Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 87 of 109
Found at i:17553038 original size:26 final size:27
Alignment explanation
Indices: 17552997--17553048 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
17552987 AATTTTTTTT
*
17552997 ATAAAAAAGATAAT-AATATGAAAATA
1 ATAAAAAAAATAATAAATATGAAAATA
* *
17553023 ATAAAAAAAATTATAAATATTAAAAT
1 ATAAAAAAAATAATAAATATGAAAAT
17553049 TTGAATATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (27 bp):
ATAAAAAAAATAATAAATATGAAAATA
Found at i:17554175 original size:180 final size:180
Alignment explanation
Indices: 17553873--17554225 Score: 706
Period size: 180 Copynumber: 2.0 Consensus size: 180
17553863 TTTTAAGATT
17553873 AATTTTATTTACTTTTTAGGATTTTAAAATTTTAAAATTAATTTTTTTATGAAATATCATTATGT
1 AATTTTATTTACTTTTTAGGATTTTAAAATTTTAAAATTAATTTTTTTATGAAATATCATTATGT
17553938 GATTGATCATTGACAGTATAAAGTATTTATATATTAACAATGCATCAATTACGGAATTGGTTTTA
66 GATTGATCATTGACAGTATAAAGTATTTATATATTAACAATGCATCAATTACGGAATTGGTTTTA
17554003 GTTATTGAAAATCGTTTTATTTTTGTTAAAAATAAATATACATTATGTGA
131 GTTATTGAAAATCGTTTTATTTTTGTTAAAAATAAATATACATTATGTGA
17554053 AATTTTATTTACTTTTTAGGATTTTAAAATTTTAAAATTAATTTTTTTATGAAATATCATTATGT
1 AATTTTATTTACTTTTTAGGATTTTAAAATTTTAAAATTAATTTTTTTATGAAATATCATTATGT
17554118 GATTGATCATTGACAGTATAAAGTATTTATATATTAACAATGCATCAATTACGGAATTGGTTTTA
66 GATTGATCATTGACAGTATAAAGTATTTATATATTAACAATGCATCAATTACGGAATTGGTTTTA
17554183 GTTATTGAAAATCGTTTTATTTTTGTTAAAAATAAATATACAT
131 GTTATTGAAAATCGTTTTATTTTTGTTAAAAATAAATATACAT
17554226 AATTATGTAC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 173 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.47
Consensus pattern (180 bp):
AATTTTATTTACTTTTTAGGATTTTAAAATTTTAAAATTAATTTTTTTATGAAATATCATTATGT
GATTGATCATTGACAGTATAAAGTATTTATATATTAACAATGCATCAATTACGGAATTGGTTTTA
GTTATTGAAAATCGTTTTATTTTTGTTAAAAATAAATATACATTATGTGA
Found at i:17555230 original size:25 final size:26
Alignment explanation
Indices: 17555202--17555256 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
17555192 CTTAATTAAA
17555202 TTTA-GATTCAAATATAAG-TATTACT
1 TTTACGATT-AAATATAAGTTATTACT
* * *
17555227 TTTACTATTATATATTAGTTATTACT
1 TTTACGATTAAATATAAGTTATTACT
17555253 TTTA
1 TTTA
17555257 AGGATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTACGATTAAATATAAGTTATTACT
Found at i:17556355 original size:29 final size:30
Alignment explanation
Indices: 17556300--17556356 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
17556290 AAATTATAAT
* **
17556300 AAAATATTTTATTATAATATTTAAATTAAG
1 AAAATATTTTAATATAATACATAAATTAAG
*
17556330 AAAA-ATTTTAATATAATACATGAATTA
1 AAAATATTTTAATATAATACATAAATTA
17556357 TAAATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAATATTTTAATATAATACATAAATTAAG
Found at i:17561512 original size:11 final size:11
Alignment explanation
Indices: 17561496--17561521 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17561486 GCAACCCAAA
17561496 ATTTTATTATT
1 ATTTTATTATT
17561507 ATTTTATTATT
1 ATTTTATTATT
17561518 ATTT
1 ATTT
17561522 AAACACCATT
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):
ATTTTATTATT
Found at i:17562611 original size:21 final size:20
Alignment explanation
Indices: 17562561--17562614 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
17562551 GTAAAAAAAT
*
17562561 TATTTTTTTATTTTTTTTAA
1 TATTTTTTTATTTTTTATAA
*
17562581 AATTTTTTTTATTTTTTATATA
1 TA-TTTTTTTATTTTTTATA-A
*
17562603 TATTATTTTATT
1 TATTTTTTTATT
17562615 AATATTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTTTATTTTTTATAA
Found at i:17562953 original size:18 final size:17
Alignment explanation
Indices: 17562913--17562956 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
17562903 ATTTTTTTTA
17562913 ATAATAAATAAAAATTG
1 ATAATAAATAAAAATTG
17562930 ATTAATAAATTAAAAATATG
1 A-TAATAAA-TAAAAAT-TG
17562950 -TAATAAA
1 ATAATAAA
17562957 AATAGGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 7 0.29
20 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAATAAATAAAAATTG
Found at i:17563151 original size:11 final size:11
Alignment explanation
Indices: 17563135--17563160 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17563125 ATTTTAATTA
17563135 AAAAAATTAAT
1 AAAAAATTAAT
17563146 AAAAAATTAAT
1 AAAAAATTAAT
17563157 AAAA
1 AAAA
17563161 TTTTTGAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAATTAAT
Found at i:17563874 original size:16 final size:16
Alignment explanation
Indices: 17563853--17563901 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
17563843 CATTTTTAGT
17563853 AAAAAAAATAA-AAAAC
1 AAAAAAAA-AACAAAAC
*
17563869 AAAAAAAAAACAAATC
1 AAAAAAAAAACAAAAC
17563885 AAAAATAAAAAGCAAAA
1 AAAAA-AAAAA-CAAAA
17563902 AAATTCACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 17 0.61
17 5 0.18
18 4 0.14
ACGTcount: A:0.84, C:0.08, G:0.02, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAACAAAAC
Found at i:17563905 original size:22 final size:21
Alignment explanation
Indices: 17563855--17563905 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
17563845 TTTTTAGTAA
17563855 AAAAAATAAAAAACAAAAAAA
1 AAAAAATAAAAAACAAAAAAA
* * *
17563876 AAACAAATCAAAAATAAAAAGCA
1 AAA-AAATAAAAAACAAAAA-AA
17563899 AAAAAAT
1 AAAAAAT
17563906 TCACACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.72
23 4 0.16
ACGTcount: A:0.82, C:0.08, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAAAATAAAAAACAAAAAAA
Found at i:17575161 original size:33 final size:33
Alignment explanation
Indices: 17575119--17575188 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
17575109 TAAAATAAAA
17575119 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
1 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
17575152 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
1 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
17575185 TTTT
1 TTTT
17575189 CCAAGATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.40
Consensus pattern (33 bp):
TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
Found at i:17575266 original size:46 final size:46
Alignment explanation
Indices: 17575152--17575841 Score: 856
Period size: 46 Copynumber: 14.8 Consensus size: 46
17575142 TGAGAGGAGC
* *
17575152 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG-CTTTTCCAAGATAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAAG--AGAA
* *
17575200 TTTTAAAGTTGTTGAACCTCTGCTGAGAGGATCCTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
** *
17575246 TTTTAAAGTCATTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGACAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAAG--AGAA
*
17575294 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* *
17575340 TTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAAG--AGAA
* *
17575388 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
** * *
17575434 TTTTAAAGTCATTGAGCCTTTGCTGAGAGGAG-CTTTTCTAAGATAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTC-AAG--AGAA
* * * *
17575482 ATTTAAAGTTATTGAGCCTCTGCTAAGAGGAGCTTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
*
17575528 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* * **
17575574 TTTTAAAGTTGTTGAGCCTATGCTGAGAGGAGCCTTTTTATTAG-A
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
17575619 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* * *
17575665 TTTTAAAGTCGTTGAGCTTCTGCTGAGAGGAG-CTTTTCCAAGATAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAAG--AGAA
* * * *
17575713 TTTTAAAGTTGTTGAACCTCTACTGAGAGAAGTCTTTTCAAGAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* * **
17575759 TTTTAAAGTCGTTGAGCCTCTGTTGAGAGGAGCCTTTTCATTAG-A
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
17575804 TTTTAAAGTTGTTGAGCCTCTGCTGA-ATGGAGCCTTTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGA-GGAGCCTTTT
17575842 AAACTTTCAA
Statistics
Matches: 560, Mismatches: 63, Indels: 41
0.84 0.09 0.06
Matches are distributed among these distances:
44 1 0.00
45 96 0.17
46 265 0.47
48 174 0.31
49 24 0.04
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (46 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAGAA
Found at i:17575314 original size:94 final size:93
Alignment explanation
Indices: 17575152--17575829 Score: 888
Period size: 94 Copynumber: 7.3 Consensus size: 93
17575142 TGAGAGGAGC
* *
17575152 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATAAAATTTTAAAGTTGTTGAAC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AAAATTTTAAAGTTGTTGAGC
*
17575217 CTCTGCTGAGAGGATCCTTTTCAAGAGAA
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
**
17575246 TTTTAAAGTCATTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGACAAAATTTTAAAGTTGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AAAATTTTAAAGTTGTTGAGC
*
17575311 CTCTGCTGAGAGGAGCTTTTTCAAGAGAA
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
*
17575340 TTTTAAAGTCGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAAAATTTTAAAGTTGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AAAATTTTAAAGTTGTTGAGC
* *
17575405 CTCTGCTGAGAGAAACCTTTTCAAGAGAA
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
** * * * *
17575434 TTTTAAAGTCATTGAGCCTTTGCTGAGAGGAGCTTTTCTAAGATAAAAATTTAAAGTTATTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AAAATTTTAAAGTTGTTGAGC
* *
17575499 CTCTGCTAAGAGGAGCTTTTTCAAGAGAA
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* *
17575528 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTT-CAAG-AGAATTTTAAAGTTGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGAAAAATTTTAAAGTTGTTGAGC
* * **
