Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 188 of 190
Found at i:56126906 original size:15 final size:16
Alignment explanation
Indices: 56126880--56126914 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
56126870 ATTTATAAAT
56126880 TTTAATATTGATAGTA
1 TTTAATATTGATAGTA
56126896 TTTAA-ATTGATAGTA
1 TTTAATATTGATAGTA
56126911 TTTA
1 TTTA
56126915 TAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAATATTGATAGTA
Found at i:56129220 original size:45 final size:45
Alignment explanation
Indices: 56129144--56129240 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
56129134 ATAAGTTTTC
* * * *
56129144 TAAATTTATAAGTTTTCTAAGTAAATTTTCTAAATTTATTAGTAT
1 TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
*
56129189 TAAAATTATAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAA
1 TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
56129234 TAAAATT
1 TAAAATT
56129241 TATTAGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (45 bp):
TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
Found at i:56129291 original size:12 final size:12
Alignment explanation
Indices: 56129274--56129299 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56129264 TTCTAAATAA
56129274 TTATATATAAGC
1 TTATATATAAGC
56129286 TTATATATAAGC
1 TTATATATAAGC
56129298 TT
1 TT
56129300 GCATAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATATATAAGC
Found at i:56129317 original size:12 final size:12
Alignment explanation
Indices: 56129302--56129489 Score: 62
Period size: 12 Copynumber: 17.1 Consensus size: 12
56129292 ATAAGCTTGC
56129302 ATAACTTACATA
1 ATAACTTACATA
56129314 ATAACTTAC---
1 ATAACTTACATA
56129323 ATAACTTACATA
1 ATAACTTACATA
* *
56129335 ATACAC-CACTTA
1 ATA-ACTTACATA
56129347 CATAACTTAC---
1 -ATAACTTACATA
*
56129357 ATAACTTATAT-
1 ATAACTTACATA
*
56129368 ATAA-TAACATA
1 ATAACTTACATA
*
56129379 ATAAATTAC---
1 ATAACTTACATA
56129388 ATAA--TACATA
1 ATAACTTACATA
*
56129398 ATAACATA-ATA
1 ATAACTTACATA
*
56129409 CATAACTTATATA
1 -ATAACTTACATA
* *
56129422 GA-AGCTTGC---
1 -ATAACTTACATA
56129431 ATAACTTACATA
1 ATAACTTACATA
56129443 ATAACTTAC---
1 ATAACTTACATA
56129452 ATAACTTACATA
1 ATAACTTACATA
* *
56129464 ATACAC-CACTTA
1 ATA-ACTTACATA
56129476 CATAACTTACATA
1 -ATAACTTACATA
56129489 A
1 A
56129490 CTTACATAGC
Statistics
Matches: 131, Mismatches: 18, Indels: 54
0.65 0.09 0.27
Matches are distributed among these distances:
7 3 0.02
8 1 0.01
9 35 0.27
10 8 0.06
11 11 0.08
12 53 0.40
13 20 0.15
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:56129326 original size:9 final size:9
Alignment explanation
Indices: 56129314--56129829 Score: 221
Period size: 9 Copynumber: 60.4 Consensus size: 9
56129304 AACTTACATA
56129314 ATAACTTAC
1 ATAACTTAC
56129323 ATAACTTAC
1 ATAACTTAC
56129332 ATAA--TAC
1 ATAACTTAC
**
56129339 ACCACTTAC
1 ATAACTTAC
56129348 ATAACTTAC
1 ATAACTTAC
*
56129357 ATAACTTAT
1 ATAACTTAC
56129366 AT-A--TA-
1 ATAACTTAC
*
56129371 ATAACATA-
1 ATAACTTAC
*
56129379 ATAAATTAC
1 ATAACTTAC
56129388 ATAA--TAC
1 ATAACTTAC
*
56129395 ATAA-TAAC
1 ATAACTTAC
56129403 ATAA--TAC
1 ATAACTTAC
*
56129410 ATAACTTAT
1 ATAACTTAC
*
56129419 ATAGAAGCTTGC
1 AT--AA-CTTAC
56129431 ATAACTTAC
1 ATAACTTAC
56129440 ATAATAACTTAC
1 ---ATAACTTAC
56129452 ATAACTTAC
1 ATAACTTAC
56129461 ATAA--TAC
1 ATAACTTAC
**
56129468 ACCACTTAC
1 ATAACTTAC
