Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 8 of 32
Found at i:1188810 original size:21 final size:21
Alignment explanation
Indices: 1188742--1188810 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1188732 ATCAACGAGT
*
1188742 TAAATTATATTTTAATTTAAAA
1 TAAATTTTA-TTTAATTTAAAA
* *
1188764 -AAATTAATT-TTTTATTTAAATT
1 TAAATT--TTATTTAATTTAAA-A
1188786 TAAATTTTATTTAATTTAAAA
1 TAAATTTTATTTAATTTAAAA
1188807 TAAA
1 TAAA
1188811 AAAATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
21 21 0.57
22 10 0.27
23 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATTTTATTTAATTTAAAA
Found at i:1189494 original size:18 final size:18
Alignment explanation
Indices: 1189471--1189531 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1189461 TTTTTATTTA
1189471 AATATAATTATAAATATT
1 AATATAATTATAAATATT
* * *
1189489 AATATAA-AATAATTTTTT
1 AATATAATTATAA-ATATT
* *
1189507 AATATTATTTTAAATATT
1 AATATAATTATAAATATT
1189525 AATATAA
1 AATATAA
1189532 ACTTTTAGAT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
17 4 0.12
18 25 0.78
19 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATAATTATAAATATT
Found at i:1189521 original size:36 final size:39
Alignment explanation
Indices: 1189448--1189532 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 39
1189438 ATTATTTAAA
*
1189448 TAATAAAAAATAATTTTTATTTAAATATAATTATAAATAT
1 TAATATAAAATAA-TTTTATTTAAATATAATTATAAATAT
* *
1189488 TAATATAAAATAA-TTT-TTT-AATATTATTTTAAATAT
1 TAATATAAAATAATTTTATTTAAATATAATTATAAATAT
1189524 TAATATAAA
1 TAATATAAA
1189533 CTTTTAGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 24 0.57
37 3 0.07
38 3 0.07
40 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
TAATATAAAATAATTTTATTTAAATATAATTATAAATAT
Found at i:1189522 original size:12 final size:12
Alignment explanation
Indices: 1189467--1189525 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
1189457 ATAATTTTTA
*
1189467 TTTAAATATAAT
1 TTTAAATATTAT
*
1189479 TATAAATATTAAT
1 TTTAAATATT-AT
* *
1189492 ATAAAATAATT-T
1 TTTAAAT-ATTAT
1189504 TTT-AATATTAT
1 TTTAAATATTAT
1189515 TTTAAATATTA
1 TTTAAATATTA
1189526 ATATAAACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
10 3 0.08
11 7 0.19
12 17 0.47
13 6 0.17
14 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAAATATTAT
Found at i:1194126 original size:14 final size:14
Alignment explanation
Indices: 1194103--1194177 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
1194093 TATTGTCAAG
*
1194103 TTTAAAATTTAAAT
1 TTTAATATTTAAAT
* *
1194117 TTTAATATTTGTATT
1 TTTAATATTT-AAAT
** *
1194132 TTTTTTATTTTAAGT
1 TTTAATA-TTTAAAT
* *
1194147 TTTAAAATTTGAAT
1 TTTAATATTTAAAT
*
1194161 TTTAATATTTATAT
1 TTTAATATTTAAAT
1194175 TTT
1 TTT
1194178 TTTAATCTTT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
14 28 0.64
15 13 0.30
16 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (14 bp):
TTTAATATTTAAAT
Found at i:1194140 original size:44 final size:44
Alignment explanation
Indices: 1194090--1194180 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
1194080 AATTTTTCTC
*
1194090 TTTTATTGTCAAG-TTTAAAATTTAAATTTTAATATTTGTATTTT
1 TTTTATT-TCAAGTTTTAAAATTTAAATTTTAATATTTATATTTT
* *
1194134 TTTTATTTTAAGTTTTAAAATTTGAATTTTAATATTTATATTTT
1 TTTTATTTCAAGTTTTAAAATTTAAATTTTAATATTTATATTTT
1194178 TTT
1 TTT
1194181 AATCTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 4 0.09
44 39 0.91
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (44 bp):
TTTTATTTCAAGTTTTAAAATTTAAATTTTAATATTTATATTTT
Found at i:1194833 original size:30 final size:30
Alignment explanation
Indices: 1194798--1194863 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1194788 ATAAAAAAAA
*
1194798 TTTTAATTTTTAATTTATATC-CAACTAAAC
1 TTTTAATTTTTAATTTATAACTCAA-TAAAC
*
1194828 TTTTAATTTTTAATTTATAACTTAATAAAC
1 TTTTAATTTTTAATTTATAACTCAATAAAC
1194858 TTTTAA
1 TTTTAA
1194864 CATAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTTAATTTTTAATTTATAACTCAATAAAC
Found at i:1195347 original size:2 final size:2
Alignment explanation
Indices: 1195340--1195374 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1195330 ATATTTCTTA
* *
1195340 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1195375 CACACACTAT
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:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1195721 original size:3 final size:3
Alignment explanation
Indices: 1195702--1195740 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
1195692 TTTTTTGACA
1195702 TAT TAT GTAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1195741 TAAAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1202194 original size:7 final size:8
Alignment explanation
Indices: 1202172--1202205 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1202162 ATTAATAAAA
1202172 TTTAATTT
1 TTTAATTT
1202180 TTTAATTT
1 TTTAATTT
1202188 TTT-ATTT
1 TTTAATTT
*
1202195 TTAAATTT
1 TTTAATTT
1202203 TTT
1 TTT
1202206 TACGAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTAATTT
Found at i:1202196 original size:15 final size:15
Alignment explanation
Indices: 1202176--1202205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1202166 ATAAAATTTA
*
1202176 ATTTTTTAATTTTTT
1 ATTTTTAAATTTTTT
1202191 ATTTTTAAATTTTTT
1 ATTTTTAAATTTTTT
1202206 TACGAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTAAATTTTTT
Found at i:1202411 original size:33 final size:33
Alignment explanation
Indices: 1202369--1202432 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1202359 AATAAAAAGA
1202369 TGAGCAAATTAATATGTAAACCAAAGAAGAAGG
1 TGAGCAAATTAATATGTAAACCAAAGAAGAAGG
1202402 TGAGCAAATTAATATGTAAACCAAAGAAGAA
1 TGAGCAAATTAATATGTAAACCAAAGAAGAA
1202433 AAAAGGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (33 bp):
TGAGCAAATTAATATGTAAACCAAAGAAGAAGG
Found at i:1202497 original size:19 final size:19
Alignment explanation
Indices: 1202473--1202531 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
1202463 TTATAGATTG
1202473 AATAAT-TTATCTTATTTAA
1 AATAATATTAT-TTATTTAA
1202492 AATAATATT-TTTATATTAA
1 AATAATATTATTTAT-TTAA
1202511 AATAATATATATTTATTTAA
1 AATAATAT-TATTTATTTAA
1202531 A
1 A
1202532 TTAAGTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.11
19 19 0.53
20 8 0.22
21 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATATTATTTATTTAA
Found at i:1202614 original size:18 final size:19
Alignment explanation
Indices: 1202587--1202622 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1202577 TAACATATAT
*
1202587 AATAATTTAAATTTAAATA
1 AATAATTTAAATTAAAATA
1202606 AATAA-TTAAATTAAAAT
1 AATAATTTAAATTAAAAT
1202623 TTGTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATTTAAATTAAAATA
Found at i:1202722 original size:4 final size:4
Alignment explanation
Indices: 1202703--1202735 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1202693 CAGGCAATAA
*
1202703 ATGC GTGC AT-C ATGC ATGC ATGC ATGC ATGC AT
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC AT
1202736 TGTAGAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (4 bp):
ATGC
Found at i:1203048 original size:17 final size:15
Alignment explanation
Indices: 1203002--1203046 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 15
