Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397280.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_77.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1703557
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 66023 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1269811 original size:19 final size:18
Alignment explanation
Indices: 1269782--1269817 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1269772 AAAAAAATTA
1269782 TAATTTAAAATTATTTAT
1 TAATTTAAAATTATTTAT
1269800 TAATTATAAAATTATTTA
1 TAATT-TAAAATTATTTA
1269818 AAATAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTTAAAATTATTTAT
Found at i:1270879 original size:170 final size:170
Alignment explanation
Indices: 1270555--1270890 Score: 358
Period size: 170 Copynumber: 2.0 Consensus size: 170
1270545 GCAAACATCC
* * *
1270555 AATTATGATTTGTTTTCACCAAAAACATAAAATATTTCAATTTAAAATCCTTTATAAGATTATAA
1 AATTATGATTTGTTTTAACCAAAAACAAAAAAGATTTCAATTTAAAATCCTTTATAAGATTATAA
* * * * *
1270620 AGCCATTTAAAGCGAGTAAATAGGCTTTCGAAGGCATGACTGACTATAAATGGACTTTTCTTGTA
66 AACCATTTAAAGCGAGGAAAAAAGCTTTCGAAGGCATGACTGACTATAAATAGACTTTTCTTGTA
* *
1270685 AATGGATGATAGCCATTTTACATTTCTCGATACAAAAAACT
131 AATGGATGATA-CCACTATACATTTCTCGATACAAAAAACT
* * *
1270726 AATTATGATTT-TTTTGAACCTAAAACAAAAAAGATTTTGAA-TTAAAATCTTTTATAA-ATTAT
1 AATTATGATTTGTTTT-AACCAAAAACAAAAAAGA-TTTCAATTTAAAATCCTTTATAAGATTAT
* * ** * * *
1270788 AAAATCTTTTAAAGCGAGGAACAAAAG-TTTCGAAGGTGTGAGTGACTATAAATAGATTTTTTTT
64 AAAACCATTTAAAGCGAGGAA-AAAAGCTTTCGAAGGCATGACTGACTATAAATAGACTTTTCTT
* * * * *
1270852 GTCAATGGTTTGCAT-CTACTATACATTTCTTGATGCAAA
128 GTAAATGG-ATG-ATACCACTATACATTTCTCGATACAAA
1270891 CATCCAAATG
Statistics
Matches: 135, Mismatches: 25, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
170 83 0.61
171 45 0.33
172 7 0.05
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
AATTATGATTTGTTTTAACCAAAAACAAAAAAGATTTCAATTTAAAATCCTTTATAAGATTATAA
AACCATTTAAAGCGAGGAAAAAAGCTTTCGAAGGCATGACTGACTATAAATAGACTTTTCTTGTA
AATGGATGATACCACTATACATTTCTCGATACAAAAAACT
Found at i:1271545 original size:171 final size:172
Alignment explanation
Indices: 1270504--1273226 Score: 1187
Period size: 171 Copynumber: 15.9 Consensus size: 172
1270494 TTCTATGGAC
* ** * **
1270504 TTTTCTTGTCAATGGATGGCATTTGTTTCATGTTT-ATCAATGCAAACATCCAATTATGATTTGT
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCT-AATGCAAACATCCAATTATGATTCAT
* * * * *
1270568 TTTCACCAAAAACAT--AAAATATTTCAATTTAAAATCCTTTATAAGATTATAAAGCCATTTAAA
65 TTT-AACAAAAA-ATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAA
* * * *
1270631 GCGAGTAA-ATAGGCTTTCGAAGGCATGACTGACTATAAATGGAC-
128 GAGAGTAACA-AGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* ** * * * * ** * * * * * *
1270675 TTTTCTTGTAAATGGATGATAGCCATTTTACATTT-CTCGATACAAAAAACTAATTATGATT-TT
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCT-AATGCAAACATCCAATTATGATTCAT
** * * * * * *
1270738 TTTGAACCTAAAA-CAAAAAAGATTT-TGAATTAAAATCTTTTATAA-ATTATAAAATCTTTTAA
65 TTT-AACAAAAAATGAAAAAA-ATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAA
* * * * **
1270800 AGCGAGGAACAAAAG-TTTCGAAGGTGTGAGTGACTATAAAT-AGA-T
127 AGAGAGTAAC-AAGGCTTTTGAAGGCATGAGTGACTATAAATGA-ACT
* * * * * *
1270845 TTTTTTTGTCAATGGTTTGCATCTACTATACA--TTTCTTGATGCAAACATCCAA--ATGTAATC
1 TTTTCTTGTCAATGGATGGCATCTACT-T-CATGTTTCCTAATGCAAACATCCAATTATG-ATTC
* * * ** * * ** * *
1270906 TATTTTACCGAAAAA-CAAAAAAATATTTTGATTTAAAATAATTTGTAACTTTACACAACCATTT
63 -ATTTTAACAAAAAATGAAAAAAAT-TTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTT
** * * * * * * *
1270970 AAACTGAGTAACTAGGCTTTTGATGGCACGAATGACTTTAAATGTATT
125 AAAGAGAGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * * * ** * * * * * * *
1271018 TTTTTTTGTTAATGGATGGCATCCACTTTAAATTTCTTTATGTAAACTTCCAAATGTGATTGATT
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCATT
** * * * * * *
1271083 TTAATTAAAAATGAAAAAGATTT-TGACTTAAAATCATTTACAAGGTTATAAAACCATTTAAAGT
66 TTAACAAAAAATGAAAAAAATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAAAGA
* * * * *
1271147 GAGTAACAAGGCTCTCGAAGGTATTAATGACTATAAAATGGAACT
130 GAGTAACAAGGCTTTTGAAGGCATGAGTGACTAT-AAAT-GAACT
* ** * * ** * * * *
1271192 TTTGT-AT-T-AATGGAAAGCATTTGCTTCACATTTCTTAATGTAAACTTCCAAATATGA-TCTA
1 TTT-TCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTC-A
* * * * * * * *
1271253 TTTGAACCAAAAAATGAAAACAATTTCAATTTAAAACCATTTATAGGATTATAAGATCAATTAAA
64 TTTTAA-CAAAAAATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAA
* ** * * * *
1271318 TAGAGTAATTAGGCTTTTGATGACATGAGTGATTATAAATGGACT
128 GAGAGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * * * *
1271363 TTTT-TTGTCAATGGATGGCATCCACTCCATCTTTCCTGATGCAAACATCCAATTATGATTCATA
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCATT
* * * *
1271427 TTAACAAAAAATGAAAAAGATTTCAGTCTAATATCATTTATAAGATTATAAAACTATTTAAAGAG
66 TTAACAAAAAATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAAGAG
* * *
1271492 AGTAACAAGGCTTTTGAAGGTATTAGTTACTATAAAT-AACT
131 AGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * *
1271533 TTTTCTTGTCAATGGATGGCTTCTACTTCATGTTTTCC-ATTGCAAACATGCAATTATGA-TCAA
1 TTTTCTTGTCAATGGATGGCATCTACTTCATG-TTTCCTAATGCAAACATCCAATTATGATTC-A
* * * * * * * * *
1271596 TTTTAACCAAAAATAAAAAAAACGTAT-GGTTTAAAATCATTTAAAAGCTTATAACATCAGTTAA
64 TTTTAACAAAAAATGAAAAAAA--TTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAA
* * * * * *
1271660 AGCGAGTAACAA-GATTTTCAAAGCCAAGAGTGACTACAAAT-AGAC-
127 AGAGAGTAACAAGGCTTTT-GAAGGCATGAGTGACTATAAATGA-ACT
* * ** **
1271705 TTTTCTTGTCAATGGATGGCTTTTGGA-TT-ATGTTTTTTAATGCAAACATCCAATTATGATTTG
1 TTTTCTTGTCAATGGATGGCATCT--ACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCA
* * * * * * *
1271768 TTGTAACTAAGAGTGAAAAATATTTC-GATTTAAAATCATTTAT-ATATTTTAAAACCATTTAAA
64 TTTTAACAAAAAATGAAAAAAATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAAA
* * * * *
1271831 GTGAGTAAAAAAGCTTTTGAAGGCATGAGTAACT-TCAAATGGAC-
128 GAGAGTAACAAGGCTTTTGAAGGCATGAGTGACTAT-AAATGAACT
* * * * * * * *
1271875 TTTTCTTGTCTATGGATGGCTTTTGCTTCATGTTTCCTAATACAAATATCCAAATATGATCCATT
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCATT
* * * * * * * *
1271940 TGAACCAAAAATGAAAAAAAATTAAATCTATAATCATTTATAAGATTATAAAACAATTTAAA-AC
66 TTAACAAAAAATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAAGA-
* * * * *
1272004 AAGTAATCAA-GCTTTCGATGGCATGAGTGACAATTAATGAAC-
130 GAGTAA-CAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * * * * * ** * * *
1272046 TTTTCTTGTC--TGCATATGACATCTGCTTCATGTTTCTTGATGCAATCATTAAATTTTGGTTGA
1 TTTTCTTGTCAATG--GATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCA
* * *
1272109 TTTTAACAAAAAAT-AAAAAATATTTCAATTTAAAATCATTTATAAGGTTATAAAACCATTTACA
64 TTTTAACAAAAAATGAAAAAA-ATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAA
* * * ** * * * *
1272173 GTGAGTAATAAGCCTTTCAAATGCATTAGTGACTGTACAT-AGACT
128 GAGAGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGA-ACT
* * * * ** * *
1272218 TTTT-TTATTAATGGATGGC-TTTCACTTCATATTTCCCCATGCAAACATTCAATTATGA-TCTG
1 TTTTCTTGTCAATGGATGGCATCT-ACTTCATGTTTCCTAATGCAAACATCCAATTATGATTC-A
** * * * *
1272280 TTTTAATTAAAAAT-AAAAAAGATTT-TGATTTAAACTCATTTATAA-ATTAAAAAATCATTTAA
64 TTTTAACAAAAAATGAAAAAA-ATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAA
* * * * *
1272342 AGCA-AGTAACGAGGCTTTCT-ATGGTATGGGTGACTACAAATGGAA--
127 AG-AGAGTAACAAGGCTTT-TGAAGGCATGAGTGACTATAAAT-GAACT
* * ** * **
1272387 TTTCCTTGTTAATGGATATCAT-TCACTTCACAT-TTTCC-AAAGCAAACACTGAAATCTA--A-
1 TTTTCTTGTCAATGGATGGCATCT-ACTT--CATGTTTCCTAATGCAAACA-TCCAAT-TATGAT
* ** * * * * *
1272446 TCTGTTTTATTAAAAACA--AAAACAATTT-TGATTTGAAATCATTTATAAGTTTATAAAACCAC
61 TC-ATTTTAACAAAAA-ATGAAAAAAATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCAT
* * * * *
1272508 TTAAAGTA-AGTAATAAGGCCTTTGAAGGCATGAGTGCCTACAAATGGA-T
123 TTAAAG-AGAGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * * * * ** * *
1272557 TTTTCTTATTAATAGAAGGC-TTTCACTTCACATTT-CTCAATGCAAACTTCCAAATATGA-TCT
1 TTTTCTTGTCAATGGATGGCATCT-ACTTCATGTTTCCT-AATGCAAACATCCAATTATGATTC-
* * * * * **
1272619 ATTTTATCCAAAAA-CAAAGGCAAA-TTC-GATTTCAAATCATTTATAAGATTATAAAATAATTT
63 ATTTTAACAAAAAATGAAA--AAAATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTT
* ** * * *
1272681 AAA-ACAAGTAATTAGGCTTTCGATA-GTATGAGTGACTATAAATGGAC-
125 AAAGA-GAGTAACAAGGCTTTTGA-AGGCATGAGTGACTATAAATGAACT
* * * *
1272728 TTTTCTTGTCAATGGATGGCATCTGCTTCATGGTTT-CTAATGGAAACATCCAATTTTGATTGAT
1 TTTTCTTGTCAATGGATGGCATCTACTTCAT-GTTTCCTAATGCAAACATCCAATTATGATTCAT
* *** * * * * * * * *
1272792 TTTAACTAAAAATGAAAGGTATTTCAATATAAAATTATTTACAATATTATAAAGCCATTAAAAGC
65 TTTAACAAAAAATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAAGA
* * * ***
1272857 GAGT-ACTAAGGCTTTCT-AAGGCATTAGTGCCAATAAATGGGTT
130 GAGTAAC-AAGGCTTT-TGAAGGCATGAGTGACTATAAATGAACT
* * * ** * * * *
1272900 TTTTCGT-TCAATGGATGGC-TTTCCCTTCATGTTTCCTAATAAAAACATCAAATTGTTATT-TT
1 TTTTCTTGTCAATGGATGGCATCT-ACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCAT
* * * *
1272962 TTTAACTAAAAGT-AAAAATGATTTC-GATTTAAAATCATTTATAA-ATTATAAAATCATTTAAA
65 TTTAACAAAAAATGAAAAA-AATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAAA
* * ** * *
1273024 GCA-AGTTACAAGGCCTTTGAAATCATGAGTGACTATATATGGAC-
128 G-AGAGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
* * * * * * *
1273068 -TTTCTTGTCAATGGAAGGCATCCATTTCATGTTTCCTTATGTAAACATCCAAATATGATTTATT
1 TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCATT
* * * * *
1273132 TTAACTAAAACA--AAAAAGATTTC-GATTTAAAATCATTTATAAAATTATAAGATCATTTAAAG
66 TTAAC-AAAAAATGAAAAAAATTTCAG-TTTAAAATCATTTATAAGATTATAAAACCATTTAAAG
* * * * *
1273194 CGAGTAACTAGGCTTTCGATGACATGAGTGACT
129 AGAGTAACAAGGCTTTTGAAGGCATGAGTGACT
1273227 GCAAATAGAT
Statistics
Matches: 1924, Mismatches: 507, Indels: 244
0.72 0.19 0.09
Matches are distributed among these distances:
167 5 0.00
168 73 0.04
169 147 0.08
170 473 0.25
171 723 0.38
172 345 0.18
173 138 0.07
174 17 0.01
175 3 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (172 bp):
TTTTCTTGTCAATGGATGGCATCTACTTCATGTTTCCTAATGCAAACATCCAATTATGATTCATT
TTAACAAAAAATGAAAAAAATTTCAGTTTAAAATCATTTATAAGATTATAAAACCATTTAAAGAG
AGTAACAAGGCTTTTGAAGGCATGAGTGACTATAAATGAACT
Found at i:1272665 original size:682 final size:679
Alignment explanation
Indices: 1271789--1273029 Score: 1530
Period size: 682 Copynumber: 1.8 Consensus size: 679
1271779 AGTGAAAAAT
* * *
1271789 ATTTCGATTTAAAATCATTTATATATTTTAAAACCATTTAAAGTGAGTAAAAAAGCTTTTGAAGG
1 ATTTCGATTTAAAATCATTTATATATTTTAAAACCACTTAAAGTAAGTAAAAAAGCCTTTGAAGG
* * * * ** **
1271854 CATGAGTAACTTCAAATGGACTTTTCTTGTCTATGGATGGCTTTTGCTTCATGTTTCCTAATACA
66 CATGAGTAACTACAAATGGACTTTTCTTATCTATAGAAGGCTTTCACTTCACATTTCCTAATACA
*
1271919 AATATCCAAATATGATCCATTTGAACCAAAAATGAAAAAAAATTAAATCTATAATCATTTATAAG
131 AATATCCAAATATGATCCATTTGAACCAAAAATCAAAAAAAATTAAATCTATAATCATTTATAAG
* *
1271984 ATTATAAAACAATTTAAAACAAGTAATCAAGCTTTCGATGGCATGAGTGACAATTAATGAACTTT
196 ATTATAAAACAATTTAAAACAAGTAATCAAGCTTTCGATAGCATGAGTGACAATAAATGAACTTT
* * * * *
1272049 TCTTGTC-TGCATATGACATCTGCTTCAT-GTTTCTTGATGCAATCATTAAATTTTGGTTGATTT
261 TCTTGTCATG--GATGACATCTGCTTCATGGTTTC-TAATGCAAACATCAAATTTTGATTGATTT
* * * * * *
1272112 TAACAAAAAATAAAAAATATTTCAATTTAAAATCATTTATAAGGTTATAAAACCATTTACAGTGA
323 TAACAAAAAATAAAAAATATTTCAATATAAAATCATTTACAAGATTATAAAACCATTAAAAGCGA
* ** * *
1272177 GTAATAAGCCTTTCAAATGCATTAGTGACTGTACATAGACTTTTTTTATT-AATGGATGGCTTTC
388 GTAATAAGCCTTTCAAAGGCATTAGTGACAATAAAT-GACTTTTTTCATTCAATGGATGGCTTTC
* ** *
1272241 ACTTCATATTTCCCCATGCAAACATTC-AATTATGATCTGTTTTAATTAAAAATAAAAAAGATTT
452 ACTTCATATTTCCCAATAAAAACA-TCAAATTATGAT-TGTTTTAACTAAAAATAAAAAAGATTT
* *
1272305 TGATTTAAACTCATTTATAAATTAAAAAATCATTTAAAGCAAGTAACGAGGCTTTCTATGGTATG
515 CGATTTAAAATCATTTATAAATTAAAAAATCATTTAAAGCAAGTAACGAGGCTTTCTATGGTATG
1272370 GGTGACTACAAATGGAATTTCCTTGTTAATGGATATCATTCACTTCACATTTTCCAAAGCAAACA
580 GGTGACTACAAATGGAATTTCCTTGTTAATGGATATCATTCACTTCACATTTTCCAAAGCAAACA
1272435 CTGAAATCTAATCTGTTTTATTAAAAACAAAAACA
645 CTGAAATCTAATCTGTTTTATTAAAAACAAAAACA
* * * *
1272470 ATTTTGATTTGAAATCATTTATA-AGTTTATAAAACCACTTAAAGTAAGTAATAAGGCCTTTGAA
1 ATTTCGATTTAAAATCATTTATATA-TTT-TAAAACCACTTAAAGTAAGTAAAAAAGCCTTTGAA
** *
1272534 GGCATGAGTGCCTACAAATGGATTTTTCTTAT-TAATAGAAGGCTTTCACTTCACATTT-CTCAA
64 GGCATGAGTAACTACAAATGGACTTTTCTTATCT-ATAGAAGGCTTTCACTTCACATTTCCT-AA
* * * * ** ** *
1272597 TGCAAACT-TCCAAATATGATCTATTTTATCCAAAAA-CAAAGGCAAATTCGATTTCA-AATCAT
127 TACAAA-TATCCAAATATGATCCATTTGAACCAAAAATCAAA-AAAAATTAAATCT-ATAATCAT
* * * * *
1272659 TTATAAGATTATAAAATAATTTAAAACAAGTAATTAGGCTTTCGATAGTATGAGTGACTATAAAT
189 TTATAAGATTATAAAACAATTTAAAACAAGTAATCAAGCTTTCGATAGCATGAGTGACAATAAAT
* * * *
1272724 GGACTTTTCTTGTCAATGGATGGCATCTGCTTCATGGTTTCTAATGGAAACATCCAATTTTGATT
254 GAACTTTTCTTGTC-ATGGATGACATCTGCTTCATGGTTTCTAATGCAAACATCAAATTTTGATT
* * ** * * *
1272789 GATTTTAACTAAAAATGAAAGGTATTTCAATATAAAATTATTTACAATATTATAAAGCCATTAAA
318 GATTTTAACAAAAAATAAAAAATATTTCAATATAAAATCATTTACAAGATTATAAAACCATTAAA
* * * * ** *
1272854 AGCGAGTACTAAGGCTTTCTAAGGCATTAGTGCCAATAAATGGGTTTTTTCGTTCAATGGATGGC
383 AGCGAGTAATAAGCCTTTCAAAGGCATTAGTGACAATAAATGACTTTTTTCATTCAATGGATGGC
* * * * * * * *
1272919 TTTCCCTTCATGTTTCCTAATAAAAACATCAAATTGTTATTTTTTTAACTAAAAGTAAAAATGAT
448 TTTCACTTCATATTTCCCAATAAAAACATCAAATTATGATTGTTTTAACTAAAAATAAAAAAGAT
*
1272984 TTCGATTTAAAATCATTTATAAATTATAAAATCATTTAAAGCAAGT
513 TTCGATTTAAAATCATTTATAAATTAAAAAATCATTTAAAGCAAGT
1273030 TACAAGGCCT
Statistics
Matches: 464, Mismatches: 84, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
680 1 0.00
681 105 0.23
682 349 0.75
683 7 0.02
684 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (679 bp):
ATTTCGATTTAAAATCATTTATATATTTTAAAACCACTTAAAGTAAGTAAAAAAGCCTTTGAAGG
CATGAGTAACTACAAATGGACTTTTCTTATCTATAGAAGGCTTTCACTTCACATTTCCTAATACA
AATATCCAAATATGATCCATTTGAACCAAAAATCAAAAAAAATTAAATCTATAATCATTTATAAG
ATTATAAAACAATTTAAAACAAGTAATCAAGCTTTCGATAGCATGAGTGACAATAAATGAACTTT
TCTTGTCATGGATGACATCTGCTTCATGGTTTCTAATGCAAACATCAAATTTTGATTGATTTTAA
CAAAAAATAAAAAATATTTCAATATAAAATCATTTACAAGATTATAAAACCATTAAAAGCGAGTA
ATAAGCCTTTCAAAGGCATTAGTGACAATAAATGACTTTTTTCATTCAATGGATGGCTTTCACTT
CATATTTCCCAATAAAAACATCAAATTATGATTGTTTTAACTAAAAATAAAAAAGATTTCGATTT
AAAATCATTTATAAATTAAAAAATCATTTAAAGCAAGTAACGAGGCTTTCTATGGTATGGGTGAC
TACAAATGGAATTTCCTTGTTAATGGATATCATTCACTTCACATTTTCCAAAGCAAACACTGAAA
TCTAATCTGTTTTATTAAAAACAAAAACA
Found at i:1273639 original size:182 final size:180
Alignment explanation
Indices: 1273267--1273705 Score: 438
Period size: 182 Copynumber: 2.4 Consensus size: 180
1273257 TCTGATTGAC
* * *
1273267 AAGAAAAGACTATTTTAAGTTAATCGGGCCATCAAAAGCTTTGTTACTCTCTTAGAAAGATATAT
1 AAGAAAAGACCATTTTAAGTTAATCAGGCCATCAAAAGCTTTGTTACTCCCTTAGAAAGATATAT
* * * * * *
1273332 TAATTCATTTATAGCCTTACAAATGGTTATAAAATGAAATATTTCGAGTTTATGGTTAAAACCTA
66 TAATTCATTTATAACCTTACAAATGATTATAAAATGAAAAATTTCGACTTTATGGCTAAAAACTA
* * * * * * *
1273397 TCATAATTTGATGTTAGGATTGGGAAATGTGAAGTGAATGCTATTTTTTG
131 TCATAATTGGATATTAGCATTAGAAAACGTGAAGTGAATGCTATTTTGTG
* ** * *
1273447 ATAGGAAAAGACCATTTTAAGTTAATCATGTGATCGAAAGCTTTGTTGCTCACCTTA-AAAGATA
1 A-A-GAAAAGACCATTTTAAGTTAATCAGGCCATCAAAAGCTTTGTTACTC-CCTTAGAAAGATA
* * * *
1273511 TATTAATTCATTTATAATCTTATAAATGATTAT-AAATTAAAAACTTTGGACTTTATGGCTAAAA
63 TATTAATTCATTTATAACCTTACAAATGATTATAAAATGAAAAA-TTTCGACTTTATGGCTAAAA
* * * * *
1273575 ACTATTATAATTGGATATTTGCATTAGAAAACGTGGAGTGGATGTTATTCATTGTG
127 ACTATCATAATTGGATATTAGCATTAGAAAACGTGAAGTGAATGCTATT--TTGTG
* * * * *
1273631 AAGAAAAGACCATTTGAAGTTAATC-GTGCCATCAATAG-TTGTGTTACTCACTTTA-AATGATG
1 AAGAAAAGACCATTTTAAGTTAATCAG-GCCATCAAAAGCTT-TGTTACTC-CCTTAGAAAGATA
*
1273693 TATTCATTCATTT
63 TATTAATTCATTT
1273706 GTAATTCATT
Statistics
Matches: 210, Mismatches: 41, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
180 1 0.00
181 11 0.05
182 188 0.90
183 5 0.02
184 5 0.02
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (180 bp):
AAGAAAAGACCATTTTAAGTTAATCAGGCCATCAAAAGCTTTGTTACTCCCTTAGAAAGATATAT
TAATTCATTTATAACCTTACAAATGATTATAAAATGAAAAATTTCGACTTTATGGCTAAAAACTA
TCATAATTGGATATTAGCATTAGAAAACGTGAAGTGAATGCTATTTTGTG
Found at i:1273714 original size:11 final size:11
Alignment explanation
Indices: 1273698--1273722 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1273688 TGATGTATTC
1273698 ATTCATTTGTA
1 ATTCATTTGTA
1273709 ATTCATTTGTA
1 ATTCATTTGTA
1273720 ATT
1 ATT
1273723 TTATAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTCATTTGTA
Found at i:1279890 original size:182 final size:180
Alignment explanation
Indices: 1278935--1281128 Score: 950
Period size: 182 Copynumber: 12.2 Consensus size: 180
1278925 NNNNNNNTTG
* * * *
1278935 GACTTTATGCTTCAAACCTATCATAATTGGATGTTTGCATTGGGAAACATGAAGT-AGATACTAT
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGA-ATGCTAT
* * * ** * * *
1278999 CTC-TTAAAAAGAAAAGACCATTCTAAGTTAATCATGTGATTGAAAGCTTTATTACTCTA-TTTA
64 C-CATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACT-TACTTTA
* *
1279062 AATGATATATTAATTAATTTATAATCTTATAAATGATTATAAA-TCAA-----A
127 AATGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGAATCTTTA
* * * ** * * *
1279110 -A-TCTTAT-GTTAAAATCTAAT-GTAATTAGATGTTTGCATTAAGCAACGTGATGTGGATGCTA
1 GACT-TTATGGTTAAAACCT-ATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTA
** * * * * * * **
1279171 -CTCATTGTGAAGAAAAGACCAA-ATTAAGTTAATTATGCCATCAATAGCTCTGTTACTCCCTTT
63 TC-CATTGAAAAGAAAAGA-CAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTT
** * * * * * ** *
1279234 ATGTAATGTAATAATTCATTTACAATCTTATAAATGATTATATATCAAAATCTTTG
