Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 6 of 26
Found at i:1116365 original size:21 final size:20
Alignment explanation
Indices: 1116336--1116379 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1116326 ATTAAATACA
1116336 TAAAATTAAT-TACATCAATT
1 TAAAATTAATCTA-ATCAATT
*
1116356 TAAAATTTAATCTAATTAATT
1 TAAAA-TTAATCTAATCAATT
1116377 TAA
1 TAA
1116380 TTATGCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 14 0.67
22 2 0.10
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATTAATCTAATCAATT
Found at i:1116899 original size:11 final size:11
Alignment explanation
Indices: 1116883--1116910 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1116873 TAAATTAAAT
1116883 TTATATTTATA
1 TTATATTTATA
1116894 TTATATTTATA
1 TTATATTTATA
1116905 TTATAT
1 TTATAT
1116911 AATAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1116901 original size:17 final size:16
Alignment explanation
Indices: 1116876--1116910 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1116866 TAATCGGTAA
1116876 ATTAAATTTATATTTAT
1 ATTAAATTTATA-TTAT
*
1116893 ATTATATTTATATTAT
1 ATTAAATTTATATTAT
1116909 AT
1 AT
1116911 AATAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTAAATTTATATTAT
Found at i:1116918 original size:24 final size:25
Alignment explanation
Indices: 1116891--1116943 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
1116881 ATTTATATTT
* *
1116891 ATATTATATTTATATTATA-TAAT-A
1 ATATTAAATTT-TAATATATTAATAA
1116915 ATA-TAAATTTTAATATATTAATAA
1 ATATTAAATTTTAATATATTAATAA
1116939 ATATT
1 ATATT
1116944 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 6 0.25
23 10 0.42
24 7 0.29
25 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTAAATTTTAATATATTAATAA
Found at i:1118606 original size:2 final size:2
Alignment explanation
Indices: 1118601--1118636 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1118591 GTGTAGGTGG
1118601 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
1118637 TGCAAAATGT
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:1118967 original size:26 final size:26
Alignment explanation
Indices: 1118918--1119001 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 26
1118908 GTTTTATAAT
*
1118918 AATTAA-A-TTAATATAATATAATTTA
1 AATTAATATTTAAT-TAATAAAATTTA
*
1118943 AATTAATATTTTATTAATAAAATTT-
1 AATTAATATTTAATTAATAAAATTTA
* * *
1118968 ATTTAA-ATTTAATT-ATAAAAATAA
1 AATTAATATTTAATTAATAAAATTTA
1118992 ATATTAATAT
1 A-ATTAATAT
1119002 AAAAATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
23 7 0.15
24 8 0.17
25 15 0.32
26 13 0.28
27 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTAATATTTAATTAATAAAATTTA
Found at i:1119016 original size:18 final size:18
Alignment explanation
Indices: 1118971--1119016 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
1118961 AAAATTTATT
1118971 TAAATTTAATTATAAAAA
1 TAAATTTAATTATAAAAA
1118989 TAAATATTAA-TATAAAAA
1 TAAAT-TTAATTATAAAAA
1119007 TAATATTTAA
1 TAA-ATTTAA
1119017 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATTTAATTATAAAAA
Found at i:1119048 original size:18 final size:17
Alignment explanation
Indices: 1119024--1119068 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
1119014 TAAATTTTTT
1119024 AAAATTAAAATAAATATA
1 AAAATTAAAATAAATA-A
* *
1119042 TAAATTAAATTAAATAA
1 AAAATTAAAATAAATAA
1119059 AAAATTAAAA
1 AAAATTAAAA
1119069 AATTTAGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTAAAATAAATAA
Found at i:1119818 original size:16 final size:16
Alignment explanation
Indices: 1119785--1119815 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1119775 TAAATAATAA
1119785 AATAAAATTTTAAATT
1 AATAAAATTTTAAATT
1119801 AATAAAA-TTTAAATT
1 AATAAAATTTTAAATT
1119816 TAAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAAATTTTAAATT
Found at i:1120500 original size:14 final size:15
Alignment explanation
Indices: 1120473--1120510 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1120463 TTTAAAAATA
1120473 ATTTTTTATTTTTAAT
1 ATTTTTTA-TTTTAAT
1120489 ATTTTTTA-TTTAAT
1 ATTTTTTATTTTAAT
1120503 ATTATTTT
1 ATT-TTTT
1120511 TATCATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTATTTTAAT
Found at i:1120511 original size:17 final size:16
Alignment explanation
Indices: 1120473--1120511 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1120463 TTTAAAAATA
*
1120473 ATTTTTTATTTTTAAT
1 ATTTTTTATTTATAAT
*
1120489 ATTTTTTATTTAATATT
1 ATTTTTTATTT-ATAAT
1120506 ATTTTT
1 ATTTTT
1120512 ATCATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTTATTTATAAT
Found at i:1120560 original size:13 final size:13
Alignment explanation
Indices: 1120544--1120568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1120534 TAATTATTTT
1120544 TTTAATTTATAAG
1 TTTAATTTATAAG
1120557 TTTAATTTATAA
1 TTTAATTTATAA
1120569 TATTTATTTT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTAATTTATAAG
Found at i:1121617 original size:23 final size:21
Alignment explanation
Indices: 1121591--1121641 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1121581 TAAATAAAAA
*
1121591 ATTTTAACAAATTATATATTTTT
1 ATTTTAA-AAATT-TAAATTTTT
*
1121614 ATTTTTAAAATTTAAATTTTT
1 ATTTTAAAAATTTAAATTTTT
1121635 ATATTTA
1 AT-TTTA
1121642 TAATTTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 8 0.33
23 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTAAAAATTTAAATTTTT
Found at i:1122584 original size:6 final size:6
Alignment explanation
Indices: 1122573--1122598 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1122563 AAAGGTAGCT
1122573 GCTTCC GCTTCC GCTTCC GCTTCC GC
1 GCTTCC GCTTCC GCTTCC GCTTCC GC
1122599 GGCTGTGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.19, T:0.31
Consensus pattern (6 bp):
GCTTCC
Found at i:1122926 original size:14 final size:14
Alignment explanation
Indices: 1122891--1122931 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1122881 ATAGAAAAGC
1122891 AAAAAAATAA-AAT
1 AAAAAAATAATAAT
1122904 AAAATAAATAATAAT
1 AAAA-AAATAATAAT
*
1122919 AATAAAATAATAA
1 AAAAAAATAATAA
1122932 CATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 15 0.60
15 6 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAAATAATAAT
Found at i:1124498 original size:23 final size:24
Alignment explanation
Indices: 1124472--1124518 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1124462 TAGTTATACA
1124472 ATAAATTT-TATTTTATATAATAT
1 ATAAATTTATATTTTATATAATAT
*
1124495 ATAAATTTAATTTTTTATATAATA
1 ATAAATTT-ATATTTTATATAATA
1124519 ATTTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATAAATTTATATTTTATATAATAT
Found at i:1124506 original size:28 final size:28
Alignment explanation
Indices: 1124475--1124568 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 28
1124465 TTATACAATA
1124475 AATTTTATTTTATATAATATATAAATTT
1 AATTTTATTTTATATAATATATAAATTT
* *
1124503 AATTTT-TTATATAATAATTTAATAAATATAT
1 AATTTTATTTTAT-ATAATAT-ATAAAT-T-T
*
1124534 AAATTTTATTATTATAAAATTAATATAAA-TT
1 -AATTTTATT-TTATATAA-T-ATATAAATTT
1124565 AATT
1 AATT
1124569 AAAAATAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
27 5 0.10
28 12 0.23
29 6 0.12
30 5 0.10
31 2 0.04
32 7 0.13
33 5 0.10
34 9 0.17
35 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTTATTTTATATAATATATAAATTT
Found at i:1125680 original size:20 final size:21
Alignment explanation
