Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 193 of 199
Found at i:56052221 original size:22 final size:21
Alignment explanation
Indices: 56052194--56052255 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 21
56052184 TAGATTAGAA
*
56052194 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTAT-AATT
56052216 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
56052237 TTTT-TATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
56052256 GTTNNNNNNN
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.37
21 8 0.21
22 16 0.42
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:56052255 original size:20 final size:20
Alignment explanation
Indices: 56052194--56052255 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
56052184 TAGATTAGAA
* *
56052194 TTTTGTATGAATATTTTAAAT
1 TTTTTTATGAATATTAT-AAT
56052215 TTTTTGTATGAATATTATAAT
1 TTTTT-TATGAATATTATAAT
*
56052236 TTTTTTATGAATATTGTAAT
1 TTTTTTATGAATATTATAAT
56052256 GTTNNNNNNN
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.38
21 12 0.32
22 11 0.30
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTTTTATGAATATTATAAT
Found at i:56052456 original size:27 final size:25
Alignment explanation
Indices: 56052398--56052727 Score: 255
Period size: 27 Copynumber: 13.8 Consensus size: 25
56052388 AATATTGTAA
*
56052398 TTTTGTATGAATATTATAA-A-T-T
1 TTTTGTATGAATATTGTAATATTAT
56052420 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
*
56052445 AGTTTTGTATGAATATTG-CA-ATT-T
1 --TTTTGTATGAATATTGTAATATTAT
* *
56052469 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAA-TAT-TAT
56052496 TTTTGTATGAATA-T-T-ATATT-T
1 TTTTGTATGAATATTGTAATATTAT
*
56052517 TTTTGAATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
56052542 AATTTTGTATGAATATTGT-A-ATT-T
1 --TTTTGTATGAATATTGTAATATTAT
* *
56052566 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAA-TAT-TAT
56052593 TTTTGTATGAATA-T-T-ATA--AT
1 TTTTGTATGAATATTGTAATATTAT
*
56052613 TTTTTTATGAATATTG---TA--A-
1 TTTTGTATGAATATTGTAATATTAT
*
56052632 TGTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
*
56052657 AATTTTGTATGAATATTG-CA-ATT-T
1 --TTTTGTATGAATATTGTAATATTAT
*
56052681 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATA-T-TAT
*
56052708 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
56052728 GTGGGGATAT
Statistics
Matches: 251, Mismatches: 21, Indels: 67
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.06
20 16 0.06
21 13 0.05
22 71 0.28
23 8 0.03
24 13 0.05
25 16 0.06
26 8 0.03
27 92 0.37
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
TTTTGTATGAATATTGTAATATTAT
Found at i:56052456 original size:49 final size:49
Alignment explanation
Indices: 56052388--56052638 Score: 382
Period size: 49 Copynumber: 5.2 Consensus size: 49
56052378 TTTTTGTATG
*
56052388 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * **
56052437 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* *
56052486 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGAATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* *
56052534 AATATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
56052583 AATTTTGTAATTTTGTATGAATATTATAA-TTTTTT-TATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
56052630 AATGTTGTA
1 AATATTGTA
56052639 TGAATATTGT
Statistics
Matches: 182, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
47 20 0.11
48 50 0.27
49 112 0.62
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
Found at i:56052548 original size:97 final size:97
Alignment explanation
Indices: 56052392--56052632 Score: 423
Period size: 97 Copynumber: 2.5 Consensus size: 97
56052382 TGTATGAATA
* *
56052392 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAATTTTTTTG-ATGAATATTGTAATATTATAATTTTGTATGA
56052457 ATATTGCAATTTTTTTGTATGAATATTGTAATT
65 ATATTGCAATTTTTTTGTATGAATATTGTAATT
56052490 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGAATGAATATTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAATTTTTTTG-ATGAATATTGTAATATTATAATTTTGTATGA
*
56052554 ATATTGTAATTTTTTTGTATGAATATTGTAATT
65 ATATTGCAATTTTTTTGTATGAATATTGTAATT
56052587 TTGTAATTTTGTATGAATATTATAATTTTTTT-ATGAATATTGTAAT
1 TTGTAATTTTGTATGAATATTATAATTTTTTTGATGAATATTGTAAT
56052633 GTTGTATGAA
Statistics
Matches: 138, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
96 14 0.10
97 93 0.67
98 31 0.22
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (97 bp):
TTGTAATTTTGTATGAATATTATAATTTTTTTGATGAATATTGTAATATTATAATTTTGTATGAA
TATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:56052673 original size:19 final size:19
Alignment explanation
Indices: 56052534--56052651 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
56052524 TGAATATTGT
56052534 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
*
56052553 AATATTGTAATTTTTTTGTATG
1 AATATTATAA---TTTTGTATG
56052575 AATATTGTAATTTTGTAATTTTGTATG
1 AATA-T-T-A-----TAATTTTGTATG
*
56052602 AATATTATAATTTTTTTATG
1 AATATTATAA-TTTTGTATG
* *
56052622 AATATTGTAATGTTGTATG
1 AATATTATAATTTTGTATG
*
56052641 AATATTGTAAT
1 AATATTATAAT
56052652 ATTATAATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
19 30 0.37
20 17 0.21
22 13 0.16
23 1 0.01
24 2 0.02
25 1 0.01
26 1 0.01
27 13 0.16
30 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:56052679 original size:19 final size:19
Alignment explanation
Indices: 56052657--56052706 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
56052647 GTAATATTAT
56052657 AATTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGC
*
56052676 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGC
*
56052698 AATATTGTA
1 AATTTTGTA
56052707 ATTTTGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.31
22 18 0.69
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
AATTTTGTATGAATATTGC
Found at i:56052696 original size:49 final size:49
Alignment explanation
Indices: 56052420--56052780 Score: 213
Period size: 49 Copynumber: 7.5 Consensus size: 49
56052410 ATTATAAATT
*
56052420 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATATTATAA
56052469 TTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATA-T-T-ATATT-T--
1 TTTTGTATGAATATTGTAA--TT-T--TTTTGTATGAATATTGTAATATTATAA
*
56052517 TTTTGAATGAATATTGTAATATTATAATTTTGTATGAATATTGT-A-ATT-T--
1 TTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATATTATAA
56052566 TTTTGTATGAATATTGTAATTTTGTAATT-T-TG--TA-TG-AATATTATAA
1 TTTTGTATGAATATTGTAATTTT-T--TTGTATGAATATTGTAATATTATAA
* *
56052612 TTTTTTTATGAATATTGTAA---TGTTGTATGAATATTGTAATATTATAA
1 -TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
* *
56052659 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
* * ** * *
56052708 TTTTGTATGAATATTATAA--TGTGGGGAT--ATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
*
56052753 TTTTTTGTATGAATATTGTAATTATTTT
1 --TTTTGTATGAATATTGTAATTTTTTT
56052781 ATAATTAATT
Statistics
Matches: 260, Mismatches: 22, Indels: 60
0.76 0.06 0.18
Matches are distributed among these distances:
41 2 0.01
42 4 0.02
43 7 0.03
44 3 0.01
45 22 0.08
46 21 0.08
47 58 0.22
48 41 0.16
49 99 0.38
50 3 0.01
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
Found at i:56052775 original size:115 final size:114
Alignment explanation
Indices: 56052527--56052774 Score: 352
Period size: 115 Copynumber: 2.1 Consensus size: 114
56052517 TTTTGAATGA
* *
56052527 ATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTGTA
1 ATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
** *
56052592 ATTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATGTTGTATG
66 ATTTTGTATGAATATTATAATTGATATATGAATATTGTAATGTTGTATG
56052641 AATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGT
1 -ATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGT
*
56052706 AATTTTGTATGAATATTATAATGTGGGGATATATTGTAATATTGTAATTTTTTGTATG
65 AATTTTGTATGAATATTATAAT-T---GATATA-TG-AATATTGTAA--TGTTGTATG
56052764 AATATTGTAAT
1 -ATATTGTAAT
56052775 TATTTTATAA
Statistics
Matches: 119, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
115 84 0.71
116 1 0.01
119 3 0.03
120 2 0.02
121 10 0.08
123 19 0.16
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (114 bp):
ATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
ATTTTGTATGAATATTATAATTGATATATGAATATTGTAATGTTGTATG
Found at i:56056381 original size:2 final size:2
Alignment explanation
Indices: 56056374--56056398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56056364 TTAGGATAGA
56056374 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 A
56056399 AAGTGGATCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56065293 original size:101 final size:101
Alignment explanation
Indices: 56065121--56065303 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 101
56065111 AATTGAGAAT
* * * * * *
56065121 TGTGGAGTACTAGATGTTGGATCTTGTGAGATCATCCTTATGATACGAAATCTTTAGATTCCAAC
1 TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