126 AAATGATATATTAATTCATTTATAATCTTATAAATGATTATAAAT-TGAATCTTTA
* * * ** * * * * * *
1279290 GACTTTATGCTTTAAACTTATTGT-ATCTAGATGCTTGCATCGGGAAATGTGAAGTTAATGCTGT
1 GACTTTATGGTTAAAACCTATCATAAT-TGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTAT
** ** * * * * * * * * * *
1279354 TTATTGTGAAGAAATGACCATTTTAAGTTTATTATGTCATCAATAGCTTTGTTACTCATTTTAAA
64 CCATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAA
* * *
1279419 TGGTGTATTGATTCATTTATAATCTTATAAATGATTATAAA-TGAAAATCTTT-
129 TGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTG--AATCTTTA
********** * * ** * * * * *
1279471 GAACTNNNNNNNNNNAACCTATTATAGTTGGATGTTTGCATACGCAAGCATGAAATGGATGCTAT
1 G-ACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTAT
* ********** * * * * * * *
1279536 CAATTGACAAA-ANNNNNNNNNNTTAAGTTAATCATGCCATTGAAAGCATTGATACATGCTTCAA
64 CCATTGA-AAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAA
* * * * * * *
1279600 ATGATATATTAATTCATATATAATCTAATAAATCATTTTTAATTGAGATATTTG
128 ATGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGA-ATCTTTA
* *
1279654 GAAC-TTATGGTTAAAACCTATCATAATTAGATGTTTGAATTGGGAAACGTGAAGTGAATGGTAT
1 G-ACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTAT
* * * * *
1279718 CCATTGACAACAAAAGACAATTTTAAATTAATCGTGGCATTAAAAACTTTGTTACTTACTTTAAA
64 CCATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAA
* * * * *
1279783 CGATATATAAATTCAATTGTAATCTTATAAATGACTATAAATTGGAATCTTTA
129 TGATATATTAATTCATTTATAATCTTATAAATGATTATAAATT-GAATCTTTA
* * * * **
1279836 GACTTTCTAGTTAAAACTTATCATAATTGGATGTTTGCATTGGGAAATGTGAAGTGGTTGCTATC
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTATC
* * * * * * * *
1279901 CCTTGACAAGAAAAGATC-ATTTTAAGCTAATCATGCCATCAATAGCTTTGTTACTCACTTTAGA
65 CATTGAAAAGAAAAGA-CAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAA
* * * *
1279965 TGATGTATTAATTCATTTATAATCTTATAAAAGATTATTAATTGAGATATTTA
129 TGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGA-ATCTTTA
* * * * * * ** *
1280018 AACTTGATGGTTAAAACATATCATAATTGGATGTTTGATGTAGAAAACGTGAAATGGTTGGTATC
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTTGAT-TGGGAAACGTGAAGTGAATGCTATC
* * * * * * *
1280083 CATTGAAAAGAAAAGA-ATATTTTAAGTTAATCGTACCGTTGAAAGCTTTGTCACTCT-CTTTGA
65 CATTGAAAAGAAAAGACA-ATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACT-TACTTTAA
* * * * * * * * *
1280146 ATGATATATTAGTTCTTTTTTCATATTATAAACGATGATAAGTTGAATTCTTTG
128 ATGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGAA-TCTTTA
* * *
1280200 GACTTTATGGTTAAAACCTATCATAATTGCATGTTTGTATTGAGAAACATGAAGT-AGATGCTAT
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGA-ATGCTAT
* * * * *
1280264 CCCTTGAAAAGAAAAGACTATTTTAAGTTAATCATGCGATTGAAAACTTTATTAC-TAGCTTTAA
64 CCATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTA-CTTTAA
* ** * **
1280328 ATGATACATTAATTCATTTATAATCTTATAAATGATTATAAATCAAATGTTCG
128 ATGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGAATCTTTA
* * * ** * *** * * * *
1280381 GACTTTATTGTTCAAATCTATTGTAATTGGGTGTTTGCATCAAGTAACATGATGTGGATGCTA-C
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTTG-ATTGGGAAACGTGAAGTGAATGCTATC
** * * ** * * * * * * *
1280445 TTGTTGCAAAGAAAGGACCCTTTTAAGTTAACCTTGCCATCAATAGCTTTCTTACTCT-CTATAA
65 -CATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACT-TACTTTAA
* * * * ** *
1280509 ATAATGTAATAATTCATTTACAATCTTATAAATGATTATAAATCAAAATCTTTG
128 ATGATATATTAATTCATTTATAATCTTATAAATGATTATAAAT-TGAATCTTTA
** * * * *** * * *
1280563 GACTTTATAATAAAAACCTATTATAATTGGATGTTTACATTCAAAAACTTGAAGTGGATGCTATT
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTTT-GATTGGGAAACGTGAAGTGAATGCTATC
* ** * * * * * * *** *
1280628 AATTGGTAGGAAAAGATC-ATTTTAAGTTAACCGTGCCATCAAAAGCTTTGATACAGGCCTTAAA
65 CATTGAAAAGAAAAGA-CAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAA
* ** * * * * *
1280692 TAATATATTAATAAATTTATAATCTTATAAATGATCATTGACTAAGACA-C-TTG
129 TGATATATTAATTCATTTATAATCTTATAAATGATTA-TAAAT-TGA-ATCTTTA
* * * * * * * *
1280745 GACTTTATCGTTAAAACCTATCATAATT-CATTATTTGAACTAGAAAACATGAAGTTG-ATGGTA
1 GACTTTATGGTTAAAACCTATCATAATTGGA-TGTTTG-ATTGGGAAACGTGAAG-TGAATGCTA
* ** * * * *
1280808 GCCATT---AAGAAAA-ACTGTTTTGAGTTAATCGTGCCATCAAAAGCTTTGTTACTTACTTTGA
63 TCCATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTT-A
* **** *
1280869 CAA--ATATATTAATTCATATATAATCTTATAAATGATTATAAA---AAAAAATG
127 -AATGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGAATCTTTA
* * * * * * * * *
1280919 GACTTTATGGTTAGAACCTATCATACTTGGATGTTCGGATTAGGAAACATGAAAT-AGTTGTTGT
1 GACTTTATGGTTAAAACCTATCATAATTGGATGTT-TGATTGGGAAACGTGAAGTGA-ATGCTAT
* * * * * * **
1280983 CCCTTGATAGGAAAAGACCATTTTAAG-CAATC--G------AAAACGTTGTTACTCGCTTTAAA
64 CCATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAA
*
1281039 TGATATATTAATTCATTTATAATCTTATAAATGATTATAAA-TGAAAAT-TATTG
129 TGATATATTAATTCATTTATAATCTTATAAATGATTATAAATTG--AATCT-TTA
* *
1281092 GACTCTATGGTTCAAACCTAT-AGTAATTGGATGTTTG
1 GACTTTATGGTTAAAACCTATCA-TAATTGGATGTTTG
1281129 CATCAGGAAA
Statistics
Matches: 1512, Mismatches: 429, Indels: 159
0.72 0.20 0.08
Matches are distributed among these distances:
167 2 0.00
168 1 0.00
169 54 0.04
172 6 0.00
173 149 0.10
174 59 0.04
175 5 0.00
177 13 0.01
178 75 0.05
179 7 0.00
180 4 0.00
181 159 0.11
182 953 0.63
183 24 0.02
184 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (180 bp):
GACTTTATGGTTAAAACCTATCATAATTGGATGTTTGATTGGGAAACGTGAAGTGAATGCTATCC
ATTGAAAAGAAAAGACAATTTTAAGTTAATCATGCCATTAAAAACTTTGTTACTTACTTTAAATG
ATATATTAATTCATTTATAATCTTATAAATGATTATAAATTGAATCTTTA
Found at i:1280675 original size:545 final size:546
Alignment explanation
Indices: 1279650--1280677 Score: 1144
Period size: 545 Copynumber: 1.9 Consensus size: 546
1279640 AATTGAGATA
* * *
1279650 TTTGGAACTTATGGTTAAAACCTATCATAATTAGATGTTTGAATTGGGAAACGTGAAGTGAATGG
1 TTTGGAACTTATGGTTAAAACCTATCATAATTAGATGTTTGAATTGAGAAACATGAAGTGAATGC
* * *
1279715 TATCCATTGACAACAAAAGACAATTTTAAATTAATCGTGGCATTAAAAACTTTGTTACTTACTTT
66 TATCCATTGAAAACAAAAGACAATTTTAAATTAATCATGGCATTAAAAACTTTATTACTTACTTT
* * ** * *
1279780 AAACGATATATAAATTCAATTGTAATCTTATAAATGACTATAAATTGGAATCTTTAGACTTTCTA
131 AAACGATACATAAATTCAATTATAATCTTATAAATGACTATAAATTCAAATCTTCAGACTTTATA
*** ** *
1279845 GTTAAAACTTATCATAATTGGATGTTTGCATTGGGAAATGTGAAGTGGTTGCTATCCCTTGACAA
196 GTTAAAACTTATCATAATTGGATGTTTGCATCAAGAAACATGAAGTGGATGCTATCCCTTGACAA
* * * * * * *
1279910 GAAAAGATCATTTTAAGCTAATCATGCCATCAATAGCTTTGTTACTCACTTTAGATGATGTATTA
261 GAAAAGACCATTTTAAGCTAACCATGCCATCAATAGCTTTCTTACTCACTATAAATAATGTAATA
* * ** * ** *
1279975 ATTCATTTATAATCTTATAAAAGATTATTAATTGAGATATTTAAACTTGATGGTTAAAACATATC
326 ATTCATTTACAATCTTATAAAAGATTATAAATCAAAATATTTAAACTTGATAATAAAAACATATC
* * * *
1280040 ATAATTGGATGTTTGATGTAGAAAACGTGAAATGGTTGGTATCCATTGAAAAGAAAAGAATATTT
391 ATAATTGGATGTTTCATGTAGAAAACGTGAAATGGATGCTATCAATTGAAAAGAAAAGAATATTT
* * **
1280105 TAAGTTAATCGTACCGTTGAAAGCTTTGTCACTCTCTTTGAATGATATATTAGTTCTTTTTTCAT
456 TAAGTTAACCGTACCATCAAAAGCTTTGTCACTCTCTTTGAATGATATATTAGTTCTTTTTTCAT
1280170 ATTATAAACGATGATAAGTTGAATTC
521 ATTATAAACGATGATAAGTTGAATTC
*
1280196 TTTGG-ACTTTATGGTTAAAACCTATCATAATT-GCATGTTTGTATTGAGAAACATGAAGT-AGA
1 TTTGGAAC-TTATGGTTAAAACCTATCATAATTAG-ATGTTTGAATTGAGAAACATGAAGTGA-A
* * * * *
1280258 TGCTATCCCTTGAAAAGAAAAGACTATTTTAAGTTAATCAT-GCGATTGAAAACTTTATTAC-TA
63 TGCTATCCATTGAAAACAAAAGACAATTTTAAATTAATCATGGC-ATTAAAAACTTTATTACTTA
* * * * * *
1280321 GCTTTAAATGATACATTAATTCATTTATAATCTTATAAATGATTATAAA-TCAAATGTTCGGACT
127 -CTTTAAACGATACATAAATTCAATTATAATCTTATAAATGACTATAAATTCAAATCTTCAGACT
* * ** * * * **
1280385 TTATTGTTCAAA-TCTATTGTAATTGGGTGTTTGCATCAAGTAACATGATGTGGATGCTA-CTTG
191 TTATAGTTAAAACT-TATCATAATTGGATGTTTGCATCAAGAAACATGAAGTGGATGCTATC-CC
* * * * *
1280448 TTG-CAAAGAAAGGACCCTTTTAAGTTAACCTTGCCATCAATAGCTTTCTTACTCTCTATAAATA
254 TTGAC-AAGAAAAGACCATTTTAAGCTAACCATGCCATCAATAGCTTTCTTACTCACTATAAATA
* * ** *
1280512 ATGTAATAATTCATTTACAATCTTATAAATGATTATAAATCAAAATCTTTGGACTTTATAATAAA
318 ATGTAATAATTCATTTACAATCTTATAAAAGATTATAAATCAAAATATTTAAACTTGATAATAAA
* * * * * ** *
1280577 AACCTATTATAATTGGATGTTTACAT-TCA-AAAACTTGAAGTGGATGCTATTAATTGGTAGGAA
383 AACATATCATAATTGGATGTTT-CATGT-AGAAAACGTGAAATGGATGCTATCAATTGAAAAGAA
*
1280640 AAG-ATCATTTTAAGTTAACCGTGCCATCAAAAGCTTTG
446 AAGAAT-ATTTTAAGTTAACCGTACCATCAAAAGCTTTG
1280678 ATACAGGCCT
Statistics
Matches: 390, Mismatches: 81, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
544 5 0.01
545 239 0.61
546 146 0.37
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (546 bp):
TTTGGAACTTATGGTTAAAACCTATCATAATTAGATGTTTGAATTGAGAAACATGAAGTGAATGC
TATCCATTGAAAACAAAAGACAATTTTAAATTAATCATGGCATTAAAAACTTTATTACTTACTTT
AAACGATACATAAATTCAATTATAATCTTATAAATGACTATAAATTCAAATCTTCAGACTTTATA
GTTAAAACTTATCATAATTGGATGTTTGCATCAAGAAACATGAAGTGGATGCTATCCCTTGACAA
GAAAAGACCATTTTAAGCTAACCATGCCATCAATAGCTTTCTTACTCACTATAAATAATGTAATA
ATTCATTTACAATCTTATAAAAGATTATAAATCAAAATATTTAAACTTGATAATAAAAACATATC
ATAATTGGATGTTTCATGTAGAAAACGTGAAATGGATGCTATCAATTGAAAAGAAAAGAATATTT
TAAGTTAACCGTACCATCAAAAGCTTTGTCACTCTCTTTGAATGATATATTAGTTCTTTTTTCAT
ATTATAAACGATGATAAGTTGAATTC
Found at i:1281228 original size:19 final size:21
Alignment explanation
Indices: 1281183--1281228 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1281173 TGTCCGAGTA
* *
1281183 CTTTATAAATTGAACTATGAT
1 CTTTATAAATTGAACTATAAC
1281204 CTTTATAAATTGAA-TA-AAC
1 CTTTATAAATTGAACTATAAC
1281223 CTTTAT
1 CTTTAT
1281229 TCCACATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (21 bp):
CTTTATAAATTGAACTATAAC
Found at i:1285098 original size:155 final size:155
Alignment explanation
Indices: 1284851--1285141 Score: 399
Period size: 155 Copynumber: 1.9 Consensus size: 155
1284841 ACACGTGAAG
* * * * *
1284851 TGGATGCTATTCATTGCGAAGAAAAGACCATTTTAAGTTAATCATGCCATCAATGGCTTTGTTAC
1 TGGATGCTATTCATTGCGAAGAAAACAACATTTTAACTTAATCATGCCACCAATAGCTTTGTTAC
* * * *
1284916 TCACTTTGAATAATGTAACACGCCATTTATAATCTTATAAATGATT-CTAAATCAATATCTTTGG
66 TCACTTTGAATAATGTAACAAGCCATTTATAATCTTATAAATGATTAC-AAATCAAAATATTTGA
1284980 ACTTTATAGTTTAAAGTTATTATATT
130 ACTTTATAGTTTAAAGTTATTATATT
*
1285006 TGGATGCTGTTCATTGCGAAGAAAACAACATTTTAACTTAATCATGCCACCAATAGCTTTGTTAC
1 TGGATGCTATTCATTGCGAAGAAAACAACATTTTAACTTAATCATGCCACCAATAGCTTTGTTAC
* ** **
1285071 TCACTTT-ATATGGA-GTATTAATTCATTTATAATCTTATAAATGATTACAAATCAAAATATTTG
66 TCACTTTGA-AT-AATGTAACAAGCCATTTATAATCTTATAAATGATTACAAATCAAAATATTTG
1285134 AACTTTAT
129 AACTTTAT
1285142 GATCAAAACC
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
154 1 0.01
155 115 0.97
156 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (155 bp):
TGGATGCTATTCATTGCGAAGAAAACAACATTTTAACTTAATCATGCCACCAATAGCTTTGTTAC
TCACTTTGAATAATGTAACAAGCCATTTATAATCTTATAAATGATTACAAATCAAAATATTTGAA
CTTTATAGTTTAAAGTTATTATATT
Found at i:1286034 original size:179 final size:179
Alignment explanation
Indices: 1285024--1287049 Score: 1119
Period size: 182 Copynumber: 11.2 Consensus size: 179
1285014 GTTCATTGCG
* * * * * ** *
1285024 AAGAAAACAACATTTTAACTTAATCATGCCA-CCAATAGCTTTGTTACTCACTTTATATGGA-GT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAA-AGCTTTGTTACTAACTTTA-AAAGATAT
* ** * *
1285087 ATTAATTCATTTATAATCTTATAAATGATTACAAATCAAAATATTT-GAACTTTATGATCAAAAC
64 ATTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAG-ACTTTATGGTTAAAAC
* * * *
1285151 CTATTATAACTGGATGTTTGCATTCA-CAAACATGAAGTGGATGCTATCAATTGAC
128 CTATCATAA-T-GATGTTTGCATT-AGAAAACGTGAAGTGGATGCTATC-CTTGAC
* * * * * *
1285206 AAG-AAA-A-CATTTTAAATTAATCATGCCATCGAAAGCATTGATAC-ATGCCTTAAATGATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTA-ACTTTAAAAGATATA
* * * *
1285267 TTAATACATTTATAATCTTATAAATGATCATTAATTGAGATATTTAGACTTTATGAG-TAAAACC
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATG-GTTAAAACC
* * * * * * *
1285331 TATCATAATTGGGTGTTTGAATTTGGAAACGTGAAATGGATGGTATCTATTGAC
129 TATCATAA-T-GATGTTTGCATTAGAAAACGTGAAGTGGATGCTATC-CTTGAC
* ** * * * *
1285385 AAGAAAAAATTATTTTAATTTAATCATGCCATAGTAAA-CTTTGTTACTTACTTTGAACA-ATAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCG-AAAGCTTTGTTACTAACTTT-AAAAGATAT
* * ** * *
1285448 ATAAATTCATTTGTAATCTTATAAATGATTATGCATTGAAATCTTTGGACTTTATGGTTAAAACC
64 ATTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACC
* * * * * *
1285513 TTTCATAATTGGATGTTTGCATT-GAGAAATGTGAAGTAGATACTTTTCCTTAAC
129 TATCATAA-T-GATGTTTGCATTAGA-AAACGTGAAGTGGATGC-TATCCTTGAC
* * * * * * * * *
1285567 AAGAATAGACCATTTTAAGCTAATCATGCCATC-AATAGCGTTGTTACTCATTTTTAATGGTGTA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAA-AGCTTTGTTACTAACTTTAAAAGATATA
* ** *
1285631 TTAATTCATTTATAATCTTATAAATGATTATTAATTGTGATATTTAGACTTTATGGTTAAAACAT
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACCT
* * * * * *
1285696 ATCATAATTAGATGTTT-CAATTGGAAGACATGAAATGGATGGTGTCCATTGAC
130 ATCATAA-T-GATGTTTGC-ATTAGAAAACGTGAAGTGGATGCTATCC-TTGAC
** * ** * * * *
1285749 AAGAAAAGAATATTTT-AGCTAGCCGTGCCATCGAAAGCTTTGTCACTCACTTTGAACA-ATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTAACTTT-AAAAGATATA
* * * * * * *
1285812 CTAGTTCATTTTTAATATTACAAATGATTATAAATTTAAATCTTTAGACTTTATGGTTAAAACCT
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACCT
** *
1285877 ATCATAA-GATGTTTGCATTAGAAAACGTGAAGTAAATGCTATTCCTTGAA
130 ATCATAATGATGTTTGCATTAGAAAACGTGAAGTGGATGCTA-TCCTTGAC
* * * * *
1285927 AAGAAAAGACCACTTTAAGTTAATCATGCAATCGCAAGCTTTATTACTAACTTTAAAAGATACAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTAACTTTAAAAGATATAT
** * * * * *
1285992 TAATTCATTTATAATCTTATAAATGATTATAAATCAAAATCTTTGGACTTTATAGTTCAAAGCTA
66 TAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACCTA
** * * * * * **
1286057 TTGTTATTGGATGTTTGCATT-GAGCAACGTGATGTGGACGCTACTCATTGTG
131 -TCATAAT-GATGTTTGCATTAGA-AAACGTGAAGTGGATGCTA-TCCTTGAC
* * * ** *
1286109 AAGAAAAGACCTTTTTAATTTAATCATGCCATCAAAAGCTTTGTTTA-TCCCTTTAAATA-ATGT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTG-TTACTAACTTTAAA-AGATAT
** * * * ** * * * *
1286172 AACAAATCATTCATAACCTTATAAACAATTATAACTT-AAAT-TCATTGGACTTTATGTTTCAAA
64 ATTAATTCATTTATAATCTTATAAATGATTATAAATTGAAATAT--TTAGACTTTATGGTTAAAA
** * * * * * * *
1286235 CCTATTGTTATTGGATATTTGCATT-GAGAAACATGAAGTTGATGTTGTTCATTG-C
127 CCTA-TCATAAT-GATGTTTGCATTAGA-AAACGTGAAGTGGATGCT-ATCCTTGAC
* * * * * ** * *
1286290 AAAGCAAAGACCATTTTAAGTTAACCATGCCATC-AATAACTTTATTTCTCGCATTAAATA-ATG
1 -AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAA-AGCTTTGTTACTAACTTTAAA-AGATA
** * * *
1286353 TATTAATTCA-TT-T-A----AT---TGATTATAAATCAAAATCA-TTGGACTTTAT-ATAAAAA
63 TATTAATTCATTTATAATCTTATAAATGATTATAAATTGAAAT-ATTTAGACTTTATGGT-TAAA
* ** * *
1286406 ACCTATTATAATTGGATGTTTGTGTTCAG-AAACCTGAAGTGGATGCTATCAATTGAC
126 ACCTATCATAA-T-GATGTTTGCATT-AGAAAACGTGAAGTGGATGCTATC-CTTGAC
* * * * * *
1286463 ATGAAAAGATCATTTTAAGTTAATCATGCTATCGAAAGCTTTGATAC-ATGCTTTAAATTGTATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTA-ACTTTAAA-AG-ATA
* * * * * * *
1286527 TATATAA---ATTTATAATCTTGTAAATGATTATTAATTGATATACTTAGACGTTATCGTTCAAA
63 TAT-TAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAA
* * * ** * * * * *
1286589 CCTATTATAATTAGTTATTTAAACTAGAAAATGTGAATTGTATGGC-ATCCATTGAG
127 CCTATCATAA-T-GATGTTTGCATTAGAAAACGTGAAGTGGAT-GCTATCC-TTGAC
* * * * * * *
1286645 AATAAAAGACTATTTTAAGTTAATCGTGCCATCAAAAACTTTGTTACTCACTTTAATAGATATAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTAACTTTAAAAGATATAT
* * * *
1286710 TCATTCATTTATAGTCTTATAAA-GATTATAAAATGAAATATTTGGACTTTATGGTTAAAACCTA
66 TAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACCTA
* * * * * *
1286774 TCAAAATTGGATGCTTGGATTGGGAAACTTGAAGTGGATGCTATCCCTTGAC
131 TCATAA-T-GATGTTTGCATTAGAAAACGTGAAGTGGATGCTAT-CCTTGAC
* * ** * * ** *
1286826 AGGAAGAGACCATTTTAAGTTAATCATGTAATAGAAAGTTTTGTTACTTGCTTTAAATGA-AGTA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTAACTTTAAAAGATA-TA
* * * *
1286890 ATACTTCATTTATAATCTTATAAATGATTATAAATCT-AAATATTT-GAACTTTATGGTTCAAAG
65 TTAATTCATTTATAATCTTATAAATGATTATAAAT-TGAAATATTTAG-ACTTTATGGTTAAAAC
* * ** * * * * * * *
1286953 CTATTATAATTGGATTTTTAAATCAGGAAACATGAAGTAGATACTATTCATT-ATG
128 CTATCATAA-T-GATGTTTGCATTAGAAAACGTGAAGTGGATGCTA-TCCTTGA-C
*
1287008 AAGAAAAGACCATTTTATGTTAATCATGCCATC-AATAGCTTT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAA-AGCTTT
1287050 CTCACCCACT
Statistics
Matches: 1417, Mismatches: 346, Indels: 162
0.74 0.18 0.08
Matches are distributed among these distances:
171 6 0.00
172 100 0.07
173 9 0.01
174 7 0.00
175 6 0.00
178 47 0.03
179 228 0.16
180 24 0.02
181 254 0.18
182 717 0.51
183 19 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (179 bp):
AAGAAAAGACCATTTTAAGTTAATCATGCCATCGAAAGCTTTGTTACTAACTTTAAAAGATATAT
TAATTCATTTATAATCTTATAAATGATTATAAATTGAAATATTTAGACTTTATGGTTAAAACCTA
TCATAATGATGTTTGCATTAGAAAACGTGAAGTGGATGCTATCCTTGAC
Found at i:1286072 original size:360 final size:361
Alignment explanation
Indices: 1285255--1286072 Score: 954
Period size: 360 Copynumber: 2.3 Consensus size: 361
1285245 GATACATGCC
* *
1285255 TTAAATGATATATTAATACATTTATAATCTTATAAATGATCATTAATTGAGATATTTAGACTTTA
1 TTAAATGATATATTAATTCATTTATAATCTTATAAATGATTATTAATTGAGATATTTAGACTTTA
* * * *
1285320 TGAG-TAAAACCTATCATAATTGGGTGTTTGAATTTGGAAACGTGAAATGGATGGTATCTATTGA
66 T-AGTTAAAA-CTATCATAATTGGATGTTTCAATTTGGAAACATGAAATGGATGGTATCCATTGA
** * * *
1285384 CAAGAAAAAATTATTTTAATTTAATCATGCCATAGTAAACTTTGTTACTTACTTTGAACAATATA
129 CAAGAAAAAATTATTTTAAGCTAACCATGCCATAGTAAACTTTGTCACTCACTTTGAACAATATA
* * ** *
1285449 TAAATTCATTTGTAATCTTATAAATGATTATGCATTGAAATCTTTGGACTTTATGGTTAAAACCT
194 TAAATTCATTTGTAATATTACAAATGATTATAAATTGAAATCTTTAGACTTTATGGTTAAAACCT
