Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 11 of 15
Found at i:1461313 original size:25 final size:25
Alignment explanation
Indices: 1461263--1461314 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1461253 TTCATACCAT
*
1461263 ATCATATTTTAATTATTTTAAACTA
1 ATCATATTTTAATTATATTAAACTA
1461288 ATCATA-TTTAA-TATCATTAAATCTA
1 ATCATATTTTAATTAT-ATTAAA-CTA
1461313 AT
1 AT
1461315 TAAAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 10 0.42
25 11 0.46
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
ATCATATTTTAATTATATTAAACTA
Found at i:1463489 original size:22 final size:24
Alignment explanation
Indices: 1463454--1463515 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 24
1463444 ATTTAAAATG
*
1463454 TTTTTAAAT-TATTTAACTT-TT-
1 TTTTTAAATAAATTTAACTTATTA
1463475 TTTTTAAATAAATTT---TTATTA
1 TTTTTAAATAAATTTAACTTATTA
1463496 TTTTTAAATAAACTTTAACT
1 TTTTTAAATAAA-TTTAACT
1463516 CTTGTCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 21 0.64
22 7 0.21
25 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTAAATAAATTTAACTTATTA
Found at i:1463615 original size:30 final size:30
Alignment explanation
Indices: 1463573--1463637 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1463563 GTTAATTTAT
* * *
1463573 ATTAAGAATTTATTTAAGTATAATTTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
*
1463603 GTTAAAAATTTATTTAAATATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
1463633 ATTAA
1 ATTAA
1463638 GAGTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAA
Found at i:1464011 original size:17 final size:18
Alignment explanation
Indices: 1463989--1464027 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1463979 TATTTATATT
* *
1463989 TAAATA-TATATTAAATA
1 TAAATATTATATAAAAAA
1464006 TAAATATTATATAAAAAA
1 TAAATATTATATAAAAAA
1464024 TAAA
1 TAAA
1464028 AAATTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATATTATATAAAAAA
Found at i:1468079 original size:2 final size:2
Alignment explanation
Indices: 1468074--1468106 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1468064 CTTTTCATTA
1468074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1468107 GAAATATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1472874 original size:20 final size:20
Alignment explanation
Indices: 1472849--1472886 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1472839 TACTATAACA
1472849 AGTTGAAAATAAAGAAAACG
1 AGTTGAAAATAAAGAAAACG
*
1472869 AGTTGAAAATGAAGAAAA
1 AGTTGAAAATAAAGAAAA
1472887 GTATATTCCT
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:0.61, C:0.03, G:0.21, T:0.16
Consensus pattern (20 bp):
AGTTGAAAATAAAGAAAACG
Found at i:1473080 original size:10 final size:10
Alignment explanation
Indices: 1473058--1473126 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
1473048 GAACATAACA
1473058 AAAATATA-T
1 AAAATATATT
1473067 -AAATATATT
1 AAAATATATT
*
1473076 AAAATTTATAT
1 AAAATATAT-T
*
1473087 AAAATAAATT
1 AAAATATATT
**
1473097 ATTGATATATT
1 A-AAATATATT
*
1473108 AAAATATATA
1 AAAATATATT
1473118 AAAATATAT
1 AAAATATAT
1473127 AATATTTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
8 7 0.15
9 1 0.02
10 24 0.51
11 15 0.32
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (10 bp):
AAAATATATT
Found at i:1473131 original size:27 final size:27
Alignment explanation
Indices: 1473031--1473137 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 27
1473021 AATACAACAT
* * *
1473031 AAAATATATAATTATATGAACATA-ACA
1 AAAATATATAA-TATATTAAAATATATA
1473058 AAAATATATAAATATATTAAAATTTATATA
1 AAAATATAT-AATATATTAAAA--TATATA
* *
1473088 AAATAAATTATTGATATATTAAAATATATA
1 AAA-ATA-TA-TAATATATTAAAATATATA
*
1473118 AAAATATATAATATTTTAAA
1 AAAATATATAATATATTAAA
1473138 TACTGTTATG
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
27 27 0.42
28 4 0.06
29 4 0.06
30 14 0.22
31 2 0.03
32 13 0.20
33 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAATATATAATATATTAAAATATATA
Found at i:1478128 original size:17 final size:17
Alignment explanation
Indices: 1478106--1478140 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1478096 AGTAACTATG
1478106 AGATCAAAAGACAGGAT
1 AGATCAAAAGACAGGAT
1478123 AGATCAAAAGACAGGAT
1 AGATCAAAAGACAGGAT
1478140 A
1 A
1478141 ACATTTCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.23, T:0.11
Consensus pattern (17 bp):
AGATCAAAAGACAGGAT
Found at i:1480694 original size:21 final size:21
Alignment explanation
Indices: 1480669--1480709 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1480659 TAAAAAAAAA
1480669 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
1480690 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
1480710 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:1480755 original size:35 final size:35
Alignment explanation
Indices: 1480681--1480744 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1480671 ATTTTATATT
1480681 AATATTTATATATTTTATAATTAAATTTAAATAAA
1 AATATTTATATATTTTATAATTAAATTTAAATAAA
1480716 AATATTTATATA-TTTA-AATT-AATTTAAAT
1 AATATTTATATATTTTATAATTAAATTTAAAT
1480745 TATAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 9 0.31
33 4 0.14
34 4 0.14
35 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
AATATTTATATATTTTATAATTAAATTTAAATAAA
Found at i:1480759 original size:33 final size:33
Alignment explanation
Indices: 1480687--1480760 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 33
1480677 TATTAATATT
1480687 TATATATTTTATAATTAAATTTAAATAAAAATA
1 TATATATTTTATAATTAAATTTAAATAAAAATA
*
1480720 TTTATATATTTA-AATT-AATTTAAATTATAAAA-A
1 TATATAT-TTTATAATTAAATTTAAA-TA-AAAATA
1480753 TATATATT
1 TATATATT
1480761 CAAAATCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
32 9 0.25
33 19 0.53
34 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TATATATTTTATAATTAAATTTAAATAAAAATA
Found at i:1486823 original size:52 final size:52
Alignment explanation
Indices: 1486758--1486863 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
1486748 TCTTAACTAT
1486758 ATTGAGATACACCAAATGGATGTTAAAACTGTTTTCTTGAATAGAGATTTAA
1 ATTGAGATACACCAAATGGATGTTAAAACTGTTTTCTTGAATAGAGATTTAA
1486810 ATTGAGATACACCAAATGGATGTTAAAACTGTTTTCTTGAATAGAGATTTAA
1 ATTGAGATACACCAAATGGATGTTAAAACTGTTTTCTTGAATAGAGATTTAA
1486862 AT
1 AT
1486864 GAAAAAAATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (52 bp):
ATTGAGATACACCAAATGGATGTTAAAACTGTTTTCTTGAATAGAGATTTAA
Found at i:1490320 original size:20 final size:20
Alignment explanation
Indices: 1490297--1490387 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
1490287 TTTATTTTTC
*
1490297 AATTATCTAATATATATAAA
1 AATTATATAATATATATAAA
*
1490317 AATTATATCAAATAAATATCATAA
1 AATTATAT--AATATATAT-A-AA
*
1490341 CA-T-TAT-AT-TATATAAA
1 AATTATATAATATATATAAA
*
1490357 TATTATATAATATATATAAA
1 AATTATATAATATATATAAA
*
1490377 TATTATATAAT
1 AATTATATAAT
1490388 TTATGTCATA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
16 3 0.05
17 2 0.03
18 7 0.12
19 4 0.07
20 26 0.45
22 11 0.19
23 2 0.03
24 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATATAATATATATAAA
Found at i:1490361 original size:11 final size:11
Alignment explanation
Indices: 1490345--1490386 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
1490335 TCATAACATT
1490345 ATATTATATAA
1 ATATTATATAA
1490356 ATATTATAT-A
1 ATATTATATAA
1490366 ATA-TATATAA
1 ATATTATATAA
1490376 ATATTATATAA
1 ATATTATATAA
1490387 TTTATGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.17
10 8 0.28
11 16 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATTATATAA
Found at i:1490420 original size:27 final size:26
Alignment explanation
Indices: 1490352--1490420 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 26
1490342 ATTATATTAT
* *
1490352 ATAAATATTATATAATATATATAAATA
1 ATAAATA-TATATAATGTATATAAAAA
* * *
1490379 TTATATA-AT-TTATGTCATATAAAAA
1 ATAAATATATATAATGT-ATATAAAAA
1490404 ATAAATATATATAATGT
1 ATAAATATATATAATGT
1490421 TAAGACATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
24 4 0.13
25 15 0.48
26 2 0.06
27 10 0.32
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAAATATATATAATGTATATAAAAA
Found at i:1491819 original size:16 final size:16