*
56065186 CGTGTGAGT-TCTTATTAACTAAGTCAGGTTGAGGAC
66 AGTGTGA-TATCTTATTAACTAAGTCAGGTTGAGGAC
* * * *
56065222 TGTGGAGTACAAAAGGTTGGGTCTTATGATAACATTCTTATGATACAAAATCTTTAGATTTCAAC
1 TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
*
56065287 ATTGTGATATCTTATTA
66 AGTGTGATATCTTATTA
56065304 TTTTGTTGTT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
100 1 0.01
101 68 0.99
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.37
Consensus pattern (101 bp):
TGTGGAGTACAAAAGGTTGGATCTTATGAGAACATCCTTATGATACAAAATCTTTAGATTCCAAC
AGTGTGATATCTTATTAACTAAGTCAGGTTGAGGAC
Found at i:56066943 original size:19 final size:19
Alignment explanation
Indices: 56066906--56066943 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56066896 TACGGTAAAA
*
56066906 TTAGGTTTTTCTCTGATAT
1 TTAGGTTTTTCTCTCATAT
56066925 TTAGG-TTTTCTCATCATAT
1 TTAGGTTTTTCTC-TCATAT
56066944 ATGTATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (19 bp):
TTAGGTTTTTCTCTCATAT
Found at i:56071626 original size:24 final size:25
Alignment explanation
Indices: 56071581--56071633 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
56071571 TAAACATTAA
56071581 AAAATTATTTTAAAAATAAAAAAAT
1 AAAATTATTTTAAAAATAAAAAAAT
56071606 AAAATTATTTTAAAAAT-AAAAAAT
1 AAAATTATTTTAAAAATAAAAAAAT
56071630 AAAA
1 AAAA
56071634 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATTATTTTAAAAATAAAAAAAT
Found at i:56071634 original size:25 final size:25
Alignment explanation
Indices: 56071561--56071634 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
56071551 GGCCCGGCCC
* * *
56071561 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAAT-AAAAATT
56071587 ATTTTAAAAATAAAAAA-ATAAAATT
1 ATTTTAAAAATAAAAAATA-AAAATT
56071612 ATTTTAAAAATAAAAAATAAAAA
1 ATTTTAAAAATAAAAAATAAAAA
56071635 AAATTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 1 0.02
25 27 0.63
26 15 0.35
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
ATTTTAAAAATAAAAAATAAAAATT
Found at i:56071640 original size:25 final size:25
Alignment explanation
Indices: 56071561--56071644 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
56071551 GGCCCGGCCC
* * *
56071561 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAA-T
*
56071587 ATTTTAAAAATAAAAAA-ATAAAATT
1 ATTTTAAAAATAAAAAATA-AAAAAT
56071612 ATTTTAAAAATAAAAAATAAAAAA-
1 ATTTTAAAAATAAAAAATAAAAAAT
*
56071636 AATTTAAAA
1 ATTTTAAAA
56071645 GTATTTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
24 8 0.16
25 23 0.46
26 19 0.38
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (25 bp):
ATTTTAAAAATAAAAAATAAAAAAT
Found at i:56071641 original size:24 final size:25
Alignment explanation
Indices: 56071589--56071644 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
56071579 AAAAAATTAT
** *
56071589 TTTAAAAATAAAAAAATAAAATTAT
1 TTTAAAAATAAAAAAATAAAAAAAA
56071614 TTTAAAAAT-AAAAAATAAAAAAAA
1 TTTAAAAATAAAAAAATAAAAAAAA
56071638 TTTAAAA
1 TTTAAAA
56071645 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TTTAAAAATAAAAAAATAAAAAAAA
Found at i:56071644 original size:35 final size:32
Alignment explanation
Indices: 56071592--56071669 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 32
56071582 AAATTATTTT
*
56071592 AAAAAT-AAAAAAATAAAATTATTTTAAAAATA
1 AAAAATAAAAAAAATAAAAGTATTTT-AAAATA
*
56071624 AAAAATAAAAAAAATTTAAAAGTATTTTAAAATT
1 AAAAATAAAAAAAA--TAAAAGTATTTTAAAATA
*
56071658 AAAATTAAAAAA
1 AAAAATAAAAAA
56071670 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.15
33 7 0.17
34 16 0.40
35 11 0.28
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (32 bp):
AAAAATAAAAAAAATAAAAGTATTTTAAAATA
Found at i:56071661 original size:6 final size:6
Alignment explanation
Indices: 56071651--56071695 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
56071641 AAAAGTATTT
* *
56071651 TAAAAT TAAAAT TAAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
56071696 TATATTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:56071670 original size:60 final size:59
Alignment explanation
Indices: 56071581--56071693 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
56071571 TAAACATTAA
* * ***
56071581 AAAATTATTTTAAAAATAAAAAAATAAAATTATTTTAAAAATAAAAAATAAAAAAAATTT
1 AAAAGTATTTTAAAAATAAAAAAATAAAATAAAAATAAAAAT-AAAAATAAAAAAAATTT
* *
56071641 AAAAGTATTTTAAAATTAAAATTAA-AAAATAAAAATAAAAATAAAAATAAAAA
1 AAAAGTATTTTAAAAATAAAA-AAATAAAATAAAAATAAAAATAAAAATAAAAA
56071694 TATATATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 11 0.24
60 32 0.71
61 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (59 bp):
AAAAGTATTTTAAAAATAAAAAAATAAAATAAAAATAAAAATAAAAATAAAAAAAATTT
Found at i:56071673 original size:13 final size:13
Alignment explanation
Indices: 56071652--56071693 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
56071642 AAAGTATTTT
* *
56071652 AAAATTAAAATTA
1 AAAAATAAAAATA
56071665 AAAAATAAAAAT-
1 AAAAATAAAAATA
56071677 AAAAATAAAAATA
1 AAAAATAAAAATA
56071690 AAAA
1 AAAA
56071694 TATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:56077910 original size:25 final size:25
Alignment explanation
Indices: 56077876--56077923 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
56077866 AAAGAATAAA
*
56077876 ATATATAATAAAAATTAAAAATTGT
1 ATATATAATAAAAAGTAAAAATTGT
*
56077901 ATATATAATAAATAGTAAAAATT
1 ATATATAATAAAAAGTAAAAATT
56077924 AAAAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAATAAAAAGTAAAAATTGT
Found at i:56080210 original size:23 final size:22
Alignment explanation
Indices: 56080167--56080211 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
56080157 AGATTAAAGG
56080167 GAGAGAAAAAAAATTAAAAAAAA
1 GAGAGAAAAAAAA-TAAAAAAAA
*
56080190 GAGAGGAAAAAAAA-AACAAAAA
1 GAGA-GAAAAAAAATAAAAAAAA
56080212 TCACAGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
GAGAGAAAAAAAATAAAAAAAA
Found at i:56087007 original size:9 final size:9
Alignment explanation
Indices: 56086993--56087017 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
56086983 TAGCCAAAGC
56086993 CAAACAATG
1 CAAACAATG
56087002 CAAACAATG
1 CAAACAATG
56087011 CAAACAA
1 CAAACAA
56087018 AATCCAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (9 bp):
CAAACAATG
Found at i:56087738 original size:12 final size:12
Alignment explanation
Indices: 56087721--56087745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56087711 CTGATTTAAG
56087721 AAAAAAAGAAAA
1 AAAAAAAGAAAA
56087733 AAAAAAAGAAAA
1 AAAAAAAGAAAA
56087745 A
1 A
56087746 CCTGAAGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:56088386 original size:29 final size:29
Alignment explanation
Indices: 56088323--56088379 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
56088313 TTTTTTTTTT
56088323 AGTCACCGAACTATGAAAAGTTACAAAAC
1 AGTCACCGAACTATGAAAAGTTACAAAAC
* * *
56088352 AGTCACCTAATTATGAAAATTTACAAAA
1 AGTCACCGAACTATGAAAAGTTACAAAA
56088380 TGATCACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.23
Consensus pattern (29 bp):
AGTCACCGAACTATGAAAAGTTACAAAAC
Found at i:56090132 original size:6 final size:6
Alignment explanation
Indices: 56090109--56090143 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
56090099 GGTAGGAGTG
* *
56090109 GAGGTA GAGGAA GAGGTA GGGGTA GAGGTA GAGGT
1 GAGGTA GAGGTA GAGGTA GAGGTA GAGGTA GAGGT
56090144 GCGCAAATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (6 bp):
GAGGTA
Found at i:56094478 original size:18 final size:18
Alignment explanation
Indices: 56094455--56094492 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
56094445 GGTACTAAAC
56094455 TATATAGTAAAATAGACA
1 TATATAGTAAAATAGACA
56094473 TATATAGTAAAATAGACA
1 TATATAGTAAAATAGACA
56094491 TA
1 TA
56094493 GAATAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (18 bp):
TATATAGTAAAATAGACA
Found at i:56094502 original size:18 final size:18
Alignment explanation
Indices: 56094458--56094502 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
56094448 ACTAAACTAT
*
56094458 ATAGTAAAATAGACATAT
1 ATAGTAAAATAGACATAA
56094476 ATAGTAAAATAGACATAGA
1 ATAGTAAAATAGACATA-A
56094495 ATAG-AAAA
1 ATAGTAAAA
56094503 GTGACAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.22
Consensus pattern (18 bp):
ATAGTAAAATAGACATAA
Found at i:56101077 original size:22 final size:24
Alignment explanation
Indices: 56101052--56101100 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
56101042 AATAAATACC
*
56101052 AAAAAATTA-TTTTAAAA-ATTTT
1 AAAAAAGTATTTTTAAAATATTTT
56101074 -AAAAAGTATTTTTAAAATATTTT
1 AAAAAAGTATTTTTAAAATATTTT
56101097 AAAA
1 AAAA
56101101 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
23 5 0.22
24 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAAAAGTATTTTTAAAATATTTT
Found at i:56101123 original size:29 final size:29
Alignment explanation
Indices: 56101087--56101158 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
56101077 AAGTATTTTT
** *
56101087 AAAA-TATTTTAAAATTAAAAAATTTTTA