* * * * *
1285514 TTCATAATTGGATGTTTGCATTGAGAAATGTGAAGTAGATACTTTTCCTTAACAAGAATAGACCA
259 ATCATAA-T-GATGTTTGCATTGAGAAACGTGAAGTAAATACTATTCCTTAACAAGAAAAGACCA
* * * * *
1285579 TTTTAAGCTAATCATGCCATCAATAGCGTTGTTACTCATT
322 CTTTAAGCTAATCATGCAATCAATAGCGTTATTACTAACT
* * * *
1285619 TTTAATGGTGTATTAATTCATTTATAATCTTATAAATGATTATTAATTGTGATATTTAGACTTTA
1 TTAAATGATATATTAATTCATTTATAATCTTATAAATGATTATTAATTGAGATATTTAGACTTTA
* * *
1285684 TGGTTAAAACATATCATAATTAGATGTTTCAA-TTGGAAGACATGAAATGGATGGTGTCCATTGA
66 TAGTTAAAAC-TATCATAATTGGATGTTTCAATTTGGAA-ACATGAAATGGATGGTATCCATTGA
* * *
1285748 CAAGAAAAGAA-TATTTT-AGCTAGCCGTGCCATCG-AAAGCTTTGTCACTCACTTTGAACAATA
129 CAAGAAAA-AATTATTTTAAGCTAACCATGCCATAGTAAA-CTTTGTCACTCACTTTGAACAATA
* * *
1285810 TACT-AGTTCATTTTTAATATTACAAATGATTATAAATTTAAATCTTTAGACTTTATGGTTAAAA
192 TA-TAAATTCATTTGTAATATTACAAATGATTATAAATTGAAATCTTTAGACTTTATGGTTAAAA
*
1285874 CCTATCATAA-GATGTTTGCATT-AGAAAACGTGAAGTAAATGCTATTCCTTGAA-AAGAAAAGA
256 CCTATCATAATGATGTTTGCATTGAG-AAACGTGAAGTAAATACTATTCCTT-AACAAGAAAAGA
* * *
1285936 CCACTTTAAGTTAATCATGCAATCGCA-AGCTTTATTACTAACT
319 CCACTTTAAGCTAATCATGCAATC-AATAGCGTTATTACTAACT
* * * ** * * *
1285979 TTAAAAGATACATTAATTCATTTATAATCTTATAAATGATTATAAATCAAAATCTTTGGACTTTA
1 TTAAATGATATATTAATTCATTTATAATCTTATAAATGATTATTAATTGAGATATTTAGACTTTA
* ** *
1286044 TAGTTCAAAGCTATTGTTATTGGATGTTT
66 TAGTT-AAAACTATCATAATTGGATGTTT
1286073 GCATTGAGCA
Statistics
Matches: 383, Mismatches: 61, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
359 2 0.01
360 145 0.38
361 7 0.02
362 3 0.01
363 104 0.27
364 120 0.31
365 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (361 bp):
TTAAATGATATATTAATTCATTTATAATCTTATAAATGATTATTAATTGAGATATTTAGACTTTA
TAGTTAAAACTATCATAATTGGATGTTTCAATTTGGAAACATGAAATGGATGGTATCCATTGACA
AGAAAAAATTATTTTAAGCTAACCATGCCATAGTAAACTTTGTCACTCACTTTGAACAATATATA
AATTCATTTGTAATATTACAAATGATTATAAATTGAAATCTTTAGACTTTATGGTTAAAACCTAT
CATAATGATGTTTGCATTGAGAAACGTGAAGTAAATACTATTCCTTAACAAGAAAAGACCACTTT
AAGCTAATCATGCAATCAATAGCGTTATTACTAACT
Found at i:1287040 original size:363 final size:361
Alignment explanation
Indices: 1285024--1287049 Score: 1377
Period size: 363 Copynumber: 5.6 Consensus size: 361
1285014 GTTCATTGCG
* * * * * * *
1285024 AAGAAAACAACATTTTAACTTAATCATGCCACCA-ATAGCTTTGTTACTCACTTTATATGGAGTA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCA-TAGAAAGCTTTGTTACTCACTTTAAAT-GAATA
* * *
1285088 T-TAATTCATTTATAATCTTATAAATGATTACAAATCAAAATATTTGAACTTTAT-GATCAAAAC
64 TATAATTCATTTATAATCTTATAAATGATTATAAAT-TAAATATTTGAACTTTATGGTTC-AAAC
* * * * * *
1285151 CTATTATAACTGGATGTTTGCATTCA-CAAACATGAAGTGGATGCTA-TCAATTGACAAG-AAA-
127 CTATTATAATTGGATTTTTG-AATCAGGAAACATGAAGTAGATGCTATTC-ATT-AGAAGAAAAG
* * * * * *
1285212 A-CATTTTAAATTAATCATGCCATCGAAAGCATTGATACATGC-CTTAAAT-GATATATTAATAC
189 ACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTAC-T-CACTTTAATAGATATATTAATTC
* * * *
1285274 ATTTATAATCTTATAAATGATCATTAATTGAGATATTTAGACTTTATGAG-TAAAACCTATCATA
252 ATTTATAATCTTATAAATGATTA-TAAATGAAATATTTGGACTTTATG-GTTAAAACCTATCATA
* * * * *
1285338 ATTGGGTGTTTGAATTTGGAAACGTGAAATGGATGGTATCTATTGAC
315 ATTGGATGTTTGAATTGGGAAACGTGAAGTGGATGCTATCAATTGAC
* ** * * * *
1285385 AAGAAAAAATTATTTTAATTTAATCATGCCATAGTAAA-CTTTGTTACTTACTTTGAA-CAATAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATAG-AAAGCTTTGTTACTCACTTTAAATGAATAT
* ** * * *
1285448 ATAAATTCATTTGTAATCTTATAAATGATTATGCATTGAAATCTTTGGACTTTATGGTTAAAACC
65 AT-AATTCATTTATAATCTTATAAATGATTATAAATT-AAATATTTGAACTTTATGGTTCAAACC
* * * ** * * * * *
1285513 T-TTCATAATTGGATGTTTGCAT-TGAGAAATGTGAAGTAGATACTTTTCCTTAACAAGAATAGA
128 TATT-ATAATTGGATTTTTGAATCAG-GAAACATGAAGTAGATGCTATTCATT-AGAAGAAAAGA
* * * * * *
1285576 CCATTTTAAGCTAATCATGCCATCAATAGCGTTGTTACTCATTTTTAAT-GGTGTATTAATTCAT
190 CCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCA-CTTTAATAGATATATTAATTCAT
* ** * *
1285640 TTATAATCTTATAAATGATTATTAATTGTGATATTTAGACTTTATGGTTAAAACATATCATAATT
254 TTATAATCTTATAAATGATTA-TAAATGAAATATTTGGACTTTATGGTTAAAACCTATCATAATT
* * * * * * *
1285705 AGATGTTTCAATT-GGAAGACATGAAATGGATGGTGTCCATTGAC
318 GGATGTTTGAATTGGGAA-ACGTGAAGTGGATGCTATCAATTGAC
** * ** * * * * *
1285749 AAGAAAAGAATATTTT-AGCTAGCCGTGCCATCGAAAGCTTTGTCACTCACTTTGAA-CAATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATAGAAAGCTTTGTTACTCACTTTAAATGAATATA
* * * * * *
1285812 CTAGTTCATTTTTAATATTACAAATGATTATAAATTTAAATCTTT-AGACTTTATGGTTAAAACC
66 -TAATTCATTTATAATCTTATAAATGATTATAAA-TTAAATATTTGA-ACTTTATGGTTCAAACC
* * * * * * * * *
1285876 TATCATAA---GATGTTTGCATTAGAAAACGTGAAGTAAATGCTATTCCTTGAAAAGAAAAGACC
128 TATTATAATTGGATTTTTGAATCAGGAAACATGAAGTAGATGCTATTCATT-AGAAGAAAAGACC
* * ** * * * *
1285938 ACTTTAAGTTAATCATGCAATCGCAAGCTTTATTACTAACTTTAAAAGATACATTAATTCATTTA
192 ATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAATAGATATATTAATTCATTTA
* * * * * ** *
1286003 TAATCTTATAAATGATTATAAATCAAAATCTTTGGACTTTATAGTTCAAAGCTATTGTTATTGGA
257 TAATCTTATAAATGATTATAAAT-GAAATATTTGGACTTTATGGTTAAAACCTATCATAATTGGA
* * * * * **
1286068 TGTTTGCATTGAGCAACGTGATGTGGACGCTACTC-ATTGTG
321 TGTTTGAATTGGGAAACGTGAAGTGGATGCTA-TCAATTGAC
* * * *
1286109 AAGAAAAGACCTTTTTAATTTAATCATGCCATCA-AAAGCTTTGTTTA-TCCCTTTAAAT-AATG
1 AAGAAAAGACCATTTTAAGTTAATCATGCCAT-AGAAAGCTTTG-TTACTCACTTTAAATGAATA
* * * * ** * * *
1286171 TAACAAATCATTCATAACCTTATAAACAATTATAACTTAAAT-TCATTGGACTTTATGTTTCAAA
64 T-ATAATTCATTTATAATCTTATAAATGATTATAAATTAAATAT--TTGAACTTTATGGTTCAAA
* * * * * * * * *
1286235 CCTATTGTTATTGGATATTTGCAT-TGAGAAACATGAAGTTGATGTTGTTCATT-GCAAAGCAAA
126 CCTATTATAATTGGATTTTTGAATCAG-GAAACATGAAGTAGATGCTATTCATTAG--AAGAAAA
* * * * * *
1286298 GACCATTTTAAGTTAACCATGCCATCAATAA-CTTTATTTCTCGCATTAAATA-ATGTATTAATT
188 GACCATTTTAAGTTAATCATGCCATCAA-AAGCTTTGTTACTCAC-TTTAATAGATATATTAATT
* * * *
1286361 CA-TT-T-A----AT---TGATTATAAATCAAA-ATCATTGGACTTTAT-ATAAAAAACCTATTA
251 CATTTATAATCTTATAAATGATTATAAATGAAATAT--TTGGACTTTATGGT-TAAAACCTATCA
** ** *
1286414 TAATTGGATGTTTGTGTTCAGAAACCTGAAGTGGATGCTATCAATTGAC
313 TAATTGGATGTTTGAATTGGGAAACGTGAAGTGGATGCTATCAATTGAC
* * * * * * *
1286463 ATGAAAAGATCATTTTAAGTTAATCATGCTATCGAAAGCTTTGATACAT-GCTTTAAATTGTATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATAGAAAGCTTTGTTAC-TCACTTTAAA-TGAATA
** * * * * * *
1286527 TAT-ATAAATTTATAATCTTGTAAATGATTATTAATTGATATACTT-AGACGTTATCGTTCAAAC
64 TATAATTCATTTATAATCTTATAAATGATTATAAATT-AAATATTTGA-ACTTTATGGTTCAAAC
* * * ** * * *
1286590 CTATTATAATTAG-TTATTT-AAACTAGAAAATGTGAA-TTGTATGGC-ATCCATTGAGAATAAA
127 CTATTATAATTGGATT-TTTGAATC-AGGAAACATGAAGTAG-AT-GCTATTCATT-AGAAGAAA
* * * *
1286651 AGACTATTTTAAGTTAATCGTGCCATCAAAAACTTTGTTACTCACTTTAATAGATATATTCATTC
187 AGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAATAGATATATTAATTC
* *
1286716 ATTTATAGTCTTATAAA-GATTATAAAATGAAATATTTGGACTTTATGGTTAAAACCTATCAAAA
252 ATTTATAATCTTATAAATGATTAT-AAATGAAATATTTGGACTTTATGGTTAAAACCTATCATAA
* * * **
1286780 TTGGATGCTTGGATTGGGAAACTTGAAGTGGATGCTATCCCTTGAC
316 TTGGATGTTTGAATTGGGAAACGTGAAGTGGATGCTATCAATTGAC
* * ** * **
1286826 AGGAAGAGACCATTTTAAGTTAATCATGTAATAGAAAGTTTTGTTACTTGCTTTAAATGAAGTA-
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATAGAAAGCTTTGTTACTCACTTTAAATGAA-TAT
* *
1286890 ATACTTCATTTATAATCTTATAAATGATTATAAATCTAAATATTTGAACTTTATGGTTCAAAGCT
65 ATAATTCATTTATAATCTTATAAATGATTATAAAT-TAAATATTTGAACTTTATGGTTCAAACCT
* *
1286955 ATTATAATTGGATTTTTAAATCAGGAAACATGAAGTAGATACTATTCATTATGAAGAAAAGACCA
129 ATTATAATTGGATTTTTGAATCAGGAAACATGAAGTAGATGCTATTCATTA-GAAGAAAAGACCA
* *
1287020 TTTTATGTTAATCATGCCATCAATAGCTTT
193 TTTTAAGTTAATCATGCCATCAAAAGCTTT
1287050 CTCACCCACT
Statistics
Matches: 1290, Mismatches: 288, Indels: 172
0.74 0.16 0.10
Matches are distributed among these distances:
352 1 0.00
353 21 0.02
354 225 0.17
355 10 0.01
356 5 0.00
357 2 0.00
359 14 0.01
360 181 0.14
361 211 0.16
362 24 0.02
363 332 0.26
364 255 0.20
365 9 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (361 bp):
AAGAAAAGACCATTTTAAGTTAATCATGCCATAGAAAGCTTTGTTACTCACTTTAAATGAATATA
TAATTCATTTATAATCTTATAAATGATTATAAATTAAATATTTGAACTTTATGGTTCAAACCTAT
TATAATTGGATTTTTGAATCAGGAAACATGAAGTAGATGCTATTCATTAGAAGAAAAGACCATTT
TAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAATAGATATATTAATTCATTTATAAT
CTTATAAATGATTATAAATGAAATATTTGGACTTTATGGTTAAAACCTATCATAATTGGATGTTT
GAATTGGGAAACGTGAAGTGGATGCTATCAATTGAC
Found at i:1287102 original size:67 final size:67
Alignment explanation
Indices: 1286994--1287129 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
1286984 ATGAAGTAGA
1286994 TACTATTCATTATGAAGAAAAGACCATTTTATGTTAATCATGCCATCAATAGCTTTCTCACCCAC
1 TACTATTCATTATGAAGAAAAGACCATTTTATGTTAATCATGCCATCAATAGCTTTCTCACCCAC
1287059 TT
66 TT
* *
1287061 TACTATTCATTATGAAGAAAAGACCATTTTTTGTTAATCATGCCATCAATAGCTTTCTCACTCAC
1 TACTATTCATTATGAAGAAAAGACCATTTTATGTTAATCATGCCATCAATAGCTTTCTCACCCAC
1287126 TT
66 TT
1287128 TA
1 TA
1287130 AATAATGTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (67 bp):
TACTATTCATTATGAAGAAAAGACCATTTTATGTTAATCATGCCATCAATAGCTTTCTCACCCAC
TT
Found at i:1287576 original size:182 final size:182
Alignment explanation
Indices: 1287075--1288987 Score: 1489
Period size: 182 Copynumber: 10.7 Consensus size: 182
1287065 ATTCATTATG
** * * * * * *
1287075 AAGAAAAGACCATTTTTTGTTAATCATGCCATCAATAGCTTTCTCACTCACTTTAAATAATGTAA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATAT
* * * * ** * **
1287140 TAGTTCATTTATAATCTCATAAATGATTATAAATCAATATCTTTTCACTTTATTGTTTTAACCTA
66 TAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCTA
** * * ** * * **
1287205 TTGTACTTGGATGCTTGCATTGGGAAACCAGAAATGGATGCTGTTTATTG-C
131 TCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * *
1287256 AAAAAAAAGACCATTTTAAGTTAATCATGCCAT--AAA---TAG---C-CACTTTAAATGGTCTA
1 -AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATA
* ** * * *
1287312 TTAATTCATTTATGAA-CTTATAAATGATCATAAACCAAAATCTTTAGACTTTATGATAAAAACC
65 TTAATTCATTTAT-AATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACC
* * * * * * * * *
1287376 AATTACAATTGGATGTTTGCATTCGTAAATGTGAAATGGATGTTATCAATTGAC
129 TATCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * * * *
1287430 AAGAAAACACCTTTTTAAGTTAATCATGCCATCAAAATCATTGATACATGA-TTCAAATGATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTAC-TCACTTTAAATGATATA
* * * * *
1287494 TTAATTCATTTATAATCTTATAAATGATTATTAATTGAGATATTTAGA-TCTTATGGTTAAAACC
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACT-TTATGGTTAAAACC
* * * * *
1287558 TATCATAATTGAATGTTTGAATTGGGAAACATGAGGTGGATGGC-ATCCATTGAG
129 TATCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGAT-GCTATCCATTGAC
* * * ** *
1287612 AAGAAAAGACTATTTTATGTTAATCGTGCCATTGAAATCTTTGTTACTCACTTTAACA-GATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAA-ATGATATA
* * * * * *
1287676 TTAATTCA-TTATAGTCTTATAAA-GATTATAAGA-CAACATATTTGGACTTTATGGTTAGAACT
65 TTAATTCATTTATAATCTTATAAATGATTATAA-ATTAAAATCTTTGGACTTTATGGTTAAAACC
* * * * * *
1287738 TATCATAATTGGATGCTTGGATTGGGAAACATAAAGCGGATGCTATCCCTTGA-
129 TATCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * *
1287791 AAAAGAAAGACCATTCTAATTTAATCATGCAATCAAAAGCTTTGTTACTCACTTTAAATGATGTA
1 AAGA-AAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATA
* * * * * * *
1287856 ATAATTCATTTATAATCTTACAAATAATTATAAATCAAATTCTTTGGACTTTATGGTTCAAAGCT
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCT
* * ** * * * **
1287921 A-CTTTAATTAGAAT-TTTGCATTAAGAAACGTGAAGTAGATACTATTCATTGTG
130 ATC-ATAATT-GGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * * * * *
1287974 AA-AAAAGTCCATTTTATGTTAATCATTCCATCAATAGCTTTCTTACTCACTTTAAATAATGTAA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATAT
* * * **
1288038 TAGTTCATTTATAATCTTATAAATGATTATAAATCAATATCTTTGGACTTTATGGTTTTAACCTA
66 TAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCTA
** * * * * * * * ** **
1288103 TTTTATTTGGATGTTAGCATTAGGAAACGTAAAATGGATACTGTTTATTGTG
131 TCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * *
1288155 AAGAAAATACCATCTTAAGTTATTCATGCCATC--AA---TAG---C-CACTTTAAATGATTTAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATAT
* * * * *
1288211 TAATTCATTTATGATCTTATAAATGATTATAAATCAAAATCTTTAGACTTTATGATCAAAACCTA
66 TAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCTA
* * * * * * * *
1288276 TTATAATTGGATGTTTGCATTTGCAAACATGAAGTTGATGTTATCAATTAAC
131 TCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * * * * * *
1288328 AAGAAAACACCATTTTAAGTTAATCATGGCATCGAAATCATTGATGCAT-GCTTCAAATGATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTAC-TCACTTTAAATGATATA
* * * * * * *
1288392 TTAATTCGTTTATAATTTTATAAATGATTATTAATTGAGATATTTGGACCTTATGGTTAAAACCT
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCT
* * *
1288457 ATCATAATTGGATGTTTGAATTGGGAAACATGAAGTGGATGGTATCCATTGAC
130 ATCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * ** *
1288510 AAGAAAAGACTA-TTTAAGTTAATTATACCATTGAAAA-C--T-TTA-TTGCTTTAAACGATATA
1 AAGAAAAGACCATTTTAAGTTAATCATGCCA-TCAAAAGCTTTGTTACTCACTTTAAATGATATA
** ** * * * *
1288569 CAAATTTGTTTACAATCTTATAAATGATTATAAATTGAAATCTTTATG-CTTTATAGTTAAAACC
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTT-GGACTTTATGGTTAAAACC
* ** * *
1288633 TA-CAATAATTGGATGTTTGCATTGAGAATTGCGAAGTGGATGCTATCCCTTGAC
129 TATC-ATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
** * * *
1288687 AAGAAAAGACCATTTTAAGTTAATCATGTAATCGAAAGCTTTGTTACTCACTTTCAATAATATAT
1 AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATAT
* * * * * *
1288752 TAATCCATTTGTGATCTTTTAAATGATTATCAATGAAAATCTTTGGACTTTATGG-TACAAACCT
66 TAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTA-AAACCT
* * * * *
1288816 ATTATAATTGGTTGTTTGAATTGGTAAACGTGAAGTGGATGCTATTCATTG-C
130 ATCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
* * * * *
1288868 AAAAAAAAGACTATTTTAAGTTAATCATGCCATCAATAGCTATGTTACTCACTTTAAATGATGTA
1 -AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATA
* * * **
1288933 TTCATACATTTATAATCTTATAAACGATTATAAATCCAAATCTTTGGACTTTATG
65 TTAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATG
1288988 ACCAAAACCT
Statistics
Matches: 1370, Mismatches: 306, Indels: 110
0.77 0.17 0.06
Matches are distributed among these distances:
173 263 0.19
174 5 0.00
175 5 0.00
176 2 0.00
177 125 0.09
178 21 0.02
179 7 0.01
180 133 0.10
181 209 0.15
182 592 0.43
183 8 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (182 bp):
AAGAAAAGACCATTTTAAGTTAATCATGCCATCAAAAGCTTTGTTACTCACTTTAAATGATATAT
TAATTCATTTATAATCTTATAAATGATTATAAATTAAAATCTTTGGACTTTATGGTTAAAACCTA
TCATAATTGGATGTTTGCATTGGGAAACGTGAAGTGGATGCTATCCATTGAC
Found at i:1288701 original size:359 final size:360
Alignment explanation
Indices: 1288224--1288892 Score: 840
Period size: 359 Copynumber: 1.9 Consensus size: 360
1288214 TTCATTTATG
**
1288224 ATCTTATAAATGATTATAAATCAAAATCTTTAGACTTTATGATCAAAACCTATTATAATTGGATG
1 ATCTTATAAATGATTATAAATCAAAATCTTTAGACTTTATGATCAAAACCTACAATAATTGGATG
* *
1288289 TTTGCATTTGCAAACATGAAGTTGATGTTATCAATTAACAAGAAAACACCATTTTAAGTTAATCA
66 TTTGCATTTGCAAACATGAAGTGGATGCTATCAATTAACAAGAAAACACCATTTTAAGTTAATCA
* * * * * * *
1288354 TGGCATCGAAATCATTGATGCAT-GC-TTCAAATGATATATTAATTCGTTTATAAT-TTTATAAA
131 TGGAATCGAAAGCATTGATAC-TCACTTTC-AATAATATATTAATCCATTTATAATCTTT-TAAA
* *
1288416 TGATTATTAATTG-AGATATTTGGACCTTATGGTTA-AAACCTATCATAATTGGATGTTTGAATT
193 TGATTATCAA-TGAAAATATTTGGACCTTATGG-TACAAACCTATCATAATTGGATGTTTGAATT
* *
1288479 GGGAAACATGAAGTGGATGGTATCCATTG-ACAAGAAAAGACTA-TTTAAGTTAATTATACCATT
256 GGGAAACATGAAGTGGATGCTATCCATTGCA-AAAAAAAGACTATTTTAAGTTAATTATACCATT
1288542 GAAAACTTTATTGCTTTAAACGATATACAAATTTGTTTACA
320 GAAAACTTTATTGCTTTAAACGATATACAAATTTGTTTACA
** *
1288583 ATCTTATAAATGATTATAAATTGAAATCTTTATG-CTTTAT-AGTTAAAACCTACAATAATTGGA
1 ATCTTATAAATGATTATAAATCAAAATCTTTA-GACTTTATGA-TCAAAACCTACAATAATTGGA
* ** * *
1288646 TGTTTGCA-TTG-AGAA-TTGCGAAGTGGATGCTATCCCTTGACAAGAAAAGACCATTTTAAGTT
64 TGTTTGCATTTGCA-AACAT--GAAGTGGATGCTATCAATTAACAAGAAAACACCATTTTAAGTT
* * * * *
1288708 AATCATGTAATCGAAAGCTTTGTTACTCACTTTCAATAATATATTAATCCATTTGTGATCTTTTA
126 AATCATGGAATCGAAAGCATTGATACTCACTTTCAATAATATATTAATCCATTTATAATCTTTTA
* * * *
1288773 AATGATTATCAATGAAAATCTTTGGACTTTATGGTACAAACCTATTATAATTGGTTGTTTGAATT
191 AATGATTATCAATGAAAATATTTGGACCTTATGGTACAAACCTATCATAATTGGATGTTTGAATT
* * *
1288838 GGTAAACGTGAAGTGGATGCTATTCATTGCAAAAAAAAGACTATTTTAAGTTAAT
256 GGGAAACATGAAGTGGATGCTATCCATTGCAAAAAAAAGACTATTTTAAGTTAAT
1288893 CATGCCATCA
Statistics
Matches: 263, Mismatches: 35, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
357 2 0.01
358 11 0.04
359 231 0.88
360 19 0.07
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (360 bp):
ATCTTATAAATGATTATAAATCAAAATCTTTAGACTTTATGATCAAAACCTACAATAATTGGATG
TTTGCATTTGCAAACATGAAGTGGATGCTATCAATTAACAAGAAAACACCATTTTAAGTTAATCA
TGGAATCGAAAGCATTGATACTCACTTTCAATAATATATTAATCCATTTATAATCTTTTAAATGA
TTATCAATGAAAATATTTGGACCTTATGGTACAAACCTATCATAATTGGATGTTTGAATTGGGAA
ACATGAAGTGGATGCTATCCATTGCAAAAAAAAGACTATTTTAAGTTAATTATACCATTGAAAAC
TTTATTGCTTTAAACGATATACAAATTTGTTTACA
Found at i:1289092 original size:27 final size:28
Alignment explanation
Indices: 1289050--1289139 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
1289040 TATCATATTA
* *
1289050 TGGCCTCGCCAC-ATATATCA-A-CCCG
1 TGGCCTTGCCACTATATATCACATACCG
*
1289075 TGGCCTTGCCACATATATATCACATACTG
1 TGGCCTTGCCAC-TATATATCACATACCG
*
1289104 TGGCCTTGCCACGTATATATCACATACTG
1 TGGCCTTGCCAC-TATATATCACATACCG
1289133 TGGCCTT
1 TGGCCTT
1289140 AACCTCATCT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.19
27 8 0.14
28 1 0.02
29 37 0.65