Indices: 1125644--1125682 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1125634 TAGTTAAAAA
*
1125644 AATTAATATTTATAAATATTT
1 AATTAATATTAATAAATATTT
1125665 AATTAA-ATTAATAAATAT
1 AATTAATATTAATAAATAT
1125683 ATAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTAATATTAATAAATATTT
Found at i:1125700 original size:27 final size:30
Alignment explanation
Indices: 1125645--1125710 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 30
1125635 AGTTAAAAAA
*
1125645 ATTAATATTTATAAATATTTAATTAAATTA-
1 ATTAA-ATATATAAATATTTAATTAAATTAT
*
1125675 A-TAAATATATAAAT-TTTAGTTAAATTAT
1 ATTAAATATATAAATATTTAATTAAATTAT
1125703 ATTAAATA
1 ATTAAATA
1125711 ATTATTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 12 0.38
28 10 0.31
29 9 0.28
30 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTAAATATATAAATATTTAATTAAATTAT
Found at i:1125743 original size:17 final size:18
Alignment explanation
Indices: 1125721--1125762 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 18
1125711 ATTATTATCT
1125721 ATTTAAATATTTTTATA-
1 ATTTAAATATTTTTATAG
1125738 ATTT-AA-ATTTTTATAG
1 ATTTAAATATTTTTATAG
1125754 ATATTAAAT
1 AT-TTAAAT
1125763 TTGAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 6 0.29
18 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTTTATAG
Found at i:1125747 original size:15 final size:17
Alignment explanation
Indices: 1125729--1125764 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
1125719 CTATTTAAAT
1125729 ATTTTTATA-AT-TTAA
1 ATTTTTATAGATATTAA
1125744 ATTTTTATAGATATTAA
1 ATTTTTATAGATATTAA
1125761 ATTT
1 ATTT
1125765 GAAGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTTATAGATATTAA
Found at i:1126180 original size:18 final size:17
Alignment explanation
Indices: 1126157--1126190 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1126147 ACGACATGAA
1126157 TAAAATATAAAAAATAAT
1 TAAAATA-AAAAAATAAT
*
1126175 TAAAATAAAAATATAA
1 TAAAATAAAAAAATAA
1126191 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAAAAAAATAAT
Found at i:1126370 original size:21 final size:21
Alignment explanation
Indices: 1126344--1126414 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1126334 ATTACAATAA
1126344 AAAATAATATAAAAATTAATT
1 AAAATAATATAAAAATTAATT
*
1126365 AAAAT-ATAATAAAAATAAATAT
1 AAAATAAT-ATAAAAATTAAT-T
* * *
1126387 GAAGTAAATATAAAAAATAA--
1 AAAAT-AATATAAAAATTAATT
1126407 AAAATAAT
1 AAAATAAT
1126415 TTATAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 16 0.41
22 4 0.10
23 9 0.23
24 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAATAATATAAAAATTAATT
Found at i:1126713 original size:27 final size:28
Alignment explanation
Indices: 1126638--1126837 Score: 264
Period size: 27 Copynumber: 7.0 Consensus size: 28
1126628 CTCCCCTTCC
1126638 CCCCCCCCCAGGCCGATTATCAGAAGACA
1 CCCCCCCCC-GGCCGATTATCAGAAGACA
*
1126667 CCCCCCCCAACCCCGCCGATTATCAGAAGACA
1 --CCCCCC--CCCGGCCGATTATCAGAAGACA
1126699 -CCCCCCCCGGCCGATTATCAGAAGACA
1 CCCCCCCCCGGCCGATTATCAGAAGACA
*
1126726 CCCCCCACCCCGCCGATTATCAGAAGACA
1 CCCCCC-CCCGGCCGATTATCAGAAGACA
1126755 --CCCCCCCGGCCGATTATCAGAAGACA
1 CCCCCCCCCGGCCGATTATCAGAAGACA
*
1126781 CCCCCCCACCCCGCCGATTATCAGAAGACA
1 -CCCCCC-CCCGGCCGATTATCAGAAGACA
*
1126811 -CCCCCCCCGGCCGAATATCAGAAGACA
1 CCCCCCCCCGGCCGATTATCAGAAGACA
1126838 AACTATCTCA
Statistics
Matches: 154, Mismatches: 7, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
26 21 0.14
27 45 0.29
28 10 0.06
29 30 0.19
30 21 0.14
31 6 0.04
32 18 0.12
33 3 0.02
ACGTcount: A:0.28, C:0.47, G:0.16, T:0.10
Consensus pattern (28 bp):
CCCCCCCCCGGCCGATTATCAGAAGACA
Found at i:1126756 original size:56 final size:57
Alignment explanation
Indices: 1126639--1126837 Score: 348
Period size: 56 Copynumber: 3.5 Consensus size: 57
1126629 TCCCCTTCCC
1126639 CCCCCCCCAGGCCGATTATCAGAAGACACCCCCCCCAACCCCGCCGATTATCAGAAGACA
1 CCCCCCCC-GGCCGATTATCAGAAGACA-CCCCCCC-ACCCCGCCGATTATCAGAAGACA
1126699 CCCCCCCCGGCCGATTATCAGAAGACA-CCCCCCACCCCGCCGATTATCAGAAGACA
1 CCCCCCCCGGCCGATTATCAGAAGACACCCCCCCACCCCGCCGATTATCAGAAGACA
1126755 -CCCCCCCGGCCGATTATCAGAAGACACCCCCCCACCCCGCCGATTATCAGAAGACA
1 CCCCCCCCGGCCGATTATCAGAAGACACCCCCCCACCCCGCCGATTATCAGAAGACA
*
1126811 CCCCCCCCGGCCGAATATCAGAAGACA
1 CCCCCCCCGGCCGATTATCAGAAGACA
1126838 AACTATCTCA
Statistics
Matches: 136, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
55 26 0.19
56 52 0.38
57 31 0.23
59 19 0.14
60 8 0.06
ACGTcount: A:0.28, C:0.46, G:0.16, T:0.10
Consensus pattern (57 bp):
CCCCCCCCGGCCGATTATCAGAAGACACCCCCCCACCCCGCCGATTATCAGAAGACA
Found at i:1127448 original size:33 final size:33
Alignment explanation
Indices: 1127406--1127473 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1127396 TGATTCGTGT
1127406 TTGAGCTTGTTTCCCTGTTTGAAATCAAAAGTC
1 TTGAGCTTGTTTCCCTGTTTGAAATCAAAAGTC
1127439 TTGAGCTTGTTTCCCTGTTTGAAATCAAAAGTC
1 TTGAGCTTGTTTCCCTGTTTGAAATCAAAAGTC
1127472 TT
1 TT
1127474 TGGGTTCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (33 bp):
TTGAGCTTGTTTCCCTGTTTGAAATCAAAAGTC
Found at i:1128273 original size:14 final size:14
Alignment explanation
Indices: 1128254--1128286 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1128244 TCTCCGTAGC
1128254 TTTTTT-CTTTTTCT
1 TTTTTTCCTTTTT-T
1128268 TTTTTTCCTTTTTT
1 TTTTTTCCTTTTTT
1128282 TTTTT
1 TTTTT
1128287 GGGGGGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTCCTTTTTT
Found at i:1128987 original size:32 final size:29
Alignment explanation
Indices: 1128940--1129009 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
1128930 AAAAATTATT
1128940 TATTATTA-AATATAAAAATAATATTT-TAA
1 TATTATTATAATAT-AAAATAA-ATTTGTAA
1128969 TATTATTATAAGTAATAAAATAAATTTGTAA
1 TATTATTATAA-T-ATAAAATAAATTTGTAA
*
1129000 -ATTAATATAA
1 TATTATTATAA
1129010 CTTAAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 8 0.22
30 15 0.42
31 11 0.31
32 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
TATTATTATAATATAAAATAAATTTGTAA
Found at i:1129756 original size:16 final size:17
Alignment explanation
Indices: 1129737--1129804 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
1129727 ATTTTTAATA
1129737 TTTTTAATTTAATAT-T
1 TTTTTAATTTAATATAT
* *
1129753 TTTTTATTTTAATATGT
1 TTTTTAATTTAATATAT
* * *
1129770 ATTATCACTTTAAT-TAT
1 -TTTTTAATTTAATATAT
1129787 TTTTTAATTT-ATATAT
1 TTTTTAATTTAATATAT
1129803 TT
1 TT
1129805 AATTCATATC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
15 2 0.05
16 26 0.63
17 3 0.07
18 10 0.24
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (17 bp):
TTTTTAATTTAATATAT
Found at i:1138882 original size:24 final size:22
Alignment explanation
Indices: 1138853--1138904 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
1138843 TGAAAATAAT
*
1138853 TATATAATAAATTTTA-TTTTA
1 TATATAATAAATTTAATTTTTA
1138874 TATAATATATAAATTTAATTTTTA
1 TAT-ATA-ATAAATTTAATTTTTA
1138898 TATATAA
1 TATATAA
1138905 ATTTAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 12 0.44
24 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATAATAAATTTAATTTTTA
Found at i:1138890 original size:17 final size:17
Alignment explanation
Indices: 1138870--1138937 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
1138860 TAAATTTTAT
1138870 TTTATATAATATATAAA
1 TTTATATAATATATAAA
* *
1138887 TTTAATTTTTATATATAAA
1 TTT-A-TATAATATATAAA
1138906 TTTA-ATAAATATATAAA
1 TTTATAT-AATATATAAA