1 AAAAGTATTTTAAAATTAAAAAATAATAA
56101115 AAAAGTATTTTAAAATTAAAAAATAATAA
1 AAAAGTATTTTAAAATTAAAAAATAATAA
56101144 AAAAGTATTTTAAAA
1 AAAAGTATTTTAAAA
56101159 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 4 0.10
29 36 0.90
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAGTATTTTAAAATTAAAAAATAATAA
Found at i:56101147 original size:40 final size:38
Alignment explanation
Indices: 56101065--56101188 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 38
56101055 AAATTATTTT
*
56101065 AAAAA-TTTTAAAAAGTATTTTTAAAATATTTTAAAAT-T-A
1 AAAAATTTTTAAAAAGTA-TTTT-AAA-A-TTAAAAATATAA
56101104 AAAAATTTTTAAAAAGTATTTTAAAATTAAAAAATAATAA
1 AAAAATTTTTAAAAAGTATTTTAAAATT-AAAAAT-ATAA
*
56101144 AAAAGTATTTTAAAAA-TATTTTAAAATTAAAAATATTAA
1 AAAAAT-TTTTAAAAAGTATTTTAAAATTAAAAATA-TAA
56101183 AAAAAT
1 AAAAAT
56101189 AAATATATTT
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
36 2 0.03
37 6 0.08
38 4 0.05
39 24 0.32
40 30 0.40
41 9 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (38 bp):
AAAAATTTTTAAAAAGTATTTTAAAATTAAAAATATAA
Found at i:56101186 original size:17 final size:17
Alignment explanation
Indices: 56101153--56101197 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56101143 AAAAAGTATT
**
56101153 TTAAAAATATTTTAAAA
1 TTAAAAATATTAAAAAA
56101170 TTAAAAATATTAAAAAA
1 TTAAAAATATTAAAAAA
* *
56101187 ATAAATATATT
1 TTAAAAATATT
56101198 TATTATATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTAAAAAA
Found at i:56104936 original size:13 final size:13
Alignment explanation
Indices: 56104918--56104942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56104908 TCAAGCTTTT
56104918 TATTTTTAATATA
1 TATTTTTAATATA
56104931 TATTTTTAATAT
1 TATTTTTAATAT
56104943 TTTTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:56108915 original size:2 final size:2
Alignment explanation
Indices: 56108908--56108954 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
56108898 TTTGCAACGA
56108908 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
56108950 AT AT A
1 AT AT A
56108955 AAGAGAGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56111849 original size:17 final size:17
Alignment explanation
Indices: 56111806--56111849 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
56111796 ATTTCAAGTC
56111806 AAAAAATAATTTAAAAAT
1 AAAAAA-AATTTAAAAAT
* * *
56111824 TATAGAAATTTAAAAAT
1 AAAAAAAATTTAAAAAT
56111841 AAAAAAAAT
1 AAAAAAAAT
56111850 CATAATAAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAAAAATTTAAAAAT
Found at i:56115458 original size:29 final size:29
Alignment explanation
Indices: 56115424--56115479 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
56115414 ATAAGGATTA
*
56115424 GATCAAATTAGTCACTT-TATTATTAAATG
1 GATCAAATTAGTC-CTTATACTATTAAATG
*
56115453 GATCAATTTAGTCCTTATACTATTAAA
1 GATCAAATTAGTCCTTATACTATTAAA
56115480 AAGAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTATACTATTAAATG
Found at i:56118260 original size:12 final size:11
Alignment explanation
Indices: 56118238--56118267 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
56118228 TTTTATATTA
56118238 AAATATATTTTT
1 AAATA-ATTTTT
56118250 AAATAATTTTT
1 AAATAATTTTT
56118261 AAATAAT
1 AAATAAT
56118268 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:56118302 original size:22 final size:21
Alignment explanation
Indices: 56118257--56118313 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
56118247 TTTAAATAAT
56118257 TTTTAAATA-ATAAAATTTAA
1 TTTTAAATATATAAAATTTAA
* *
56118277 -TTTAAATATGTATAATTTATA
1 TTTTAAATATATAAAATTTA-A
*
56118298 TTTTAGATAT-TAAAAT
1 TTTTAAATATATAAAAT
56118314 AAAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.27
20 8 0.27
21 6 0.20
22 8 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTTAAATATATAAAATTTAA
Found at i:56121678 original size:31 final size:31
Alignment explanation
Indices: 56121629--56121694 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
56121619 TTATTACTAT
* *
56121629 TTTTCTAATTAGTTAATTTTAGTT-TTTATAC
1 TTTTCGAATTAGTCAATTTTA-TTCTTTATAC
* *
56121660 TTTTCGAATTGGTCAATTTTATTCTTTTTAC
1 TTTTCGAATTAGTCAATTTTATTCTTTATAC
56121691 TTTT
1 TTTT
56121695 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTTCGAATTAGTCAATTTTATTCTTTATAC
Found at i:56122384 original size:19 final size:22
Alignment explanation
Indices: 56122343--56122384 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
56122333 AAAATTTATT
56122343 TTTAATATATTTTTATATAAAA
1 TTTAATATATTTTTATATAAAA
56122365 TTTAA-ATA-TTTTAT-TAAAA
1 TTTAATATATTTTTATATAAAA
56122384 T
1 T
56122385 AATAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 3 0.15
22 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATATATTTTTATATAAAA
Found at i:56123752 original size:31 final size:31
Alignment explanation
Indices: 56123717--56123779 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
56123707 GCAACTATAC
56123717 AAATAAAACTTGAATTGTGATTC-ATATGTAT
1 AAATAAAACTTGAATTGTGATTCAAT-TGTAT
* *
56123748 AAATAAAACTTTAATTTTGATTCAATTGTAT
1 AAATAAAACTTGAATTGTGATTCAATTGTAT
56123779 A
1 A
56123780 TATTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (31 bp):
AAATAAAACTTGAATTGTGATTCAATTGTAT
Found at i:56124601 original size:5 final size:5
Alignment explanation
Indices: 56124591--56124629 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
56124581 CGTATTAAAA
56124591 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT
56124630 ATAAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:56138167 original size:16 final size:17
Alignment explanation
Indices: 56138141--56138172 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56138131 CAATTTGAAA
56138141 ATTTATCAATTTAATTG
1 ATTTATCAATTTAATTG
56138158 ATTTAT-AATTTAATT
1 ATTTATCAATTTAATT
56138173 ACCAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTATCAATTTAATTG
Found at i:56138801 original size:37 final size:38
Alignment explanation
Indices: 56138735--56138851 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 38
56138725 AAAAATTTAT
*
56138735 TTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAATA
1 TTTAAAAATT--AA-AAAAATT--AAAAAGTATTTTAAAAAAA
*
56138778 TTTTAAAATTAAAAAAATT-AAAAGTATTTTAAAAAAA
1 TTTAAAAATTAAAAAAATTAAAAAGTATTTTAAAAAAA
** *
56138815 TTTAAAAATTTTAAAATTTAAAAAAAGTATTTTAAAA
1 TTTAAAAATTAAAAAAATT--AAAAAGTATTTTAAAA
56138852 TTAAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
37 32 0.49
40 22 0.34
41 2 0.03
43 9 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (38 bp):
TTTAAAAATTAAAAAAATTAAAAAGTATTTTAAAAAAA
Found at i:56138809 original size:20 final size:20
Alignment explanation
Indices: 56138786--56138851 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
56138776 TATTTTAAAA
56138786 TTAAAAAAATTAAAAGTATT
1 TTAAAAAAATTAAAAGTATT
56138806 TTAAAAAAATTTAAAA--ATT
1 TTAAAAAAA-TTAAAAGTATT
56138825 TTAAAATTTAAA--AAAAGTATT
1 TTAAAA---AAATTAAAAGTATT
56138846 TTAAAA
1 TTAAAA
56138852 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 13 0.32
20 9 0.22
21 15 0.38
22 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAAAAATTAAAAGTATT
Found at i:56138857 original size:20 final size:21
Alignment explanation
Indices: 56138822--56138860 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
56138812 AAATTTAAAA
56138822 ATTTTAAAATTTAAAAAAAGT
1 ATTTTAAAATTTAAAAAAAGT
56138843 ATTTTAAAA-TTAAAAAAA
1 ATTTTAAAATTTAAAAAAA
56138861 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
ATTTTAAAATTTAAAAAAAGT
Found at i:56138858 original size:28 final size:27
Alignment explanation
Indices: 56138790--56138874 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
56138780 TTAAAATTAA
*
56138790 AAAAATTAAAAGTATTTTAAAAAA-ATTT
1 AAAAATTAAAA--ATTTAAAAAAATATTT
*
56138818 AAAAATTTTAAAATTTAAAAAAAGTATTT
1 AAAAA-TTAAAAATTTAAAAAAA-TATTT
* **
56138847 TAAAATTAAAAAAATAAAAAAATATTT
1 AAAAATTAAAAATTTAAAAAAATATTT
56138874 A
1 A
56138875 TTATATTCGG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 15 0.32
28 19 0.40
29 13 0.28
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAAATTAAAAATTTAAAAAAATATTT
Found at i:56142272 original size:21 final size:20
Alignment explanation
Indices: 56142217--56142262 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
56142207 AAGAAAAAAA
* *
56142217 AGAAAGAAAAAAAG-GAA-G
1 AGAAAGAACAAAGGAGAAGG
56142235 AGAAAGAACAAAGGAGAAGG
1 AGAAAGAACAAAGGAGAAGG
56142255 AGAAAGAA
1 AGAAAGAA
56142263 AAGTAGGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 3 0.12
20 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (20 bp):
AGAAAGAACAAAGGAGAAGG
Found at i:56152396 original size:25 final size:25
Alignment explanation
Indices: 56152368--56152423 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
56152358 ATTTTAAAAA
56152368 TTAAAA-CAAAAATTAAAAAAGTATT
1 TTAAAATCAAAAATT-AAAAAGTATT
*
56152393 TTAAAATTAAAAATTAAAAAGTATT
1 TTAAAATCAAAAATTAAAAAGTATT