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (28 bp):
TGGCCTTGCCACTATATATCACATACCG
Found at i:1289106 original size:29 final size:29
Alignment explanation
Indices: 1289074--1289139 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
1289064 ATATCAACCC
1289074 GTGGCCTTGCCACATATATATCACATACT
1 GTGGCCTTGCCACATATATATCACATACT
*
1289103 GTGGCCTTGCCACGTATATATCACATACT
1 GTGGCCTTGCCACATATATATCACATACT
1289132 GTGGCCTT
1 GTGGCCTT
1289140 AACCTCATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (29 bp):
GTGGCCTTGCCACATATATATCACATACT
Found at i:1289523 original size:2 final size:2
Alignment explanation
Indices: 1289518--1289543 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1289508 TATATAGCTA
1289518 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1289544 TCAAAGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1292087 original size:15 final size:16
Alignment explanation
Indices: 1292058--1292090 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1292048 CTTGTGGATG
1292058 ATGCAATTTGCTTTTA
1 ATGCAATTTGCTTTTA
*
1292074 ATGC-ATTTGTTTTTA
1 ATGCAATTTGCTTTTA
1292089 AT
1 AT
1292091 TTAGGCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (16 bp):
ATGCAATTTGCTTTTA
Found at i:1297708 original size:6 final size:6
Alignment explanation
Indices: 1297697--1297721 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1297687 TCAGTTAAGA
1297697 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
1297722 GATCATGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:1299397 original size:168 final size:169
Alignment explanation
Indices: 1298881--1300053 Score: 762
Period size: 168 Copynumber: 6.9 Consensus size: 169
1298871 AACACCATCA
* * * * * * *
1298881 ACAAGAGAACTCTATTTATAGTCACTCATACCTTTGAAAGCC-ATGTTACTGT-CTTTCAGTGGT
1 ACAAGAAAAGTCTATTTATATTCACTCATGCCTTCGAAAGCCTA-GTTACT-TACTTTAAATGGT
* * * * *
1298944 TTTATAAGT-TTATAAATGATTTTAAGAT-AAGTTTTTTTTTTCATTTTTAGTTAAAACATCTCA
64 TTTATAA-TCTTATAAATGATTTTAAGTTGAA---TTTTGTTTCA-TTTTGGTTAAAATA-ATCA
* * ** * *
1299007 TAATTGGATGTTT-CTCTTGGAAAACATGAAGTGAAAGCCATCTATTA
123 TAATTAGATGTTTGC-CTTGGAAAACGTGAAGCAAAAGCCATCCATTG
* * * * * **
1299054 ACAAGAAAAGTTTATTTATAGTCACTCATGCCTTCGAAATCCTTA-TTAGTCTA-TTTAAGTCAT
1 ACAAGAAAAGTCTATTTATATTCACTCATGCCTTCGAAAGCC-TAGTTACT-TACTTTAAATGGT
* * * * *
1299117 TGTACAA-CATTATAAAAGATTTTAAATTG-A-TTT-TTTCATTTTAGGTTAAAACATATCATAA
64 TTTATAATC-TTATAAATGATTTTAAGTTGAATTTTGTTTCATTTT-GGTTAAAATA-ATCATAA
* ** * ***
1299178 TTAGATGTTTACC-TCAAGAAACATGAAATGAAAGCCATCCATTCG
126 TTAGATGTTTGCCTTGGA-AAACGTGAAGCAAAAGCCATCCATT-G
*** * *
1299223 -CAAGAAAAGTCTATTTATATTCACTCATATTTTTGAAAGTCTAGTTACTTACTTTAAATGGTTT
1 ACAAGAAAAGTCTATTTATATTCACTCATGCCTTCGAAAGCCTAGTTACTTACTTTAAATGGTTT
* * * * *
1299287 TATAATCTCAT-AGTGAGTTTAAGTTGAATTTTGTTTCATTTATGGTTAAGATAGGTCAT-ATTA
66 TATAATCTTATAAATGATTTTAAGTTGAATTTTGTTTCATTT-TGGTTAAAATA-ATCATAATTA
* * *
1299350 GATGTTTGCCTTGGCAAACGTGAAGCAAAAGTCA-CCTTTG
129 GATGTTTGCCTTGGAAAACGTGAAGCAAAAGCCATCCATTG
* * * *
1299390 ACAAGAAAAGTCTGTTTGTGA-TCACTCATGCCTTCGAAACCCTAGTTACTTA-TTT-TATGCGA
1 ACAAGAAAAGTCTATTTAT-ATTCACTCATGCCTTCGAAAGCCTAGTTACTTACTTTAAATG-G-
* * *
1299452 TTTTATAATCTTATAAATGATTTTAAGTTGAGTTTTTTTGTTTTTCATTTTTTGTTAGAGCA-AA
63 TTTTATAATCTTATAAATGATTTTAAGTTGA---ATTTTG--TTTCA-TTTTGGTTA-A-AATAA
* * ** * *
1299516 TCATAATTGGATGTTTCCCTCAGAAAATGTGAAGTAAAAGCCATCCATTG
120 TCATAATTAGATGTTTGCCTTGGAAAACGTGAAGCAAAAGCCATCCATTG
* * * ** *
1299566 ACAAGAAAAGTCCATTTATACTCACTCAAGCC-TCGAAAGCCTAGTTACTCGCTTT-AAT-TTCT
1 ACAAGAAAAGTCTATTTATATTCACTCATGCCTTCGAAAGCCTAGTTACTTACTTTAAATGGT-T
* ** *
1299628 TTATAATCTTATAAATGATTTTAAGTTG-ATTTT-TTTTATTTTCACTTAAAATAATCATAATTG
65 TTATAATCTTATAAATGATTTTAAGTTGAATTTTGTTTCATTTT-GGTTAAAATAATCATAATTA
* * * *
1299691 GATATTTACCTTGGAAAAAGTGAAGTGAAAA-CCATCCATTG
129 GATGTTTGCCTTGGAAAACGTGAAG-CAAAAGCCATCCATTG
* * * * * * *
1299732 ACAAGAAAAGTCTATTTATAGTT-ACTCATGCCCTCAAAAACCTTA-TTACTAACGTGAAGTGGT
1 ACAAGAAAAGTCTATTTATA-TTCACTCATGCCTTCGAAAGCC-TAGTTACTTACTTTAAATGGT
* *
1299795 TTTATAA-CTTTATAAATGATTTTAAGAT-AATTTTTTTTCATTTTAGGTTGAAACA-AATCATA
64 TTTATAATC-TTATAAATGATTTTAAGTTGAATTTTGTTTCATTTT-GGTT-AAA-ATAATCATA
* *
1299857 ATT-GAATGTTTGCCTTGGGAAACGTGAAGCAAAAGCCATCCGTTG
125 ATTAG-ATGTTTGCCTTGGAAAACGTGAAGCAAAAGCCATCCATTG
* * * ** *
1299902 AGAAGAAAAGT-TCA-TTATAATCACTCATG-CTTCCGAAAGTCTAGTTACTTGTTTTAAATAGT
1 ACAAGAAAAGTCT-ATTTATATTCACTCATGCCTT-CGAAAGCCTAGTTACTTACTTTAAATGGT
* * * * * * * *
1299964 TTTATAATCTCA-AAATGAGTTTAAGTGGAATTCTGCTTCATTTTATGATAAAATAGATTATAAT
64 TTTATAATCTTATAAATGATTTTAAGTTGAATTTTGTTTCATTTT-GGTTAAAATA-ATCATAAT
* * *
1300028 TAGATGTTAGCCTTGGGAAACATGAA
127 TAGATGTTTGCCTTGGAAAACGTGAA
1300054 ACGATAGTTA
Statistics
Matches: 791, Mismatches: 149, Indels: 124
0.74 0.14 0.12
Matches are distributed among these distances:
165 1 0.00
166 76 0.10
167 54 0.07
168 220 0.28
169 149 0.19
170 80 0.10
171 2 0.00
172 5 0.01
173 71 0.09
174 43 0.05
175 53 0.07
176 37 0.05
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (169 bp):
ACAAGAAAAGTCTATTTATATTCACTCATGCCTTCGAAAGCCTAGTTACTTACTTTAAATGGTTT
TATAATCTTATAAATGATTTTAAGTTGAATTTTGTTTCATTTTGGTTAAAATAATCATAATTAGA
TGTTTGCCTTGGAAAACGTGAAGCAAAAGCCATCCATTG
Found at i:1299989 original size:510 final size:511
Alignment explanation
Indices: 1298975--1299989 Score: 1082
Period size: 510 Copynumber: 2.0 Consensus size: 511
1298965 TTAAGATAAG
** * ** *
1298975 TTTTTTTTTTCATTTTTAGTTAAAACATCTCATAATTGGATGTTTCTCTTGGAAAACATGAAGTG
1 TTTTTTTTTTCATTTTTAGTTAAAACAAATCATAATTGGATGTTTCCCTCAGAAAACATGAAGTA
* ** * * * *
1299040 AAAGCCATCTATTAACAAGAAAAGTTTATTTATAGTCACTCATGCCTTCGAAATCCTTATTAGTC
66 AAAGCCATCCATTAACAAGAAAAGTCCATTTATACTCACTCAAGCCTTCGAAAGCCTTATTACTC
* *
1299105 TATTTAAGTCATTGTACAACATTATAAAAGATTTTAAATTGATTTTTTCATTTTAGGTTAAAACA
131 GATTTAAGTCATTGTACAACATTATAAAAGATTTTAAATTGATTTTTTCATTTTAGCTTAAAACA
* * *
1299170 TATCATAATTAGATGTTTACCTCAAGAAACATGAAATGAAAGCCATCCATTCGCAAGAAAAGTCT
196 TATCATAATTAGATATTTACCTCAAGAAAAATGAAATGAAAACCATCCATTCGCAAGAAAAGTCT
*** ** ** * * * *
1299235 ATTTATATTCACTCATATTTTTGAAAGTCTAGTTACTTACTTTAAATGGTTTTATAATCTCATAG
261 ATTTATATTCACTCATACCCTCAAAAACCTAGTTACTAACGTGAAATGGTTTTATAATCTCATAA
* * **
1299300 TGAGTTTAAGTTGAATTTTGTTTCATTTATGGTTAAGATAGGTCATATTAGATGTTTGCCTTGGC
326 TGAGTTTAAGATGAATTTTGTTTCATTTATGGTTAAGACAAATCATATTAGATGTTTGCCTTGGC
* * ** * *
1299365 AAACGTGAAGCAAAAGTCACCTTTGACAAGAAAAGTCTGTTTGTGATCACTCATGCCTTCGAAAC
391 AAACGTGAAGCAAAAGCCACCGTTGACAAGAAAAGTCTCATTATAATCACTCATGCCTTCGAAAC
* * *
1299430 CCTAGTTACTTATTTTATGCGATTTTATAATCTTATAAATGATTTTAAGTTGAGTT
456 CCTAGTTACTTATTTTATGAGATTTTATAATCTCATAAATGAGTTTAAGTTGAGTT
* * * **
1299486 TTTTTGTTTTTCATTTTTTGTTAGAGCAAATCATAATTGGATGTTTCCCTCAGAAAATGTGAAGT
1 TTTTT-TTTTTCATTTTTAGTTAAAACAAATCATAATTGGATGTTTCCCTCAGAAAACATGAAGT
*
1299551 AAAAGCCATCCATTGACAAGAAAAGTCCATTTATACTCACTCAAGCC-TCGAAAGCC-TAGTTAC
65 AAAAGCCATCCATTAACAAGAAAAGTCCATTTATACTCACTCAAGCCTTCGAAAGCCTTA-TTAC
* * * * * *
1299614 TCGCTTTAATTTC-TT-TATAATC-TTATAAATGATTTTAAGTTGATTTTTTTTATTTTCA-CTT
129 TCGATTTAA-GTCATTGTACAA-CATTATAAAAGATTTTAAATTGA-TTTTTTCATTTT-AGCTT
* * ** *
1299675 AAAATA-ATCATAATTGGATATTTACCT-TGGAAAAAGTGAAGTGAAAACCATCCATT-GACAAG
190 AAAACATATCATAATTAGATATTTACCTCAAGAAAAA-TGAAATGAAAACCATCCATTCG-CAAG
* *
1299737 AAAAGTCTATTTATAGTT-ACTCATGCCCTCAAAAACCTTA-TTACTAACGTGAAGTGGTTTTAT
253 AAAAGTCTATTTATA-TTCACTCATACCCTCAAAAACC-TAGTTACTAACGTGAAATGGTTTTAT
* * *
1299800 AA-CTTTATAAATGATTTTAAGAT-AATTTTTTTTCATTT-TAGGTTGAA-ACAAATCATAATT-
316 AATC-TCAT-AATGAGTTTAAGATGAATTTTGTTTCATTTAT-GGTT-AAGACAAATCAT-ATTA
* *
1299860 GAATGTTTGCCTTGGGAAACGTGAAGCAAAAGCCATCCGTTGAGAAGAAAAGT-TCATTATAATC
376 G-ATGTTTGCCTTGGCAAACGTGAAGCAAAAGCCA-CCGTTGACAAGAAAAGTCTCATTATAATC
** *
1299924 ACTCATG-CTTCCGAAAGTCTAGTTACTTGTTTTAAAT-AG-TTTTATAATCTCA-AAATGAGTT
439 ACTCATGCCTT-CGAAACCCTAGTTACTTATTTT--ATGAGATTTTATAATCTCATAAATGAGTT
1299985 TAAGT
501 TAAGT
1299990 GGAATTCTGC
Statistics
Matches: 415, Mismatches: 69, Indels: 41
0.79 0.13 0.08
Matches are distributed among these distances:
509 8 0.02
510 157 0.38
511 140 0.34
512 108 0.26
513 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (511 bp):
TTTTTTTTTTCATTTTTAGTTAAAACAAATCATAATTGGATGTTTCCCTCAGAAAACATGAAGTA
AAAGCCATCCATTAACAAGAAAAGTCCATTTATACTCACTCAAGCCTTCGAAAGCCTTATTACTC
GATTTAAGTCATTGTACAACATTATAAAAGATTTTAAATTGATTTTTTCATTTTAGCTTAAAACA
TATCATAATTAGATATTTACCTCAAGAAAAATGAAATGAAAACCATCCATTCGCAAGAAAAGTCT
ATTTATATTCACTCATACCCTCAAAAACCTAGTTACTAACGTGAAATGGTTTTATAATCTCATAA
TGAGTTTAAGATGAATTTTGTTTCATTTATGGTTAAGACAAATCATATTAGATGTTTGCCTTGGC
AAACGTGAAGCAAAAGCCACCGTTGACAAGAAAAGTCTCATTATAATCACTCATGCCTTCGAAAC
CCTAGTTACTTATTTTATGAGATTTTATAATCTCATAAATGAGTTTAAGTTGAGTT
Found at i:1300482 original size:31 final size:31
Alignment explanation
Indices: 1300447--1300506 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1300437 ACATAGAAGA
** *
1300447 AAATTGGAATTGAAGAAATGTTGGAAGGGCC
1 AAATTGGAAAGGAAGAAAAGTTGGAAGGGCC
* *
1300478 AAATTGTAAAGGATGAAAAGTTGGAAGGG
1 AAATTGGAAAGGAAGAAAAGTTGGAAGGG
1300507 TATATGGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.33, T:0.22
Consensus pattern (31 bp):
AAATTGGAAAGGAAGAAAAGTTGGAAGGGCC
Found at i:1304311 original size:171 final size:171
Alignment explanation
Indices: 1302632--1305586 Score: 1800
Period size: 170 Copynumber: 17.4 Consensus size: 171
1302622 GAGCCAATAG
* ** * * **
1302632 ATGGATGGCTTTTGCTTGACATTTT-GGAAGGCAAACATCTAATTATGATTTGTTTTAACCAAAA
1 ATGGATGGCTTTTGCTTCAC-TTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
* * * * *
1302696 ATGAAAACCAA-TGCAACTTAAAATTATTTAT-GAGATTATAAAACCATTTAAAGCGAGTAACTA
65 ATGAAAA-AAACT-TAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACTA
* *
1302759 GGCTTTCGAAGGCATGAGTGATTATAAATGGACTTTTCTTGTCA
128 GGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
** * *** * ** * ** *
1302803 ATGGATGGCTTTCACTTCACGTTTTC-CAATCCAAACATCAAATTAAAATATAATTTAA-TGAAA
1 ATGGATGGCTTTTGCTTCAC-TTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACT-TAA
* * * * *
1302866 AATGAAAAAAA-TTAATTTAAAATCACTTATAAAG-TTCTAAAATCA-TTGAAAG-TGAG-AAGC
64 AATGAAAAAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTT-AAAGCT-AGTAA-C
* * * *
1302926 AAGGCTTTCGAAGGTATGAATAACTATAAA-AGGAAC-TTTCTTGTCA
126 TAGGCTTTCGAAGGCATGAGTGACTATAAATA-G-ACTTTTCTTGTCA
* * * * * * * **
1302972 ATGGATGACTTTTGTTTCA-TGTTTTTTAAGGCAAACATCCAATTATAATCTATTTTAACCAAAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
* * * * * * *
1303036 AT-AAAAAAAATTCAAGTTCAAAA-AATTTAT-GAGATTCTAAAACAATTTAAAGCAAGTAACTA
65 ATGAAAAAAACTT-AACTT-AAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACTA
* **** * * *
1303098 GGATTTCGAAAATTTTAGTGACTATAAATGGACTTTTCTTATCA
128 GGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * * ** *
1303142 ATGGACGGCTTTCGCTTCACTTTTTTTGA-GACAAACATCCAATTATGATTTACTTTAAC-CATA
1 ATGGATGGCTTTTGCTTCACTTTTCTTAAGGA-AAACATCCAATTATGATTTGTTTTAACTTA-A
* * * ** *
1303205 AATGAAAAAGAAAACTCAACCTAAAATCATTTATA-ATATTATAAAA-CTGTGTAAAGCAAGTAA
64 AATG--AAA-AAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACT-TAAAGCTAGTAA
* * *
1303268 CTAGGCTTTCAAAGGCATGAGTGACTATTAAT-GAACTTTTCTTATCA
125 CTAGGCTTTCGAAGGCATGAGTGACTATAAATAG-ACTTTTCTTGTCA
* * * * * * * * *
1303315 AGGGATGGCTTCTGCTTCACGTTTCCTATGGCAAACATCTAATTATGATCTGTTTT-ACAATAAA
1 ATGGATGGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAAC-TTAAA
* * *
1303379 ATGAAACAAAA-TTCAACTTAAACTCA-TTAT-GAGATTATAAAACCATTTAAA-ATGAGTAACT
65 ATGAAA-AAAACTT-AACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCT-AGTAACT
** ** * * *
1303440 AGGCTTTTAAAAACATGAGTGATTATAAACAGACTTTTCTTCTCA
127 AGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * * *
1303485 ACGGATGGCTTTTGCTTCA-TGTTTCTTGAGGTAAACATTCAATTATGATTTGTTTTAACCTAAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
** * *
1303549 ATTTTAAAAAA-TTATCTTAAAATCATTTATAGA-TTTATAAAACCACTTAAAGCTAGTAA-TAA
65 A-TGAAAAAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACT-A
** * **
1303611 GATTTTCGACGATATGAGTGACTATAAATAGACTTCTT-TTGTCA
128 GGCTTTCGAAGGCATGAGTGACTATAAATAGACTT-TTCTTGTCA
** * * * * *
1303655 ATGGATGGCTTTCACTTCACTTTT-TTCGAGGCAAACATCCAATTATGATTTATTTTAAGTGAAA
1 ATGGATGGCTTTTGCTTCACTTTTCTT-AAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
* * * * *
1303719 ATGAAAAAAATTTAACTTAAAATCATTTAT-GAGATTATAAAGA-AAC-TAAAGCGAATAATTAG
65 ATGAAAAAAACTTAACTTAAAATCATTTATAGAGATTATAAA-ACCACTTAAAGCTAGTAACTAG
* *
1303781 GCTTTCG-AGGCATAAGTGACTATAAATTGACTTTTCTTGTCA
129 GCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * ** *
1303823 ATGGATGGCTTTTGCTCCACGTTTTC-TAAAGAAAACATCCAATTATGACTTGCCTTAA-TAAAA
1 ATGGATGGCTTTTGCTTCAC-TTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACT-TAA
* * * * * *
1303886 AAGGAAAAGAAAAGCTCAACCTAAAATCATTTACA-AGATTATAAAACCATTTAAA-ATAAGTAA
64 AATG-AAA-AAAA-CTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCT-AGTAA
* * * * **
1303949 CTAGGCTTTCGAAGGTATGGGTGACCATAAATAGACTTTTGTTACCA
125 CTAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* ** * * * * *
1303996 AGGGATGGCTTTTGCTTCACTTTTCCCCAA-GAAAACATCTAAATATGATATGTTGTACACATAA
1 ATGGATGGCTTTTGCTTCACTTTT-CTTAAGGAAAACATCCAATTATGATTTGTTTTA-ACTTAA
* *
1304060 AATGAAACAAAA-TTCAACTTAAACTCA-TTAT-GAGATTATAAAACCATTTTAAA--TGAGTAA
64 AATGAAA-AAAACTT-AACTTAAAATCATTTATAGAGATTATAAAACCA-CTTAAAGCT-AGTAA
** * * * *
1304120 CTAGGCTTTTAAAAGCATGAGTGATTATAAATAGACTTTCCTTCTCA
125 CTAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
** * * *
1304167 ACAGATGGCTTTTGCTTCA-TATTTCTTGAGGTAAACATTCAATTATGATTTGTTTTAACTTAAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
*
1304231 ATGGATACAAAAA-TTATCTTAAAATCATTTATAGAG-TTATAAAACCACTTAAAGCTAGTAA-T
65 AT-GA-A-AAAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACT
* * *
1304293 AAGG-TTTCGACGGCATGAGTGACTATAAACAGACTTCTCTTGTCA
127 -AGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * *
1304338 ATGGATAGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTATTTTAAGTGAAAA
1 ATGGATGGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAAA
* * * * *
1304403 TGAAAAAAATTTAACTTAAAATCATTTAT-GAGATTATAAAA-AAATTAAAGCGAGTAACTAGTC
66 TGAAAAAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACTAGGC
* * * * *
1304466 TTTTG-AGGCATAAATGACTATAACTTGACTTTTCTTGTCA
131 TTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * * *
1304506 ATAGATGGCTTTTGCTTCA-TCTTTCCTAAAGAAAACATCCAATTATGACTTT-CTTTAA-TAAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTTAAGGAAAACATCCAATTATGA-TTTGTTTTAACT-TA
* * * * *
1304568 AAATGAAAAAAAAGCTCAACTTAAAACCATTTATA-AGATTATAAAACCATTTAAATCAAGTAAC
63 AAATG-AAAAAAA-CTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAAC
* * * *
1304632 TAGGCTTTCGAAGGCATGAGTGACCATAAATGGACTTTTATTATCA
126 TAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * ** * * * * *
1304678 AGGGATAGCTTTTGCTTCAGTTTTCCCCAA-GCAAACATCTAATTATGATATGCTTTAAC-CATA
1 ATGGATGGCTTTTGCTTCACTTTT-CTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTA-A
* * ** * *
1304741 AATGAAATAGAA-TTCAACTTAAACTCA-TTAT-GATTTTAGAAAACCATTTAAAG-TGAGTAAC
64 AATGAAA-AAAACTT-AACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCT-AGTAAC
* * * * ** *
1304802 TAGACTTTTC-AAAGTATGAGTGAATATAAACGGACTTTTCTTGTAA
126 TAGGC-TTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * * * *
1304848 ATGGATGGC-TTT-CTTGA---GTC-------AAACATCTAATTATGATCTATTTTAACCTAAAA
1 ATGGATGGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAAA
* * * * * ** *
1304901 TGAAAAAATA-TCAATTTAAAATAATTTATA-AGGTTATACAATGACTTAAA--TAGACTAACAA
66 TGAAAAAA-ACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAG--TAACTA
* * *
1304962 GGCTTTCAAAGGTATGAGTGACCATAAATAGACTTTTCTTGTCA
128 GGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
* * * * * * *
1305006 ATGGATGGCTTTTGCTTCA-TGTTTCCTAA-GACAAATAGT-GAATTATGATCTATTTTAAGTAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTTAAGGA-AAACA-TCCAATTATGATTTGTTTTAACTTA
* *
1305068 AAAT-AAAAAAA-TTCAACTTAAAATCATTTAT-GAGATTATAAAGA--AATTAAAGCGAGTAAC
63 AAATGAAAAAAACTT-AACTTAAAATCATTTATAGAGATTATAAA-ACCACTTAAAGCTAGTAAC
* * *
1305128 TAGGCTTTCG-AGGCATGAGTGATTATAAATAGACTTGTCTTATCA
126 TAGGCTTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
** * * * * * * * **
1305173 ATAAATAGCTTTTGCTTCACATTTCTTTAGGTAAATATCTAATTATGATCTAATTTAA-TTAAAA
1 ATGGATGGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTT-AAA
* * * * * * *
1305237 ATGAAAAAAA-TTCAGTCTGAAATCATTTATA-ACG-TTTTATAACCTCTTAAAGCGAGTAAC-A
65 ATGAAAAAAACTTAACT-TAAAATCATTTATAGA-GATTATAAAACCACTTAAAGCTAGTAACTA
* * * *
1305298 AGCTTTTCAAAGGCATGGGTGACTACAAAT-GAGCTTTTCTTGTCA
128 GGC-TTTCGAAGGCATGAGTGACTATAAATAGA-CTTTTCTTGTCA
* ** * * * * * * **
1305343 ATAGATGTATTTTGTTTCACCTTTT-TTAAGGCAGACATCTAATTATGATCTGATTTAACCAAAA
1 ATGGATGGCTTTTGCTTCA-CTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAA
** * * *
1305407 ATGAAAAAGAA-TTCAGTTTAAACA-CATTTAT-GAGATTATAAAACTATTTAAAG-TGAGTAAT
65 ATGAAAAA-AACTT-AACTTAAA-ATCATTTATAGAGATTATAAAACCACTTAAAGCT-AGTAAC
* * * *
1305468 TACGCTTTCGAAAGCATGAGTGATTATAAATTA-ACTTTTTTTGTCA
126 TAGGCTTTCGAAGGCATGAGTGACTATAAA-TAGACTTTTCTTGTCA
** * * * * *
1305514 ATGGATGGCTTTCACTTTA-TGTTT-TTCAAGGCAAACAT-CAATTATGATCTATTTTAACCTAA
1 ATGGATGGCTTTTGCTTCACT-TTTCTT-AAGGAAAACATCCAATTATGATTTGTTTTAACTTAA
*
1305576 AATTAAAAAAA
64 AATGAAAAAAA
1305587 AATTAATTCA
Statistics
Matches: 2188, Mismatches: 440, Indels: 314
0.74 0.15 0.11
Matches are distributed among these distances:
156 2 0.00
157 16 0.01
