Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 6 of 45
Found at i:1149557 original size:15 final size:14
Alignment explanation
Indices: 1149535--1149569 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
1149525 TCAATTCTAA
1149535 TTTTATTTATTATT
1 TTTTATTTATTATT
1149549 TTATTATTTATTATT
1 TT-TTATTTATTATT
1149564 TTTTAT
1 TTTTAT
1149570 GTTGGGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTATT
Found at i:1153281 original size:2 final size:2
Alignment explanation
Indices: 1153274--1153317 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1153264 GGGCCAAAAC
*
1153274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1153316 AT
1 AT
1153318 CAATTTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1164700 original size:2 final size:2
Alignment explanation
Indices: 1164695--1164727 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1164685 TATATCAACT
1164695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1164728 GTATTAAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1165568 original size:6 final size:6
Alignment explanation
Indices: 1165531--1165564 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1165521 TATTCCAATC
*
1165531 TCATGG TCATGG TCATGG TCATGG TCATAG TCAT
1 TCATGG TCATGG TCATGG TCATGG TCATGG TCAT
1165565 AGTCTTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (6 bp):
TCATGG
Found at i:1168736 original size:2 final size:2
Alignment explanation
Indices: 1168731--1168765 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1168721 AAAAAAAACC
1168731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168766 TCTACTGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1170056 original size:184 final size:184
Alignment explanation
Indices: 1169747--1170112 Score: 635
Period size: 184 Copynumber: 2.0 Consensus size: 184
1169737 ATTGCAATGA
*
1169747 GGAATCTAAATTGTTCAGACTTTCAGGTGGTTCATAGGCTTGTCTTTGTATACACTGTACAGACA
1 GGAATCTAAATTGTTCAGACTTTCAGATGGTTCATAGGCTTGTCTTTGTATACACTGTACAGACA
* *
1169812 GTTCAAGGATTGCACCTGCTTGTTGTTTAACTAAGCAAAGTTAATTCAACGACCTTTGGAAATAT
66 GTTCAAAGATTGCACCTGCTTGTTGTTTAACTAAGCAAAGTTAATTAAACGACCTTTGGAAATAT
1169877 AAATGTCAGCTGGTGAGCTGAATCAAAAACTAAAAAAAGGCTATTTGGATATGT
131 AAATGTCAGCTGGTGAGCTGAATCAAAAACTAAAAAAAGGCTATTTGGATATGT
* *
1169931 GGAATCTAAATTGTTCAGACTTTCAGATGGTTCATAGGCTTGTCTTTGTATACATTGTACAGTCA
1 GGAATCTAAATTGTTCAGACTTTCAGATGGTTCATAGGCTTGTCTTTGTATACACTGTACAGACA
* * *
1169996 GTTCAAAGATTGCATCTGCTTGTTGTTTAACTAAGCAGAGTTAATTAAACTTA-CTTTGGAAATA
66 GTTCAAAGATTGCACCTGCTTGTTGTTTAACTAAGCAAAGTTAATTAAAC-GACCTTTGGAAATA
*
1170060 TAAATGTCAGCTGGTGAGCTGAATCAAAAACTAGAAAAAGGCTATTTGGATAT
130 TAAATGTCAGCTGGTGAGCTGAATCAAAAACTAAAAAAAGGCTATTTGGATAT
1170113 ACTGTCATAA
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 171 0.99
185 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (184 bp):
GGAATCTAAATTGTTCAGACTTTCAGATGGTTCATAGGCTTGTCTTTGTATACACTGTACAGACA
GTTCAAAGATTGCACCTGCTTGTTGTTTAACTAAGCAAAGTTAATTAAACGACCTTTGGAAATAT
AAATGTCAGCTGGTGAGCTGAATCAAAAACTAAAAAAAGGCTATTTGGATATGT
Found at i:1171148 original size:64 final size:64
Alignment explanation
Indices: 1171043--1171166 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 64
1171033 TATACATAGT
* *
1171043 TCCCAAACTTTTTGAGCTGCATTTATTTTTTTGATGATGGCCTACACTGCTAATAACAAAAATC
1 TCCCAAACTTTTTGAGCTGCATTTATGTTTTCGATGATGGCCTACACTGCTAATAACAAAAATC
*
1171107 TCCCAAACTTTTTGAGCTGCATTTATGTTTTCGATGCTGGCCTACACTGCTAATAACAAA
1 TCCCAAACTTTTTGAGCTGCATTTATGTTTTCGATGATGGCCTACACTGCTAATAACAAA
1171167 GATCAAATAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (64 bp):
TCCCAAACTTTTTGAGCTGCATTTATGTTTTCGATGATGGCCTACACTGCTAATAACAAAAATC
Found at i:1172115 original size:20 final size:20
Alignment explanation
Indices: 1172092--1172147 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1172082 ATTTTTTTTA
* *
1172092 TTATTATCAAATTATTATTT
1 TTATTATTAAATTAATATTT
1172112 TTA-TATTAATATTAATATTT
1 TTATTATTAA-ATTAATATTT
1172132 TTATTATTAAA-TAATA
1 TTATTATTAAATTAATA
1172148 ATTTAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 10 0.31
20 16 0.50
21 6 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTAAATTAATATTT
Found at i:1172875 original size:21 final size:22
Alignment explanation
Indices: 1172851--1172891 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1172841 TAGAATTACG
*
1172851 ATTTAAATTT-TTTTAATTTTT
1 ATTTAAATTTAATTTAATTTTT
1172872 ATTTAAATTTAATTTAATTT
1 ATTTAAATTTAATTTAATTT
1172892 ACAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTAAATTTAATTTAATTTTT
Found at i:1176597 original size:2 final size:2
Alignment explanation
Indices: 1176587--1176619 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1176577 GTATATATCT
*
1176587 AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1176620 TGGAAGTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1180077 original size:2 final size:2
Alignment explanation
Indices: 1180070--1180116 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1180060 TCTCAAATAT
1180070 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1180112 TC TC T
1 TC TC T
1180117 TTGTCTATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1182528 original size:2 final size:2
Alignment explanation
Indices: 1182521--1182559 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1182511 GACTCTAAAA
1182521 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1182560 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1182564 original size:2 final size:2
Alignment explanation
Indices: 1182559--1182585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1182549 TCTCTCTCTC
1182559 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1182586 GGACTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1183524 original size:1 final size:1
Alignment explanation
Indices: 1183518--1183542 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1183508 AGAAGAATAA
1183518 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1183543 ACATCAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1183799 original size:2 final size:2
Alignment explanation
Indices: 1183788--1183821 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1183778 CAAAAACAAT
1183788 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1183822 GCAATGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1184694 original size:21 final size:21
Alignment explanation
Indices: 1184637--1184688 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1184627 ATTTAATGTA
*
1184637 TAATATATTTATA-TAAATTT
1 TAATATATTTATATTATATTT
1184657 TAATATATTTATATTATATTT
1 TAATATATTTATATTATATTT
*
1184678 TATTATTATTT
1 TAATA-TATTT
1184689 TTTTATGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.46
21 10 0.36
22 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATATATTTATATTATATTT
Found at i:1184802 original size:3 final size:3
Alignment explanation
Indices: 1184794--1184823 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1184784 CTCTATAAGC