56152418 TTAAAA
1 TTAAAA
56152424 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (25 bp):
TTAAAATCAAAAATTAAAAAGTATT
Found at i:56152404 original size:26 final size:25
Alignment explanation
Indices: 56152375--56152486 Score: 97
Period size: 25 Copynumber: 4.5 Consensus size: 25
56152365 AAATTAAAAC
56152375 AAAAATTAAAAAAGTATTTTAAAATT
1 AAAAATT-AAAAAGTATTTTAAAATT
56152401 AAAAATTAAAAAGTATTTTAAAAATTTT
1 AAAAATTAAAAAGTATTTT-AAAA--TT
* *
56152429 TAAAATTTAAAA--A-TTTAAAA-T
1 AAAAATTAAAAAGTATTTTAAAATT
** * *
56152450 AGTATTTTAAAAGTATTTTAAAATT
1 AAAAATTAAAAAGTATTTTAAAATT
*
56152475 AAAAAATAAAAA
1 AAAAATTAAAAA
56152487 ATAATAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
21 9 0.13
23 1 0.01
24 11 0.16
25 23 0.34
26 12 0.18
28 12 0.18
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
AAAAATTAAAAAGTATTTTAAAATT
Found at i:56152422 original size:38 final size:37
Alignment explanation
Indices: 56152383--56152486 Score: 151
Period size: 37 Copynumber: 2.8 Consensus size: 37
56152373 ACAAAAATTA
56152383 AAAAAGTATTTTAAAATTAAAAATTAAAAAGTATTTT
1 AAAAAGTATTTTAAAATTAAAAATTAAAAAGTATTTT
56152420 AAAAA-T-TTTTAAAATTTAAAAATTTAAAATAGTATTTT
1 AAAAAGTATTTTAAAA-TTAAAAA-TTAAAA-AGTATTTT
*
56152458 -AAAAGTATTTTAAAATTAAAAAATAAAAA
1 AAAAAGTATTTTAAAATTAAAAATTAAAAA
56152487 ATAATAAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
35 8 0.13
36 9 0.15
37 20 0.33
38 16 0.26
39 8 0.13
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (37 bp):
AAAAAGTATTTTAAAATTAAAAATTAAAAAGTATTTT
Found at i:56152848 original size:15 final size:15
Alignment explanation
Indices: 56152828--56152858 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56152818 GAAACTTGTC
56152828 ATTATTCATTTCTTG
1 ATTATTCATTTCTTG
*
56152843 ATTATTGATTTCTTG
1 ATTATTCATTTCTTG
56152858 A
1 A
56152859 AGAGATTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.58
Consensus pattern (15 bp):
ATTATTCATTTCTTG
Found at i:56154798 original size:3 final size:3
Alignment explanation
Indices: 56154790--56154815 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56154780 TACTAAACTA
56154790 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
56154816 GTATATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56155104 original size:32 final size:31
Alignment explanation
Indices: 56155056--56155179 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 31
56155046 ATGTACATAC
56155056 ATATATA-TTATTTATATTTTAAAATATATT
1 ATATATATTTATTTATATTTTAAAATATATT
* *
56155086 ATATATATTTTTTATATATTTTATAATTTACATATACAT
1 ATATATATTTATT-TATA-TTT-TAA---A-ATATA-TT
*
56155125 ACATATATATTATTTATATTTTAAAATATATT
1 ATATATAT-TTATTTATATTTTAAAATATATT
*
56155157 ATATATATTTTTTATATATTTTA
1 ATATATATTTATT-TATATTTTA
56155180 TAATTTACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
30 7 0.09
31 8 0.11
32 21 0.28
33 8 0.11
34 4 0.05
37 4 0.05
38 8 0.11
39 12 0.16
40 4 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
ATATATATTTATTTATATTTTAAAATATATT
Found at i:56155109 original size:39 final size:37
Alignment explanation
Indices: 56155057--56155220 Score: 131
Period size: 37 Copynumber: 4.4 Consensus size: 37
56155047 TGTACATACA
* *
56155057 TATATATTATTTATATTTTAAAATATATTATATATATTTTT
1 TATATA-T-TTTATATTTT-AAATATA-CATACATATTTTT
* * *
56155098 TATATATTTTATAATTTACATATACATACATA---TA
1 TATATATTTTATATTTTAAATATACATACATATTTTT
* *
56155132 TAT-TA-TTTATATTTTAAAATATATTATATATATTTTT
1 TATATATTTTATATTTT-AAATATA-CATACATATTTTT
* *
56155169 TATATATTTTATAATTTACATATACATACATATTTTT
1 TATATATTTTATATTTTAAATATACATACATATTTTT
* *
56155206 AATTTATATTTATAT
1 TATATAT-TTTATAT
56155221 ACATATATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
32 9 0.09
33 8 0.08
34 10 0.10
37 26 0.27
38 20 0.20
39 18 0.18
40 1 0.01
41 6 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (37 bp):
TATATATTTTATATTTTAAATATACATACATATTTTT
Found at i:56155141 original size:71 final size:71
Alignment explanation
Indices: 56155049--56155216 Score: 311
Period size: 71 Copynumber: 2.4 Consensus size: 71
56155039 TTACTTCATG
56155049 TACATACATATATATTATTTATATTTTAAAATATATTATATATATTTTTTATATATTTTATAATT
1 TACATACATATATATTATTTATATTTTAAAATATATTATATATATTTTTTATATATTTTATAATT
56155114 TACATA
66 TACATA
56155120 TACATACATATATATTATTTATATTTTAAAATATATTATATATATTTTTTATATATTTTATAATT
1 TACATACATATATATTATTTATATTTTAAAATATATTATATATATTTTTTATATATTTTATAATT
56155185 TACATA
66 TACATA
*
56155191 TACATACATAT-TTTTAATTTATATTT
1 TACATACATATATATT-ATTTATATTT
56155217 ATATACATAT
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
70 3 0.03
71 92 0.97
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (71 bp):
TACATACATATATATTATTTATATTTTAAAATATATTATATATATTTTTTATATATTTTATAATT
TACATA
Found at i:56155602 original size:22 final size:24
Alignment explanation
Indices: 56155576--56155619 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56155566 GAAAAATATT
56155576 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
56155598 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
56155620 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:56155730 original size:9 final size:9
Alignment explanation
Indices: 56155716--56155743 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56155706 TTTTGTTACA
56155716 ACAATTAAT
1 ACAATTAAT
56155725 ACAATTAAT
1 ACAATTAAT
56155734 ACAATTAAT
1 ACAATTAAT
56155743 A
1 A
56155744 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:56155765 original size:68 final size:68
Alignment explanation
Indices: 56155686--56155886 Score: 298
Period size: 59 Copynumber: 3.1 Consensus size: 68
56155676 TCAAGTTTGT
*
56155686 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
56155751 AAA
66 AAA
*
56155754 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-GCAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
56155810 AAA
66 AAA
56155813 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
56155876 AAT
66 AAA
56155879 TTTACTAA
1 TTTACTAA
56155887 CAATTAATTT
Statistics
Matches: 120, Mismatches: 4, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
59 55 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 31 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:56155896 original size:16 final size:16
Alignment explanation
Indices: 56155875--56155916 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
56155865 AATAATTTGA
*
56155875 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
56155891 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
56155907 TAGTTTTAAT
1 TAATTTTAAT
56155917 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:56155940 original size:23 final size:22
Alignment explanation
Indices: 56155890--56155963 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
56155880 TTACTAACAA
* * * *
56155890 TTAATTTTAATAACAATTAGTT
1 TTAATTTTATTAAAAAATAATT
56155912 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTATT-AAAAAATAATT
56155935 TTAATTTTATTAAAAAATAATT
1 TTAATTTTATTAAAAAATAATT
56155957 TTAATTT
1 TTAATTT
56155964 AAAACGGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 28 0.60
23 19 0.40
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAATTTTATTAAAAAATAATT
Found at i:56164768 original size:13 final size:14
Alignment explanation
Indices: 56164743--56164771 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56164733 AAAGGGGAAT
56164743 GAAGAACAAAATGG
1 GAAGAACAAAATGG
56164757 GAAGAA-AAAATGG
1 GAAGAACAAAATGG
56164770 GA
1 GA
56164772 GTGAAGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.31, T:0.07
Consensus pattern (14 bp):
GAAGAACAAAATGG
Found at i:56174840 original size:52 final size:52
Alignment explanation
Indices: 56174767--56174871 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
56174757 ACTTAAGTTA
56174767 AATTACAAAAATGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
1 AATTACAAAAATGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
* **
56174819 AATTACAGAAATGCTATACTTAGGCAATTAAAGAGGTGAACTCTTAGAAATT
1 AATTACAAAAATGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
56174871 A
1 A
56174872 GTGACTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (52 bp):
AATTACAAAAATGCTATACTTAGGCAATTAAAGAGGCAAACTCTTAGAAATT
Found at i:56174909 original size:9 final size:9
Alignment explanation
Indices: 56174895--56174930 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56174885 AGTGAGTGCT
56174895 TCCCCCCCC
1 TCCCCCCCC
56174904 TCCCCCCCC
1 TCCCCCCCC
56174913 T-CCCCCCC
1 TCCCCCCCC
56174921 TCCCCCCCC
1 TCCCCCCCC
56174930 T
1 T
56174931 TTACCCTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.00, C:0.86, G:0.00, T:0.14
Consensus pattern (9 bp):
TCCCCCCCC
Found at i:56174910 original size:8 final size:8
Alignment explanation
Indices: 56174897--56174928 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
56174887 TGAGTGCTTC
56174897 CCCCCCCT
1 CCCCCCCT
56174905 CCCCCCCCT