1202992 GTTTAACTTG
1203002 ATAAATTTAATTTAAA
1 ATAAA-TTAATTTAAA
1203018 ATAAATTAAGTTTAAA
1 ATAAATTAA-TTTAAA
1203034 ATTAAATTAATTT
1 A-TAAATTAATTT
1203047 TATTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATAAATTAATTTAAA
Found at i:1203094 original size:40 final size:38
Alignment explanation
Indices: 1203006--1203123 Score: 113
Period size: 37 Copynumber: 3.2 Consensus size: 38
1202996 AACTTGATAA
* * * * *
1203006 ATTTAATTTAAAATAAATTAAGTTTAAAATTAAAT-TA-
1 ATTTTATTTAAATTAAATTAAATTTTAAA-TAAATAAAT
* *
1203043 ATTTTATTTAAATTATTATTTAA--TT-AATAAA-AAAT
1 ATTTTATTTAAATTA-AATTAAATTTTAAATAAATAAAT
1203078 ATTTTATTTAAATTAAATTAAATTTTAAATAAATAAAT
1 ATTTTATTTAAATTAAATTAAATTTTAAATAAATAAAT
1203116 ATTTTATT
1 ATTTTATT
1203124 ATATGGTCTC
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
34 10 0.15
35 17 0.26
36 3 0.05
37 19 0.29
38 16 0.25
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
ATTTTATTTAAATTAAATTAAATTTTAAATAAATAAAT
Found at i:1203106 original size:17 final size:17
Alignment explanation
Indices: 1203084--1203121 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1203074 AAATATTTTA
*
1203084 TTTAAATTAAATTAA-AT
1 TTTAAA-TAAATAAATAT
1203101 TTTAAATAAATAAATAT
1 TTTAAATAAATAAATAT
1203118 TTTA
1 TTTA
1203122 TTATATGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATAAATAAATAT
Found at i:1204141 original size:14 final size:13
Alignment explanation
Indices: 1204122--1204160 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
1204112 TTAAATAAGA
1204122 ATATATATTAAATT
1 ATATAT-TTAAATT
*
1204136 ATATATTTATATT
1 ATATATTTAAATT
1204149 -TATATTTAAATT
1 ATATATTTAAATT
1204161 TGTGTGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 6 0.26
14 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATTTAAATT
Found at i:1204361 original size:2 final size:2
Alignment explanation
Indices: 1204356--1204400 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1204346 AATTACACAC
* *
1204356 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT 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 AT AT AT
1204398 AT A
1 AT A
1204401 CACACACGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1205708 original size:3 final size:3
Alignment explanation
Indices: 1205700--1205726 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1205690 TGAAATGATC
1205700 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1205727 AGAAGTCACG
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1207616 original size:2 final size:2
Alignment explanation
Indices: 1207609--1207643 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1207599 ATATGCATAC
1207609 AT AT AT 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 AT AT AT A
1207644 GAGAGAGAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1207648 original size:2 final size:2
Alignment explanation
Indices: 1207643--1207690 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1207633 ATATATATAT
*
1207643 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1207685 AG AG AG
1 AG AG AG
1207691 CAGCACCTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1213719 original size:17 final size:18
Alignment explanation
Indices: 1213682--1213720 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1213672 ATATATTCAC
1213682 ATTAAATATATATTTAAAT
1 ATTAAATATATATTT-AAT
*
1213701 ATTAAATATATGTTT-AT
1 ATTAAATATATATTTAAT
1213718 ATT
1 ATT
1213721 TAACTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
19 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAAATATATATTTAAT
Found at i:1214604 original size:15 final size:15
Alignment explanation
Indices: 1214584--1214615 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1214574 CGATTCGGTT
1214584 TCCGAAAGATTTACA
1 TCCGAAAGATTTACA
1214599 TCCGAAAGATTTACA
1 TCCGAAAGATTTACA
1214614 TC
1 TC
1214616 GTAGAATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (15 bp):
TCCGAAAGATTTACA
Found at i:1214921 original size:2 final size:2
Alignment explanation
Indices: 1214914--1214946 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1214904 ATCAAAGGAA
1214914 AT AT 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 AT AT A
1214947 CATGCGTGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1214957 original size:2 final size:2
Alignment explanation
Indices: 1214952--1215008 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
1214942 ATATACATGC
* * * * *
1214952 GT GT GT GT GC GT GC GT GT GT GT GT GC GT GC AT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1214994 GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT G
1215009 GAAGAACATA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.07, G:0.49, T:0.42
Consensus pattern (2 bp):
GT
Found at i:1214973 original size:16 final size:16
Alignment explanation
Indices: 1214952--1215008 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
1214942 ATATACATGC
1214952 GTGTGTGTGCGTGCGT
1 GTGTGTGTGCGTGCGT
*
1214968 GTGTGTGTGCGTGCAT
1 GTGTGTGTGCGTGCGT
* *
1214984 GTGTGTGTGTGTGTGT
1 GTGTGTGTGCGTGCGT
1215000 GTGTGTGTG
1 GTGTGTGTG
1215009 GAAGAACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.02, C:0.07, G:0.49, T:0.42
Consensus pattern (16 bp):
GTGTGTGTGCGTGCGT
Found at i:1218993 original size:19 final size:19
Alignment explanation
Indices: 1218971--1219038 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
1218961 AAATTTGATT
1218971 TAAATTATTATTTAAATAA
1 TAAATTATTATTTAAATAA
*
1218990 TAAA-TATTAATATAAAT--
1 TAAATTATT-ATTTAAATAA
1219007 T-AATT-TT-TTTAAA-AA
1 TAAATTATTATTTAAATAA
*
1219022 TAAATTTTTATATTAAA
1 TAAATTATTAT-TTAAA
1219039 ACAAATCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
14 5 0.13
15 1 0.03
16 8 0.21
17 4 0.10
18 5 0.13
19 16 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTATTATTTAAATAA
Found at i:1219158 original size:11 final size:11
Alignment explanation
Indices: 1219144--1219179 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1219134 ATTATTTTTT
1219144 ATTTAAATTTA
1 ATTTAAATTTA
*
1219155 ATTTAAATTAA
1 ATTTAAATTTA
1219166 ATTTAAA-TTA
1 ATTTAAATTTA
1219176 ATTT
1 ATTT
1219180 TATAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:1222844 original size:29 final size:28
Alignment explanation
Indices: 1222780--1222865 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
1222770 ATATAAATTT
1222780 AATA-ATTTACATATTTATATATATATA
1 AATATATTTACATATTTATATATATATA
* * * *
1222807 TATCTTATTTATATATTTTTATATATAATA
1 AAT-ATATTTACATATTTATATATAT-ATA
* *
1222837 AATATATTTAAAATATTATATATTTATAT
1 AATATATTT-ACATATT-TATATATATAT
1222866 TAACACGATT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.04
29 23 0.51
30 13 0.29
31 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
AATATATTTACATATTTATATATATATA
Found at i:1223062 original size:2 final size:2
Alignment explanation
Indices: 1223055--1223081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1223045 AAATACAGTG
1223055 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
1223082 GTGAATTATC
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:1223408 original size:5 final size:5
Alignment explanation
Indices: 1223390--1223574 Score: 82
