Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:1073586 original size:27 final size:28
Alignment explanation
Indices: 1073533--1073587 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1073523 AATTAAAACA
* *
1073533 TTTTATTTCCTTTTCGTTTTTCTTTTTC
1 TTTTATTTCCTTTTCGTTTATCCTTTTC
1073561 TTTTATTT-CTTTTC-TTCTATCCTTTTC
1 TTTTATTTCCTTTTCGTT-TATCCTTTTC
1073588 ACCTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 14 0.58
28 8 0.33
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTATTTCCTTTTCGTTTATCCTTTTC
Found at i:1076711 original size:32 final size:34
Alignment explanation
Indices: 1076674--1076792 Score: 109
Period size: 34 Copynumber: 3.5 Consensus size: 34
1076664 CACTTGATTA
1076674 AAATTGTATAATTAAGTT-GT-GTCTAATTAATT
1 AAATTGTATAATTAAGTTAGTAGTCTAATTAATT
* *
1076706 AAATTGTTTAATTAAGTTATTAGGTCTAATTAATT
1 AAATTGTATAATTAAGTTAGTA-GTCTAATTAATT
** * * * *
1076741 -AATTAAACAATTAAGTTATTAGGCTTAATTGATT
1 AAATTGTATAATTAAGTTAGTAGTC-TAATTAATT
*
1076775 AAATTTGTTTAATTAAGT
1 AAA-TTGTATAATTAAGT
1076793 CATTGGGTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
32 17 0.25
33 3 0.04
34 25 0.36
35 14 0.20
36 10 0.14
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (34 bp):
AAATTGTATAATTAAGTTAGTAGTCTAATTAATT
Found at i:1076719 original size:17 final size:19
Alignment explanation
Indices: 1076682--1076742 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 19
1076672 TAAAATTGTA
*
1076682 TAATTAAGTTGTGTCTAAT
1 TAATTAAATTGTGTCTAAT
1076701 TAATTAAATTGT-T-TAAT
1 TAATTAAATTGTGTCTAAT
1076718 TAAGTT--ATTAG-GTCTAAT
1 TAA-TTAAATT-GTGTCTAAT
1076736 TAATTAA
1 TAATTAA
1076743 TTAAACAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
16 3 0.09
17 11 0.31
18 10 0.29
19 11 0.31
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (19 bp):
TAATTAAATTGTGTCTAAT
Found at i:1079470 original size:2 final size:2
Alignment explanation
Indices: 1079457--1079488 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1079447 AGGTATCACA
*
1079457 AT AT AT AC 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 AT AT
1079489 TGCAATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1084812 original size:171 final size:170
Alignment explanation
Indices: 1084272--1085686 Score: 1254
Period size: 170 Copynumber: 8.3 Consensus size: 170
1084262 GTTACACATG
* * * * * * * *
1084272 CCTTCAAATGTCTTATTACTCGTTTTAAATGATTTTTAATCTTATAAAGAAGTTTATATCAAACT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTTTAATCTTATAAATAATTTTAAATCAAAAT
* * * * * * * * *
1084337 CTTTTTTGTTTGTAGTTAAAATAGATTATAATTGGATATTTATA-TCGAAAA-ATGTCAAGCGGA
66 ATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGAAAACATG--AAACGAA
* * * *
1084400 AGCTATCCATTGACAAGAAAAGTCCATTTATAGTCACTTATA
129 AACCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
* * ** ** * * *
1084442 CCTTCAAAAGCCTTATTACTAACTTTAAATCATTTTTTATCTTATAAATGATCTTAAATCAAAAT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTTTAATCTTATAAATAATTTTAAATCAAAAT
* * * * *
1084507 ATTTTTCATTTTTGGTT-AAACTAGATCATAATTGGATATTAGTATCACG-AAACAT-AAA-GCA
66 ATTTTTTATTTTTAGTTAAAAC-AGATCATAATTAGATATTTGTAT-TCGAAAACATGAAACG-A
* * * * * *
1084568 AAAGCTATCCATTGACAATAAAAATCTATTTATAGTCACTTATA
128 AAA-CCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
* * * *
1084612 CCTTCAATAGTCTTATTACTTGCTTTAAATGGTTTTTGAATCTTATAAATTATTTTAAATCAAAA
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTTT-AATCTTATAAATAATTTTAAATCAAAA
* * * * *
1084677 TATATTTTATTTTTAGTTAAAACAGATCATAATTGGATGTTTGCATTGGAAAACATGAAACGAAA
65 TATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGAAAACATGAAACGAAA
* * * *
1084742 GCCATCCATTGATAAGAAAAGTCCATTTATGGT-AGCTTATG
130 ACCATCCATTGATAAGAAAAGTCCATTTATAGTCA-CTCATA
* * * * * *
1084783 CTTTCGAAAGCCTTGTTACTCGTTTTAAATGGTTTTATAATCTTATAAATGATTTTACATGC-AA
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTT-TAATCTTATAAATAATTTTAAAT-CAAA
* * * * * **
1084847 AGATTTTTTATTTTTTTGTTAAAATAGATCAAAATTAGATATTAGTA-TCGAGAAATGTGAAACG
64 ATATTTTTTA-TTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGA-AAACATGAAACG
* *
1084911 AAAACCATTCATTGATAAGAAAAGTCCATTTATAATCACTCATA
127 AAAACCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
* *
1084955 CCTTCAATAA-TCTTGTTACTCGCTTTAAATAGTTTTTGAATCTTATAAATAATTTTAAATTAAA
1 CCTTCAA-AAGTCTTGTTACTCGCTTTAAATGGTTTTT-AATCTTATAAATAATTTTAAATCAAA
* * * **
1085019 ATATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATGTTTGCATT-GGAAACATGAAGTGAA
64 ATATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGAAAACATGAAACGAA
* *
1085083 AACCATCCATTGATAAGAAAAGTCCATTTATAGTCACACATG
129 AACCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
* ** * *
1085125 CCTTCGAAAGTCTTGTTACTTACTTTAAATGGTTTTATAATCTTATAAA-ATTTTTTAAATTAAA
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTT-TAATCTTATAAATA-ATTTTAAATCAAA
* * * *
1085189 ATATTTTTTATTTTTAGTTCAAACAAATCATAATT-GAATATTTGTA-TCAGGAAACGT-AAA-G
64 ATATTTTTTATTTTTAGTTAAAACAGATCATAATTAG-ATATTTGTATTC-GAAAACATGAAACG
* * *
1085250 CAAAAGCCA-CCATTAATAAGAAAAGTCTATTTATAATCACTCATA
127 -AAAA-CCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
** * * * * * **
1085295 TTTTCAAAAATCTTTTTATTCGCTTTAAATGATTTTTAATCTTATAAATGATTTCCAATCAAAAT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTTTAATCTTATAAATAATTTTAAATCAAAAT
* * * * * * * * ** ** *
1085360 CTTTTTTATTGTTAGTTAAAACAGATTAAAATTAGATGTTTGCATTAGTAAATGTGAGGCAAAAA
66 ATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGAAAACATGAAACGAAAA
* * * *
1085425 CCATCTATTGAAAAAAAAAATCCATTTATAAGT-ACTCATA
131 CCATCCATTGATAAGAAAAGTCCATTTAT-AGTCACTCATA
* * * *
1085465 CTTTCAAAAGTCTTGTTACTCACTTTAAATAGTTTTTTAATCATATAAATAATTTTAAAT-AGAA
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAAT-GGTTTTTAATCTTATAAATAATTTTAAATCA-AA
* *
1085529 ATATTTTTTAATTTTT-GATTAAAACAGATCATAATTAGATATTTGTA-TCGAGAAACGTGAAGC
64 ATATTTTTT-ATTTTTAG-TTAAAACAGATCATAATTAGATATTTGTATTCGA-AAACATGAAAC
** * *
1085592 GAAAACCATTTATTGATAAAAAAAGTCTATTTATAGTCACAT-ATA
126 GAAAACCATCCATTGATAAGAAAAGTCCATTTATAGTCAC-TCATA
* ** *
1085637 CCTTTAAAAGTCTTGTTTTTCGCTTTAAATGGTTTTTTAATCTTACAAAT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATGG-TTTTTAATCTTATAAAT
1085687 TAGCAATGTT
Statistics
Matches: 1012, Mismatches: 189, Indels: 86
0.79 0.15 0.07
Matches are distributed among these distances:
168 1 0.00
169 79 0.08
170 416 0.41
171 247 0.24
172 264 0.26
173 5 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (170 bp):
CCTTCAAAAGTCTTGTTACTCGCTTTAAATGGTTTTTAATCTTATAAATAATTTTAAATCAAAAT
ATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATATTTGTATTCGAAAACATGAAACGAAAA
CCATCCATTGATAAGAAAAGTCCATTTATAGTCACTCATA
Found at i:1085579 original size:682 final size:681
Alignment explanation
Indices: 1084272--1085686 Score: 1666
Period size: 682 Copynumber: 2.1 Consensus size: 681
1084262 GTTACACATG
* * * * * *
1084272 CCTTCAAATGTCTTATTACTCGTTTTAAATGATTTTTAATCTTATAAAGAAGTTTATATCAAACT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAATG-TTTTTAATCTTATAAATAAGTTTAAATCAAAAT
* * * * * * *
1084337 CTTTTTTGTTTGTAGTTAAAATAGATTATAATTGGATATTTATATCGAAAAATGTCAAGCGGAAG
65 ATTTTTTATTTGTAGTTAAAACAGATCATAATTAGATATTTATATCGAAAAATG-CAAGCGAAAA
* **
1084402 CTATCCATTGACAAGAAAAGTCCATTTATAGTCACTTATACCTTCAAAAGCCTTATTACTAACTT
129 CCATCCATTGACAAGAAAAGTCCATTTATAGTCACACATACCTTCAAAAGCCTTATTACTAACTT
* * *
1084467 TAAATCATTTTTTATCTTATAAATGATCTTAAATCAAAATATTTTTCATTTTTGGTTAAACTAGA
194 TAAATCATTTTTAATCTTATAAATGATCTTAAATCAAAATATTTTTCATTTTTAGTTAAACTAAA
* * * *
1084532 TCATAATTGGATATTAGTATCACGAAACATAAAGCAAAAGCTATCCATTGACAATAAAAATCTAT
259 TCATAATTGAATATTAGTATCACGAAACATAAAGCAAAAGCCATCCATTAACAAGAAAAATCTAT
* * * * *
1084597 TTATAGTCACTTATACCTTCAATAGTCTTATTACTTGCTTTAAATGGTTTTTGAATCTTATAAAT
324 TTATAATCACTCATACCTTCAAAAATCTTATTACTTGCTTTAAATGATTTTTGAATCTTATAAAT
* * * * * *
1084662 TATTTTAAATCAAAATATATTTTATTTTTAGTTAAAACAGATCATAATTGGATGTTTGCATTGGA
389 GATTTCAAATCAAAATATATTTTATTGTTAGTTAAAACAGATCAAAATTAGATGTTTGCATTAGA
* * * * * * * * *
1084727 AAACATGAAACGAAAGCCATCCATTGATAAGAAAAGTCCATTTATGGTAGCTTATGCTTTCGAAA
454 AAACATGAAACAAAAACCATCCATTGAAAAAAAAAATCCATTTATAGTAGCTCATACTTTCAAAA
** * * * *
1084792 GCCTTGTTACTCGTTTTAAATGGTTTTATAATCTTATAAATGATTTTACATGCAAAGATTTTTTA
519 GCCTTGTTACTCACTTTAAATAGTTTTATAATCATATAAATAATTTTAAATGCAAAGATTTTTTA
* * *
1084857 TTTTTTTGTTAAAATAGATCAAAATTAGATATTAGTATCGAGAAATGTGAAACGAAAACCATTCA
584 TATTTTTGTTAAAACAGATCAAAATTAGATATTAGTATCGAGAAACGTGAAACGAAAACCATTCA
*
1084922 TTGATAAGAAAAGTCCATTTATAATCAC-TCATA
649 TTGATAAAAAAAGTCCATTTATAATCACAT-ATA
* *
1084955 CCTTCAATAA-TCTTGTTACTCGCTTTAAATAGTTTTTGAATCTTATAAATAATTTTAAATTAAA
1 CCTTCAA-AAGTCTTGTTACTCGCTTTAAAT-GTTTTT-AATCTTATAAATAAGTTTAAATCAAA
* * * * *
1085019 ATATTTTTTATTTTTAGTTAAAACAGATCATAATTAGATGTTTGCAT-TGGAAACATG-AAGTGA
63 ATATTTTTTATTTGTAGTTAAAACAGATCATAATTAGATATTT--ATATCGAAAAATGCAAGCGA
* * * * * *
1085082 AAACCATCCATTGATAAGAAAAGTCCATTTATAGTCACACATGCCTTCGAAAGTCTTGTTACTTA
126 AAACCATCCATTGACAAGAAAAGTCCATTTATAGTCACACATACCTTCAAAAGCCTTATTACTAA
** * * * *
1085147 CTTTAAATGGTTTTATAATCTTATAAAAT-TTTTTAAATTAAAATATTTTTTATTTTTAGTTCAA
191 CTTTAAATCATTTT-TAATCTTAT-AAATGATCTTAAATCAAAATATTTTTCATTTTTAGTT-AA
* * * *
1085211 AC-AAATCATAATTGAATATTTGTATCAGGAAACGTAAAGCAAAAGCCA-CCATTAATAAGAAAA
253 ACTAAATCATAATTGAATATTAGTATCACGAAACATAAAGCAAAAGCCATCCATTAACAAGAAAA
* ** *
1085274 GTCTATTTATAATCACTCATATTTTCAAAAATCTTTTTA-TTCGCTTTAAATGATTTTT-AATCT
318 ATCTATTTATAATCACTCATACCTTCAAAAATCTTATTACTT-GCTTTAAATGATTTTTGAATCT
* * * *
1085337 TATAAATGATTTCCAATCAAAATCTTTTTTATTGTTAGTTAAAACAGATTAAAATTAGATGTTTG
382 TATAAATGATTTCAAATCAAAATATATTTTATTGTTAGTTAAAACAGATCAAAATTAGATGTTTG