1 -CCCCCCCT
56174914 CCCCCCCT
1 CCCCCCCT
56174922 CCCCCCC
1 CCCCCCC
56174929 CTTTACCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.91, G:0.00, T:0.09
Consensus pattern (8 bp):
CCCCCCCT
Found at i:56174919 original size:17 final size:17
Alignment explanation
Indices: 56174897--56174930 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56174887 TGAGTGCTTC
56174897 CCCCCCCTCCCCCCCCT
1 CCCCCCCTCCCCCCCCT
56174914 CCCCCCCTCCCCCCCCT
1 CCCCCCCTCCCCCCCCT
56174931 TTACCCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.88, G:0.00, T:0.12
Consensus pattern (17 bp):
CCCCCCCTCCCCCCCCT
Found at i:56181549 original size:31 final size:28
Alignment explanation
Indices: 56181514--56181588 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
56181504 TTTCGCTATT
*
56181514 ATATTGTTACTATTTTGTTGTTATTGTTTGG
1 ATATTGTTACTATTTTGTT-TTATTG-TT-A
56181545 ATATTG-TA-TAACTTTTGTTTTATTGTTA
1 ATATTGTTACT-A-TTTTGTTTTATTGTTA
*
56181573 ATTTTGTTACTATTTT
1 ATATTGTTACTATTTT
56181589 AGAGGTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
28 9 0.24
29 6 0.16
30 10 0.26
31 13 0.34
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (28 bp):
ATATTGTTACTATTTTGTTTTATTGTTA
Found at i:56181579 original size:17 final size:19
Alignment explanation
Indices: 56181546--56181580 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
56181536 ATTGTTTGGA
56181546 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
56181565 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
56181581 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:56205491 original size:18 final size:21
Alignment explanation
Indices: 56205444--56205496 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
56205434 CAAGAGTAAA
56205444 ATATAATTTCAAATTCATGAGT
1 ATATAATTTCAAATTCAT-AGT
56205466 ATTATAATTTCAAATTC-T-G-
1 A-TATAATTTCAAATTCATAGT
56205485 ATATAATTTCAA
1 ATATAATTTCAA
56205497 TTTCGATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 1 0.03
22 2 0.07
23 15 0.50
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (21 bp):
ATATAATTTCAAATTCATAGT
Found at i:56206566 original size:245 final size:245
Alignment explanation
Indices: 56206134--56206633 Score: 901
Period size: 245 Copynumber: 2.0 Consensus size: 245
56206124 AGTAAGCATA
56206134 TATTGACTTTTTTTTTAACAATATCATTATAGGTTAAGATCATATTTGTTATTTTTAACATAATA
1 TATTGACTTTTTTTTTAACAATATCATTATAGGTTAAGATCATATTTGTTATTTTTAACATAATA
*
56206199 CTTAGAATTATTCATAGTTCTTCCCTAACTCATAAATAAAAAGATAATGCATTTCAGCACACTCA
66 CTTAGAATTATTCATAGTTCTTCCCTAACTCATAAATAAAAAGATAATACATTTCAGCACACTCA
*
56206264 AACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAAATTAATTTATATGAGAATAGAG
131 AACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAAATTAATTAATATGAGAATAGAG
* * *
56206329 TGGGGAGTGAAGGAGTAAGCATAGAGACCGCACCCCAATATTGTCGTGAT
196 TGAGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCAATATTGTCGTAAT
* *
56206379 TATTGACTTTTTTTTTTACAATATCATTATAGGTTAAGATCATATTTGTTCTTTTTAACATAATA
1 TATTGACTTTTTTTTTAACAATATCATTATAGGTTAAGATCATATTTGTTATTTTTAACATAATA
*
56206444 CTTAGAATTATTCATAGTTCTTCCCTAATTCATAAATAAAAAGATAATACATTTCAGCACACTCA
66 CTTAGAATTATTCATAGTTCTTCCCTAACTCATAAATAAAAAGATAATACATTTCAGCACACTCA
*
56206509 AACTTACGTATCGTGTATTGACAATAATATTTATACTAATCAAATTAATTAATATGAGAATAGAG
131 AACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAAATTAATTAATATGAGAATAGAG
* *
56206574 TGAGGAGTGAAGGAGTAAGCATGGAGACCCCACCCCACTATTGTCGTAAT
196 TGAGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCAATATTGTCGTAAT
56206624 TATTGACTTT
1 TATTGACTTT
56206634 GCAATTTGCA
Statistics
Matches: 244, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
245 244 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (245 bp):
TATTGACTTTTTTTTTAACAATATCATTATAGGTTAAGATCATATTTGTTATTTTTAACATAATA
CTTAGAATTATTCATAGTTCTTCCCTAACTCATAAATAAAAAGATAATACATTTCAGCACACTCA
AACTTACGTATCGTGTATTGACAATAATATTCATACTAATCAAATTAATTAATATGAGAATAGAG
TGAGGAGTGAAGGAGTAAGCATAGAGACCCCACCCCAATATTGTCGTAAT
Found at i:56211295 original size:30 final size:30
Alignment explanation
Indices: 56211217--56211295 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 30
56211207 TAAATTTTTG
* * **
56211217 GGGGTCTAATTAAAATTTTTAAAAAATCTA
1 GGGGTCTAATGAAAATTTTAAAAAAAAATA
* * * *
56211247 GGAGTTTAATG-AGA-TTTAAAAAAAAATT
1 GGGGTCTAATGAAAATTTTAAAAAAAAATA
56211275 GGGGTCTAATGAAAATTTTAA
1 GGGGTCTAATGAAAATTTTAA
56211296 TTTTTTGTGA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
28 19 0.53
29 4 0.11
30 13 0.36
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (30 bp):
GGGGTCTAATGAAAATTTTAAAAAAAAATA
Found at i:56211568 original size:28 final size:28
Alignment explanation
Indices: 56211532--56211592 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
56211522 AATTACTAGT
*
56211532 GTCTCGATCCCAATTTTCTACTGAAACG
1 GTCTTGATCCCAATTTTCTACTGAAACG
*
56211560 GTCTTGATCTCAATTTTCTACTGAAACG
1 GTCTTGATCCCAATTTTCTACTGAAACG
*
56211588 ATCTT
1 GTCTT
56211593 AAAAGTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (28 bp):
GTCTTGATCCCAATTTTCTACTGAAACG
Found at i:56214539 original size:8 final size:8
Alignment explanation
Indices: 56214526--56214552 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
56214516 TATTAAATCT
56214526 AAATTTTA
1 AAATTTTA
56214534 AAATTTTA
1 AAATTTTA
56214542 AAATTTTA
1 AAATTTTA
56214550 AAA
1 AAA
56214553 ATAGAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:56214566 original size:31 final size:31
Alignment explanation
Indices: 56214534--56214591 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
56214524 CTAAATTTTA
*
56214534 AAATTTTAAAATTTT-AAAAATAGAAAGATT
1 AAATTTTAAAATTTTGAAAAATACAAAGATT
* *
56214564 AAATTTTTAATTTTTGAAAAATACAAAG
1 AAATTTTAAAATTTTGAAAAATACAAAG
56214592 GCTATACGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (31 bp):
AAATTTTAAAATTTTGAAAAATACAAAGATT
Found at i:56216994 original size:7 final size:7
Alignment explanation
Indices: 56216982--56217007 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
56216972 AAAATATTAA
56216982 AAAATAC
1 AAAATAC
56216989 AAAATAC
1 AAAATAC
56216996 AAAATAC
1 AAAATAC
56217003 AAAAT
1 AAAAT
56217008 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAC
Found at i:56219282 original size:16 final size:16
Alignment explanation
Indices: 56219263--56219300 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
56219253 ATATATAATA
56219263 TATATAATATATTTTT
1 TATATAATATATTTTT
*
56219279 TATATAATGTATTTTT
1 TATATAATATATTTTT
56219295 TATATA
1 TATATA
56219301 TGTTTTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATAATATATTTTT
Found at i:56220132 original size:16 final size:15
Alignment explanation
Indices: 56220111--56220160 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
56220101 ACTGAATTAA
*
56220111 ATAATATATATTATAT
1 ATAATATAT-TTTTAT
56220127 ATAATATATTTTTAT
1 ATAATATATTTTTAT
*
56220142 ATAATGTATTTTTTAT
1 ATAATATA-TTTTTAT
56220158 ATA
1 ATA
56220161 TGTTTTATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATAATATATTTTTAT
Found at i:56220823 original size:856 final size:856
Alignment explanation
Indices: 56218777--56221336 Score: 4200
Period size: 861 Copynumber: 3.0 Consensus size: 856
56218767 CCGGCAGCGC
*
56218777 GTGTGGAATGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCAACATATTTCC
1 GTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCAACATATTTCC
56218842 TTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAATG
66 TTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAATG
* * *
56218907 GCACAGGTCAAAATAAGATTCAAATTTTAAACCCAAAATTAGCATGAAAAACTTAGACTCGTTTA
131 GCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAAATTTAGACACGTTTA
* *
56218972 AGATTATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGTGGTTAAAAT
196 AGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGTGGTTAAAAA
* * * *
56219037 ATAAAATCGAGGAAGCTGTAACCATTTGATCAAATTACAACAGAAATTAGAGGTGCTCATAGTTC
261 ATAAAATCGAGGAGGCTGTAACCGTTTGATCAAATCACAACAGAAATTAGAGGTGTTCATAGTTC
*
56219102 GGTTAAAGTCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTAG
326 GGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTAG
* * *
56219167 TTCGGTCTGATGTGGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCAGTTCGAAATCA
391 TTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGTTCGAAATCG
* *
56219232 AGTATTTAACTGAATTAAATAATATATAATATATATAATATATTTTTTATATAATGTATTTTTTA
456 AGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAATGTATTTTTTA
*
56219297 TATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATACAAATTTTAGTTAATTCAGTTAAG
521 TATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTTAAG
*
56219362 TTATTGGGTTGCTAAGTTTTCTTTTTAAATCCAGCTAGTGAGCTCCAAGTGTCGATTCGACAAAT
586 TTATTGGGTTGCTAAGTTTTC-TTTTAAATCCAGCTAGTGAGCTCCAAGTGTCGATTCGACAAAC
*
56219427 GGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTACATCCAAGTCGATTTGATG
650 GGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGTCGATTTGATG
* * * * *
56219492 GTCAGTGTTAGAGATTGGAGAATAAAACTATTTAAATTTTAATATATAGATTTGTAAATTTTAAA
715 GTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGTGAATTTTAAA
*
56219557 GTTGTTTAATG-AAAAAA-AAACTAAACTATAGAAGAGAAGATGAATGAAAGCTTTCGATTGGTG
780 GTTGTTTAATGAAAAAAATAAACT-AA-TATAGAAGAGAAGATGAATGAAAGCTTTCGACTGGTG
*
56219620 CCCTAAACCGGCAGTGT
843 -CC--AACCAGCAGTGT
* *
56219637 GTGTGGACTGAACTGTAAATTGCGGCAAGACTCGTACAAGTACATGAACTTGGGCAACATATTTC
1 GTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATG-ACTTGGGCAACATATTTC
56219702 CTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAAT
65 CTTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAAT
*
56219767 GGCACACGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAAATTTAGACACGTTT
130 GGCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAAATTTAGACACGTTT
* * *
56219832 AAGATGATATTTTAGTATAATGAGATATCGTCTAATCTTTTCTAAATTAATGATTGTTGTTAAAA
195 AAGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGTGGTTAAAA
* *
56219897 AATAAAATCGAGGAGGCTGTAACCGTTTGATCAAATCACAACAGAAACTAAAGGTGTTCATAGTT
260 AATAAAATCGAGGAGGCTGTAACCGTTTGATCAAATCACAACAGAAATTAGAGGTGTTCATAGTT
* *
56219962 CGGTTAAAATCGAATTAACAGACCGAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTA
325 CGGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTA
* * *
56220027 GTTTGGTCTGATGTTGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGTTCAAAATC
390 GTTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGTTCGAAATC
56220092 GAGTAATTAACTGAATTAAATAATATATATTATATATAATATA-TTTTTATATAATGTATTTTTT
455 GAGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAATGTATTTTTT
* *
56220156 ATATATGTTTTATGCTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTGAA
520 ATATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTTAA
* * *
56220221 GTTATTGGGTTGCTAAATTTTCTTTATAAATCTAGCTAGTGAGCTCCAAATGTCGATTCGACAAA
585 GTTATTGGGTTGCTAAGTTTTCTTT-TAAATCCAGCTAGTGAGCTCCAAGTGTCGATTCGACAAA
* * * * *
56220286 CGGTGCGGTGGATCAGTACCTATCGACGAATAGAATAACATATCTTAGATTCAAGTCGATTTGAT
649 CGGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGTCGATTTGAT
* * *
56220351 GGCCAGTGTTAGAGATTGAAGGATAAAACTATTTAAATTTTGATTTATAGATTCGCGAATTTTAA
714 GGTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGTGAATTTTAA
* * * * *
56220416 AATTGTTGAATGAAAAAAATTAAACTATATATAAAAGAGAAAATGAATGAAAGTTTTCGACTGGT
779 AGTTGTTTAATGAAAAAAA-TAAACTA-ATATAGAAGAGAAGATGAATGAAAGCTTTCGACTGGT
**
56220481 GCC-GGCAGC-GTGT
842 GCCAACCAGCAGTGT
*
56220494 GTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCATATGACTTGGGCAACATATTTCC
1 GTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCAACATATTTCC
56220559 TTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAATG
66 TTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAATG
*
56220624 GCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAATTTTAGACACGTTTA
131 GCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAAATTTAGACACGTTTA
*
56220689 AGATGATATTTTAGTACAATGAGATATCGTGTAACCTTTTCTAAATTAATGATTGTGGTTAAAAA
196 AGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGTGGTTAAAAA
* * * * *
56220754 ATAAAATTGAAGAGGTTGTAATCGTTTGATCAAATCACAACAGAAATTAGAGATGTTCATAGTTC
261 ATAAAATCGAGGAGGCTGTAACCGTTTGATCAAATCACAACAGAAATTAGAGGTGTTCATAGTTC
* * *
56220819 GGTTAAAATCGAATTAACTGACCAAACCTATCTAATTCAATTTATCGATCAATGCTCGAATTTAG
326 GGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTAG
* * *
56220884 TTCGGTCTGATGTCGATTAATGATTTTTTAAAATTTCAATTATCAATTAATTCGGTTCGAAATCG
391 TTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGTTCGAAATCG
* *
56220949 AGTAATTAACTGAATTAAATAATATATATTATATTTAATATATTTTTTATATAATTTATTTTTTA
456 AGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAATGTATTTTTTA
56221014 TATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTTAAG
521 TATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTTAAG
* * *
56221079 TTATTGGGTTGCTAAGTTTTCTTTTCAAATCCAACTAGTGAGCTCCAAGTGTCGATTCAACGAAC
586 TTATTGGGTTGCTAAGTTTTCTTTT-AAATCCAGCTAGTGAGCTCCAAGTGTCGATTCGACAAAC
*
56221144 GGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATATTAAATCCAAGTCGATTTGATG
650 GGTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGTCGATTTGATG
** *
56221209 GTCAGTGTTAGAGATTGAAGAATAAAACTATTTGGATTTTGATTTATAGATTCGTGAATTTCAAA
715 GTCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGTGAATTTTAAA
*
56221274 GTTGTTTAATGAAATAAAACTAAAC---TATAGAAGATAAGATGAATGAAAGCTTTCGACTGGTG
780 GTTGTTTAATGAAA-AAAA-TAAACTAATATAGAAGAGAAGATGAATGAAAGCTTTCGACTGGTG
56221336 C
843 C
56221337 AAATGACGCA
Statistics
Matches: 1578, Mismatches: 113, Indels: 24
0.92 0.07 0.01
Matches are distributed among these distances:
854 34 0.02
856 427 0.27
857 318 0.20
858 12 0.01
859 3 0.00
860 310 0.20
861 434 0.28
862 34 0.02
863 6 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (856 bp):
GTGTGGACTGAACTGAAAATTGCGGCAAGACTCGTACAAGCACATGACTTGGGCAACATATTTCC
TTACATGCGACTTATTTCAATCACTAGGACCCTACTATGATGCCCACTGCAGAGCCACCCTAATG
GCACAGGTCAAAATAAGATTGAAATTTTAAACCCAAAATTAGCATGAAAAATTTAGACACGTTTA
AGATGATATTTTAGTACAATGAGATATCGTGTAATCTTTTCTAAATTAATGATTGTGGTTAAAAA
ATAAAATCGAGGAGGCTGTAACCGTTTGATCAAATCACAACAGAAATTAGAGGTGTTCATAGTTC
GGTTAAAATCGAATTAACTGACCAAACCGATCTAATTCAGTTAATCGATCAATGCTCGAATTTAG
TTCGGTCTGATGTCGATTAATGATTTTTTGAAATTTTAATTATCAGTTAATTCGGTTCGAAATCG
AGTAATTAACTGAATTAAATAATATATATTATATATAATATATTTTTTATATAATGTATTTTTTA
TATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTAGTTAATTCAGTTAAG
TTATTGGGTTGCTAAGTTTTCTTTTAAATCCAGCTAGTGAGCTCCAAGTGTCGATTCGACAAACG
GTGCGATGGATCAGTATCTATCGACGAGTAGAATAACATATCTTAAATCCAAGTCGATTTGATGG
TCAGTGTTAGAGATTGAAGAATAAAACTATTTAAATTTTGATTTATAGATTCGTGAATTTTAAAG
TTGTTTAATGAAAAAAATAAACTAATATAGAAGAGAAGATGAATGAAAGCTTTCGACTGGTGCCA
ACCAGCAGTGT
Found at i:56221003 original size:16 final size:16
Alignment explanation
Indices: 56220967--56221017 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
56220957 ACTGAATTAA
* *
56220967 ATAATATATATTATAT
1 ATAATATATTTTTTAT
*
56220983 TTAATATATTTTTTAT
1 ATAATATATTTTTTAT
*
56220999 ATAATTTATTTTTTAT
1 ATAATATATTTTTTAT
56221015 ATA
1 ATA
56221018 TGTTTTATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAATATATTTTTTAT
Found at i:56224517 original size:25 final size:25
Alignment explanation
Indices: 56224455--56224531 Score: 111
Period size: 26 Copynumber: 3.1 Consensus size: 25
56224445 ATCGCAGCTT
* *
56224455 TTATGAGCGTCCCGATATATGGCTC
1 TTATGAGCTTCCCGATAAATGGCTC
56224480 TTCATGAGCTTCCCGATAAATGGCTC
1 TT-ATGAGCTTCCCGATAAATGGCTC
*
56224506 TTATGAGCTTCCCG-TTAATGGCTC
1 TTATGAGCTTCCCGATAAATGGCTC
56224530 TT
1 TT
56224532 CGGAACTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 11 0.23
25 14 0.29
26 23 0.48
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (25 bp):
TTATGAGCTTCCCGATAAATGGCTC
Found at i:56227542 original size:2 final size:2
Alignment explanation
Indices: 56227537--56227575 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56227527 ATATTTTCTC
56227537 AT AT 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 AT AT A
56227576 AAAGAGGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56228320 original size:17 final size:16
Alignment explanation
Indices: 56228296--56228334 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
56228286 CTTTTCATTA
56228296 TGTTTTCCTTTCTTTT-
1 TGTTTTCCTTT-TTTTC
56228312 TGTTGTTCCTTTTTTTC
1 TGTT-TTCCTTTTTTTC
56228329 TGTTTT
1 TGTTTT
56228335 GTGCATGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTTTTCCTTTTTTTC
Found at i:56234588 original size:14 final size:15
Alignment explanation
Indices: 56234560--56234588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56234550 AATCCTGTTT
56234560 AATATTTTAATATAA
1 AATATTTTAATATAA
56234575 AATATTTT-ATATAA
1 AATATTTTAATATAA
56234589 TACATCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATATAA
Found at i:56236336 original size:36 final size:35
Alignment explanation
Indices: 56236287--56236366 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 35
56236277 TAAACTTAAA
56236287 ATTAAAAA-ATAAAACTTCAATAAATTCTTCAATC
1 ATTAAAAACATAAAACTTCAATAAATTCTTCAATC
* * *
56236321 ATTAAAAACAGTAAAACTTTAATAAATTCTTTAATT
1 ATTAAAAACA-TAAAACTTCAATAAATTCTTCAATC
56236357 ATTAAAAACA
1 ATTAAAAACA
56236367 AATAATGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 8 0.20
35 1 0.02
36 32 0.78
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (35 bp):
ATTAAAAACATAAAACTTCAATAAATTCTTCAATC
Found at i:56236701 original size:17 final size:17
Alignment explanation
Indices: 56236679--56236712 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56236669 AATTAAACAA
56236679 GTTTTACTAATCTGGGT
1 GTTTTACTAATCTGGGT
56236696 GTTTTACTAATCTGGGT
1 GTTTTACTAATCTGGGT
56236713 TGATTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (17 bp):
GTTTTACTAATCTGGGT