17575591 CTATGCTGAGAGGAGCCTTTTTATTAG-A
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
* *
17575619 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-CAAG-AGAATTTTAAAGTCGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGAAAAATTTTAAAGTTGTTGAGC
* *
17575682 TTCTGCTGAGAGGAG-CTTTTCCAAGATAAAA
65 CTCTGCTGAGAGGAGCCTTTT-CAAG--AGAA
* * * * *
17575713 TTTTAAAGTTGTTGAACCTCTACTGAGAGAAGTCTTTT-CAAG-AGAATTTTAAAGTCGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGAAAAATTTTAAAGTTGTTGAGC
* **
17575776 CTCTGTTGAGAGGAGCCTTTTCATTAG-A
65 CTCTGCTGAGAGGAGCCTTTTCAAGAGAA
17575804 TTTTAAAGTTGTTGAGCCTCTGCTGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGA
17575830 ATGGAGCCTT
Statistics
Matches: 524, Mismatches: 54, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
90 5 0.01
91 101 0.19
92 40 0.08
93 1 0.00
94 367 0.70
95 10 0.02
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (93 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAAAAATTTTAAAGTTGTTGAGCC
TCTGCTGAGAGGAGCCTTTTCAAGAGAA
Found at i:17576115 original size:22 final size:20
Alignment explanation
Indices: 17576051--17576116 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
17576041 TATTTAATTT
*
17576051 TTTCTTTTTCTTTCTTTCTCC
1 TTTCTTTTTTTTTC-TTCTCC
*
17576072 TTT-TTGTTTTCTTCTTCTTCC
1 TTTCTT-TTTTTTTCTTC-TCC
17576093 TTTCTTTTCTTTTTCTTCATCC
1 TTTCTTTT-TTTTTCTTC-TCC
17576115 TT
1 TT
17576117 ATCTGGTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.14
21 17 0.46
22 15 0.41
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTCTTTTTTTTTCTTCTCC
Found at i:17577098 original size:19 final size:17
Alignment explanation
Indices: 17577054--17577099 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
17577044 TAAAAAAATT
17577054 TTTTTTATTTTTTTAAA
1 TTTTTTATTTTTTTAAA
*
17577071 TTTTCTTATTTTTTATATA
1 TTTT-TTATTTTTT-TAAA
17577090 TTATTTTATT
1 TT-TTTTATT
17577100 AATATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 9 0.36
19 10 0.40
20 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTATTTTTTTAAA
Found at i:17577441 original size:18 final size:17
Alignment explanation
Indices: 17577401--17577444 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
17577391 ATTTTTTTTA
17577401 ATAATAAATAAAAATTG
1 ATAATAAATAAAAATTG
17577418 ATTAATAAATTAAAAATATG
1 A-TAATAAA-TAAAAAT-TG
17577438 -TAATAAA
1 ATAATAAA
17577445 AATAGGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 7 0.29
20 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAATAAATAAAAATTG
Found at i:17578047 original size:189 final size:189
Alignment explanation
Indices: 17577698--17578070 Score: 660
Period size: 189 Copynumber: 2.0 Consensus size: 189
17577688 ACATGACATA
* * *
17577698 ATTTTTTACGAAAAGTAAATTTAGACCTCCCAAAGATGAGATTCTAAAAGTATTTTGAGTAGAGA
1 ATTTTTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATTTCGAGTAGAGA
*
17577763 TGCTTTAAGAAATCTTTAGGTGAGAAAAAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTA
66 TGCTTTAAGAAATCTCTAGGTGAGAAAAAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTA
*
17577828 AGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTTTAAC
131 AGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTTAAC
17577887 ATTTTCTTACGAAAAATAAATTCGAG-CCT-CCAAAGATGAGATTCTAAAAGTATTTCGAGTAGA
1 ATTTT-TTACGAAAAATAAATT-GAGACCTCCCAAAGATGAGATTCTAAAAGTATTTCGAGTAGA
*
17577950 GATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTT
64 GATGCTTTAAGAAATCTCTAGGTGAGAAAAAGTTCTTTTAATGTTACCAACGTACTGGAACATTT
17578015 TAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
129 TAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
17578071 AATAAATAAA
Statistics
Matches: 176, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
189 156 0.89
190 18 0.10
191 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (189 bp):
ATTTTTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATTTCGAGTAGAGA
TGCTTTAAGAAATCTCTAGGTGAGAAAAAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTA
AGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTTAAC
Found at i:17579382 original size:96 final size:96
Alignment explanation
Indices: 17579272--17579459 Score: 281
Period size: 96 Copynumber: 2.0 Consensus size: 96
17579262 AGTATTTTTT
* * **
17579272 TCCCTTGTTCTTGATACTTTGTTCAATTTAAGTGTAAGGGTA-AAA-AAAAGCTTTTTGTACTTA
1 TCCCTTGTTCTTGATACATTGTTCAATTTAAGTGT--GGGGAGAAATAAAAGCTTTTTAAACTTA
17579335 AATGATTTTTGAAAATTATGATTCCATTTCTTC
64 AATGATTTTTGAAAATTATGATTCCATTTCTTC
* * *
17579368 TCCCTTGTTTTTGATGCATTGTTCAATTTAAGTGTGGGGAGAAATGAAAGCTTTTTAAACTTAAA
1 TCCCTTGTTCTTGATACATTGTTCAATTTAAGTGTGGGGAGAAATAAAAGCTTTTTAAACTTAAA
17579433 TGATTTTTGAAAATTATGATTCCATTT
66 TGATTTTTGAAAATTATGATTCCATTT
17579460 TTGCTTTCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
94 4 0.05
95 3 0.04
96 76 0.92
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (96 bp):
TCCCTTGTTCTTGATACATTGTTCAATTTAAGTGTGGGGAGAAATAAAAGCTTTTTAAACTTAAA
TGATTTTTGAAAATTATGATTCCATTTCTTC
Found at i:17580456 original size:21 final size:22
Alignment explanation
Indices: 17580432--17580473 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17580422 TTCAACAATC
17580432 TTACTTATTGTT-TTTAAGATT
1 TTACTTATTGTTATTTAAGATT
*
17580453 TTACTTATTGTTATTTTAGAT
1 TTACTTATTGTTATTTAAGAT
17580474 CTAGTTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.62
Consensus pattern (22 bp):
TTACTTATTGTTATTTAAGATT
Found at i:17600313 original size:22 final size:22
Alignment explanation
Indices: 17600288--17600332 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17600278 CAAACATTAG
17600288 TGTCTAGTTCAAAGATATCTTA
1 TGTCTAGTTCAAAGATATCTTA
*
17600310 TGTCTAGTTCAGAGATATCTTA
1 TGTCTAGTTCAAAGATATCTTA
17600332 T
1 T
17600333 AGGGTAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (22 bp):
TGTCTAGTTCAAAGATATCTTA
Found at i:17604062 original size:24 final size:22
Alignment explanation
Indices: 17604035--17604078 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
17604025 AAGCACAAAT
17604035 AATCAAGCTCTTTTTTAGTATAAA
1 AATCAAGCT-TTTTTTA-TATAAA
*
17604059 AATCGAGCTTTTTTTATATA
1 AATCAAGCTTTTTTTATATA
17604079 TTAATCGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (22 bp):
AATCAAGCTTTTTTTATATAAA
Found at i:17604078 original size:22 final size:24
Alignment explanation
Indices: 17604035--17604088 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
17604025 AAGCACAAAT
*
17604035 AATCAAGCTCTTTTTTAGTATAAA
1 AATCGAGCTCTTTTTTAGTATAAA
**
17604059 AATCGAGCT-TTTTTTA-TATATT
1 AATCGAGCTCTTTTTTAGTATAAA
17604081 AATCGAGC
1 AATCGAGC
17604089 GAGCTTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 7 0.26
24 8 0.30
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (24 bp):
AATCGAGCTCTTTTTTAGTATAAA
Found at i:17609698 original size:14 final size:15
Alignment explanation
Indices: 17609673--17609706 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17609663 ATTAAAGTAA
17609673 ACAAAAATTTATCAT
1 ACAAAAATTTATCAT
17609688 ACAAAAA-TTATCAT
1 ACAAAAATTTATCAT
*
17609702 GCAAA
1 ACAAA
17609707 TAACATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (15 bp):
ACAAAAATTTATCAT
Found at i:17609906 original size:25 final size:26
Alignment explanation
Indices: 17609871--17609919 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
17609861 TAGAAATCAA
* *
17609871 AAAATGGAAAATAATAA-AAAAAATC
1 AAAATGAAAAATAAAAAGAAAAAATC
17609896 AAAATGAAAAATAAAAAGAAAAAA
1 AAAATGAAAAATAAAAAGAAAAAA
17609920 AAATCTGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (26 bp):
AAAATGAAAAATAAAAAGAAAAAATC
Found at i:17610888 original size:14 final size:15
Alignment explanation
Indices: 17610863--17610910 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
17610853 TTCCTTCTCA
*
17610863 TTTGATTTTTTTATT
1 TTTGATTTTTTTACT
17610878 TTTGA-TTTTTTACT
1 TTTGATTTTTTTACT
*
17610892 TTTGACCTTTTTTAACT
1 TTTGA--TTTTTTTACT
17610909 TT
1 TT
17610911 GACTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
15 5 0.18
17 10 0.36
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTGATTTTTTTACT
Found at i:17611666 original size:35 final size:35
Alignment explanation
Indices: 17611549--17611663 Score: 149
Period size: 35 Copynumber: 3.3 Consensus size: 35
17611539 AAGGTTTTAG
* * *
17611549 ATTTACAAAGATTTCAAGTTTCGCAAAGGTTCTAA
1 ATTTGCAAAGATTTCAAGTTTCGCAGAGATTCTAA
* * *
17611584 ATTTGTAAAGATTTTAAGTTTCGCAGAGATTCTGA
1 ATTTGCAAAGATTTCAAGTTTCGCAGAGATTCTAA
* *
17611619 ATTTGCAAAGGTTTCAAGTTTTGCAGAGATTCTAA
1 ATTTGCAAAGATTTCAAGTTTCGCAGAGATTCTAA
*
17611654 ATTCGCAAAG
1 ATTTGCAAAG
17611664 GTTCTAAGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (35 bp):
ATTTGCAAAGATTTCAAGTTTCGCAGAGATTCTAA
Found at i:17611670 original size:17 final size:17
Alignment explanation
Indices: 17611568--17611670 Score: 55
Period size: 17 Copynumber: 5.9 Consensus size: 17
17611558 GATTTCAAGT
*
17611568 TTCGCAAAGGTTCTAAA
1 TTCGCAAAGATTCTAAA
* * * *
17611585 TTTGTAAAGATTTTAAGT
1 TTCGCAAAGATTCTAA-A
* *
17611603 TTCGCAGAGATTCTGAA
1 TTCGCAAAGATTCTAAA
* * *
17611620 TTTGCAAAGGTT-TCAAGT
1 TTCGCAAAGATTCT-AA-A
* *
17611638 TTTGCAGAGATTCTAAA
1 TTCGCAAAGATTCTAAA
*
17611655 TTCGCAAAGGTTCTAA
1 TTCGCAAAGATTCTAA
17611671 GTTCACAAGA
Statistics
Matches: 60, Mismatches: 22, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
16 1 0.02
17 35 0.58
18 23 0.38
19 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (17 bp):
TTCGCAAAGATTCTAAA
Found at i:17611695 original size:18 final size:18
Alignment explanation
Indices: 17611672--17611720 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