* ** ** *
1085402 CATTAGTAAATGTGAGGCAAAAACCATCTATTGAAAAAAAAAATCCATTTATAAGTA-CTCATAC
447 CATTAGAAAACATGAAACAAAAACCATCCATTGAAAAAAAAAATCCATTTAT-AGTAGCTCATAC
* *
1085466 TTTCAAAAGTCTTGTTACTCACTTTAAATAGTTTTTTAATCATATAAATAATTTTAAATAG-AAA
511 TTTCAAAAGCCTTGTTACTCACTTTAAATAGTTTTATAATCATATAAATAATTTTAAAT-GCAAA
* * * *
1085530 TATTTTTTA-ATTTTTGATTAAAACAGATCATAATTAGATATTTGTATCGAGAAACGTGAAGCGA
575 GATTTTTTATATTTTTG-TTAAAACAGATCAAAATTAGATATTAGTATCGAGAAACGTGAAACGA
* * *
1085594 AAACCATTTATTGATAAAAAAAGTCTATTTATAGTCACATATA
639 AAACCATTCATTGATAAAAAAAGTCCATTTATAATCACATATA
* ** *
1085637 CCTTTAAAAGTCTTGTTTTTCGCTTTAAATGGTTTTTTAATCTTACAAAT
1 CCTTCAAAAGTCTTGTTACTCGCTTTAAAT-G-TTTTTAATCTTATAAAT
1085687 TAGCAATGTT
Statistics
Matches: 613, Mismatches: 104, Indels: 31
0.82 0.14 0.04
Matches are distributed among these distances:
681 8 0.01
682 284 0.46
683 169 0.28
684 134 0.22
685 16 0.03
686 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (681 bp):
CCTTCAAAAGTCTTGTTACTCGCTTTAAATGTTTTTAATCTTATAAATAAGTTTAAATCAAAATA
TTTTTTATTTGTAGTTAAAACAGATCATAATTAGATATTTATATCGAAAAATGCAAGCGAAAACC
ATCCATTGACAAGAAAAGTCCATTTATAGTCACACATACCTTCAAAAGCCTTATTACTAACTTTA
AATCATTTTTAATCTTATAAATGATCTTAAATCAAAATATTTTTCATTTTTAGTTAAACTAAATC
ATAATTGAATATTAGTATCACGAAACATAAAGCAAAAGCCATCCATTAACAAGAAAAATCTATTT
ATAATCACTCATACCTTCAAAAATCTTATTACTTGCTTTAAATGATTTTTGAATCTTATAAATGA
TTTCAAATCAAAATATATTTTATTGTTAGTTAAAACAGATCAAAATTAGATGTTTGCATTAGAAA
ACATGAAACAAAAACCATCCATTGAAAAAAAAAATCCATTTATAGTAGCTCATACTTTCAAAAGC
CTTGTTACTCACTTTAAATAGTTTTATAATCATATAAATAATTTTAAATGCAAAGATTTTTTATA
TTTTTGTTAAAACAGATCAAAATTAGATATTAGTATCGAGAAACGTGAAACGAAAACCATTCATT
GATAAAAAAAGTCCATTTATAATCACATATA
Found at i:1087840 original size:20 final size:20
Alignment explanation
Indices: 1087815--1087874 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1087805 TTCTAGACCA
*
1087815 AATGTATGGATACATTTTGG
1 AATGTATCGATACATTTTGG
* *
1087835 AATGTATTGATACA-TTTGAA
1 AATGTATCGATACATTTTG-G
*
1087855 AATGTATCCATACATTTTGG
1 AATGTATCGATACATTTTGG
1087875 GCAGAACCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 4 0.12
20 25 0.76
21 4 0.12
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTTGG
Found at i:1088038 original size:21 final size:21
Alignment explanation
Indices: 1088014--1088063 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1088004 TGCATAGGAG
*
1088014 GTTTAAAA-CTAATTTAAACAA
1 GTTTAAAAGCT-ATTCAAACAA
1088035 GTTTAAAAGCTATTCAAACAA
1 GTTTAAAAGCTATTCAAACAA
*
1088056 GTTCAAAA
1 GTTTAAAA
1088064 ATCGTTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (21 bp):
GTTTAAAAGCTATTCAAACAA
Found at i:1088181 original size:21 final size:21
Alignment explanation
Indices: 1088157--1088223 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1088147 AAAAAAAATT
* *
1088157 AAAACCTATTCAAACAGGTTC
1 AAAAACTATTCAAACAAGTTC
* * *
1088178 AAAAACTCATTCTAACAATTTT
1 AAAAACT-ATTCAAACAAGTTC
*
1088200 AAAAATTATTCAAACAAGTTC
1 AAAAACTATTCAAACAAGTTC
1088221 AAA
1 AAA
1088224 GATCATTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAACTATTCAAACAAGTTC
Found at i:1088364 original size:21 final size:21
Alignment explanation
Indices: 1088309--1088393 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
1088299 TAACATTAAT
1088309 AAACTAAGTTCAAAAA-CATTTTC
1 AAAC-AAGTTCAAAAATCA--TTC
**
1088332 AAACAACATCAAAAATCATTC
1 AAACAAGTTCAAAAATCATTC
** *
1088353 AAACAAGTTCAAGGATCACTC
1 AAACAAGTTCAAAAATCATTC
* *
1088374 AAAGAAGTTCAAAGATCATT
1 AAACAAGTTCAAAAATCATT
1088394 GAAGCAATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 36 0.71
22 9 0.18
23 6 0.12
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (21 bp):
AAACAAGTTCAAAAATCATTC
Found at i:1091892 original size:3 final size:3
Alignment explanation
Indices: 1091884--1091924 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1091874 CTCTAAACCC
* *
1091884 TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1091925 GCTCTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1093013 original size:2 final size:2
Alignment explanation
Indices: 1093006--1093030 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1092996 CAAACACTAT
1093006 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1093031 CGTATCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1094124 original size:166 final size:167
Alignment explanation
Indices: 1093849--1094164 Score: 392
Period size: 166 Copynumber: 1.9 Consensus size: 167
1093839 ACACGTAATG
* * *
1093849 TAAATTTGAAACTTAATTAAAAGTATTGTTATATCATTGAAATATCATCTCATTAGCTTCATAAA
1 TAAATTTAAAACTTAATTAAAAGTATTGTCATATCATTGAAATATCATCTCATTAGCTTCAGAAA
* * *
1093914 TAGTAACTTTTTTCTACCAAAATTTAAAAGCAAATAATAACTTAAAATATC-TTCATACTATTGT
66 TAGTAACTTTTTTCTA-CAAAAATCAAAAGCAAATAACAACTTAAAATATCTTTCATACTATTGT
*
1093978 CAATGATAATAATAATAATAGCTAAAAATAATGCAATT
130 CAATAATAATAATAATAATAGCTAAAAATAATGCAATT
* * *
1094016 TAAATTTAAAACTTAATTAAAAG-A-TGCTCATATTATTGAAATAAT-ATC-CGTTTGGCTTCAG
1 TAAATTTAAAACTTAATTAAAAGTATTG-TCATATCATTGAAAT-ATCATCTC-ATTAGCTTCAG
* ** *
1094077 AAATAGTAACTTTTTTTTCTA-AAAAATCAAAAGCAAATAGCAACTTAAAATATCTTTTTTGTAT
63 AAATAGTAAC--TTTTTTCTACAAAAATCAAAAGCAAATAACAACTTAAAATATC--TTTCATAC
1094141 TATTGTCAATAATAATAATAATAA
124 TATTGTCAATAATAATAATAATAA
1094165 CAATTGTCGA
Statistics
Matches: 127, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
165 3 0.02
166 64 0.50
167 24 0.19
168 9 0.07
169 27 0.21
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (167 bp):
TAAATTTAAAACTTAATTAAAAGTATTGTCATATCATTGAAATATCATCTCATTAGCTTCAGAAA
TAGTAACTTTTTTCTACAAAAATCAAAAGCAAATAACAACTTAAAATATCTTTCATACTATTGTC
AATAATAATAATAATAATAGCTAAAAATAATGCAATT
Found at i:1105323 original size:2 final size:2
Alignment explanation
Indices: 1105316--1105344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1105306 AGGGCAATTC
1105316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1105345 CACACACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1106525 original size:11 final size:11
Alignment explanation
Indices: 1106511--1106543 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1106501 AAAAGACCAA
*
1106511 GTAAAGAGAGG
1 GTAAAGAGAAG
1106522 GTAAAGAGAAG
1 GTAAAGAGAAG
1106533 GTAAAGAGAAG
1 GTAAAGAGAAG
1106544 TGGACAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.09
Consensus pattern (11 bp):
GTAAAGAGAAG
Found at i:1107928 original size:29 final size:29
Alignment explanation
Indices: 1107886--1107946 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1107876 ATAAAATATT
1107886 TATAATATCCATAGTAGCTAACCAAGATA
1 TATAATATCCATAGTAGCTAACCAAGATA
* *
1107915 TATAATATCTATAGTAGCTAAGCAAGATA
1 TATAATATCCATAGTAGCTAACCAAGATA
1107944 TAT
1 TAT
1107947 TGAATATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (29 bp):
TATAATATCCATAGTAGCTAACCAAGATA
Found at i:1108630 original size:19 final size:19
Alignment explanation
Indices: 1108591--1108632 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1108581 AATAAGTGAC
*
1108591 AATTTTAAAGCTTAATGCT
1 AATTTTAAAGCTTAATACT
1108610 AATTTTAAAGC-TAGATACT
1 AATTTTAAAGCTTA-ATACT
1108629 AATT
1 AATT
1108633 AAGAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (19 bp):
AATTTTAAAGCTTAATACT
Found at i:1116848 original size:82 final size:82
Alignment explanation
Indices: 1116711--1116869 Score: 291
Period size: 82 Copynumber: 1.9 Consensus size: 82
1116701 ACAAAGGAGG
1116711 GAGTTTTTAACTATACTTTGAGCGAGCAAAGAGGGCAACAATTGACTTTTTCTTCTTTCTCACAA
1 GAGTTTTTAACTATACTTTGAGCGAGCAAAGAGGGCAACAATTGACTTTTTCTTCTTTCTCACAA
1116776 GCTTAACTGAAAAAGGA
66 GCTTAACTGAAAAAGGA
* * *
1116793 GAGTTTTTAACTATACTTTGTGCGAGCAAAGAGGGCAACAGTTGCCTTTTTCTTCTTTCTCACAA
1 GAGTTTTTAACTATACTTTGAGCGAGCAAAGAGGGCAACAATTGACTTTTTCTTCTTTCTCACAA
1116858 GCTTAACTGAAA
66 GCTTAACTGAAA
1116870 CTTTTTTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (82 bp):
GAGTTTTTAACTATACTTTGAGCGAGCAAAGAGGGCAACAATTGACTTTTTCTTCTTTCTCACAA
GCTTAACTGAAAAAGGA
Found at i:1119356 original size:18 final size:19
Alignment explanation
Indices: 1119333--1119372 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1119323 CAAGTAGAAA
1119333 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
* *
1119351 ATTTTATTAATAAAATATT
1 ATTTTATGAATAAAATAAT
1119370 ATT
1 ATT
1119373 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1119369 original size:11 final size:11
Alignment explanation
Indices: 1119355--1119384 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1119345 AATAATATTT
1119355 TATTAATAAAA
1 TATTAATAAAA
*
1119366 TATTATTAAAA
1 TATTAATAAAA
1119377 TATTAATA
1 TATTAATA
1119385 TTTTTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:1130784 original size:12 final size:12
Alignment explanation
Indices: 1130769--1130815 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
1130759 GAGATTTTTT
1130769 GAGGCAGCAAGA
1 GAGGCAGCAAGA
1130781 GAGGCAGC-AGA
1 GAGGCAGCAAGA
1130792 GAGGCAGCAA-A
1 GAGGCAGCAAGA
1130803 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
1130816 AACTATTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.38
12 19 0.59
13 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:1130796 original size:23 final size:23
Alignment explanation
Indices: 1130769--1130812 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1130759 GAGATTTTTT
1130769 GAGGCAGC-AAGAGAGGCAGCAGA
1 GAGGCAGCAAAG-GAGGCAGCAGA
1130792 GAGGCAGCAAAGGAGGCAGCA
1 GAGGCAGCAAAGGAGGCAGCA
1130813 AGAAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (23 bp):
GAGGCAGCAAAGGAGGCAGCAGA
Found at i:1145285 original size:277 final size:274
Alignment explanation
Indices: 1144816--1145315 Score: 729