Found at i:56238930 original size:2 final size:2
Alignment explanation
Indices: 56238925--56238951 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56238915 AAATCATGTT
56238925 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
56238952 CTGTGGCTAT
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:56240884 original size:18 final size:18
Alignment explanation
Indices: 56240861--56240926 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
56240851 TGTAATTAAT
56240861 TTCACTGTATATTACTAA
1 TTCACTGTATATTACTAA
* *
56240879 TTCACTTTACCATAAATTACTCAT
1 TTCACTGT---AT--ATTACT-AA
56240903 TTCACTGTATATTACTAA
1 TTCACTGTATATTACTAA
56240921 TTCACT
1 TTCACT
56240927 TTATTATCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 14 0.37
19 6 0.16
21 4 0.11
23 6 0.16
24 8 0.21
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (18 bp):
TTCACTGTATATTACTAA
Found at i:56245999 original size:16 final size:18
Alignment explanation
Indices: 56245973--56246005 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56245963 TTGAATTATC
56245973 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
56245990 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
56246006 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:56248023 original size:22 final size:21
Alignment explanation
Indices: 56247991--56248036 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
56247981 TATATCAAAT
* *
56247991 ACCCAAGACCATAAACTCTTAA
1 ACCCAAAACCATAAA-TCCTAA
56248013 ACCCAAAACCATAAATCCTAA
1 ACCCAAAACCATAAATCCTAA
56248034 ACC
1 ACC
56248037 ATAGATCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (21 bp):
ACCCAAAACCATAAATCCTAA
Found at i:56255754 original size:2 final size:2
Alignment explanation
Indices: 56255747--56255780 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
56255737 TGTGCGTGCA
*
56255747 TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
56255781 AGAGAGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:56264402 original size:31 final size:30
Alignment explanation
Indices: 56264329--56264407 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
56264319 ATGCAATTTG
* *
56264329 ATACATGAAA-TTTGATTTGGTACAATTAT
1 ATACATGAAACTTTGATTTAGTACAAATAT
* * * *
56264358 ACACATAAAACTTTGATTGTAGTTCAAATGT
1 ATACATGAAACTTTGATT-TAGTACAAATAT
56264389 ATACATGAAACTTTGATTT
1 ATACATGAAACTTTGATTT
56264408 TGATTCGATC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 8 0.20
30 8 0.20
31 24 0.60
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (30 bp):
ATACATGAAACTTTGATTTAGTACAAATAT
Found at i:56265769 original size:40 final size:40
Alignment explanation
Indices: 56265714--56265794 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
56265704 CCAGCAACAC
56265714 ATACCATACCAAACAGCATACTGTGTTTCCATGGTAGTCT
1 ATACCATACCAAACAGCATACTGTGTTTCCATGGTAGTCT
*
56265754 ATACCATACCAAACAGCATATTGTGTTTCCATGGTAGTCT
1 ATACCATACCAAACAGCATACTGTGTTTCCATGGTAGTCT
56265794 A
1 A
56265795 ATAGTCTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (40 bp):
ATACCATACCAAACAGCATACTGTGTTTCCATGGTAGTCT
Found at i:56269075 original size:38 final size:38
Alignment explanation
Indices: 56269033--56269113 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
56269023 GTAGCCTTTC
56269033 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
1 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
*
56269071 ACTTATAAAAACAAACAAAAAGATATCTTTATTTTCTT
1 ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
56269109 ACTTA
1 ACTTA
56269114 ATGCTGCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (38 bp):
ACTTATAAAAACAAACAAAAAGATACCTTTATTTTCTT
Found at i:56269863 original size:35 final size:35
Alignment explanation
Indices: 56269824--56269895 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
56269814 AGTAATAGAG
56269824 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
1 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
56269859 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
1 AATGGCAATTGAGAACAGTATAACACCATTTTAAT
56269894 AA
1 AA
56269896 ACCCGAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (35 bp):
AATGGCAATTGAGAACAGTATAACACCATTTTAAT
Found at i:56277421 original size:9 final size:10
Alignment explanation
Indices: 56277391--56277442 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
56277381 AGATGGATTA
56277391 TTATATATTT
1 TTATATATTT
* *
56277401 TTAAATTTTT
1 TTATATATTT
*
56277411 TTATGTATTT
1 TTATATATTT
56277421 TTATATATTT
1 TTATATATTT
*
56277431 TTA-AAATTT
1 TTATATATTT
56277440 TTA
1 TTA
56277443 AAATTAAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
9 8 0.23
10 27 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATATATTT
Found at i:56279451 original size:32 final size:32
Alignment explanation
Indices: 56279410--56279470 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
56279400 CAAATTTAGC
56279410 TATACATTCAATTTCTAGGAAGAGAACTTGTA
1 TATACATTCAATTTCTAGGAAGAGAACTTGTA
56279442 TATACATTCAATTTCTAGGAAGAGAACTT
1 TATACATTCAATTTCTAGGAAGAGAACTT
56279471 TACTTATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TATACATTCAATTTCTAGGAAGAGAACTTGTA
Found at i:56281165 original size:98 final size:98
Alignment explanation
Indices: 56281048--56281243 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
56281038 ATTGTGTCGA
56281048 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
1 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
56281113 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
66 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
56281146 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
1 TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
56281211 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
66 CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
56281244 ATACTTAAAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.51
Consensus pattern (98 bp):
TTGTTTGGTTGTTTTTTCTTGGATAATTTCTTATTGATTGTTTTGTTTTAAAAATTGCTAAGAGT
CACAAGTATTTGAACTTCTCTTTCTACTGGCAT
Found at i:56289184 original size:6 final size:6
Alignment explanation
Indices: 56289173--56289201 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56289163 CATTACTGTT
56289173 TACATC TACATC TACATC TACATC TACAT
1 TACATC TACATC TACATC TACATC TACAT
56289202 ATTATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATC
Found at i:56310012 original size:29 final size:31
Alignment explanation
Indices: 56309974--56310037 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
56309964 AATATATATA
56309974 TTTTATTTTTAAAAATA-TTTTAAAATACTT
1 TTTTATTTTTAAAAATATTTTTAAAATACTT
56310004 TTTTATTTTT-AAAATATTTTTAAAATACTT
1 TTTTATTTTTAAAAATATTTTTAAAATACTT
56310034 TTTT
1 TTTT
56310038 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTATTTTTAAAAATATTTTTAAAATACTT
Found at i:56310743 original size:21 final size:20
Alignment explanation
Indices: 56310719--56310758 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56310709 AAATCAAAAC
56310719 AATTTTCAAAATTTCAAAATT
1 AATTTTCAAAA-TTCAAAATT
* *
56310740 AATTTTTAGAATTCAAAAT
1 AATTTTCAAAATTCAAAAT
56310759 ACTTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTTTCAAAATTCAAAATT
Found at i:56310941 original size:16 final size:16
Alignment explanation
Indices: 56310922--56310952 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56310912 TTGAAAGAGT
56310922 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
56310938 TTTCAAATTTATATG
1 TTTCAAATATATATG
56310953 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:56311696 original size:24 final size:23
Alignment explanation
Indices: 56311644--56311697 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
56311634 TTCTATCTTT
**
56311644 TATTTAATATATAATTAATTTTA
1 TATTTAATATATAAAAAATTTTA
* *
56311667 TTTTTATTATATAAAAATATTTTA
1 TATTTAATATATAAAAA-ATTTTA
56311691 TATTTAA
1 TATTTAA
56311698 AATAATGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTAATATATAAAAAATTTTA
Found at i:56312960 original size:19 final size:20
Alignment explanation
Indices: 56312907--56312961 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
56312897 ATTTTTTAAA
56312907 ATTAAAAAATATAAATATTCT
1 ATTAAAAAATATAAA-ATTCT
* *
56312928 TTTTAAAAAT-TAAAATTC-
1 ATTAAAAAATATAAAATTCT
56312946 ATTAAAAAATATAAAA
1 ATTAAAAAATATAAAA
56312962 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 4 0.14
21 8 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAAATATAAAATTCT
Found at i:56313200 original size:28 final size:29
Alignment explanation
Indices: 56313156--56313211 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
56313146 TTAACTAGCT
56313156 TTTTTAAAAATTAAAAAATTA-TAAAAATC
1 TTTTTAAAAATT-AAAAATTATTAAAAATC
*
56313185 TTTTT-AAAATTTAAAATTATTAAAAAT
1 TTTTTAAAAATTAAAAATTATTAAAAAT
56313212 ATAAAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 13 0.52