*
1184794 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1184824 GTAGTAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1186349 original size:18 final size:19
Alignment explanation
Indices: 1186309--1186352 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1186299 ATATAAGATA
1186309 AATTTT-TAAAGAAAATAT
1 AATTTTATAAAGAAAATAT
1186327 AATTTTATAAA-AAAAT-T
1 AATTTTATAAAGAAAATAT
1186344 ATATTTTAT
1 A-ATTTTAT
1186353 TACTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 18 0.75
19 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTATAAAGAAAATAT
Found at i:1186637 original size:18 final size:18
Alignment explanation
Indices: 1186614--1186651 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1186604 TTTAATATAT
1186614 AATAATA-TTATTATAATA
1 AATAATACTT-TTATAATA
*
1186632 AATAATACTTTTATGATA
1 AATAATACTTTTATAATA
1186650 AA
1 AA
1186652 AGTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AATAATACTTTTATAATA
Found at i:1186650 original size:21 final size:21
Alignment explanation
Indices: 1186606--1186650 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1186596 TTATTATATT
* *
1186606 TAATATATAATAATATTATTA
1 TAATAAATAATAATATTATGA
* *
1186627 TAATAAATAATACTTTTATGA
1 TAATAAATAATAATATTATGA
1186648 TAA
1 TAA
1186651 AAGTTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATAAATAATAATATTATGA
Found at i:1190301 original size:2 final size:2
Alignment explanation
Indices: 1190294--1190329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1190284 GCAAACCAAG
1190294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1190330 CCTTTTGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1191394 original size:2 final size:2
Alignment explanation
Indices: 1191387--1191424 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1191377 TATCAATTTC
1191387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1191425 TTTTCCCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1191489 original size:2 final size:2
Alignment explanation
Indices: 1191482--1191518 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1191472 TAATTTGGGC
1191482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1191519 TGCTTTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1192109 original size:13 final size:13
Alignment explanation
Indices: 1192091--1192115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192081 TAATAAAAAA
1192091 TTAAAAAATTTAT
1 TTAAAAAATTTAT
1192104 TTAAAAAATTTA
1 TTAAAAAATTTA
1192116 AAATTTTAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAAAATTTAT
Found at i:1192110 original size:21 final size:21
Alignment explanation
Indices: 1192084--1192123 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1192074 TAAAATATAA
1192084 TAAAAAATTAAAAAATTTATT
1 TAAAAAATTAAAAAATTTATT
* *
1192105 TAAAAAATTTAAAATTTTA
1 TAAAAAATTAAAAAATTTA
1192124 AATCTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATTAAAAAATTTATT
Found at i:1195651 original size:20 final size:22
Alignment explanation
Indices: 1195633--1195713 Score: 60
Period size: 23 Copynumber: 3.7 Consensus size: 22
1195623 TGAATAATAA
1195633 ATAATATATTTAATAAATATA-
1 ATAATATATTTAATAAATATAC
* ** *
1195654 AAAATA-ATAAAATAAATATGAT
1 ATAATATATTTAATAAATAT-AC
*
1195676 ATAATATATTTAA-ATATATTAAC
1 ATAATATATTTAATAAATA-T-AC
*
1195699 ATGATATATTTAATA
1 ATAATATATTTAATA
1195714 TATTTTATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 11 0.24
21 6 0.13
22 9 0.20
23 18 0.40
24 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATATATTTAATAAATATAC
Found at i:1195714 original size:32 final size:33
Alignment explanation
Indices: 1195625--1195718 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 33
1195615 AATAATTTTG
* *
1195625 AATAAT-AAAT-AATATATTTAATAAATATAAA
1 AATAATAAAATAAATATATTTAATATATTTAAA
*
1195656 AATAATAAAATAAATATGATATAATATATTTAAA
1 AATAATAAAATAAATAT-ATTTAATATATTTAAA
* * * *
1195690 TATATTAACAT-GATATATTTAATATATTT
1 AATAATAAAATAAATATATTTAATATATTT
1195719 TATTTAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 6 0.12
32 16 0.31
33 9 0.17
34 21 0.40
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (33 bp):
AATAATAAAATAAATATATTTAATATATTTAAA
Found at i:1197396 original size:29 final size:28
Alignment explanation
Indices: 1197344--1197412 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 28
1197334 CTTTGGAACG
1197344 TTTTTATATTTTTATTATATTTAAAT-AA
1 TTTTTAT-TTTTTATTATATTTAAATGAA
*
1197372 TTTTTATTTTTTATTTTATGCTTAAATGAA
1 TTTTTATTTTTTATTATAT--TTAAATGAA
1197402 TTTTTATTTTT
1 TTTTTATTTTT
1197413 AAATTCTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 11 0.30
28 7 0.19
29 6 0.16
30 13 0.35
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTTATTTTTTATTATATTTAAATGAA
Found at i:1197413 original size:29 final size:26
Alignment explanation
Indices: 1197345--1197413 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
1197335 TTTGGAACGT
1197345 TTTTATATTTTTATTATATTTAAATAA
1 TTTT-TATTTTTATTATATTTAAATAA
*
1197372 TTTTTATTTTTTATTTTATGCTTAAATGAA
1 TTTTTA-TTTTTATTATAT--TTAAAT-AA
1197402 TTTTTATTTTTA
1 TTTTTATTTTTA
1197414 AATTCTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.05
27 15 0.41
29 12 0.32
30 8 0.22
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTTATTTTTATTATATTTAAATAA
Found at i:1202729 original size:2 final size:2
Alignment explanation
Indices: 1202722--1202749 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1202712 TTTCACATTA
1202722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1202750 TATTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1204121 original size:12 final size:12
Alignment explanation
Indices: 1204106--1204139 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1204096 ACACACAGAT
1204106 ATACATATATAC
1 ATACATATATAC
*
1204118 ATACATATATAT
1 ATACATATATAC
*
1204130 ATATATATAT
1 ATACATATAT
1204140 TGGTGGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ATACATATATAC
Found at i:1206455 original size:40 final size:41
Alignment explanation
Indices: 1206368--1206456 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 41
1206358 TATTAATAAT
* *
1206368 AAATTT-TTTAATTTTATAAATAAAATTAAAAAATATTATA
1 AAATTTATTTAATTTTATAAATAAAATTAAAAAACATTAAA
* * * *
1206408 TATTTTATTT-ATTTTTTAAAT-ATATTAAAAATACATTAAA
1 AAATTTATTTAATTTTATAAATAAAATTAAAAA-ACATTAAA
1206448 AAATTTATT
1 AAATTTATT
1206457 ATTCATATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
39 9 0.23
40 27 0.69
41 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (41 bp):
AAATTTATTTAATTTTATAAATAAAATTAAAAAACATTAAA
Found at i:1207569 original size:21 final size:21
Alignment explanation
Indices: 1207539--1207583 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1207529 TAATTTAATA
1207539 AATTTAAAATT-TTAATTTTTT
1 AATTTAAAATTATT-ATTTTTT
*
1207560 AATTTTAAATTATTATTTTTT
1 AATTTAAAATTATTATTTTTT
1207581 AAT
1 AAT