*
1138923 TTT-TATTAT-TATAAA
1 TTTATATAATATATAAA
1138938 ATTAATATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 6 0.14
16 3 0.07
17 17 0.40
18 2 0.05
19 14 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTATATAATATATAAA
Found at i:1138918 original size:19 final size:19
Alignment explanation
Indices: 1138878--1138920 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1138868 ATTTTATATA
***
1138878 ATATATAAATTTAATTTTT
1 ATATATAAATTTAATAAAT
1138897 ATATATAAATTTAATAAAT
1 ATATATAAATTTAATAAAT
1138916 ATATA
1 ATATA
1138921 AATTTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATAAATTTAATAAAT
Found at i:1143108 original size:17 final size:17
Alignment explanation
Indices: 1143086--1143136 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1143076 TATGTTTAAT
1143086 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1143103 ATTTTA-ATTTAT-TAA
1 ATTTTATATTTATATAA
*
1143118 TAATTTATA-TTATATAA
1 -ATTTTATATTTATATAA
1143135 AT
1 AT
1143137 ATTAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 16 0.55
17 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1143121 original size:11 final size:11
Alignment explanation
Indices: 1143107--1143160 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
1143097 ATATAAATTT
*
1143107 TAATTTATTAA
1 TAATATATTAA
1143118 TAATTTATATTATA
1 TAA--TATATTA-A
1143132 TAA-ATATTAA
1 TAATATATTAA
1143142 TAATATATTAA
1 TAATATATTAA
*
1143153 TATTATAT
1 TAATATAT
1143161 CATATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 4 0.11
11 23 0.62
13 6 0.16
14 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATATATTAA
Found at i:1143136 original size:32 final size:33
Alignment explanation
Indices: 1143081--1143142 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1143071 ATAATTATGT
* *
1143081 TTAATATTTTATATTTATATAAATTTTAATTTA
1 TTAATAATTTATATTTATATAAATATTAATTTA
1143114 TTAATAATTTATA-TTATATAAATATTAAT
1 TTAATAATTTATATTTATATAAATATTAAT
1143143 AATATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATAATTTATATTTATATAAATATTAATTTA
Found at i:1143137 original size:18 final size:17
Alignment explanation
Indices: 1143083--1143165 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
1143073 AATTATGTTT
1143083 AATATTTTATATTTATATA
1 AATA-TTTATA-TTATATA
*
1143102 AAT-TTTA-ATT-TATT
1 AATATTTATATTATATA
1143116 AATAATTTATATTATATA
1 AAT-ATTTATATTATATA
* * *
1143134 AATATTAATAATATATT
1 AATATTTATATTATATA
*
1143151 AATA-TTATATCATAT
1 AATATTTATATTATAT
1143166 TTTAATTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 13 0.25
17 22 0.42
18 6 0.12
19 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTATATTATATA
Found at i:1143165 original size:27 final size:27
Alignment explanation
Indices: 1143115--1143207 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 27
1143105 TTTAATTTAT
* *
1143115 TAATA-ATTTATATTATATAAATATTAA
1 TAATATATTAATATTATAT-CATATTAA
*
1143142 TAATATATTAATATTATATCATATT-T
1 TAATATATTAATATTATATCATATTAA
1143168 TAAT-TATTATATATATATATCATATTTATA
1 TAATATATTA-ATAT-TATATCATA-TTA-A
1143198 TAACTATATT
1 TAA-TATATT
1143208 TAAAATTACC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
25 5 0.09
26 8 0.15
27 19 0.35
28 14 0.26
30 3 0.06
31 1 0.02
32 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATATATTAATATTATATCATATTAA
Found at i:1143166 original size:38 final size:37
Alignment explanation
Indices: 1143081--1143199 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 37
1143071 ATAATTATGT
* *
1143081 TTAATATTTTATAT-TTATATAAAT-TT--TAATTTA
1 TTAATATTATATATATTATATAAATATTAATAATATA
*
1143114 TTAATA--ATTTATATTATATAAATATTAATAATATA
1 TTAATATTATATATATTATATAAATATTAATAATATA
*
1143149 TTAATATTATATCATATT-T-TAATTATT-ATATATATA
1 TTAATATTATAT-ATATTATATAAATATTAATA-ATATA
*
1143185 TATCATATT-TATATA
1 T-TAATATTATATATA
1143200 ACTATATTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
31 4 0.06
32 10 0.14
33 8 0.11
35 18 0.25
36 16 0.23
37 10 0.14
38 5 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (37 bp):
TTAATATTATATATATTATATAAATATTAATAATATA
Found at i:1147570 original size:20 final size:21
Alignment explanation
Indices: 1147520--1147577 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
1147510 AAAAGATATC
**
1147520 TTTGGATGAAATGATGCATTG
1 TTTGGATGAAAAAATGCATTG
* *
1147541 GTTAGATGAAAAAATGCATT-
1 TTTGGATGAAAAAATGCATTG
1147561 TTTGGATG-AAAAATGCA
1 TTTGGATGAAAAAATGCA
1147578 ACTTTTAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 9 0.29
20 6 0.19
21 16 0.52
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (21 bp):
TTTGGATGAAAAAATGCATTG
Found at i:1147583 original size:20 final size:20
Alignment explanation
Indices: 1147545--1147583 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147535 GCATTGGTTA
*
1147545 GATGAAAAAATGCATTTTTG
1 GATGAAAAAATGCACTTTTG
1147565 GATG-AAAAATGCAACTTTT
1 GATGAAAAAATGC-ACTTTT
1147584 AATGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (20 bp):
GATGAAAAAATGCACTTTTG
Found at i:1151053 original size:25 final size:25
Alignment explanation
Indices: 1151028--1151092 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
1151018 AAAAATTTTA
* *
1151028 AATT-AAATTATTTTTTATTAGATT
1 AATTAAAAATATTTATTATTAGATT
1151052 AATTAAAAATATTTATTATT--ATT
1 AATTAAAAATATTTATTATTAGATT
*
1151075 ATTTAAAAACT-TTTATTA
1 AATTAAAAA-TATTTATTA
1151093 CATTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 18 0.50
24 5 0.14
25 13 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
AATTAAAAATATTTATTATTAGATT
Found at i:1151080 original size:23 final size:22
Alignment explanation
Indices: 1151040--1151098 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1151030 TTAAATTATT
1151040 TTTTATTAGATTAATTAAAAA-
1 TTTTATTAGATTAATTAAAAAC
* *
1151061 TATTTATTATTATTATTTAAAAAC
1 T-TTTATTA-GATTAATTAAAAAC
*
1151085 TTTTATTACATTAA
1 TTTTATTAGATTAA
1151099 AAATATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 11 0.35
23 18 0.58
24 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTATTAGATTAATTAAAAAC
Found at i:1153195 original size:73 final size:71
Alignment explanation
Indices: 1153071--1153332 Score: 263
Period size: 73 Copynumber: 3.6 Consensus size: 71
1153061 GTAGCTAGTA
* * * * * *
1153071 CATTGTTTGTGCCTAAGGTAGTTCCATGTACGAACCATTTGCCCTGTTTTTATACCCCTATTTAT
1 CATTGTTTGTGCCTAAGGCAGTTCCATGTATGAACCGTTT-TCCGGGTTTTATACCCC-ATTTAT
1153136 ACTCAGTT
64 ACTCAGTT
* * * *
1153144 TATTGTTTGTGCCTAAGGCAATTCCATGTATGAACCGCTTTCCGGGATTTTATACCCCATTTTTT
1 CATTGTTTGTGCCTAAGGCAGTTCCATGTATGAACCGTTTTCCGGG-TTTTATACCCCA-TTTAT
**
1153209 ACAGAGTT
64 ACTCAGTT
* * * * * * * **
1153217 CATTGATAGTTCCTAAGGCAGTTCTATTTATGAATCGTTTTCCTGGGTTTTATACCCAAATTCGT
1 CATTGTTTGTGCCTAAGGCAGTTCCATGTATGAACCGTTTTCC-GGGTTTTATACCC-CATTTAT
1153282 ACTCAGTT
64 ACTCAGTT
* *
1153290 CATTGTTTATGCCAAAGGCAGTTCCATGTATGAACCGTTTTCC
1 CATTGTTTGTGCCTAAGGCAGTTCCATGTATGAACCGTTTTCC
1153333 CTGATATTAT
Statistics
Matches: 151, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
72 4 0.03
73 143 0.95
74 4 0.03
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (71 bp):
CATTGTTTGTGCCTAAGGCAGTTCCATGTATGAACCGTTTTCCGGGTTTTATACCCCATTTATAC
TCAGTT
Found at i:1158646 original size:2 final size:2
Alignment explanation
Indices: 1158639--1158675 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1158629 TAAATAGCTT