158 97 0.04
159 4 0.00
160 4 0.00
163 2 0.00
164 1 0.00
165 1 0.00
166 2 0.00
167 88 0.04
168 246 0.11
169 265 0.12
170 625 0.29
171 461 0.21
172 161 0.07
173 198 0.09
174 15 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (171 bp):
ATGGATGGCTTTTGCTTCACTTTTCTTAAGGAAAACATCCAATTATGATTTGTTTTAACTTAAAA
TGAAAAAAACTTAACTTAAAATCATTTATAGAGATTATAAAACCACTTAAAGCTAGTAACTAGGC
TTTCGAAGGCATGAGTGACTATAAATAGACTTTTCTTGTCA
Found at i:1304501 original size:683 final size:676
Alignment explanation
Indices: 1302662--1305586 Score: 2862
Period size: 682 Copynumber: 4.3 Consensus size: 676
1302652 ATTTTGGAAG
* * * * *
1302662 GCAAACATCTAATTATGATTTGTTTTAACCA-AAAATGAAA-ACCAATGCAACTTAAAATTATTT
1 GCAAACATCTAATTATGATATGTTTTAACCATAAAATGAAACA-AAATTCAACTTAAACTCA-TT
* ** * **
1302725 ATGAGATTATAAAACCATTTAAAGCGAGTAACTAGGCTTTCGAAGGCATGAGTGATTATAAATGG
64 ATGAGATTATAAAACCATTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAACAG
* ** ** ** *** ** *
1302790 ACTTTTCTTGTCAATGGATGGCTTTCACTTCACGTTTTC-CAATCCAAACATCAAATTAAAATAT
129 ACTTTTCTTCTCAACAGATGGCTTTTGCTTCA--TTTTCTTGAGGTAAACATCAAATTATGATTT
* *** * * * *
1302854 AATTTAATGAAAAATGAAAAAAATTAATTTAAAATCACTTATAAAGTTCTAAAATCA-TTGAAAG
192 ATTTTAACCTAAAATGAAAAAAATT-ATTTAAAATCATTTATAGAGTTATAAAACCACTT-AAAG
* * *
1302918 TGAG-AAGCAAGGCTTTCGAAGGTATGAATAACTATAAA-AGGAACTT-TCTTGTCAATGGATGA
255 T-AGTAA-CAAGGCTTTCGAAGGTATGAGTGACTATAAATA-G-ACTTCTCTTGTCAATGGATGG
* * * * ** *
1302980 CTTTTGTTTCATGTTTTTTAAGGCAAACATCCAATTATAATCTATTTTAACCAAAAATAAAAAAA
316 CTTTTGCTTCATGTTTCTTAAGGAAAACATCCAATTATGATCTATTTTAAGTAAAAATGAAAAAA
* * * * * * *
1303045 ATTCAAGTTCAAAA-AATTTATGAGATTCTAAAACAATTTAAAGCAAGTAACTAGGATTTCGA-A
381 ATTCAACTT-AAAATCATTTATGAGATTATAAAA-AAATTAAAGCGAGTAACTAGGCTTTCGAGG
* * * * * * * **
1303108 AATTTTAGTGACTATAAATGGACTTTTCTTATCAATGGACGGCTTTCGCTTCACTTTTTTTGAGA
444 CA--TAAGTGACTATAAATTGACTTTTCTTATCAATAGATGGCTTTTGCTTCACTTTTCTAAAGA
* * * * *
1303173 CAAACATCCAATTATGATTTACTTTAACCATAAATGAAAAAGAAAA-CTCAACCTAAAATCATTT
507 -AAACATCCAATTATGACTTACTTTAA-TAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTT
* ** * ** * * *
1303237 ATAATATTATAAAACTGTGTAAAGCAAGTAACTAGGCTTTCAAAGGCATGAGTGACTATTAATGA
570 ATAAGATTATAAAACCATTTAAAATAAGTAACTAGGCTTTCGAAGGCATGAGTGACCATAAATG-
* * * * *
1303302 ACTTTTCTTATCAAGGGATGGCTTCTGCTTCACGTTT-CCTATG
634 ACTTTTATTATCAAGGGATGGCTTTTGCTTCACTTTTCCCCA-A
* *
1303345 GCAAACATCTAATTATGATCTGTTTT-ACAATAAAATGAAACAAAATTCAACTTAAACTCATTAT
1 GCAAACATCTAATTATGATATGTTTTAACCATAAAATGAAACAAAATTCAACTTAAACTCATTAT
* *
1303409 GAGATTATAAAACCATTTAAAATGAGTAACTAGGCTTTTAAAAACATGAGTGATTATAAACAGAC
66 GAGATTATAAAACCATTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAACAGAC
* *
1303474 TTTTCTTCTCAACGGATGGCTTTTGCTTCATGTTTCTTGAGGTAAACATTC-AATTATGATTTGT
131 TTTTCTTCTCAACAGATGGCTTTTGCTTCAT-TTTCTTGAGGTAAACA-TCAAATTATGATTTAT
** *
1303538 TTTAACCTAAAATTTTAAAAAATTATCTTAAAATCATTTATAGATTTATAAAACCACTTAAAGCT
194 TTTAACCTAAAA-TGAAAAAAATTAT-TTAAAATCATTTATAGAGTTATAAAACCACTTAAAG-T
* ** * * * *
1303603 AGTAATAAGATTTTCGACGATATGAGTGACTATAAATAGACTTCTTTTGTCAATGGATGGCTTTC
256 AGTAACAAGGCTTTCGAAGGTATGAGTGACTATAAATAGACTTCTCTTGTCAATGGATGGCTTTT
* * * * *
1303668 ACTTCACT-TTT-TTCGAGGCAAACATCCAATTATGATTTATTTTAAGTGAAAATGAAAAAAATT
321 GCTTCA-TGTTTCTT-AAGGAAAACATCCAATTATGATCTATTTTAAGTAAAAATGAAAAAAATT
* * * * *
1303731 TAACTTAAAATCATTTATGAGATTATAAAGAAACTAAAGCGAATAATTAGGCTTTCGAGGCATAA
384 CAACTTAAAATCATTTATGAGATTATAAAAAAATTAAAGCGAGTAACTAGGCTTTCGAGGCATAA
* * *
1303796 GTGACTATAAATTGACTTTTCTTGTCAATGGATGGCTTTTGCTCCACGTTTTCTAAAGAAAACAT
449 GTGACTATAAATTGACTTTTCTTATCAATAGATGGCTTTTGCTTCAC-TTTTCTAAAGAAAACAT
* * *
1303861 CCAATTATGACTTGCCTTAATAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTTACAAGATT
513 CCAATTATGACTTACTTTAATAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTTATAAGATT
* * *
1303926 ATAAAACCATTTAAAATAAGTAACTAGGCTTTCGAAGGTATGGGTGACCATAAATAGACTTTTGT
578 ATAAAACCATTTAAAATAAGTAACTAGGCTTTCGAAGGCATGAGTGACCATAAAT-GACTTTTAT
*
1303991 TACCAAGGGATGGCTTTTGCTTCACTTTTCCCCAA
642 TATCAAGGGATGGCTTTTGCTTCACTTTTCCCCAA
* * *
1304026 GAAAACATCTAAATATGATATGTTGT-ACACATAAAATGAAACAAAATTCAACTTAAACTCATTA
1 GCAAACATCTAATTATGATATGTTTTAAC-CATAAAATGAAACAAAATTCAACTTAAACTCATTA
*
1304090 TGAGATTATAAAACCATTTTAAA-TGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAATAG
65 TGAGATTATAAAACCA-TTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAACAG
*
1304154 ACTTTCCTTCTCAACAGATGGCTTTTGCTTCATATTTCTTGAGGTAAACATTC-AATTATGATTT
129 ACTTTTCTTCTCAACAGATGGCTTTTGCTTCAT-TTTCTTGAGGTAAACA-TCAAATTATGATTT
* *
1304218 GTTTTAACTTAAAATGGATACAAAAATTATCTTAAAATCATTTATAGAGTTATAAAACCACTTAA
192 ATTTTAACCTAAAAT-GA-A-AAAAATTAT-TTAAAATCATTTATAGAGTTATAAAACCACTTAA
* * * * *
1304283 AGCTAGTAATAAGG-TTTCGACGGCATGAGTGACTATAAACAGACTTCTCTTGTCAATGGATAGC
253 AG-TAGTAACAAGGCTTTCGAAGGTATGAGTGACTATAAATAGACTTCTCTTGTCAATGGATGGC
* *
1304347 TTTTGCTTCACT-TTTCTTAAGGAAAACATCCAATTATGATTTATTTTAAGTGAAAATGAAAAAA
317 TTTTGCTTCA-TGTTTCTTAAGGAAAACATCCAATTATGATCTATTTTAAGTAAAAATGAAAAAA
* * *
1304411 ATTTAACTTAAAATCATTTATGAGATTATAAAAAAATTAAAGCGAGTAACTAGTCTTTTGAGGCA
381 ATTCAACTTAAAATCATTTATGAGATTATAAAAAAATTAAAGCGAGTAACTAGGCTTTCGAGGCA
* * * *
1304476 TAAATGACTATAACTTGACTTTTCTTGTCAATAGATGGCTTTTGCTTCATCTTTCCTAAAGAAAA
446 TAAGTGACTATAAATTGACTTTTCTTATCAATAGATGGCTTTTGCTTCA-CTTTTCTAAAGAAAA
* * * *
1304541 CATCCAATTATGACTTTCTTTAATAAAAAATGAAAA-AAAAGCTCAACTTAAAACCATTTATAAG
510 CATCCAATTATGACTTACTTTAATAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTTATAAG
1304605 ATTATAAAACCATTT-AAATCAAGTAACTAGGCTTTCGAAGGCATGAGTGACCATAAATGGACTT
575 ATTATAAAACCATTTAAAAT-AAGTAACTAGGCTTTCGAAGGCATGAGTGACCATAAAT-GACTT
* *
1304669 TTATTATCAAGGGATAGCTTTTGCTTCAGTTTTCCCCAA
638 TTATTATCAAGGGATGGCTTTTGCTTCACTTTTCCCCAA
* * *
1304708 GCAAACATCTAATTATGATATGCTTTAACCAT-AAATGAAATAGAATTCAACTTAAACTCATTAT
1 GCAAACATCTAATTATGATATGTTTTAACCATAAAATGAAACAAAATTCAACTTAAACTCATTAT
** * * * * * *
1304772 GATTTTAGAAAACCATTTAAAGTGAGTAACTAGACTTTTCAAAGTATGAGTGAATATAAACGGAC
66 GAGATTATAAAACCATTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAACAGAC
* * * * *
1304837 TTTTCTTGT--A-A-ATGG---ATG--GC--TTTCTTGA-GTCAAACATCTAATTATGATCTATT
131 TTTTCTTCTCAACAGATGGCTTTTGCTTCATTTTCTTGAGGT-AAACATCAAATTATGATTTATT
* * * **
1304890 TTAACCTAAAATGAAAAAATATCAATTTAAAATAATTTATA-AGGTTATACAATGACTTAAA-TA
195 TTAACCTAAAATGAAAAAA-AT-TATTTAAAATCATTTATAGA-GTTATAAAACCACTTAAAGTA
* * *
1304953 GACTAACAAGGCTTTCAAAGGTATGAGTGACCATAAATAGACTTTTCTTGTCAATGGATGGCTTT
257 G--TAACAAGGCTTTCGAAGGTATGAGTGACTATAAATAGACTTCTCTTGTCAATGGATGGCTTT
* * *
1305018 TGCTTCATGTTTCCTAA-GACAAATAGT-GAATTATGATCTATTTTAAGTAAAAAT-AAAAAAAT
320 TGCTTCATGTTTCTTAAGGA-AAACA-TCCAATTATGATCTATTTTAAGTAAAAATGAAAAAAAT
* *
1305080 TCAACTTAAAATCATTTATGAGATTATAAAGAAATTAAAGCGAGTAACTAGGCTTTCGAGGCATG
383 TCAACTTAAAATCATTTATGAGATTATAAAAAAATTAAAGCGAGTAACTAGGCTTTCGAGGCATA
* * * * * * * * * *
1305145 AGTGATTATAAATAGACTTGTCTTATCAATAAATAGCTTTTGCTTCACATTTCTTTAGGTAAATA
448 AGTGACTATAAATTGACTTTTCTTATCAATAGATGGCTTTTGCTTCACTTTTC-TAAAGAAAACA
* * * * * ** *
1305210 TCTAATTATGA-TCTAATTTAATTAAAAATG-AAA-AAAA-TTCAGTCTGAAATCATTTATAACG
512 TCCAATTATGACT-TACTTTAATAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTTATAA-G
* * *** * * * * *
1305271 -TTTTATAACC-TCTTAAAGCGAGTAAC-AAGCTTTTCAAAGGCATGGGTGACTACAAATGAGCT
575 ATTATAAAACCAT-TTAAAATAAGTAACTAGGC-TTTCGAAGGCATGAGTGACCATAAATGA-CT
* * ** ** * **
1305333 TTTCTTGTCAATAGATGTATTTTGTTTCACCTTTT--TTAA
637 TTTATTATCAAGGGATGGCTTTTGCTTCA-CTTTTCCCCAA
* * * ** *
1305372 GGCAGACATCTAATTATGATCTGATTTAACCA-AAAATGAAA-AAGAATTCAGTTTAAACACATT
1 -GCAAACATCTAATTATGATATGTTTTAACCATAAAATGAAACAA-AATTCAACTTAAACTCA-T
* * * ** *
1305435 TATGAGATTATAAAACTATTTAAAGTGAGTAATTACGCTTTCGAAAGCATGAGTGATTATAAATT
63 TATGAGATTATAAAACCATTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAA-C
* * ** ** * * *
1305500 A-ACTTTTTTTGTCAATGGATGGCTTTCACTTTATGTTT-TTCAAGGCAAACATC-AATTATGAT
127 AGACTTTTCTTCTCAACAGATGGCTTTTGCTTCAT-TTTCTT-GAGGTAAACATCAAATTATGAT
* *
1305562 CTATTTTAACCTAAAATTAAAAAAA
190 TTATTTTAACCTAAAATGAAAAAAA
1305587 AATTAATTCA
Statistics
Matches: 1902, Mismatches: 272, Indels: 143
0.82 0.12 0.06
Matches are distributed among these distances:
664 9 0.00
665 130 0.07
666 87 0.05
667 180 0.09
668 97 0.05
669 37 0.02
670 4 0.00
672 1 0.00
674 2 0.00
676 1 0.00
677 38 0.02
678 12 0.01
679 2 0.00
680 21 0.01
681 288 0.15
682 463 0.24
683 463 0.24
684 67 0.04
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (676 bp):
GCAAACATCTAATTATGATATGTTTTAACCATAAAATGAAACAAAATTCAACTTAAACTCATTAT
GAGATTATAAAACCATTTAAAGTGAGTAACTAGGCTTTTAAAAGCATGAGTGATTATAAACAGAC
TTTTCTTCTCAACAGATGGCTTTTGCTTCATTTTCTTGAGGTAAACATCAAATTATGATTTATTT
TAACCTAAAATGAAAAAAATTATTTAAAATCATTTATAGAGTTATAAAACCACTTAAAGTAGTAA
CAAGGCTTTCGAAGGTATGAGTGACTATAAATAGACTTCTCTTGTCAATGGATGGCTTTTGCTTC
ATGTTTCTTAAGGAAAACATCCAATTATGATCTATTTTAAGTAAAAATGAAAAAAATTCAACTTA
AAATCATTTATGAGATTATAAAAAAATTAAAGCGAGTAACTAGGCTTTCGAGGCATAAGTGACTA
TAAATTGACTTTTCTTATCAATAGATGGCTTTTGCTTCACTTTTCTAAAGAAAACATCCAATTAT
GACTTACTTTAATAAAAAAGGAAAAGAAAAGCTCAACCTAAAATCATTTATAAGATTATAAAACC
ATTTAAAATAAGTAACTAGGCTTTCGAAGGCATGAGTGACCATAAATGACTTTTATTATCAAGGG
ATGGCTTTTGCTTCACTTTTCCCCAA
Found at i:1320115 original size:24 final size:24
Alignment explanation
Indices: 1320088--1320141 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1320078 TTTTTTTTCA
1320088 ATTTGTATTATT-ATTTTTATTTAT
1 ATTTGTATTATTCATTTTTA-TTAT
* * * *
1320112 ATTTATTTTTTTCATTTTTATTCT
1 ATTTGTATTATTCATTTTTATTAT
1320136 ATTTGT
1 ATTTGT
1320142 TCATATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (24 bp):
ATTTGTATTATTCATTTTTATTAT
Found at i:1320117 original size:19 final size:19
Alignment explanation
Indices: 1320079--1320139 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1320069 AATTTTAAAT
*
1320079 TTTTTTTCAATTTGTA-TTA
1 TTTTTTTC-ATTTATATTTA
1320098 TTATTTTT-ATTTATATTTA
1 TT-TTTTTCATTTATATTTA
*
1320117 TTTTTTTCATTTTTATTCTA
1 TTTTTTTCATTTATATT-TA
1320137 TTT
1 TTT
1320140 GTTCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 11 0.31
19 15 0.42
20 10 0.28
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTCATTTATATTTA
Found at i:1323885 original size:29 final size:30
Alignment explanation
Indices: 1323828--1323885 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1323818 TGAGGGGTAA
* *
1323828 AGTTTTTATAATTTTATTTTAAGTTAAATT
1 AGTTTTTATAATTTTATTTGAAGTAAAATT
* *
1323858 AGTTTTTATATTTTTATTTGGA-TAAAAT
1 AGTTTTTATAATTTTATTTGAAGTAAAAT
1323886 ACCCCCACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (30 bp):
AGTTTTTATAATTTTATTTGAAGTAAAATT
Found at i:1326372 original size:20 final size:22
Alignment explanation
Indices: 1326335--1326380 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
1326325 TATTTAACTA
*
1326335 TTTATATTTTATGTATTATAAT
1 TTTATATTTTATGTATTATAAG
1326357 TTTATA-TTTA-GTATTATAAG
1 TTTATATTTTATGTATTATAAG
1326377 TTTA
1 TTTA
1326381 AATAGAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTATATTTTATGTATTATAAG
Found at i:1327097 original size:15 final size:15
Alignment explanation
Indices: 1327077--1327230 Score: 82
Period size: 15 Copynumber: 10.8 Consensus size: 15
1327067 GATATTATGT
1327077 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
1327092 TTAAATTT-AATATAA
1 TTAAATTTAAATA-AA
1327107 TT-AATCCTT--AT---
1 TTAAAT--TTAAATAAA
*
1327118 TTAAATTTAAACAAA
1 TTAAATTTAAATAAA
1327133 TTAAATTTAAATATAA
1 TTAAATTTAAATA-AA
* * *
1327149 -TAGA--TAGATAAT
1 TTAAATTTAAATAAA
*
1327161 TTAAATTTAAACAAA
1 TTAAATTTAAATAAA
1327176 TTAAATTTAAATATAA
1 TTAAATTTAAATA-AA
* * * *
1327192 -TAGA--CAGATAAT
1 TTAAATTTAAATAAA
*
1327204 TTAAATTTAAACAAA
1 TTAAATTTAAATAAA
1327219 TTAAATTTAAAT
1 TTAAATTTAAAT
1327231 TTATATCCTA
Statistics
Matches: 102, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
10 2 0.02
11 2 0.02
12 6 0.06
13 15 0.15
14 7 0.07
15 64 0.63
16 6 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:1327164 original size:22 final size:21
Alignment explanation
Indices: 1327136--1327209 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
1327126 AAACAAATTA
1327136 AATTTAAATATAATAGATAGAT
1 AATTTAAATATAATAGA-AGAT
* *
1327158 AATTTAAATTTAA-ACAA-ATT
1 AATTTAAATATAATAGAAGA-T
1327178 AAATTTAAATATAATAGACAGAT
1 -AATTTAAATATAATAGA-AGAT
1327201 AATTTAAAT
1 AATTTAAAT
1327210 TTAAACAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 2 0.05
21 14 0.33
22 23 0.53
23 2 0.05
24 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
AATTTAAATATAATAGAAGAT
Found at i:1327175 original size:43 final size:43
Alignment explanation
Indices: 1327076--1327230 Score: 235
Period size: 43 Copynumber: 3.7 Consensus size: 43
1327066 GGATATTATG
* ** *
1327076 TTTAAATTTAAATAAATTAAATTT-AATATAATTA-AT-CCTTA
1 TTTAAATTTAAACAAATTAAATTTAAATATAA-TAGATAGATAA
1327117 TTTAAATTTAAACAAATTAAATTTAAATATAATAGATAGATAA
1 TTTAAATTTAAACAAATTAAATTTAAATATAATAGATAGATAA
*
1327160 TTTAAATTTAAACAAATTAAATTTAAATATAATAGACAGATAA
1 TTTAAATTTAAACAAATTAAATTTAAATATAATAGATAGATAA
1327203 TTTAAATTTAAACAAATTAAATTTAAAT
1 TTTAAATTTAAACAAATTAAATTTAAAT
1327231 TTATATCCTA
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
41 25 0.24
42 9 0.08
43 72 0.68
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (43 bp):
TTTAAATTTAAACAAATTAAATTTAAATATAATAGATAGATAA
Found at i:1333068 original size:43 final size:45
Alignment explanation
Indices: 1332961--1333070 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 45
1332951 TGCATACAAG
* * * * *
1332961 TTTACTTAACAAATAAGCAAAATAATTATATTATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAACAATTACATCATGCATTTTAT--AT
1333008 TTTACCTAACAAATAAGTAAAACAATTACATCATGCATTTT-T-T
1 TTTACCTAACAAATAAGTAAAACAATTACATCATGCATTTTATAT
1333051 TTTACCTAACAAATAAGTAA
1 TTTACCTAACAAATAAGTAA
1333071 TCATGCTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 21 0.36
46 1 0.02
47 36 0.62
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (45 bp):
TTTACCTAACAAATAAGTAAAACAATTACATCATGCATTTTATAT
Found at i:1333074 original size:33 final size:35
Alignment explanation
Indices: 1333037--1333106 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
1333027 AAACAATTAC
1333037 ATCATGCATTTT-T-TTTTACCTAACAAATAAGTA
1 ATCATGCATTTTATATTTTACCTAACAAATAAGTA
* * *
1333070 ATCATGCTTTTTATAATTTTGCCTAATAAATAAGTA
1 ATCATGCATTTTAT-ATTTTACCTAACAAATAAGTA
1333106 A
1 A
1333107 AATCATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 11 0.35
34 1 0.03
36 19 0.61
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (35 bp):
ATCATGCATTTTATATTTTACCTAACAAATAAGTA
Found at i:1335171 original size:15 final size:16
Alignment explanation
Indices: 1335146--1335185 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1335136 GATAGGATAT
*
1335146 TATATTTAAATTTAAA
1 TATAATTAAATTTAAA
1335162 TA-AATTAAATTTAAA
1 TATAATTAAATTTAAA
1335177 TATAATTAA
1 TATAATTAA
1335186 TTCTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATTAAATTTAAA
Found at i:1335173 original size:21 final size:21
Alignment explanation
Indices: 1335144--1335250 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 21
1335134 GAGATAGGAT
*
1335144 ATTATATTTAAATTTAAATAA
1 ATTAAATTTAAATTTAAATAA
* *
1335165 ATTAAATTTAAATAT-AATTA
1 ATTAAATTTAAATTTAAATAA
**
1335185 ATTCTTATTTAAATTTAAATATA
1 ATT-AAATTTAAATTTAAATA-A
*
1335208 ATGGATAGATAATTTAAATTTAAAAAA
1 AT---T--A-AATTTAAATTTAAATAA
1335235 ATTAAATTTAAATTTA
1 ATTAAATTTAAATTTA
1335251 TATCCTATCT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 7 0.10
21 34 0.51
22 4 0.06
23 3 0.04
24 1 0.01
26 1 0.01
27 3 0.04
28 14 0.21
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTAAATTTAAATTTAAATAA
Found at i:1335824 original size:29 final size:29
Alignment explanation
Indices: 1335788--1335911 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
1335778 ATTAATATCA
*
1335788 ATTAATTTCTAGATTTACACTGATATGAT
1 ATTAATTTCTAGATTTACACAGATATGAT
*
1335817 ATTAATTTCTAGATTTACACAGGTATGAT
1 ATTAATTTCTAGATTTACACAGATATGAT
* ** **
1335846 ATTAATTTTTATCTTTACACAAGA-ACAAT
1 ATTAATTTCTAGATTTACAC-AGATATGAT
1335875 ATTAATTT-TCAGATTTACACAGATATGAT
1 ATTAATTTCT-AGATTTACACAGATATGAT
1335904 ATTAATTT
1 ATTAATTT
1335912 TTATGTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.05
29 74 0.93
30 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (29 bp):
ATTAATTTCTAGATTTACACAGATATGAT
Found at i:1336292 original size:3 final size:3
Alignment explanation
Indices: 1336279--1336308 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1336269 ATTCCTTTGG
*
1336279 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1336309 GTTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1339154 original size:23 final size:24
Alignment explanation
Indices: 1339109--1339155 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1339099 TTATACTAGG
*
1339109 TACCATCACAACGTGATGGAATGC
1 TACCATCACAACGTGATGAAATGC
1339133 TACC-TCACAACGTG-TAGAAATGC
1 TACCATCACAACGTGAT-GAAATGC
1339156 AAATAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 16 0.76
24 4 0.19
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (24 bp):
TACCATCACAACGTGATGAAATGC
Found at i:1342882 original size:129 final size:122
Alignment explanation
Indices: 1342659--1342908 Score: 401
Period size: 129 Copynumber: 2.0 Consensus size: 122
1342649 CATTGCAGTC
* * *
1342659 CTGGCTAGGGAATAGGAGAATGAAAGTTTAGCCGTCTGCTTTTTTGATATATGAATAGAAATAAC
1 CTGGCGAGGGAATAGGAGAATGAAAGTTTAGCCCTCTGCTTTTTAGATATATGAATAGAAATAAC