56129477 ATAACTTAC
1 ATAACTTAC
56129486 ATAACTTAC
1 ATAACTTAC
*
56129495 ATAGCTTAC
1 ATAACTTAC
*
56129504 AT-TC-TAC
1 ATAACTTAC
* *
56129511 ACAACTTGC
1 ATAACTTAC
* *
56129520 ATAACATAT
1 ATAACTTAC
*
56129529 ATAA--TGC
1 ATAACTTAC
*
56129536 AGAACTTAC
1 ATAACTTAC
* *
56129545 ATAA--AAT
1 ATAACTTAC
56129552 ATAACTTAC
1 ATAACTTAC
*
56129561 ATATCTTAC
1 ATAACTTAC
56129570 ATAA--TAC
1 ATAACTTAC
56129577 ATAACTTAC
1 ATAACTTAC
56129586 ATAA--TAC
1 ATAACTTAC
56129593 A-ACACTTAC
1 ATA-ACTTAC
* *
56129602 ACAACTTAA
1 ATAACTTAC
*
56129611 ATAACTTGC
1 ATAACTTAC
56129620 ATAA--TAC
1 ATAACTTAC
* *
56129627 ATAGCCTAC
1 ATAACTTAC
*
56129636 ATCAA-TTAT
1 AT-AACTTAC
*
56129645 ATAACTTTC
1 ATAACTTAC
**
56129654 ATAAAATA-
1 ATAACTTAC
56129662 A-AACTTAC
1 ATAACTTAC
**
56129670 ATATTTTAC
1 ATAACTTAC
*
56129679 ATAAAACTTAT
1 AT--AACTTAC
56129690 ATAA--TAC
1 ATAACTTAC
56129697 ATAACTTAC
1 ATAACTTAC
56129706 ATAA--TAC
1 ATAACTTAC
**
56129713 AGCACTTAC
1 ATAACTTAC
* *
56129722 ACAACTTAA
1 ATAACTTAC
*
56129731 ATAACTTGC
1 ATAACTTAC
56129740 ATAA--TAC
1 ATAACTTAC
* *
56129747 ATAGCCTAC
1 ATAACTTAC
*
56129756 ATAACTTAT
1 ATAACTTAC
*
56129765 ATAACTTTC
1 ATAACTTAC
**
56129774 ATAAAATAC
1 ATAACTTAC
56129783 --AACTTAC
1 ATAACTTAC
**
56129790 ATATTTTAC
1 ATAACTTAC
*
56129799 ATAAAACTTAT
1 AT--AACTTAC
56129810 ATAA--TAC
1 ATAACTTAC
56129817 ATAACTTAC
1 ATAACTTAC
56129826 ATAA
1 ATAA
56129830 TACAGCACTT
Statistics
Matches: 373, Mismatches: 85, Indels: 98
0.67 0.15 0.18
Matches are distributed among these distances:
5 2 0.01
6 4 0.01
7 84 0.23
8 21 0.06
9 230 0.62
10 4 0.01
11 14 0.04
12 14 0.04
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:56129345 original size:25 final size:21
Alignment explanation
Indices: 56129292--56129505 Score: 158
Period size: 21 Copynumber: 10.0 Consensus size: 21
56129282 AAGCTTATAT
*
56129292 ATAAGCTTGCATAACTTACATA
1 ATAA-CTTACATAACTTACATA
56129314 ATAACTTACATAACTTACATA
1 ATAACTTACATAACTTACATA
56129335 ATACACCACTTACATAACTTAC---
1 AT--A--ACTTACATAACTTACATA
* * *
56129357 ATAACTTATATATAATAACATA
1 ATAACTTACATA-ACTTACATA
*
56129379 ATAAATTACATAA--TACATA
1 ATAACTTACATAACTTACATA
*
56129398 ATAACATAATACATAACTTATATA
1 ATAAC-T--TACATAACTTACATA
* *
56129422 GA-AGCTTGCATAACTTACATA
1 -ATAACTTACATAACTTACATA
56129443 ATAACTTACATAACTTACATA
1 ATAACTTACATAACTTACATA
56129464 ATACACCACTTACATAACTTAC---
1 AT--A--ACTTACATAACTTACATA
*
56129486 ATAACTTACATAGCTTACAT
1 ATAACTTACATAACTTACAT
56129506 TCTACACAAC
Statistics
Matches: 156, Mismatches: 15, Indels: 44
0.73 0.07 0.20
Matches are distributed among these distances:
18 22 0.14
19 13 0.08
20 4 0.03
21 51 0.33
22 25 0.16
23 3 0.02
24 7 0.04
25 31 0.20
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (21 bp):
ATAACTTACATAACTTACATA
Found at i:56129357 original size:34 final size:32
Alignment explanation
Indices: 56129314--56129625 Score: 167
Period size: 34 Copynumber: 9.8 Consensus size: 32
56129304 AACTTACATA
56129314 ATAACTTACATAACTTACATAATACACCACTTAC
1 ATAACTTACATAACTTACATAATA-A-CACTTAC
*
56129348 ATAACTTACATAACTTATATATAATAACA--TA-
1 ATAACTTACATAAC-T-TACATAATAACACTTAC
*
56129379 ATAAATTACATAA--TACATAATAACA-TAATAC
1 ATAACTTACATAACTTACATAATAACACT--TAC
* * *
56129410 ATAACTTATATAGAAGCTTGCATAACTTACA--TA-
1 ATAACTTACAT--AA-CTTACATAA-TAACACTTAC
56129443 ATAACTTACATAACTTACATAATACACCACTTAC