*
1158639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1158676 GGACCTAAAA
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1163579 original size:25 final size:24
Alignment explanation
Indices: 1163528--1163579 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
1163518 AATAATATTA
*
1163528 ATATGATATTTATAAAATATTAAAT
1 ATATGATATATATAAAATA-TAAAT
1163553 ATATGATATA-ATATAAA-ATAAAT
1 ATATGATATATATA-AAATATAAAT
1163576 ATAT
1 ATAT
1163580 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 9 0.36
24 4 0.16
25 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATATGATATATATAAAATATAAAT
Found at i:1163600 original size:33 final size:34
Alignment explanation
Indices: 1163558--1163638 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 34
1163548 TAAATATATG
*
1163558 ATATAATATAAAATAAATATATT-T-TTAAAATTT
1 ATATAATATAAAATAAAT-TATTGTATCAAAATTT
*
1163591 ATATAATAT-AAAT-TATTATTGTATCAAAATTT
1 ATATAATATAAAATAAATTATTGTATCAAAATTT
1163623 ATATAAGTATAAAATA
1 ATATAA-TATAAAATA
1163639 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 3 0.07
32 18 0.44
33 12 0.29
34 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (34 bp):
ATATAATATAAAATAAATTATTGTATCAAAATTT
Found at i:1165041 original size:8 final size:8
Alignment explanation
Indices: 1165017--1165056 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
1165007 AATTAAAGCT
1165017 TTATATATA
1 TTATATA-A
*
1165026 TAATATAA
1 TTATATAA
1165034 TTATATAA
1 TTATATAA
1165042 TTATATAA
1 TTATATAA
1165050 TTATATA
1 TTATATA
1165057 TGCTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTATATAA
Found at i:1165461 original size:68 final size:67
Alignment explanation
Indices: 1165335--1165463 Score: 152
Period size: 68 Copynumber: 1.9 Consensus size: 67
1165325 TTTTTAATCG
* ** *
1165335 ATATGATAAAAAAATTAAATCGATTTAAAATTATACGATAAGTATGATTATATTACTAAATCAAT
1 ATATGATAAAAAAATTAAATCGATTCAAAATTATAC-ATAAGTACAATTATATAACTAAATCAAT
1165400 ATA
65 ATA
* * * *
1165403 ATATGATAGAGAAATTAAATTGATTCAAAACTTTATA-ATAAGTACAATTGTATAACTAAAT
1 ATATGATAAAAAAATTAAATCGATTCAAAA--TTATACATAAGTACAATTATATAACTAAAT
1165464 TCACTGATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
68 46 0.90
70 5 0.10
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (67 bp):
ATATGATAAAAAAATTAAATCGATTCAAAATTATACATAAGTACAATTATATAACTAAATCAATA
TA
Found at i:1169888 original size:2 final size:2
Alignment explanation
Indices: 1169881--1169933 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
1169871 GTTCGGGATC
* *
1169881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1169923 AT AT AT -T AT AT
1 AT AT AT AT AT AT
1169934 GGTTCCGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1172133 original size:2 final size:2
Alignment explanation
Indices: 1172126--1172155 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1172116 TTTTTAACCC
1172126 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
1172156 TTATAGTCTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1172389 original size:17 final size:18
Alignment explanation
Indices: 1172328--1172389 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
1172318 ATAATTATAA
*
1172328 TTAAATATTTTATATTTAT
1 TTAAATATTTAATA-TTAT
*
1172347 ATAAAT-TTTAATA-TA-
1 TTAAATATTTAATATTAT
*
1172362 TT-AATAATTAATATTAT
1 TTAAATATTTAATATTAT
1172379 TTAAAT-TTTAA
1 TTAAATATTTAA
1172390 AATATATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 4 0.12
17 6 0.18
18 9 0.26
19 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATATTTAATATTAT
Found at i:1175371 original size:1 final size:1
Alignment explanation
Indices: 1175367--1175397 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1175357 TTGTTCAGCG
*
1175367 CCCCCCCCCCCCCACCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1175398 ATCTTTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1176635 original size:24 final size:25
Alignment explanation
Indices: 1176607--1176671 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 25
1176597 AAAATTTAAA
*
1176607 TTTTAATATATGTA-ATTTTTT-TAT
1 TTTTAATATATATATATTTTTTAT-T
1176631 TTTTAA-AT-TATATATTTTTTATT
1 TTTTAATATATATATATTTTTTATT
1176654 TTTTAAATATATATATAT
1 TTTT-AATATATATATAT
1176672 ATATATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.09
23 14 0.40
24 9 0.26
25 2 0.06
26 7 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTAATATATATATATTTTTTATT
Found at i:1176651 original size:22 final size:24
Alignment explanation
Indices: 1176623--1176669 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
1176613 TATATGTAAT
1176623 TTTTTTA-TTTTTAAAT-TATATA
1 TTTTTTATTTTTTAAATATATATA
1176645 TTTTTTATTTTTTAAATATATATA
1 TTTTTTATTTTTTAAATATATATA
1176669 T
1 T
1176670 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTTATTTTTTAAATATATATA
Found at i:1177020 original size:22 final size:22
Alignment explanation
Indices: 1176994--1177119 Score: 89
Period size: 22 Copynumber: 5.6 Consensus size: 22
1176984 TCTAAATTTG
1176994 ATATTATATTTATATAATTTTT
1 ATATTATATTTATATAATTTTT
* ***
1177016 ATATTATAATTATAT--TTAAA
1 ATATTATATTTATATAATTTTT
1177036 ATATTATATATTTATATAATTTTT
1 ATA-T-TATATTTATATAATTTTT
* *
1177060 -TAATATATTTATATATTTATATT
1 ATATTATATTTATATAATT-T-TT
1177083 ATATTATATTT-TAATTAATTTTAT
1 ATATTATATTTAT-A-TAATTTT-T
* *
1177107 ATCTTATAATTAT
1 ATATTATATTTAT
1177120 TTTATGTTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.06
21 15 0.19
22 25 0.32
23 6 0.08
24 23 0.29
25 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATATTTATATAATTTTT
Found at i:1177028 original size:11 final size:11
Alignment explanation
Indices: 1176994--1177124 Score: 61
Period size: 11 Copynumber: 12.6 Consensus size: 11
1176984 TCTAAATTTG
*
1176994 ATATTATATTT
1 ATATTATAATT
* **
1177005 ATATAATTTTT
1 ATATTATAATT
1177016 ATATTATAATT
1 ATATTATAATT
*
1177027 ATATT-TAA-A
1 ATATTATAATT
1177036 ATATTATATATT
1 ATATTATA-ATT
1177048 -TA-TATAATT
1 ATATTATAATT
1177057 -T-TT-TAA-T
1 ATATTATAATT
1177064 ATATTTATATATTT
1 ATA-TTATA-A-TT
1177078 ATATTAT-ATT
1 ATATTATAATT
*
1177088 ATATTTTAATT
1 ATATTATAATT
*
1177099 A-ATT-TTA-T
1 ATATTATAATT
*
1177107 ATCTTATAATT
1 ATATTATAATT
*
1177118 ATTTTAT
1 ATATTAT
1177125 GTTTAATATT
Statistics
Matches: 93, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
7 1 0.01
8 6 0.06
9 14 0.15
10 24 0.26
11 39 0.42
12 1 0.01
13 4 0.04
14 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTATAATT
Found at i:1177052 original size:8 final size:8
Alignment explanation
Indices: 1176998--1177095 Score: 62
Period size: 8 Copynumber: 12.0 Consensus size: 8
1176988 AATTTGATAT
1176998 TATATTTA
1 TATATTTA
*
1177006 TATAATTTT
1 TAT-ATTTA
1177015 TATATTATAA
1 TATATT-T-A
1177025 TTATATTTA
1 -TATATTTA
*
1177034 -AAATATTA
1 TATAT-TTA
1177042 TATATTTA
1 TATATTTA
*
1177050 TATAATT-
1 TATATTTA
*
1177057 T-T-TTAA
1 TATATTTA
1177063 TATATTTA
1 TATATTTA
1177071 TATATTTA
1 TATATTTA
1177079 TATTATATTA
1 TA-TAT-TTA
1177089 TAT-TTTA
1 TATATTTA
1177096 ATTAATTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 23
0.70 0.08 0.23
Matches are distributed among these distances:
5 1 0.01
6 2 0.03
7 8 0.11
8 32 0.45
9 16 0.23
10 6 0.08
11 6 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATATTTA
Found at i:1177055 original size:44 final size:46