17611662 AGGTTCTAAG
*
17611672 TTCACAAGAATTTTCAAA
1 TTCACAAGAATTTTAAAA
17611690 TTCACAAGAA--TTAAAA
1 TTCACAAGAATTTTAAAA
*
17611706 TTCGCAAGAATTTTA
1 TTCACAAGAATTTTA
17611721 GGTTCGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (18 bp):
TTCACAAGAATTTTAAAA
Found at i:17611728 original size:17 final size:17
Alignment explanation
Indices: 17611706--17611749 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
17611696 AGAATTAAAA
*
17611706 TTCGCAAGAATTTTAGG
1 TTCGCAAGAATTTCAGG
* *
17611723 TTCGCAAAAATTTCAGT
1 TTCGCAAGAATTTCAGG
17611740 TTCGCAAGAA
1 TTCGCAAGAA
17611750 CTCAAAGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (17 bp):
TTCGCAAGAATTTCAGG
Found at i:17611828 original size:16 final size:16
Alignment explanation
Indices: 17611807--17611838 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17611797 AAGAAGTCAA
*
17611807 AGATTCGTAAGAATTT
1 AGATTCATAAGAATTT
17611823 AGATTCATAAGAATTT
1 AGATTCATAAGAATTT
17611839 TCAGATTTGC
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:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
AGATTCATAAGAATTT
Found at i:17611841 original size:52 final size:50
Alignment explanation
Indices: 17611694--17611854 Score: 150
Period size: 52 Copynumber: 3.1 Consensus size: 50
17611684 TTCAAATTCA
* * * * *
17611694 CAAGAATTAAA-ATTCGCAAGAATTTTAGGTTCGCAAAAATTTCAGTTTCG
1 CAAGAATCAAAGATTCGTAAGAACTTTAGATTCACAAAAATTTCAGTTT-G
*
17611744 CAAGAACTCAAAGACTT-GTAA-AACTTTCAGATTTACAAAAATTTCAAGTTTG
1 CAAGAA-TCAAAGA-TTCGTAAGAACTTT-AGATTCACAAAAATTTC-AGTTTG
* *
17611796 CAAGAAGTCAAAGATTCGTAAGAA-TTTAGATTCATAAGAATTTTCAGATTTG
1 CAAGAA-TCAAAGATTCGTAAGAACTTTAGATTCACAA-AAATTTCAG-TTTG
17611848 CAAGAAT
1 CAAGAAT
17611855 TTCAAGATTC
Statistics
Matches: 92, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
50 6 0.07
51 22 0.24
52 55 0.60
53 9 0.10
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (50 bp):
CAAGAATCAAAGATTCGTAAGAACTTTAGATTCACAAAAATTTCAGTTTG
Found at i:17611862 original size:18 final size:17
Alignment explanation
Indices: 17611768--17611863 Score: 54
Period size: 18 Copynumber: 5.5 Consensus size: 17
17611758 CTTGTAAAAC
* *
17611768 TTTCAGATTTACAAAAA
1 TTTCAGATTTGCAAGAA
17611785 TTTCA-AGTTTGCAAGAA
1 TTTCAGA-TTTGCAAGAA
* * *
17611802 -GTCAAAGATTCGTAAGAA
1 TTTC--AGATTTGCAAGAA
***
17611820 TTT-AGATTCATAAGAA
1 TTTCAGATTTGCAAGAA
17611836 TTTTCAGATTTGCAAGAA
1 -TTTCAGATTTGCAAGAA
17611854 TTTCAAGATT
1 TTTC-AGATT
17611864 CTTAGGCTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
16 15 0.25
17 20 0.33
18 24 0.39
19 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
TTTCAGATTTGCAAGAA
Found at i:17612211 original size:44 final size:45
Alignment explanation
Indices: 17612157--17612272 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 45
17612147 ATTGTAAGTC
* * * *
17612157 AAAAATTTTAAAGATTCACACCCAAAAGTT-AAGGATATT-CATTT
1 AAAAAATTTAAAGATTCACATCCAAAAGTTCAAAGAT-TTACATTA
* * *
17612201 AAAAAATTTAAATATTCACTTCCAAAATTTCAAAGATTTACATTA
1 AAAAAATTTAAAGATTCACATCCAAAAGTTCAAAGATTTACATTA
*
17612246 AAAAAATTTTAGAGATTCACATCCAAA
1 AAAAAA-TTTAAAGATTCACATCCAAA
17612273 GTTTTACAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 27 0.46
45 15 0.25
46 17 0.29
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (45 bp):
AAAAAATTTAAAGATTCACATCCAAAAGTTCAAAGATTTACATTA
Found at i:17612215 original size:21 final size:22
Alignment explanation
Indices: 17612191--17612254 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
17612181 AAAGTTAAGG
17612191 ATATTCATTTAAAAAATTT-AA
1 ATATTCATTTAAAAAATTTCAA
* **
17612212 ATATTCACTTCCAAAATTTCAA
1 ATATTCATTTAAAAAATTTCAA
* *
17612234 AGATTTACATTAAAAAAATTT
1 ATA-TT-CATTTAAAAAATTT
17612255 TAGAGATTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 16 0.50
22 4 0.12
23 2 0.06
24 10 0.31
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATTCATTTAAAAAATTTCAA
Found at i:17613459 original size:16 final size:16
Alignment explanation
Indices: 17613440--17613470 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17613430 TTTCTCTTTT
17613440 TTTTTTTGCTTTTGCC
1 TTTTTTTGCTTTTGCC
*
17613456 TTTTTTTTCTTTTGC
1 TTTTTTTGCTTTTGC
17613471 TTTCATTTTT
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:0.00, C:0.16, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTTTTTGCTTTTGCC
Found at i:17613459 original size:17 final size:16
Alignment explanation
Indices: 17613439--17613470 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
17613429 TTTTCTCTTT
17613439 TTTTTTTTGCTTTTGCC
1 TTTTTTTT-CTTTTGCC
17613456 TTTTTTTTCTTTTGC
1 TTTTTTTTCTTTTGC
17613471 TTTCATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (16 bp):
TTTTTTTTCTTTTGCC
Found at i:17613821 original size:1 final size:1
Alignment explanation
Indices: 17613773--17613802 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
17613763 GCTCCATCAA
*
17613773 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17613803 GCACTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:17617091 original size:32 final size:32
Alignment explanation
Indices: 17617055--17617115 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
17617045 TACAAAGAAT
*
17617055 AATATATAAATATAAAGAACAACATAAAAAAC
1 AATATATAAATACAAAGAACAACATAAAAAAC
*
17617087 AATATATAAATACAAAGAACAATATAAAA
1 AATATATAAATACAAAGAACAACATAAAA
17617116 GGTTAGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.20
Consensus pattern (32 bp):
AATATATAAATACAAAGAACAACATAAAAAAC
Found at i:17618471 original size:3 final size:3
Alignment explanation
Indices: 17618463--17618490 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17618453 TAACAATTAC
17618463 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17618491 CATAGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17618540 original size:22 final size:18
Alignment explanation
Indices: 17618496--17618559 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 18
17618486 TAATACATAG
**
17618496 TAAAAAAATAAAAAAATG
1 TAAAAAAATAAAAAAAAA
* *
17618514 GAAAATAATAAGGAAAAAAA
1 TAAAAAAATAA--AAAAAAA
17618534 TAAAAAAATAAAAAGAAAA
1 TAAAAAAATAAAAA-AAAA
17618553 TAAAAAA
1 TAAAAAA
17618560 GAAAAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 12 0.32
19 11 0.30
20 14 0.38
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAAA
Found at i:17618558 original size:12 final size:12
Alignment explanation
Indices: 17618500--17618564 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
17618490 ACATAGTAAA
17618500 AAAATAAAAAAATGG
1 AAAAT-AAAAAA--G
* *
17618515 AAAATAATAAGG
1 AAAATAAAAAAG
17618527 AAAA-AAATAAA-
1 AAAATAAA-AAAG
17618538 AAAAT-AAAAAG
1 AAAATAAAAAAG
17618549 AAAATAAAAAAG
1 AAAATAAAAAAG
17618561 AAAA
1 AAAA
17618565 AACTTGCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 13 0.31
12 17 0.40
14 4 0.10
15 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (12 bp):
AAAATAAAAAAG
Found at i:17618564 original size:34 final size:36
Alignment explanation
Indices: 17618496--17618566 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 36
17618486 TAATACATAG
* *
17618496 TAAAAAAATAAAAAAATGGAAAATAATAAGGAAAAAAA
1 TAAAAAAAT-AAAAAA-GGAAAATAAAAAAGAAAAAAA
17618534 TAAAAAAAT-AAAAA-GAAAATAAAAAAGAAAAAA
1 TAAAAAAATAAAAAAGGAAAATAAAAAAGAAAAAA
17618567 CTTGCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 17 0.55
36 5 0.16
38 9 0.29
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.11
Consensus pattern (36 bp):
TAAAAAAATAAAAAAGGAAAATAAAAAAGAAAAAAA
Found at i:17627280 original size:23 final size:19
Alignment explanation
Indices: 17627232--17627271 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17627222 TTCTTGTAAA
17627232 GAAGGAAGAAAAAATTGAT
1 GAAGGAAGAAAAAATTGAT
17627251 GAAGGAAGAAAAAATTGAT
1 GAAGGAAGAAAAAATTGAT
17627270 GA
1 GA
17627272 GAACAGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (19 bp):
GAAGGAAGAAAAAATTGAT
Found at i:17630571 original size:25 final size:26
Alignment explanation
Indices: 17630537--17630597 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 26
17630527 TTTATAATCA
*
17630537 ATCAAAATTATTGTAATATTT-TCTT
1 ATCAAAATTATTGAAATATTTCTCTT
17630562 ATCAAAATTATTGAAATATTTCTCTT
1 ATCAAAATTATTGAAATATTTCTCTT
17630588 AT-AATAATTA
1 ATCAA-AATTA
17630598 GTCAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (26 bp):
ATCAAAATTATTGAAATATTTCTCTT
Found at i:17632632 original size:23 final size:23
Alignment explanation
Indices: 17632605--17632652 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17632595 AAAAGAATCG
* *
17632605 TAAAATTTATA-TAAACTATATAA
1 TAAAATTAATATTAAAATATA-AA
17632628 TAAAATTAATATTAAAATATAAA
1 TAAAATTAATATTAAAATATAAA
17632651 TA
1 TA
17632653 TTTATATCAC
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:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATTAATATTAAAATATAAA
Found at i:17633086 original size:20 final size:21
Alignment explanation
Indices: 17633058--17633101 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
17633048 GAAAGAGGAT
*
17633058 AAGAAAGAAAGATGGGAG-GC
1 AAGAAAGAAAGATGAGAGAGC
*
17633078 AAGATAGAAAGATGAGAGAGC
1 AAGAAAGAAAGATGAGAGAGC
17633099 AAG
1 AAG
17633102 GGAACGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.52, C:0.05, G:0.36, T:0.07
Consensus pattern (21 bp):
AAGAAAGAAAGATGAGAGAGC
Found at i:17644359 original size:17 final size:16
Alignment explanation
Indices: 17644338--17644368 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17644328 TCGAGCTTGA
17644338 AAAAAAAAGAAAAAAT
1 AAAAAAAAGAAAAAAT