1342724 TCTAGGGCAGGAGCCTGTTATCTCATAGTGTTCACATATATATAAAATCTCTAGTTT
66 TCTAGGGCAGGAGCCTGTTATCTCATAGTGTTCACATATATATAAAATCTCTAGTTT
1342781 CTGGCGAGGGAATAGGAGAATGAAAGTTTAGCTCTCTACTTTGCACTTTTTAGATATATGAATAG
1 CTGGCGAGGGAATAGGAGAATGAAAGTTTAGC-C-CT-C--TG--CTTTTTAGATATATGAATAG
*
1342846 AAATAACTCTAGGGCAGGAGCCTGTTATCTCATAGTGTTCACATTTATATAAAATCTCTAGTT
59 AAATAACTCTAGGGCAGGAGCCTGTTATCTCATAGTGTTCACATATATATAAAATCTCTAGTT
1342909 ACAAGCCATA
Statistics
Matches: 117, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
122 31 0.26
123 1 0.01
124 1 0.01
125 1 0.01
127 2 0.02
129 81 0.69
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (122 bp):
CTGGCGAGGGAATAGGAGAATGAAAGTTTAGCCCTCTGCTTTTTAGATATATGAATAGAAATAAC
TCTAGGGCAGGAGCCTGTTATCTCATAGTGTTCACATATATATAAAATCTCTAGTTT
Found at i:1348129 original size:25 final size:24
Alignment explanation
Indices: 1348095--1348146 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 24
1348085 TAAAAAGGTA
1348095 GTTTATGTGGTTAGAACTTTTTATT
1 GTTTATGTGGTTAGAACTTTTT-TT
*
1348120 GTTTTTGTGGTTAGAACTTTTTTT
1 GTTTATGTGGTTAGAACTTTTTTT
1348144 GTT
1 GTT
1348147 CATATCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (24 bp):
GTTTATGTGGTTAGAACTTTTTTT
Found at i:1354847 original size:17 final size:18
Alignment explanation
Indices: 1354798--1354847 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1354788 AAAAAGCTCC
*
1354798 TTATATTTTTTAAAAAATT
1 TTAT-TTTTTTAAAAAATG
*
1354817 TTA-TTCTTTAAAAAGA-G
1 TTATTTTTTTAAAAA-ATG
1354834 TTATTTTTTTAAAA
1 TTATTTTTTTAAAA
1354848 TTTATGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.50
18 10 0.38
19 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (18 bp):
TTATTTTTTTAAAAAATG
Found at i:1354932 original size:16 final size:15
Alignment explanation
Indices: 1354891--1354935 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1354881 AGATAAGTTT
1354891 TTTTAAAAAATTTTA
1 TTTTAAAAAATTTTA
***
1354906 TTTTTTTAAATTATTA
1 TTTTAAAAAATT-TTA
1354922 TTTTAAAAAATTTT
1 TTTTAAAAAATTTT
1354936 CAAAATCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAAAAAATTTTA
Found at i:1362004 original size:12 final size:13
Alignment explanation
Indices: 1361987--1362019 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1361977 TTGGAGAATT
1361987 TTTATTTACTT-A
1 TTTATTTACTTCA
1361999 TTTATTTACTTCA
1 TTTATTTACTTCA
1362012 TTTATTTA
1 TTTATTTA
1362020 TTTAAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTTACTTCA
Found at i:1362313 original size:22 final size:21
Alignment explanation
Indices: 1362280--1362341 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
1362270 TACTTCATTC
*
1362280 ATTTA-TTT-AATTTAATTTT
1 ATTTATTTTAAATTTATTTTT
*
1362299 ATTTCTTTTAGAATTT-TTATTT
1 ATTTATTTTA-AATTTATT-TTT
1362321 ATTTATTTTAAATTTATTTTT
1 ATTTATTTTAAATTTATTTTT
1362342 CAAATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.11
20 3 0.09
21 9 0.26
22 19 0.54
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTATTTTAAATTTATTTTT
Found at i:1362322 original size:261 final size:260
Alignment explanation
Indices: 1361812--1362330 Score: 675
Period size: 261 Copynumber: 2.0 Consensus size: 260
1361802 TTTGTATTTA
* * *
1361812 TTTATTTATTTTAAATTTGTTTTATTATTTTTCAAATAAATAAAATTCCTTTGAGAGTGAAATTT
1 TTTATTTATTTCAAATTTGTTGTATTATTTTTCAAATAAATAAAAATCCTTTGAGAGTGAAATTT
** * *
1361877 CTTTAAAATTTTCCAACACTTTTGGTAAAATTTAAGAAAAATTTCTAACCTAAAAATTTTCAAGA
66 CTCCAAAATTTACCAACACTTTTGCTAAAATTTAAGAAAAATTTCTAACCTAAAAATTTTCAAGA
* * *
1361942 TAATTATTACTTCTAACATGTTTGAAATTCCATCATTGGAGAATTTTTATTTACTTATTTATTTA
131 AAATTATCACTTATAACATGTTTGAAATTCCATCATTGGAGAATTTTTATTTACTTATTTATTTA
*
1362007 CTTCATTTATTTATTTAAGTTTATCTTATTCCTTTTAGAATTTTTATATATTTATTTTATTATTA
196 CTTCATTCATTTATTTAAGTTTATCTTATTCCTTTTAGAA-TTTTATATATTTATTTTATTATTA
1362072 T
260 T
* * *
1362073 TTTATTTATTTCAAATTTGTTGTATT-TTGTTTCAAATAAATAAAAATCTTTTGATATTGAAATT
1 TTTATTTATTTCAAATTTGTTGTATTATT-TTTCAAATAAATAAAAATCCTTTGAGAGTGAAATT
* * * * * ** *
1362137 TCTCCCAAATTTACCAACACTTTTGCTAAAATTTATGAAAATTTTGTCACCTGGAAATTTTCTAG
65 TCTCCAAAATTTACCAACACTTTTGCTAAAATTTAAGAAAAATTTCTAACCTAAAAATTTTCAAG
* * * *
1362202 AAAATTATCACTTATAAC-TTTTCTGAAATTTCATCATTGGAGAATTTTTATTTATTTTTTTACT
130 AAAATTATCACTTATAACATGTT-TGAAATTCCATCATTGGAGAATTTTTATTTACTTATTTA--
* * *
1362266 TACTTACTTCATTCATTTATTTAA-TTTAATTTTATTTCTTTTAGAATTTTTATTTATTTATTTT
192 T--TTACTTCATTCATTTATTTAAGTTT-ATCTTATTCCTTTTAGAA-TTTTATATATTTATTTT
1362330 A
253 A
1362331 AATTTATTTT
Statistics
Matches: 222, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
260 5 0.02
261 159 0.72
263 1 0.00
264 3 0.01
265 54 0.24
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (260 bp):
TTTATTTATTTCAAATTTGTTGTATTATTTTTCAAATAAATAAAAATCCTTTGAGAGTGAAATTT
CTCCAAAATTTACCAACACTTTTGCTAAAATTTAAGAAAAATTTCTAACCTAAAAATTTTCAAGA
AAATTATCACTTATAACATGTTTGAAATTCCATCATTGGAGAATTTTTATTTACTTATTTATTTA
CTTCATTCATTTATTTAAGTTTATCTTATTCCTTTTAGAATTTTATATATTTATTTTATTATTAT
Found at i:1364850 original size:2 final size:2
Alignment explanation
Indices: 1364843--1364870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1364833 TCAAGTAAGA
1364843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364871 TAATACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367453 original size:35 final size:35
Alignment explanation
Indices: 1367414--1367562 Score: 162
Period size: 35 Copynumber: 4.3 Consensus size: 35
1367404 TAATTGTTTT
* *
1367414 ATTTAATCAATT-AGACCCAATAACTTTATTAAACA
1 ATTTAATCAATTAAG-CCCAACAACTTAATTAAACA
* * *
1367449 ATTTAATTAACTAAGCCCAACAATTTAATTAAACA
1 ATTTAATCAATTAAGCCCAACAACTTAATTAAACA
**
1367484 ATTTTAATCAATTAAGCCCAATGACTTAATTAAACA
1 A-TTTAATCAATTAAGCCCAACAACTTAATTAAACA
* *
1367520 ATTTAATTAATT-AG-GC-ACAACTTAATTAAACA
1 ATTTAATCAATTAAGCCCAACAACTTAATTAAACA
1367552 ATTTTAATCAA
1 A-TTTAATCAA
1367563 GTGCTTGAGA
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
32 15 0.16
33 9 0.09
34 2 0.02
35 38 0.40
36 32 0.33
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.34
Consensus pattern (35 bp):
ATTTAATCAATTAAGCCCAACAACTTAATTAAACA
Found at i:1367466 original size:71 final size:71
Alignment explanation
Indices: 1367415--1367562 Score: 214
Period size: 71 Copynumber: 2.1 Consensus size: 71
1367405 AATTGTTTTA
* *
1367415 TTTAATCAATT-AGACCCAATAACTTTATTAAACAATTTAATTAACTAAGCCCAACAATTTAATT
1 TTTAATCAATTAAG-CCCAATAACTTAATTAAACAATTTAATTAACTAAGCCCAACAACTTAATT
1367479 AAACAAT
65 AAACAAT
* * *
1367486 TTTAATCAATTAAGCCCAATGACTTAATTAAACAATTTAATTAA-TTAG-GC-ACAACTTAATTA
1 TTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATTAACTAAGCCCAACAACTTAATTA
1367548 AACAAT
66 AACAAT
1367554 TTTAATCAA
1 TTTAATCAA
1367563 GTGCTTGAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
68 26 0.37
69 1 0.01
70 3 0.04
71 39 0.55
72 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (71 bp):
TTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATTAACTAAGCCCAACAACTTAATTA
AACAAT
Found at i:1374619 original size:23 final size:21
Alignment explanation
Indices: 1374567--1374631 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
1374557 GTTCAAAGTT
1374567 ATAC-TAAAATAAAATAATAATA
1 ATACATAAAATAAAATAA-AA-A
*
1374589 ATTCATAAAATAAAATAAAAA
1 ATACATAAAATAAAATAAAAA
*
1374610 ATAACAATAAAA-ATAATAAAAA
1 AT-AC-ATAAAATAAAATAAAAA
1374632 GAAATCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 3 0.08
22 15 0.41
23 19 0.51
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
ATACATAAAATAAAATAAAAA
Found at i:1374625 original size:12 final size:12
Alignment explanation
Indices: 1374571--1374622 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
1374561 AAAGTTATAC
1374571 TAAAATAAAATAA
1 TAAAATAAAA-AA
*
1374584 TAATAATTCATAAAA
1 TAA-AA-T-AAAAAA
1374599 TAAAATAAAAAA
1 TAAAATAAAAAA
1374611 TAACAATAAAAA
1 TAA-AATAAAAA
1374623 TAATAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 8 0.24
13 12 0.36
14 4 0.12
15 6 0.18
16 3 0.09
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:1374719 original size:2 final size:2
Alignment explanation
Indices: 1374665--1374703 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
1374655 AGTGTTTACA
* *
1374665 AT AT AT AT AT AT AT AT AT AT AT AT AC AGT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1374704 GCACACAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1384631 original size:34 final size:34
Alignment explanation
Indices: 1384523--1384916 Score: 188
Period size: 33 Copynumber: 11.6 Consensus size: 34
1384513 TCGATAATGA
* *
1384523 AAAGTATTGTAAGGTTAAAAGAG--TC-AGAATTGT
1 AAAGCATTGTAAGGTTAAAAG-GTTTCAAG-ATTGG
** *
1384556 AAAGC-TTGTAAGGTTTCAAGGTTTCAAGA-TCG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
* * *
1384588 AAAGTATTGTAAGGTTAAAAGGTTTTAAGACTGG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
** * *
1384622 AAAGCATTGTAAGGTTAAAAACTGTCAGGATTGG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
* * *
1384656 AAAAC-GTGCAAGGTTAAAAGGTTTCAAGATTGG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
* *
1384689 AAAGCATTGAAAGGTTAAAACTTCAAAGCTTTCAAGATTGG
1 AAAGCATTGTAAGGTT---A----AAAGGTTTCAAGATTGG
* ** * * *
1384730 GAAGC-TTGTACTGTTAGAAGATTTCAAGATTAG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
* * ** * * *
1384763 AAAGCATTGTAAGCTCAAAAGGTCACAGGGTTTG
1 AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
* * *
1384797 AAAAC-TTGTAAAGTTACAAA-GTTTCAAGATGGG
1 AAAGCATTGTAAGGTTA-AAAGGTTTCAAGATTGG
* *
1384830 AAA-CTATTGTACA-ATTAAATGGTTTCAAGATTTGG
1 AAAGC-ATTGTA-AGGTTAAAAGGTTTCAAGA-TTGG
* * * *
1384865 -AA-CATTATAAGGGTACAAGATTTCAAGGA-T-G
1 AAAGCATTGTAAGGTTAAAAGGTTTCAA-GATTGG
*
1384896 AAAGGCATTGTAAGTTTAAAA
1 AAA-GCATTGTAAGGTTAAAA
1384917 TGTTGGGAAA
Statistics
Matches: 266, Mismatches: 70, Indels: 49
0.69 0.18 0.13
Matches are distributed among these distances:
31 2 0.01
32 23 0.09
33 107 0.40
34 101 0.38
35 4 0.02
37 2 0.01
40 7 0.03
41 20 0.08
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (34 bp):
AAAGCATTGTAAGGTTAAAAGGTTTCAAGATTGG
Found at i:1385573 original size:42 final size:42
Alignment explanation
Indices: 1385496--1385575 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1385486 TGTAATTTGC
* *
1385496 TAATTAGTCCTTACACTTAATTGAACCCTTCAATTAAGGTTT
1 TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAGGTTT
* * * *
1385538 TAATTGGTCCTTGCACTTAATTAAATCATTTAATTAAG
1 TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAG
1385576 TGTAATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (42 bp):
TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAGGTTT
Found at i:1386822 original size:34 final size:33
Alignment explanation
Indices: 1386673--1386914 Score: 181
Period size: 33 Copynumber: 7.2 Consensus size: 33
1386663 TATTCCAACA
* * * **
1386673 TAAAAGGTGTCAAGATTGGAAAGCTAGTAACTT
1 TAAAAAGTTTCAAGATTGGAAAGCTTGTAAGGT
* *
1386706 TAAAAAGGTTTCAAGATTGAAAAGCATTGTGAGGT
1 TAAAAA-GTTTCAAGATTGGAAAGC-TTGTAAGGT
* * *
1386741 T-AAAGGTTTCAAGATTGGGCAA-CTTGTGAGGT
1 TAAAAAGTTTCAAGATT-GGAAAGCTTGTAAGGT
* *
1386773 TAGAAGGTTT-AAGATTGGAAAGCATTGTAAGGT
1 TAAAAAGTTTCAAGATTGGAAAGC-TTGTAAGGT
1386806 TAAAAAGTTTCAAGATTAGG-AAGCTTGTAAATAAGGT
1 TAAAAAGTTTCAAGATT-GGAAAGCTTG----TAAGGT
* * *
1386843 TAGAAAA--TTCAAGGTTGGGAAGCATTGTAAGAT
1 TA-AAAAGTTTCAAGATTGGAAAGC-TTGTAAGGT
* *
1386876 TAAAAGGTATCAAGATTGGAAAGCTTGTAAGGT
1 TAAAAAGTTTCAAGATTGGAAAGCTTGTAAGGT
*
1386909 TGAAAA
1 TAAAAA
1386915 CTTTTAAGGA
Statistics
Matches: 168, Mismatches: 24, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
31 4 0.02
32 20 0.12
33 62 0.37
34 45 0.27
35 10 0.06
36 12 0.07
37 11 0.07
38 4 0.02
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (33 bp):
TAAAAAGTTTCAAGATTGGAAAGCTTGTAAGGT
Found at i:1386864 original size:36 final size:37
Alignment explanation
Indices: 1386800--1386872 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
1386790 GAAAGCATTG
1386800 TAAGGTTAAAAAGTTTCAAGATTAGGAAGC-TTGTAAA
1 TAAGGTTAAAAAG-TTCAAGATTAGGAAGCATTGTAAA
* *
1386837 TAAGGTTAGAAAA-TTCAAGGTTGGGAAGCATTGTAA
1 TAAGGTTA-AAAAGTTCAAGATTAGGAAGCATTGTAA
1386873 GATTAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 14 0.44
37 14 0.44
38 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (37 bp):
TAAGGTTAAAAAGTTCAAGATTAGGAAGCATTGTAAA
Found at i:1386868 original size:70 final size:70
Alignment explanation
Indices: 1386769--1386905 Score: 186
Period size: 70 Copynumber: 2.0 Consensus size: 70
1386759 GCAACTTGTG
** * * *
1386769 AGGTTAGAAGGTTTAAGATTGGAAAGCATTGTAAGGTTAAAAAGTTTCAAGATTAGG-AAGCTTG
1 AGGTTAGAAAATTCAAGATTGGAAAGCATTGTAAGATTAAAAAGTATCAAGATT-GGAAAGCTTG
1386833 TAAATA
65 TAAATA
* * *
1386839 AGGTTAGAAAATTCAAGGTTGGGAAGCATTGTAAGATTAAAAGGTATCAAGATTGGAAAGCTTGT
1 AGGTTAGAAAATTCAAGATTGGAAAGCATTGTAAGATTAAAAAGTATCAAGATTGGAAAGCTTGT
1386904 AA
66 AA
1386906 GGTTGAAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 2 0.03
70 56 0.97
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.28
Consensus pattern (70 bp):
AGGTTAGAAAATTCAAGATTGGAAAGCATTGTAAGATTAAAAAGTATCAAGATTGGAAAGCTTGT
AAATA
Found at i:1387048 original size:34 final size:35
Alignment explanation
Indices: 1386996--1387077 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
1386986 TTAAAGACTA
* * *
1386996 CAAAACATGC-AAGGTTGAAAAGCCTTAAGGATTG
1 CAAAGCATGCTAAGATTGAAAAACCTTAAGGATTG
* * *
1387030 GAAAGTATG-TAAGATTGAAAAACTTTAAGGATTG
1 CAAAGCATGCTAAGATTGAAAAACCTTAAGGATTG
1387064 CAAAGCATGCTAAG
1 CAAAGCATGCTAAG
1387078 TTGTCATGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (35 bp):
CAAAGCATGCTAAGATTGAAAAACCTTAAGGATTG
Found at i:1393042 original size:6 final size:6
Alignment explanation
Indices: 1393031--1393055 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1393021 ACCAAAGGTG
1393031 ATGAAA ATGAAA ATGAAA ATGAAA A
1 ATGAAA ATGAAA ATGAAA ATGAAA A
1393056 GAATGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGAAA
Found at i:1393400 original size:10 final size:10
Alignment explanation
Indices: 1393387--1393430 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1393377 AAATAATATT
1393387 TTTAAAAAAA
1 TTTAAAAAAA
** *
1393397 TTTAAATTAT
1 TTTAAAAAAA
1393407 TTTAAAAAAA
1 TTTAAAAAAA
1393417 TTTAAATAAAA
1 TTTAAA-AAAA
1393428 TTT
1 TTT
1393431 TATATTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:1393411 original size:20 final size:20
Alignment explanation
Indices: 1393386--1393423 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1393376 TAAATAATAT
1393386 TTTTAAAAAAATTTAAATTA
1 TTTTAAAAAAATTTAAATTA
1393406 TTTTAAAAAAATTTAAAT
1 TTTTAAAAAAATTTAAAT
1393424 AAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAAAAAAATTTAAATTA
Found at i:1401334 original size:29 final size:29
Alignment explanation
Indices: 1401292--1401354 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1401282 TTTAGGATTT
*
1401292 ATACTTTGTTTTTCTATTCT-GAGCGGAGG
1 ATACTTTGTTTTTCTATTATCG-GCGGAGG
1401321 ATACTTTGTTTTTCTATTATCGGCGGAGG
1 ATACTTTGTTTTTCTATTATCGGCGGAGG
1401350 ATACT
1 ATACT
1401355 GTACAGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (29 bp):
ATACTTTGTTTTTCTATTATCGGCGGAGG
Found at i:1409906 original size:26 final size:26
Alignment explanation
Indices: 1409877--1410002 Score: 108
Period size: 26 Copynumber: 5.2 Consensus size: 26
1409867 GGTATTACAA
*
1409877 GACTGAATATTTGTTAAGCATTGCGT
1 GACTGAATATTTGTTAAGCATTACGT
* *
1409903 GACT---TATTTG-TATGTATTACGT
1 GACTGAATATTTGTTAAGCATTACGT
* *
1409925 GACTGAATATTTGTTGAGCATTGCGT
1 GACTGAATATTTGTTAAGCATTACGT
* *
1409951 GACTTGATTATATG-T----ATTACGT
1 GAC-TGAATATTTGTTAAGCATTACGT
*
1409973 GACTGAATATTTGTTGAGCATTACGT
1 GACTGAATATTTGTTAAGCATTACGT
1409999 GACT
1 GACT
1410003 TGTTTGTAGG
Statistics
Matches: 78, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
21 8 0.10
22 23 0.29
23 6 0.08
25 6 0.08
26 27 0.35
27 8 0.10
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (26 bp):
GACTGAATATTTGTTAAGCATTACGT
Found at i:1409929 original size:48 final size:48
Alignment explanation
Indices: 1409868--1410024 Score: 226
Period size: 48 Copynumber: 3.3 Consensus size: 48
1409858 TATTTATTTG
** *
1409868 GTATTACAAGACTGAATATTTGTTAAGCATTGCGTGACTTATTTGTAT
1 GTATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTTATTTGTAT
*
1409916 GTATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTTGA-TTATAT
1 GTATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTT-ATTTGTAT
* * *
1409964 GTATTACGTGACTGAATATTTGTTGAGCATTACGTGACTTGTTTGTAG
1 GTATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTTATTTGTAT
*
1410012 GTATTATGTGACT
1 GTATTACGTGACT
1410025 TATTTGTAGG
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
48 97 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (48 bp):
GTATTACGTGACTGAATATTTGTTGAGCATTGCGTGACTTATTTGTAT
Found at i:1410033 original size:22 final size:22
Alignment explanation
Indices: 1409900--1410034 Score: 92
Period size: 22 Copynumber: 5.8 Consensus size: 22
1409890 TTAAGCATTG
*
1409900 CGTGACTTATTTGTATGTATTA
1 CGTGACTTATTTGTAGGTATTA
* * *
1409922 CGTGACTGAATATTTGTTGAGCATTG
1 CGTGACT---TATTTGTAG-GTATTA
* *
1409948 CGTGACTTGA-TTATATGTATTA
1 CGTGACTT-ATTTGTAGGTATTA
* *
1409970 CGTGACTGAATATTTGTTGAGCATTA
1 CGTGACT---TATTTGTAG-GTATTA
*
1409996 CGTGACTTGTTTGTAGGTATTA
1 CGTGACTTATTTGTAGGTATTA
*
1410018 TGTGACTTATTTGTAGG
1 CGTGACTTATTTGTAGG
1410035 CATTGTTTGA
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
22 38 0.45
23 11 0.13
24 2 0.02
25 11 0.13
26 23 0.27
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.44