1207584 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTAAAATTATTATTTTTT
Found at i:1207988 original size:3 final size:3
Alignment explanation
Indices: 1207980--1208013 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1207970 TCCATATTAT
1207980 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1208014 CAAAACAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1208583 original size:22 final size:20
Alignment explanation
Indices: 1208543--1208604 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
1208533 ATTTAATACA
1208543 TTTTAAATTATAAAATAAAT
1 TTTTAAATTATAAAATAAAT
1208563 TTTTAAATT-T--AATAAAT
1 TTTTAAATTATAAAATAAAT
* *
1208580 TAAATTAAATT-TTAAATAAAT
1 T--TTTAAATTATAAAATAAAT
1208601 TTTT
1 TTTT
1208605 TTTATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 8 0.22
19 11 0.31
20 9 0.25
21 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAAATTATAAAATAAAT
Found at i:1208588 original size:39 final size:38
Alignment explanation
Indices: 1208489--1208604 Score: 114
Period size: 38 Copynumber: 3.0 Consensus size: 38
1208479 TCCACTTATA
* * *
1208489 TAAATATTAATATATTAATATAAAATA-AAAATAATTTTAT
1 TAAAT-TTAATAAATTAAT-TAAATTATAAAATAAATTT-T
*
1208529 TAATATTTAATACATT--TTAAATTATAAAATAAATTTT
1 TAA-ATTTAATAAATTAATTAAATTATAAAATAAATTTT
*
1208566 TAAATTTAATAAATTAAATTAAATT-TTAAATAAATTTT
1 TAAATTTAATAAATT-AATTAAATTATAAAATAAATTTT
1208604 T
1 T
1208605 TTTATTATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
36 11 0.17
37 10 0.15
38 24 0.36
39 7 0.11
40 12 0.18
41 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
TAAATTTAATAAATTAATTAAATTATAAAATAAATTTT
Found at i:1209667 original size:3 final size:3
Alignment explanation
Indices: 1209644--1209690 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1209634 ACATTTCATC
*
1209644 AAT AA- AAT AAAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1209689 AA
1 AA
1209691 AGAATAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1210040 original size:59 final size:59
Alignment explanation
Indices: 1209948--1210062 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
1209938 ACAGCTCCAG
* * *
1209948 TCCGTTGATTCTTGCCCCGTTGTCGGATTAAAGAATAAATTCCTTATTCTAATATTTGA
1 TCCGTTAATTCTTGCCCCATTGTCGGATTAAAGAATAAATTCCGTATTCTAATATTTGA
* * *
1210007 TCCGTTAATTCTTGCCCCATTGTCGGGTTAAAGAATGAATTTCGTATTCTAATATT
1 TCCGTTAATTCTTGCCCCATTGTCGGATTAAAGAATAAATTCCGTATTCTAATATT
1210063 ATATTTTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (59 bp):
TCCGTTAATTCTTGCCCCATTGTCGGATTAAAGAATAAATTCCGTATTCTAATATTTGA
Found at i:1214785 original size:16 final size:16
Alignment explanation
Indices: 1214766--1214805 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1214756 ATTTATCGGA
*
1214766 TAATTTA-ATAATTTAT
1 TAATTTATATAA-TAAT
1214782 TAATTTATATAATAAT
1 TAATTTATATAATAAT
1214798 TAATTTAT
1 TAATTTAT
1214806 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTATATAATAAT
Found at i:1214819 original size:21 final size:23
Alignment explanation
Indices: 1214774--1214826 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
1214764 GATAATTTAA
1214774 TAATTTATTAATTTATATAATAAT
1 TAATTTATT-ATTTATATAATAAT
*
1214798 TAATTTATT-TTT-TATTATAAT
1 TAATTTATTATTTATATAATAAT
1214819 TATATTTA
1 TA-ATTTA
1214827 AAATATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 10 0.37
22 8 0.30
24 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATTTATTATTTATATAATAAT
Found at i:1214840 original size:8 final size:8
Alignment explanation
Indices: 1214774--1214902 Score: 62
Period size: 8 Copynumber: 17.0 Consensus size: 8
1214764 GATAATTTAA
*
1214774 TAATTTAT
1 TAATATAT
*
1214782 TAATTTAT
1 TAATATAT
1214790 ATAATA-AT
1 -TAATATAT
*
1214798 TAATTTAT
1 TAATATAT
* *
1214806 T-TTTTAT
1 TAATATAT
1214813 T-ATA-AT
1 TAATATAT
1214819 T-ATAT-T
1 TAATATAT
*
1214825 TAAAATAT
1 TAATATAT
1214833 TAATATA-
1 TAATATAT
*
1214840 TAA-ATTT
1 TAATATAT
1214847 TAATATAT
1 TAATATAT
1214855 TAATA-AT
1 TAATATAT
*
1214862 TTATATTAT
1 TAATA-TAT
*
1214871 ATAA-ATTT
1 -TAATATAT
1214879 TAATATAT
1 TAATATAT
*
1214887 TTATATAT
1 TAATATAT
*
1214895 TTATATAT
1 TAATATAT
1214903 CATAATTAAA
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
6 10 0.10
7 29 0.30
8 48 0.50
9 7 0.07
10 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TAATATAT
Found at i:1214844 original size:14 final size:14
Alignment explanation
Indices: 1214827--1214886 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
1214817 ATTATATTTA
1214827 AAATATTAATATAT
1 AAATATTAATATAT
*
1214841 AAATTTTAATATAT
1 AAATATTAATATAT
*
1214855 TAATAATTTATATTATAT
1 AAAT-A-TTA-A-TATAT
*
1214873 AAATTTTAATATAT
1 AAATATTAATATAT
1214887 TTATATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 6 0.16
17 1 0.03
18 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTAATATAT
Found at i:1214849 original size:22 final size:22
Alignment explanation
Indices: 1214823--1214886 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1214813 TATAATTATA
1214823 TTTAAAATATTAATATATAAAT
1 TTTAAAATATTAATATATAAAT
* * *
1214845 TTTAATATATTAATAATTTATAT
1 TTTAAAATATTAAT-ATATAAAT
* *
1214868 TATATAAATTTTAATATAT
1 TTTA-AAATATTAATATAT
1214887 TTATATATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 13 0.39
23 12 0.36
24 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAATATTAATATATAAAT
Found at i:1214875 original size:32 final size:33
Alignment explanation
Indices: 1214836--1214900 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1214826 AAAATATTAA
1214836 TATATAAATTTTAATATATTAATA-ATTTATAT
1 TATATAAATTTTAATATATTAATATATTTATAT
*
1214868 TATATAAATTTTAATATATTTATATATTTATAT
1 TATATAAATTTTAATATATTAATATATTTATAT
1214901 ATCATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATATAAATTTTAATATATTAATATATTTATAT
Found at i:1215246 original size:2 final size:2
Alignment explanation
Indices: 1215239--1215265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1215229 TAATTTTTAA
1215239 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 A
1215266 AAGATTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1216011 original size:26 final size:27
Alignment explanation
Indices: 1215982--1216036 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1215972 ATTTTACTTA
*
1215982 ATAT-AATTAACAATTAAAAAATTTTT
1 ATATAAATAAACAATTAAAAAATTTTT
* *
1216008 ATATCAAATAAATAATTAAAATATTTTT
1 ATAT-AAATAAACAATTAAAAAATTTTT
1216036 A
1 A
1216037 AGTAGTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
28 20 0.83
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAAATAAACAATTAAAAAATTTTT
Found at i:1218650 original size:9 final size:9
Alignment explanation
Indices: 1218636--1218681 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
1218626 AAATATGAGA
1218636 AAAATTTAT
1 AAAATTTAT
*
1218645 AAAATTTTT
1 AAAATTTAT
1218654 AAAATTTAT
1 AAAATTTAT
1218663 AAAAATTT-T
1 -AAAATTTAT
1218672 AAAATTTAT
1 AAAATTTAT
1218681 A
1 A
1218682 TAATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.21