17644354 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
17644369 GTTTAGCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAT
Found at i:17647180 original size:413 final size:413
Alignment explanation
Indices: 17646413--17647231 Score: 1593
Period size: 413 Copynumber: 2.0 Consensus size: 413
17646403 TTTTTGTTAG
17646413 ATTTTGTAGTAAACTTGTTGATTTAGCTTACCTTAGCTTTACTCAAGTTCATTTTCTCTAGAAAA
1 ATTTTGTAGTAAACTTGTTGATTTAGCTTACCTTAGCTTTACTCAAGTTCATTTTCTCTAGAAAA
*
17646478 TTTCAGATCTAAATTTTTTTCTATTCAATCAATAATTAATAAGCTAAAATCAGTTTCTGTTTTAC
66 TTTCAGATCTAAATTTTTTTCTATTCAATCAATAATTAATAAGCTAAAATCAGTTTATGTTTTAC
17646543 ACTTTTACTTATTGATTCTTGTAATTCCTTCCAATTTTTGTTCTCCAATTTAGTTTTTCATGTTG
131 ACTTTTACTTATTGATTCTTGTAATTCCTTCCAATTTTTGTTCTCCAATTTAGTTTTTCATGTTG
17646608 TTCCTTCAATTTACTATCAATTTTCAGTTCATATTCATTTGATTTTACATGAATTAAATCTAAAT
196 TTCCTTCAATTTACTATCAATTTTCAGTTCATATTCATTTGATTTTACATGAATTAAATCTAAAT
17646673 TTGCAGTTTGAAGTTCTAGTTTCCAGATTTCACTATACTTTCGATTTTCATGTTCTAGCTTAGAT
261 TTGCAGTTTGAAGTTCTAGTTTCCAGATTTCACTATACTTTCGATTTTCATGTTCTAGCTTAGAT
17646738 TTTACAACTTTTTTTATTGCTTGCATTTCAAATCTATTTTTACTTTAAATTATGTTCAGTTCATT
326 TTTACAACTTTTTTTATTGCTTGCATTTCAAATCTATTTTTACTTTAAATTATGTTCAGTTCATT
17646803 ACATTTTAATTTACTTTAAATAT
391 ACATTTTAATTTACTTTAAATAT
*
17646826 ATTTTGTAGTAAACTTGTTGATTTAGCTTACCTTAGCTTTATTCAAGTTCATTTTCTCTAGAAAA
1 ATTTTGTAGTAAACTTGTTGATTTAGCTTACCTTAGCTTTACTCAAGTTCATTTTCTCTAGAAAA
17646891 TTTCAGATCTAAATTTTTTTCTATTCAATCAATAATTAATAAGCTAAAATCAGTTTATGTTTTAC
66 TTTCAGATCTAAATTTTTTTCTATTCAATCAATAATTAATAAGCTAAAATCAGTTTATGTTTTAC
*
17646956 ACTTTTACTTATTGATTCTTGTAATTCCTTCCAATTTTTGTTCTTCAATTTAGTTTTTCATGTTG
131 ACTTTTACTTATTGATTCTTGTAATTCCTTCCAATTTTTGTTCTCCAATTTAGTTTTTCATGTTG
17647021 TTCCTTCAATTTACTATCAATTTTCAGTTCATATTCATTTGATTTTACATGAATTAAATCTAAAT
196 TTCCTTCAATTTACTATCAATTTTCAGTTCATATTCATTTGATTTTACATGAATTAAATCTAAAT
* *
17647086 TTGCAGTTTGAAGTTCTAGTTTTCAGATTTCACTATACTTTTGATTTTCATGTTCTAGCTTAGAT
261 TTGCAGTTTGAAGTTCTAGTTTCCAGATTTCACTATACTTTCGATTTTCATGTTCTAGCTTAGAT
17647151 TTTACAACTTTTTTTATTGCTTGCATTTCAAATCTATTTTTACTTTAAATTATGTTCAGTTCATT
326 TTTACAACTTTTTTTATTGCTTGCATTTCAAATCTATTTTTACTTTAAATTATGTTCAGTTCATT
17647216 ACATTTTAATTTACTT
391 ACATTTTAATTTACTT
17647232 ACTATTTTTG
Statistics
Matches: 401, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
413 401 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.50
Consensus pattern (413 bp):
ATTTTGTAGTAAACTTGTTGATTTAGCTTACCTTAGCTTTACTCAAGTTCATTTTCTCTAGAAAA
TTTCAGATCTAAATTTTTTTCTATTCAATCAATAATTAATAAGCTAAAATCAGTTTATGTTTTAC
ACTTTTACTTATTGATTCTTGTAATTCCTTCCAATTTTTGTTCTCCAATTTAGTTTTTCATGTTG
TTCCTTCAATTTACTATCAATTTTCAGTTCATATTCATTTGATTTTACATGAATTAAATCTAAAT
TTGCAGTTTGAAGTTCTAGTTTCCAGATTTCACTATACTTTCGATTTTCATGTTCTAGCTTAGAT
TTTACAACTTTTTTTATTGCTTGCATTTCAAATCTATTTTTACTTTAAATTATGTTCAGTTCATT
ACATTTTAATTTACTTTAAATAT
Found at i:17658801 original size:21 final size:20
Alignment explanation
Indices: 17658777--17658816 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
17658767 TTTTTTATAT
17658777 TTAT-CATATTTAAAATAAAAA
1 TTATGCATA-TTAAAA-AAAAA
17658798 TTATGCATATTAAAAAAAA
1 TTATGCATATTAAAAAAAA
17658817 GTTGAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (20 bp):
TTATGCATATTAAAAAAAAA
Found at i:17663035 original size:19 final size:19
Alignment explanation
Indices: 17663011--17663047 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17663001 GATGGAATGA
*
17663011 AATAGTTTTAAATTTTAAG
1 AATAGTATTAAATTTTAAG
17663030 AATAGTATTAAATTTTAA
1 AATAGTATTAAATTTTAA
17663048 ACAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
AATAGTATTAAATTTTAAG
Found at i:17663931 original size:22 final size:23
Alignment explanation
Indices: 17663883--17663935 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
17663873 AAAATAAAAG
17663883 TTAT-ATT-TTAAAATTATATAT
1 TTATAATTATTAAAATTATATAT
*
17663904 TT-TAATTATTAAAATTTTAT-T
1 TTATAATTATTAAAATTATATAT
17663925 TTATAA-TATTA
1 TTATAATTATTA
17663936 CTACTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 13 0.46
22 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATAATTATTAAAATTATATAT
Found at i:17675355 original size:25 final size:25
Alignment explanation
Indices: 17675323--17675373 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
17675313 ACCGGTATAT
17675323 TAATCAAACTAGATTTTATACCTTA
1 TAATCAAACTAGATTTTATACCTTA
*
17675348 TAATCAAACTTGATTTTATACCTTA
1 TAATCAAACTAGATTTTATACCTTA
17675373 T
1 T
17675374 TTTGTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (25 bp):
TAATCAAACTAGATTTTATACCTTA
Found at i:17677782 original size:20 final size:20
Alignment explanation
Indices: 17677757--17677794 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17677747 GATGGAATGA
*
17677757 AATAGTTTTAAATTTTAAGT
1 AATAGTATTAAATTTTAAGT
17677777 AATAGTATTAAATTTTAA
1 AATAGTATTAAATTTTAA
17677795 ACAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
AATAGTATTAAATTTTAAGT
Found at i:17677949 original size:12 final size:12
Alignment explanation
Indices: 17677932--17677959 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17677922 TACCATAAAA
17677932 AAATTTAATTTT
1 AAATTTAATTTT
17677944 AAATTTAATTTT
1 AAATTTAATTTT
17677956 AAAT
1 AAAT
17677960 AACTATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATTTAATTTT
Found at i:17678663 original size:22 final size:21
Alignment explanation
Indices: 17678636--17678681 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
17678626 AGTTATTATT
17678636 TTAAAATTATATATTTA-AATTA
1 TTAAAATTATAT-TTTATAA-TA
*
17678658 TTAAAATTTTATTTTATAATA
1 TTAAAATTATATTTTATAATA
17678679 TTA
1 TTA
17678682 CTACTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAAATTATATTTTATAATA
Found at i:17679234 original size:5 final size:5
Alignment explanation
Indices: 17679224--17679257 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
17679214 TTGAACTTGG
*
17679224 GTTTA GTTTA GTTTA ATTTA GTTTA G-TTA GTTTA
1 GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA GTTTA
17679258 TAGCATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (5 bp):
GTTTA
Found at i:17683340 original size:16 final size:16
Alignment explanation
Indices: 17683319--17683353 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17683309 CTCTAACTTT
* *
17683319 TAATTCAATCAAGTAC
1 TAATTCAATAAAATAC
17683335 TAATTCAATAAAATAC
1 TAATTCAATAAAATAC
17683351 TAA
1 TAA
17683354 AAATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (16 bp):
TAATTCAATAAAATAC
Found at i:17684029 original size:26 final size:26
Alignment explanation
Indices: 17684000--17684050 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
17683990 TGCTATTATT
17684000 TTTAATTTAATTTAATTTTCTTAATC
1 TTTAATTTAATTTAATTTTCTTAATC
* * *
17684026 TTTATTTTATTTTAATTTTTTTAAT
1 TTTAATTTAATTTAATTTTCTTAAT
17684051 TTTTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTAATTTAATTTAATTTTCTTAATC
Found at i:17685037 original size:22 final size:24
Alignment explanation
Indices: 17684982--17685039 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
17684972 TTAGTTTAAG
*
17684982 TTTTT-TTTTTTTATATTTTCTTA
1 TTTTTATTTTATTATATTTTCTTA
*
17685005 TTTTTA--CTATTATA-TTT-TTA
1 TTTTTATTTTATTATATTTTCTTA
17685025 TTTTTATTTTATTAT
1 TTTTTATTTTATTAT
17685040 TATGAATGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 9 0.31
21 3 0.10
22 12 0.41
23 5 0.17
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTATTTTATTATATTTTCTTA
Found at i:17692102 original size:73 final size:73
Alignment explanation
Indices: 17691981--17692126 Score: 204
Period size: 73 Copynumber: 2.0 Consensus size: 73
17691971 CTACTAGTAA
* * * * *
17691981 GCAAGTCCTTAACCACCTTATACGTAGAAGTTGCTGAAGAGGCGTTGGAATGTTCTTTTAGACCT
1 GCAAGTCCTTAACCACATTATACATAGAAGCTGCTGAAGAGGCATTGGAATGTTCCTTTAGACCT
17692046 TTTGAATT
66 TTTGAATT
* * *
17692054 GCAAG-CCTTTAACCACATTGTACATAGAAGCTGTTGAAGAGGCATTGGAATGTTCCTTTAGATC
1 GCAAGTCC-TTAACCACATTATACATAGAAGCTGCTGAAGAGGCATTGGAATGTTCCTTTAGACC
17692118 TTTTGAATT
65 TTTTGAATT
17692127 TACTAATGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 2 0.03
73 62 0.97
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (73 bp):
GCAAGTCCTTAACCACATTATACATAGAAGCTGCTGAAGAGGCATTGGAATGTTCCTTTAGACCT
TTTGAATT
Found at i:17693267 original size:23 final size:24
Alignment explanation
Indices: 17693218--17693270 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
17693208 CACAGTGCAG
*
17693218 CAACCATTACCCTTGCACATTGAC
1 CAACCATTACCCTTACACATTGAC
*
17693242 CAACCATTACCC-TACACATTGCC
1 CAACCATTACCCTTACACATTGAC
17693265 CAACCA
1 CAACCA
17693271 CCATCTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.32, C:0.42, G:0.06, T:0.21
Consensus pattern (24 bp):
CAACCATTACCCTTACACATTGAC
Found at i:17694307 original size:21 final size:21
Alignment explanation
Indices: 17694281--17694327 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17694271 TTGCCAAACT
17694281 AAAAAAGATAAAGAG-AGAAAA
1 AAAAAAGA-AAAGAGAAGAAAA
* *
17694302 AAAAAAGAGAAGGGAAGAAAA
1 AAAAAAGAAAAGAGAAGAAAA
17694323 AAAAA
1 AAAAA
17694328 GGTAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAGAGAAGAAAA
Found at i:17700350 original size:46 final size:45
Alignment explanation
Indices: 17700195--17700362 Score: 167
Period size: 46 Copynumber: 3.7 Consensus size: 45
17700185 TTTAGATAAA
* * *
17700195 ATTTTTAAAGTTGTTGGGCCTTTAATGAGAGGACCCTTTT-AATTTG
1 ATTTTTAAAGTTGTTGAGCCTTTAATAAGAGGA--GTTTTCAATTTG
* ** * ** *
17700241 ATTTTTAGAGTTGTCAACCCTTTAATAAGAGGAGCATTCTAGTTTG
1 ATTTTTAAAGTTGTTGAGCCTTTAATAAGAGGAGTTTTC-AATTTG
*