1 ATAACTTACATAACTTACATAATA-A-CACTTAC
* * *
56129477 ATAACTTACATAACTTACATAGCTTACATTCTAC
1 ATAACTTACATAACTTACATA-ATAACACT-TAC
* * * *
56129511 ACAACTTGCATAACATATATAATGCAGA-ACTTAC
1 ATAACTTACATAACTTACATAAT--A-ACACTTAC
* *
56129545 ATAA--AATATAACTTACAT-AT----CTTAC
1 ATAACTTACATAACTTACATAATAACACTTAC
56129570 ATAA--TACATAACTTACATAATACAACACTTAC
1 ATAACTTACATAACTTACATAAT--AACACTTAC
* * *
56129602 ACAACTTAAATAACTTGCATAATA
1 ATAACTTACATAACTTACATAATA
56129626 CATAGCCTAC
Statistics
Matches: 216, Mismatches: 31, Indels: 64
0.69 0.10 0.21
Matches are distributed among these distances:
25 21 0.10
26 2 0.01
27 11 0.05
29 1 0.00
30 11 0.05
31 27 0.12
32 20 0.09
33 18 0.08
34 81 0.38
35 5 0.02
36 15 0.07
37 4 0.02
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31
Consensus pattern (32 bp):
ATAACTTACATAACTTACATAATAACACTTAC
Found at i:56129381 original size:8 final size:7
Alignment explanation
Indices: 56129368--56129413 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
56129358 TAACTTATAT
56129368 ATAATAAC
1 ATAAT-AC
56129376 ATAATA-
1 ATAATAC
*
56129382 A-ATTAC
1 ATAATAC
56129388 ATAATAC
1 ATAATAC
56129395 ATAATAAC
1 ATAAT-AC
56129403 ATAATAC
1 ATAATAC
56129410 ATAA
1 ATAA
56129414 CTTATATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:56129406 original size:15 final size:15
Alignment explanation
Indices: 56129368--56129413 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
56129358 TAACTTATAT
56129368 ATAATAACATAAT--
1 ATAATAACATAATAC
*
56129381 A-AATTACATAATAC
1 ATAATAACATAATAC
56129395 ATAATAACATAATAC
1 ATAATAACATAATAC
56129410 ATAA
1 ATAA
56129414 CTTATATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:56129415 original size:53 final size:56
Alignment explanation
Indices: 56129311--56129421 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
56129301 CATAACTTAC
* * * *
56129311 ATAATAACTTACATAACTTACATAATACACCACTTACATAACTTACATAACTTATAT
1 ATAATAACATACATAAATTACATAATACACCAATAACATAAC-TACATAACTTATAT
*
56129368 ATAATAACATA-ATAAATTACATAATACA-TAATAACATAA-TACATAACTTATAT
1 ATAATAACATACATAAATTACATAATACACCAATAACATAACTACATAACTTATAT
56129421 A
1 A
56129422 GAAGCTTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 15 0.31
55 8 0.16
56 16 0.33
57 10 0.20
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (56 bp):
ATAATAACATACATAAATTACATAATACACCAATAACATAACTACATAACTTATAT
Found at i:56129568 original size:25 final size:25
Alignment explanation
Indices: 56129540--56129588 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
56129530 TAATGCAGAA
*
56129540 CTTACATAAAATATAACTTACATAT
1 CTTACATAAAACATAACTTACATAT
*
56129565 CTTACATAATACATAACTTACATA
1 CTTACATAAAACATAACTTACATA
56129589 ATACAACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (25 bp):
CTTACATAAAACATAACTTACATAT
Found at i:56129577 original size:16 final size:16
Alignment explanation
Indices: 56129558--56129833 Score: 149
Period size: 16 Copynumber: 16.2 Consensus size: 16
56129548 AAATATAACT
*
56129558 TACATATCTTACATAA
1 TACATAACTTACATAA
56129574 TACATAACTTACATAA
1 TACATAACTTACATAA
*
56129590 TACA-ACACTTACACAA
1 TACATA-ACTTACATAA
* *
56129606 CTTAAATAACTTGCATAA
1 --TACATAACTTACATAA
* *
56129624 TACATAGCCTACATCAA
1 TACATAACTTACAT-AA
* *
56129641 TTATATAACTTTCATAA
1 -TACATAACTTACATAA
* * * *
56129658 AATAAAACTTACATATTT
1 TACATAACTTACATA--A
*
56129676 TACATAAAACTTATATAA