Alignment explanation
Indices: 1491798--1491829 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1491788 AATCAGAATA
*
1491798 TAATTTAATAATAATT
1 TAATTTAACAATAATT
1491814 TAATTTAACAATAATT
1 TAATTTAACAATAATT
1491830 AAAGATAGTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAACAATAATT
Found at i:1492449 original size:20 final size:20
Alignment explanation
Indices: 1492424--1492463 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1492414 AAAAGAATTT
1492424 TAATGAAATTTAAATTCTTA
1 TAATGAAATTTAAATTCTTA
1492444 TAATGAAATTTAAATTCTTA
1 TAATGAAATTTAAATTCTTA
1492464 CTTACAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATGAAATTTAAATTCTTA
Found at i:1493541 original size:16 final size:16
Alignment explanation
Indices: 1493501--1493543 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1493491 ATTCTTTTTT
*
1493501 AATTTATTTTTTTAAA
1 AATTTAATTTTTTAAA
**
1493517 AAAAT-ATTTTTTAAA
1 AATTTAATTTTTTAAA
1493532 AATTTAATTTTT
1 AATTTAATTTTT
1493544 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTAATTTTTTAAA
Found at i:1496428 original size:3 final size:3
Alignment explanation
Indices: 1496420--1496458 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1496410 CAAGTACCGT
1496420 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TT
1496459 TCTTTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1507082 original size:19 final size:18
Alignment explanation
Indices: 1507060--1507110 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1507050 ATGTTTATTC
* *
1507060 TTATATGATATAAATTACA
1 TTATATAATATAAAATA-A
1507079 TTATATAATATAAAATAA
1 TTATATAATATAAAATAA
*
1507097 TATATATTATATAA
1 T-TATATAATATAA
1507111 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATATAATATAAAATAA
Found at i:1507282 original size:43 final size:43
Alignment explanation
Indices: 1507228--1507311 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
1507218 TAATATTTTA
1507228 ATTTAAATTCTTTAAAATATTAGATAAAACTTAAGTTGAACTT
1 ATTTAAATTCTTTAAAATATTAGATAAAACTTAAGTTGAACTT
1507271 ATTTAAATTCTTTAAAATATTAGATAAAACTTAAGTTGAAC
1 ATTTAAATTCTTTAAAATATTAGATAAAACTTAAGTTGAAC
1507312 ACATATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (43 bp):
ATTTAAATTCTTTAAAATATTAGATAAAACTTAAGTTGAACTT
Found at i:1514215 original size:20 final size:20
Alignment explanation
Indices: 1514168--1514242 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1514158 AAAAAGACAT
*
1514168 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1514187 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1514208 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1514228 AATGTATCGATACAT
1 AATGTATCGATACAT
1514243 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1514236 original size:40 final size:39
Alignment explanation
Indices: 1514165--1514242 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1514155 GGTAAAAAGA
* *
1514165 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1514204 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1514243 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1514819 original size:32 final size:32
Alignment explanation
Indices: 1514770--1515602 Score: 944
Period size: 32 Copynumber: 27.2 Consensus size: 32
1514760 AATATGGTGA
* **
1514770 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1514802 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1514834 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* * *
1514866 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1514898 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1514930 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1514962 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1514994 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515026 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515058 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1515090 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1515122 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515154 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515186 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
*
1515218 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACTGACTTGTGTGGGC
* *
1515250 TTTGGAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515278 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1515307 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGTGGGC
* *
1515336 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1515365 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGTGGGC
1515394 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGTGGGC
* * *
1515423 TTTAAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* * * *
1515452 TTTGAAAAGAGTT-CCACTAAC-T-TGTAGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1515481 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGTGGGC
1515510 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
* *
1515538 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1515567 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACTGACTTGTGTGGGC
1515596 TTTGAAA
1 TTTGAAA
1515603 GGGATGAACA
Statistics
Matches: 742, Mismatches: 39, Indels: 43
0.90 0.05 0.05
Matches are distributed among these distances:
28 44 0.06
29 252 0.34
30 11 0.01
31 3 0.00
32 432 0.58
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
Found at i:1516852 original size:12 final size:12
Alignment explanation
Indices: 1516827--1516869 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
1516817 GACCCTTCTA
*
1516827 TTTTTTGCTATTT
1 TTTTTTG-TTTTT
1516840 TTTTTTGTTTTT
1 TTTTTTGTTTTT
1516852 TTGTTTTGTTTTT
1 TT-TTTTGTTTTT
1516865 TTTTT
1 TTTTT
1516870 GGGTGTAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:1530922 original size:20 final size:20
Alignment explanation
Indices: 1530875--1530949 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1530865 AAAAAGACAT
*
1530875 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1530894 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1530915 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1530935 AATGTATCGATACAT
1 AATGTATCGATACAT
1530950 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1530943 original size:40 final size:39
Alignment explanation
Indices: 1530872--1530949 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1530862 GGTAAAAAGA
* *
1530872 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1530911 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1530950 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1532020 original size:33 final size:32
Alignment explanation
Indices: 1531978--1532039 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1531968 CACACCCAAA
*
1531978 TGTATCGATACAT-TATGCTTTGTATCGATATAT
1 TGTATCGATACATGT-T-CATTGTATCGATATAT
1532011 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTTCATTGTATCGATA
1532040 CATGAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATATAT
Found at i:1532131 original size:10 final size:10
Alignment explanation
Indices: 1532113--1532143 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1532103 CATTGCTTGT
*
1532113 AACGACTATA
1 AACGGCTATA
1532123 AACGGCTATA
1 AACGGCTATA
1532133 AACGGCTATA
1 AACGGCTATA
1532143 A
1 A
1532144 TTTCAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (10 bp):
AACGGCTATA
Found at i:1532995 original size:370 final size:370
Alignment explanation
Indices: 1532314--1533059 Score: 1438
Period size: 370 Copynumber: 2.0 Consensus size: 370
1532304 GCTGAAATGC
1532314 AAGAGAATTAACCAAGAGACACTAAGAGTTCAAAGTATTCAAAGTTTGTTTTGTTTTCTCATTTT
1 AAGAGAATTAACCAAGAGACACTAAGAGTTCAAAGTATTCAAAGTTTGTTTTGTTTTCTCATTTT
1532379 CAAGAGCTTTTGCTTTCATTGTTGTTATTTTAAAAATGCTCTTTTGTATTTATTTTGAGCTTATT
66 CAAGAGCTTTTGCTTTCATTGTTGTTATTTTAAAAATGCTCTTTTGTATTTATTTTGAGCTTATT
1532444 CTTTCCCAAACACTAGCCTACTTAGAGGCAATTCTTGTTTGTACAATTTCTTTGTCTAGATAAGG
131 CTTTCCCAAACACTAGCCTACTTAGAGGCAATTCTTGTTTGTACAATTTCTTTGTCTAGATAAGG
1532509 TTGTGTTCAACCGAAGAGTATTAATCTTTTAGGAACTTGGGGTATAGTTCTTGAAGAGATTGAGA
196 TTGTGTTCAACCGAAGAGTATTAATCTTTTAGGAACTTGGGGTATAGTTCTTGAAGAGATTGAGA