Consensus pattern (22 bp):
CGTGACTTATTTGTAGGTATTA
Found at i:1410045 original size:22 final size:22
Alignment explanation
Indices: 1409980--1410047 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
1409970 CGTGACTGAA
* *
1409980 TATTTGTTGAGCATTACGTGACT
1 TATTTGTAG-GCATTATGTGACT
* *
1410003 TGTTTGTAGGTATTATGTGACT
1 TATTTGTAGGCATTATGTGACT
* *
1410025 TATTTGTAGGCATTGTTTGACT
1 TATTTGTAGGCATTATGTGACT
1410047 T
1 T
1410048 TATCTACCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 30 0.81
23 7 0.19
ACGTcount: A:0.19, C:0.09, G:0.24, T:0.49
Consensus pattern (22 bp):
TATTTGTAGGCATTATGTGACT
Found at i:1411136 original size:203 final size:203
Alignment explanation
Indices: 1410783--1411185 Score: 558
Period size: 203 Copynumber: 2.0 Consensus size: 203
1410773 ATGTATATGG
* * * * *
1410783 TGACTTGTTGTTATGTATTGCTTGACATTGGGTCAGTACGTGACTGGTTATGTTGGCATAACGTG
1 TGACCTGTTGTTATGTATTGCGTGACATTGGGCCAGTACATGACTAGTTATGTTGGCATAACGTG
* * * *
1410848 AGTGGATCTTAAGCATCGAGTGACTTATTATTAGGTATTGCGAGACTGGAGATGCGTGACTTGTG
66 AGTAGATATTAAGCATCGAGTGACTTATTATTAGGTATTGCAAGACTGGAGATGCATGACTTGTG
* * * * * *
1410913 CAATTCTTGTCTTGTTTTGAGGCTTTTGTTCACTAGTTTGTAGGTATTACATGACTAATTTTTAT
131 CAATTCTTCTCTTATTTTGAGGCTTTTGTTCACTAGTTTGTAAGCATAACATGACCAATTTTTAT
1410978 GTATTGCT
196 GTATTGCT
* * *
1410986 TGACCTGTTGTTATGTATTTCGTGACATTGGGCCATTACATGACTAGTTATGTTGGCATAATGTG
1 TGACCTGTTGTTATGTATTGCGTGACATTGGGCCAGTACATGACTAGTTATGTTGGCATAACGTG
* *
1411051 AGTAGATATTATGCATCGAGTGACTTATTATTAGGTATTGCAAGACTGGAGGTGCAT-ACCTTGT
66 AGTAGATATTAAGCATCGAGTGACTTATTATTAGGTATTGCAAGACTGGAGATGCATGA-CTTGT
* * * *
1411115 GTAATT-TATCTCTTATTTTGAGGCTTTTGTTGACTAGTTTGTAAGCATAACGTGACCGATTTTT
130 GCAATTCT-TCTCTTATTTTGAGGCTTTTGTTCACTAGTTTGTAAGCATAACATGACCAATTTTT
1411179 ATGTATT
194 ATGTATT
1411186 ACGTGACATT
Statistics
Matches: 174, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
202 2 0.01
203 172 0.99
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (203 bp):
TGACCTGTTGTTATGTATTGCGTGACATTGGGCCAGTACATGACTAGTTATGTTGGCATAACGTG
AGTAGATATTAAGCATCGAGTGACTTATTATTAGGTATTGCAAGACTGGAGATGCATGACTTGTG
CAATTCTTCTCTTATTTTGAGGCTTTTGTTCACTAGTTTGTAAGCATAACATGACCAATTTTTAT
GTATTGCT
Found at i:1415092 original size:17 final size:17
Alignment explanation
Indices: 1415066--1415099 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1415056 TTTTTTTATG
1415066 AAGTAATGGTTGTGAGC
1 AAGTAATGGTTGTGAGC
*
1415083 AAGTAGTGGTTGTGAGC
1 AAGTAATGGTTGTGAGC
1415100 TTTTGATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.38, T:0.29
Consensus pattern (17 bp):
AAGTAATGGTTGTGAGC
Found at i:1417208 original size:23 final size:23
Alignment explanation
Indices: 1417140--1417491 Score: 107
Period size: 23 Copynumber: 15.3 Consensus size: 23
1417130 GATAAATAAT
* *
1417140 TAGTCACGCGACTCCATATTTAC
1 TAGTCACGCGACTCAATATTAAC
* * * ** *
1417163 TACTCAGGCGATTTTATAATAAC
1 TAGTCACGCGACTCAATATTAAC
* *
1417186 TAGTCACGCGATTCAATAGTAAC
1 TAGTCACGCGACTCAATATTAAC
* * * *
1417209 TAGTAACGCTACTCCATATTTAC
1 TAGTCACGCGACTCAATATTAAC
* * * *
1417232 TACTCACGCGAGTCAATATCAAT
1 TAGTCACGCGACTCAATATTAAC
* * * * *
1417255 TAGTCATGCAACTCCATATTTAT
1 TAGTCACGCGACTCAATATTAAC
* * * ** *
1417278 TACTTA-GCGATTTTATAATAAC
1 TAGTCACGCGACTCAATATTAAC
* * *
1417300 TAGTTACGCGATTCAATAATAAC
1 TAGTCACGCGACTCAATATTAAC
* * * * ** *
1417323 AAGTAATGCCACTTTATATTTAC
1 TAGTCACGCGACTCAATATTAAC
* * * *
1417346 TACTCACGAGAGTCAATATCAAC
1 TAGTCACGCGACTCAATATTAAC
* *
1417369 TAGTCACGCGAAC-CCATATTTAC
1 TAGTCACGCG-ACTCAATATTAAC
** * ** *
1417392 TACCCACGCGATTTTATAATAAC
1 TAGTCACGCGACTCAATATTAAC
* * * *
1417415 TAGTCACACAATTCAATAATAAC
1 TAGTCACGCGACTCAATATTAAC
* * *
1417438 TAGTAACGTC-ACTCTATATTTAC
1 TAGTCACG-CGACTCAATATTAAC
* * * *
1417461 TACTCATGCGAGTCAATATCAAC
1 TAGTCACGCGACTCAATATTAAC
1417484 TAGTCACG
1 TAGTCACG
1417492 TGAACCCATA
Statistics
Matches: 225, Mismatches: 99, Indels: 10
0.67 0.30 0.03
Matches are distributed among these distances:
22 16 0.07
23 207 0.92
24 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (23 bp):
TAGTCACGCGACTCAATATTAAC
Found at i:1417457 original size:115 final size:116
Alignment explanation
Indices: 1417140--1417606 Score: 577
Period size: 115 Copynumber: 4.1 Consensus size: 116
1417130 GATAAATAAT
* * *
1417140 TAGTCACGCG-ACTCCATATTTACTACTCAGGCGATTTTATAATAACTAGTCACGCGATTCAATA
1 TAGTCACGCGAACTCCATATTTACTACTCACGCGATTTTATAATAACTAGTCACACAATTCAATA
* *
1417204 GTAACTAGTAACG-CTACTCCATATTTACTACTCACGCGAGTCAATATCAAT
66 ATAACTAGTAACGTC-ACTCCATATTTACTACTCACGCGAGTCAATATCAAC
* * * * * *
1417255 TAGTCATGC-AACTCCATATTTATTACTTA-GCGATTTTATAATAACTAGTTACGCGATTCAATA
1 TAGTCACGCGAACTCCATATTTACTACTCACGCGATTTTATAATAACTAGTCACACAATTCAATA
* * * ** *
1417318 ATAACAAGTAATGCCACTTTATATTTACTACTCACGAGAGTCAATATCAAC
66 ATAACTAGTAACGTCACTCCATATTTACTACTCACGCGAGTCAATATCAAC
*
1417369 TAGTCACGCGAAC-CCATATTTACTACCCACGCGATTTTATAATAACTAGTCACACAATTCAATA
1 TAGTCACGCGAACTCCATATTTACTACTCACGCGATTTTATAATAACTAGTCACACAATTCAATA
* *
1417433 ATAACTAGTAACGTCACTCTATATTTACTACTCATGCGAGTCAATATCAAC
66 ATAACTAGTAACGTCACTCCATATTTACTACTCACGCGAGTCAATATCAAC
* ** * * * *
1417484 TAGTCACGTGAAC-CCATATTTACTACTCACATGATTTTATAATAACTAGTTATATAATTCTATA
1 TAGTCACGCGAACTCCATATTTACTACTCACGCGATTTTATAATAACTAGTCACACAATTCAATA
* * ** ** *
1417548 ATTACTAGTAACGTCACTCCATATTTACAACTTGCGTTACTCAATATCAAC
66 ATAACTAGTAACGTCACTCCATATTTACTACTCACGCGAGTCAATATCAAC
1417599 TAGTCACG
1 TAGTCACG
1417607 TGATTCTATA
Statistics
Matches: 307, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
114 96 0.31
115 211 0.69
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (116 bp):
TAGTCACGCGAACTCCATATTTACTACTCACGCGATTTTATAATAACTAGTCACACAATTCAATA
ATAACTAGTAACGTCACTCCATATTTACTACTCACGCGAGTCAATATCAAC
Found at i:1417622 original size:23 final size:23
Alignment explanation
Indices: 1417591--1417634 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1417581 GCGTTACTCA
1417591 ATATCAACTAGTCACGTGATTCT
1 ATATCAACTAGTCACGTGATTCT
* *
1417614 ATATTAACTAGTTACGTGATT
1 ATATCAACTAGTCACGTGATT
1417635 TCAAATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (23 bp):
ATATCAACTAGTCACGTGATTCT
Found at i:1418641 original size:21 final size:22
Alignment explanation
Indices: 1418616--1418659 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1418606 AAGTAATTAA
1418616 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1418637 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1418659 T
1 T
1418660 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1423505 original size:21 final size:20
Alignment explanation
Indices: 1423481--1423525 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1423471 CTCTTAAAGT
*
1423481 AATTTAAAATAAAATACCTAA
1 AATTT-AAATAAAATAACTAA
* *
1423502 AATTTAACTAAAATAACTTA
1 AATTTAAATAAAATAACTAA
1423522 AATT
1 AATT
1423526 AATCACTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTAAATAAAATAACTAA
Found at i:1425435 original size:74 final size:74
Alignment explanation
Indices: 1425349--1425500 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 74
1425339 ATGCCATGCC
* * ** * * *
1425349 TAAATCCAGTCATGCTGTCATACAATGATTTATCAATAAGTCACGTAATGACCTATAAACTAGTC
1 TAAATCCAGTCATGCTGTCACACAACGACCTATCAATAAGTCACGTAATCACATATAAACCAGTC
1425414 CCGCAATAT
66 CCGCAATAT
* * * *
1425423 TAAATCCAGTCATGTTGTCACGCAACGACCTATCAATATGTCACGTAATCACATATCAACCAGTC
1 TAAATCCAGTCATGCTGTCACACAACGACCTATCAATAAGTCACGTAATCACATATAAACCAGTC
* *
1425488 CTGCAATGT
66 CCGCAATAT
1425497 TAAA
1 TAAA
1425501 CCCTTATGCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (74 bp):
TAAATCCAGTCATGCTGTCACACAACGACCTATCAATAAGTCACGTAATCACATATAAACCAGTC
CCGCAATAT
Found at i:1428443 original size:158 final size:158
Alignment explanation
Indices: 1428146--1428459 Score: 412
Period size: 158 Copynumber: 2.0 Consensus size: 158
1428136 TTTTTCTCTA
*
1428146 ACAACTCCTCGACTTGTCTTTGTACCACCAAAGACTAACCTTGTGCATGATAAACATCAATTTCC
1 ACAACTCCTCGACTTGTCTTTATACCACCAAAGACTAACCTTGTGCATGATAAACATCAATTTCC
** ** * * * *
1428211 TTTATCTCCTCATCATATTCATTGTAAATTGAATCTAATTCTTCCCAATTCAAATAATCCTCCAC
66 TCAATCTCCTCATCATATTCATCATAAAATCAATCTAATTCTTCCCAATCCAAATAATCCTACAC
* * *
1428276 TTGTTACTTCCCATGAGAATCGACTATT
131 CTATAACTTCCCATGAGAATCGACTATT
* * * * *
1428304 ACAACTGCTCGACTTGTCTTTATAGCACCAAGGACTCACCTTGTGCATGATGAACATCAATTTCC
1 ACAACTCCTCGACTTGTCTTTATACCACCAAAGACTAACCTTGTGCATGATAAACATCAATTTCC
* * * * **
1428369 TCAATGTCCTTATCATATTCATCATAAAATCATTCTAATTCTTTCCAATCCAAATAATCCTATGC
66 TCAATCTCCTCATCATATTCATCATAAAATCAATCTAATTCTTCCCAATCCAAATAATCCTACAC
*
1428434 CTATAACTTCTCATGAGAATCGACTA
131 CTATAACTTCCCATGAGAATCGACTA
1428460 CTTCAATCTT
Statistics
Matches: 132, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
158 132 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (158 bp):
ACAACTCCTCGACTTGTCTTTATACCACCAAAGACTAACCTTGTGCATGATAAACATCAATTTCC
TCAATCTCCTCATCATATTCATCATAAAATCAATCTAATTCTTCCCAATCCAAATAATCCTACAC
CTATAACTTCCCATGAGAATCGACTATT
Found at i:1433559 original size:16 final size:16
Alignment explanation
Indices: 1433538--1433571 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1433528 TAGTCTTAGC
*
1433538 CCCTCTTTTCTCTCTT
1 CCCTCTTTACTCTCTT
1433554 CCCTCTTTACTCTCTT
1 CCCTCTTTACTCTCTT
1433570 CC
1 CC
1433572 TCGTCATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (16 bp):
CCCTCTTTACTCTCTT
Found at i:1444318 original size:77 final size:75
Alignment explanation
Indices: 1444232--1444456 Score: 285
Period size: 77 Copynumber: 2.9 Consensus size: 75
1444222 TGAATCTTCC
*
1444232 AAATTAAAATGCTTGCCTTAATTTTAAGAATTTCATTTAAGGTAGGAAACAATATT-CTATTCTT
1 AAATTAAAAT-CTT-CCTTAATTTTAAGAATTTCATTTAAAGTAGGAAACAAT-TTCCTATTCTT
*
1444296 TAGGAATCACCTA
63 TATGAATCACCTA
* * *
1444309 AAATTAAAATTTTATCCTTAATTTT-AGAAATTTCTTTTAAAGTAGGGAACAATTTCCTATTCTT
1 AAATTAAAA-TCT-TCCTTAATTTTAAG-AATTTCATTTAAAGTAGGAAACAATTTCCTATTCTT
1444373 TATGAATCACCTA
63 TATGAATCACCTA
* *
1444386 AAATTAAGATTCTATCCTTAATTTTAAGAA-TTCACTTTAAAGTAGGAAACAATTTCCTATTTTT
1 AAATTAA-AATCT-TCCTTAATTTTAAGAATTTCA-TTTAAAGTAGGAAACAATTTCCTATTCTT
1444450 TATGAAT
63 TATGAAT
1444457 TACTCAAACT
Statistics
Matches: 131, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
76 7 0.05
77 119 0.91
78 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (75 bp):
AAATTAAAATCTTCCTTAATTTTAAGAATTTCATTTAAAGTAGGAAACAATTTCCTATTCTTTAT
GAATCACCTA
Found at i:1450639 original size:20 final size:21
Alignment explanation
Indices: 1450597--1450641 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1450587 ATGGATAAAG
1450597 AAATATCTCATACATTATATA
1 AAATATCTCATACATTATATA
*
1450618 AAATATC-CATA-ATGTATTTA
1 AAATATCTCATACAT-TATATA
1450638 AAAT
1 AAAT
1450642 GAAATATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 13 0.59
21 7 0.32
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATATCTCATACATTATATA
Found at i:1453460 original size:21 final size:19
Alignment explanation
Indices: 1453434--1453474 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1453424 AATTTAAAAC
1453434 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
1453455 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
1453474 A
1 A
1453475 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:1461177 original size:19 final size:20
Alignment explanation
Indices: 1461153--1461192 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1461143 TTGACATTGG
1461153 TATTATTTTA-ATTAAAAAT
1 TATTATTTTATATTAAAAAT
*
1461172 TATTATTTTATTTTAAAAAT
1 TATTATTTTATATTAAAAAT
1461192 T
1 T
1461193 TCCTTTAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTATATTAAAAAT
Found at i:1461301 original size:11 final size:11
Alignment explanation
Indices: 1461285--1461310 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1461275 CTCAATAAGA
1461285 TATTATTATTT
1 TATTATTATTT
1461296 TATTATTATTT
1 TATTATTATTT
1461307 TATT
1 TATT
1461311 GCATACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:1462854 original size:23 final size:25
Alignment explanation
Indices: 1462801--1462863 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
1462791 TGGCAATACT
1462801 ATTTT-TAAAA-TTTTTTTACTTAGA
1 ATTTTATAAAACTTTTTTTAC-TAGA
*
1462825 ATATTATAAAACTTTTTTTA-TA-A
1 ATTTTATAAAACTTTTTTTACTAGA
* *
1462848 ATTTTATTAAGCTTTT
1 ATTTTATAAAACTTTT
1462864 ATAAAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 14 0.42
24 6 0.18
25 5 0.15
26 8 0.24
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTTTATAAAACTTTTTTTACTAGA
Found at i:1463747 original size:21 final size:20
Alignment explanation
Indices: 1463721--1463764 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1463711 TCGCGCCAAC
1463721 AAATTTATA-AAATTTTTTTAT
1 AAATTT-TACAAA-TTTTTTAT
*
1463742 AAATTTTACTAATTTTTTAT
1 AAATTTTACAAATTTTTTAT
1463762 AAA
1 AAA
1463765 AAATAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTTTACAAATTTTTTAT
Found at i:1463936 original size:2 final size:2
Alignment explanation
Indices: 1463929--1463960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1463919 ATTAATTTCG
1463929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1463961 AGTAATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1470675 original size:30 final size:30
Alignment explanation
Indices: 1470640--1470707 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1470630 CTTGATTGAG
*
1470640 AATGAAGAAGATGACATGCAAAGAGATGAA
1 AATGAAGAAGATGACACGCAAAGAGATGAA
* *
1470670 GATGAAGAAGATGACACGGAAAGAGATGAA
1 AATGAAGAAGATGACACGCAAAGAGATGAA
1470700 AATGAAGA
1 AATGAAGA
1470708 TGAAGAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.29, T:0.12
Consensus pattern (30 bp):
AATGAAGAAGATGACACGCAAAGAGATGAA
Found at i:1476480 original size:35 final size:35
Alignment explanation
Indices: 1476441--1476507 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
1476431 TTTTATGCAA
* * * *
1476441 AACAACTATAATAAGTGAAGTGCTACTTCACGCAG
1 AACAACTAGAACAAGTAAAGCGCTACTTCACGCAG
* *
1476476 AACAATTAGAACAAGTAAAGCGTTACTTCACG
1 AACAACTAGAACAAGTAAAGCGCTACTTCACG
1476508 TAGAGTACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (35 bp):
AACAACTAGAACAAGTAAAGCGCTACTTCACGCAG
Found at i:1476778 original size:29 final size:29
Alignment explanation
Indices: 1476755--1476859 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
1476745 CTTATTTTTG
* *
1476755 TATACCTGTTCACATATAGCTTATTT-TCT
1 TATACCTATTCACATATAGCTT-TTTCTAT
* *
1476784 TGTACCTATTCACATACAGCTTTTTCTAT
1 TATACCTATTCACATATAGCTTTTTCTAT
*
1476813 TGTACCTATTCACATATAGCTTTTTCTAT
1 TATACCTATTCACATATAGCTTTTTCTAT
* *
1476842 TATACTTGTTCACATATA
1 TATACCTATTCACATATA
1476860 CCTCTTCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 3 0.04
29 64 0.96
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (29 bp):
TATACCTATTCACATATAGCTTTTTCTAT
Found at i:1479684 original size:20 final size:21
Alignment explanation
Indices: 1479644--1479688 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1479634 AATATAGCAT
*
1479644 AAAAATATAAATACAAATAAA
1 AAAAATAAAAATACAAATAAA
*
1479665 AAAAATAAAAAT-CAATTAAA
1 AAAAATAAAAATACAAATAAA
1479685 AAAA
1 AAAA
1479689 GAGCTGCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAATAAAAATACAAATAAA
Found at i:1480258 original size:2 final size:2
Alignment explanation
Indices: 1480253--1480279 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1480243 TATATATATA
1480253 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1480280 ATAATTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1493383 original size:35 final size:35
Alignment explanation
Indices: 1493333--1493427 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
1493323 NNNNNNNNNN
*
1493333 CCACAACCTTTAACAATGGTTTTTCAAAGGCTCAA
1 CCACAACCTTCAACAATGGTTTTTCAAAGGCTCAA
* * *
1493368 CCACAACCTTCAACAATGGCTTTTCAATGGCTCAG
1 CCACAACCTTCAACAATGGTTTTTCAAAGGCTCAA
* *
1493403 CCATAAACTTCAACAATGGTTTTTC
1 CCACAACCTTCAACAATGGTTTTTC
1493428 TCAAAATCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (35 bp):
CCACAACCTTCAACAATGGTTTTTCAAAGGCTCAA
Found at i:1496581 original size:76 final size:77
Alignment explanation
Indices: 1496499--1496662 Score: 231
Period size: 76 Copynumber: 2.1 Consensus size: 77
1496489 TGAATTTTCC
* * *
1496499 AAATTAAAGTACTATCCTTAATTTTAAGAATTTCTTTTAAAGTAGGAAACAATTACTTATTTT-T
1 AAATTAAAATACTATCCATAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTACTTATTTTGT
*
1496563 ATGAATCACCTA
66 ACGAATCACCTA
* * * * *
1496575 AAATTAAAATTCTATCCATAATTTTAGGAATTGCTTTTAAAGTAGGAAATAATTTCTTTTTTTGT
1 AAATTAAAATACTATCCATAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTACTTATTTTGT
*
1496640 ACGAATTACCTA
66 ACGAATCACCTA
1496652 AAATTAAAATA
1 AAATTAAAATA
1496663 GATGATATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
76 55 0.72
77 21 0.28
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (77 bp):
AAATTAAAATACTATCCATAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTACTTATTTTGT
ACGAATCACCTA
Found at i:1499605 original size:80 final size:80
Alignment explanation
Indices: 1499469--1499667 Score: 247
Period size: 80 Copynumber: 2.5 Consensus size: 80
1499459 TGGCCTATAA
* *
1499469 TGTATATGACTATCTCAACACATACATATAATGGCATACATTTCACAGTCTCATAAATCACTTAC
1 TGTATATGACTATCTCAACACATACATCTAATGGCATACATTTCACAGCCTCATAAATCACTTAC
* *
1499534 AAGCTTAGCCCATAG
66 AAGATTAGCACATAG
* ** *
1499549 TGTATATGACTATCTCAACATATACATCTAATGGCATACATTTCATGGCCTTATAAATCACTTAC
1 TGTATATGACTATCTCAACACATACATCTAATGGCATACATTTCACAGCCTCATAAATCACTTAC
* *
1499614 ATGATTAGCACATGG