Period size: 277 Copynumber: 1.8 Consensus size: 274
1144806 AAAGAGGGTG
*
1144816 GAAATACCACCAACCTTTAGGTGATCACACCCTTGATTTATGTTTGTAGTAACAACTCCATACGT
1 GAAATACCACCAACC-TTAGGTGATCACACCCTTAATTTATGTTTGTAGTAACAACTCCATACGT
* * * *
1144881 GTTGAAACACAATTATATATGGAAAATTAGAGGTTGATGCGAATGATTTCTATAATTATGTTCAT
65 GTTGAAACACAATTAGATATGGAAAATTAGAGATTGATGCAAATGAGTTCTATAATTATGTTCAT
* *
1144946 GATTTACAAATTCATTATTGTTAAGAATTGTTTACGTAAGTAGTGCTTTATATGAGTATAGTAAC
130 GATCTACAAATTCATTATTGTTAAGAATTGTTTACATAAGTAGTGCTTTATATGAGTATAGTAAC
*
1145011 TTAAGTTATATGTGGATGATGTTGAATTAAACATAGTAGAGTGGAGATATAACTCATTAATATTT
195 TCAAGTTATATGTGGATGATGTTGAATTAAACATAGTAGAGTGGAGATATAACTCATTAATATTT
1145076 CCTGAAAGTGGGATA
260 CCTGAAAGTGGGATA
* * ** *
1145091 GAAATACCACCAGCACC-TAGGTTATCACACCTTTAATGTT-TGTTTGTAGTAATGACTCCATAT
1 GAAATACCACCA--ACCTTAGGTGATCACACCCTTAAT-TTATGTTTGTAGTAACAACTCCATAC
* *
1145154 GTGTTGAAACACATAATTAGATTATAGG-AAATTAGAGATTTATGCAAATG-GTTGTATAATTAT
63 GTGTTGAAACAC--AATTAGA-TAT-GGAAAATTAGAGATTGATGCAAATGAGTTCTATAATTAT
* * *
1145217 GTTCATGATCTACAAATTCATTCTTGTTGAGAATTGTTTACATAAGTAGTGTTTTATATGAGTAT
124 GTTCATGATCTACAAATTCATTATTGTTAAGAATTGTTTACATAAGTAGTGCTTTATATGAGTAT
*
1145282 AGTAACTCAAGTTATATGTGGATTATGTTGAATT
189 AGTAACTCAAGTTATATGTGGATGATGTTGAATT
1145316 GAGCCTATAA
Statistics
Matches: 199, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
275 61 0.31
276 2 0.01
277 112 0.56
278 22 0.11
279 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (274 bp):
GAAATACCACCAACCTTAGGTGATCACACCCTTAATTTATGTTTGTAGTAACAACTCCATACGTG
TTGAAACACAATTAGATATGGAAAATTAGAGATTGATGCAAATGAGTTCTATAATTATGTTCATG
ATCTACAAATTCATTATTGTTAAGAATTGTTTACATAAGTAGTGCTTTATATGAGTATAGTAACT
CAAGTTATATGTGGATGATGTTGAATTAAACATAGTAGAGTGGAGATATAACTCATTAATATTTC
CTGAAAGTGGGATA
Found at i:1157868 original size:15 final size:16
Alignment explanation
Indices: 1157848--1157877 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1157838 TAATTTAAGT
1157848 TTCAAGA-GAAATGTA
1 TTCAAGATGAAATGTA
1157863 TTCAAGATGAAATGT
1 TTCAAGATGAAATGT
1157878 TGAATGAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (16 bp):
TTCAAGATGAAATGTA
Found at i:1166726 original size:13 final size:13
Alignment explanation
Indices: 1166708--1166732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1166698 ATCAACAACA
1166708 TGGACTTTTAGCT
1 TGGACTTTTAGCT
1166721 TGGACTTTTAGC
1 TGGACTTTTAGC
1166733 ATAACTAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
TGGACTTTTAGCT
Found at i:1179362 original size:2 final size:2
Alignment explanation
Indices: 1179355--1179390 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1179345 GTTAAATCTC
1179355 TG TG TG TG T- 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 TG TG TG TG TG T
1179391 AAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:1182935 original size:28 final size:28
Alignment explanation
Indices: 1182903--1182961 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1182893 AATCAAGGAA
1182903 CCCTAGATGTGAAGCTTAGGATCTTTCT
1 CCCTAGATGTGAAGCTTAGGATCTTTCT
1182931 CCCTAGATGTGAAGCTTAGGATCTTTCT
1 CCCTAGATGTGAAGCTTAGGATCTTTCT
1182959 CCC
1 CCC
1182962 CTTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (28 bp):
CCCTAGATGTGAAGCTTAGGATCTTTCT
Found at i:1185364 original size:1 final size:1
Alignment explanation
Indices: 1185320--1185348 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1185310 TTTCAAGTTC
1185320 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1185349 AGCCTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1191886 original size:14 final size:14
Alignment explanation
Indices: 1191860--1191895 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1191850 GAGAAAAGCC
1191860 AATAATAATAATAAA
1 AATAAT-ATAATAAA
*
1191875 TATAATATAATAAA
1 AATAATATAATAAA
1191889 AATAATA
1 AATAATA
1191896 ATAGAGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAATATAATAAA
Found at i:1191886 original size:17 final size:17
Alignment explanation
Indices: 1191864--1191898 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1191854 AAAGCCAATA
1191864 ATAATAATAAAT-ATAAT
1 ATAATAA-AAATAATAAT
1191881 ATAATAAAAATAATAAT
1 ATAATAAAAATAATAAT
1191898 A
1 A
1191899 GAGGTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAATAAAAATAATAAT
Found at i:1198818 original size:21 final size:21
Alignment explanation
Indices: 1198790--1198850 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1198780 TGCATTCTAT
1198790 TTCA-AATGTATCGATACATA
1 TTCATAATGTATCGATACATA
* *
1198810 TTTATAATGTA-CTGATATATA
1 TTCATAATGTATC-GATACATA
*
1198831 TTCATAATGTATTGATACAT
1 TTCATAATGTATCGATACAT
1198851 TTAGCCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (21 bp):
TTCATAATGTATCGATACATA
Found at i:1200442 original size:29 final size:30
Alignment explanation
Indices: 1200403--1200586 Score: 161
Period size: 29 Copynumber: 6.4 Consensus size: 30
1200393 CATTGGTTGA
* *
1200403 GTTTTAGGGATTGAAT-AATGATTACTTGA
1 GTTTTATGGATTGAATAAATGATTACTTGG
*
1200432 GTTATATGGATTG-ATAAATGATTACTTGG
1 GTTTTATGGATTGAATAAATGATTACTTGG
* * * * *
1200461 GTTTTATGGATTGGA-CATTGATCAC-TGC
1 GTTTTATGGATTGAATAAATGATTACTTGG
*
1200489 GTTTTATGGACT-AATAAATGATTACTTGG
1 GTTTTATGGATTGAATAAATGATTACTTGG
* * * *
1200518 GTTTTATGGA-T-AAGACATTGATCA-TTGT
1 GTTTTATGGATTGAATA-AATGATTACTTGG
*
1200546 GTTATATGGATTG-ATAAATGATTACTTGG
1 GTTTTATGGATTGAATAAATGATTACTTGG
*
1200575 GTTATATGGATT
1 GTTTTATGGATT
1200587 AGGTGTTGAT
Statistics
Matches: 124, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.01
28 44 0.35
29 78 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (30 bp):
GTTTTATGGATTGAATAAATGATTACTTGG
Found at i:1200507 original size:57 final size:57
Alignment explanation
Indices: 1200432--1200588 Score: 242
Period size: 57 Copynumber: 2.8 Consensus size: 57
1200422 GATTACTTGA
*
1200432 GTTATATGGATTGATAAATGATTACTTGGGTTTTATGGATTGGACATTGATCACTGC
1 GTTATATGGATTGATAAATGATTACTTGGGTTTTATGGATTAGACATTGATCACTGC
* * * * * *
1200489 GTTTTATGGACTAATAAATGATTACTTGGGTTTTATGGATAAGACATTGATCATTGT
1 GTTATATGGATTGATAAATGATTACTTGGGTTTTATGGATTAGACATTGATCACTGC
*
1200546 GTTATATGGATTGATAAATGATTACTTGGGTTATATGGATTAG
1 GTTATATGGATTGATAAATGATTACTTGGGTTTTATGGATTAG
1200589 GTGTTGATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 88 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (57 bp):
GTTATATGGATTGATAAATGATTACTTGGGTTTTATGGATTAGACATTGATCACTGC
Found at i:1201447 original size:21 final size:20
Alignment explanation
Indices: 1201417--1201458 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1201407 AAGTGATTAA
1201417 TTTAGTTATTTTAGTTAAAT
1 TTTAGTTATTTTAGTTAAAT
*
1201437 TTTAGGTTATTTTATTTAAAT
1 TTTA-GTTATTTTAGTTAAAT
1201458 T
1 T
1201459 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTAGTTATTTTAGTTAAAT
Found at i:1202124 original size:12 final size:12
Alignment explanation
Indices: 1202107--1202154 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
1202097 AGAGATTTTT
1202107 GAGGCAGCAAGA
1 GAGGCAGCAAGA
*
1202119 GTGGCAGCAAGA
1 GAGGCAGCAAGA
1202131 GAGGCAGCAA-A
1 GAGGCAGCAAGA
*
1202142 GGAGGTAGCAAGA
1 -GAGGCAGCAAGA
1202155 AACTATTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.42, T:0.04
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:1205308 original size:27 final size:27
Alignment explanation
Indices: 1205270--1205326 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1205260 AACCAAATCT
1205270 CATAGTTTTTATCACATTACTCACAAA
1 CATAGTTTTTATCACATTACTCACAAA
1205297 CATAGTTTTTATCACATTACTCACAAA
1 CATAGTTTTTATCACATTACTCACAAA
1205324 CAT
1 CAT
1205327 TTATCACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (27 bp):
CATAGTTTTTATCACATTACTCACAAA
Found at i:1206168 original size:17 final size:17
Alignment explanation
Indices: 1206148--1206180 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1206138 TTTCTTGATT
1206148 TCCTTATTCAT-TCTTTC
1 TCCTT-TTCATCTCTTTC
1206165 TCCTTTTCATCTCTTT
1 TCCTTTTCATCTCTTT
1206181 ATTTGCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (17 bp):
TCCTTTTCATCTCTTTC
Found at i:1207630 original size:12 final size:12
Alignment explanation
Indices: 1207615--1207639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1207605 AATAATTTGC
1207615 ATACATACATAT
1 ATACATACATAT
1207627 ATACATACATAT
1 ATACATACATAT
1207639 A
1 A
1207640 GGCATATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATACATACATAT
Found at i:1227314 original size:27 final size:27
Alignment explanation
Indices: 1227272--1227583 Score: 231
Period size: 27 Copynumber: 11.6 Consensus size: 27
1227262 TGGAAAAAAT
*
1227272 GTTGTTA-TTGCCATGTTGAAAAATGTA
1 GTTGTTACATGCCATGTTG-AAAATGTA
* *
1227299 G-TATTACATGCCATGTTTG-AAATTTA
1 GTTGTTACATGCCATG-TTGAAAATGTA
** *
1227325 GTTGTTACACACAATGTT-AGAAA--TA
1 GTTGTTACATGCCATGTTGA-AAATGTA
* **
1227350 ATTGTTACACACCATGTTGAAAATGTA
1 GTTGTTACATGCCATGTTGAAAATGTA
*
1227377 GTTGTTACATGTCATGTTGAAAAATGTA
1 GTTGTTACATGCCATGTTG-AAAATGTA
* * * * *
1227405 GTTATTATACGTCATGTTGAAAATTTA
1 GTTGTTACATGCCATGTTGAAAATGTA
* * *
1227432 GTTGTTACATGTCTTGTTGAAAAATATA
1 GTTGTTACATGCCATGTTG-AAAATGTA
* **** * * *
1227460 GTTATTACACATTATGTTTAAGATTTA
1 GTTGTTACATGCCATGTTGAAAATGTA
* ** *
1227487 GTTGTTACATGCCATGGTGAGGATTTA
1 GTTGTTACATGCCATGTTGAAAATGTA
1227514 GTTGTTACATGCCATGTTGAAAATGTA
1 GTTGTTACATGCCATGTTGAAAATGTA
* * *
1227541 GTTGTTACATGCCATGTTGAAGATTTT
1 GTTGTTACATGCCATGTTGAAAATGTA
*
1227568 GTTGTTACACGCCATG
1 GTTGTTACATGCCATG
1227584 ATGATGAAGT
Statistics
Matches: 229, Mismatches: 46, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
25 21 0.09
26 14 0.06
27 147 0.64
28 47 0.21