17700287 ATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGAGTTTTTCAATTTG
1 ATTTTTAAAGTTGTTGAGCCTTTAATAAGAGGAG-TTTTCAATTTG
* * *
17700333 ATTTTTAAAGTTATTGAGCCTCTGATAAGA
1 ATTTTTAAAGTTGTTGAGCCTTTAATAAGA
17700363 AAAGCCTTTT
Statistics
Matches: 97, Mismatches: 22, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
44 2 0.02
46 92 0.95
47 3 0.03
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (45 bp):
ATTTTTAAAGTTGTTGAGCCTTTAATAAGAGGAGTTTTCAATTTG
Found at i:17700361 original size:92 final size:92
Alignment explanation
Indices: 17700195--17700386 Score: 224
Period size: 92 Copynumber: 2.1 Consensus size: 92
17700185 TTTAGATAAA
* * * * *
17700195 ATTTTTAAAGTTGTTGGGCCTTTAATGAGAGGACCCTTTTAATTTGATTTTTAGAGTTGTCAACC
1 ATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGACCCTTTTAATTTGATTTTTAAAGTTATCAACC
* **
17700260 CTTTAATAAGAGGAGCATTCTAGTTTG
66 CTCTAATAAGAAAAGCATTCTAGTTTG
** ** *
17700287 ATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGA-GTTTTTCAATTTGATTTTTAAAGTTATTGAG
1 ATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGACCCTTTT-AATTTGATTTTTAAAGTTATCAAC
* * *
17700351 CCTCTGATAAGAAAAGCCTTTTAGTTTG
65 CCTCTAATAAGAAAAGCATTCTAGTTTG
17700379 ATTTTAAA
1 ATTTTAAA
17700387 GTTTTCTGAG
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
91 4 0.05
92 79 0.95
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (92 bp):
ATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGACCCTTTTAATTTGATTTTTAAAGTTATCAACC
CTCTAATAAGAAAAGCATTCTAGTTTG
Found at i:17700379 original size:46 final size:45
Alignment explanation
Indices: 17700230--17700585 Score: 134
Period size: 46 Copynumber: 7.6 Consensus size: 45
17700220 TGAGAGGACC
* * * ** * * **
17700230 CTTTTAATTTGATTTTTAGAGTTGTCAACCCTTTAATAAGAGGAG
1 CTTTTAGTTTGATTTTTAAAGTTATTGAGCCTCTAATAAGAAAAG
* * * * **
17700275 CATTCTAGTTTGATTTTAAAAGTTGTTGAGCCTTTAATAAGAGGAG
1 C-TTTTAGTTTGATTTTTAAAGTTATTGAGCCTCTAATAAGAAAAG
* * *
17700321 TTTTTCAATTTGATTTTTAAAGTTATTGAGCCTCTGATAAGAAAAG
1 CTTTT-AGTTTGATTTTTAAAGTTATTGAGCCTCTAATAAGAAAAG
* *
17700367 CCTTTTAGTTTGA-TTTTAAAGTTTTCTGAGCAAGATTCATAAGTCATCTAGAAAA-
1 -CTTTTAGTTTGATTTTTAAAGTTAT-TGAGC----CTC-TAA-T-A---AGAAAAG
** * * * ** * *
17700422 --AATACTTTAAAATTTTAAAGCTT-TCAAGCCTCTAATTAGATAAG
1 CTTTTAGTTT-GATTTTTAAAG-TTATTGAGCCTCTAATAAGAAAAG
*
17700466 CATTTCAGTTTGATTTTTAAAAGTTATTGAGCCTCTAATGAAAGAAGAA-
1 C-TTTTAGTTTGATTTTT-AAAGTTATTGAGCCTCTAAT--AAGAA-AAG
* *
17700515 -TTTTAGTTTGATTTTTAAAAGTTGTTGAGCCTTTAATAAGAAGAA-
1 CTTTTAGTTTGATTTTT-AAAGTTATTGAGCCTCTAATAAGAA-AAG
* *
17700560 CATTCAGTTTGATTTTTAAAAGTTAT
1 CTTTTAGTTTGATTTTT-AAAGTTAT
17700586 CGAACCTTTA
Statistics
Matches: 238, Mismatches: 46, Indels: 53
0.71 0.14 0.16
Matches are distributed among these distances:
43 5 0.02
45 23 0.10
46 110 0.46
47 58 0.24
48 3 0.01
49 5 0.02
50 4 0.02
51 2 0.01
52 6 0.03
53 5 0.02
54 9 0.04
55 2 0.01
56 6 0.03
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (45 bp):
CTTTTAGTTTGATTTTTAAAGTTATTGAGCCTCTAATAAGAAAAG
Found at i:17700502 original size:47 final size:46
Alignment explanation
Indices: 17700448--17700585 Score: 172
Period size: 47 Copynumber: 3.0 Consensus size: 46
17700438 AAAGCTTTCA
*
17700448 AGCCTCTAATTAGATAAGCATTTCAGTTTGATTTTTAAAAGTTATTG
1 AGCCTCTAATAAGA-AAGCATTTCAGTTTGATTTTTAAAAGTTATTG
* * *
17700495 AGCCTCTAATGAA-AGAAGAATTTTAGTTTGATTTTTAAAAGTTGTTG
1 AGCCTCTAAT-AAGA-AAGCATTTCAGTTTGATTTTTAAAAGTTATTG
* *
17700542 AGCCTTTAATAAGAAGAACA-TTCAGTTTGATTTTTAAAAGTTAT
1 AGCCTCTAATAAGAA-AGCATTTCAGTTTGATTTTTAAAAGTTAT
17700586 CGAACCTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
46 25 0.32
47 52 0.67
48 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (46 bp):
AGCCTCTAATAAGAAAGCATTTCAGTTTGATTTTTAAAAGTTATTG
Found at i:17700594 original size:46 final size:46
Alignment explanation
Indices: 17700469--17700597 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 46
17700459 AGATAAGCAT
* *
17700469 TTCAGTTTGATTTTTAAAAGTTATTGAGCCTCTAATGAAAGAAGAAT
1 TTCAGTTTGATTTTTAAAAGTTATTGAGCCTTTAAT-AAAGAAGAAA
* *
17700516 TTTAGTTTGATTTTTAAAAGTTGTTGAGCCTTTAAT-AAGAAGAACA
1 TTCAGTTTGATTTTTAAAAGTTATTGAGCCTTTAATAAAGAAGAA-A
* *
17700562 TTCAGTTTGATTTTTAAAAGTTATCGAACCTTTAAT
1 TTCAGTTTGATTTTTAAAAGTTATTGAGCCTTTAAT
17700598 GAAATGAGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
45 8 0.11
46 32 0.44
47 33 0.45
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (46 bp):
TTCAGTTTGATTTTTAAAAGTTATTGAGCCTTTAATAAAGAAGAAA
Found at i:17701107 original size:25 final size:25
Alignment explanation
Indices: 17701066--17701115 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
17701056 TCTTTCATCT
17701066 TTATTTTATTTTGTTTTTGTTTTTG
1 TTATTTTATTTTGTTTTTGTTTTTG
* * *
17701091 TTATTTTGTTTCTTTTTTTTTTTTT
1 TTATTTTATTT-TGTTTTTGTTTTT
17701116 TGGTTCCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.06, C:0.02, G:0.08, T:0.84
Consensus pattern (25 bp):
TTATTTTATTTTGTTTTTGTTTTTG
Found at i:17704040 original size:28 final size:29
Alignment explanation
Indices: 17704009--17704076 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
17703999 ATTTATTTTT
* *
17704009 TAAAATAAAAT-AGAATAATAAAAA-ATAA
1 TAAAATAAAATCAAAACAA-AAAAATATAA
17704037 TAAAAATGAAAATCAAAACAAAAAAATATAA
1 T-AAAAT-AAAATCAAAACAAAAAAATATAA
17704068 -AAAATAAAA
1 TAAAATAAAA
17704077 AGCCAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 5 0.15
29 10 0.29
30 10 0.29
31 9 0.26
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (29 bp):
TAAAATAAAATCAAAACAAAAAAATATAA
Found at i:17704275 original size:10 final size:10
Alignment explanation
Indices: 17704260--17704297 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
17704250 TAAAATTATT
17704260 TTTTAATAAA
1 TTTTAATAAA
17704270 TTTTAATAAA
1 TTTTAATAAA
17704280 TTTT-A-AAA
1 TTTTAATAAA
*
17704288 TTTTATTAAA
1 TTTTAATAAA
17704298 AAAATAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:17713851 original size:3 final size:3
Alignment explanation
Indices: 17713845--17713880 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
17713835 CGAAAAAAAT
17713845 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
17713881 TTGGTTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17721885 original size:21 final size:23
Alignment explanation
Indices: 17721859--17721910 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
17721849 CCAAAAAGAA
17721859 ATTATAAATAT-TAAAAT-TTAT
1 ATTATAAATATATAAAATGTTAT
*
17721880 ATTATAAATATATTAAATGTTAT
1 ATTATAAATATATAAAATGTTAT
*
17721903 ATTTTAAA
1 ATTATAAA
17721911 AATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
22 5 0.19
23 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTATAAATATATAAAATGTTAT
Found at i:17721896 original size:23 final size:22
Alignment explanation
Indices: 17721859--17721911 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
17721849 CCAAAAAGAA
17721859 ATTAT-AAATATTAAAAT-TTAT
1 ATTATAAAATATT-AAATGTTAT
17721880 ATTATAAATATATTAAATGTTAT
1 ATTATAAA-ATATTAAATGTTAT
*
17721903 ATTTTAAAA
1 ATTATAAAA
17721912 ATAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.18
22 7 0.25
23 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTATAAAATATTAAATGTTAT
Found at i:17726813 original size:26 final size:26
Alignment explanation
Indices: 17726765--17726823 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
17726755 TTTTTTTTTC
* *
17726765 ATTTATTTTGTATATTTCAAAATTAT
1 ATTTTTTTTGAATATTTCAAAATTAT
* *
17726791 ATTATTTTTTGAATATTT-TAAATTTT
1 ATT-TTTTTTGAATATTTCAAAATTAT
17726817 ATTTTTT
1 ATTTTTT
17726824 ATCTGTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTTTTTTGAATATTTCAAAATTAT
Found at i:17737770 original size:31 final size:31
Alignment explanation
Indices: 17737735--17737797 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
17737725 ATAAACTTTG
*
17737735 TGTCATAGCAATAAAATTATTGTATTTGTTT
1 TGTCATAGAAATAAAATTATTGTATTTGTTT
*
17737766 TGTCATAGAAATAGAATTATTGTATTTGTTT
1 TGTCATAGAAATAAAATTATTGTATTTGTTT
17737797 T
1 T
17737798 CCTGTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (31 bp):
TGTCATAGAAATAAAATTATTGTATTTGTTT
Found at i:17740672 original size:24 final size:24
Alignment explanation
Indices: 17740622--17740685 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 24
17740612 TATTAATATA
17740622 ATTATTAAAATATTTAAAATTTGTT
1 ATTATTAAAATA-TTAAAATTTGTT
17740647 ATTATTAAAATATTAAAATTAT-TT
1 ATTATTAAAATATTAAAATT-TGTT
*
17740671 ATTATTAAATTATTA
1 ATTATTAAAATATTA
17740686 TGTATTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 24 0.65
25 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATTAAAATATTAAAATTTGTT
Found at i:17740691 original size:15 final size:16
Alignment explanation
Indices: 17740657--17740720 Score: 51
Period size: 18 Copynumber: 3.8 Consensus size: 16
17740647 ATTATTAAAA
17740657 TATTAAAATTATTTAT
1 TATTAAAATTATTTAT
*
17740673 TATTAAATTATTATGTAT
1 TATTAAA--ATTATTTAT
*
17740691 T-TTAATAATAATATTTAA
1 TATTAA-AAT--TATTTAT
17740709 TATT-AAATTATT
1 TATTAAAATTATT
17740721 AAGTTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
15 4 0.10
16 9 0.23
17 7 0.18
18 17 0.44
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTAAAATTATTTAT
Found at i:17740753 original size:25 final size:26
Alignment explanation
Indices: 17740670--17740753 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 26
17740660 TAAAATTATT
* *
17740670 TATTATTAAATTATTATGTATTTTAATAA
1 TATTATTTAA-TATTA-ATATTTTAA-AA
* **
17740699 TAATATTTAATATTAA-ATTATTAAGT
1 TATTATTTAATATTAATATT-TTAAAA
*
17740725 TATTATTT-ATGTTAATATTTTAAAA