Period size: 5 Copynumber: 36.2 Consensus size: 5
1223380 TAAAAAAATT
*
1223390 ATATG ATATAA ATATA ATATA A-A-A ATA-A ATATA ATATA ATATA ATATTAA
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA-T-A
* * * * *
1223440 AAATA ATATAA ATATA ATATA ATATA TTAAA AT-TT ATAAA ATATTA ATTAATA
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATA-TA A-T-ATA
* * * * *
1223493 ATATA TTATA AT-TT TTATAA ATATA A-ATTA TTTTAA ATATA ATTATA
1 ATATA ATATA ATATA ATAT-A ATATA ATA-TA ATAT-A ATATA A-TATA
*
1223540 ATATA AT-TA A-AT- ATATAA ATATG ATATAA ATATA A
1 ATATA ATATA ATATA ATAT-A ATATA ATAT-A ATATA A
1223575 GAATTATGAA
Statistics
Matches: 136, Mismatches: 23, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
3 3 0.02
4 17 0.12
5 75 0.55
6 33 0.24
7 7 0.05
8 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1223426 original size:28 final size:27
Alignment explanation
Indices: 1223378--1223465 Score: 108
Period size: 27 Copynumber: 3.2 Consensus size: 27
1223368 TAAATTTATG
* * *
1223378 AATAAAAAAATTATATGATATAAATAT
1 AATATAAAAATAATATAATATAAATAT
1223405 AATATAAAAATAAATATAATAT-AATAT
1 AATATAAAAAT-AATATAATATAAATAT
1223432 AATATTAAAAATAATATAA-ATATAATAT
1 AATA-TAAAAATAATATAATATA-AATAT
1223460 AATATA
1 AATATA
1223466 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.04
27 28 0.52
28 24 0.44
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (27 bp):
AATATAAAAATAATATAATATAAATAT
Found at i:1223427 original size:22 final size:22
Alignment explanation
Indices: 1223395--1223456 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1223385 AAATTATATG
1223395 ATATAAATATAATATAAAAATAA
1 ATAT-AATATAATATAAAAATAA
* *
1223418 ATATAATATAATATAATATTAA
1 ATATAATATAATATAAAAATAA
*
1223440 AAATAATATAAATATAA
1 ATATAATAT-AATATAA
1223457 TATAATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAATATAATATAAAAATAA
Found at i:1223477 original size:28 final size:28
Alignment explanation
Indices: 1223395--1223574 Score: 108
Period size: 28 Copynumber: 6.2 Consensus size: 28
1223385 AAATTATATG
*
1223395 ATATAAATATAATATA--AAAATAAATATA
1 ATAT-AATATAATATATTAAAATATATA-A
*
1223423 ATATAATATAATAT-TAAAAATAATATAA
1 ATATAATATAATATATTAAAAT-ATATAA
*
1223451 ATATAATATAATATATTAAAATTTATAAA
1 ATATAATATAATATATTAAAATATAT-AA
* *
1223480 ATATTAATTAATAATATATTATAATTTTTATAA
1 ATA-TAA-T-ATAATATATTA-AA-ATATATAA
*
1223513 ATATAA-AT--TAT-TTTAAATATAATTATA
1 ATATAATATAATATATTAAAATAT-A-TA-A
1223540 ATATAAT-TAA-ATATATAAATATGATATAA
1 ATATAATATAATATAT-TAAA-AT-ATATAA
1223569 ATATAA
1 ATATAA
1223575 GAATTATGAA
Statistics
Matches: 124, Mismatches: 8, Indels: 39
0.73 0.05 0.23
Matches are distributed among these distances:
24 2 0.02
25 3 0.02
26 4 0.03
27 21 0.17
28 29 0.23
29 25 0.20
30 8 0.06
31 4 0.03
32 16 0.13
33 7 0.06
34 5 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATAATATAATATATTAAAATATATAA
Found at i:1223483 original size:17 final size:16
Alignment explanation
Indices: 1223457--1223521 Score: 53
Period size: 17 Copynumber: 4.0 Consensus size: 16
1223447 ATAAATATAA
*
1223457 TATAATATATTAAAATT
1 TATAAAATATT-AAATT
1223474 TATAAAATATT-AATT
1 TATAAAATATTAAATT
* *
1223489 AATAATATATTATAATT
1 TATAAAATATTA-AATT
*
1223506 TTTATAAATA-TAAATT
1 TATA-AAATATTAAATT
1223522 ATTTTAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
15 13 0.33
16 4 0.10
17 18 0.46
18 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAAATATTAAATT
Found at i:1223517 original size:15 final size:15
Alignment explanation
Indices: 1223499--1223538 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1223489 AATAATATAT
1223499 TATAATT-TTTATAAA
1 TATAATTATTT-TAAA
1223514 TATAAATTATTTTAAA
1 TAT-AATTATTTTAAA
1223530 TATAATTAT
1 TATAATTAT
1223539 AATATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 11 0.48
17 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAATTATTTTAAA
Found at i:1224005 original size:19 final size:19
Alignment explanation
Indices: 1223981--1224021 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1223971 TTAATTAAAA
1223981 ATTATTTTATATTTAA-TAT
1 ATTATTTT-TATTTAATTAT
1224000 ATTATTTTTATTTAATTAT
1 ATTATTTTTATTTAATTAT
1224019 ATT
1 ATT
1224022 TTTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTTTTATTTAATTAT
Found at i:1224724 original size:15 final size:16
Alignment explanation
Indices: 1224690--1224721 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1224680 ACAGATGTTA
1224690 AATATAAATATATTTTT
1 AATATAAATATA-TTTT
1224707 AATATAAATATATTT
1 AATATAAATATATTT
1224722 AATTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATAAATATATTTT
Found at i:1226046 original size:10 final size:11
Alignment explanation
Indices: 1225994--1226047 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
1225984 ATCATTAGTT
1225994 ATTTAATATAA
1 ATTTAATATAA
* *
1226005 ATTTTATTTAA
1 ATTTAATATAA
1226016 ATTTAATTATAA
1 ATTTAA-TATAA
*
1226028 A-AT-ATATAA
1 ATTTAATATAA
1226037 A-TTAATATAA
1 ATTTAATATAA
1226047 A
1 A
1226048 AATAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 7 0.20
10 8 0.23
11 15 0.43
12 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTAATATAA
Found at i:1226049 original size:20 final size:21
Alignment explanation
Indices: 1226013--1226060 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
1226003 AAATTTTATT
1226013 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1226034 TAAA-TTAA-TATAAAA-ATA
1 TAAATTTAATTATAAAATATA
*
1226052 -ATATTTAAT
1 TAAATTTAAT
1226061 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 2 0.08
18 7 0.29
19 7 0.29
20 4 0.17
21 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1226061 original size:18 final size:21
Alignment explanation
Indices: 1226015--1226062 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1226005 ATTTTATTTA
1226015 AATTTAAT-TATAAAATATAT
1 AATTTAATATATAAAATATAT
*
1226035 AAATTAATATA-AAAATA-AT
1 AATTTAATATATAAAATATAT
1226054 -ATTTAATAT
1 AATTTAATAT
1226063 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.32
19 2 0.08
20 13 0.52
21 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAATATATAAAATATAT
Found at i:1236034 original size:21 final size:21
Alignment explanation
Indices: 1235977--1236036 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
1235967 TCAAATTCAT
*
1235977 ATTTAATAATAAAAAATATTTAA
1 ATTTAAT-AT-AAAAATATATAA
1236000 ATTTAAT-TATAAAATATAT-A
1 ATTTAATATA-AAAATATATAA
1236020 ATATTAATATAAAAATA
1 AT-TTAATATAAAAATA
1236037 AATTTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.12
21 20 0.61
22 2 0.06
23 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTAATATAAAAATATATAA
Found at i:1236706 original size:21 final size:22
Alignment explanation
Indices: 1236658--1236706 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
1236648 TTTTAAAATT
*
1236658 TATTTTTATATTTAAATTTATA
1 TATTTTTATATTTAAATTTAAA
1236680 TA-TTTTATA-TTAAATTTAAA
1 TATTTTTATATTTAAATTTAAA
1236700 TATTTTT
1 TATTTTT
1236707 TAATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 11 0.44
22 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTATATTTAAATTTAAA
Found at i:1236712 original size:21 final size:21
Alignment explanation
Indices: 1236658--1236712 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1236648 TTTTAAAATT