1 TACAT--AACTTACATAA
56129694 TACATAACTTACATAA
1 TACATAACTTACATAA
** *
56129710 TACAGCACTTACACAA
1 TACATAACTTACATAA
* *
56129726 CTTAAATAACTTGCATAA
1 --TACATAACTTACATAA
* *
56129744 TACATAGCCTACATAA
1 TACATAACTTACATAA
* *
56129760 CTTATATAACTTTCATAA
1 --TACATAACTTACATAA
* * * *
56129778 AATACAACTTACATATTT
1 TACATAACTTACATA--A
*
56129796 TACATAAAACTTATATAA
1 TACAT--AACTTACATAA
56129814 TACATAACTTACATAA
1 TACATAACTTACATAA
56129830 TACA
1 TACA
56129834 GCACTTACAC
Statistics
Matches: 193, Mismatches: 49, Indels: 36
0.69 0.18 0.13
Matches are distributed among these distances:
15 1 0.01
16 111 0.58
17 4 0.02
18 58 0.30
19 1 0.01
20 18 0.09
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:56129727 original size:120 final size:120
Alignment explanation
Indices: 56129565--56129843 Score: 515
Period size: 120 Copynumber: 2.3 Consensus size: 120
56129555 ACTTACATAT
* *
56129565 CTTACATAATACATAACTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATA
1 CTTATATAATACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATA
56129630 GCCTACATCAA-TTATATAACTTTCATAAAATAAAACTTACATATTTTACATAAAA
66 GCCTACAT-AACTTATATAACTTTCATAAAATAAAACTTACATATTTTACATAAAA
56129685 CTTATATAATACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATA
1 CTTATATAATACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATA
*
56129750 GCCTACATAACTTATATAACTTTCATAAAATACAACTTACATATTTTACATAAAA
66 GCCTACATAACTTATATAACTTTCATAAAATAAAACTTACATATTTTACATAAAA
56129805 CTTATATAATACATAACTTACATAATACAGCACTTACAC
1 CTTATATAATACATAACTTACATAATACAGCACTTACAC
56129844 GACAGAACAC
Statistics
Matches: 155, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
119 2 0.01
120 153 0.99
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (120 bp):
CTTATATAATACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATA
GCCTACATAACTTATATAACTTTCATAAAATAAAACTTACATATTTTACATAAAA
Found at i:56129791 original size:34 final size:33
Alignment explanation
Indices: 56129697--56129829 Score: 97
Period size: 34 Copynumber: 3.8 Consensus size: 33
56129687 TATATAATAC
* * *
56129697 ATAACTTACATAATACAGCACTTACACAACTTAA
1 ATAACTTGCATAATACA-TACTTACATAACTTAA
* *
56129731 ATAACTTGCATAATACATAGCCTACATAACTTAT
1 ATAACTTGCATAATACATA-CTTACATAACTTAA
* **
56129765 ATAACTTTCATAAAATACA-ACTTACATATTTTACA
1 ATAACTTGCAT--AATACATACTTACATAACTTA-A
* **
56129800 TAAAACTTATATAATACATAACTTACATAA
1 -ATAACTTGCATAATACAT-ACTTACATAA
56129830 TACAGCACTT
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
33 1 0.01
34 53 0.68
35 1 0.01
36 23 0.29
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (33 bp):
ATAACTTGCATAATACATACTTACATAACTTAA
Found at i:56129839 original size:16 final size:16
Alignment explanation
Indices: 56129803--56129842 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
56129793 TTTTACATAA
* *
56129803 AACTTATATAATACAT
1 AACTTACATAATACAG
56129819 AACTTACATAATACAG
1 AACTTACATAATACAG
*
56129835 CACTTACA
1 AACTTACA
56129843 CGACAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (16 bp):
AACTTACATAATACAG
Found at i:56130729 original size:10 final size:10
Alignment explanation
Indices: 56130714--56130770 Score: 66
Period size: 10 Copynumber: 5.9 Consensus size: 10
56130704 AAATTTTTAA
56130714 TTTAAAATAT
1 TTTAAAATAT
56130724 TTTAAAATAT
1 TTTAAAATAT
56130734 TTTAAAATACT
1 TTTAAAATA-T
*
56130745 TTT-TAAT-T
1 TTTAAAATAT