9 19 0.58
10 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAAATTTAT
Found at i:1218659 original size:18 final size:18
Alignment explanation
Indices: 1218636--1218681 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1218626 AAATATGAGA
*
1218636 AAAATTTATAAAATTTTT
1 AAAATTTATAAAAATTTT
1218654 AAAATTTATAAAAATTTT
1 AAAATTTATAAAAATTTT
1218672 AAAATTTATA
1 AAAATTTATA
1218682 TAATAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTATAAAAATTTT
Found at i:1218782 original size:17 final size:17
Alignment explanation
Indices: 1218702--1218780 Score: 65
Period size: 17 Copynumber: 4.5 Consensus size: 17
1218692 TTAATATACC
1218702 AAAAT-TTAT-AAATA-
1 AAAATATTATAAAATAT
*
1218716 AAAATATTTTAAACATAATT
1 AAAATATTATAAA-AT-A-T
* *
1218736 ATAATATAATAAAATAT
1 AAAATATTATAAAATAT
1218753 AAAATATTATAAAATAT
1 AAAATATTATAAAATAT
1218770 ATAAATTATTA
1 A-AAA-TATTA
1218781 AATTTAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 2 0.04
17 19 0.37
18 5 0.10
19 7 0.14
20 10 0.20
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATTATAAAATAT
Found at i:1218867 original size:21 final size:19
Alignment explanation
Indices: 1218821--1218870 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
1218811 TTAAAATTAT
*
1218821 TAAAAATAAATAATTAAAA
1 TAAAATTAAATAATTAAAA
* *
1218840 TATAATTAAATAAATTTAATA
1 TAAAATTAAAT-AA-TTAAAA
1218861 TAAAATTAAA
1 TAAAATTAAA
1218871 AATAAATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAATTAAATAATTAAAA
Found at i:1219433 original size:3 final size:3
Alignment explanation
Indices: 1219425--1219461 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1219415 TTTTACTCTC
1219425 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1219462 GAACTAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1225201 original size:2 final size:2
Alignment explanation
Indices: 1225194--1225219 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1225184 AAATAAGGTG
1225194 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1225220 GACTTTCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1226422 original size:10 final size:10
Alignment explanation
Indices: 1226403--1226433 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1226393 TTGCACGTTA
1226403 TTTTATAATTT
1 TTTTA-AATTT
1226414 TTTTAAATTT
1 TTTTAAATTT
1226424 TTTTAAATTT
1 TTTTAAATTT
1226434 ACATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:1231311 original size:2 final size:2
Alignment explanation
Indices: 1231304--1231330 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1231294 GAACACCCCA
1231304 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1231331 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1238808 original size:11 final size:11
Alignment explanation
Indices: 1238792--1238821 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1238782 GGTTTTTTAA
1238792 AAAATTAAATT
1 AAAATTAAATT
1238803 AAAATTAAATT
1 AAAATTAAATT
1238814 AAATATTA
1 AAA-ATTA
1238822 TATCTAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:1238982 original size:21 final size:21
Alignment explanation
Indices: 1238930--1238982 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1238920 TTTTTTTTTT
**
1238930 ATTTTAAAAATAAAATATTTA
1 ATTTTAATTATAAAATATTTA
*
1238951 TTTTTATATTATAAAAT-TTTAA
1 ATTTTA-ATTATAAAATATTT-A
1238973 ATTTTAATTA
1 ATTTTAATTA
1238983 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAATTATAAAATATTTA
Found at i:1248217 original size:23 final size:23
Alignment explanation
Indices: 1248191--1248237 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1248181 AGTAACACTT
*
1248191 TTAACAATTAATTTTCATCTAGG
1 TTAACAATTAATTTTCATCAAGG
1248214 TTAACAATTAATTTTCATCAAGG
1 TTAACAATTAATTTTCATCAAGG
1248237 T
1 T
1248238 GGCCGTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
TTAACAATTAATTTTCATCAAGG
Found at i:1255102 original size:34 final size:33
Alignment explanation
Indices: 1255054--1255274 Score: 275
Period size: 34 Copynumber: 6.5 Consensus size: 33
1255044 TGTTAAAAAC
1255054 CACCATTTAATCAACAATGGTAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1255087 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1255121 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1255155 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1255189 CTCTCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CAC-CATTTAATCAACAATGG-TAACCTACCAAAT
*
1255223 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1255257 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1255275 TCTCCCACTT
Statistics
Matches: 164, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
33 23 0.14
34 135 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1255233 original size:102 final size:101
Alignment explanation
Indices: 1255054--1255274 Score: 363
Period size: 102 Copynumber: 2.2 Consensus size: 101
1255044 TGTTAAAAAC
* *
1255054 CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
1255119 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** *
1255155 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGTAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAACCACC
1255219 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1255257 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1255275 TCTCCCACTT
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 17 0.15
102 93 0.85
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1259719 original size:34 final size:33
Alignment explanation
Indices: 1259676--1259898 Score: 207
Period size: 34 Copynumber: 6.6 Consensus size: 33
1259666 GGTTTGGTAA
*
1259676 AAATCACCATTTAATCAACAATGACAACCTACC
1 AAATCACCATTTAATCAACAATGATAACCTACC
* *
1259709 AAATCTACCATTTAGTCAACAATGGTAAGCC-ACC
1 AAATC-ACCATTTAATCAACAATGATAA-CCTACC
* * * *
1259743 AAATCACCCATTTAATTAATAATGGTAAGCTACC
1 AAATCA-CCATTTAATCAACAATGATAACCTACC
** *
1259777 AAATTTCTCATTTAATCAACAATGATAAGCTACC
1 AAATCAC-CATTTAATCAACAATGATAACCTACC
* * * *
1259811 AAATCTCCCATTTAGTTAACAATGGTAAACC-ACC
1 AAATC-ACCATTTAATCAACAATGAT-AACCTACC
* * *
1259845 AAATCACCCATTTAATTAACAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGATAACCTACC
*
1259879 TAATCACCATTTAATCAACA
1 AAATCACCATTTAATCAACA
1259899 TAAACCACGA
Statistics
Matches: 158, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
33 24 0.15
34 128 0.81
35 6 0.04
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.27
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGATAACCTACC
Found at i:1259789 original size:68 final size:66
Alignment explanation
Indices: 1259676--1259898 Score: 239
Period size: 68 Copynumber: 3.3 Consensus size: 66
1259666 GGTTTGGTAA
* ** * * *
1259676 AAATCACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATTAACAATGGTAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTA
1259741 CC
65 CC
* * * *
1259743 AAATCACCCATTTAATTAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGATAAGCT
1 AAATCA-CCATTTAATTAACAATGGTAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCT
1259808 ACC
64 ACC
* * * * * *
1259811 AAATCTCCCATTTAGTTAACAATGGTAAACCACCAAATCACCCATTTAATTAACAATGGTAAACT
1 AAATC-ACCATTTAATTAACAATGGTAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCT
1259876 ACC
64 ACC
* *
1259879 TAATCACCATTTAATCAACA
1 AAATCACCATTTAATTAACA
1259899 TAAACCACGA
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
67 20 0.16
68 108 0.84
69 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.27
Consensus pattern (66 bp):
AAATCACCATTTAATTAACAATGGTAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTAC
C
Found at i:1259859 original size:102 final size:101
Alignment explanation
Indices: 1259676--1259898 Score: 347
Period size: 102 Copynumber: 2.2 Consensus size: 101
1259666 GGTTTGGTAA
*
1259676 AAATCACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCA
* *
1259741 CCAAATCACCCATTTAATTAATAATGGTAAGCTACC
66 CCAAATCACCCATTTAATTAACAATGGTAAACTACC
** * * * *
1259777 AAATTTCTCATTTAATCAACAATGATAAGCTACCAAATCTCCCATTTAGTTAACAATGGTAAACC
1 AAATCAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACC
1259842 ACCAAATCACCCATTTAATTAACAATGGTAAACTACC
65 ACCAAATCACCCATTTAATTAACAATGGTAAACTACC
*
1259879 TAATCACCATTTAATCAACA
1 AAATCACCATTTAATCAACA
1259899 TAAACCACGA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
101 18 0.17
102 91 0.83
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.27
Consensus pattern (101 bp):
AAATCACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCA
CCAAATCACCCATTTAATTAACAATGGTAAACTACC
Found at i:1261698 original size:2 final size:2
Alignment explanation
Indices: 1261691--1261718 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1261681 ATTATCATTA
1261691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1261719 CCAAAATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1262407 original size:22 final size:22
Alignment explanation
Indices: 1262382--1262439 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1262372 TTTTGTATAT
1262382 AATATTTTTTA-AAATATTCATC
1 AATATTTTTTATAAA-ATTCATC
* *
1262404 AATA-CTTTTATGAAATTCATC
1 AATATTTTTTATAAAATTCATC
*
1262425 AA-ATTTTTTAGAAAA
1 AATATTTTTTATAAAA
1262440 CATAAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (22 bp):
AATATTTTTTATAAAATTCATC
Found at i:1263477 original size:23 final size:23
Alignment explanation
Indices: 1263442--1263495 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1263432 TTTAATGATA
1263442 TTAA-ATAAATATATTAAAATAT
1 TTAATATAAATATATTAAAATAT
* *
1263464 TTAATATAATTATATTATAATAT
1 TTAATATAAATATATTAAAATAT
*
1263487 CTAAT-TAAA
1 TTAATATAAA
1263496 AATAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATATAAATATATTAAAATAT
Found at i:1263516 original size:29 final size:30
Alignment explanation
Indices: 1263484--1263540 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1263474 TATATTATAA
*
1263484 TATCT-AAT-TAAAAATAAAAATTCGTAAAC
1 TATCTAAATATAAAAAAAAAAATT-GTAAAC
1263513 TATCTAAATATAAAAAAAAAAATTGTAA
1 TATCTAAATATAAAAAAAAAAATTGTAA
1263541 GGACAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 7 0.28
31 13 0.52
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.30
Consensus pattern (30 bp):
TATCTAAATATAAAAAAAAAAATTGTAAAC
Found at i:1273138 original size:18 final size:19
Alignment explanation
Indices: 1273107--1273150 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1273097 ATTAAAATAG
1273107 ATAAATTAAAATAAT-TAA
1 ATAAATTAAAATAATATAA
** *
1273125 ATAAATTATTATAATATAT
1 ATAAATTAAAATAATATAA
1273144 ATAAATT
1 ATAAATT
1273151 TACTTGTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAATTAAAATAATATAA
Found at i:1273309 original size:19 final size:19
Alignment explanation
Indices: 1273281--1273324 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1273271 AAAAATATAA
* * *
1273281 ATTAAATGAAACTTAAATT
1 ATTAATTGAAAATAAAATT
1273300 ATTAATTGAAAATAAAATT
1 ATTAATTGAAAATAAAATT
1273319 ATTAAT
1 ATTAAT
1273325 AATTAGTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTAATTGAAAATAAAATT
Found at i:1274164 original size:18 final size:18
Alignment explanation
Indices: 1274141--1274191 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1274131 AAACACATTG
1274141 TATTAAATATATATATAT
1 TATTAAATATATATATAT
*
1274159 TATTAAATATAT-TAAAAT
1 TATTAAATATATAT-ATAT
*
1274177 TA-TAAATATAAATAT
1 TATTAAATATATATAT
1274192 CATATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTAAATATATATATAT
Found at i:1278492 original size:27 final size:27
Alignment explanation
Indices: 1278462--1278524 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
1278452 TAAAGTATAA
*
1278462 ACTCAAGTTCAAAAGAGATTTTTAGAG
1 ACTCAAGTTCAAAAGAGATTCTTAGAG
1278489 ACTCAAGTTCAAAAGAGATTCTTAGAG
1 ACTCAAGTTCAAAAGAGATTCTTAGAG
*
1278516 AATCAAGTT
1 ACTCAAGTT
1278525 TGTTTCCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (27 bp):
ACTCAAGTTCAAAAGAGATTCTTAGAG
Found at i:1280674 original size:14 final size:13
Alignment explanation
Indices: 1280611--1280683 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
1280601 AATAATATTA
1280611 AATATTTAAATTT
1 AATATTTAAATTT
* *
1280624 ATTA-TCAAATTT
1 AATATTTAAATTT
*
1280636 --TAATTAAATTT
1 AATATTTAAATTT
* *
1280647 ATTAATAATAAATTT
1 AAT-AT-TTAAATTT
1280662 AATTATTTAAATTT
1 AA-TATTTAAATTT
1280676 AATATTTA
1 AATATTTA
1280684 TTTAAAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 2 0.04
11 7 0.15
12 7 0.15
13 10 0.21
14 10 0.21
15 10 0.21
16 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTAAATTT
Found at i:1280859 original size:3 final size:3
Alignment explanation
Indices: 1280851--1280879 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1280841 GTAAGTTGAA
1280851 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1280880 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1281357 original size:14 final size:14
Alignment explanation
Indices: 1281338--1281372 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1281328 CCATTACCTC
*
1281338 TATTCATAAATAAA
1 TATTCACAAATAAA
1281352 TATTCACAAATAAA
1 TATTCACAAATAAA
1281366 TAATTCA
1 T-ATTCA
1281373 AAACATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (14 bp):
TATTCACAAATAAA
Found at i:1281571 original size:26 final size:26
Alignment explanation
Indices: 1281525--1281583 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1281515 TTTTTATACG
* *
1281525 ATAAAAATAATTTAATATATAAAAAT
1 ATAAAATTAATATAATATATAAAAAT
* *
1281551 ATAAAATTAATAT-ATATTATATAATT
1 ATAAAATTAATATAATA-TATAAAAAT
1281577 ATAAAAT
1 ATAAAAT
1281584 AAAAATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATAAAATTAATATAATATATAAAAAT
Found at i:1281968 original size:22 final size:22
Alignment explanation
Indices: 1281940--1281981 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1281930 CACCCTCGTG
1281940 GGATGCTGGATGCGAGAGGGTA
1 GGATGCTGGATGCGAGAGGGTA
* *
1281962 GGATGCTGGCTGCGTGAGGG
1 GGATGCTGGATGCGAGAGGG