1 TATTATTTAATATTAATATTTTAAAA
17740750 TATT
1 TATT
17740754 TAAAATAGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
25 14 0.32
26 13 0.30
27 4 0.09
28 5 0.11
29 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TATTATTTAATATTAATATTTTAAAA
Found at i:17741040 original size:17 final size:17
Alignment explanation
Indices: 17741018--17741068 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
17741008 AAAATAGTCA
17741018 TATTATTAAACTAATAT
1 TATTATTAAACTAATAT
17741035 TATTATATAAAC-AATAT
1 TATTAT-TAAACTAATAT
*
17741052 TAATTATTAAAATAATA
1 T-ATTATTAAACTAATA
17741069 AAAATTACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTATTAAACTAATAT
Found at i:17741560 original size:14 final size:14
Alignment explanation
Indices: 17741501--17741561 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
17741491 GATTTAAATT
17741501 AAATTATATTTAAAA
1 AAATT-TATTTAAAA
* *
17741516 ATATCTTATTTATAA
1 AAAT-TTATTTAAAA
* * **
17741531 ATAGTTATTTTTAA
1 AAATTTATTTAAAA
17741545 AAATTTATTTAAAA
1 AAATTTATTTAAAA
17741559 AAA
1 AAA
17741562 GATAATTTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 22 0.59
15 14 0.38
16 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
AAATTTATTTAAAA
Found at i:17741584 original size:15 final size:15
Alignment explanation
Indices: 17741503--17741585 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
17741493 TTTAAATTAA
17741503 ATTATATTTAAAAATAT
1 ATTAT-TTTAAAAA-AT
* *
17741520 CTTA-TTT-ATAAAT
1 ATTATTTTAAAAAAT
*
17741533 AGTTATTTTTAAAAAT
1 A-TTATTTTAAAAAAT
* *
17741549 -TTATTTAAAAAAAG
1 ATTATTTTAAAAAAT
* *
17741563 ATAATTTTCAAAAAT
1 ATTATTTTAAAAAAT
17741578 ATTATTTT
1 ATTATTTT
17741586 TTATCAATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
13 2 0.04
14 17 0.34
15 23 0.46
16 5 0.10
17 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
ATTATTTTAAAAAAT
Found at i:17742036 original size:18 final size:16
Alignment explanation
Indices: 17742003--17742033 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17741993 CCAAAAAACC
17742003 CCTTTTTTTTTCTCTT
1 CCTTTTTTTTTCTCTT
*
17742019 CCTTTCTTTTTCTCT
1 CCTTTTTTTTTCTCT
17742034 CTTTCGATAT
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:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
CCTTTTTTTTTCTCTT
Found at i:17744380 original size:7 final size:7
Alignment explanation
Indices: 17744365--17744394 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
17744355 TTCGATCTGC
17744365 AAAAGAA
1 AAAAGAA
*
17744372 AAAAAAA
1 AAAAGAA
17744379 AAAAGAA
1 AAAAGAA
17744386 AAAAGAA
1 AAAAGAA
17744393 AA
1 AA
17744395 TTACTTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:17745499 original size:35 final size:35
Alignment explanation
Indices: 17745425--17745500 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
17745415 TAGATACCCA
* * *
17745425 TATTTACTACGGGTGAATTCCAAAACTTGTTGCCG
1 TATTTACAACGGGTGAATTCCAAAACCTGGTGCCG
17745460 TATTTACAACGGGTGAATTCCAAAAACCTGGTGCC-
1 TATTTACAACGGGTGAATTCC-AAAACCTGGTGCCG
17745495 TATTTA
1 TATTTA
17745501 GATTCAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 26 0.70
36 11 0.30
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (35 bp):
TATTTACAACGGGTGAATTCCAAAACCTGGTGCCG
Found at i:17745803 original size:21 final size:21
Alignment explanation
Indices: 17745779--17745825 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
17745769 AACGTGGCTG
* *
17745779 TTGATTATGTTAACATGATAA
1 TTGATTATGTTAACATAACAA
*
17745800 TTGAATATGTTAACATAACAA
1 TTGATTATGTTAACATAACAA
17745821 TTGAT
1 TTGAT
17745826 AAAATTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (21 bp):
TTGATTATGTTAACATAACAA
Found at i:17745891 original size:31 final size:30
Alignment explanation
Indices: 17745855--17745946 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
17745845 TACAAATGAT
*
17745855 TTTTATATTTATATGAAATTTAAAATTTAG
1 TTTTATATTTATATGAAATTTAAAATTTAA
* * *
17745885 TCTTTATTTTTGTATAAAATTTAAAATTTAA
1 T-TTTATATTTATATGAAATTTAAAATTTAA
* *
17745916 TTATTATATTCATACGAAA-TTAAAATTTAA
1 TT-TTATATTTATATGAAATTTAAAATTTAA
17745946 T
1 T
17745947 CTCTCTAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 14 0.27
31 37 0.73
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
TTTTATATTTATATGAAATTTAAAATTTAA
Found at i:17746064 original size:19 final size:17
Alignment explanation
Indices: 17746001--17746065 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
17745991 AATATTAAAA
* *
17746001 TTTAAAAATATTTTAAT
1 TTTAATAATATATTAAT
*
17746018 TTCT-CTAATATATTAAT
1 TT-TAATAATATATTAAT
*
17746035 TTTATTAAATATAATTAAT
1 TTTAAT-AATAT-ATTAAT
17746054 TATTAATAATAT
1 T-TTAATAATAT
17746066 TATATTAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 15 0.39
18 6 0.16
19 12 0.32
20 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATAATATATTAAT
Found at i:17746072 original size:17 final size:17
Alignment explanation
Indices: 17746048--17746085 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17746038 ATTAAATATA
*
17746048 ATTA-ATTATTAATAAT
1 ATTATATTAATAATAAT
*
17746064 ATTATATTAATAATATT
1 ATTATATTAATAATAAT
17746081 ATTAT
1 ATTAT
17746086 CATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATTAATAATAAT
Found at i:17746078 original size:14 final size:14
Alignment explanation
Indices: 17746054--17746082 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17746044 TATAATTAAT
17746054 TATTAATAATATTA
1 TATTAATAATATTA
17746068 TATTAATAATATTA
1 TATTAATAATATTA
17746082 T
1 T
17746083 TATCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTAATAATATTA
Found at i:17746304 original size:20 final size:21
Alignment explanation
Indices: 17746274--17746313 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17746264 ACATGAAATT
17746274 AATATAGTAAAAATATATTAC
1 AATATAGTAAAAATATATTAC
*
17746295 AATA-AGTAAAAATTTATTA
1 AATATAGTAAAAATATATTA
17746314 AAAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AATATAGTAAAAATATATTAC
Found at i:17746933 original size:20 final size:21
Alignment explanation
Indices: 17746908--17746950 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
17746898 ACATTTATTT
17746908 TTTTAATAAATTTTTACT-TA
1 TTTTAATAAATTTTTACTATA
**
17746928 TTTTAATGTATTTTTACTATA
1 TTTTAATAAATTTTTACTATA
17746949 TT
1 TT
17746951 AATTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTAATAAATTTTTACTATA
Found at i:17747129 original size:29 final size:29
Alignment explanation
Indices: 17747097--17747173 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
17747087 ACTTTGATAT
17747097 ATTAATTTAAATTATTAATATTATAATTG
1 ATTAATTTAAATTATTAATATTATAATTG
* * *
17747126 ATTAATATAAA-TAATAATATTATTATTG
1 ATTAATTTAAATTATTAATATTATAATTG
* *
17747154 -TTAATATGATATTATTAATA
1 ATTAAT-TTAAATTATTAATA
17747174 ATTAATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.13
28 17 0.44
29 17 0.44
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTAATTTAAATTATTAATATTATAATTG
Found at i:17751336 original size:2 final size:2
Alignment explanation
Indices: 17751325--17751356 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17751315 CAGGTACTGC
17751325 AT AT -T 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 AT AT A
17751357 AACTAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17754478 original size:14 final size:14
Alignment explanation
Indices: 17754459--17754487 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17754449 TATTCAATTT
17754459 AAGATGTTGGCTAA
1 AAGATGTTGGCTAA
17754473 AAGATGTTGGCTAA
1 AAGATGTTGGCTAA
17754487 A
1 A
17754488 TGATACTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
AAGATGTTGGCTAA
Found at i:17759694 original size:25 final size:25
Alignment explanation
Indices: 17759666--17759736 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 25
17759656 ATATGAAACA
* *
17759666 TGAAAAATAAGAAGTATTAGGTGAT
1 TGAAAAATAAAAAATATTAGGTGAT
*
17759691 TGAAAAAAGTAAAAAATATTAGGTGTT
1 TG-AAAAA-TAAAAAATATTAGGTGAT
17759718 TGAAAAATGAAAAGAATAT
1 TGAAAAAT-AAAA-AATAT
17759737 CTCGAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.08
26 14 0.36
27 22 0.56
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (25 bp):
TGAAAAATAAAAAATATTAGGTGAT
Found at i:17759735 original size:27 final size:28
Alignment explanation
Indices: 17759674--17759736 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
17759664 CATGAAAAAT
17759674 AAGAAGTATTAGGTGATTGAAAAAAGTAA
1 AAGAA-TATTAGGTGATTGAAAAAAGTAA
* *
17759703 AA-AATATTAGGTGTTTGAAAAATG-AA
1 AAGAATATTAGGTGATTGAAAAAAGTAA
17759729 AAGAATAT
1 AAGAATAT
17759737 CTCGAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.13
27 23 0.74
28 2 0.06
29 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (28 bp):
AAGAATATTAGGTGATTGAAAAAAGTAA
Found at i:17762113 original size:21 final size:21
Alignment explanation
Indices: 17762074--17762113 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17762064 AAAGTGTATG
* * *
17762074 AATTAAATTAAATATTTAACT
1 AATTAAAATAAAAAATTAACT
17762095 AATTAAAATAAAAAATTAA
1 AATTAAAATAAAAAATTAA
17762114 TTTATACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTAAAATAAAAAATTAACT
Found at i:17763748 original size:19 final size:19
Alignment explanation
Indices: 17763724--17763760 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17763714 GTTACCCTAG
17763724 GTAGGAATACCAAATTAAA
1 GTAGGAATACCAAATTAAA
* *
17763743 GTAGGATTTCCAAATTAA
1 GTAGGAATACCAAATTAA
17763761 GGTAAGGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
GTAGGAATACCAAATTAAA
Found at i:17763770 original size:20 final size:19