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (27 bp):
GTTGTTACATGCCATGTTGAAAATGTA
Found at i:1227434 original size:55 final size:55
Alignment explanation
Indices: 1227272--1227583 Score: 271
Period size: 55 Copynumber: 5.8 Consensus size: 55
1227262 TGGAAAAAAT
* *
1227272 GTTGTTA-TTGCCATGTTGAAAAATGTAG-TATTACATGCCATGTTTG-AAATTTA
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATG-TTGAAAATTTA
** * * * * * *
1227325 GTTGTTACACACAATGTT-AGAAA--TAATTGTTACACACCATGTTGAAAATGTA
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATGTTGAAAATTTA
* * *
1227377 GTTGTTACATGTCATGTTGAAAAATGTAGTTATTATACGTCATGTTGAAAATTTA
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATGTTGAAAATTTA
* * * *** * *
1227432 GTTGTTACATGTCTTGTTGAAAAATATAGTTATTACACATTATGTTTAAGATTTA
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATGTTGAAAATTTA
* ** * * * *
1227487 GTTGTTACATGCCATGGTG-AGGATTTAGTTGTTACATGCCATGTTGAAAATGTA
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATGTTGAAAATTTA
* * * *
1227541 GTTGTTACATGCCATGTTG-AAGATTTTGTTGTTACACGCCATG
1 GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATG
1227584 ATGATGAAGT
Statistics
Matches: 207, Mismatches: 46, Indels: 11
0.78 0.17 0.04
Matches are distributed among these distances:
51 5 0.02
52 31 0.15
53 15 0.07
54 69 0.33
55 87 0.42
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (55 bp):
GTTGTTACATGCCATGTTGAAAAATGTAGTTATTACACGCCATGTTGAAAATTTA
Found at i:1227453 original size:82 final size:82
Alignment explanation
Indices: 1227272--1227583 Score: 228
Period size: 82 Copynumber: 3.9 Consensus size: 82
1227262 TGGAAAAAAT
* * * * *
1227272 GTTGTTA-TTGCCATGTTGAAAAATGTAG-TATTACATGCCATGTTTG--AAATTTAGTTGTTAC
1 GTTGTTACATGCCATGTTG-AAAATGTAGTTGTTACATGTCATG-TTGAAAAATGTAGTTATTAC
* * *
1227333 ACACAAT-GTTAGAAA--TA
64 ACGCCATGGTGA-AAATTTA
* ** *
1227350 ATTGTTACACACCATGTTGAAAATGTAGTTGTTACATGTCATGTTGAAAAATGTAGTTATTATAC
1 GTTGTTACATGCCATGTTGAAAATGTAGTTGTTACATGTCATGTTGAAAAATGTAGTTATTACAC
* *
1227415 GTCATGTTGAAAATTTA
66 GCCATGGTGAAAATTTA
* * * * ** * * * * *
1227432 GTTGTTACATGTCTTGTTGAAAAATATAGTTATTACACATTATGTT-TAAGATTTAGTTGTTACA
1 GTTGTTACATGCCATGTTG-AAAATGTAGTTGTTACATGTCATGTTGAAAAATGTAGTTATTACA
* **
1227496 TGCCATGGTGAGGATTTA
65 CGCCATGGTGAAAATTTA
* * * * *
1227514 GTTGTTACATGCCATGTTGAAAATGTAGTTGTTACATGCCATGTTG-AAGATTTTGTTGTTACAC
1 GTTGTTACATGCCATGTTGAAAATGTAGTTGTTACATGTCATGTTGAAAAATGTAGTTATTACAC
1227578 GCCATG
66 GCCATG
1227584 ATGATGAAGT
Statistics
Matches: 181, Mismatches: 44, Indels: 15
0.75 0.18 0.06
Matches are distributed among these distances:
78 18 0.10
79 20 0.11
80 19 0.10
81 44 0.24
82 59 0.33
83 21 0.12
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (82 bp):
GTTGTTACATGCCATGTTGAAAATGTAGTTGTTACATGTCATGTTGAAAAATGTAGTTATTACAC
GCCATGGTGAAAATTTA
Found at i:1227596 original size:27 final size:26
Alignment explanation
Indices: 1227487--1227597 Score: 105
Period size: 27 Copynumber: 4.1 Consensus size: 26
1227477 TTAAGATTTA
* * *
1227487 GTTGTTACATGCCATGGTGAGGATTT
1 GTTGTTACATGCCATGTTGAGAAGTT
* *
1227513 AGTTGTTACATGCCATGTTGAAAATGTA
1 -GTTGTTACATGCCATGTTGAGAA-GTT
**
1227541 GTTGTTACATGCCATGTTGAAGATTTT
1 GTTGTTACATGCCATGTTG-AGAAGTT
* *
1227568 GTTGTTACACGCCATGATGATGAAGTT
1 GTTGTTACATGCCATGTTGA-GAAGTT
1227595 GTT
1 GTT
1227598 ACACAACACG
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
26 1 0.01
27 64 0.94
28 3 0.04
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (26 bp):
GTTGTTACATGCCATGTTGAGAAGTT
Found at i:1227600 original size:51 final size:52
Alignment explanation
Indices: 1227486--1227600 Score: 151
Period size: 54 Copynumber: 2.2 Consensus size: 52
1227476 TTTAAGATTT
* * * *
1227486 AGTTGTTACATGCCATGGTGAGGATTTAGTTGTTACATGCCATGTTGAAAATGT
1 AGTTGTTACATGCCATGGTGAAGATTTAGTTGTTACACGCCATGATG--AATGA
* *
1227540 AGTTGTTACATGCCATGTTGAAGATTTTGTTGTTACACGCCATGATG-ATGA
1 AGTTGTTACATGCCATGGTGAAGATTTAGTTGTTACACGCCATGATGAATGA
1227591 AGTTGTTACA
1 AGTTGTTACA
1227601 CAACACGCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 13 0.24
54 42 0.76
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (52 bp):
AGTTGTTACATGCCATGGTGAAGATTTAGTTGTTACACGCCATGATGAATGA
Found at i:1228388 original size:35 final size:35
Alignment explanation
Indices: 1228347--1228418 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1228337 TTAATGTAAA
1228347 ATGCCCAACATTGGCAACATTAACATAACATGTTC
1 ATGCCCAACATTGGCAACATTAACATAACATGTTC
1228382 ATGCCCAACATTGGCAACATTAACATAACATGTTC
1 ATGCCCAACATTGGCAACATTAACATAACATGTTC
1228417 AT
1 AT
1228419 AATCTGTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (35 bp):
ATGCCCAACATTGGCAACATTAACATAACATGTTC
Found at i:1231999 original size:20 final size:20
Alignment explanation
Indices: 1231961--1232001 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1231951 TAACAGCTAG
*
1231961 TAACGACTAGAAACTATCTC
1 TAACGACTAGAAACAATCTC
* *
1231981 TAACGGCTAGAATCAATCTC
1 TAACGACTAGAAACAATCTC
1232001 T
1 T
1232002 CAAGTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
TAACGACTAGAAACAATCTC
Found at i:1235149 original size:20 final size:20
Alignment explanation
Indices: 1235124--1235195 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 20
1235114 AACTTTCGCA
*
1235124 CTTTAATTGGTTAATGCAAG
1 CTTTAATCGGTTAATGCAAG
**
1235144 CTTTAATCAATTAAAGTGCTAAAG
1 CTTTAATCGGTT-AA-TGC--AAG
1235168 CTTTAATCGGTTAATGCAAG
1 CTTTAATCGGTTAATGCAAG
1235188 CTTTAATC
1 CTTTAATC
1235196 AATTAAAGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 20 0.47
21 2 0.05
22 6 0.14
23 2 0.05
24 13 0.30
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (20 bp):
CTTTAATCGGTTAATGCAAG
Found at i:1235201 original size:20 final size:20
Alignment explanation
Indices: 1235134--1235201 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
1235124 CTTTAATTGG
1235134 TTAATGCAAGCTTTAATCAA
1 TTAATGCAAGCTTTAATCAA
**
1235154 TTAAAGTGCTAAAGCTTTAATCGG
1 TT-AA-TGC--AAGCTTTAATCAA
1235178 TTAATGCAAGCTTTAATCAA
1 TTAATGCAAGCTTTAATCAA
1235198 TTAA
1 TTAA
1235202 AGTGCTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 17 0.43
21 2 0.05
22 6 0.15
23 2 0.05
24 13 0.32
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
TTAATGCAAGCTTTAATCAA
Found at i:1235218 original size:44 final size:44
Alignment explanation
Indices: 1235124--1235209 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
1235114 AACTTTCGCA
*
1235124 CTTTAATTGGTTAATGCAAGCTTTAATCAATTAAAGTGCTAAAG
1 CTTTAATCGGTTAATGCAAGCTTTAATCAATTAAAGTGCTAAAG
1235168 CTTTAATCGGTTAATGCAAGCTTTAATCAATTAAAGTGCTAA
1 CTTTAATCGGTTAATGCAAGCTTTAATCAATTAAAGTGCTAA
1235210 TGACTTAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (44 bp):
CTTTAATCGGTTAATGCAAGCTTTAATCAATTAAAGTGCTAAAG
Found at i:1238560 original size:18 final size:18
Alignment explanation
Indices: 1238534--1238569 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1238524 ATTTTGAAAT
*
1238534 TCATTATATGAAATATCA
1 TCATCATATGAAATATCA
1238552 TCATCATATGAAATATCA
1 TCATCATATGAAATATCA
1238570 CATAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (18 bp):
TCATCATATGAAATATCA
Found at i:1240544 original size:35 final size:35
Alignment explanation
Indices: 1240502--1240757 Score: 248
Period size: 35 Copynumber: 7.3 Consensus size: 35
1240492 TTCATTGTTT
1240502 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
1240537 AACTTAATTAATTAAGCCCAATAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
1240572 AATTTTAATCAATTAGGCCCACTGACGTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ***
1240608 AAATTTAATCAATTAAGCCCAATAACTTAATTATTT
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * ** *
1240644 AATTTAATTAATTAGACTGAATAACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ** * * *
1240679 AATTTAATTAATTAGGCTTAATGATTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
1240714 AATTTATTTAATTAGG--C-ATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1240746 AATTTTAATCAA
1 AA-TTTAATCAA
1240758 GTGCTTAGCT
Statistics
Matches: 182, Mismatches: 36, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
32 14 0.08
33 7 0.04
35 107 0.59
36 52 0.29
37 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.38
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:1240628 original size:107 final size:106
Alignment explanation
Indices: 1240502--1240695 Score: 273
Period size: 107 Copynumber: 1.8 Consensus size: 106
1240492 TTCATTGTTT
* *
1240502 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAACTTAATTAATTA-AGCCCAATAATTTAA
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAACAACTTAATTAATTAGA-CCCAATAACTTAA
1240566 TTAAACAATTTTAATCAATTAGGCCCACTGACGTAATTAAACA
65 TTAAACAA-TTTAATCAATTAGGCCCACTGACGTAATTAAACA
*** * **
1240609 AATTTAATCAATTAAGCCCAATAACTTAATTATTTAATTTAATTAATTAGACTGAATAACTTAAT
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAACAACTTAATTAATTAGACCCAATAACTTAAT
* *
1240674 TAAATAATTTAATTAATTAGGC
66 TAAACAATTTAATCAATTAGGC
1240696 TTAATGATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
106 14 0.18
107 61 0.80
108 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (106 bp):
AATTTAATCAATTAAGCCCAATAACTTAATTAAACAACTTAATTAATTAGACCCAATAACTTAAT
TAAACAATTTAATCAATTAGGCCCACTGACGTAATTAAACA
Found at i:1240781 original size:142 final size:141
Alignment explanation
Indices: 1240479--1240757 Score: 348
Period size: 142 Copynumber: 2.0 Consensus size: 141
1240469 AGTCCTTAAG
* * * *
1240479 AAGCCCAGTTAACTTCATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAACTTAA
1 AAGCCCA-ATAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAACAACTTAA
*