29 5 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTTAAAAATTAAAAATTATTAAAAATC
Found at i:56313244 original size:37 final size:38
Alignment explanation
Indices: 56313161--56313244 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 38
56313151 TAGCTTTTTT
56313161 AAAAATTAAAAAATTATAAAAATCTTTTTAAAATTTAA
1 AAAAATTAAAAAATTATAAAAATCTTTTTAAAATTTAA
**
56313199 AATTATT-AAAAA-TATAAAAA-CATTTTTTAAAATTTAA
1 AAAAATTAAAAAATTATAAAAATC--TTTTTAAAATTTAA
56313236 AAAAATTAA
1 AAAAATTAA
56313245 TTAAATGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 1 0.03
36 8 0.21
37 24 0.62
38 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (38 bp):
AAAAATTAAAAAATTATAAAAATCTTTTTAAAATTTAA
Found at i:56313248 original size:20 final size:19
Alignment explanation
Indices: 56313197--56313249 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
56313187 TTTAAAATTT
56313197 AAAATTATTAAAAATATAAA
1 AAAATTATT-AAAATATAAA
* * *
56313217 AACATTTTTTAAAATTTAAA
1 AA-AATTATTAAAATATAAA
56313237 AAAATTAATTAAA
1 AAAATT-ATTAAA
56313250 TGATGGCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATTAAAATATAAA
Found at i:56313630 original size:16 final size:16
Alignment explanation
Indices: 56313609--56313639 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56313599 TTTGCAACTC
56313609 GATTTAAATTTAGACG
1 GATTTAAATTTAGACG
56313625 GATTTAAATTTAGAC
1 GATTTAAATTTAGAC
56313640 AAATTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (16 bp):
GATTTAAATTTAGACG
Found at i:56313645 original size:16 final size:16
Alignment explanation
Indices: 56313610--56313647 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
56313600 TTGCAACTCG
**
56313610 ATTTAAATTTAGACGG
1 ATTTAAATTTAGACAA
56313626 ATTTAAATTTAGACAA
1 ATTTAAATTTAGACAA
56313642 ATTTAA
1 ATTTAA
56313648 GCATAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (16 bp):
ATTTAAATTTAGACAA
Found at i:56314081 original size:2 final size:2
Alignment explanation
Indices: 56314074--56314100 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56314064 CATGGTTGTG
56314074 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
56314101 TTCTTGAGTG
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:56314410 original size:33 final size:31
Alignment explanation
Indices: 56314352--56314414 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
56314342 AACTTTGGTT
*
56314352 TTCTGAATTTTTTGAATTAATTATTTTATTTA
1 TTCTGAATTTTTTGAACTAATTA-TTTATTTA
*
56314384 TTCTCGAATTTTTTTATACTAA-TATTTATTT
1 TTCT-GAATTTTTTGA-ACTAATTATTTATTT
56314415 TTCGTTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 11 0.41
33 12 0.44
34 4 0.15
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (31 bp):
TTCTGAATTTTTTGAACTAATTATTTATTTA
Found at i:56314485 original size:35 final size:35
Alignment explanation
Indices: 56314407--56314487 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
56314397 TTATACTAAT
*
56314407 ATTTATTTTTCGTTGGAAAATATTTTATTTAACTCA
1 ATTT-TTTTTCGTTGGAAAATATTTGATTTAACTCA
*
56314443 ATCTTTTTTTCGTT-GACAAATATTTGGTTTAAC-CAA
1 AT-TTTTTTTCGTTGGA-AAATATTTGATTTAACTC-A
56314479 ATTTTTTTT
1 ATTTTTTTT
56314488 GTGTAGTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 10 0.25
36 28 0.70
37 2 0.05
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (35 bp):
ATTTTTTTTCGTTGGAAAATATTTGATTTAACTCA
Found at i:56316256 original size:42 final size:43
Alignment explanation
Indices: 56316196--56316297 Score: 188
Period size: 42 Copynumber: 2.4 Consensus size: 43
56316186 TAACTGAAAT
56316196 GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
1 GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
56316239 -ATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
1 GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
*
56316281 GATATACATTCTTTAAC
1 GATACACATTCTTTAAC
56316298 CGAAATGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
42 42 0.74
43 15 0.26
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (43 bp):
GATACACATTCTTTAACAGCTAACTACAAACAAAGATACTCAA
Found at i:56317305 original size:20 final size:20
Alignment explanation
Indices: 56317258--56317306 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
56317248 AATTTAGTAC
* * *
56317258 TTTAATAAATAATAATTATA
1 TTTATTAAAAAATAAATATA
56317278 -TTATTTAAAAAATAAATATA
1 TTTA-TTAAAAAATAAATATA
56317298 TTTATTAAA
1 TTTATTAAA
56317307 GAAACTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTATTAAAAAATAAATATA
Found at i:56319166 original size:169 final size:169
Alignment explanation
Indices: 56318966--56319392 Score: 784
Period size: 169 Copynumber: 2.5 Consensus size: 169
56318956 CCAAGTAATT
*
56318966 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTCAAACCAT
1 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTTAAACCAT
*
56319031 ACATTATCATATTCATAAAGTAT-TCGTTACTCAACCGCATTAAACACCACAAACATATTAAGCC
66 ACATTATCATATTCATAAAGTATCT-GTTACTCAACCACATTAAACACCACAAACATATTAAGCC
56319095 ACACATACATATACATATCAAAATATGTCCAACTCAAGCC
130 ACACATACATATACATATCAAAATATGTCCAACTCAAGCC
56319135 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTTAAACCAT
1 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTTAAACCAT
*
56319200 ACATTATCATATTCATAAATTATCTGTTACTCAACCACATTAAACACCACAAACATATTAAGCCA
66 ACATTATCATATTCATAAAGTATCTGTTACTCAACCACATTAAACACCACAAACATATTAAGCCA
*
56319265 CACATACATATACATATCAAAATGTGTCCAACTCAAGCC
131 CACATACATATACATATCAAAATATGTCCAACTCAAGCC
*
56319304 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTGTCTTAAACCAT
1 AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTTAAACCAT
*
56319369 ACATTATCATATTCATAAATTATC
66 ACATTATCATATTCATAAAGTATC
56319393 CGTGGGGAAG
Statistics
Matches: 252, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
169 251 1.00
170 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (169 bp):
AATCTTACCTAATTGACCATATAAACCTATTTGCATATTTCTCCGATCATATTATCTTAAACCAT
ACATTATCATATTCATAAAGTATCTGTTACTCAACCACATTAAACACCACAAACATATTAAGCCA
CACATACATATACATATCAAAATATGTCCAACTCAAGCC
Found at i:56321586 original size:10 final size:9
Alignment explanation
Indices: 56321568--56321627 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
56321558 TTATTTTTTT
56321568 AAATT-TAA
1 AAATTATAA
*
56321576 AACTTCATAA
1 AAATT-ATAA
56321586 AAATTATAAA
1 AAATTAT-AA
*
56321596 AATATTTTTAA
1 AA-A-TTATAA
56321607 AAATTATAA
1 AAATTATAA
56321616 AATATTATAA
1 AA-ATTATAA
56321626 AA
1 AA
56321628 TATTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 4 0.10
9 9 0.21
10 21 0.50
11 5 0.12
12 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATTATAA
Found at i:56321609 original size:21 final size:20
Alignment explanation
Indices: 56321583--56321621 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
56321573 TAAAACTTCA
56321583 TAAAAATTATAAAAATATTTT
1 TAAAAATTAT-AAAATATTTT
56321604 TAAAAATTATAAAATATT
1 TAAAAATTATAAAATATT
56321622 ATAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTATAAAATATTTT
Found at i:56321628 original size:10 final size:10
Alignment explanation
Indices: 56321582--56321631 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
56321572 TTAAAACTTC
56321582 ATAAAA-ATT
1 ATAAAATATT
56321591 ATAAAAATATTT
1 AT-AAAATA-TT
*
56321603 TTAAAA-ATT
1 ATAAAATATT
56321612 ATAAAATATT
1 ATAAAATATT
56321622 ATAAAATATT
1 ATAAAATATT
56321632 TTTAATATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 9 0.26
10 18 0.51
11 5 0.14
12 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAAAATATT
Found at i:56321628 original size:30 final size:31
Alignment explanation
Indices: 56321571--56321636 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
56321561 TTTTTTTAAA
*
56321571 TTTAAAACTTCATAAAAATTATAAAAATATT
1 TTTAAAAATTCATAAAAATTATAAAAATATT
56321602 TTTAAAAATT-ATAAAATATTAT-AAAATATT
1 TTTAAAAATTCATAAAA-ATTATAAAAATATT
56321632 TTTAA
1 TTTAA
56321637 TATACCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTAAAAATTCATAAAAATTATAAAAATATT
Found at i:56324231 original size:30 final size:30
Alignment explanation
Indices: 56324197--56324254 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
56324187 TATTATCATG
56324197 GGAATTCCTTGATGCTGGACCAACCTTTAA
1 GGAATTCCTTGATGCTGGACCAACCTTTAA
* *
56324227 GGAATTCCTTTATGTTGGACCAACCTTT
1 GGAATTCCTTGATGCTGGACCAACCTTT
56324255 GAGAAATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (30 bp):
GGAATTCCTTGATGCTGGACCAACCTTTAA
Found at i:56328429 original size:44 final size:44
Alignment explanation
Indices: 56328365--56328451 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
56328355 GCTAAGTCTT
* **
56328365 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTC
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCTC
* *
56328409 ATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATCT
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCT
56328452 TGTACCTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCGACAAATCTC
Done.