Alignment explanation
Indices: 17763733--17763771 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
17763723 GGTAGGAATA
17763733 CCAAATTAAAGTAGGATTT
1 CCAAATTAAAGTAGGATTT
*
17763752 CCAAATTAAGGTAAGGATTT
1 CCAAATTAAAGT-AGGATTT
17763772 TAAAATTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
CCAAATTAAAGTAGGATTT
Found at i:17763777 original size:20 final size:19
Alignment explanation
Indices: 17763735--17763778 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17763725 TAGGAATACC
*
17763735 AAATTAAAGTAGGATTTCC
1 AAATTAAAGTAGGATTTCA
* *
17763754 AAATTAAGGTAAGGATTTTA
1 AAATTAAAGT-AGGATTTCA
17763774 AAATT
1 AAATT
17763779 GAGAAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (19 bp):
AAATTAAAGTAGGATTTCA
Found at i:17764589 original size:21 final size:20
Alignment explanation
Indices: 17764530--17764591 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
17764520 TACTTTTTAT
17764530 TTATAATAATAATTTTTACA
1 TTATAATAATAATTTTTACA
*
17764550 TT-TCCAAT-TTAATTATTTACA
1 TTAT--AATAATAATT-TTTACA
17764571 TTATAATAATATATTTTTACA
1 TTATAATAATA-ATTTTTACA
17764592 CTTGTTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
19 1 0.03
20 10 0.29
21 19 0.56
22 4 0.12
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATAATAATAATTTTTACA
Found at i:17764813 original size:215 final size:213
Alignment explanation
Indices: 17764516--17764904 Score: 516
Period size: 214 Copynumber: 1.8 Consensus size: 213
17764506 TTTTGGTTTG
* *
17764516 AAATTACTTTTTATTTATAATAATAATTTTTACATTTCCAATTTAATTATTTACATTATAATAAT
1 AAATTACTTTTTATTTATAATAATAATTTTTACATTTCCAACTTAATTATTTACATTAAAATAAT
* * **
17764581 ATATTTTTACACTTGTTCTTATATTTTATTATGTTTAAAAGTATCACAACTGTTT-TCTTATGGT
66 ATATTTTTACACTTGTTCTTATATTTCATTATATTTAAAAGTATCACAACT-TTTCT-TTAAAGT
**
17764645 GTTACAACACTTCTAATATATTTTAGGCCAAATGATACAAATTTTACGATTATTCTTATATTTTT
129 GTTACAACACTTCTAATATATTTTACACCAAATGATACAAATTTTACGATTATTCTTATATTTTT
17764710 ACATAAAAACTTTTTTTATT
194 ACATAAAAACTTTTTTTATT
*
17764730 AAATTATTTTTTAATTTATAATAATAATTTTTTTACATTGT-CAACTTAATTATTTACATTAAAA
1 AAATTACTTTTT-ATTTATAATAATAA--TTTTTACATT-TCCAACTTAATTATTTACATTAAAA
** * * *
17764794 TAAT-T-TTTTTATGCTTGTTCTTATATTTCATTATATTTATAATTATTACAACTTTTCTTTAAA
62 TAATATATTTTTACACTTGTTCTTATATTTCATTATATTTAAAAGTATCACAACTTTTCTTTAAA
* * * * * *
17764857 TTGTTACGATAGTTCTAATATATTTTACACCAAATTATACTAATTTTA
127 GTGTTACAACACTTCTAATATATTTTACACCAAATGATACAAATTTTA
17764905 TGACTATTTT
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
214 57 0.38
215 56 0.37
216 1 0.01
217 35 0.23
218 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.51
Consensus pattern (213 bp):
AAATTACTTTTTATTTATAATAATAATTTTTACATTTCCAACTTAATTATTTACATTAAAATAAT
ATATTTTTACACTTGTTCTTATATTTCATTATATTTAAAAGTATCACAACTTTTCTTTAAAGTGT
TACAACACTTCTAATATATTTTACACCAAATGATACAAATTTTACGATTATTCTTATATTTTTAC
ATAAAAACTTTTTTTATT
Found at i:17765717 original size:21 final size:20
Alignment explanation
Indices: 17765668--17765734 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
17765658 AGAGTAATTG
*
17765668 TTTAT-TTGTAATAATAATTCT
1 TTTATGTTGTAATAAT-ATT-A
*
17765689 TTTGTGTTGCATAA-AATATTA
1 TTTATGTTG--TAATAATATTA
*
17765710 TTTATGTTGTAATAATATTT
1 TTTATGTTGTAATAATATTA
17765730 TTTAT
1 TTTAT
17765735 ACTTGTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 3 0.08
20 11 0.29
21 12 0.32
22 6 0.16
23 3 0.08
24 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTATGTTGTAATAATATTA
Found at i:17765777 original size:217 final size:215
Alignment explanation
Indices: 17765293--17765789 Score: 476
Period size: 216 Copynumber: 2.3 Consensus size: 215
17765283 CAATAATATC
* * * * * * *
17765293 TTTTTACATTTTTTGTTACTTTTAATTATGTTTAAAATTATTAC-AATTTTTTGTTAAGGTGTAA
1 TTTTTACACTTGTTGTTACTTTTTATTATGTTT-AAATTATCACTACTTTTTT-TAAAGGTGTTA
* * *
17765357 CAAAACTTCTAACCATTTTACGTAAAATAATACAAATTCTACGATTTTCTCACCATTTTATATTA
64 CAAAACTTCTAAACATTTTACATAAAATAATACAAATTCTACGATTCTCTCACCATTTTATATTA
* * * * * **
17765422 ATTCTTATTTTTTGTTTAAATTATTTTTTATTTGTAATAATAATTTTTTTTATATTGCCAATTTA
129 AATCTTATTTTTGGTTTAAATAATTGTTTATTTGTAATAATAATTTCTTTTATATTGCCAAAATA
17765487 ATTATTTATATTATAACAAGTT
194 ATTATTTATATTATAACAAGTT
* *
17765509 TTTTTACGCTTGTTGTTACGTTTTATTACT-TTTAAGATTATCA-TAACTTTTTTTAAAGGTGTT
1 TTTTTACACTTGTTGTTACTTTTTATTA-TGTTTAA-ATTATCACT-ACTTTTTTTAAAGGTGTT
* * * * * *
17765572 ACAATACTTCTAAATATTTTACATCAAATAATATC-AATTTTATGATTACTCTCACCTTTTTTAT
63 ACAAAACTTCTAAACATTTTACATAAAATAATA-CAAATTCTACGATT-CTCTCACC-ATTTTAT
* * *
17765636 ATTAACAT-TTATTTTGTGGTTTAGAGTAATTGTTTATTTGTAATAATAA-TTCTTTTGTGTTGC
125 ATTAA-ATCTTATTTT-TGGTTTA-AATAATTGTTTATTTGTAATAATAATTTCTTTTATATTGC
* * * *
17765699 ATAAAAT-ATTATTTATGTTGTAATAA-TAT
187 -CAAAATAATTATTTATATTATAACAAGT-T
* *
17765728 TTTTTATACTTGTT-TT-TTTTTTATTATGTTTAGAATTATCACTACTTTTTGTTAAA-GTGTTA
1 TTTTTACACTTGTTGTTACTTTTTATTATGTTTA-AATTATCACTACTTTTT-TTAAAGGTGTTA
17765790 TGACACTTCC
Statistics
Matches: 229, Mismatches: 36, Indels: 31
0.77 0.12 0.10
Matches are distributed among these distances:
215 2 0.01
216 79 0.34
217 48 0.21
218 28 0.12
219 47 0.21
220 25 0.11
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (215 bp):
TTTTTACACTTGTTGTTACTTTTTATTATGTTTAAATTATCACTACTTTTTTTAAAGGTGTTACA
AAACTTCTAAACATTTTACATAAAATAATACAAATTCTACGATTCTCTCACCATTTTATATTAAA
TCTTATTTTTGGTTTAAATAATTGTTTATTTGTAATAATAATTTCTTTTATATTGCCAAAATAAT
TATTTATATTATAACAAGTT
Found at i:17766304 original size:214 final size:211
Alignment explanation
Indices: 17765928--17766623 Score: 644
Period size: 214 Copynumber: 3.2 Consensus size: 211
17765918 GGTTAATATG
*
17765928 TTTTTT-TTAGAATTATTTTTTATTTATAATAATAAATTTTTTATATTGTCAACTTATATTTACA
1 TTTTTTATT-GAATTATTTTTTATTTATAATAATAATTTTTTTATATTGTCAACTT-TA-TTACA
* * * * * * * * *
17765992 TTACAATAAAATATTTTACGTTTATTCTTACCATTTATTATGTTTAGAATTATATCACAA-GTTT
63 TTTCAATAATATTTTTTACATTTGTTATTA-CTTTTATTATGTTTAGAATT-T-TTACAATTTTT
* * * * * *
17766056 TTCTTAAGGTATTAGGACATTTTTAATATATTTTACACCAAATAATACCAATTTTATAATTATTC
125 TTCTTAAGGTATTACGATACTTTTAA-CTATTTTACATCAAATAATACTAATTTTATAATTATTC
17766121 TCACATTTTTATATTAACACTTA
189 TCACATTTTTATATTAACACTTA
** * **
17766144 TTTTTTAATTGAATTATTTTTTCATTTATAATTCTAATTTTTTTATGTTACCAA-TTTATTACAT
1 TTTTTT-ATTGAATTATTTTTT-ATTTATAATAATAATTTTTTTATATTGTCAACTTTATTACAT
*
17766208 TTCAATAATATTTGTTTACATTTGTTGTTACTTTTTATTATGTTTAGAATTTTTACAATTTTTTT
64 TTCAATAATATTT-TTTACATTTGTTATTAC-TTTTATTATGTTTAGAATTTTTACAATTTTTTT
* * * *
17766273 CTTAAGGTATAACGATACTTTTAACTATTTTACATTAAATAATACTAATTTTATAACTATTTTCA
127 CTTAAGGTATTACGATACTTTTAACTATTTTACATCAAATAATACTAATTTTATAATTATTCTCA
** * *
17766338 C-TATTTTACGTTAACTCCTA
192 CAT-TTTTATATTAACACTTA
* * * * * * *
17766358 GTTTTTTATTTAATTTTTTTTTGTTTGTAATAATTATTTTTTTATATTGTCAACTTAATTATTTA
1 -TTTTTTATTGAATTATTTTTTATTTATAATAATAATTTTTTTATATTGTCAACTTTATTA--CA
* * * * * *
17766423 TGTTATAATAATATTTTTTATATTTGTTATTAACTTTCATTATGTTTAAAAGTATTACAATGTTT
63 T-TT-CAATAATATTTTTTACATTTGTTATT-ACTTTTATTATGTTTAGAATTTTTACAAT-TTT
* * * * ** *
17766488 TTTTTTAAAGGTATTATGATGCTTTTTACTATTTTATGTCAAATAATACTAATTTTATAATTACT
124 TTTCTT-AAGGTATTACGATACTTTTAACTATTTTACATCAAATAATACTAATTTTATAATTATT
* *
17766553 CTCACATTTTTTATACTAACACTTT
188 CTCACA-TTTTTATATTAACACTTA
* ** * *
17766578 TTTTTTGTTTAGAATTATTAATTATTTGTAATAATAATTCTTTTAT
1 TTTTTT-ATT-GAATTATTTTTTATTTATAATAATAATTTTTTTAT
17766624 GTTGCCAAAA
Statistics
Matches: 387, Mismatches: 73, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
213 24 0.06
214 73 0.19
215 49 0.13
216 41 0.11
217 52 0.13
218 47 0.12
219 59 0.15
220 13 0.03
221 29 0.07
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.54
Consensus pattern (211 bp):
TTTTTTATTGAATTATTTTTTATTTATAATAATAATTTTTTTATATTGTCAACTTTATTACATTT
CAATAATATTTTTTACATTTGTTATTACTTTTATTATGTTTAGAATTTTTACAATTTTTTTCTTA
AGGTATTACGATACTTTTAACTATTTTACATCAAATAATACTAATTTTATAATTATTCTCACATT
TTTATATTAACACTTA
Found at i:17766513 original size:24 final size:24
Alignment explanation
Indices: 17766467--17766514 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17766457 TTTCATTATG
*
17766467 TTTAAAAGTATTACAATGTTTTTT
1 TTTAAAAGTATTACAATGCTTTTT
* **
17766491 TTTAAAGGTATTATGATGCTTTTT
1 TTTAAAAGTATTACAATGCTTTTT
17766515 ACTATTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.54
Consensus pattern (24 bp):
TTTAAAAGTATTACAATGCTTTTT
Found at i:17766656 original size:20 final size:22
Alignment explanation
Indices: 17766607--17766664 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
17766597 AATTATTTGT
*
17766607 AATAATAATTCTTTTATGTTGCC
1 AATAATAATT-TTTTATGTTGAC
*
17766630 AAAAAT-ATTTTTTATGTT-AC
1 AATAATAATTTTTTATGTTGAC
17766650 AATAATAATTTTTTA
1 AATAATAATTTTTTA
17766665 CACTTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 6 0.19
21 17 0.55
22 3 0.10
23 5 0.16
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AATAATAATTTTTTATGTTGAC
Found at i:17769157 original size:32 final size:31
Alignment explanation
Indices: 17769092--17769157 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
17769082 GAAAGATGAG
* *
17769092 AAAAAAAAAGAAAAAAAATGGTGAAATGTAAA
1 AAAAAAAAAGAAAAAAAAAGGTAAAATG-AAA
*
17769124 AAATAAAAAGAAAAAAAAAGG-AAAATGAAA
1 AAAAAAAAAGAAAAAAAAAGGTAAAATGAAA
17769154 AAAA
1 AAAA
17769158 GAGAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.20
31 5 0.17
32 19 0.63
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (31 bp):
AAAAAAAAAGAAAAAAAAAGGTAAAATGAAA
Found at i:17769165 original size:17 final size:16
Alignment explanation
Indices: 17769121--17769165 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