1240544 TTAATTAAGCCCAATAATTTAATTAAACAATTTTAATCAATTAGGCCCACTGACGTAATTAAACA
65 TTAATTAAGCCCAATAATTTAATTAAACAATTTTAATCAATTAGG-CCACTAACGTAATTAAACA
1240609 AATTTAATCAATT
129 AATTTAATCAATT
* ** * *
1240622 AAGCCCAATAACTTAATTATTTAATTTAATTAATTAGACTGAATAACTTAATTAAATAATTTAAT
1 AAGCCCAATAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAACAACTTAAT
* ** * * * * * *
1240687 TAATTAGGCTTAATGATTTAATTAAATAA-TTTATTTAATTAGG-CA-TAACTTAATTAAACAAT
66 TAATTAAGCCCAATAATTTAATTAAACAATTTTAATCAATTAGGCCACTAACGTAATTAAACAAA
1240749 TTTAATCAA
131 TTTAATCAA
1240758 GTGCTTAGCT
Statistics
Matches: 117, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
138 23 0.20
139 2 0.02
141 12 0.10
142 73 0.62
143 7 0.06
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (141 bp):
AAGCCCAATAACTTAATTATTTAATTTAATCAATTAGACCCAATAACTTAATTAAACAACTTAAT
TAATTAAGCCCAATAATTTAATTAAACAATTTTAATCAATTAGGCCACTAACGTAATTAAACAAA
TTTAATCAATT
Found at i:1245657 original size:2 final size:2
Alignment explanation
Indices: 1245650--1245694 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1245640 AATAAGTGTT
* * * *
1245650 TA TA TA TA AA TA TA TA TA TA TA TA CA TA TA CA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1245692 TA T
1 TA T
1245695 TCTATATCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1246137 original size:14 final size:14
Alignment explanation
Indices: 1246118--1246144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1246108 ATTTATATTG
1246118 GATGTTTACATTTA
1 GATGTTTACATTTA
1246132 GATGTTTACATTT
1 GATGTTTACATTT
1246145 GTATTACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
GATGTTTACATTTA
Found at i:1249132 original size:28 final size:28
Alignment explanation
Indices: 1249084--1249168 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 28
1249074 TTAAAACAAT
* *
1249084 ACATATGT-TCTTGTCGAAATTGAGACA
1 ACATATGTATCTTGTCTAAATTAAGACA
*
1249111 ACATATGTATCTTGTCTTAATTAAGACA
1 ACATATGTATCTTGTCTAAATTAAGACA
* *
1249139 ACTTATGTACCTTGTCTAAATTAAGACA
1 ACATATGTATCTTGTCTAAATTAAGACA
1249167 AC
1 AC
1249169 TTTTATCTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 8 0.16
28 43 0.84
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (28 bp):
ACATATGTATCTTGTCTAAATTAAGACA
Found at i:1255821 original size:20 final size:22
Alignment explanation
Indices: 1255796--1255844 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
1255786 TTTTATTTTT
*
1255796 ATATAAACTTAAAATA-AT-AA
1 ATATAAAATTAAAATACATAAA
*
1255816 ATATAAAATTATAATACATAAA
1 ATATAAAATTAAAATACATAAA
1255838 ATATAAA
1 ATATAAA
1255845 TAATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.56
21 2 0.08
22 9 0.36
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
ATATAAAATTAAAATACATAAA
Found at i:1255822 original size:14 final size:13
Alignment explanation
Indices: 1255796--1255846 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
1255786 TTTTATTTTT
1255796 ATATAAACT-TAAA
1 ATATAAA-TATAAA
1255809 ATAATAAATATAAA
1 AT-ATAAATATAAA
*
1255823 ATTATAATACATAAA
1 A-TATAA-ATATAAA
1255838 ATATAAATA
1 ATATAAATA
1255847 ATTAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.16
14 19 0.59
15 8 0.25
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAATATAAA
Found at i:1255846 original size:15 final size:14
Alignment explanation
Indices: 1255805--1255855 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1255795 TATATAAACT
1255805 TAAAATAATAAAT-A
1 TAAAAT-ATAAATAA
1255819 TAAAAT-TATAATACA
1 TAAAATATA-AATA-A
1255834 TAAAATATAAATAA
1 TAAAATATAAATAA
*
1255848 TTAAATAT
1 TAAAATAT
1255856 GATATACAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 2 0.06
13 3 0.09
14 14 0.44
15 11 0.34
16 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATATAAATAA
Found at i:1257546 original size:15 final size:16
Alignment explanation
Indices: 1257512--1257543 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1257502 ACATTTGAAA
1257512 CAAAACACATGTACCC
1 CAAAACACATGTACCC
*
1257528 CAAAACATATGTACCC
1 CAAAACACATGTACCC
1257544 AAAGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.34, G:0.06, T:0.16
Consensus pattern (16 bp):
CAAAACACATGTACCC
Found at i:1257774 original size:33 final size:33
Alignment explanation
Indices: 1257732--1257797 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1257722 TTGCGAGGCA
1257732 TGTGGTTAATATTATACAGGGAAGGAAACCGGT
1 TGTGGTTAATATTATACAGGGAAGGAAACCGGT
1257765 TGTGGTTAATATTATACAGGGAAGGAAACCGGT
1 TGTGGTTAATATTATACAGGGAAGGAAACCGGT
1257798 GGCAGACGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (33 bp):
TGTGGTTAATATTATACAGGGAAGGAAACCGGT
Found at i:1266752 original size:42 final size:42
Alignment explanation
Indices: 1266693--1266787 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
1266683 TTTAAACAAA
* *
1266693 TTAAATTTAAATGTAATGGATTATCACATAGATAATCTTTAT
1 TTAAATTTAAATGTAATGGATTATCACATAAATAACCTTTAT
1266735 TTAAATTTAAATGTAATGGATTATCACATAAATAACCTTTAT
1 TTAAATTTAAATGTAATGGATTATCACATAAATAACCTTTAT
*
1266777 TTAAATATAAA
1 TTAAATTTAAA
1266788 CAAATTAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (42 bp):
TTAAATTTAAATGTAATGGATTATCACATAAATAACCTTTAT
Found at i:1271114 original size:29 final size:27
Alignment explanation
Indices: 1271038--1271115 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
1271028 TAAAAAGGCT
* *
1271038 GAGGTTTTGTCTAATCCTTGAAAACGTT
1 GAGGTTATGTCTAATCCTTG-AAACGTA
* * * *
1271066 GAGGTTATGTTTGATGCTTGAAAGGTA
1 GAGGTTATGTCTAATCCTTGAAACGTA
1271093 GAGAAGTTATGTCTAATCCTTGA
1 GAG--GTTATGTCTAATCCTTGA
1271116 TTTGTGCTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 8 0.21
28 16 0.41
29 15 0.38
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (27 bp):
GAGGTTATGTCTAATCCTTGAAACGTA
Found at i:1271169 original size:36 final size:37
Alignment explanation
Indices: 1271120--1271214 Score: 117
Period size: 36 Copynumber: 2.7 Consensus size: 37
1271110 CCTTGATTTG
* *
1271120 TGCTTGATATTCTTGAAAAGGCAATGTATG-AGGTTA
1 TGCTTGATCTTCTTGAAAAGGCAATGTATGAAAGTTA
* *
1271156 TGCTTAATCTTCTTG-AAAGGCAATGTGTGAAAGTTA
1 TGCTTGATCTTCTTGAAAAGGCAATGTATGAAAGTTA
*
1271192 TGCTTGATC--CTTTAAAAGGCAAT
1 TGCTTGATCTTCTTGAAAAGGCAAT
1271215 TTTTTAATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 3 0.06
35 22 0.43
36 26 0.51
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (37 bp):
TGCTTGATCTTCTTGAAAAGGCAATGTATGAAAGTTA
Found at i:1271210 original size:35 final size:35
Alignment explanation
Indices: 1271130--1271214 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
1271120 TGCTTGATAT
* *
1271130 TCTTGAAAAGGCAATGTATGAGGTTATGCTTAATCT
1 TCTT-AAAAGGCAATGTATGAAGTTATGCTTAATCC
* * *
1271166 TCTTGAAAGGCAATGTGTGAAAGTTATGCTTGATCC
1 TCTTAAAAGGCAATGTATG-AAGTTATGCTTAATCC
1271202 T-TTAAAAGGCAAT
1 TCTTAAAAGGCAAT
1271215 TTTTTAATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.57
36 18 0.43
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (35 bp):
TCTTAAAAGGCAATGTATGAAGTTATGCTTAATCC
Found at i:1275906 original size:4 final size:4
Alignment explanation
Indices: 1275897--1275923 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1275887 TAAAGACCCA
1275897 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1275924 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1287975 original size:22 final size:22
Alignment explanation
Indices: 1287945--1288013 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
1287935 ATGTTGAGAC
* *
1287945 ATTGTGTGACTGGTTTTTATGT
1 ATTGAGTGACTAGTTTTTATGT
1287967 ATTGAGTGACTAGTTTTTATGT
1 ATTGAGTGACTAGTTTTTATGT
* * * *
1287989 ATTGCGTGACTTGTTGTTAAGT
1 ATTGAGTGACTAGTTTTTATGT
1288011 ATT
1 ATT
1288014 ACGTGACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.51
Consensus pattern (22 bp):
ATTGAGTGACTAGTTTTTATGT
Found at i:1293035 original size:29 final size:29
Alignment explanation
Indices: 1292986--1293046 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1292976 ATCCACATTA
* *
1292986 TAGGGAAAGATCAATCGTTTAAGATATGT
1 TAGGGAAAGATCAATCATTTAAGACATGT
* *
1293015 TAGGGAAAGATTAGTCATTTAAGACATGT
1 TAGGGAAAGATCAATCATTTAAGACATGT
1293044 TAG
1 TAG
1293047 CGCTAAGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (29 bp):
TAGGGAAAGATCAATCATTTAAGACATGT
Found at i:1294400 original size:23 final size:23
Alignment explanation
Indices: 1294374--1294612 Score: 118
Period size: 23 Copynumber: 10.4 Consensus size: 23
1294364 TCAAAAAGTT
*
1294374 ACGCGATTCCATATTTACTACTC
1 ACGCGATTCCATATTAACTACTC
* * * * *
1294397 ACGCGATTCCTTGTCAAATACTT
1 ACGCGATTCCATATTAACTACTC
** * * * *
1294420 GTGCGATTCTATAATAACTAGTA
1 ACGCGATTCCATATTAACTACTC
* *
1294443 ACGTGATTCCATATTTACTACTC
1 ACGCGATTCCATATTAACTACTC
** *
1294466 ACGCGATTCCATAGCAACTAGTC
1 ACGCGATTCCATATTAACTACTC
** * * *
1294489 ACATGATTCCCTATCAAATACTC
1 ACGCGATTCCATATTAACTACTC
* * * *
1294512 ACGCGATTCTATAATAACTAGTG
1 ACGCGATTCCATATTAACTACTC
** * *
1294535 GTGCGATTCCATCTTCACTACTC
1 ACGCGATTCCATATTAACTACTC
* * * * * *
1294558 ATGCAATTCCATATCAGCTAGTA
1 ACGCGATTCCATATTAACTACTC
* * *
1294581 ACACGATTCCATATTTACTACTT
1 ACGCGATTCCATATTAACTACTC
*
1294604 ACGTGATTC
1 ACGCGATTC
1294613 AAAATCAATT
Statistics
Matches: 146, Mismatches: 70, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
23 146 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (23 bp):
ACGCGATTCCATATTAACTACTC
Found at i:1294451 original size:46 final size:46
Alignment explanation
Indices: 1294422--1294533 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 46
1294412 AAATACTTGT
* ** *
1294422 GCGATTCTATAATAACTAGTAACGTGATTCCATATTTACTACTCAC
1 GCGATTCTATAATAACTAGTAACATGATTCCATATCAAATACTCAC
* ** * *
1294468 GCGATTCCATAGCAACTAGTCACATGATTCCCTATCAAATACTCAC