* *
1236658 TATTTTTATATTTAAATTTATA
1 TATTTTT-TAATTAAATTTAAA
*
1236680 TATTTTAT-ATTAAATTTAAA
1 TATTTTTTAATTAAATTTAAA
1236700 TATTTTTTAATTA
1 TATTTTTTAATTA
1236713 TTAAATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.61
21 5 0.18
22 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTTAATTAAATTTAAA
Found at i:1236936 original size:2 final size:2
Alignment explanation
Indices: 1236929--1236973 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1236919 CATTGGCATG
1236929 AT AT AT 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 AT AT AT
1236971 AT A
1 AT A
1236974 CCAGTTTGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1237350 original size:13 final size:13
Alignment explanation
Indices: 1237334--1237359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1237324 ATTTTAATTT
1237334 TTTTTTAAAAATA
1 TTTTTTAAAAATA
1237347 TTTTTTAAAAATA
1 TTTTTTAAAAATA
1237360 CTCGTGACAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAAATA
Found at i:1237747 original size:21 final size:21
Alignment explanation
Indices: 1237723--1237762 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1237713 TATATTTATT
1237723 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
1237744 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
1237763 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:1237765 original size:32 final size:32
Alignment explanation
Indices: 1237703--1237765 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1237693 TATTTTAAAT
* * **
1237703 TAAAATAATATATATTTATTTAAATTTAATTA
1 TAAAATAATAAATATTTAATTAAAAATAATTA
1237735 TAAAATATATAAATA-TTAATTAAAAATAATT
1 TAAAATA-ATAAATATTTAATTAAAAATAATT
1237766 TTTAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAAAATAATAAATATTTAATTAAAAATAATTA
Found at i:1238037 original size:2 final size:2
Alignment explanation
Indices: 1238030--1238057 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1238020 ACATCCATGG
1238030 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
1238058 TTATCATATG
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:1241071 original size:13 final size:13
Alignment explanation
Indices: 1241050--1241079 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1241040 CCTTAGTTTA
1241050 TTTTATTTTATTT
1 TTTTATTTTATTT
*
1241063 TTTTCTTTTATTT
1 TTTTATTTTATTT
1241076 TTTT
1 TTTT
1241080 GTTTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:1246644 original size:6 final size:6
Alignment explanation
Indices: 1246635--1246667 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1246625 GCTTTCGCTT
1246635 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCT
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCT
1246668 TTTTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCCC
Found at i:1250622 original size:19 final size:20
Alignment explanation
Indices: 1250598--1250635 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1250588 CGATTATATT
1250598 TAAAAGAATT-AATTTTAAG
1 TAAAAGAATTAAATTTTAAG
*
1250617 TAAAAGTATTAAATTTTAA
1 TAAAAGAATTAAATTTTAA
1250636 AATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAAAGAATTAAATTTTAAG
Found at i:1251016 original size:16 final size:18
Alignment explanation
Indices: 1250979--1251018 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
1250969 AATATTTATT
*
1250979 TTTATTTTATTTAATGAA
1 TTTATTTTATTTAATAAA
1250997 TTTATTTT-TTT-ATAAA
1 TTTATTTTATTTAATAAA
1251013 TTTATT
1 TTTATT
1251019 AATTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 3 0.14
18 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTATTTTATTTAATAAA
Found at i:1251034 original size:14 final size:13
Alignment explanation
Indices: 1251009--1251038 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1250999 TATTTTTTTA
1251009 TAAATTTATTAAT
1 TAAATTTATTAAT
1251022 TAAATTATATTAAT
1 TAAATT-TATTAAT
1251036 TAA
1 TAA
1251039 CTCATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATTTATTAAT
Found at i:1251373 original size:73 final size:72
Alignment explanation
Indices: 1251299--1251438 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 72
1251289 TAAATCGATA
*
1251299 AAAATT-CATATTTTTTAATTTTTTTATAAAATTATTGTATATTATAAGGTTAAAATCATTAATT
1 AAAATTACA-ATTTTTTAATTTTTTTATAAAATTATTGTATATTATAAGGTTAAAACCATTAATT
1251363 TTTTTAAT
65 TTTTTAAT
* * * *
1251371 AAATTTAACAATTTTTTTATTTTTTTATAAATTTATTGTATATTATAAGGTTAAAACCTTTAATT
1 AAAATT-ACAATTTTTTAATTTTTTTATAAAATTATTGTATATTATAAGGTTAAAACCATTAATT
1251436 TTT
65 TTT
1251439 GAATTTATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
72 5 0.08
73 54 0.89
74 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (72 bp):
AAAATTACAATTTTTTAATTTTTTTATAAAATTATTGTATATTATAAGGTTAAAACCATTAATTT
TTTTAAT
Found at i:1251480 original size:17 final size:17
Alignment explanation
Indices: 1251460--1251494 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1251450 AAAAACACAA
1251460 TTTAATAAATATATATT
1 TTTAATAAATATATATT
* *
1251477 TTTATTAAATATTTATT
1 TTTAATAAATATATATT
1251494 T
1 T
1251495 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATAAATATATATT
Found at i:1253704 original size:144 final size:144
Alignment explanation
Indices: 1253444--1253735 Score: 521
Period size: 144 Copynumber: 2.0 Consensus size: 144
1253434 TTTTATGCTG
* * *
1253444 TAGTAGCAGGAGTATGGTAAATTTTTTCATAGAGTTGTCTGATAGTTTTGAAGGATTTTTAGCCA
1 TAGTAGCAGAAGTATGGTAAATTTTTTCATAAAGTTGTCTGATAGTTTTGAAGGATTTATAGCCA
1253509 AACTGGTTGGCTTATCAAACGAATTCAATGAATTTTATCTTTTATTTTGTGCACTTAGTATTTGT
66 AACTGGTTGGCTTATCAAACGAATTCAATGAATTTTATCTTTTATTTTGTGCACTTAGTATTTGT
1253574 GATTTTGAATATAT
131 GATTTTGAATATAT
1253588 TAGTAGCAGAAGTATGGTAAATTTTTTCATAAAGTTGTCTGATAGTTTTGAAGGATTTATAGCCA
1 TAGTAGCAGAAGTATGGTAAATTTTTTCATAAAGTTGTCTGATAGTTTTGAAGGATTTATAGCCA
* * * *
1253653 AACTGGTTGGCTTATCGAATGAATTCAATGATTTTTATCTTTTATTTTGTGCACTTAGTGTTTGT
66 AACTGGTTGGCTTATCAAACGAATTCAATGAATTTTATCTTTTATTTTGTGCACTTAGTATTTGT
1253718 GATTTTGAATATAT
131 GATTTTGAATATAT
1253732 TAGT
1 TAGT
1253736 TTAATGTCAG
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 141 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.44
Consensus pattern (144 bp):
TAGTAGCAGAAGTATGGTAAATTTTTTCATAAAGTTGTCTGATAGTTTTGAAGGATTTATAGCCA
AACTGGTTGGCTTATCAAACGAATTCAATGAATTTTATCTTTTATTTTGTGCACTTAGTATTTGT
GATTTTGAATATAT
Found at i:1255589 original size:2 final size:2
Alignment explanation
Indices: 1255582--1255607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1255572 TTAGGGTTTT
1255582 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
1255608 ATCTTTCTAG
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:1257943 original size:2 final size:2
Alignment explanation
Indices: 1257936--1257961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1257926 AAGAATCTTC
1257936 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
1257962 TAAATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1258100 original size:18 final size:19
Alignment explanation
Indices: 1258067--1258102 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1258057 TTACCTATGT
1258067 ATATATTTTATATATATAC
1 ATATATTTTATATATATAC
*
1258086 ATATA-TTTATTTATATA