1281982 GCGAGCCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.52, T:0.19
Consensus pattern (22 bp):
GGATGCTGGATGCGAGAGGGTA
Found at i:1288034 original size:2 final size:2
Alignment explanation
Indices: 1288029--1288060 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1288019 AGTAAAAAAG
1288029 TC TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1288061 TTGTCAAAAT
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1288051 original size:15 final size:15
Alignment explanation
Indices: 1288031--1288061 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1288021 TAAAAAAGTC
1288031 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
1288046 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
1288061 T
1 T
1288062 TGTCAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCTCTCTCTCTCT
Found at i:1289061 original size:174 final size:172
Alignment explanation
Indices: 1288745--1289063 Score: 430
Period size: 174 Copynumber: 1.8 Consensus size: 172
1288735 AATAATTATT
* *
1288745 ATAAATGATATAATATTATAACAAAAATTAAATAAAAATTTTAATACGTATTTTTTTAATATCAT
1 ATAAATGATATAATATTATAACAAAAATTAAATAAAAATTTAAATACGCATTTTTTTAATATCAT
* * *
1288810 TTATAAAATTATAAAAAAATTATATTATTAATGCGTTAACGATGAACCCATCTTACAAATCTATT
66 TTATAAAAATATAAAAAAATTATATTATTAATACGTTAACGATGAACCCATCTCACAAATCTATT
1288875 AAATCTACATAATTATTTAACATTAATTGTATTACAATAATC
131 AAATCTACATAATTATTTAACATTAATTGTATTACAATAATC
* *
1288917 ATAAATGATAT-ATTTTAATAATAAAAATTAAATAAAAAATTTAAATACATGACATTTTTTTAAT
1 ATAAATGATATAATATT-ATAACAAAAATTAAAT-AAAAATTTAAATAC--G-CATTTTTTTAAT
* * * * **
1288981 TTTATCTT-TAAAAAT-TAAAAAAATT-TATTGTTAATACGTTAATGATGAACCCATCTCATGAA
61 ATCAT-TTATAAAAATATAAAAAAATTATATTATTAATACGTTAACGATGAACCCATCTCACAAA
*
1289043 TCTGTTAAATCTACATAATTA
125 TCTATTAAATCTACATAATTA
1289064 CTTCTATTAT
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
171 4 0.03
172 26 0.20
173 13 0.10
174 51 0.40
175 11 0.09
176 20 0.16
177 2 0.02
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (172 bp):
ATAAATGATATAATATTATAACAAAAATTAAATAAAAATTTAAATACGCATTTTTTTAATATCAT
TTATAAAAATATAAAAAAATTATATTATTAATACGTTAACGATGAACCCATCTCACAAATCTATT
AAATCTACATAATTATTTAACATTAATTGTATTACAATAATC
Found at i:1290903 original size:2 final size:2
Alignment explanation
Indices: 1290896--1290930 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1290886 CTTGTAACTG
* *
1290896 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1290931 GGCTATAGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1291946 original size:13 final size:13
Alignment explanation
Indices: 1291928--1291952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1291918 CCTAAACTAA
1291928 TCTTGGATTAGAT
1 TCTTGGATTAGAT
1291941 TCTTGGATTAGA
1 TCTTGGATTAGA
1291953 ATTTAAATAA
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:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
TCTTGGATTAGAT
Found at i:1292068 original size:2 final size:2
Alignment explanation
Indices: 1292019--1292049 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1292009 TGTGTGTGTG
1292019 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1292050 ACAATCTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1293557 original size:22 final size:22
Alignment explanation
Indices: 1293532--1293577 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1293522 CGGATATCAC
* * *
1293532 TTTTTATATATTGTTAATAAAA
1 TTTTTAAATATTATAAATAAAA
*
1293554 TTTTTAAATTTTATAAATAAAA
1 TTTTTAAATATTATAAATAAAA
1293576 TT
1 TT
1293578 AGAATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTTAAATATTATAAATAAAA
Found at i:1295176 original size:3 final size:3
Alignment explanation
Indices: 1295168--1295194 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1295158 TTTTAATGCT
1295168 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1295195 TAAGTTAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1297454 original size:21 final size:22
Alignment explanation
Indices: 1297425--1297466 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1297415 TTTTTAAAAA
1297425 ATATCAAATATAAATATATTTG
1 ATATCAAATATAAATATATTTG
*
1297447 ATAT-AAATATAAATTTATTT
1 ATATCAAATATAAATATATTT
1297467 TTTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATCAAATATAAATATATTTG
Found at i:1297500 original size:26 final size:24
Alignment explanation
Indices: 1297457--1297506 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
1297447 ATATAAATAT
1297457 AAATTTATTTTTTATATATTTAAA
1 AAATTTATTTTTTATATATTTAAA
1297481 AAATTATATTTTTATATATATTTAAA
1 AAATT-TATTTTT-TATATATTTAAA
1297507 TATATATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.21
25 7 0.29
26 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATTTATTTTTTATATATTTAAA
Found at i:1297507 original size:23 final size:23
Alignment explanation
Indices: 1297435--1297514 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 23
1297425 ATATCAAATA
* * *
1297435 TAAA-TATA-TTTGATATAAATA
1 TAAATTATATTTTTATATATATT
1297456 TAAATT-TATTTTT-TATATATT
1 TAAATTATATTTTTATATATATT
1297477 TAAAAAATTATATTTTTATATATATT
1 T---AAATTATATTTTTATATATATT
1297503 TAAATATATATT
1 TAAAT-TATATT
1297515 GAACCATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
21 13 0.27
22 4 0.08
23 4 0.08
24 11 0.23
25 7 0.15
26 9 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TAAATTATATTTTTATATATATT
Found at i:1297512 original size:24 final size:24
Alignment explanation
Indices: 1297438--1297514 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 24
1297428 TCAAATATAA
* * *
1297438 ATATA-TTTGATATAAATATAAAT
1 ATATATTTTTATATATATTTAAAT
*
1297461 -T-TATTTTT-TATATATTTAAAAA
1 ATATATTTTTATATATATTT-AAAT
1297483 ATTATATTTTTATATATATTTAAAT
1 A-TATATTTTTATATATATTTAAAT
1297508 ATATATT
1 ATATATT
1297515 GAACCATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
21 9 0.21
22 7 0.16
24 7 0.16
25 11 0.26
26 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
ATATATTTTTATATATATTTAAAT
Found at i:1298216 original size:16 final size:16
Alignment explanation
Indices: 1298195--1298252 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
1298185 TTGGTAATTT
1298195 ATATTATATTTATATA
1 ATATTATATTTATATA
*
1298211 ATATTATGTTT-TATA
1 ATATTATATTTATATA
*
1298226 ATTAATCATATTTA-A-A
1 A-T-ATTATATTTATATA
1298242 ATATTATATTT
1 ATATTATATTT
1298253 TATTTATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.23
15 6 0.17
16 13 0.37
17 8 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
ATATTATATTTATATA
Found at i:1298334 original size:22 final size:22
Alignment explanation
Indices: 1298308--1298373 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
1298298 ATATGTTTAT
* *
1298308 TTTTTCATTTCATATTTATTTTA
1 TTTTTCATTACAT-TTTATATTA
*
1298331 TTTTTTATTACATTTTATATTA
1 TTTTTCATTACATTTTATATTA
* *
1298353 -TTTTAATTA-TTTTTATATTA
1 TTTTTCATTACATTTTATATTA
1298373 T
1 T
1298374 ATTTGATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.27
21 8 0.22
22 8 0.22
23 11 0.30