Alignment explanation
Indices: 1176998--1177124 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 46
1176988 AATTTGATAT
1176998 TATATTTATATAATTTTTATATTATAATTATATTTA-A-AATATTA
1 TATATTTATATAATTTTTATATTATAATTATATTTATATAATATTA
* * *
1177042 TATATTTATATAATTTTT-TAATATATTTATATATTTATATTATATTA
1 TATATTTATATAATTTTTATATTATA-AT-TATATTTATATAATATTA
*
1177089 TAT-TTTA-ATTAATTTTATATCTTATAATTAT-TTTAT
1 TATATTTATA-TAATTTT-TATATTATAATTATATTTAT
1177125 GTTTAATATT
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
43 6 0.09
44 19 0.27
45 14 0.20
46 15 0.21
47 11 0.16
48 5 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (46 bp):
TATATTTATATAATTTTTATATTATAATTATATTTATATAATATTA
Found at i:1177095 original size:17 final size:17
Alignment explanation
Indices: 1176997--1177136 Score: 77
Period size: 17 Copynumber: 8.5 Consensus size: 17
1176987 AAATTTGATA
*
1176997 TTATATTTATATAAT-TT
1 TTATA-TTATATTATATT
1177014 TTATATTATAATTATA-T
1 TTATATTAT-ATTATATT
*
1177031 TTA-A-AATATTATATAT
1 TTATATTATATTATAT-T
1177047 TTATA-TA-ATT-T-TT
1 TTATATTATATTATATT
*
1177060 TAATA-TAT-TTATATAT
1 TTATATTATATTATAT-T
1177076 TTATATTATATTATATT
1 TTATATTATATTATATT
* *
1177093 TTA-ATTAATTTTATATC
1 TTATATT-ATATTATATT
* *
1177110 TTATAATTATTTTATGTT
1 TTAT-ATTATATTATATT
*
1177128 TAATATTAT
1 TTATATTAT
1177137 TACTTGAGCA
Statistics
Matches: 99, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
13 9 0.09
14 8 0.08
15 4 0.04
16 20 0.20
17 38 0.38
18 17 0.17
19 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:1177098 original size:42 final size:43
Alignment explanation
Indices: 1176989--1177098 Score: 97
Period size: 42 Copynumber: 2.6 Consensus size: 43
1176979 GAGCATCTAA
* *
1176989 ATTTGATATTATATT-TA-TATAATTTTTATATTATAATTATAT
1 ATTT-ATATTATATTATATTTTAATTTTTATAATATAATTATAT
* *
1177031 -TTAAAATATTATA-TAT-TTATATAATTTTT-TAATATATTTATAT
1 ATT--TATATTATATTATATT-T-TAATTTTTATAATATAATTATAT
1177074 ATTTATATTATATTATATTTTAATT
1 ATTTATATTATATTATATTTTAATT
1177099 AATTTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
41 3 0.06
42 23 0.43
43 16 0.30
44 12 0.22
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (43 bp):
ATTTATATTATATTATATTTTAATTTTTATAATATAATTATAT
Found at i:1177340 original size:6 final size:6
Alignment explanation
Indices: 1177330--1177361 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1177320 TTATCAAGCA
*
1177330 CACTGA CACTGC CACTGC CACTGC CACTGC CA
1 CACTGC CACTGC CACTGC CACTGC CACTGC CA
1177362 TTGAAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.22, C:0.47, G:0.16, T:0.16
Consensus pattern (6 bp):
CACTGC
Found at i:1177656 original size:2 final size:2
Alignment explanation
Indices: 1177649--1177676 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1177639 TTGAAGAATG
1177649 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
1177677 GACAATTCAG
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):
TA
Found at i:1178002 original size:25 final size:24
Alignment explanation
Indices: 1177962--1178008 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1177952 ATAAAAATAA
1177962 AAATTTTATAAATATTTAAATATTT
1 AAATTTTATAAATA-TTAAATATTT
**
1177987 AAATTTTATATTTATTAAATAT
1 AAATTTTATAAATATTAAATAT
1178009 GATATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATTTTATAAATATTAAATATTT
Found at i:1178326 original size:2 final size:2
Alignment explanation
Indices: 1178321--1178352 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1178311 TATGTGTGTG
*
1178321 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1178353 ACAGTAAATT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1179427 original size:29 final size:28
Alignment explanation
Indices: 1179385--1179461 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 28
1179375 TGCTAATCGA
* * *
1179385 TAAATAATATTAATTAAAATAATATTTTTT
1 TAAAAAATA-TAATAAAAATAATA-ATTTT
* * *
1179415 TAAAAAATATAATCAATATATTAATTTT
1 TAAAAAATATAATAAAAATAATAATTTT
*
1179443 T-AAAAATTTAATAAAAATA
1 TAAAAAATATAATAAAAATA
1179462 TCTAAAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 15 0.38
28 5 0.13
29 11 0.28
30 8 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAAAATATAATAAAAATAATAATTTT
Found at i:1181310 original size:2 final size:2
Alignment explanation
Indices: 1181303--1181328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1181293 TTTATAACTT
1181303 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
1181329 AAAGTTTCAA
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:1183023 original size:2 final size:2
Alignment explanation
Indices: 1183018--1183059 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1183008 TCCATGACAT
*
1183018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1183060 GCTAGAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1183198 original size:18 final size:19
Alignment explanation
Indices: 1183169--1183205 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1183159 TTAGCATAAA
1183169 ATTTATTAATTTTATATAT
1 ATTTATTAATTTTATATAT
1183188 ATTTA-TAATTTTATATAT
1 ATTTATTAATTTTATATAT
1183206 GATTAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTAATTTTATATAT
Found at i:1183260 original size:21 final size:21
Alignment explanation
Indices: 1183212--1183252 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1183202 ATATGATTAA
1183212 GATTTTAATAAATTAATTATT
1 GATTTTAATAAATTAATTATT
*
1183233 GAATTTAATAAATTAATTAT
1 GATTTTAATAAATTAATTAT
1183253 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
GATTTTAATAAATTAATTATT
Found at i:1183376 original size:25 final size:23
Alignment explanation
Indices: 1183314--1183387 Score: 62
Period size: 25 Copynumber: 3.1 Consensus size: 23
1183304 AAAAAATATC
*
1183314 ATTTTTAATATATTTAATGATTAAT
1 ATTTTTAAT-TATTT-ATAATTAAT
*
1183339 TTTTTTAA-T-TTTATAATTAAAT
1 ATTTTTAATTATTTATAATT-AAT
*
1183361 ATTTTTAATTTATTTAAAATTTAAT
1 ATTTTTAA-TTATTTATAA-TTAAT
1183386 AT
1 AT
1183388 ATATAATCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 5 0.12
22 13 0.32
23 1 0.03
24 1 0.03
25 18 0.45
26 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
ATTTTTAATTATTTATAATTAAT
Found at i:1184260 original size:26 final size:27
Alignment explanation
Indices: 1184210--1184260 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1184200 TAAAATTTAA
* * *
1184210 AATTTATATTAAAAATATTATATTATT
1 AATTAATATTAAAAATATAAAATTATT
1184237 AATTAATA-TAAAAATATAAAATTA
1 AATTAATATTAAAAATATAAAATTA
1184261 ACTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTAATATTAAAAATATAAAATTATT
Found at i:1184815 original size:3 final size:3
Alignment explanation
Indices: 1184794--1184834 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1184784 TCCCCTCTCA
* * *
1184794 CAT CAT CAC CAT CAC CAT CAT CAT CAT CAT CCT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1184835 AAAGCCAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (3 bp):
CAT
Found at i:1185908 original size:15 final size:15
Alignment explanation
Indices: 1185888--1185919 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1185878 AAGACCTAGA
*
1185888 TTTTCTTTTCCGTTG
1 TTTTCTTTTCCGCTG
1185903 TTTTCTTTTCCGCTG
1 TTTTCTTTTCCGCTG
1185918 TT
1 TT
1185920 ACATTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.12, T:0.66