1 ATATATTTTATATATATA
1258103 TTTGATACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATATTTTATATATATAC
Found at i:1259161 original size:2 final size:2
Alignment explanation
Indices: 1259154--1259185 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1259144 GAAGTCAAGT
1259154 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
1259186 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1259190 original size:2 final size:2
Alignment explanation
Indices: 1259185--1259218 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1259175 ATATATATAT
1259185 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1259219 TAGATCTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1263620 original size:21 final size:20
Alignment explanation
Indices: 1263582--1263621 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1263572 AAATTTTATA
*
1263582 TTTTGATTTTGATATATTTG
1 TTTTGATTTTAATATATTTG
*
1263602 TTTTGTATTTTAATTTATTT
1 TTTTG-ATTTTAATATATTT
1263622 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (20 bp):
TTTTGATTTTAATATATTTG
Found at i:1263847 original size:2 final size:2
Alignment explanation
Indices: 1263840--1263883 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1263830 GCAATTCTTC
1263840 AT AT AT 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 AT AT AT
1263882 AT
1 AT
1263884 GAATGTTACG
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):
AT
Found at i:1266351 original size:13 final size:13
Alignment explanation
Indices: 1266314--1266360 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
1266304 TAAAATTAAA
1266314 ATTAAT-TTTTAT
1 ATTAATATTTTAT
1266326 ATTAATA-TTTAT
1 ATTAATATTTTAT
*
1266338 ATTTATATTTTAT
1 ATTAATATTTTAT
1266351 AATTAA-ATTT
1 -ATTAATATTT
1266361 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 17 0.57
13 9 0.30
14 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTAATATTTTAT
Found at i:1266881 original size:20 final size:21
Alignment explanation
Indices: 1266844--1266882 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1266834 AAATGTTGAG
*
1266844 TTATTCACTAAGTTAAAAAAC
1 TTATTCAATAAGTTAAAAAAC
1266865 TTATTCAATAA-TTAAAAA
1 TTATTCAATAAGTTAAAAA
1266883 GATTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (21 bp):
TTATTCAATAAGTTAAAAAAC
Found at i:1267566 original size:16 final size:14
Alignment explanation
Indices: 1267518--1267562 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
1267508 TTTTAATATT
1267518 TTTAAATAAAAAAA
1 TTTAAATAAAAAAA
*
1267532 TTTAAA-AATAAAA
1 TTTAAATAAAAAAA
1267545 TTTAAATAAAAAATA
1 TTTAAATAAAAAA-A
1267560 TTT
1 TTT
1267563 TAAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 11 0.41
15 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTAAATAAAAAAA
Found at i:1273610 original size:2 final size:2
Alignment explanation
Indices: 1273605--1273635 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1273595 TGTGTGTGTA
1273605 AT 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 AT A
1273636 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1273640 original size:2 final size:2
Alignment explanation
Indices: 1273635--1273664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1273625 ATATATATAT
1273635 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1273665 GGCTAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1274418 original size:14 final size:15
Alignment explanation
Indices: 1274398--1274432 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1274388 TTAAAATATA
*
1274398 ATAAAAATTAAATTT
1 ATAAAAAGTAAATTT
1274413 -TAAAAAGTAAATTT
1 ATAAAAAGTAAATTT
1274427 ATAAAA
1 ATAAAA
1274433 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAAAAAGTAAATTT
Found at i:1274427 original size:13 final size:12
Alignment explanation
Indices: 1274382--1274446 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 12
1274372 TTAATTTATT
*
1274382 TAAATTTTAAAA
1 TAAATTTAAAAA
1274394 TATAA--TAAAAA
1 TA-AATTTAAAAA
1274405 TTAAATTTTAAAAA
1 -TAAA-TTTAAAAA
1274419 GTAAATTTATAAAA
1 -TAAATTTA-AAAA
1274433 TAAA-TTAAAAA
1 TAAATTTAAAAA
1274444 TAA
1 TAA
1274447 TATAAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 7 0.16
13 10 0.22
14 14 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:1274471 original size:19 final size:20
Alignment explanation
Indices: 1274430--1274472 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1274420 TAAATTTATA
1274430 AAATAAATTAAAAATAATAT
1 AAATAAATTAAAAATAATAT
*
1274450 AAAT-AATTATAAAA-AATTT
1 AAATAAATTA-AAAATAATAT
1274469 AAAT
1 AAAT
1274473 TACTTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAATTAAAAATAATAT
Found at i:1276149 original size:16 final size:17
Alignment explanation
Indices: 1276108--1276149 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1276098 ATAAAATTTA
*
1276108 ATTTAAAAATAATTTTT
1 ATTTAAAATTAATTTTT
*
1276125 ATTT-TAATTAATTTTT
1 ATTTAAAATTAATTTTT
1276141 -TTTAAAATT
1 ATTTAAAATT
1276150 CCTCATAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTAATTTTT
Found at i:1277823 original size:49 final size:45
Alignment explanation
Indices: 1277769--1277877 Score: 137
Period size: 49 Copynumber: 2.3 Consensus size: 45
1277759 ATAAATTTTT
1277769 AAAATAATTTTTATTTAAAATTAATTATAAATTATATAAATATAATATA
1 AAAAT-ATTTTTATTTAAAATTAATTATAAA-TA-ATAAATATAAT-TA
* *
1277818 AAAATATTTTTAATTTTATATTAATTATAAATAATAAATATAATTA
1 AAAATATTTTT-ATTTAAAATTAATTATAAATAATAAATATAATTA
1277864 AAAATTATTGTTTA
1 AAAA-TATT-TTTA
1277878 ACCCATAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
46 6 0.11
47 16 0.29
48 11 0.20
49 22 0.40
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (45 bp):
AAAATATTTTTATTTAAAATTAATTATAAATAATAAATATAATTA
Found at i:1278077 original size:21 final size:21
Alignment explanation
Indices: 1278051--1278097 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1278041 ATTTATTAAT
*
1278051 ATTAACATAATAAAACATTCG
1 ATTAACAAAATAAAACATTCG
1278072 ATTAACAAAATAAAACATTCG
1 ATTAACAAAATAAAACATTCG
1278093 ATTAA
1 ATTAA
1278098 ATCAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (21 bp):
ATTAACAAAATAAAACATTCG
Found at i:1282943 original size:20 final size:20
Alignment explanation
Indices: 1282920--1282957 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1282910 GAATTAGTTT
1282920 AAAT-TATTATTTAATTAATA
1 AAATATATT-TTTAATTAATA
*
1282940 AAATATATTTTTATTTAA
1 AAATATATTTTTAATTAA
1282958 ATTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATATATTTTTAATTAATA
Found at i:1283923 original size:31 final size:31
Alignment explanation
Indices: 1283868--1283938 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
1283858 TTTAATTTTT
*
1283868 TAAAAAAATTAAATAAAAATATTAAGTTTAA
1 TAAAAAAATTAAATAAAAATATTAAATTTAA
* * *
1283899 TAAATAAATTTAAGTAAAAA-ATTAAATTTATT
1 TAAA-AAAATTAAATAAAAATATTAAATTTA-A
1283931 TAAAAAAA
1 TAAAAAAA
1283939 AGATGAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAAAAAATTAAATAAAAATATTAAATTTAA
Found at i:1283934 original size:18 final size:17
Alignment explanation
Indices: 1283894--1283937 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1283884 AAATATTAAG
*
1283894 TTTAATAAATAAATTTA
1 TTTAAAAAATAAATTTA
**
1283911 AGTAAAAAATTAAATTTA