1532574 GGTTGTTATCTTGGCCTTTAAAAGATAAGGTTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCA
261 GGTTGTTATCTTGGCCTTTAAAAGATAAGGTTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCA
*
1532639 ATTCTAGTAGTGAATTGGATAACCACTCGATAAGGAAGTGTCGAG
326 ATTCTAGTAGTGAATCGGATAACCACTCGATAAGGAAGTGTCGAG
*
1532684 AAGAGAATTAACCAAGAGACACTAAGAGTTCAAAGTATTCAGAGTTTGTTTTGTTTTCTCATTTT
1 AAGAGAATTAACCAAGAGACACTAAGAGTTCAAAGTATTCAAAGTTTGTTTTGTTTTCTCATTTT
**
1532749 CAAGAGCTTTTGCTTTCATTGTTGTTATTTTACGAATGCTCTTTTGTATTTATTTTGAGCTTATT
66 CAAGAGCTTTTGCTTTCATTGTTGTTATTTTAAAAATGCTCTTTTGTATTTATTTTGAGCTTATT
* *
1532814 CTTTCCCAAACACTAGCCTACTTAGAGGTAATTCTTGTTTGTACAATTTCTTTGTTTAGATAAGG
131 CTTTCCCAAACACTAGCCTACTTAGAGGCAATTCTTGTTTGTACAATTTCTTTGTCTAGATAAGG
1532879 TTGTGTTCAACCGAAGAGTATTAATCTTTTAGGAACTTGGGGTATAGTTCTTGAAGAGATTGAGA
196 TTGTGTTCAACCGAAGAGTATTAATCTTTTAGGAACTTGGGGTATAGTTCTTGAAGAGATTGAGA
1532944 GGTTGTTATCTTGGCCTTTAAAAGATAAGGTTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCA
261 GGTTGTTATCTTGGCCTTTAAAAGATAAGGTTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCA
1533009 ATTCTAGTAGTGAATCGGATAACCACTCGATAAGGAAGTGTCGAG
326 ATTCTAGTAGTGAATCGGATAACCACTCGATAAGGAAGTGTCGAG
1533054 AAGAGA
1 AAGAGA
1533060 GGACGTAGGT
Statistics
Matches: 370, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
370 370 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (370 bp):
AAGAGAATTAACCAAGAGACACTAAGAGTTCAAAGTATTCAAAGTTTGTTTTGTTTTCTCATTTT
CAAGAGCTTTTGCTTTCATTGTTGTTATTTTAAAAATGCTCTTTTGTATTTATTTTGAGCTTATT
CTTTCCCAAACACTAGCCTACTTAGAGGCAATTCTTGTTTGTACAATTTCTTTGTCTAGATAAGG
TTGTGTTCAACCGAAGAGTATTAATCTTTTAGGAACTTGGGGTATAGTTCTTGAAGAGATTGAGA
GGTTGTTATCTTGGCCTTTAAAAGATAAGGTTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCA
ATTCTAGTAGTGAATCGGATAACCACTCGATAAGGAAGTGTCGAG
Found at i:1536735 original size:13 final size:13
Alignment explanation
Indices: 1536717--1536742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1536707 TACAGCAAGT
1536717 ATGTATCGATACA
1 ATGTATCGATACA
1536730 ATGTATCGATACA
1 ATGTATCGATACA
1536743 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1538993 original size:21 final size:21
Alignment explanation
Indices: 1538960--1539004 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1538950 TTGCAAGTTG
*
1538960 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1538982 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1539002 AAA
1 AAA
1539005 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1540828 original size:15 final size:15
Alignment explanation
Indices: 1540808--1540838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1540798 TAAAAATGTC
*
1540808 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1540823 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1540838 C
1 C
1540839 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1542931 original size:20 final size:20
Alignment explanation
Indices: 1542852--1542931 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1542842 AATGTCCAAA
*
1542852 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1542872 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1542897 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1542917 TTGTATCGATACATT
1 ATGTATCGATACATT
1542932 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1542935 original size:13 final size:13
Alignment explanation
Indices: 1542917--1542942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1542907 ACATTTTTCT
1542917 TTGTATCGATACA
1 TTGTATCGATACA
1542930 TTGTATCGATACA
1 TTGTATCGATACA
1542943 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1543087 original size:21 final size:21
Alignment explanation
Indices: 1543063--1543109 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1543053 AAATCTTTTG
1543063 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1543084 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1543104 CAAAAT
1 CAAAAT
1543110 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1543106 original size:20 final size:19
Alignment explanation
Indices: 1543065--1543107 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1543055 ATCTTTTGCA
1543065 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1543085 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1543105 AAA
1 AAA
1543108 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1545502 original size:13 final size:13
Alignment explanation
Indices: 1545484--1545509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1545474 TACAGCAAGT
1545484 ATGTATCGATACA
1 ATGTATCGATACA
1545497 ATGTATCGATACA
1 ATGTATCGATACA
1545510 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1549529 original size:13 final size:13
Alignment explanation
Indices: 1549511--1549537 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1549501 ACATTATGCT
1549511 TTGTATCGATACA
1 TTGTATCGATACA
1549524 TTGTATCGATACA
1 TTGTATCGATACA
1549537 T
1 T
1549538 GTTCATTGTA
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:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1549534 original size:33 final size:32
Alignment explanation
Indices: 1549492--1549553 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1549482 CACACCCAAA
*
1549492 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
1549525 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTTCATTGTATCGATA
1549554 TATGGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:1549567 original size:20 final size:19
Alignment explanation
Indices: 1549521--1549577 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1549511 TTGTATCGAT
*
1549521 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
1549540 TCATTGTATCGATATATGG
1 ACATTGTATCGATACATGG
1549559 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1549578 AAACTGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1549662 original size:33 final size:33
Alignment explanation
Indices: 1549609--1549673 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1549599 CCACTATTTG
* **
1549609 TATCGATACATGGTACATTGTATTGATACATTA
1 TATCGATACATGATACATTGTATCAATACATTA
1549642 TATCGATACATGATGA-ATTGTATCAATACATT
1 TATCGATACATGAT-ACATTGTATCAATACATT
1549674 GCTTGTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (33 bp):
TATCGATACATGATACATTGTATCAATACATTA
Found at i:1556455 original size:9 final size:9
Alignment explanation
Indices: 1556429--1556475 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1556419 TGAATTTTTA
*
1556429 TTTATTTGT
1 TTTATTTCT
1556438 TTT-TTTCT
1 TTTATTTCT
1556446 TTTATTTCT
1 TTTATTTCT
*
1556455 TTTTTTTCAT
1 TTTATTTC-T
1556465 TTTATCTTCT
1 TTTAT-TTCT
1556475 T
1 T
1556476 GATAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 15 0.47
10 7 0.22
11 3 0.09
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTATTTCT
Found at i:1556461 original size:19 final size:20
Alignment explanation
Indices: 1556437--1556475 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
1556427 TATTTATTTG
1556437 TTTTTTTC-TTTTAT-TTCT
1 TTTTTTTCATTTTATCTTCT
1556455 TTTTTTTCATTTTATCTTCT
1 TTTTTTTCATTTTATCTTCT
1556475 T
1 T
1556476 GATAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTCATTTTATCTTCT
Found at i:1556533 original size:18 final size:17
Alignment explanation
Indices: 1556510--1556551 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1556500 AAATTTTACA
1556510 TTATAAT-TTAAATTAATT
1 TTATAATATTAAA-TAA-T
1556528 TTATAAATATTAAATAAT
1 TTAT-AATATTAAATAAT
1556546 TTATAA
1 TTATAA
1556552 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 6 0.27
20 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATAATATTAAATAAT
Found at i:1556672 original size:26 final size:26
Alignment explanation
Indices: 1556652--1556705 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1556642 TATAATATTA
1556652 TAATTTCAATTAATTTTATAAAAATAT
1 TAATTT-AATTAATTTTATAAAAATAT
* *
1556679 TTATTTGATTAATTTTATAAAAATAT
1 TAATTTAATTAATTTTATAAAAATAT
1556705 T
1 T
1556706 TAAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TAATTTAATTAATTTTATAAAAATAT
Found at i:1556848 original size:20 final size:20