17769111 GGTGAAATGT
*
17769121 AAAAAATAAAAAGAAA
1 AAAAAAGAAAAAGAAA
*
17769137 AAAAAAGGAAAATGAAA
1 AAAAAA-GAAAAAGAAA
*
17769154 AAAAGAGAAAAA
1 AAAAAAGAAAAA
17769166 AAAGATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:17770360 original size:22 final size:22
Alignment explanation
Indices: 17770326--17770382 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
17770316 GAATATTTTG
* *
17770326 ATGAAAATTTTTGAGAACTC-AA
1 ATGAGAATCTTTGAG-ACTCAAA
**
17770348 ATGAGAATCTTTGAGTTTCAAA
1 ATGAGAATCTTTGAGACTCAAA
17770370 ATGAGAATCTTTG
1 ATGAGAATCTTTG
17770383 GGGAGTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
ATGAGAATCTTTGAGACTCAAA
Found at i:17771030 original size:43 final size:43
Alignment explanation
Indices: 17770971--17771230 Score: 333
Period size: 43 Copynumber: 6.0 Consensus size: 43
17770961 TAGATGAGCC
* * * *
17770971 ATTTATTTTTTCAAAGTCATTGAACCTCTAAGTAGAGGAGCTTT
1 ATTTA-TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
* * * * *
17771015 ATTTATTTTTAAAAGTTGTTGAGCCTCTGTTTAGAAGAGTTTT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
*
17771058 ATTTATTTTTCAAAGTCGTTGACCCTCTGATTAGAGGAGCTTT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
*
17771101 ATTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
* * *
17771144 ATTCA-TTTTCAAAGTCGTTAAGCCTCTGATTAAAGGAGCTTT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
* * *
17771186 GTTTATGTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAGAAGCTTT
1 ATTTA--TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
17771231 GATCAAAATT
Statistics
Matches: 186, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
42 37 0.20
43 111 0.60
44 5 0.03
45 33 0.18
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (43 bp):
ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTT
Found at i:17771085 original size:86 final size:86
Alignment explanation
Indices: 17770941--17771230 Score: 338
Period size: 86 Copynumber: 3.4 Consensus size: 86
17770931 ATTAGAGGAG
* * * * * * * *
17770941 AAAGTTGTGGTGCCTTTGATTAGATGAGC--CATTTATTTTTTCAAAGTCATTGAACCTCTAAGT
1 AAAGTTGTTGAGCCTCTGATTAGAAGAGCTTTATTTA-TTTTTCAAAGTCGTTGAACCTCTGATT
*
17771004 AGAGGAGCTTTATTTATTTTTA
65 AGAGGAGCTTTATTTATTTTTC
* * *
17771026 AAAGTTGTTGAGCCTCTGTTTAGAAGAGTTTTATTTATTTTTCAAAGTCGTTGACCCTCTGATTA
1 AAAGTTGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTGATTA
17771091 GAGGAGCTTTATTTATTTTTC
66 GAGGAGCTTTATTTATTTTTC
* *
17771112 AAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTATTCA-TTTTCAAAGTCGTT-AAGCCTCTGATT
1 AAAGTTGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTCAAAGTCGTTGAA-CCTCTGATT
* *
17771175 AAAGGAGCTTTGTTTATGTTTTTC
65 AGAGGAGCTTTATTTA--TTTTTC
* *
17771199 AAAGTCGTTGAGCCTCTGCTTAG-AGAAGCTTT
1 AAAGTTGTTGAGCCTCTGATTAGAAG-AGCTTT
17771231 GATCAAAATT
Statistics
Matches: 177, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 60 0.34
86 78 0.44
87 38 0.21
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (86 bp):
AAAGTTGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTGATTA
GAGGAGCTTTATTTATTTTTC
Found at i:17771471 original size:3 final size:3
Alignment explanation
Indices: 17771463--17771568 Score: 70
Period size: 3 Copynumber: 31.7 Consensus size: 3
17771453 TTTTATTTAT
* *
17771463 TTA TTA TTA TTTA TCTA TTA TTA CTA TTTA TTA ATA TATA TT- TTA TTA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA
*
17771511 TTAA TTA TCTGT TTA TTTA TCTA TTA TATA TTA TTA TTTA TCTA TTA TTA
1 TT-A TTA T-T-A TTA -TTA T-TA TTA T-TA TTA TTA -TTA T-TA TTA TTA
17771561 TTA TTA TT
1 TTA TTA TT
17771569 TATCTATTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 26
0.72 0.05 0.22
Matches are distributed among these distances:
2 2 0.02
3 50 0.60
4 31 0.37
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17771472 original size:14 final size:14
Alignment explanation
Indices: 17771451--17771621 Score: 84
Period size: 14 Copynumber: 11.8 Consensus size: 14
17771441 TTGTATTTTG
17771451 TATT-TTATTTATT
1 TATTATTATTTATT
*
17771464 TATTATTATTTATC
1 TATTATTATTTATT
*
17771478 TATTATTA-CTATT
1 TATTATTATTTATT
* *
17771491 TATTAATATATATTT
1 TATTATTATTTA-TT
*
17771506 TATTATTAATTATCT
1 TATTATTATTTAT-T
*
17771521 GT-TTATTTATCTATTATA
1 -TATTA-TTA--T-TTATT
*
17771539 TATTATTATTTATC
1 TATTATTATTTATT
17771553 TATTATTA-TTA-T
1 TATTATTATTTATT
**
17771565 TATTTATCTATTTACA
1 TA-TTAT-TATTTATT
* *
17771581 TATTATCATTTATC
1 TATTATTATTTATT
*
17771595 TATTAATATATTTTTTT
1 TATT-AT-TA-TTTATT
17771612 TATT-TTATTT
1 TATTATTATTT
17771622 TTTTCTTGGT
Statistics
Matches: 122, Mismatches: 19, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.02
13 24 0.20
14 44 0.36
15 26 0.21
16 7 0.06
17 12 0.10
18 3 0.02
19 4 0.03
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (14 bp):
TATTATTATTTATT
Found at i:17771620 original size:75 final size:74
Alignment explanation
Indices: 17771451--17771620 Score: 164
Period size: 75 Copynumber: 2.2 Consensus size: 74
17771441 TTGTATTTTG
* *
17771451 TATTTTATTTATTTATTATTATTTATCTATTATTACTATTTATTAATATATATTTTATTATTAAT
1 TATTTTTTTTA-TT-TTATTATTTATCTATTATTACTATTTATT-ATATATATTTTATTATCAAT
* * *
17771516 TATCTGTTTATT
63 TATCTATTAATA
* * * * * * *
17771528 TATCTATTATATATTATTATTTATCTATTATTATTA-TTATT-TATCTATTTACATATTATCATT
1 TATTTTTTTTATTTTATTATTTATCTATTATTACTATTTATTATATATATTT---TATTATCAAT
17771591 TATCTATTAATA
63 TATCTATTAATA
17771603 TATTTTTTTTATTTTATT
1 TATTTTTTTTATTTTATT
17771621 TTTTTCTTGG
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
72 8 0.11
74 5 0.07
75 53 0.72
76 1 0.01
77 7 0.09
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (74 bp):
TATTTTTTTTATTTTATTATTTATCTATTATTACTATTTATTATATATATTTTATTATCAATTAT
CTATTAATA
Found at i:17772538 original size:3 final size:3
Alignment explanation
Indices: 17772532--17772588 Score: 69
Period size: 3 Copynumber: 17.7 Consensus size: 3
17772522 TTTTTCATTT
*
17772532 TTA TTA TTTA TTTA TTTA TTTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17772581 TTA TTA TT
1 TTA TTA TT
17772589 TATTGATTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 36 0.71
4 15 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17772552 original size:12 final size:11
Alignment explanation
Indices: 17772531--17772597 Score: 58
Period size: 9 Copynumber: 6.6 Consensus size: 11
17772521 TTTTTTCATT
17772531 TTTATTATTTA
1 TTTATTATTTA
17772542 TTTATTTATTTA
1 TTTA-TTATTTA
17772554 -TTATTA-TTA
1 TTTATTATTTA
*
17772563 -TTATTA-TCA
1 TTTATTATTTA
17772572 -TTATTA-TTA
1 TTTATTATTTA
17772581 -TTATTATTTA
1 TTTATTATTTA
*
17772591 TTGATTA
1 TTTATTA
17772598 GATTAGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
9 25 0.50
10 6 0.12
11 12 0.24
12 7 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:17772644 original size:12 final size:11
Alignment explanation
Indices: 17772617--17772654 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
17772607 TGTTTAATAC
17772617 TTTTTATTTTA
1 TTTTTATTTTA
17772628 TTTTTATTTTA
1 TTTTTATTTTA
17772639 TGTTTTATTTTA
1 T-TTTTATTTTA
17772651 TTTT
1 TTTT
17772655 CTTTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:17772751 original size:61 final size:59
Alignment explanation
Indices: 17772670--17772908 Score: 310
Period size: 58 Copynumber: 4.1 Consensus size: 59
17772660 AATAAAATTC
* *
17772670 AAAAAAATA-TTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTCT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTTCT
* * *
17772729 GAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAGCTTTCT
1 -AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCT
*
17772789 -AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC-
1 AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCT
* * * *
17772846 AAAAATAGATTTTT-AGGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC-
1 AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCT
17772904 AAAAA
1 AAAAA
17772909 TGGATTTTTG
Statistics
Matches: 164, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
57 2 0.01
58 105 0.64
59 2 0.01
60 14 0.09
61 41 0.25
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCT
Found at i:17772826 original size:58 final size:56
Alignment explanation
Indices: 17772671--17772988 Score: 309
Period size: 58 Copynumber: 5.7 Consensus size: 56
17772661 ATAAAATTCA
** *
17772671 AAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTC
1 AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTTC
* * *
17772728 TGAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATAAGCTTTC
1 ---AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
*
17772788 TAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC
1 -AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
* * *
17772846 AAAAATAGATTTTTAGGGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC
1 AAAAA-ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
*** *
17772904 --AAAA-A----T-GG-ATTTTTG--AGCATCAATTTTCCTTAAAAATAAGTTTTC
1 AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
*
17772949 -AAAAGTGAATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAT--ATTTTTG-GGAAAAGTTGAAAGTATCAATTTT
17772989 TTCTGTACAA
Statistics
Matches: 220, Mismatches: 21, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
45 28 0.13
46 3 0.01
47 4 0.02
48 2 0.01
49 1 0.00
50 1 0.00
53 1 0.00
54 1 0.00
55 3 0.01
56 7 0.03
57 7 0.03
58 107 0.49
59 3 0.01
60 16 0.07
61 36 0.16
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (56 bp):
AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
Done.