1 GCGATTCTATAATAACTAGTAACATGATTCCATATCAAATACTCAC
1294514 GCGATTCTATAATAACTAGT
1 GCGATTCTATAATAACTAGT
1294534 GGTGCGATTC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (46 bp):
GCGATTCTATAATAACTAGTAACATGATTCCATATCAAATACTCAC
Found at i:1294518 original size:92 final size:92
Alignment explanation
Indices: 1294422--1294590 Score: 230
Period size: 92 Copynumber: 1.8 Consensus size: 92
1294412 AAATACTTGT
* * *
1294422 GCGATTCTATAATAACTAGTAACGTGATTCCATATTTACTACTCACGCGATTCCATAGCAACTAG
1 GCGATTCTATAATAACTAGTAACGCGATTCCATATTCACTACTCACGCAATTCCATAGCAACTAG
* *
1294487 TCACATGATTCCCTATCAAATACTCAC
66 TAACACGATTCCCTATCAAATACTCAC
*** * * * *
1294514 GCGATTCTATAATAACTAGTGGTGCGATTCCATCTTCACTACTCATGCAATTCCATATCAGCTAG
1 GCGATTCTATAATAACTAGTAACGCGATTCCATATTCACTACTCACGCAATTCCATAGCAACTAG
1294579 TAACACGATTCC
66 TAACACGATTCC
1294591 ATATTTACTA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
92 65 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (92 bp):
GCGATTCTATAATAACTAGTAACGCGATTCCATATTCACTACTCACGCAATTCCATAGCAACTAG
TAACACGATTCCCTATCAAATACTCAC
Found at i:1294557 original size:46 final size:46
Alignment explanation
Indices: 1294422--1294612 Score: 136
Period size: 46 Copynumber: 4.2 Consensus size: 46
1294412 AAATACTTGT
* *
1294422 GCGATTCTATAATAACTAGTAACGTGATTCCATATTTACTACTCAC
1 GCGATTCTATAATAACTAGTAACGTGATTCCATCTTCACTACTCAC
* ** * * *
1294468 GCGATTCCATAGCAACTAGTCACATGATTCC--CTATCAAATACTCAC
1 GCGATTCTATAATAACTAGTAACGTGATTCCATCT-TC-ACTACTCAC
*** * *
1294514 GCGATTCTATAATAACTAGTGGTGCGATTCCATCTTCACTACTCAT
1 GCGATTCTATAATAACTAGTAACGTGATTCCATCTTCACTACTCAC
* * * ** * * *
1294560 GCAATTCCAT-ATCAGCTAGTAACACGATTCCATATTTACTACTTAC
1 GCGATTCTATAAT-AACTAGTAACGTGATTCCATCTTCACTACTCAC
*
1294606 GTGATTC
1 GCGATTC
1294613 AAAATCAATT
Statistics
Matches: 109, Mismatches: 31, Indels: 10
0.73 0.21 0.07
Matches are distributed among these distances:
44 1 0.01
45 3 0.03
46 101 0.93
47 2 0.02
48 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (46 bp):
GCGATTCTATAATAACTAGTAACGTGATTCCATCTTCACTACTCAC
Found at i:1297987 original size:4 final size:4
Alignment explanation
Indices: 1297978--1298022 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
1297968 ATTATCAATA
1297978 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1298023 AATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1309043 original size:32 final size:32
Alignment explanation
Indices: 1309007--1309139 Score: 225
Period size: 32 Copynumber: 4.2 Consensus size: 32
1308997 AAGCATTAAT
*
1309007 ATTAATACTTTGTATTAATGCA-GCTTAGCAAC
1 ATTAATGCTTTGTATTAATG-ATGCTTAGCAAC
1309039 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
1 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
1309071 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
1 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
*
1309103 ATTAATGCTTTGTATT-ATGATGCTTAGCAGC
1 ATTAATGCTTTGTATTAATGATGCTTAGCAAC
1309134 ATTAAT
1 ATTAAT
1309140 CCAAAGCATG
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
31 21 0.21
32 77 0.79
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (32 bp):
ATTAATGCTTTGTATTAATGATGCTTAGCAAC
Found at i:1309062 original size:16 final size:16
Alignment explanation
Indices: 1309043--1309127 Score: 55
Period size: 16 Copynumber: 5.4 Consensus size: 16
1309033 AGCAACATTA
1309043 ATGCTTTGTATTAATG
1 ATGCTTTGTATTAATG
* * ** * *
1309059 ATGCTTAGCAACATTA
1 ATGCTTTGTATTAATG
1309075 ATGCTTTGTATTAATG
1 ATGCTTTGTATTAATG
* * ** * *
1309091 ATGCTTAGCAACATTA
1 ATGCTTTGTATTAATG
1309107 ATGCTTTGTATT-ATG
1 ATGCTTTGTATTAATG
1309122 ATGCTT
1 ATGCTT
1309128 AGCAGCATTA
Statistics
Matches: 45, Mismatches: 24, Indels: 1
0.64 0.34 0.01
Matches are distributed among these distances:
15 7 0.16
16 38 0.84
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGCTTTGTATTAATG
Found at i:1309076 original size:19 final size:19
Alignment explanation
Indices: 1309052--1309109 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 19
1309042 AATGCTTTGT
1309052 ATTAATGATGCTTAGCAAC
1 ATTAATGATGCTTAGCAAC
* *
1309071 ATT-A--ATGCTTTG---T
1 ATTAATGATGCTTAGCAAC
1309084 ATTAATGATGCTTAGCAAC
1 ATTAATGATGCTTAGCAAC
1309103 ATTAATG
1 ATTAATG
1309110 CTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
16 14 0.48
18 1 0.03
19 10 0.34
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTAATGATGCTTAGCAAC
Found at i:1311970 original size:2 final size:2
Alignment explanation
Indices: 1311963--1311994 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1311953 GGAAACATAG
1311963 AT AT 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 AT AT
1311995 GTATGTGTGT
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):
AT
Found at i:1315861 original size:21 final size:21
Alignment explanation
Indices: 1315832--1315920 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
1315822 TTGAATAGAG
* *
1315832 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTATCATGAAT
* * *
1315853 GCATTAGTCTTTGTTATGAAT
1 GCATCAGTCTTTATCATGAAT
1315874 GCATCAGTCTTTATCATGAAT
1 GCATCAGTCTTTATCATGAAT
* *
1315895 GCATTAGTCTTTGTCATGAATT
1 GCATCAGTCTTTATCATGAA-T
1315917 GCAT
1 GCAT
1315921 GAATATATCT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
21 52 0.91
22 5 0.09
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (21 bp):
GCATCAGTCTTTATCATGAAT
Found at i:1315888 original size:42 final size:43
Alignment explanation
Indices: 1315832--1315920 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 43
1315822 TTGAATAGAG
*
1315832 GCATCAGTCCTTATCATAAATGCATTAGTCTTTGTTATGAA-T
1 GCATCAGTCCTTATCATAAATGCATTAGTCTTTGTCATGAATT
* *
1315874 GCATCAGTCTTTATCATGAATGCATTAGTCTTTGTCATGAATT
1 GCATCAGTCCTTATCATAAATGCATTAGTCTTTGTCATGAATT
1315917 GCAT
1 GCAT
1315921 GAATATATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 38 0.88
43 5 0.12
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (43 bp):
GCATCAGTCCTTATCATAAATGCATTAGTCTTTGTCATGAATT
Found at i:1318922 original size:8 final size:8
Alignment explanation
Indices: 1318909--1318936 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1318899 TATTATTTAT
1318909 TTTTATTC
1 TTTTATTC
1318917 TTTTATTC
1 TTTTATTC
1318925 TTTTATTC
1 TTTTATTC
1318933 TTTT
1 TTTT
1318937 TTTTTCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTC
Found at i:1318953 original size:28 final size:27
Alignment explanation
Indices: 1318901--1318988 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
1318891 ACTTTGTTTA
*
1318901 TTATTTATTTTTATTCTTT-TA-TTCTT
1 TTATTT-TTTTTTTTCTTTATATTTCTT
1318927 TTATTCTTTTTTTTTCTTTATATTTCTT
1 TTATT-TTTTTTTTTCTTTATATTTCTT
**
1318955 TCCCTTTTTTTTTTTCTTCTTATATTT-TT
1 T-TATTTTTTTTTTTC-T-TTATATTTCTT
1318984 TTATT
1 TTATT
1318989 GTTAACTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 16 0.31
27 3 0.06
28 18 0.35
29 6 0.12
30 8 0.16
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (27 bp):
TTATTTTTTTTTTTCTTTATATTTCTT
Found at i:1327178 original size:31 final size:31
Alignment explanation
Indices: 1327140--1327229 Score: 162
Period size: 31 Copynumber: 2.9 Consensus size: 31
1327130 TCTTTTTTCT
* *
1327140 TTACATACATTGTGCTCACAAAAAAATATGC
1 TTACATACATTGTGCTCATAGAAAAATATGC
1327171 TTACATACATTGTGCTCATAGAAAAATATGC
1 TTACATACATTGTGCTCATAGAAAAATATGC
1327202 TTACATACATTGTGCTCATAGAAAAATA
1 TTACATACATTGTGCTCATAGAAAAATA
1327230 AGGTAACTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (31 bp):
TTACATACATTGTGCTCATAGAAAAATATGC
Found at i:1330465 original size:24 final size:24
Alignment explanation
Indices: 1330438--1330483 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1330428 TTGATGTTAG
1330438 TACCTTTTTTTAATTTTACAATAA
1 TACCTTTTTTTAATTTTACAATAA
1330462 TACCTTTTTTTAATTTTACAAT
1 TACCTTTTTTTAATTTTACAAT
1330484 TTCATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (24 bp):
TACCTTTTTTTAATTTTACAATAA
Found at i:1341479 original size:17 final size:17
Alignment explanation
Indices: 1341453--1341495 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1341443 GGATACAATA
*
1341453 AAAATATAAAAAAAATC
1 AAAATCTAAAAAAAATC
*
1341470 AAAATCT-AAACAAATC
1 AAAATCTAAAAAAAATC
*
1341486 AAAACCTAAA
1 AAAATCTAAA
1341496 TTTTAGTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATCTAAAAAAAATC
Found at i:1341486 original size:16 final size:16
Alignment explanation
Indices: 1341465--1341495 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1341455 AATATAAAAA
*
1341465 AAATCAAAATCTAAAC
1 AAATCAAAACCTAAAC
1341481 AAATCAAAACCTAAA
1 AAATCAAAACCTAAA
1341496 TTTTAGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATCAAAACCTAAAC
Found at i:1342503 original size:346 final size:346
Alignment explanation
Indices: 1341862--1342546 Score: 919
Period size: 346 Copynumber: 2.0 Consensus size: 346
1341852 GTTTCACATT
* **
1341862 TATGCTTGTACATTTTCTACTCTTTGGGTGACAAGGCAACTACATAGTTGATGTTCAATTTGTGG
1 TATGCTTGTACATTTTCTACTCTTTAGGTGACAAGGCAACTACATAGTTGATGTTCAATTTGTAA
* * * *
1341927 ATCATTTTCTTGGGTTATCCTTATGATATTATTGTAAATCACTTCCTACCAATGTTTGAAAATAT
66 ATCATTTTCTTGGGCTATCCTTATAATATTATTGCAAATCACTGCCTACCAATGTTTGAAAATAT
* * * * *
1341992 TAGATATTGATTATTGGGAAATTGGTATGTTTTCATGCTTGATGGTTGTTTATTTGCGTTTGTGA
131 TAGATATTAATTATTGGGAAATTAGTATGCTTTAATGCTTGATGGTTGTTTATTTGAGTTTGTGA
*
1342057 TTTTTAGCGATGCTAATTCAATCATTGTTGAATATCTAATTATTGTTTTATTGCTGCAAATGTCA
196 TTTTTAGCGATGCTAATTCAATCATTATTGAATATCTAATTATTGTTTTATTGCTGCAAATGTCA
* * * ** *
1342122 ACATACTTACATATGGCAGAGTGTTGCCTAAATTTTTTGGACAATTCTAAACTATGTTATATGTT
261 ACATACTTACATATGGCAAAATGTTGCCAAAATTTTTTGGACAACACTAAACTATGATATATGTT
1342187 TGTTGAGAACTCCCCCAAACA