Alignment explanation
Indices: 1556797--1556848 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1556787 TACAAATTAA
* *
1556797 ATTTAATTTAAAAATAAATAT
1 ATTT-ATTTAAATATAAAAAT
**
1556818 -TTTATAAAAATATAAAAAT
1 ATTTATTTAAATATAAAAAT
1556837 ATTTATTTAAAT
1 ATTTATTTAAAT
1556849 TAATTTAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTATTTAAATATAAAAAT
Found at i:1556955 original size:10 final size:10
Alignment explanation
Indices: 1556918--1556960 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1556908 CTTATTTGAC
1556918 ATAAATAAATT
1 ATAAATAAA-T
*
1556929 ATAATTATAAT
1 ATAAATA-AAT
1556940 -TAAATAAAT
1 ATAAATAAAT
1556949 ATAAATAAAT
1 ATAAATAAAT
1556959 AT
1 AT
1556961 TTATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 3 0.11
10 16 0.57
11 7 0.25
12 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:1557116 original size:20 final size:20
Alignment explanation
Indices: 1557093--1557170 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1557083 TTAATAAAAT
1557093 AATTATTTATATTTTTAATA
1 AATTATTTATATTTTTAATA
* *
1557113 AATTATTAATTTTTTTAA-A
1 AATTATTTATATTTTTAATA
* * * **
1557132 AGTCATTTAAATTATAAAATAA
1 AATTATTTATATT-TTTAAT-A
1557154 TAATTATTTATATTTTT
1 -AATTATTTATATTTTT
1557171 TGCTTATTGA
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
19 9 0.22
20 19 0.47
22 2 0.05
23 10 0.25
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
AATTATTTATATTTTTAATA
Found at i:1557813 original size:17 final size:15
Alignment explanation
Indices: 1557779--1557817 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1557769 AATCTTTAAA
1557779 TTAAAATATAATTAT
1 TTAAAATATAATTAT
*
1557794 TTAATAATATAAATTTT
1 TTAA-AATAT-AATTAT
1557811 TTAAAAT
1 TTAAAAT
1557818 TTTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAAATATAATTAT
Found at i:1562870 original size:17 final size:17
Alignment explanation
Indices: 1562837--1562895 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
1562827 TTTAATATAT
1562837 TTTTAT-ATTATTTTTTA
1 TTTTATAATTA-TTTTTA
1562854 TTTTATAATTATTTTTA
1 TTTTATAATTATTTTTA
*
1562871 ---TATAA-TATTTATA
1 TTTTATAATTATTTTTA
*
1562884 TTGTATAATTAT
1 TTTTATAATTAT
1562896 ATAATATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 7 0.19
14 5 0.14
16 5 0.14
17 15 0.42
18 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTATAATTATTTTTA
Found at i:1562879 original size:24 final size:23
Alignment explanation
Indices: 1562855--1562914 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
1562845 TATTTTTTAT
**
1562855 TTTATAATTATTTTTATATAATA
1 TTTATAATTATAATTATATAATA
*
1562878 TTTATATTGTATAATTATATAATA
1 TTTATAAT-TATAATTATATAATA
*
1562902 TTTAAAATTATAA
1 TTTATAATTATAA
1562915 AATCAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTATAATTATAATTATATAATA
Found at i:1562893 original size:30 final size:29
Alignment explanation
Indices: 1562829--1562895 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
1562819 TATAAAAATT
* * *
1562829 TAATATATTTTTATATTATTTTTTATTTTA
1 TAAT-TATTTTTATATAATTTTATATTGTA
1562859 TAATTATTTTTATATAATATTTATATTGTA
1 TAATTATTTTTATATAAT-TTTATATTGTA
1562889 TAATTAT
1 TAATTAT
1562896 ATAATATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
TAATTATTTTTATATAATTTTATATTGTA
Found at i:1563293 original size:23 final size:23
Alignment explanation
Indices: 1563217--1563299 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 23
1563207 AAAATAAAAA
*
1563217 TTTAAAATTTAACTTAATTAATATAT
1 TTTAAAATTTAA-AT-ATTAATAT-T
* * **
1563243 GTTAAAAAATT-AATATTTAATAAA
1 -TTTAAAATTTAAATA-TTAATATT
1563267 TTTAAAATTTAAATATTAATATT
1 TTTAAAATTTAAATATTAATATT
*
1563290 TTTAATATTT
1 TTTAAAATTT
1563300 CTTTTATTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
23 23 0.52
24 5 0.11
25 7 0.16
26 1 0.02
27 8 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TTTAAAATTTAAATATTAATATT
Found at i:1564460 original size:36 final size:35
Alignment explanation
Indices: 1564420--1564491 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
1564410 TTTTAATATT
*
1564420 AATATTATATATT-TTTAATAATTAAATTTAAATAAA
1 AATATTATATATTATTAAATAA-T-AATTTAAATAAA
* * *
1564456 AATATTTTTTATTATTAAATAATAATTTGAATAAA
1 AATATTATATATTATTAAATAATAATTTAAATAAA
1564491 A
1 A
1564492 TCAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 12 0.39
36 12 0.39
37 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
AATATTATATATTATTAAATAATAATTTAAATAAA
Found at i:1565549 original size:12 final size:11
Alignment explanation
Indices: 1565533--1565586 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
1565523 AAAATATTAT
1565533 ATTTTATATAA
1 ATTTTATATAA
1565544 ATTTT-TAT-A
1 ATTTTATATAA
* *
1565553 TTTTTATATTTA
1 ATTTTATA-TAA
1565565 ATTTTATATAA
1 ATTTTATATAA
1565576 ATTTTAATATA
1 ATTTT-ATATA
1565587 TTATTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.14
10 5 0.14
11 13 0.36
12 13 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTATATAA
Found at i:1565562 original size:62 final size:60
Alignment explanation
Indices: 1565485--1565601 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 60
1565475 AAATTGATAA
1565485 TTTATATATTTATA-TTATATTTTATTATAATTATATTTAAAATATTA-TA-TTTTATATAAATT
1 TTTATATATTTATATTTA-ATTTTA-TATAA--AT-TTTAAAATATTATTATTTTTATATAAATT
* *
1565547 TTTATATTTTTATATTTAATTTTATATAAATTTTAATATATTATTATTTTTATAT
1 TTTATATATTTATATTTAATTTTATATAAATTTTAAAATATTATTATTTTTATAT
1565602 TATATTATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
58 11 0.22
59 4 0.08
60 8 0.16
61 5 0.10
62 19 0.38
63 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (60 bp):
TTTATATATTTATATTTAATTTTATATAAATTTTAAAATATTATTATTTTTATATAAATT
Found at i:1565595 original size:32 final size:32
Alignment explanation
Indices: 1565533--1565595 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1565523 AAAATATTAT
* *
1565533 ATTTTATATAAATTTTTATATTTTTATATTTA
1 ATTTTATATAAATTTTAATATTTATATATTTA
1565565 ATTTTATATAAATTTTAATATATTAT-TATTT
1 ATTTTATATAAATTTTAATAT-TTATATATTT
1565596 TTATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
ATTTTATATAAATTTTAATATTTATATATTTA
Found at i:1565611 original size:58 final size:60
Alignment explanation
Indices: 1565485--1565631 Score: 148
Period size: 58 Copynumber: 2.5 Consensus size: 60
1565475 AAATTGATAA
*
1565485 TTTATATATTTATA-TTATATTTTATTATAATTATATTTAAAATATTATATTTTATATAAATT
1 TTTATATTTTTATATTTA-ATTTTATTATAA-TATATTTAAAATATTATATTTTATAT-AATT
*
1565547 TTTATATTTTTATATTTAATTTTA-TATAA-AT-TTTAATATATTATTATTTT-TAT-ATT
1 TTTATATTTTTATATTTAATTTTATTATAATATATTTAAAATATTA-TATTTTATATAATT
*
1565603 ATATTATA-TTTTATTTATTAATTTT-TTAT
1 -T-TTATATTTTTATAT-TTAATTTTATTAT
1565632 TACATGCATA
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
56 3 0.04
57 8 0.11
58 30 0.39
59 8 0.11
61 5 0.07
62 19 0.25
63 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (60 bp):
TTTATATTTTTATATTTAATTTTATTATAATATATTTAAAATATTATATTTTATATAATT
Found at i:1565620 original size:16 final size:16
Alignment explanation
Indices: 1565491--1565620 Score: 75
Period size: 15 Copynumber: 8.4 Consensus size: 16
1565481 ATAATTTATA
1565491 TATTTATATTATATTT
1 TATTTATATTATATTT
1565507 TA-TTATAATTATA-TT
1 TATTTAT-ATTATATTT
**
1565522 TA-AAATATTATATTT
1 TATTTATATTATATTT
*
1565537 TA--TATA-AAT-TTT
1 TATTTATATTATATTT
1565549 TATATT-T-TTATATTT
1 TAT-TTATATTATATTT
* *
1565564 AATTT-TATATAAATTT
1 TATTTATAT-TATATTT
*
1565580 TA-ATATATTATTATTTT
1 TATTTATATTA-TA-TTT
1565597 TATATTATATTATATTT
1 TAT-TTATATTATATTT
1565614 TATTTAT
1 TATTTAT
1565621 TAATTTTTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 15 0.17
15 24 0.27
16 23 0.26
17 11 0.12
18 2 0.02
19 7 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATATTATATTT
Found at i:1565622 original size:33 final size:32
Alignment explanation
Indices: 1565536--1565631 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 32
1565526 ATATTATATT
* * * * * *
1565536 TTATATAAATTTTTATATTTTTATATTTAATT
1 TTATATAAATTTTAATATATTAATTTTTTATA
*
1565568 TTATATAAATTTTAATATATTATTATTTTTATA
1 TTATATAAATTTTAATATATTAAT-TTTTTATA
* *
1565601 TTATATTATATTTT-ATTTATTAATTTTTTAT