1 TTTAAAAAA-TAAATTTA
1283929 TTTAAAAAA
1 TTTAAAAAA
1283938 AAGATGAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTAAAAAATAAATTTA
Found at i:1284118 original size:33 final size:34
Alignment explanation
Indices: 1284081--1284159 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 34
1284071 ATATAAATAT
*
1284081 TAAAAAATATATTAA-T-TTAAAGTTTAAATTTAA
1 TAAAAAATATATAAATTATTAAAGTTT-AATTTAA
**
1284114 T-AAAAATAT-TAAATTATTAAAGTTTAATTTTT
1 TAAAAAATATATAAATTATTAAAGTTTAATTTAA
1284146 TAAAAAATTATATA
1 TAAAAAA-TATATA
1284160 TATTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 3 0.08
32 15 0.39
33 15 0.39
34 3 0.08
35 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAAAAATATATAAATTATTAAAGTTTAATTTAA
Found at i:1284155 original size:23 final size:23
Alignment explanation
Indices: 1284124--1284177 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
1284114 TAAAAATATT
* *
1284124 AAATTATTAAAGTTTAATTTTTTA
1 AAATAATTAAA-TATAATTTTTTA
* *
1284148 AAA-AATTATATATATTTTTTTA
1 AAATAATTAAATATAATTTTTTA
1284170 AAATAATT
1 AAATAATT
1284178 TAGAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 13 0.52
23 9 0.36
24 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATAATTAAATATAATTTTTTA
Found at i:1284788 original size:17 final size:16
Alignment explanation
Indices: 1284753--1284798 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1284743 TGTGAAAAAA
1284753 TAAAATTTAAAT-A--
1 TAAAATTTAAATAATT
1284766 TAAAATTATAAATAATT
1 TAAAATT-TAAATAATT
*
1284783 TAAAATTTAATTAATT
1 TAAAATTTAAATAATT
1284799 ACTTAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 1 0.04
16 8 0.29
17 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTTAAATAATT
Found at i:1285219 original size:14 final size:15
Alignment explanation
Indices: 1285167--1285212 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 15
1285157 TTGAAAATAA
1285167 ATATTTAATATAAAT
1 ATATTTAATATAAAT
1285182 ATGTATTTAATATAAAT
1 A--TATTTAATATAAAT
1285199 ATATTTAAT-TAAAT
1 ATATTTAATATAAAT
1285213 TTTTTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.17
15 9 0.31
17 15 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTTAATATAAAT
Found at i:1286916 original size:24 final size:24
Alignment explanation
Indices: 1286888--1286940 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1286878 TCGAGATTTA
*
1286888 AATTACGATCATAAATATATTTTT
1 AATTACAATCATAAATATATTTTT
* *
1286912 AATTATAATTATAAATATATTTTT
1 AATTACAATCATAAATATATTTTT
1286936 AATTA
1 AATTA
1286941 TTTTATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTACAATCATAAATATATTTTT
Found at i:1288320 original size:15 final size:15
Alignment explanation
Indices: 1288295--1288327 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1288285 TAATTAAAAA
1288295 TTATAATTAATATCTT
1 TTATAATTAATAT-TT
1288311 TTAT-ATTAATATTT
1 TTATAATTAATATTT
1288325 TTA
1 TTA
1288328 AAAACAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATAATTAATATTT
Found at i:1291964 original size:18 final size:19
Alignment explanation
Indices: 1291927--1291964 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1291917 TATATTAAAA
*
1291927 TTTATATAATATAAATTAT
1 TTTATATAATATAAACTAT
*
1291946 TTTATA-AATATATACTAT
1 TTTATATAATATAAACTAT
1291964 T
1 T
1291965 ATTTACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATAATATAAACTAT
Found at i:1292127 original size:27 final size:26
Alignment explanation
Indices: 1292090--1292144 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1292080 ATTTAAAATT
*
1292090 TTTTAATATTTA-ATAATTATATTAAA
1 TTTTAATATTTATA-AATTAAATTAAA
*
1292116 TTTTAATTATTTTTAAATTAAATTAAA
1 TTTTAA-TATTTATAAATTAAATTAAA
1292143 TT
1 TT
1292145 AAATCTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 18 0.72
28 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTAATATTTATAAATTAAATTAAA
Found at i:1292337 original size:2 final size:2
Alignment explanation
Indices: 1292326--1292369 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1292316 AATAATTAAT
1292326 TA TA -A 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
1292367 TA T
1 TA T
1292370 CGTTAGTAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1292707 original size:3 final size:3
Alignment explanation
Indices: 1292699--1292732 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1292689 GGCCTGTTAG
1292699 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1292733 TCTTCTTTGC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1304913 original size:8 final size:8
Alignment explanation
Indices: 1304900--1304925 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1304890 GGTAGACAAC
1304900 TACATGTG
1 TACATGTG
1304908 TACATGTG
1 TACATGTG
1304916 TACATGTG
1 TACATGTG
1304924 TA
1 TA
1304926 AACTAGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (8 bp):
TACATGTG
Found at i:1309114 original size:30 final size:30
Alignment explanation
Indices: 1309065--1309166 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 30
1309055 TAAAATTACG
* *
1309065 TAAAAAAT-TATTAACTTTTTAAAATTTTA
1 TAAAAAATATATTTATTTTTTAAAATTTTA
*
1309094 TAAAAAATATATTTATTTTTTAATA-TTTA
1 TAAAAAATATATTTATTTTTTAAAATTTTA
* *
1309123 -AAAAATATTTATTTATTTTTTTAAAATTTAA
1 TAAAAA-ATATATTTA-TTTTTTAAAATTTTA
*
1309154 TTAAAAATATATT
1 TAAAAAATATATT
1309167 GATTCGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
28 5 0.08
29 20 0.33
30 22 0.37
31 9 0.15
32 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAAAAATATATTTATTTTTTAAAATTTTA
Found at i:1309361 original size:16 final size:16
Alignment explanation
Indices: 1309296--1309361 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
1309286 ATTATTATTA
*
1309296 AATTATATTTTAATTC
1 AATTATATATTAATTC
* *
1309312 AAATATATATTAAATATTTT
1 AATTATATATT--A-A-TTC
*
1309332 AATTAT-TTTTAATTC
1 AATTATATATTAATTC
1309347 AATTATATATTAATT
1 AATTATATATTAATT
1309362 TTGAAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
15 8 0.21
16 17 0.45
17 1 0.03
18 1 0.03
19 4 0.11
20 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATATATTAATTC
Found at i:1310239 original size:15 final size:16
Alignment explanation
Indices: 1310219--1310257 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1310209 TTAATGCAAA
*
1310219 TTTAAAATTAAG-TAT
1 TTTAAAAATAAGTTAT
1310234 TTTAAAAATAAGTTTAT
1 TTTAAAAATAAG-TTAT
1310251 TTTAAAA
1 TTTAAAA
1310258 CATCCGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TTTAAAAATAAGTTAT
Found at i:1312472 original size:4 final size:4
Alignment explanation
Indices: 1312463--1312491 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1312453 ACTGATTCAA
1312463 CCAT CCAT CCAT CCAT CCAT CCAT CCAT C
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT C
1312492 TAATTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (4 bp):
CCAT
Found at i:1313041 original size:25 final size:25
Alignment explanation
Indices: 1312990--1313042 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1312980 ATTCAGATTA
* *
1312990 ATTAAAATTTAATAAATTTTTTGAT
1 ATTAAAATTTAATAAAATATTTGAT
*
1313015 ATTAAAATTTTATAAAAATATTT-AT
1 ATTAAAATTTAAT-AAAATATTTGAT
1313040 ATT
1 ATT
1313043 TATATTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTAAAATTTAATAAAATATTTGAT
Found at i:1313291 original size:51 final size:51
Alignment explanation
Indices: 1313235--1313362 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 51
1313225 TAATCGAATT
1313235 AATATTTAATAATTAAAAT-TTTTTAATATAATTTTAATTAT-AA-AATATATA
1 AATATTTAATAATTAAAATATTTTT-AT-TAATTTTAATTATCAATAA-ATATA
* *
1313286 AATATTATAAT-ATAAAAATAATTTTTATTATTTTTAATTATCAATAAATATA
1 AATATT-TAATAATTAAAAT-ATTTTTATTAATTTTAATTATCAATAAATATA
* *
1313338 AATAATTTAAATAATTTAATTATTT
1 AAT-ATTT-AATAATTAAAATATTT
1313363 AAATTAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
51 25 0.39
52 17 0.27
53 17 0.27
54 5 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (51 bp):
AATATTTAATAATTAAAATATTTTTATTAATTTTAATTATCAATAAATATA
Found at i:1315561 original size:2 final size:2
Alignment explanation
Indices: 1315548--1315581 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1315538 TTCATCTTAA
*
1315548 AT AT AT AC AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
1315582 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1319011 original size:21 final size:21
Alignment explanation
Indices: 1318973--1319017 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
1318963 AAGATAATCG
*
1318973 TAAAATTGAATATTATAATAA
1 TAAAATTGAAAATTATAATAA
1318994 TAAAATT-AAAA-T-TAATAA
1 TAAAATTGAAAATTATAATAA
1319012 TAAAAT
1 TAAAAT
1319018 ATATATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 1 0.04
20 3 0.13
21 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATTGAAAATTATAATAA
Found at i:1333895 original size:5 final size:5
Alignment explanation
Indices: 1333885--1333909 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1333875 TCGGAGACAA
1333885 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
1333910 CACCAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:1334419 original size:16 final size:16
Alignment explanation
Indices: 1334400--1334446 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1334390 AAATAACCTA
*
1334400 AACTCGAAATGATTCG
1 AACTCGAAATGATCCG
*
1334416 AACTCGAAATTATCCG
1 AACTCGAAATGATCCG
1334432 AA-TCCGAAATGATCC
1 AACT-CGAAATGATCC
1334447 AGATAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 1 0.04
16 26 0.96
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (16 bp):
AACTCGAAATGATCCG
Found at i:1335282 original size:16 final size:16
Alignment explanation
Indices: 1335263--1335346 Score: 87
Period size: 16 Copynumber: 5.2 Consensus size: 16
1335253 ACCTGAATCT
*
1335263 GAAATGACCCCAACCC
1 GAAATGACCCAAACCC
*
1335279 GAAATGACTCAAACCC
1 GAAATGACCCAAACCC
* *
1335295 GAAATGATCCGAACCC
1 GAAATGACCCAAACCC
* **
1335311 GAAATAATTCAAACCC
1 GAAATGACCCAAACCC
* *
1335327 AAAATGACCCAAACCT
1 GAAATGACCCAAACCC
1335343 GAAA
1 GAAA
1335347 ATAACTCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.45, C:0.31, G:0.12, T:0.12
Consensus pattern (16 bp):
GAAATGACCCAAACCC
Found at i:1335310 original size:32 final size:32
Alignment explanation
Indices: 1335263--1335356 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 32
1335253 ACCTGAATCT
* *
1335263 GAAATGACCCCAACCCGAAATGACTCAAACCC
1 GAAATGACCCAAACCCGAAATAACTCAAACCC
* * *
1335295 GAAATGATCCGAACCCGAAATAATTCAAACCC
1 GAAATGACCCAAACCCGAAATAACTCAAACCC
* *
1335327 AAAATGACCCAAACCTGAAAATAACTCAAA
1 GAAATGACCCAAACCCG-AAATAACTCAAA
1335357 AATTTTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 41 0.79
33 11 0.21
ACGTcount: A:0.47, C:0.30, G:0.11, T:0.13
Consensus pattern (32 bp):
GAAATGACCCAAACCCGAAATAACTCAAACCC
Found at i:1335356 original size:17 final size:16
Alignment explanation
Indices: 1335274--1335356 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 16
1335264 AAATGACCCC
* *
1335274 AACCCGAAATGACTCA
1 AACCCAAAATAACTCA
* * *
1335290 AACCCGAAATGA-TCCG
1 AACCCAAAATAACT-CA
* *
1335306 AACCCGAAATAATTCA
1 AACCCAAAATAACTCA
* *
1335322 AACCCAAAATGACCCA
1 AACCCAAAATAACTCA
*
1335338 AACCTGAAAATAACTCA
1 AACC-CAAAATAACTCA
1335355 AA
1 AA
1335357 AATTTTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 41 0.76
17 12 0.22
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.13
Consensus pattern (16 bp):
AACCCAAAATAACTCA
Found at i:1335389 original size:15 final size:15
Alignment explanation
Indices: 1335365--1335403 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1335355 AAAATTTTAA
* *
1335365 AACTCAAAATGATCC
1 AACTCGAAATGACCC
*
1335380 AATTCGAAATGACCC
1 AACTCGAAATGACCC
1335395 AACTCGAAA
1 AACTCGAAA
1335404 CTAACTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (15 bp):
AACTCGAAATGACCC
Found at i:1336482 original size:24 final size:22
Alignment explanation
Indices: 1336450--1336500 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1336440 TTTAAAAAAA
*
1336450 TTTTAAAATCTAATCTATTTTAAT
1 TTTTAAAAT-TAATCTAATTT-AT
*
1336474 TTTTAAAATTAATTTAATTTAT
1 TTTTAAAATTAATCTAATTTAT
1336496 TTTTA
1 TTTTA
1336501 TGAAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 9 0.36
24 9 0.36
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAAATTAATCTAATTTAT
Found at i:1336688 original size:24 final size:24
Alignment explanation
Indices: 1336644--1336698 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
1336634 ATTATTATTT
*
1336644 TTAATAAAAAATAATATTTAATTAAC
1 TTAA-AAAAAATAATATTTAA-TAAA
*
1336670 TTAAAAAAAATTATA-TTAATAAA
1 TTAAAAAAAATAATATTTAATAAA
1336693 TTAAAA
1 TTAAAA
1336699 TATTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 4 0.15
25 10 0.37
26 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAAAAAATAATATTTAATAAA
Found at i:1336778 original size:118 final size:119
Alignment explanation
Indices: 1336650--1336950 Score: 371
Period size: 118 Copynumber: 2.5 Consensus size: 119
1336640 ATTTTTAATA
* * *
1336650 AAAAATAATATTTAATTAACTTAAAAAAAATTATATTAATAAATTAAAATATTAATTATTTTT-T
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTATATTAACAAATTAAAATATTAATTATTTTTAT
* * * *
1336714 -AAA-AAAACAAATTAAATTAAAAAGGGTTTATTATTATTATTTTTTAAT-AAACTT
66 AAAATAAAAAAAATTAAAATAAAAAAGGTTTATTATTA-TAATTTTTAATGAAA--T
*
1336768 AAAAATAATATTTAATTAAGTTTAAAAATATTATATTAACAAATTAAAATATTAATTATTATATT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTATATTAACAAATTAAAATATT-A--A-T-TATT
* *
1336833 TTTATAAAAATAAAAAAAATTAAAATAAAAAATGTTTTTTATTATAATTTTTAATGAAAT
61 TTTAT-AAAATAAAAAAAATTAAAATAAAAAAGGTTTATTATTATAATTTTTAATGAAAT
* *
1336893 -AAAA-AATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTATATTAACAAATTAAAATATTAATTATT
1336951 ATGTTTTTTA
Statistics
Matches: 160, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
118 53 0.33
119 2 0.01
120 1 0.01
121 1 0.01
122 2 0.01
123 51 0.32
124 5 0.03
125 1 0.01
126 13 0.08
127 31 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (119 bp):
AAAAATAATATTTAATTAAGTTTAAAAAAATTATATTAACAAATTAAAATATTAATTATTTTTAT
AAAATAAAAAAAATTAAAATAAAAAAGGTTTATTATTATAATTTTTAATGAAAT
Found at i:1336782 original size:22 final size:21
Alignment explanation
Indices: 1336756--1336816 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
1336746 ATTATTATTT
1336756 TTTAATAAACTTAAAAATAATA
1 TTTAATAAA-TTAAAAATAATA
* *
1336778 TTTAATTAAGTTTAAAAATATTA
1 TTTAA-TAA-ATTAAAAATAATA
*
1336801 TATTAACAAATTAAAA
1 T-TTAATAAATTAAAA