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTCATTACATTTTATATTA
Found at i:1298363 original size:9 final size:10
Alignment explanation
Indices: 1298322--1298373 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
1298312 TCATTTCATA
*
1298322 TTTATTTTAT
1 TTTATATTAT
*
1298332 TTTTTATTACAT
1 TTTATATT--AT
1298344 TTTATATTAT
1 TTTATATTAT
1298354 TTTA-ATTATT
1 TTTATATTA-T
1298364 TTTATATTAT
1 TTTATATTAT
1298374 ATTTGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.11
10 18 0.51
11 4 0.11
12 9 0.26
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATATTAT
Found at i:1298382 original size:27 final size:26
Alignment explanation
Indices: 1298304--1298392 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
1298294 TTTAATATGT
*
1298304 TTATTTTTTCATTTCATATTTATTTT-A
1 TTATTTTTACA-TT-ATATTTATTTTAA
* *
1298331 TTTTTTATTACATTTTATATTATTTTAA
1 TTATTT-TTACATTATAT-TTATTTTAA
*
1298359 TTATTTTTATATTATATTTGA-TTTAA
1 TTATTTTTACATTATATTT-ATTTTAA
*
1298385 TTGTTTTT
1 TTATTTTT
1298393 CTTAATTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
26 17 0.33
27 24 0.47
28 10 0.20
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTTTTACATTATATTTATTTTAA
Found at i:1306192 original size:35 final size:34
Alignment explanation
Indices: 1306152--1306227 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
1306142 AAATTATATT
*
1306152 TTTATATTTTTTTA-AAATATAAATATATTTAA-AA
1 TTTATATTTTTATATAAAT-TAAATATA-TTAATAA
*
1306186 TATTATATTTTTATATAAATTTAATATATTAATAA
1 T-TTATATTTTTATATAAATTAAATATATTAATAA
1306221 TTTATAT
1 TTTATAT
1306228 CATAAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 11 0.30
35 22 0.59
36 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTATATTTTTATATAAATTAAATATATTAATAA
Found at i:1306198 original size:16 final size:17
Alignment explanation
Indices: 1306160--1306198 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1306150 TTTTTATATT
1306160 TTTTTAAAATATAAATA
1 TTTTTAAAATATAAATA
* *
1306177 TATTTAAAATAT-TATA
1 TTTTTAAAATATAAATA
1306193 TTTTTA
1 TTTTTA
1306199 TATAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTTAAAATATAAATA
Found at i:1306209 original size:43 final size:42
Alignment explanation
Indices: 1306144--1306224 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 42
1306134 TATAATTTAA
***
1306144 ATTATATTTTTATATTTTTTTAAAATATAAATATATTTAAAAT
1 ATTATATTTTTATATAAATTTAAAATATAAATA-ATTTAAAAT
* *
1306187 ATTATATTTTTATATAAATTTAATATATTAATAATTTA
1 ATTATATTTTTATATAAATTTAAAATATAAATAATTTA
1306225 TATCATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 5 0.15
43 28 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (42 bp):
ATTATATTTTTATATAAATTTAAAATATAAATAATTTAAAAT
Found at i:1306224 original size:26 final size:26
Alignment explanation
Indices: 1306178--1306227 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1306168 ATATAAATAT
*
1306178 ATTTAAAATATTATATTTTTATATAA
1 ATTTAAAATATTATATATTTATATAA
*
1306204 ATTTAATATATTA-ATAATTTATAT
1 ATTTAAAATATTATAT-ATTTATAT
1306228 CATAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAAATATTATATATTTATATAA
Found at i:1307365 original size:17 final size:18
Alignment explanation
Indices: 1307335--1307369 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
1307325 AAAATTTTAA
1307335 AAATATATGATATATATTT
1 AAATATAT-ATATATATTT
1307354 AAATATAT-TATATATT
1 AAATATATATATATATT
1307370 ATATCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATATATATATATATTT
Found at i:1308397 original size:11 final size:10
Alignment explanation
Indices: 1308378--1308429 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
1308368 TGAGATTCAA
*
1308378 ATATGTTATT
1 ATATTTTATT
*
1308388 ATATTATTATA
1 ATATT-TTATT
1308399 ATATTTATATT
1 ATATTT-TATT
1308410 ATATTTTATAT
1 ATATTTTAT-T
1308421 CATATTTTA
1 -ATATTTTA
1308430 AATATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 8 0.23
11 19 0.54
12 8 0.23
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
ATATTTTATT
Found at i:1308417 original size:12 final size:12
Alignment explanation
Indices: 1308384--1308429 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1308374 TCAAATATGT
1308384 TATTATATTATTA
1 TATTATATT-TTA
1308397 TA--ATA-TTTA
1 TATTATATTTTA
1308406 TATTATATTTTA
1 TATTATATTTTA
*
1308418 TATCATATTTTA
1 TATTATATTTTA
1308430 AATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
9 5 0.17
10 1 0.03
11 6 0.21
12 15 0.52
13 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1312653 original size:2 final size:2
Alignment explanation
Indices: 1312646--1312689 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1312636 CAGCTCCCCT
1312646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1312688 TA
1 TA
1312690 AAACTTTGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1322652 original size:22 final size:20
Alignment explanation
Indices: 1322598--1322652 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 20
1322588 ATTTAAATAA
1322598 ATATTT-AATATAAATTTAT
1 ATATTTAAATATAAATTTAT
*
1322617 AT-TTTAATTA-AAATTGTGAT
1 ATATTTAAATATAAATT-T-AT
*
1322637 TTATTTAAATATAAAT
1 ATATTTAAATATAAAT
1322653 AAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 8 0.29
19 6 0.21
20 3 0.11
21 7 0.25
22 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATATTTAAATATAAATTTAT
Found at i:1323146 original size:3 final size:3
Alignment explanation
Indices: 1323140--1323169 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1323130 AATAATGACA
1323140 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1323170 TAAATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1324054 original size:31 final size:30
Alignment explanation
Indices: 1323995--1324055 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1323985 ATTTGATCTC
* *
1323995 GTTTATTATATAATTTTTGTTTTATATTCA
1 GTTTAATATATAATTTATGTTTTATATTCA
* *
1324025 GTTTAATATATTATGTTATGTTTTGTATTCA
1 GTTTAATATATAAT-TTATGTTTTATATTCA
1324056 AAATTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.61
Consensus pattern (30 bp):
GTTTAATATATAATTTATGTTTTATATTCA
Found at i:1325716 original size:2 final size:2
Alignment explanation
Indices: 1325703--1325732 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1325693 GAATCCATTA
*
1325703 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1325733 GCAAAGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1326713 original size:2 final size:2
Alignment explanation
Indices: 1326708--1326736 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1326698 ACACACACAC
1326708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1326737 AACGATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1327636 original size:25 final size:23
Alignment explanation
Indices: 1327602--1327651 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
1327592 AGGTATAAAA
*
1327602 TTTTAATTTTAATATATGTAATTTT
1 TTTTAATTTTAA-AT-TATAATTTT
*
1327627 TTTTATTTTTAAATTATAATTTT
1 TTTTAATTTTAAATTATAATTTT
1327650 TT