1 TTATA-TAAATTTTAATATATTAATTTTTTAT
1565632 TACATGCATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 27 0.52
33 18 0.35
34 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TTATATAAATTTTAATATATTAATTTTTTATA
Found at i:1567524 original size:22 final size:22
Alignment explanation
Indices: 1567499--1567540 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1567489 TTTTAATATG
*
1567499 TTAAATATTTAAAATTAAAAAA
1 TTAAATATTTAAAACTAAAAAA
* *
1567521 TTAATTTTTTAAAACTAAAA
1 TTAAATATTTAAAACTAAAA
1567541 TTATACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATATTTAAAACTAAAAAA
Found at i:1568059 original size:18 final size:17
Alignment explanation
Indices: 1568038--1568142 Score: 72
Period size: 18 Copynumber: 5.9 Consensus size: 17
1568028 TTTAAATTTA
1568038 AAAAAATATGTAAAAATT
1 AAAAAATAT-TAAAAATT
*
1568056 AAAATATAATTAAAAATAT
1 AAAAAAT-ATTAAAAAT-T
* *
1568075 AAGAATAATTTTTTAAAA-T
1 AA-AA-AA-TATTAAAAATT
1568094 AAAAAAT-TTAAAATATT
1 AAAAAATATTAAAA-ATT
* *
1568111 ATAAAAATCTAAAAAATT
1 A-AAAAATATTAAAAATT
1568129 AAAAAA-ATTAAAAA
1 AAAAAATATTAAAAA
1568143 ATATCATCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
15 5 0.07
16 8 0.11
17 9 0.13
18 25 0.36
19 13 0.19
20 2 0.03
21 7 0.10
22 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAAATATTAAAAATT
Found at i:1568131 original size:8 final size:8
Alignment explanation
Indices: 1568089--1568144 Score: 60
Period size: 9 Copynumber: 6.6 Consensus size: 8
1568079 ATAATTTTTT
1568089 AAAA-TAA
1 AAAATTAA
1568096 AAAATTTAA
1 AAAA-TTAA
*
1568105 AATATTATA
1 AAAATTA-A
1568114 AAAATCTAA
1 AAAAT-TAA
1568123 AAAATTAAA
1 AAAATT-AA
1568132 AAAATTAA
1 AAAATTAA
1568140 AAAAT
1 AAAAT
1568145 ATCATCAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 4 0.10
8 11 0.26
9 25 0.60
10 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAATTAA
Found at i:1568143 original size:18 final size:17
Alignment explanation
Indices: 1568089--1568144 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1568079 ATAATTTTTT
*
1568089 AAAA-TAAAAAATTTAA
1 AAAATTAAAAAAATTAA
* *
1568105 AATATTATAAAAATCTAA
1 AAAATTAAAAAAAT-TAA
1568123 AAAATTAAAAAAATTAA
1 AAAATTAAAAAAATTAA
1568140 AAAAT
1 AAAAT
1568145 ATCATCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 15 0.45
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTAAAAAAATTAA
Found at i:1568363 original size:13 final size:13
Alignment explanation
Indices: 1568345--1568370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1568335 GAGAGGGTAG
1568345 TTGGCCACCGATC
1 TTGGCCACCGATC
1568358 TTGGCCACCGATC
1 TTGGCCACCGATC
1568371 AGCATTGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.23, T:0.23
Consensus pattern (13 bp):
TTGGCCACCGATC
Found at i:1568626 original size:14 final size:15
Alignment explanation
Indices: 1568592--1568633 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
1568582 TTCCCTCTTC
*
1568592 CTTTTCTCTCTCCTTT
1 CTTTTCTTTCTCC-TT
1568608 CTTTTCTTTCTCC-T
1 CTTTTCTTTCTCCTT
1568622 CTTTTCTTTCTC
1 CTTTTCTTTCTC
1568634 TAAAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
CTTTTCTTTCTCCTT
Found at i:1568703 original size:19 final size:20
Alignment explanation
Indices: 1568678--1568723 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1568668 ATTTAGTTTA
*
1568678 TATTTTTTAAAAAGCATTTT
1 TATTTTTTAAAAAACATTTT
*
1568698 TATTTTTTAAAAAATATTTT
1 TATTTTTTAAAAAACATTTT
1568718 TATTTT
1 TATTTT
1568724 ATTTTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTTTAAAAAACATTTT
Found at i:1568928 original size:27 final size:27
Alignment explanation
Indices: 1568892--1568959 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1568882 ATGCGGCATT
1568892 AATATTTATTTAAAAATATTAATAA-A-A
1 AATATTTATTTAAAAA-ATT-ATAATATA
*
1568919 AATATATATTTTAAAAAATTATAATATA
1 AATATTTA-TTTAAAAAATTATAATATA
1568947 AATATTTATTTAA
1 AATATTTATTTAA
1568960 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 4 0.11
27 16 0.44
28 16 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATTTATTTAAAAAATTATAATATA
Found at i:1569787 original size:27 final size:26
Alignment explanation
Indices: 1569739--1569816 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
1569729 TTAATATGCA
*
1569739 TATTTTTAATTATATTCGTATATTTT
1 TATTTTTAATTATATTCATATATTTT
1569765 TATTTTATAATTATATGT-ATATATTTAT
1 TATTTT-TAATTATAT-TCATATATTT-T
* *
1569793 ATAATTTTAA-TATATTAATA-ATTT
1 -TATTTTTAATTATATTCATATATTT
1569817 ATTTGTATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 11 0.24
27 24 0.53
28 5 0.11
29 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (26 bp):
TATTTTTAATTATATTCATATATTTT
Found at i:1569793 original size:6 final size:6
Alignment explanation
Indices: 1569738--1569909 Score: 58
Period size: 6 Copynumber: 28.8 Consensus size: 6
1569728 ATTAATATGC
* * * *
1569738 ATATTT TTAATT ATATTCGT ATATTT TTATTTT ATAATT ATATGTAT ATATTT
1 ATATTT ATATTT ATATT--T ATATTT ATA-TTT ATATTT ATAT-T-T ATATTT
* * * * * *
1569791 ATA-TA AT-TTT AATATATT AATAATT -TATTT GTATGT AAATTT -TAATAT
1 ATATTT ATATTT -ATAT-TT -ATATTT ATATTT ATATTT ATATTT AT-ATTT
* * * *
1569839 ATATAT ATATTC ATA-TT ATATTT ATA-TT AT-TTT ATATTT TTAATT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
*
1569884 ATTTTT AT-TTT ATA-TT ATA-TT ATATT
1 ATATTT ATATTT ATATTT ATATTT ATATT
1569910 GTATTATATA
Statistics
Matches: 123, Mismatches: 26, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
5 35 0.28
6 60 0.49
7 11 0.09
8 17 0.14
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (6 bp):
ATATTT
Found at i:1569868 original size:5 final size:5
Alignment explanation
Indices: 1569838--1569930 Score: 70
Period size: 5 Copynumber: 18.6 Consensus size: 5
1569828 AATTTTAATA
*
1569838 TATAT ATATAT TCATAT TATATT TATAT TATTT TATAT T-T-T TA-AT
1 TATAT -TATAT T-ATAT TATA-T TATAT TATAT TATAT TATAT TATAT
* * *
1569883 TATTTT TATTT TATAT TATAT TATAT TGTAT TATA- TATCA- TATAT TAT
1 TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TAT
1569931 TTAAAATTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
3 2 0.03
4 8 0.11
5 45 0.62
6 18 0.25
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:1569872 original size:10 final size:10
Alignment explanation
Indices: 1569851--1569942 Score: 60
Period size: 10 Copynumber: 8.9 Consensus size: 10
1569841 ATATATATTC
1569851 ATATTATATTT
1 ATATTAT-TTT
1569862 ATATTATTTT
1 ATATTATTTT
*
1569872 ATATTTTTAATT
1 ATATTATT--TT
*
1569884 ATTTTTATTTT
1 A-TATTATTTT
*
1569895 ATATTATATT
1 ATATTATTTT
* *
1569905 ATATTGTATT
1 ATATTATTTT
**
1569915 ATA-TATCAT
1 ATATTATTTT
*
1569924 ATATTATTTA
1 ATATTATTTT
*
1569934 AAATTATTT
1 ATATTATTT
1569943 CATCTAAGAA
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
9 6 0.09
10 40 0.62
11 10 0.16
12 3 0.05
13 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
ATATTATTTT
Found at i:1569889 original size:18 final size:16
Alignment explanation
Indices: 1569838--1569909 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
1569828 AATTTTAATA
* *
1569838 TATATATATATTCATAT
1 TATATTTATATT-ATTT
1569855 TATATTTATATTATTT
1 TATATTTATATTATTT
*
1569871 TATATTTTTAATTATTT
1 TATATTTAT-ATTATTT
*
1569888 T-TATTTTATATTATAT
1 TATA-TTTATATTATTT
1569904 TATATT
1 TATATT
1569910 GTATTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 22 0.47
17 25 0.53
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTATATTATTT
Found at i:1569914 original size:28 final size:27
Alignment explanation
Indices: 1569844--1569930 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 27
1569834 AATATATATA
1569844 TATATTCATATTATATTTA-TATTATTT
1 TATATT-ATATTATATTTATTATTATTT
*
1569871 TATATT-T-TTA-A-TTATTTTTATTT
1 TATATTATATTATATTTATTATTATTT
**
1569894 TATATTATATTATATTGTATTATATATCA
1 TATATTATATTATATT-TATTAT-TATTT
1569923 TATATTAT
1 TATATTAT
1569931 TTAAAATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
22 3 0.06
23 14 0.29
24 4 0.08
25 4 0.08
26 1 0.02
27 7 0.14
28 5 0.10
29 11 0.22
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (27 bp):
TATATTATATTATATTTATTATTATTT
Found at i:1570382 original size:29 final size:30
Alignment explanation