326 TGTTGAGAACTCCCCCAAACA
* *
1342208 TATGCTTGTACATTTTCTGCTCTTTAGGTGACAAGGCAACTACGTAGTTGATGTTCAATTTGTAA
1 TATGCTTGTACATTTTCTACTCTTTAGGTGACAAGGCAACTACATAGTTGATGTTCAATTTGTAA
* * *
1342273 ATTATTTTCTTGTGCTATCCTTATAATATTATTGCAAATCACTGCCTACCTATGTTTGAAAATAT
66 ATCATTTTCTTGGGCTATCCTTATAATATTATTGCAAATCACTGCCTACCAATGTTTGAAAATA-
* *
1342338 TTA-TTATTAATTATTGGGAAATTAGTGTGCTTTAATGCTTGATGGTTGTTTATTTGAG-TTGTG
130 TTAGATATTAATTATTGGGAAATTAGTATGCTTTAATGCTTGATGGTTGTTTATTTGAGTTTGTG
* *** * ** * *
1342401 ATTTTTTTAGTGATGCTAATTTTGTTATTATTTTATATCTGATTATT-TTGTT-TTGTTGCAAAT
195 A--TTTTTAGCGATGCTAATTCAATCATTATTGAATATCTAATTATTGTT-TTATTGCTGCAAAT
* * * * * * * *
1342464 GTGAACATACTTACCTCTGGTAAAATGTTGTCAAAATTTTTTGGAGAACACTAAATTGTGATATA
257 GTCAACATACTTACATATGGCAAAATGTTGCCAAAATTTTTTGGACAACACTAAACTATGATATA
1342529 TGTTTGTTGAGAACTCCC
322 TGTTTGTTGAGAACTCCC
1342547 TTAAATATAT
Statistics
Matches: 292, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
345 6 0.02
346 246 0.84
347 40 0.14
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (346 bp):
TATGCTTGTACATTTTCTACTCTTTAGGTGACAAGGCAACTACATAGTTGATGTTCAATTTGTAA
ATCATTTTCTTGGGCTATCCTTATAATATTATTGCAAATCACTGCCTACCAATGTTTGAAAATAT
TAGATATTAATTATTGGGAAATTAGTATGCTTTAATGCTTGATGGTTGTTTATTTGAGTTTGTGA
TTTTTAGCGATGCTAATTCAATCATTATTGAATATCTAATTATTGTTTTATTGCTGCAAATGTCA
ACATACTTACATATGGCAAAATGTTGCCAAAATTTTTTGGACAACACTAAACTATGATATATGTT
TGTTGAGAACTCCCCCAAACA
Found at i:1346180 original size:36 final size:36
Alignment explanation
Indices: 1346133--1346289 Score: 194
Period size: 35 Copynumber: 4.4 Consensus size: 36
1346123 NNNNNNNNNN
1346133 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
1 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
**** *
1346169 CCTAATTGATTAAA-TTCAACAATTAAGTTATTGGG
1 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
* * *
1346204 CCTCATTGATTAAATTTGTCTAATCAAGCTATTGGG
1 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
* *
1346240 CCTAATTGATTAAA-TTGTTTAATTAAGTTAATGGG
1 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
*
1346275 CTTAATTGA-TAAATT
1 CCTAATTGATTAAATT
1346290 AAACAATTAA
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
34 4 0.04
35 55 0.54
36 42 0.42
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (36 bp):
CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGG
Found at i:1346264 original size:71 final size:71
Alignment explanation
Indices: 1346133--1346289 Score: 226
Period size: 71 Copynumber: 2.2 Consensus size: 71
1346123 NNNNNNNNNN
* *
1346133 CCTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTGATTAAATTCAACAATTAAGTT
1 CCTAATTGATTAAATTTGTCTAATCAAGCTATTGGGCCTAATTGATTAAATTCAACAATTAAGTT
*
1346198 ATTGGG
66 AATGGG
* ****
1346204 CCTCATTGATTAAATTTGTCTAATCAAGCTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTT
1 CCTAATTGATTAAATTTGTCTAATCAAGCTATTGGGCCTAATTGATTAAATTCAACAATTAAGTT
1346269 AATGGG
66 AATGGG
*
1346275 CTTAATTGA-TAAATT
1 CCTAATTGATTAAATT
1346290 AAACAATTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
70 6 0.08
71 70 0.92
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (71 bp):
CCTAATTGATTAAATTTGTCTAATCAAGCTATTGGGCCTAATTGATTAAATTCAACAATTAAGTT
AATGGG
Found at i:1346312 original size:35 final size:35
Alignment explanation
Indices: 1346158--1346310 Score: 164
Period size: 35 Copynumber: 4.3 Consensus size: 35
1346148 TTGTTTAATC
*
1346158 AAGTTATTGGGCCTAATTGATTAAATTCAACAATT
1 AAGTTATTGGGCCTAATTGATTAAATTAAACAATT
* *** *
1346193 AAGTTATTGGGCCTCATTGATTAAATTTGTCTAATC
1 AAGTTATTGGGCCTAATTGATTAAATTAAAC-AATT
* ****
1346229 AAGCTATTGGGCCTAATTGATTAAATTGTTTAATT
1 AAGTTATTGGGCCTAATTGATTAAATTAAACAATT
* *
1346264 AAGTTAATGGGCTTAATTGA-TAAATTAAACAATT
1 AAGTTATTGGGCCTAATTGATTAAATTAAACAATT
1346298 AAGTTAATTGGGC
1 AAGTT-ATTGGGC
1346311 TTCTTAAGGA
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
34 15 0.15
35 53 0.55
36 29 0.30
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (35 bp):
AAGTTATTGGGCCTAATTGATTAAATTAAACAATT
Found at i:1353587 original size:35 final size:35
Alignment explanation
Indices: 1353541--1353676 Score: 157
Period size: 35 Copynumber: 3.9 Consensus size: 35
1353531 NNNNAATTTG
*
1353541 TTTAATCAAGTTATTGGGCCTAATTGATTTAATTA
1 TTTAATCAAGTTATTGGGCCTAATTGATTAAATTA
* * *
1353576 TTTAATTAAGTTATTGGGCCTCATTTATTAAATTA
1 TTTAATCAAGTTATTGGGCCTAATTGATTAAATTA
** * * *
1353611 AATAA-CTAAGTTATTGGACTTAATTGATTAAATTTG
1 TTTAATC-AAGTTATTGGGCCTAATTGATTAAA-TTA
*
1353647 TTTAATCAAGTTATTAGGCCTAATTGATTA
1 TTTAATCAAGTTATTGGGCCTAATTGATTA
1353677 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 17, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
35 55 0.68
36 25 0.31
37 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTAATCAAGTTATTGGGCCTAATTGATTAAATTA
Found at i:1353726 original size:35 final size:35
Alignment explanation
Indices: 1353543--1353729 Score: 124
Period size: 35 Copynumber: 5.3 Consensus size: 35
1353533 NNAATTTGTT
* * * **
1353543 TAATCAAGTTATTGGGCCTAATTGATTTAATTATT
1 TAATTAAGTTATTAGGCCTAATTGATTAAATTAAA
* * *
1353578 TAATTAAGTTATTGGGCCTCATTTATTAAATTAAA
1 TAATTAAGTTATTAGGCCTAATTGATTAAATTAAA
* * ***
1353613 TAACTAAGTTATT-GGACTTAATTGATTAAATTTGTT
1 TAATTAAGTTATTAGG-CCTAATTGATTAAA-TTAAA
* *******
1353649 TAATCAAGTTATTAGGCCTAATTGATTANNNNNNN
1 TAATTAAGTTATTAGGCCTAATTGATTAAATTAAA
***
1353684 NNNTTAAGTTATTAGGCCTAATTGATTAAATTAAA
1 TAATTAAGTTATTAGGCCTAATTGATTAAATTAAA
*
1353719 CAATTAAGTTA
1 TAATTAAGTTA
1353730 ACTGGGCTTC
Statistics
Matches: 112, Mismatches: 37, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
34 2 0.02
35 84 0.75
36 24 0.21
37 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.41
Consensus pattern (35 bp):
TAATTAAGTTATTAGGCCTAATTGATTAAATTAAA
Found at i:1363067 original size:12 final size:11
Alignment explanation
Indices: 1363045--1363084 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1363035 AGCCCTCTTC
1363045 CAAAAAAATTT
1 CAAAAAAATTT
1363056 CAAAACAAATTT
1 CAAAA-AAATTT
* *
1363068 TAAAAAAAATT
1 CAAAAAAATTT
1363079 CAAAAA
1 CAAAAA
1363085 CAAAATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (11 bp):
CAAAAAAATTT
Found at i:1363093 original size:23 final size:23
Alignment explanation
Indices: 1363046--1363093 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1363036 GCCCTCTTCC
* *
1363046 AAAAAAATTTCAAAACAAATTTT
1 AAAAAAAATTCAAAACAAATATT
1363069 AAAAAAAATTCAAAAACAAA-ATT
1 AAAAAAAATTC-AAAACAAATATT
1363092 AA
1 AA
1363094 GGAATGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAAAATTCAAAACAAATATT
Found at i:1366618 original size:35 final size:35
Alignment explanation
Indices: 1366573--1366643 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1366563 TTTGTAAGTT
1366573 AGTTTCATTTTTATGTTTTGTACAAGGACTAGTAA
1 AGTTTCATTTTTATGTTTTGTACAAGGACTAGTAA
1366608 AGTTTCATTTTTATGTTTTGTACAAGGACTAGTAA
1 AGTTTCATTTTTATGTTTTGTACAAGGACTAGTAA
1366643 A
1 A
1366644 ATATTAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (35 bp):
AGTTTCATTTTTATGTTTTGTACAAGGACTAGTAA
Found at i:1373777 original size:6 final size:6
Alignment explanation
Indices: 1373766--1373791 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1373756 AGTTTATTAG
1373766 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
1373792 GTTTGGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:1379454 original size:15 final size:15
Alignment explanation
Indices: 1379434--1379464 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1379424 TACGAAGCTG
1379434 ATTTTGATGATGCTA
1 ATTTTGATGATGCTA
*
1379449 ATTTTGATGGTGCTA
1 ATTTTGATGATGCTA
1379464 A
1 A
1379465 ACTATGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (15 bp):
ATTTTGATGATGCTA
Found at i:1379629 original size:13 final size:13
Alignment explanation
Indices: 1379611--1379637 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1379601 AATATGCTGG
1379611 TGACAGACTGTTA
1 TGACAGACTGTTA
1379624 TGACAGACTGTTA
1 TGACAGACTGTTA
1379637 T
1 T
1379638 AATGAGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TGACAGACTGTTA
Found at i:1383951 original size:15 final size:15
Alignment explanation
Indices: 1383931--1383959 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1383921 GAATGAATTA
1383931 CATTGAAAGATTGAT
1 CATTGAAAGATTGAT
1383946 CATTGAAAGATTGA
1 CATTGAAAGATTGA
1383960 GTTAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (15 bp):
CATTGAAAGATTGAT
Found at i:1384293 original size:35 final size:35
Alignment explanation
Indices: 1384254--1384322 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
1384244 TTAAAATTGC
** * *
1384254 TTAATTAAGTTGTTAGGCTTAATTAATTAAATTAT
1 TTAATTAAGTCATTAGACCTAATTAATTAAATTAT
*
1384289 TTAATTAAGTCATTAGACCTAATTGATTAAATTA
1 TTAATTAAGTCATTAGACCTAATTAATTAAATTA
1384323 AACAATTAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (35 bp):
TTAATTAAGTCATTAGACCTAATTAATTAAATTAT
Found at i:1386950 original size:17 final size:19
Alignment explanation
Indices: 1386915--1386952 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1386905 ATTTCCTAGC
1386915 TTTTCAAAAATATCCTAAA
1 TTTTCAAAAATATCCTAAA
1386934 TTTTC-AAAATA-CCTAAA
1 TTTTCAAAAATATCCTAAA
1386951 TT
1 TT
1386953 CAATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTTCAAAAATATCCTAAA
Found at i:1387443 original size:14 final size:14
Alignment explanation
Indices: 1387424--1387453 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1387414 CTCTCTACTT
*
1387424 CAAATGTATTGATA
1 CAAATGTATCGATA
1387438 CAAATGTATCGATA
1 CAAATGTATCGATA
1387452 CA
1 CA
1387454 TTGGAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
CAAATGTATCGATA