66 AAGATTAGCACATAG
* * * * *
1499629 TGTACAT-AATATGCTTAACACATTCATCTCATGGCATAC
1 TGTATATGACTAT-CTCAACACATACATCTAATGGCATAC
1499668 GTGTTGCAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
79 4 0.04
80 98 0.96
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (80 bp):
TGTATATGACTATCTCAACACATACATCTAATGGCATACATTTCACAGCCTCATAAATCACTTAC
AAGATTAGCACATAG
Found at i:1500552 original size:73 final size:73
Alignment explanation
Indices: 1500464--1500659 Score: 180
Period size: 73 Copynumber: 2.7 Consensus size: 73
1500454 GCAAACTGTG
* * * * **
1500464 AGACAAAGAAC-ACTTAGTCGACCAAGAGACAATGTTAGTCGACTAAGAGCTTATTGTCAAAAAC
1 AGACAAA-AACGACTTAATCGACAAAGAGACAATGTTAGTCGACTAAGAGCCTACTACCAAAAAC
1500528 TAGGTTCAA
65 TAGGTTCAA
* * *** * *
1500537 AGACAAAAACGACTTAATC-AGCTAAGATATTTTTTTAGTCGACTAAGAGCCTACTACCAGAAAC
1 AGACAAAAACGACTTAATCGA-CAAAGAGACAATGTTAGTCGACTAAGAGCCTACTACCAAAAAC
* *
1500601 TGGGTTCAG
65 TAGGTTCAA
* * * * *
1500610 AGATAAAGATGACTTAATCGACAAAGTGGCAATGTTAGTCGACTAAGAGC
1 AGACAAAAACGACTTAATCGACAAAGAGACAATGTTAGTCGACTAAGAGC
1500660 ATTCTGTCTA
Statistics
Matches: 95, Mismatches: 25, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
72 4 0.04
73 90 0.95
74 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (73 bp):
AGACAAAAACGACTTAATCGACAAAGAGACAATGTTAGTCGACTAAGAGCCTACTACCAAAAACT
AGGTTCAA
Found at i:1501897 original size:21 final size:20
Alignment explanation
Indices: 1501869--1501907 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1501859 TTGAAATCGA
*
1501869 TGAAATGTATCAATACATTT
1 TGAAATGTAGCAATACATTT
*
1501889 TGAACATGTAGCGATACAT
1 TGAA-ATGTAGCAATACAT
1501908 GTTCATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
TGAAATGTAGCAATACATTT
Found at i:1502905 original size:15 final size:15
Alignment explanation
Indices: 1502887--1502936 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1502877 ACCTAAAGAA
*
1502887 TTACTGGCTAAGATG
1 TTACTGGCTAAGGTG
** *
1502902 TTACTGTTTAAGGTA
1 TTACTGGCTAAGGTG
1502917 TTACTGGCTAAGGTG
1 TTACTGGCTAAGGTG
1502932 TTACT
1 TTACT
1502937 ATCTGAGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (15 bp):
TTACTGGCTAAGGTG
Found at i:1502905 original size:30 final size:30
Alignment explanation
Indices: 1502869--1502937 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1502859 AGATAGTAAC
1502869 ATGTTACTACCTAAAGAATTACTGGCTAAG
1 ATGTTACTACCTAAAGAATTACTGGCTAAG
*** * *
1502899 ATGTTACTGTTTAAGGTATTACTGGCTAAG
1 ATGTTACTACCTAAAGAATTACTGGCTAAG
*
1502929 GTGTTACTA
1 ATGTTACTA
1502938 TCTGAGGTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (30 bp):
ATGTTACTACCTAAAGAATTACTGGCTAAG
Found at i:1503214 original size:35 final size:35
Alignment explanation
Indices: 1503147--1503217 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
1503137 ACACTATTTT
* *
1503147 ATGCGGAACAACTAAAGCAAGTGAAGTACTACTTC
1 ATGCAGAACAACTAAAGCAACTGAAGTACTACTTC
* *
1503182 ATGCAGAACAACTAGAA-CAACTGATGTGCTACTTC
1 ATGCAGAACAACTA-AAGCAACTGAAGTACTACTTC
1503217 A
1 A
1503218 CATAGAGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 29 0.94
36 2 0.06
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (35 bp):
ATGCAGAACAACTAAAGCAACTGAAGTACTACTTC
Found at i:1505547 original size:29 final size:28
Alignment explanation
Indices: 1505488--1505576 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
1505478 GTATACTTGC
*
1505488 TCACATACACCTTCTTTC-TTGTACCTAT
1 TCACATACAACTT-TTTCTTTGTACCTAT
*
1505516 TCACATACAACTTTTTCTATTGTACCTGT
1 TCACATACAACTTTTTCT-TTGTACCTAT
* *
1505545 TCACATACAACTTCTTCTCTTGTACCTTT
1 TCACATACAACTTTTTCT-TTGTACCTAT
1505574 TCA
1 TCA
1505577 TGTATACCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 4 0.07
28 12 0.22
29 38 0.70
ACGTcount: A:0.22, C:0.29, G:0.04, T:0.44
Consensus pattern (28 bp):
TCACATACAACTTTTTCTTTGTACCTAT
Found at i:1507349 original size:71 final size:72
Alignment explanation
Indices: 1507224--1507381 Score: 162
Period size: 71 Copynumber: 2.2 Consensus size: 72
1507214 CTTATGGTAA
* * * * * * *
1507224 TTTAATAAATTAAAATAATATTGGAATGGATTTTGAGAAAGACATAAAGCTTTT-AATCAATTAA
1 TTTAATAGATTAAAACAACATTGGAATGCACTCTGAGAAAGACAGAAAGCTTTTAAATCAATTAA
*
1507288 AACCCA-T
66 AA-CAAGT
*
1507295 TTTAATAGATTAAAACAACATTGGAATGCACTCTGAGATAAG-CAGAAA-CATTTTAAATCGATT
1 TTTAATAGATTAAAACAACATTGGAATGCACTCTGAGA-AAGACAGAAAGC-TTTTAAATCAATT
*
1507358 AACACAAGT
64 AAAACAAGT
*
1507367 TTTAATTGATTAAAA
1 TTTAATAGATTAAAA
1507382 TTCAAAGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
70 1 0.01
71 43 0.60
72 28 0.39
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (72 bp):
TTTAATAGATTAAAACAACATTGGAATGCACTCTGAGAAAGACAGAAAGCTTTTAAATCAATTAA
AACAAGT
Found at i:1507646 original size:63 final size:62
Alignment explanation
Indices: 1507508--1507646 Score: 145
Period size: 62 Copynumber: 2.2 Consensus size: 62
1507498 ATAGAGAAGC
* * * * *
1507508 TTTAATTGATCAAAGACAATTTTATCTAATTAACCTAAAGCAATGGGAATAGACAGAATGGT
1 TTTAATTGATTAAAGACAATTTTATCTAATTAACCTAAAGCAATAGGAATAGACAAAAAGAT
** * * * *
1507570 TTTAATCAATTAAAGCCAATTTTAATC-AATTATCCTGAAGCACTAGGAGATAGACAAAAAGAT
1 TTTAATTGATTAAAGACAATTTT-ATCTAATTAACCTAAAGCAATAGGA-ATAGACAAAAAGAT
*
1507633 TTTAATTGGTTAAA
1 TTTAATTGATTAAA
1507647 ATCCATTTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
62 36 0.59
63 25 0.41
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (62 bp):
TTTAATTGATTAAAGACAATTTTATCTAATTAACCTAAAGCAATAGGAATAGACAAAAAGAT
Found at i:1509871 original size:25 final size:25
Alignment explanation
Indices: 1509815--1509864 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1509805 ATGGTCTATG
* *
1509815 ATTATACATGGCAAGGCCATGGGTT
1 ATTATACATGGCAAGGCCACGAGTT
1509840 ATTATACATGGCAAGGCCACGAGTT
1 ATTATACATGGCAAGGCCACGAGTT
1509865 GATATACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (25 bp):
ATTATACATGGCAAGGCCACGAGTT
Found at i:1513017 original size:25 final size:25
Alignment explanation
Indices: 1512989--1513044 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1512979 TTGCAACTAA
* * *
1512989 GTATATCAACTCGTGGCCTAGCCAC
1 GTATAACAACTCATGACCTAGCCAC
* *
1513014 GTATAACAACTCATGACTTTGCCAC
1 GTATAACAACTCATGACCTAGCCAC
1513039 GTATAA
1 GTATAA
1513045 TCACAGATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (25 bp):
GTATAACAACTCATGACCTAGCCAC
Found at i:1513065 original size:28 final size:25
Alignment explanation
Indices: 1513002--1513074 Score: 65
Period size: 28 Copynumber: 2.8 Consensus size: 25
1512992 TATCAACTCG
*
1513002 TGGCCTAGCCACGTATAACAACTCA
1 TGGCCTAGCCACGTATAACAAATCA
* * *
1513027 TGACTTTGCCACGTATAATCACAGATCA
1 TGGCCTAGCCACGTATAA-CA-A-ATCA
* *
1513055 TGGCCTAGCCATGTTTAACA
1 TGGCCTAGCCACGTATAACA
1513075 GCCCAACGGC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
25 15 0.42
26 2 0.06
27 3 0.08
28 16 0.44
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (25 bp):
TGGCCTAGCCACGTATAACAAATCA
Found at i:1515026 original size:18 final size:18
Alignment explanation
Indices: 1515005--1515047 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1514995 TTATTTGTTG
*
1515005 AGTTAGGTTA-TTTTGAGA
1 AGTTAGGATATTTTTGA-A
1515023 AGTT-GGATATTTTTGAA
1 AGTTAGGATATTTTTGAA
1515040 AGTTAGGA
1 AGTTAGGA
1515048 AAAGAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (18 bp):
AGTTAGGATATTTTTGAA
Found at i:1527541 original size:20 final size:20
Alignment explanation
Indices: 1527518--1527564 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1527508 CAATGTATCA
* *
1527518 ATACATTGGACAATATATTG
1 ATACATTCGACAATATATTC
*
1527538 ATACATTCGCCAATATATTC
1 ATACATTCGACAATATATTC
1527558 ATACATT
1 ATACATT
1527565 TTATCGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (20 bp):
ATACATTCGACAATATATTC
Found at i:1528756 original size:79 final size:80
Alignment explanation
Indices: 1528557--1528943 Score: 387
Period size: 79 Copynumber: 4.9 Consensus size: 80
1528547 AGATAGTAAC
* * * *
1528557 ATGCATGCTATGA-A-ATGTGTGATT-GGATAGTCATATACACTATAGGCTAAACATGTGAGTCA
1 ATGCATGCCATGAGATATATGTG-TTGGGATAGTCATATACACTATAGGCTAAGCATGTGAGTTA
* *
1528619 TTTATGAGATTGT-AA
65 TTTATGAGGTTATGAA
* * * * * *
1528634 CATACATGGCATAAAATGTATGTGTTGGGATAGTCATATACACTATAGGCTAAGCATGTGGGTTA
1 -ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATAGGCTAAGCATGTGAGTTA
1528699 -TTATGAGGTTATGAA
65 TTTATGAGGTTATGAA
* * **
1528714 ATGCATGCCATGAGATATATGTGTTGGGATAGTCATAAACACTAT-GAGCTAAGCATGTCAACTA
1 ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATAG-GCTAAGCATGTGAGTTA
*
1528778 TTTATGA-GATATGAA
65 TTTATGAGGTTATGAA
* * * * * * * *
1528793 ATGCATGCCATGAGATGTATGTGTTGAGATAGTCATATGCACTTTGGGCTAAGTATGTAAGTGAT
1 ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATAGGCTAAGCATGTGAGTTAT
1528858 TTATGAGGTTATGAA
66 TTATGAGGTTATGAA
* * * * * *
1528873 ATGTATGCCATGAGATGA-ATGTGTTGAGATAATCATATACACTATGGGCTAAGAATGATGA-TG
1 ATGCATGCCATGAGAT-ATATGTGTTGGGATAGTCATATACACTATAGGCTAAGCATG-TGAGTT
1528936 ATTTATGA
64 ATTTATGA
1528944 AAATGTTATA
Statistics
Matches: 259, Mismatches: 40, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
78 10 0.04
79 131 0.51
80 116 0.45
81 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (80 bp):
ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATAGGCTAAGCATGTGAGTTAT
TTATGAGGTTATGAA
Found at i:1528870 original size:159 final size:159
Alignment explanation
Indices: 1528557--1528925 Score: 430
Period size: 159 Copynumber: 2.3 Consensus size: 159
1528547 AGATAGTAAC
* * * * *
1528557 ATGCATGCTATGA-A-ATGTGTGATT-GGATAGTCATATACACTAT-AGGCTAAACATGTGAGTC
1 ATGCATGCCATGAGATATATGTG-TTGGGATAGTCATATACACTATGA-GCTAAGCATGTAACTC
* *
1528618 ATTTATGAGATTGTAACATACATGGCATAAAATGTATGTGTTGGGATAGTCATATACACTATAGG
64 ATTTATGAGATTGTAACATACATGCCATAAAATGTATGTGTTGAGATAGTCATATACACTATAGG
** *
1528683 CTAAGCATGTGGGTTATTATGAGGTTATGAA
129 CTAAGCATGTAAGTGATTATGAGGTTATGAA
*
1528714 ATGCATGCCATGAGATATATGTGTTGGGATAGTCATAAACACTATGAGCTAAGCATGTCAACT-A
1 ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATGAGCTAAGCATGT-AACTCA
* * * * * *
1528778 TTTATGAGATATG-AA-ATGCATGCCATGAGATGTATGTGTTGAGATAGTCATATGCACTTTGGG
65 TTTATGAGAT-TGTAACATACATGCCATAAAATGTATGTGTTGAGATAGTCATATACACTATAGG
*
1528841 CTAAGTATGTAAGTGATTTATGAGGTTATGAA
129 CTAAGCATGTAAGTGA-TTATGAGGTTATGAA
* * * *
1528873 ATGTATGCCATGAGATGA-ATGTGTTGAGATAATCATATACACTATGGGCTAAG
1 ATGCATGCCATGAGAT-ATATGTGTTGGGATAGTCATATACACTATGAGCTAAG
1528926 AATGATGATG
Statistics
Matches: 181, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
157 12 0.07
158 55 0.30
159 108 0.60
160 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (159 bp):
ATGCATGCCATGAGATATATGTGTTGGGATAGTCATATACACTATGAGCTAAGCATGTAACTCAT
TTATGAGATTGTAACATACATGCCATAAAATGTATGTGTTGAGATAGTCATATACACTATAGGCT
AAGCATGTAAGTGATTATGAGGTTATGAA
Found at i:1544939 original size:14 final size:14
Alignment explanation
Indices: 1544915--1544954 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1544905 AGGTTAAAAT
1544915 TTAATTT-TTTTAA
1 TTAATTTATTTTAA
* *
1544928 TTAGTTTATTTTTA
1 TTAATTTATTTTAA
1544942 TTAATTTATTTTA
1 TTAATTTATTTTA
1544955 TTTTATGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTAATTTATTTTAA
Found at i:1544940 original size:18 final size:19
Alignment explanation
Indices: 1544918--1544958 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1544908 TTAAAATTTA
1544918 ATTTTT-TTAA-TTAGTTT
1 ATTTTTATTAATTTAGTTT
*
1544935 ATTTTTATTAATTTATTTT
1 ATTTTTATTAATTTAGTTT
1544954 ATTTT
1 ATTTT
1544959 ATGCCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 4 0.19
19 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTATTAATTTAGTTT
Found at i:1544959 original size:18 final size:17
Alignment explanation
Indices: 1544913--1544960 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1544903 TGAGGTTAAA
* *
1544913 ATTTAATTTTTTTAATT
1 ATTTTATTTTATTAATT
*
1544930 AGTTTATTTTTATTAATTT
1 ATTTTA-TTTTATTAA-TT
1544949 ATTTTATTTTAT
1 ATTTTATTTTAT
1544961 GCCAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 4 0.16
18 14 0.56
19 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTATTTTATTAATT
Found at i:1550911 original size:24 final size:25
Alignment explanation
Indices: 1550861--1550917 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
1550851 TATTTTATGC
1550861 CTTTATTTACTTTTGAGTTGTTGAT
1 CTTTATTTACTTTTGAGTTGTTGAT
* *
1550886 CTTTATTTA-TTTTTATTTGCTT-AT
1 CTTTATTTACTTTTGAGTTG-TTGAT
1550910 CTTTATTT
1 CTTTATTT
1550918 TATTATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (25 bp):
CTTTATTTACTTTTGAGTTGTTGAT
Found at i:1552161 original size:21 final size:21
Alignment explanation
Indices: 1552137--1552245 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
1552127 AATCCATTAT
*
1552137 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTATTTAA
** * *
1552158 ATTTAAATATGGA-TTAATTAC
1 ATTTAAAT-TTAATTTATTTAA
*
1552179 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTATTTAA
** * *
1552200 ATTTAAATATGGA-TTAATTAC
1 ATTTAAAT-TTAATTTATTTAA
1552221 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
1552242 ATTT
1 ATTT
1552246 TTTAAAAAAA
Statistics
Matches: 65, Mismatches: 19, Indels: 8
0.71 0.21 0.09
Matches are distributed among these distances:
20 4 0.06
21 57 0.88
22 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:1552189 original size:42 final size:42
Alignment explanation
Indices: 1552132--1552245 Score: 210
Period size: 42 Copynumber: 2.7 Consensus size: 42
1552122 TGAATAATCC
*
1552132 ATTATATTTAAATTTAATTTGTTTAAATTTAAATATGGATTA
1 ATTACATTTAAATTTAATTTGTTTAAATTTAAATATGGATTA
1552174 ATTACATTTAAATTTAATTTGTTTAAATTTAAATATGGATTA
1 ATTACATTTAAATTTAATTTGTTTAAATTTAAATATGGATTA
*
1552216 ATTACATTTAAATTTAATTTATTTAAATTT
1 ATTACATTTAAATTTAATTTGTTTAAATTT
1552246 TTTAAAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (42 bp):
ATTACATTTAAATTTAATTTGTTTAAATTTAAATATGGATTA
Found at i:1561347 original size:28 final size:28
Alignment explanation
Indices: 1561315--1561454 Score: 151
Period size: 28 Copynumber: 5.0 Consensus size: 28
1561305 TGACAACTTT
*
1561315 AACATGTTTGTCTTATTTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
1561343 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
1561372 AATATGTTTGTCTTAATTTAAAACAAAAGAA
1 AACATGTTTGTCTTAATTT-AGAC--AAGAA
* *
1561403 AA-A--TTTGTTTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* * *
1561428 AACATATTTGTCTCAAATTAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA
1561455 TAAAATATTT
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
25 7 0.07
26 1 0.01
27 3 0.03
28 47 0.49
29 29 0.31
30 1 0.01
31 7 0.07
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:1562719 original size:32 final size:31
Alignment explanation
Indices: 1562665--1562726 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
1562655 TATTACTTTT
1562665 TTTTTAAGAAAAAAGAGATTTTCATGTATATTC
1 TTTTTAAGAAAAAAGAGATTTTC-T-TATATTC
*
1562698 TTTTTAAG-AAAAAGAGTTTTTCTTATATT
1 TTTTTAAGAAAAAAGAGATTTTCTTATATT
1562727 AAAATCTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 6 0.21
31 1 0.04
32 13 0.46
33 8 0.29
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTTTAAGAAAAAAGAGATTTTCTTATATTC
Found at i:1568758 original size:29 final size:28
Alignment explanation
Indices: 1568718--1568871 Score: 143
Period size: 29 Copynumber: 5.4 Consensus size: 28
1568708 CTTTAACATG
*
1568718 TTTGTCTTAATTTAGACAAGAAAACATA
1 TTTGTCTTAATTTAGACAAGAAAAAATA
* * *
1568746 TTTGGTCTTAATTTAGATAAGAAAATATG
1 TTT-GTCTTAATTTAGACAAGAAAAAATA
* *
1568775 TTTGTCCTAATTTAAAACAA-AAAAAATA
1 TTTGTCTTAATTT-AGACAAGAAAAAATA
* *
1568803 TTTTATCTTAATCTAGA-AA-AAAAAATA
1 -TTTGTCTTAATTTAGACAAGAAAAAATA
* * *
1568830 TTTGTCTCAATTTATACAAGATAAAATATT
1 TTTGTCTTAATTTAGACAAGA-AAAA-ATA
1568860 TTTGTCTTAATT
1 TTTGTCTTAATT
1568872 AAACACAAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
26 12 0.12
27 12 0.12
28 21 0.21
29 43 0.43
30 13 0.13
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAAAATA
Found at i:1568804 original size:57 final size:55
Alignment explanation
Indices: 1568715--1568871 Score: 165
Period size: 57 Copynumber: 2.8 Consensus size: 55
1568705 CAGCTTTAAC
* * * * *
1568715 ATGTTTGTCTTAATTTAGACAAGAAAACATATTTGGTCTTAATTTAGATAAGAAAAT
1 ATGTTTGTCCTAATTTAAACAAGAAAAAATATTTTGTCTTAATTTAGA-AA-AAAAA
* *
1568772 ATGTTTGTCCTAATTTAAAACAA-AAAAAATATTTTATCTTAATCTAGAAAAAAAA
1 ATGTTTGTCCTAATTT-AAACAAGAAAAAATATTTTGTCTTAATTTAGAAAAAAAA
* * *
1568827 ATATTTGT-CTCAATTTATACAAGATAAAATATTTTTGTCTTAATT
1 ATGTTTGTCCT-AATTTAAACAAGAAAAAATA-TTTTGTCTTAATT
1568872 AAACACAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
54 7 0.08
55 23 0.27
56 13 0.15
57 36 0.43
58 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (55 bp):
ATGTTTGTCCTAATTTAAACAAGAAAAAATATTTTGTCTTAATTTAGAAAAAAAA
Found at i:1569059 original size:18 final size:17
Alignment explanation
Indices: 1569024--1569057 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1569014 ATAATAATAA
1569024 AATAAGAGTTGTTATTT
1 AATAAGAGTTGTTATTT
1569041 AATAAGGAGTT-TTATTT
1 AATAA-GAGTTGTTATTT
1569058 TATCAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
AATAAGAGTTGTTATTT
Found at i:1575027 original size:17 final size:18
Alignment explanation
Indices: 1574990--1575029 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1574980 TCCACAATAT
1574990 CACAATATCTCAAAAATG
1 CACAATATCTCAAAAATG
*
1575008 CACAATATCTTAAAAA-G
1 CACAATATCTCAAAAATG
1575025 CACAA
1 CACAA
1575030 GTGTGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (18 bp):
CACAATATCTCAAAAATG
Done.