Indices: 1570307--1570382 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
1570297 AAATTTAAAA
* * *
1570307 TAATATATATTTATATAAATTTTAATTTTTAT
1 TAATTTATA-TTATATAAATGTTAA-TTATAT
1570339 TAATTTAT-TTAATATAAATGTTAA-TATAT
1 TAATTTATATT-ATATAAATGTTAATTATAT
1570368 TAATTTATATTATAT
1 TAATTTATATTATAT
1570383 TTTAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 16 0.41
30 4 0.10
31 12 0.31
32 7 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TAATTTATATTATATAAATGTTAATTATAT
Found at i:1570387 original size:17 final size:17
Alignment explanation
Indices: 1570360--1570412 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1570350 ATATAAATGT
1570360 TAATATATTAATTTATA
1 TAATATATTAATTTATA
* * **
1570377 TTATATTTTAAAATATA
1 TAATATATTAATTTATA
*
1570394 TAATATATAAATTTATA
1 TAATATATTAATTTATA
1570411 TA
1 TA
1570413 TTACAATATT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATATTAATTTATA
Found at i:1573461 original size:9 final size:9
Alignment explanation
Indices: 1573449--1573487 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1573439 TTTTTATTTT
1573449 TTAAAAAAA
1 TTAAAAAAA
*
1573458 TTAAAAATA
1 TTAAAAAAA
1573467 TATAAAAAAA
1 T-TAAAAAAA
*
1573477 TTTAAAAAA
1 TTAAAAAAA
1573486 TT
1 TT
1573488 GAACAAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1573485 original size:10 final size:10
Alignment explanation
Indices: 1573448--1573485 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1573438 TTTTTTATTT
1573448 TTTAAAAAAA
1 TTTAAAAAAA
*
1573458 -TTAAAAATA
1 TTTAAAAAAA
*
1573467 TATAAAAAAA
1 TTTAAAAAAA
1573477 TTTAAAAAA
1 TTTAAAAAA
1573486 TTGAACAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:1577747 original size:13 final size:13
Alignment explanation
Indices: 1577729--1577753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577719 CATAAAGTGT
1577729 TGTATCGATACAA
1 TGTATCGATACAA
1577742 TGTATCGATACA
1 TGTATCGATACA
1577754 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1577751 original size:33 final size:33
Alignment explanation
Indices: 1577709--1577775 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1577699 TCAAACGATT
1577709 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1577742 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1577775 T
1 T
1577776 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1577834 original size:13 final size:13
Alignment explanation
Indices: 1577816--1577840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577806 ATCACTTAAA
1577816 TGTATCGATACAT
1 TGTATCGATACAT
1577829 TGTATCGATACA
1 TGTATCGATACA
1577841 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1577905 original size:52 final size:52
Alignment explanation
Indices: 1577849--1577977 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1577839 CACTGATCTT
* * *
1577849 TGTATCGATACATGCAGGAAAATTTGTCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1577901 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1577953 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1577978 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1582051 original size:20 final size:20
Alignment explanation
Indices: 1582026--1582172 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
1582016 TTTTTAACCA
1582026 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* *** *
1582046 AATGTATTGATACATGCATG
1 AATGTATCGATACATTTTTC
* *
1582066 AATGTGTCGATACATTCTTC
1 AATGTATCGATACATTTTTC
1582086 AATGTATCGATACATTCTGTCTTTTTACCC
1 AATGTATCGATACA-------TTTTT---C
1582116 AGATGTATCGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * *
1582137 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
1582157 AATGTATCGATACATT
1 AATGTATCGATACATT
1582173 CTGTCTTTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
20 74 0.74
21 2 0.02
24 5 0.05
27 4 0.04
30 2 0.02
31 13 0.13
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1582125 original size:31 final size:31
Alignment explanation
Indices: 1582087--1582203 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
1582077 ACATTCTTCA
1582087 ATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATTCTGTCTTTTTACCCAG
* * **
1582118 ATGTATCGATACATT-TTTCAATGTATCGATACATGTATG
1 ATGTATCGATACATTCTGTC--T-T-T--TTAC--CCA-G
1582157 AATGTATCGATACATTCTGTCTTTTTACCCAG
1 -ATGTATCGATACATTCTGTCTTTTTACCCAG
*
1582189 ATATATCGATACATT
1 ATGTATCGATACATT
1582204 TATATCGATA
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
30 3 0.05
31 29 0.44
32 2 0.03
33 2 0.03
34 1 0.02
35 3 0.05
36 3 0.05
37 1 0.02
38 2 0.03
39 2 0.03
40 15 0.23
41 3 0.05
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (31 bp):
ATGTATCGATACATTCTGTCTTTTTACCCAG
Found at i:1582209 original size:14 final size:14
Alignment explanation
Indices: 1582190--1582217 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1582180 TTTACCCAGA
1582190 TATATCGATACATT
1 TATATCGATACATT
1582204 TATATCGATACATT
1 TATATCGATACATT
1582218 GAATAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TATATCGATACATT
Found at i:1585667 original size:47 final size:47
Alignment explanation
Indices: 1585614--1585714 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
1585604 TTCTAGCATT
* * * * * *
1585614 ATTTTAGTCATTTTTCATGACTTAGAGACT-TTTATGTCATTTTATGC
1 ATTTTAGTAATTTGTCATGACTTA-AGAATATTTATATAATTTCATGC
*
1585661 ATTTTAGTAATTTGTCATGATTTAAGAATATTTATATAATTTCATGC
1 ATTTTAGTAATTTGTCATGACTTAAGAATATTTATATAATTTCATGC
1585708 ATTTTAG
1 ATTTTAG
1585715 GGTCATTCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
46 4 0.09
47 42 0.91
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (47 bp):
ATTTTAGTAATTTGTCATGACTTAAGAATATTTATATAATTTCATGC
Found at i:1585693 original size:29 final size:30
Alignment explanation
Indices: 1585660--1585745 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
1585650 TCATTTTATG
1585660 CATTTTAGTAATTTGTCATGATTTAAGAAT
1 CATTTTAGTAATTTGTCATGATTTAAGAAT
* **
1585690 -ATTTATA-TAA-TT-TCATGCATTTTAGGGT
1 CATTT-TAGTAATTTGTCATG-ATTTAAGAAT
*
1585718 CATTCTAGTAATTTGTCATGATTTAAGA
1 CATTTTAGTAATTTGTCATGATTTAAGA
1585746 CCATTTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 5 0.11
28 11 0.25
29 13 0.30
30 10 0.23
31 5 0.11
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (30 bp):
CATTTTAGTAATTTGTCATGATTTAAGAAT
Found at i:1585758 original size:29 final size:29
Alignment explanation
Indices: 1585660--1585760 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
1585650 TCATTTTATG
1585660 CATTT-TAGTAATTTGTCATGATTTAAGAA
1 CATTTATA-TAATTTGTCATGATTTAAGAA
* * **
1585689 TATTTATATAA-TT-TCATGCATTTTAGGGT
1 CATTTATATAATTTGTCATG-A-TTTAAGAA
* *
1585718 CATTCTA-GTAATTTGTCATGATTTAAGAC
1 CATT-TATATAATTTGTCATGATTTAAGAA
1585747 CATTTATATAATTT
1 CATTTATATAATTT
1585761 CATGCGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
27 5 0.09
28 5 0.09
29 33 0.60
30 7 0.13
31 5 0.09
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
CATTTATATAATTTGTCATGATTTAAGAA
Found at i:1585795 original size:58 final size:58
Alignment explanation
Indices: 1585660--1585800 Score: 194
Period size: 58 Copynumber: 2.4 Consensus size: 58
1585650 TCATTTTATG
*
1585660 CATTTTAGTAATTTGTCATGATTTAAGAATATTTATATAATTTCATGCATTTTAGGGT
1 CATTTTAGTAATTTGTCATGATTTAAGAACATTTATATAATTTCATGCATTTTAGGGT
* * * *
1585718 CATTCTAGTAATTTGTCATGATTTAAGACCATTTATATAATTTCATGCGTTTTGGAGGT
1 CATTTTAGTAATTTGTCATGATTTAAGAACATTTATATAATTTCATGCATTTTAG-GGT
* * *
1585777 -ATTTTAATTATTTTTCATGATTTA
1 CATTTTAGTAATTTGTCATGATTTA
1585801 GGGATTATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 70 0.96
59 3 0.04
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (58 bp):
CATTTTAGTAATTTGTCATGATTTAAGAACATTTATATAATTTCATGCATTTTAGGGT
Found at i:1586010 original size:144 final size:145
Alignment explanation
Indices: 1585700--1586011 Score: 324
Period size: 144 Copynumber: 2.2 Consensus size: 145
1585690 ATTTATATAA
* * * *
1585700 TTTCATGCATTTTAGGGTCATTCTAGTAATTTGTCATGATTTAAGACCATTTATATAATTTCATG
1 TTTCATGCATTTTAGGGTTATTTTAGTAATTTGTCATGATTTAAGACCATTCATATAATTTCATA
* * ** * * * * * *
1585765 CGTTTTGGAGGTATTTTAATTATTTTTCATGATTTAGGGATTATTATGTAATTTTATGCATTATA