Found at i:1388576 original size:25 final size:25
Alignment explanation
Indices: 1388543--1388602 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
1388533 GTGGTCGTAA
**
1388543 CCACGTATATCAACTTGTGGCCTAG
1 CCACGTATATCAACCCGTGGCCTAG
* *
1388568 CCACATATATCAACCCGTGGCCTTG
1 CCACGTATATCAACCCGTGGCCTAG
1388593 CCACGTATAT
1 CCACGTATAT
1388603 ATCATATACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.27
Consensus pattern (25 bp):
CCACGTATATCAACCCGTGGCCTAG
Found at i:1397650 original size:22 final size:22
Alignment explanation
Indices: 1397608--1397650 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1397598 TGTGGTCCAA
*
1397608 TAAGAAACTAAAGAAACAAAAC
1 TAAGAAACTAAAAAAACAAAAC
*
1397630 TAAGAAA-TAACAAAAAGAAAA
1 TAAGAAACTAA-AAAAACAAAA
1397651 GGGAAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.09
Consensus pattern (22 bp):
TAAGAAACTAAAAAAACAAAAC
Found at i:1399447 original size:25 final size:25
Alignment explanation
Indices: 1399419--1399467 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1399409 TATATGCGGC
* *
1399419 AAGGCCACAATATGTTATACGTGGA
1 AAGGCCACAAGATGATATACGTGGA
* *
1399444 AAGGTCACGAGATGATATACGTGG
1 AAGGCCACAAGATGATATACGTGG
1399468 TTTCGACCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (25 bp):
AAGGCCACAAGATGATATACGTGGA
Found at i:1401384 original size:73 final size:73
Alignment explanation
Indices: 1401265--1401411 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
1401255 TTCCTAGTTT
*
1401265 AGGCTCACTCCACATAGGCCATAGGTGGCTTGCTTTAAGGCACACAACACAATACATGATCAGAT
1 AGGCTCACTCCACATAGGCCATAGGTGGCTTGCTTTAAGGCACACAACACAATACATGATCACAT
1401330 ATATTTTC
66 ATATTTTC
1401338 AGGCTCACTCCACATAGGCCATAGGTGGCTTGCTTTAAGGCACACAACACAATACATGATCACAT
1 AGGCTCACTCCACATAGGCCATAGGTGGCTTGCTTTAAGGCACACAACACAATACATGATCACAT
1401403 ATATTTTC
66 ATATTTTC
1401411 A
1 A
1401412 TTCTCTAGCC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (73 bp):
AGGCTCACTCCACATAGGCCATAGGTGGCTTGCTTTAAGGCACACAACACAATACATGATCACAT
ATATTTTC
Found at i:1419130 original size:18 final size:18
Alignment explanation
Indices: 1419107--1419153 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1419097 AAAAATCAGC
1419107 AAATAAAAATAT-AGTTAA
1 AAATAAAAATATAAG-TAA
*
1419125 AAATAAAAATGTAAGTAA
1 AAATAAAAATATAAGTAA
*
1419143 CAATAAAAATA
1 AAATAAAAATA
1419154 AAATAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATAAAAATATAAGTAA
Found at i:1423437 original size:8 final size:8
Alignment explanation
Indices: 1423417--1423495 Score: 85
Period size: 8 Copynumber: 10.1 Consensus size: 8
1423407 AGATTCAGCT
1423417 AGGAAGCAA
1 AGGAAG-AA
1423426 AGGAAGAA
1 AGGAAGAA
1423434 AGGAAGAA
1 AGGAAGAA
*
1423442 AGAAAGAA
1 AGGAAGAA
*
1423450 AGG-AGAG
1 AGGAAGAA
1423457 AGGAAGAA
1 AGGAAGAA
1423465 AGGAAGAA
1 AGGAAGAA
*
1423473 AGGGAGAGA
1 AGGAAGA-A
1423482 A--AAGAA
1 AGGAAGAA
1423488 A-GAAGAA
1 AGGAAGAA
1423495 A
1 A
1423496 AGAGAAAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
6 2 0.03
7 15 0.25
8 36 0.59
9 8 0.13
ACGTcount: A:0.62, C:0.01, G:0.37, T:0.00
Consensus pattern (8 bp):
AGGAAGAA
Found at i:1423505 original size:23 final size:23
Alignment explanation
Indices: 1423437--1423507 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
1423427 GGAAGAAAGG
* *
1423437 AAGAAAGAAAGAAAGGAGAGAG-G
1 AAGAAAG-AAGAAAAGAGAGAGAA
*
1423460 AAGAAAGGAAG-AAAGGGAGAGAA
1 AAGAAA-GAAGAAAAGAGAGAGAA
*
1423483 AAGAAAGAAGAAAAGAGAAAGAA
1 AAGAAAGAAGAAAAGAGAGAGAA
1423506 AA
1 AA
1423508 AGTTCTGCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 12 0.30
23 27 0.68
24 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAGAAAAGAGAGAGAA
Found at i:1424300 original size:2 final size:2
Alignment explanation
Indices: 1424288--1424326 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1424278 CTTTGAATAA
*
1424288 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
1424327 GTAAAGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1435959 original size:18 final size:19
Alignment explanation
Indices: 1435936--1435978 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1435926 AGGTAGAAAG
*
1435936 AATATTTT-TGAATAACAT
1 AATATTTTATGAATAAAAT
1435954 AATATTTTATGAATAAAAT
1 AATATTTTATGAATAAAAT
1435973 AATATT
1 AATATT
1435979 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (19 bp):
AATATTTTATGAATAAAAT
Found at i:1444667 original size:35 final size:35
Alignment explanation
Indices: 1444627--1444708 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
1444617 ACAAGGTCAG
* * * *
1444627 GCATAACCTTTACAACATGCCTTTTGCAGGATTAA
1 GCATAACCTCTACAACATGCCTTTTGAAAGATCAA
*
1444662 GCATAACCTCTACAACATGCCTTTTGAAAGATCAG
1 GCATAACCTCTACAACATGCCTTTTGAAAGATCAA
1444697 GCATAACCTCTA
1 GCATAACCTCTA
1444709 TCAAGACACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (35 bp):
GCATAACCTCTACAACATGCCTTTTGAAAGATCAA
Found at i:1469944 original size:43 final size:43
Alignment explanation
Indices: 1469861--1469944 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
1469851 TATATAAAGG
**
1469861 ATATCAAGCAATATAATTGGAACTGTAGCACCTCGTATCAAAA
1 ATATCAAGCAATATAATTGGAACTGTAGCACCTCAAATCAAAA
* *
1469904 ATATCAAGCATTATACTTGGAAAC-GTAGCA-CTACAAATCAA
1 ATATCAAGCAATATAATTGG-AACTGTAGCACCT-CAAATCAA
1469945 GGATATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 30 0.86
44 3 0.09
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (43 bp):
ATATCAAGCAATATAATTGGAACTGTAGCACCTCAAATCAAAA
Found at i:1474388 original size:11 final size:11
Alignment explanation
Indices: 1474372--1474396 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1474362 TTTGTATGTG
1474372 ATAAAATAATA
1 ATAAAATAATA
1474383 ATAAAATAATA
1 ATAAAATAATA
1474394 ATA
1 ATA
1474397 TCTTATTTAG
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:1474515 original size:19 final size:19
Alignment explanation
Indices: 1474491--1474529 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1474481 CCTAAAGGAA
1474491 AATTTTGAAATAAAATAAT
1 AATTTTGAAATAAAATAAT
* *
1474510 AATTTTTAGATAAAATAAT
1 AATTTTGAAATAAAATAAT
1474529 A
1 A
1474530 GTAAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AATTTTGAAATAAAATAAT
Found at i:1474838 original size:30 final size:30
Alignment explanation
Indices: 1474804--1474862 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1474794 GGGAGGACCC
*
1474804 AATTAAAAAGAAT-AAGAAGTTGAGGGGTGG
1 AATTAAAAAGAATGAA-AAGTTAAGGGGTGG
* *
1474834 AATTATAAATAATGAAAAGTTAAGGGGTG
1 AATTAAAAAGAATGAAAAGTTAAGGGGTG
1474863 AAGTTGCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (30 bp):
AATTAAAAAGAATGAAAAGTTAAGGGGTGG
Found at i:1477099 original size:25 final size:25
Alignment explanation
Indices: 1477071--1477129 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
1477061 TTTGTGATAT
*
1477071 ATATACATGACAAGGCCACAGGTTG
1 ATATACATGACAAGGCCACAAGTTG
** * *
1477096 ATATATGTGGCTAGGCCACAAGTTG
1 ATATACATGACAAGGCCACAAGTTG
*
1477121 ATAAACATG
1 ATATACATG
1477130 GTTATGACTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (25 bp):
ATATACATGACAAGGCCACAAGTTG
Found at i:1485941 original size:19 final size:19
Alignment explanation
Indices: 1485891--1485944 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
1485881 CTTTGTAGAC
*
1485891 AATTAATTAAAACTAAATTT
1 AATTAA-TAAAACTAAATCT
1485911 AA-TAATAAAACTAAA-CT
1 AATTAATAAAACTAAATCT
1485928 AATTAATGAAAACTAAA
1 AATTAAT-AAAACTAAA
1485945 AATTCACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 14 0.45
19 12 0.39
20 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
AATTAATAAAACTAAATCT
Found at i:1487724 original size:71 final size:71
Alignment explanation
Indices: 1487576--1487714 Score: 167
Period size: 71 Copynumber: 2.0 Consensus size: 71
1487566 TCTGGGCAGA
* * * *
1487576 ATCTATCAATAGATGTACATCATCTATTGAGAGATTAAACCTAAAAAGTTTTTAAATGAGATTTG
1 ATCTATCAACAGATGGACATCATCTATTGAGAAATTAAACCTAAAAAGTTTTTAAAAGAGATTTG
1487641 AAGAAC
66 AAGAAC
* * *
1487647 ATCTATCAACAGATGGACA-CATCTATTGATAAATTGCAA-CTAGAAAGCTTTTTAAAAG-GACT
1 ATCTATCAACAGATGGACATCATCTATTGAGAAATT-AAACCTAAAAAG-TTTTTAAAAGAGA-T
1487709 TTGAAG
63 TTGAAG
1487715 GCTATCTATC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
70 23 0.40
71 35 0.60
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (71 bp):
ATCTATCAACAGATGGACATCATCTATTGAGAAATTAAACCTAAAAAGTTTTTAAAAGAGATTTG
AAGAAC
Found at i:1513269 original size:21 final size:21
Alignment explanation
Indices: 1513245--1513285 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1513235 TTCCAAGCCT
1513245 TTTTCTTCTTCTTCCTTTCTC
1 TTTTCTTCTTCTTCCTTTCTC
*
1513266 TTTTCTTCTTTTTCCTTTCT
1 TTTTCTTCTTCTTCCTTTCT
1513286 TTCTTGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTTCTTCTTCCTTTCTC
Found at i:1513276 original size:14 final size:15
Alignment explanation
Indices: 1513242--1513286 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1513232 CTCTTCCAAG
1513242 CCTTTTTCTTCTTCTT
1 CCTTTTTCTT-TTCTT
*
1513258 CCTTTCTCTTTTCTT
1 CCTTTTTCTTTTCTT
*
1513273 -CTTTTTCCTTTCTT
1 CCTTTTTCTTTTCTT
1513287 TCTTGTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 12 0.46
15 5 0.19
16 9 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
CCTTTTTCTTTTCTT
Found at i:1518246 original size:17 final size:20
Alignment explanation
Indices: 1518227--1518262 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1518217 AATGAAAAAG
1518227 AAAA-GAAAAAAA-AGAAGA
1 AAAATGAAAAAAATAGAAGA
1518245 AAAATGAAAAAAATAGAA
1 AAAATGAAAAAAATAGAA
1518263 TAAATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 8 0.50
20 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (20 bp):
AAAATGAAAAAAATAGAAGA
Done.