Consensus pattern (15 bp):
TTTTCTTTTCCGCTG
Found at i:1186469 original size:22 final size:21
Alignment explanation
Indices: 1186429--1186469 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1186419 ACAGAAAAAT
*
1186429 CTTTTTATTTTTTATTTATGG
1 CTTTTTATTTTTTAATTATGG
*
1186450 CTTTTTCTTTTCTTAATTAT
1 CTTTTTATTTT-TTAATTAT
1186470 ATGTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.71
Consensus pattern (21 bp):
CTTTTTATTTTTTAATTATGG
Found at i:1189498 original size:2 final size:2
Alignment explanation
Indices: 1189493--1189522 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1189483 TGTGTGTGTG
1189493 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
1189523 GAGAGAGAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1189527 original size:2 final size:2
Alignment explanation
Indices: 1189522--1189549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1189512 ATATATATAT
1189522 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
1189550 TATAGGAACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1189601 original size:2 final size:2
Alignment explanation
Indices: 1189594--1189624 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1189584 AATAGGATAC
1189594 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
1189625 CACAAAAAAA
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:1190697 original size:21 final size:18
Alignment explanation
Indices: 1190665--1190724 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 18
1190655 TATTATTTAA
1190665 AAATTT-ATTTTTATATT
1 AAATTTAATTTTTATATT
1190682 AATATTTATATATTTTATAATT
1 AA-ATTTA-AT-TTTTAT-ATT
1190704 AAATTTAATTTTT-TATT
1 AAATTTAATTTTTATATT
1190721 AAAT
1 AAAT
1190725 AGATAGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.24
18 5 0.13
19 4 0.11
20 4 0.11
21 11 0.29
22 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTAATTTTTATATT
Found at i:1194488 original size:20 final size:20
Alignment explanation
Indices: 1194463--1194500 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1194453 GAATAGACTT
1194463 AAAATA-TTATTTATTTAATA
1 AAAATAGTT-TTTATTTAATA
1194483 AAAATAGTTTTTATTTAA
1 AAAATAGTTTTTATTTAA
1194501 ATATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAAATAGTTTTTATTTAATA
Found at i:1202649 original size:15 final size:15
Alignment explanation
Indices: 1202629--1202682 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1202619 GAGTGAGATA
1202629 TTTAAATTTGATTTG
1 TTTAAATTTGATTTG
* ** *
1202644 TTTAAATATTAAAATA
1 TTTAAAT-TTGATTTG
*
1202660 TTTAAATTTGATTCG
1 TTTAAATTTGATTTG
1202675 TTTAAATT
1 TTTAAATT
1202683 ATTTAAGTTG
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (15 bp):
TTTAAATTTGATTTG
Found at i:1205001 original size:24 final size:24
Alignment explanation
Indices: 1204972--1205019 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1204962 ACACTCTTTA
*
1204972 AGGTTATAATATATAGTAATGTTT
1 AGGTTATAATATATAATAATGTTT
*
1204996 AGGTTATTATATATAATAATGTTT
1 AGGTTATAATATATAATAATGTTT
1205020 TTATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (24 bp):
AGGTTATAATATATAATAATGTTT
Found at i:1205222 original size:2 final size:2
Alignment explanation
Indices: 1205211--1205244 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1205201 ATTAGAATGC
1205211 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1205245 GTTTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1206492 original size:17 final size:17
Alignment explanation
Indices: 1206452--1206498 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1206442 AATTAAAAAT
1206452 TTTG-TATATATTTATA
1 TTTGATATATATTTATA
**
1206468 TTAAATATATATTTATA
1 TTTGATATATATTTATA
*
1206485 TTTGATATTTATTT
1 TTTGATATATATTT
1206499 TAAATTTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTGATATATATTTATA
Found at i:1206760 original size:2 final size:2
Alignment explanation
Indices: 1206753--1206777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1206743 AATAGTAAGT
1206753 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1206778 TGTATACTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1209302 original size:13 final size:13
Alignment explanation
Indices: 1209279--1209317 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1209269 TTCAATTTTT
1209279 TTTAT-TTTAATA
1 TTTATATTTAATA
1209291 TTTATATTTAATA
1 TTTATATTTAATA
* *
1209304 TCTATATTTGATA
1 TTTATATTTAATA
1209317 T
1 T
1209318 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTATATTTAATA
Found at i:1209863 original size:26 final size:28
Alignment explanation
Indices: 1209828--1209886 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
1209818 ATGGATTTGT
1209828 AGAGAAAAAAACTA-AAA-ATG-AAATGG
1 AGAGAAAAAAA-TATAAAGATGAAAATGG
1209854 AGAGAAAAAAATATAAAGATGAAAATGG
1 AGAGAAAAAAATATAAAGATGAAAATGG
*
1209882 GGAGA
1 AGAGA
1209887 CTAAAGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 14 0.48
27 3 0.10
28 10 0.34
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.12
Consensus pattern (28 bp):
AGAGAAAAAAATATAAAGATGAAAATGG
Found at i:1210043 original size:15 final size:15
Alignment explanation
Indices: 1210023--1210066 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1210013 CGTGTGAAAT
1210023 TATAAAAATATAATC
1 TATAAAAATATAATC
* * *
1210038 TATAAAATTATGATG
1 TATAAAAATATAATC
*
1210053 TTTAAAAATATAAT
1 TATAAAAATATAAT
1210067 TTATGTCTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (15 bp):
TATAAAAATATAATC
Found at i:1210192 original size:32 final size:32
Alignment explanation
Indices: 1210156--1210218 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1210146 TATTTCAACG
*
1210156 TCAAGTATCATAAGTTGTGATAATGAAGAACT
1 TCAAGTATCATAAGTTGTGATAACGAAGAACT
*
1210188 TCAAGTATCATAGGTTGTGATAACGAAGAAC
1 TCAAGTATCATAAGTTGTGATAACGAAGAAC
1210219 CTGCCAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.29
Consensus pattern (32 bp):
TCAAGTATCATAAGTTGTGATAACGAAGAACT
Found at i:1212229 original size:21 final size:21
Alignment explanation
Indices: 1212205--1212275 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 21
1212195 TTTTAAGTTT
*
1212205 TAATTAATATTAAATTTTTAA
1 TAATTAATAATAAATTTTTAA
* *
1212226 TAATATAAAAAT-AATTTTTTA
1 TAAT-TAATAATAAATTTTTAA
*
1212247 -AATTAATAA-AAAATTTTAA
1 TAATTAATAATAAATTTTTAA
1212266 -AATATAATAA
1 TAAT-TAATAA
1212276 AAAAGATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 15 0.37
20 9 0.22
21 12 0.29
22 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTAATAATAAATTTTTAA
Found at i:1212237 original size:18 final size:18
Alignment explanation
Indices: 1212202--1212235 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1212192 CTTTTTTAAG
*
1212202 TTTTAATTAATATTAAAT
1 TTTTAATTAATATAAAAT
1212220 TTTTAA-TAATATAAAA
1 TTTTAATTAATATAAAA
1212236 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAATTAATATAAAAT
Found at i:1212261 original size:20 final size:21
Alignment explanation
Indices: 1212216--1212279 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 21
1212206 AATTAATATT
1212216 AAATTTTTAATAATATAA-AAA
1 AAATTTTTAA-AATATAATAAA
* *
1212237 TAATTTTTTAAAT-TAATAAA
1 AAATTTTTAAAATATAATAAA
1212257 AAA-TTTTAAAATATAATAAA
1 AAATTTTTAAAATATAATAAA
1212277 AAA
1 AAA
1212280 GATATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.30
20 18 0.49