1336817 TATTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 11 0.34
23 17 0.53
24 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTAATAAATTAAAAATAATA
Found at i:1336914 original size:123 final size:118
Alignment explanation
Indices: 1336629--1336983 Score: 409
Period size: 123 Copynumber: 3.0 Consensus size: 118
1336619 AATAATAACG
* * * * *
1336629 TATTAATTATTATTTTTAATAAA-AAATAATATTTAATTAACTTAAAAAAAATTATATTAATAAA
1 TATT-ATTATAATTTTTAATAAATAAAAAATATTTAATTAAGTT-TAAAAAATTATATTAACAAA
* * *
1336693 TTAAAATATT-A--A-T-TATTTTTT-AAAAAAACAAATTAAATTAAAAAGGGTT
64 TTAAAATATTAATTATTATATTTTTTAAAAAAAAAAAATTAAAATAAAAAAGGTT
*
1336742 TATTATTATTATTTTTTAATAAACTTAAAAATAATATTTAATTAAGTTTAAAAATATTATATTAA
1 TATTATTA-TAATTTTTAATAAA--T-AAAA-AATATTTAATTAAGTTTAAAAA-ATTATATTAA
*
1336807 CAAATTAAAATATTAATTATTATATTTTTATAAAAATAAAAAAAATTAAAATAAAAAATGTT
60 CAAATTAAAATATTAATTATTATATTTTT-T-AAAA-AAAAAAAATTAAAATAAAAAAGGTT
* *
1336869 TTTTATTATAATTTTTAATGAAATAAAAAATATTTAATTAAGTTTAAAAAATTTACATTAACAAA
1 TATTATTATAATTTTTAAT-AAATAAAAAATATTTAATTAAGTTTAAAAAA-TTATATTAACAAA
* * *
1336934 TTAAAATATTAATTATTATGTTTTTTAAAACAAAAAAATTAAAATTAAAA
64 TTAAAATATTAATTATTATATTTTTTAAAAAAAAAAAATTAAAATAAAAA
1336984 TTTTATTAAT
Statistics
Matches: 208, Mismatches: 16, Indels: 29
0.82 0.06 0.11
Matches are distributed among these distances:
112 4 0.02
113 16 0.08
117 8 0.04
118 38 0.18
119 1 0.00
120 18 0.09
121 5 0.02
122 3 0.01
123 65 0.31
124 5 0.02
125 1 0.00
126 13 0.06
127 31 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (118 bp):
TATTATTATAATTTTTAATAAATAAAAAATATTTAATTAAGTTTAAAAAATTATATTAACAAATT
AAAATATTAATTATTATATTTTTTAAAAAAAAAAAATTAAAATAAAAAAGGTT
Found at i:1340058 original size:32 final size:33
Alignment explanation
Indices: 1340022--1340083 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1340012 ACCAATCTTA
*
1340022 AAATTTTACAA-TTTTAT-AATTAAATTAAAATT
1 AAATTTTA-AATTTTTATAAATCAAATTAAAATT
1340054 AAATTTTAAATTTTTATAAATCAAATTAAA
1 AAATTTTAAATTTTTATAAATCAAATTAAA
1340084 TTACATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 2 0.07
32 14 0.52
33 11 0.41
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATTTTAAATTTTTATAAATCAAATTAAAATT
Found at i:1340763 original size:24 final size:22
Alignment explanation
Indices: 1340729--1340778 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
1340719 ATAAATTTCA
*
1340729 TAAAAATAAATCAAATT-GATTT
1 TAAAAATAAAT-AAATTAGATAT
1340751 TAAAAATAAAAATAAATTAGATAT
1 TAAAAAT--AAATAAATTAGATAT
1340775 TAAA
1 TAAA
1340779 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 5 0.21
24 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
TAAAAATAAATAAATTAGATAT
Found at i:1341286 original size:13 final size:13
Alignment explanation
Indices: 1341268--1341320 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
1341258 CGTATTCATA
1341268 AAAAAATTATTTT
1 AAAAAATTATTTT
1341281 AAAAAA-TATTTTAT
1 AAAAAATTA-TTT-T
1341295 AAAAAATT-TATTT
1 AAAAAATTAT-TTT
*
1341308 ACAAAATTATTTT
1 AAAAAATTATTTT
1341321 TTTTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 21 0.62
14 10 0.29
15 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAAAATTATTTT
Found at i:1341305 original size:28 final size:28
Alignment explanation
Indices: 1341265--1341320 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1341255 TAACGTATTC
1341265 ATAAAAAAATTATTTTA-AAAAATATTTT
1 ATAAAAAAATTA-TTTACAAAAATATTTT
* *
1341293 ATAAAAAATTTATTTACAAAATTATTTT
1 ATAAAAAAATTATTTACAAAAATATTTT
1341321 TTTTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATAAAAAAATTATTTACAAAAATATTTT
Found at i:1341308 original size:15 final size:15
Alignment explanation
Indices: 1341260--1341313 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
1341250 TTTCTTAACG
* *
1341260 TATTCATAAAAAAAT
1 TATTTATAAAAAATT
*
1341275 TATTT-TAAAAAATA
1 TATTTATAAAAAATT
1341289 T-TTTATAAAAAATT
1 TATTTATAAAAAATT
*
1341303 TATTTACAAAA
1 TATTTATAAAA
1341314 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 3 0.09
14 17 0.53
15 12 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTTATAAAAAATT
Found at i:1342667 original size:33 final size:33
Alignment explanation
Indices: 1342630--1342695 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1342620 AACTTATGCC
1342630 TATGTCCTCGGACACCACCAATTCTATTATGAG
1 TATGTCCTCGGACACCACCAATTCTATTATGAG
1342663 TATGTCCTCGGACACCACCAATTCTATTATGAG
1 TATGTCCTCGGACACCACCAATTCTATTATGAG
1342696 AAAGAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (33 bp):
TATGTCCTCGGACACCACCAATTCTATTATGAG
Found at i:1342861 original size:27 final size:27
Alignment explanation
Indices: 1342829--1342902 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1342819 AAACAACATG
*
1342829 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* * *
1342856 CTACCATTTTTGACAAACACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
**
1342883 CCATAATTTTTGACAAACAA
1 CCACCATTTTTGACAAACAA
1342903 TGAGTGGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:1347427 original size:27 final size:27
Alignment explanation
Indices: 1347388--1347460 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1347378 AAATAACATG
* *
1347388 TCATCATTTTTTACAAATA-AAAAGAAA
1 TCATAATTTTTTACAAACACAAAA-AAA
* * *
1347415 TTATTATTTTTTACAAACACAAAATAA
1 TCATAATTTTTTACAAACACAAAAAAA
1347442 TCATAATTTTTTACAAACA
1 TCATAATTTTTTACAAACA
1347461 ATAGGTGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 35 0.90
28 4 0.10
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.38
Consensus pattern (27 bp):
TCATAATTTTTTACAAACACAAAAAAA
Found at i:1351181 original size:2 final size:2
Alignment explanation
Indices: 1351174--1351200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1351164 AATGCTCAAT
1351174 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
1351201 GGATGATGTT
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:1351257 original size:156 final size:154
Alignment explanation
Indices: 1351002--1351311 Score: 489
Period size: 156 Copynumber: 2.0 Consensus size: 154
1350992 TTTTTTGTTT
* * * *
1351002 AATATTTAAATGTTCAGTTATATATATATATATATATATATGTTGATGATGTTTGCTTTGTATTT
1 AATATTTAAATGCTCAATTATATATATATATATATATATATATTGATGATGTTTGCTTTGTATTC
* * * * *
1351067 GAGGTATATGATATTATTGAGTTTGTTATTTATTTATTTTTGATTTATGCTT-TTAAATGAATTT
66 AAGGTATATGATATTATTGAGTTTATTATGTATTTATTTTTAATTTATG-TTATTAAATGAATGT
1351131 TAAAATGCTTAAATTATCTATTGTA
130 TAAAATGCTTAAATTATCTATTGTA
1351156 AATATTTAAATGCTCAATTATATATATATATATATATATATATATGGATGATGTTTGCTTTGTAT
1 AATATTTAAATGCTCAATTATATATATATATATATATATATAT-T-GATGATGTTTGCTTTGTAT
1351221 TCAAGGTATATGATATTATTGA-TTTAATTATGTATTTATTTTTAATTTATGTTATTAAATGAAT
64 TCAAGGTATATGATATTATTGAGTTT-ATTATGTATTTATTTTTAATTTATGTTATTAAATGAAT
1351285 GTTAAAATGCTTAAATTATCTATTGTA
128 GTTAAAATGCTTAAATTATCTATTGTA
1351312 TTAAAATGAG
Statistics
Matches: 143, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
154 40 0.28
155 6 0.04
156 97 0.68
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.51
Consensus pattern (154 bp):
AATATTTAAATGCTCAATTATATATATATATATATATATATATTGATGATGTTTGCTTTGTATTC
AAGGTATATGATATTATTGAGTTTATTATGTATTTATTTTTAATTTATGTTATTAAATGAATGTT
AAAATGCTTAAATTATCTATTGTA
Done.