1 TT
1327652 AAAATAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 2 0.09
25 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTAATTTTAAATTATAATTTT
Found at i:1335301 original size:16 final size:17
Alignment explanation
Indices: 1335258--1335301 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1335248 TATATAAATA
1335258 TAAATTTTAAA-ATTAT
1 TAAATTTTAAATATTAT
1335274 T-AATATTT-AATATT-T
1 TAAAT-TTTAAATATTAT
1335289 TAAATTTTAAATA
1 TAAATTTTAAATA
1335302 AATAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTTTAAATATTAT
Found at i:1335755 original size:8 final size:8
Alignment explanation
Indices: 1335742--1335786 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
1335732 AGAAATAAAT
1335742 TTTTTATA
1 TTTTTATA
1335750 TTTTTATA
1 TTTTTATA
*
1335758 TTTTT-TC
1 TTTTTATA
*
1335765 TTTTTATT
1 TTTTTATA
*
1335773 TTTTTTTA
1 TTTTTATA
1335781 TTTTTA
1 TTTTTA
1335787 CTTAACACGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATA
Found at i:1335776 original size:23 final size:23
Alignment explanation
Indices: 1335742--1335785 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1335732 AGAAATAAAT
1335742 TTTTTATATTTTTATATTTTTTC
1 TTTTTATATTTTTATATTTTTTC
* *
1335765 TTTTTATTTTTTTTTATTTTT
1 TTTTTATATTTTTATATTTTT
1335786 ACTTAACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTATATTTTTATATTTTTTC
Found at i:1335778 original size:15 final size:15
Alignment explanation
Indices: 1335740--1335786 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1335730 ACAGAAATAA
*
1335740 ATTTTTTATATTTTT
1 ATTTTTTTTATTTTT
* *
1335755 ATATTTTTTCTTTTT
1 ATTTTTTTTATTTTT
1335770 ATTTTTTTTTATTTTT
1 A-TTTTTTTTATTTTT
1335786 A
1 A
1335787 CTTAACACGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTTTTTATTTTT
Found at i:1339715 original size:16 final size:16
Alignment explanation
Indices: 1339694--1339724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1339684 ATTTTGATGA
1339694 TTTTATAATTTTAATT
1 TTTTATAATTTTAATT
*
1339710 TTTTATATTTTTAAT
1 TTTTATAATTTTAAT
1339725 AATAAATTAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATAATTTTAATT
Found at i:1341886 original size:27 final size:26
Alignment explanation
Indices: 1341856--1341948 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
1341846 TACTTTTTGT
1341856 TAAATAAT-TTAAAATATAATACGAATA
1 TAAA-AATATTAAAATATAATA-GAATA
* *
1341883 TAAAAATAATTAAAATAAAATATAATA
1 TAAAAAT-ATTAAAATATAATAGAATA
1341910 TAAAAATATTATAAATAT-AT--AATA
1 TAAAAATATTA-AAATATAATAGAATA
*
1341934 TAAATATATTAAAAT
1 TAAAAATATTAAAAT
1341949 TTATATAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.07
24 14 0.24
26 9 0.15
27 20 0.34
28 12 0.20
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (26 bp):
TAAAAATATTAAAATATAATAGAATA
Found at i:1341917 original size:13 final size:13
Alignment explanation
Indices: 1341879--1341942 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
1341869 ATATAATACG
1341879 AATATAAAAATAATT
1 AATATAAAAAT-A-T
*
1341894 AAAAT-AAAATAT
1 AATATAAAAATAT
1341906 AATATAAAAATAT
1 AATATAAAAATAT
*
1341919 --TATAAATATAT
1 AATATAAAAATAT
*
1341930 AATATAAATATAT
1 AATATAAAAATAT
1341943 TAAAATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
11 10 0.23
12 5 0.12
13 19 0.44
14 5 0.12
15 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATAAAAATAT
Found at i:1341925 original size:22 final size:22
Alignment explanation
Indices: 1341899--1341947 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
1341889 TAATTAAAAT
1341899 AAAATATAATATAAAAATATTA
1 AAAATATAATATAAAAATATTA
*
1341921 TAAATATATAATATAAATATATTA
1 -AAA-ATATAATATAAAAATATTA
1341945 AAA
1 AAA
1341948 TTTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATATAATATAAAAATATTA
Found at i:1341959 original size:32 final size:32
Alignment explanation
Indices: 1341907--1341999 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
1341897 ATAAAATATA
*
1341907 ATATAAAAATATTATA-AATATATAATATAAAT
1 ATATTAAAAT-TTATATAATATATAATATAAAT
*
1341939 ATATTAAAATTTATATAATAT-TAATTATTAAT
1 ATATTAAAATTTATATAATATATAA-TATAAAT
*
1341971 ATATTAAAATTTATTTAAATATATAATAT
1 ATATTAAAATTTATAT-AATATATAATAT
1342000 TTTAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.15
32 35 0.65
33 8 0.15
34 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATTAAAATTTATATAATATATAATATAAAT
Found at i:1341992 original size:18 final size:18
Alignment explanation
Indices: 1341939--1341992 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 18
1341929 TAATATAAAT
*
1341939 ATATTAAAATTTATAT-A
1 ATATTAAAATTTATTTAA
1341956 ATATT--AA-TTA-TTAA
1 ATATTAAAATTTATTTAA
1341970 TATATTAAAATTTATTTAA
1 -ATATTAAAATTTATTTAA
1341989 ATAT
1 ATAT
1341993 ATAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 7 0.23
17 7 0.23
18 7 0.23
19 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTAAAATTTATTTAA
Found at i:1342012 original size:32 final size:32
Alignment explanation
Indices: 1341909--1342012 Score: 83
Period size: 32 Copynumber: 3.2 Consensus size: 32
1341899 AAAATATAAT
* *
1341909 ATAAAAA--TATTATAAATATATAATATAAATAT
1 ATAAAAATTTATT-TAAATATATAATAT-ATTAA
* *
1341941 ATTAAAATTTATAT-AATAT-TAAT-TATTAA
1 ATAAAAATTTATTTAAATATATAATATATTAA
*
1341970 TATATTAAAATTTATTTAAATATATAATATTTTAA
1 -ATA--AAAATTTATTTAAATATATAATATATTAA
1342005 ATAAAAAT
1 ATAAAAAT
1342013 ATATAAATAC
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
29 3 0.05
30 3 0.05
31 4 0.07
32 26 0.46
33 6 0.11
34 10 0.18
35 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATAAAAATTTATTTAAATATATAATATATTAA
Found at i:1346981 original size:2 final size:2
Alignment explanation
Indices: 1346974--1347005 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1346964 CAAATTCCAA
*
1346974 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1347006 TTCTTAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1347093 original size:19 final size:19
Alignment explanation
Indices: 1347069--1347112 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1347059 ACTACAGCTA
*
1347069 GTGCATG-AGTTTCGTGAGG
1 GTGCATGTAGTTTC-TGAAG
1347088 GTGCATGTTAGTTTCTGAAG
1 GTGCATG-TAGTTTCTGAAG
1347108 GTGCA
1 GTGCA
1347113 AATATGGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.18, C:0.11, G:0.36, T:0.34
Consensus pattern (19 bp):
GTGCATGTAGTTTCTGAAG
Found at i:1349247 original size:2 final size:2
Alignment explanation
Indices: 1349240--1349276 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1349230 AACGAGGAAC
*
1349240 AT AT AT AT AT AT AT AT AC 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 AT AT A
1349277 ATTTAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1352498 original size:2 final size:2
Alignment explanation
Indices: 1352491--1352523 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1352481 ACAATCATGA
*
1352491 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1352524 ATTTCTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Done.