66 CATTTTAGAGCCATTTTAATCATTTTTCATGATTTAAGAACTATTATATAATTTCATGCATTATA
*
1585830 TCAACATTCTAGCAT
131 TCAACATTCTAACAT
* *** * **
1585845 TTTCATACATTTTAAAATTATTTTAGTAATTTG-CTATGATTTAGGACCA-TCATATAATTTTGT
1 TTTCATGCATTTTAGGGTTATTTTAGTAATTTGTC-ATGATTTAAGACCATTCATATAATTTCAT
* * * *
1585908 ACATTTTA-AGACCATTTTAGTCATTTTTCATTATTTAATAACTATTATATAATTTCATGCATTT
65 ACATTTTAGAG-CCATTTTAATCATTTTTCATGATTTAAGAACTATTATATAATTTCATGCATTA
* *
1585972 TATCACCATTCTAATAT
129 TATCAACATTCTAACAT
*
1585989 TTTCATGCTTTTTAGGGTTATTT
1 TTTCATGCATTTTAGGGTTATTT
1586012 AGGCTATTTC
Statistics
Matches: 132, Mismatches: 33, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
143 2 0.02
144 90 0.68
145 40 0.30
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (145 bp):
TTTCATGCATTTTAGGGTTATTTTAGTAATTTGTCATGATTTAAGACCATTCATATAATTTCATA
CATTTTAGAGCCATTTTAATCATTTTTCATGATTTAAGAACTATTATATAATTTCATGCATTATA
TCAACATTCTAACAT
Found at i:1586496 original size:78 final size:77
Alignment explanation
Indices: 1586412--1586589 Score: 178
Period size: 77 Copynumber: 2.3 Consensus size: 77
1586402 TCGAGTTCGT
** ** * * *
1586412 AGATCATATGGAAACCTTTGTGTCAAAACATGTTTGTTAGGGGCATTTAGGTAAAAGTATCTTTA
1 AGATCATATGGAAACCTTTGTGTCAAAACATGTCCGTTAGGGG-ATTTAAATAAAAATACCTTAA
1586477 AACCGAGTCTTTA
65 AACCGAGTCTTTA
* * **
1586490 AGATCATAT-GAGAACTTTTATGTTGAAACATGTCCGTTAGGGGATTTAAATAAAAATACCTTAA
1 AGATCATATGGA-AACCTTTGTGTCAAAACATGTCCGTTAGGGGATTTAAATAAAAATACCTTAA
* *
1586554 AATCGAGTCTTTT
65 AACCGAGTCTTTA
* * * *
1586567 GGATTATGTGGGAACCTTTGTGT
1 AGATCATATGGAAACCTTTGTGT
1586590 TAAAGCATAG
Statistics
Matches: 79, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
77 44 0.56
78 35 0.44
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (77 bp):
AGATCATATGGAAACCTTTGTGTCAAAACATGTCCGTTAGGGGATTTAAATAAAAATACCTTAAA
ACCGAGTCTTTA
Found at i:1587538 original size:17 final size:18
Alignment explanation
Indices: 1587506--1587543 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1587496 AATTTTTAAA
1587506 TAATATTAAAATAATT-T
1 TAATATTAAAATAATTAT
1587523 TAAT-TTAAAATAAATTAT
1 TAATATTAAAAT-AATTAT
1587541 TAA
1 TAA
1587544 AATATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATTAAAATAATTAT
Found at i:1587558 original size:29 final size:27
Alignment explanation
Indices: 1587497--1587559 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
1587487 AGTGTACTTA
*
1587497 ATTTTTAAATAATATTAAAATAATTTT
1 ATTTTAAAATAATATTAAAATAATTTT
*
1587524 AATTTAAAATAAATTATTAAAAT-ATTATT
1 ATTTTAAAAT-AA-TATTAAAATAATT-TT
1587553 ATTTTAA
1 ATTTTAA
1587560 CTAGTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 8 0.27
28 5 0.17
29 17 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTTAAAATAATATTAAAATAATTTT
Found at i:1587751 original size:53 final size:51
Alignment explanation
Indices: 1587694--1587859 Score: 188
Period size: 55 Copynumber: 3.1 Consensus size: 51
1587684 AAAATTTTTA
* *
1587694 AATAATTAGACAATTACAACTATTAATATAAAATAATTAGAATTATAACTCAT
1 AATAATTAGACGATTATAA-T-TTAATATAAAATAATTAGAATTATAACTCAT
1587747 AATAATTAGACGATTATAATTTTTAATATAAAATAATTAGATAATTATAACTCAT
1 AATAATTAGACGATTATAA--TTTAATATAAAATAATTAG--AATTATAACTCAT
* * * *
1587802 AATAATCAGATGATTATAATTTAAATTTAAAAATAATTAGATGATTATAACTCTT
1 AATAATTAGACGATTATAATTT-AATAT-AAAATAATTAGA--ATTATAACTCAT
1587857 AAT
1 AAT
1587860 TTAAATTCAA
Statistics
Matches: 99, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
53 39 0.39
54 5 0.05
55 55 0.56
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (51 bp):
AATAATTAGACGATTATAATTTAATATAAAATAATTAGAATTATAACTCAT
Found at i:1587805 original size:31 final size:31
Alignment explanation
Indices: 1587747--1587805 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
1587737 TATAACTCAT
* * **
1587747 AATAATTAGACGATTATAATTTTTAATATAA
1 AATAATTAGACAATTATAACTCATAATATAA
*
1587778 AATAATTAGATAATTATAACTCATAATA
1 AATAATTAGACAATTATAACTCATAATA
1587806 ATCAGATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (31 bp):
AATAATTAGACAATTATAACTCATAATATAA
Found at i:1587817 original size:55 final size:54
Alignment explanation
Indices: 1587716--1587859 Score: 202
Period size: 55 Copynumber: 2.7 Consensus size: 54
1587706 ATTACAACTA
*
1587716 TTAATATAAAATAATTAG--AATTATAACTCATAATAATTAGACGATTATAATTT
1 TTAATATAAAATAATTAGATAATTATAACTCATAATAATCAGACGATTATAA-TT
*
1587769 TTAATATAAAATAATTAGATAATTATAACTCATAATAATCAGATGATTATAATT
1 TTAATATAAAATAATTAGATAATTATAACTCATAATAATCAGACGATTATAATT
* * * *
1587823 TAAATTTAAAAATAATTAGATGATTATAACTCTTAAT
1 TTAATAT-AAAATAATTAGATAATTATAACTCATAAT
1587860 TTAAATTCAA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
53 18 0.22
54 7 0.09
55 57 0.70
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (54 bp):
TTAATATAAAATAATTAGATAATTATAACTCATAATAATCAGACGATTATAATT
Found at i:1587838 original size:31 final size:32
Alignment explanation
Indices: 1587802--1587864 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
1587792 TATAACTCAT
1587802 AATAATCAGATGATTATAA-T-TTAAATTTAAA
1 AATAATCAGATGATTATAACTCTT-AATTTAAA
*
1587833 AATAATTAGATGATTATAACTCTTAATTTAAA
1 AATAATCAGATGATTATAACTCTTAATTTAAA
1587865 TTCAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 18 0.62
32 9 0.31
33 2 0.07
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (32 bp):
AATAATCAGATGATTATAACTCTTAATTTAAA
Found at i:1587915 original size:18 final size:19
Alignment explanation
Indices: 1587892--1587928 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1587882 TGATTACGAC
*
1587892 TTAAATTAAA-ATTTTAAA
1 TTAAATAAAATATTTTAAA
1587910 TTAAATAAAATATTTTAAA
1 TTAAATAAAATATTTTAAA
1587929 ATAATAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATAAAATATTTTAAA
Found at i:1588275 original size:14 final size:13
Alignment explanation
Indices: 1588256--1588310 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 13
1588246 TAAAAATTAA
1588256 AATAATAATATTTT
1 AATAAT-ATATTTT
*
1588270 AATAATTTATTTT
1 AATAATATATTTT
1588283 CAATAAATATTATTTT
1 -AAT-AATA-TATTTT
1588299 AATAATATATTT
1 AATAATATATTT
1588311 CAAAATTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 11 0.31
14 13 0.36
15 6 0.17
16 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
AATAATATATTTT
Found at i:1588282 original size:13 final size:13
Alignment explanation
Indices: 1588264--1588310 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
1588254 AAAATAATAA
1588264 TATTTTAATAATT
1 TATTTTAATAATT
1588277 TATTTTCAATAAATAT
1 TATTTT-AAT-AAT-T
*
1588293 TATTTTAATAATA
1 TATTTTAATAATT
1588306 TATTT
1 TATTT
1588311 CAAAATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.37
14 6 0.20
15 6 0.20
16 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:1591855 original size:62 final size:61
Alignment explanation
Indices: 1591774--1591893 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 61
1591764 ATAGTTTTAA
* *
1591774 ATTTTTTAAAAATCAATATTAATTTAAAAATTATAACTTTAAAAT-TTTTAT-TTTTAATTT
1 ATTTTTTAAAAATCAATATTAATTTAAAAA-TATAAATTTAAAATATTGTATATTTTAATTT
*
1591834 ATTTTATTAAAAAAT-AGATATTAATTTAAAAATATAAATTTTAAATATTGTATATTTTAA
1 ATTTT-TT-AAAAATCA-ATATTAATTTAAAAATATAAATTTAAAATATTGTATATTTTAA
1591894 AAAAGATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
60 5 0.10
61 15 0.29
62 26 0.50
63 6 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (61 bp):
ATTTTTTAAAAATCAATATTAATTTAAAAATATAAATTTAAAATATTGTATATTTTAATTT
Found at i:1591966 original size:15 final size:15
Alignment explanation
Indices: 1591927--1591970 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1591917 ACTTTTTTAT
1591927 TTTTTAAAATGTAAAA
1 TTTTTAAAAT-TAAAA
** *
1591943 TACTTAAAATTATAA
1 TTTTTAAAATTAAAA
1591958 TTTTTAAAATTAA
1 TTTTTAAAATTAA
1591971 TATCTATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
TTTTTAAAATTAAAA
Found at i:1592161 original size:18 final size:19
Alignment explanation
Indices: 1592138--1592176 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1592128 ATATCTAAAA
1592138 TAAAAA-TAAAAATAATTT
1 TAAAAATTAAAAATAATTT
* *
1592156 TAAAAATTAAATATGATTT
1 TAAAAATTAAAAATAATTT
1592175 TA
1 TA
1592177 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAAATTAAAAATAATTT
Found at i:1592763 original size:20 final size:21
Alignment explanation
Indices: 1592705--1592769 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1592695 TATTTTTCTA
* * *
1592705 TTAATACATCATATTTAATAT
1 TTAATATATTATATTTAATTT
* *
1592726 ATATTATATTATATTTAATATT
1 TTAATATATTATATTTAAT-TT
1592748 TTAATATATT-TA-TTAATTT
1 TTAATATATTATATTTAATTT
1592767 TTA
1 TTA
1592770 TAAAAAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 17 0.47
22 9 0.25
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATATATTATATTTAATTT
Found at i:1592766 original size:8 final size:9
Alignment explanation
Indices: 1592715--1592759 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
1592705 TTAATACATC
1592715 ATATTTAAT
1 ATATTTAAT
1592724 ATATATTATATT
1 ATAT-TTA-A-T
1592736 ATATTTAAT
1 ATATTTAAT
1592745 AT-TTTAAT
1 ATATTTAAT
1592753 ATATTTA
1 ATATTTA
1592760 TTAATTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 8 0.25
9 11 0.34
10 4 0.12
11 4 0.12
12 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATATTTAAT
Found at i:1592923 original size:15 final size:15
Alignment explanation
Indices: 1592899--1592952 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 15
1592889 CTACGGTTAG
1592899 AATA-TAAATATGTT
1 AATATTAAATATGTT
1592913 AATATTAAATATGATT
1 AATATTAAATATG-TT
*
1592929 -ATATT-AATAT-TA
1 AATATTAAATATGTT
*
1592941 AATATTATATAT
1 AATATTAAATAT
1592953 AATATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 1 0.03
13 5 0.15
14 13 0.38
15 13 0.38
16 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
AATATTAAATATGTT
Found at i:1592923 original size:21 final size:21
Alignment explanation
Indices: 1592899--1592998 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
1592889 CTACGGTTAG
*
1592899 AATATAAATATGTTAATATTA
1 AATATAAATATATTAATATTA
* *
1592920 AATATGATTATATTAATATTA
1 AATATAAATATATTAATATTA
* *
1592941 AATAT-TATATA-TAATATAAA
1 AATATAAATATATTAATAT-TA
*
1592961 AAAATTAAA-ATA-TAAT-TTA
1 AATA-TAAATATATTAATATTA
*
1592980 AA-ATAAATATATAAATATT
1 AATATAAATATATTAATATT
1592999 TTAAAATTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
17 4 0.06
18 4 0.06
19 12 0.19
20 11 0.17
21 31 0.49
22 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATAAATATATTAATATTA
Found at i:1592960 original size:18 final size:18
Alignment explanation
Indices: 1592911--1592957 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
1592901 TATAAATATG
1592911 TTAATATTAAATATGATTATA
1 TTAATATT-AA-AT-ATTATA
1592932 TTAATATTAAATATTATA
1 TTAATATTAAATATTATA
1592950 TATAATAT
1 T-TAATAT
1592958 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 2 0.08
21 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATATTAAATATTATA
Found at i:1592965 original size:22 final size:20
Alignment explanation
Indices: 1592940--1593020 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
1592930 TATTAATATT
1592940 AAATATTATATATAATATAAAA
1 AAAT-TTATATA-AATATAAAA
* * *
1592962 AAATTAAAATATAATTTAAAA
1 AAATTTATATA-AATATAAAA
***
1592983 TAAA--TATATAAATATTTTA
1 -AAATTTATATAAATATAAAA
1593002 AAATTTATATAAATATAAA
1 AAATTTATATAAATATAAA
1593021 TTATTAAAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
18 3 0.07
19 5 0.11
20 15 0.34
21 14 0.32
22 7 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTTATATAAATATAAAA
Found at i:1592993 original size:34 final size:34
Alignment explanation
Indices: 1592929--1593095 Score: 107
Period size: 33 Copynumber: 5.0 Consensus size: 34
1592919 AAATATGATT
* *
1592929 ATATTAATATTAA-ATATTATATATAATATA-AAAA
1 ATATTAAAATTAATATA-AATATA-AATATATAAAA
* *
1592963 A-ATTAAAATATAATTTAAA-ATAAATATATAAAT
1 ATATTAAAAT-TAATATAAATATAAATATATAAAA
* * *
1592996 ATTTTAAAATTTATATAAATATAAAT-TATTAAA
1 ATATTAAAATTAATATAAATATAAATATATAAAA
* * **
1593029 ATATTAAAATTTATATAAA-A-ATATAT-TAATT
1 ATATTAAAATTAATATAAATATAAATATATAAAA
* *
1593060 ATAATTATAATATAATAAAATATATAAATATATAAA
1 AT-ATTAAAAT-TAATATAA-ATATAAATATATAAA
1593096 TTATTAATTT
Statistics
Matches: 102, Mismatches: 19, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
31 7 0.07
32 15 0.15
33 50 0.49
34 19 0.19
35 3 0.03
36 5 0.05
37 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
ATATTAAAATTAATATAAATATAAATATATAAAA
Found at i:1592995 original size:8 final size:8
Alignment explanation
Indices: 1592982--1593096 Score: 52
Period size: 8 Copynumber: 14.8 Consensus size: 8
1592972 ATAATTTAAA
1592982 ATAAATAT
1 ATAAATAT
1592990 ATAAATATT
1 ATAAATA-T
* *
1592999 TTAAAATTT
1 AT-AAATAT
1593008 ATATAA-AT
1 ATA-AATAT
1593016 ATAAAT-T
1 ATAAATAT
1593023 ATTAAA-AT
1 A-TAAATAT
1593031 ATTAAA-AT
1 A-TAAATAT
*
1593039 -T-TATAT
1 ATAAATAT
*
1593045 AAAAATAT
1 ATAAATAT
*
1593053 ATTAAT-T
1 ATAAATAT
1593060 AT-AAT-T
1 ATAAATAT
1593066 AT-AATAT
1 ATAAATAT
1593073 AATAAAATAT
1 -AT-AAATAT
1593083 ATAAATAT
1 ATAAATAT
1593091 ATAAAT
1 ATAAAT
1593097 TATTAATTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
5 1 0.01
6 12 0.14
7 8 0.09
8 47 0.55
9 8 0.09
10 9 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAAATAT
Found at i:1593558 original size:16 final size:15
Alignment explanation
Indices: 1593515--1593565 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 15
1593505 TATAATATAA
*
1593515 TATTAAGATTTTTAT
1 TATTAATATTTTTAT
1593530 T-TT-ATATTTTTAT
1 TATTAATATTTTTAT
1593543 TATTAATATTTATTAT
1 TATTAATATTT-TTAT
*
1593559 AATTAAT
1 TATTAAT
1593566 TATAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.32
14 4 0.13
15 7 0.23
16 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTAATATTTTTAT
Found at i:1593580 original size:15 final size:15
Alignment explanation
Indices: 1593560--1593600 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1593550 ATTTATTATA
1593560 ATTAATTATAATAAT
1 ATTAATTATAATAAT
*
1593575 ATTAATTAT-AT-TT
1 ATTAATTATAATAAT
1593588 A-TAATTATAATAA
1 ATTAATTATAATAA
1593601 ATATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 2 0.09
15 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAATTATAATAAT
Found at i:1593605 original size:21 final size:21
Alignment explanation
Indices: 1593565--1593605 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1593555 TTATAATTAA
* *
1593565 TTATAATAATATTAATTATAT
1 TTATAATAATAATAAATATAT
*
1593586 TTATAATTATAATAAATATA
1 TTATAATAATAATAAATATA
1593606 ATATTATCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATAATAATAATAAATATAT
Found at i:1593607 original size:15 final size:14
Alignment explanation
Indices: 1593552--1593607 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
1593542 TTATTAATAT
*
1593552 TTATTATAAT-TAA
1 TTATAATAATATAA
1593565 TTATAATAATATTAA
1 TTATAATAATA-TAA
*
1593580 TTAT-AT-TTATAA
1 TTATAATAATATAA
1593592 TTATAATAAATATAA
1 TTATAAT-AATATAA
1593607 T
1 T
1593608 ATTATCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.20
13 13 0.37
14 2 0.06
15 13 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATAATAATATAA
Found at i:1594006 original size:19 final size:20
Alignment explanation
Indices: 1593979--1594018 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1593969 AATATATTTT
1593979 ATTAATTAAAAAAT-TTAAA
1 ATTAATTAAAAAATATTAAA
* *
1593998 ATTATTTAATAAATATTAAA
1 ATTAATTAAAAAATATTAAA
1594018 A
1 A
1594019 AATCTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATTAAAAAATATTAAA
Found at i:1594147 original size:16 final size:16
Alignment explanation
Indices: 1594098--1594152 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1594088 TAAAAATATA
*
1594098 TAAAAATATAATATGT
1 TAAATATATAATATGT
** * *
1594114 TATTTAAAT-ATATTT
1 TAAATATATAATATGT
1594129 TAAATATATAATATGT
1 TAAATATATAATATGT
1594145 TAAATATA
1 TAAATATA
1594153 ATTTTAACAC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (16 bp):
TAAATATATAATATGT
Found at i:1594306 original size:17 final size:16
Alignment explanation
Indices: 1594271--1594306 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1594261 TTAATTAAAA
*
1594271 TTATATTTAAAATATT
1 TTATATTTAAAAAATT
1594287 TTATATTTAAATAAATT
1 TTATATTTAAA-AAATT
1594304 TTA
1 TTA
1594307 ATCCGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTAAAAAATT
Done.