21 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTTTAAAATATAATAAA
Found at i:1212666 original size:4 final size:4
Alignment explanation
Indices: 1212659--1212689 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1212649 TATATATATA
1212659 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
1212690 TCGTTTAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1216795 original size:2 final size:2
Alignment explanation
Indices: 1216788--1216828 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1216778 GTTAAGTATG
* * *
1216788 TA TA TA TA TA TA TA TA TA TA TT TA TA TA AA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1216829 TTATGTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1218945 original size:6 final size:6
Alignment explanation
Indices: 1218934--1218964 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1218924 AACGTTCAAA
*
1218934 GAAAAT GAAAAT GATAAT GAAAAT GAAAAT G
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT G
1218965 CTATATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
GAAAAT
Found at i:1219306 original size:195 final size:195
Alignment explanation
Indices: 1218959--1219319 Score: 582
Period size: 195 Copynumber: 1.9 Consensus size: 195
1218949 AATGAAAATG
*
1218959 AAAATGCTATATTTCATGATCCGAAAAAAAGCTCAGAGCTCAGAAGTCAGAACCCTATGACCACC
1 AAAATGCTATATTTCATGATCCGAAAAAAAGCTCAGAGCTCAGAAGTCAGAACCCTACGACCACC
*
1219024 ACATGAACATGCTAAAATAGGTAGAATTCCTCCAATGAATAAGTCATATGGATGGTAAATTGGTA
66 ACATGAACATGCTAAAATAGGTAGAATTCCTCCAATGAATAACTCATATGGATGGTAAATTGGTA
**
1219089 ACCAAACATTAAAATTAGCAAACAAG-TTCGTAAATTACACAAGAAAACAACGTTCAAAGATAAT
131 ACCAAACATTAAAACCAGCAAACAAGATT-GTAAATTACACAAGAAAACAACGTTCAAAGATAAT
1219153 A
195 A
* * **
1219154 AAAATGTTGTATTTCATGATCCGAAAAAAAGCTCATCGCTCAGAAGTCAGAACCCTACGACCACC
1 AAAATGCTATATTTCATGATCCGAAAAAAAGCTCAGAGCTCAGAAGTCAGAACCCTACGACCACC
* * * *
1219219 ACATGAACATGCTAAAATTGGTATACTT-CTACCTATGAATAACTCATATGGATGGTAAATTGGT
66 ACATGAACATGCTAAAATAGGTAGAATTCCT-CCAATGAATAACTCATATGGATGGTAAATTGGT
1219283 AACCAAACATTAAAACCAGCAAACAAGATTGTAAATT
130 AACCAAACATTAAAACCAGCAAACAAGATTGTAAATT
1219320 TGCTACTAAT
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
194 2 0.01
195 148 0.97
196 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (195 bp):
AAAATGCTATATTTCATGATCCGAAAAAAAGCTCAGAGCTCAGAAGTCAGAACCCTACGACCACC
ACATGAACATGCTAAAATAGGTAGAATTCCTCCAATGAATAACTCATATGGATGGTAAATTGGTA
ACCAAACATTAAAACCAGCAAACAAGATTGTAAATTACACAAGAAAACAACGTTCAAAGATAATA
Found at i:1227618 original size:19 final size:19
Alignment explanation
Indices: 1227594--1227633 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1227584 AAATTTTGTC
1227594 TTTAACCTTGGATTAGAGT
1 TTTAACCTTGGATTAGAGT
1227613 TTTAACCTTGGATTAGAGT
1 TTTAACCTTGGATTAGAGT
1227632 TT
1 TT
1227634 AGCATGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTAACCTTGGATTAGAGT
Found at i:1230951 original size:32 final size:30
Alignment explanation
Indices: 1230915--1230978 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1230905 AAATATTATT
* * *
1230915 AATTTGAATTAAATTGATTTATCAGTTTTTTA
1 AATTT-AAATAAATT-ATATATAAGTTTTTTA
*
1230947 AATTTAAATATATTATATATAAGTTTTTTA
1 AATTTAAATAAATTATATATAAGTTTTTTA
1230977 AA
1 AA
1230979 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 16 0.57
31 7 0.25
32 5 0.18
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (30 bp):
AATTTAAATAAATTATATATAAGTTTTTTA
Found at i:1233023 original size:17 final size:16
Alignment explanation
Indices: 1233001--1233073 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
1232991 ACTCTTCCTG
1233001 ATATATTTAAAGA-ATT
1 ATATATTTAAA-ATATT
1233017 AATATATTTAAAATATT
1 -ATATATTTAAAATATT
* *
1233034 ATATATTTATATATTTT
1 ATATATTTA-AAATATT
* *
1233051 TTAATATTT-TAATATT
1 AT-ATATTTAAAATATT
1233067 ATATATT
1 ATATATT
1233074 ATTATATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
15 5 0.11
16 15 0.33
17 20 0.43
18 6 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
ATATATTTAAAATATT
Found at i:1233045 original size:8 final size:8
Alignment explanation
Indices: 1233018--1233111 Score: 63
Period size: 8 Copynumber: 11.5 Consensus size: 8
1233008 TAAAGAATTA
1233018 ATATATTT
1 ATATATTT
*
1233026 A-AAATATT
1 ATATAT-TT
1233034 ATATATTT
1 ATATATTT
1233042 ATATATTTT
1 ATATA-TTT
*
1233051 TTAATATTT
1 AT-ATATTT
1233060 -TA-ATATT
1 ATATAT-TT
1233067 ATATA-TT
1 ATATATTT
1233074 ATTATATTT
1 A-TATATTT
1233083 -TATATTT
1 ATATATTT
*
1233090 TTATATTAT
1 ATATATT-T
1233099 ATTATATTT
1 A-TATATTT
1233108 ATAT
1 ATAT
1233112 TATTATATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 24
0.71 0.04 0.24
Matches are distributed among these distances:
6 2 0.03
7 16 0.23
8 27 0.39
9 16 0.23
10 9 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:1233057 original size:18 final size:17
Alignment explanation
Indices: 1233019--1233115 Score: 80
Period size: 18 Copynumber: 5.9 Consensus size: 17
1233009 AAAGAATTAA
* *
1233019 TATATTTA-AAATATTA
1 TATATTTATATATATTT
*
1233035 TATATTTATATATTTTT
1 TATATTTATATATATTT
*
1233052 TAATATTT-TA-ATATTA
1 T-ATATTTATATATATTT
1233068 TATA-TTAT-TATATTT
1 TATATTTATATATATTT
* *
1233083 TATATTTTTATATTATAT
1 TATATTTATATA-TATTT
1233101 TATATTTATAT-TATT
1 TATATTTATATATATT
1233116 ATATTCATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.03
15 13 0.20
16 19 0.30
17 10 0.16
18 20 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTATATATATTT
Found at i:1233065 original size:33 final size:30
Alignment explanation
Indices: 1233019--1233120 Score: 107
Period size: 30 Copynumber: 3.2 Consensus size: 30
1233009 AAAGAATTAA
* *
1233019 TATATTTAAAATATTATATATTTATATATTTTT
1 TATATTT-TAATATTATATA-TTAT-TATATTT
1233052 TAATATTTTAATATTATATATTATTATATTT
1 T-ATATTTTAATATTATATATTATTATATTT
*
1233083 TATATTTTTATATTATAT-TATATTTATATTAT
1 TATATTTTAATATTATATAT-TA-TTATATT-T
1233115 TATATT
1 TATATT
1233121 CATATGATGT
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
29 1 0.02
30 18 0.29
31 14 0.23
32 11 0.18
33 12 0.19
34 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TATATTTTAATATTATATATTATTATATTT
Found at i:1233068 original size:25 final size:24
Alignment explanation
Indices: 1233028--1233120 Score: 63
Period size: 23 Copynumber: 3.9 Consensus size: 24
1233018 ATATATTTAA
*
1233028 AATATTATATATTTATATATTTTTT
1 AATATTATATATTTAT-TATATTTT
*
1233053 AATATTTTA-ATATTA-TATATTATT
1 AATATTATATAT-TTATTATATT-TT
*
1233077 -ATATTTTATATTT-TTATATTATAT
1 AATATTATATATTTATTATATT-T-T
*
1233101 TATATT-TATA-TTATTATATT
1 AATATTATATATTTATTATATT
1233121 CATATGATGT
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
23 25 0.42
24 18 0.31
25 16 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
AATATTATATATTTATTATATTTT
Found at i:1233119 original size:8 final size:8
Alignment explanation
Indices: 1233062--1233120 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
1233052 TAATATTTTA
1233062 ATATTA-T
1 ATATTATT
1233069 ATATTATT
1 ATATTATT
1233077 ATATT-TT
1 ATATTATT
*
1233084 ATATTTTT
1 ATATTATT
1233092 ATATTA-T
1 ATATTATT
1233099 AT-TATATTT
1 ATAT-TA-TT
1233108 ATATTATT
1 ATATTATT
1233116 ATATT
1 ATATT
1233121 CATATGATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
6 1 0.02
7 18 0.40
8 20 0.44
9 5 0.11
10 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATATTATT
Found at i:1233125 original size:25 final size:25
Alignment explanation
Indices: 1233035--1233146 Score: 60
Period size: 26 Copynumber: 4.5 Consensus size: 25
1233025 TAAAATATTA
* * *
1233035 TATATTTATATATT-TTTTAATATTT
1 TATATTT-TATATTATTATATTATAT
*
1233060 TAATATTATATATTATTATA-T-T-T
1 T-ATATTTTATATTATTATATTATAT
1233083 TATATTTT-TA-TATTATATTATATT
1 TATATTTTATATTATTATATTATA-T
1233107 TATATTATTATATTCA-TATGATGTA-AT
1 TATATT-TTATATT-ATTAT-AT-TATAT
*
1233134 TATAATTTATATT
1 TATATTTTATATT
1233147 TATTTAATAA
Statistics
Matches: 71, Mismatches: 4, Indels: 23
0.72 0.04 0.23
Matches are distributed among these distances:
20 7 0.10
21 3 0.04
22 7 0.10
23 2 0.03
24 8 0.11
25 10 0.14
26 18 0.25
27 10 0.14
28 4 0.06
29 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (25 bp):
TATATTTTATATTATTATATTATAT
Found at i:1236250 original size:17 final size:17
Alignment explanation
Indices: 1236228--1236272 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1236218 TAAATTATTA
1236228 TTTAATATTAAAAATAT
1 TTTAATATTAAAAATAT
1236245 TTTAAT-TATAAAAATAT
1 TTTAATAT-TAAAAATAT
* *
1236262 ATAAATATTAA
1 TTTAATATTAA
1236273 TATAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATATTAAAAATAT
Found at i:1236302 original size:19 final size:19
Alignment explanation
Indices: 1236240--1236304 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
1236230 TAATATTAAA
1236240 AATATTTTAATTATAAAAATAT
1 AATATTTTAA-TA-AAAAA-AT
* * *
1236262 ATAAATATTAATATAAAAAT
1 A-ATATTTTAATAAAAAAAT
1236282 AATATTTTAATAAAAAAAT
1 AATATTTTAATAAAAAAAT
1236301 AATA
1 AATA
1236305 ATAACAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
19 19 0.53
20 3 0.08
21 4 0.11
22 3 0.08
23 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATTTTAATAAAAAAAT
Found at i:1240565 original size:11 final size:11
Alignment explanation
Indices: 1240536--1240564 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1240526 TAGAAATTTC
1240536 TTTCTTTTCTT
1 TTTCTTTTCTT
1240547 TTTCTTTTCTT
1 TTTCTTTTCTT
1240558 TTT-TTTT
1 TTTCTTTT
1240565 TTATATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:1240565 original size:16 final size:15
Alignment explanation
Indices: 1240532--1240564 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1240522 ACTTTAGAAA
1240532 TTTCTTTCTTTTCTT
1 TTTCTTTCTTTTCTT
1240547 TTTCTTTTCTTTT-TT
1 TTTC-TTTCTTTTCTT
1240562 TTT
1 TTT
1240565 TTATATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTCTTTTCTT
Found at i:1242506 original size:2 final size:2
Alignment explanation
Indices: 1242499--1242526 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1242489 GCTAGCTACC
1242499 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
1242527 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1243196 original size:2 final size:2
Alignment explanation
Indices: 1243189--1243214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1243179 TTTAGCCCCA
1243189 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
1243215 TGATATTTCC
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:1244001 original size:20 final size:19
Alignment explanation
Indices: 1243976--1244044 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 19
1243966 TAAAATTGTT
1243976 TATTATTAAATTTAATATAA
1 TATTATTAAATTTAA-ATAA
* *
1243996 TATTA-TAACTATAAATGATA
1 TATTATTAAATTTAAAT-A-A
1244016 TATTAATTAAATTTAAA-ATA
1 TATT-ATTAAATTTAAATA-A
1244036 TATT-TTAAA
1 TATTATTAAA
1244045 GAAATTCGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 7 0.17
19 8 0.20
20 17 0.41
21 1 0.02
22 8 0.20
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
TATTATTAAATTTAAATAA
Found at i:1244848 original size:18 final size:18
Alignment explanation
Indices: 1244825--1244863 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1244815 TTTTTTATTT
*
1244825 TTTATATTATAATTA-ATA
1 TTTATATCAT-ATTACATA
1244843 TTTATATCATATTACATA
1 TTTATATCATATTACATA
1244861 TTT
1 TTT
1244864 TCATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATCATATTACATA
Found at i:1244957 original size:15 final size:16
Alignment explanation
Indices: 1244921--1244958 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1244911 TCATCTCAAA
1244921 TTTT-AATATTTAATT
1 TTTTAAATATTTAATT
1244936 TTTTAAATATTT-ATT
1 TTTTAAATATTTAATT
1244951 TTTTAAAT
1 TTTTAAAT
1244959 TGATGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTAAATATTTAATT
Found at i:1245736 original size:19 final size:18
Alignment explanation
Indices: 1245714--1245757 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1245704 AACTAAAATT
1245714 AAAAGTGAAAAAAAAGAAA
1 AAAAGTGAAAAAAAA-AAA
* *
1245733 AAAATTTAAAAAAAAAAA
1 AAAAGTGAAAAAAAAAAA
1245751 AACAAGT
1 AA-AAGT
1245758 TTGTCAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAAGTGAAAAAAAAAAA
Found at i:1248459 original size:26 final size:27
Alignment explanation
Indices: 1248413--1248474 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
1248403 GACAAGGTTG
***
1248413 TAAAAATAAAAATATTTATAAA-AAT-
1 TAAAAATAAAAATAAAAATAAATAATA
1248438 TAAAAATTAAAAATAAAAATAAATAATA
1 TAAAAA-TAAAAATAAAAATAAATAATA
1248466 TAAATAATA
1 TAAA-AATA
1248475 TATTATCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.20
26 13 0.43
27 3 0.10
28 6 0.20
29 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
TAAAAATAAAAATAAAAATAAATAATA
Found at i:1248465 original size:7 final size:6
Alignment explanation
Indices: 1248413--1248472 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
1248403 GACAAGGTTG
***
1248413 TAAAAA TAAAAA TATTTA TAAAAA TTAAAAA TTAAAAA TAAAAA TAAATAA
1 TAAAAA TAAAAA TAAAAA TAAAAA -TAAAAA -TAAAAA TAAAAA TAAA-AA
*
1248464 TATAAA TAA
1 TAAAAA TAA
1248473 TATATTATCC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 26 0.59
7 18 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
TAAAAA
Found at i:1249082 original size:12 final size:14
Alignment explanation
Indices: 1249065--1249096 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1249055 ACTACTTTAT
1249065 TATTTAA-A-ATTA
1 TATTTAACATATTA
1249077 TATTTAACATATTA
1 TATTTAACATATTA
1249091 TATTTA
1 TATTTA
1249097 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTAACATATTA
Found at i:1251113 original size:3 final size:3
Alignment explanation
Indices: 1251105--1251132 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1251095 TAAATTCTTT
1251105 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1251133 ATTGTTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1251878 original size:21 final size:20
Alignment explanation
Indices: 1251848--1251886 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1251838 TATTTTAATT
*
1251848 TTAATTTTTATATTTAATAA
1 TTAATTTTTAAATTTAATAA
1251868 TTAATTTTTTAAATTTAAT
1 TTAA-TTTTTAAATTTAAT
1251887 TTTTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTTTTAAATTTAATAA
Found at i:1256980 original size:8 final size:8
Alignment explanation
Indices: 1256967--1256992 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1256957 CTGATATTTT
1256967 AAATTACA
1 AAATTACA
1256975 AAATTACA
1 AAATTACA
1256983 AAATTACA
1 AAATTACA
1256991 AA
1 AA
1256993 TAAATAAATA
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:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (8 bp):
AAATTACA
Done.