*
56130753 TTAAAAAT-T
1 TTTAAAATAT
56130762 TTTAAAATA
1 TTTAAAATA
56130771 AAAATGGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.08
9 11 0.28
10 22 0.55
11 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:56130755 original size:18 final size:16
Alignment explanation
Indices: 56130704--56130766 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 16
56130694 AATACTTTTT
56130704 AAATTTTTAA-TTTAA
1 AAATTTTTAATTTTAA
*
56130719 AATATTTTAAAATATTTTAA
1 AA-ATTTT--TA-ATTTTAA
56130739 AATACTTTTTAATTTTAA
1 AA-A-TTTTTAATTTTAA
56130757 AAATTTTTAA
1 AAATTTTTAA
56130767 AATAAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 2 0.05
16 12 0.30
17 1 0.03
18 10 0.25
19 2 0.05
20 9 0.22
21 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTTTAATTTTAA
Found at i:56132012 original size:19 final size:19
Alignment explanation
Indices: 56131988--56132025 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56131978 GTAAATATTT
*
56131988 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
56132007 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
56132026 CATTTTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:56132356 original size:43 final size:42
Alignment explanation
Indices: 56132224--56132583 Score: 472
Period size: 43 Copynumber: 8.4 Consensus size: 42
56132214 CATTAAAAAA
* * *
56132224 AAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GG
56132267 AAAAGCGCCGCTAAAGGT-ATGGTCTTTAGCGGCGTTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
* * *
56132308 AAAAAGCGTCACTAAAGGTCATGGTCTTTAACGGCGTTAT-TGG
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTT-TGTGG
* * *
56132351 TAAAAGCGCCGCTAAAGATTATGGTCTATAGCGGCGTTTGTGG
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
56132394 TAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
1 --AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
*
56132438 AAAAGGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAG
1 AAAA-GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTG-G
* * * *
56132482 AAAAGCGCGGCTAAATGTCTTGGTCTTTAGTGGCGTTTGTGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
* *
56132524 AAAAAGCGCCGCTAAAGGTCTTAGTCTTTAGCGGCGTTTGTGGG
1 -AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GG
56132568 AAAAGCGCCGCTAAAG
1 AAAAGCGCCGCTAAAG
56132584 TTAGCGACGC
Statistics
Matches: 283, Mismatches: 25, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
41 2 0.01
42 43 0.15
43 191 0.67
44 47 0.17
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG
Found at i:56132465 original size:130 final size:129
Alignment explanation
Indices: 56132224--56132583 Score: 491
Period size: 130 Copynumber: 2.8 Consensus size: 129
56132214 CATTAAAAAA
* * * *
56132224 AAAAACGCCACTAAAAGTC-ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-AT
1 AAAAGCGCCGCTAAATGTCTATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCAT
* *
56132287 GGTCTTTAGCGGCGTTTGTGGAAAAAGCGTCACTAAAGGTCATGGTCTTTAACGGCGTTAT-TG-
66 GGTCTTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTT-TGTGA
56132350 G
129 G
*
56132351 TAAAAGCGCCGCTAAA-GAT-TATGGTCTATAGCGGCGTTTGTGGTAAAAAGCGCCGCTAAAGGT
1 -AAAAGCGCCGCTAAATG-TCTATGGTCTTTAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAGGT
* *
56132414 CATGGTCTTTAGCGGCGTTTGTGGAAAAGGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT
63 CATGGTCTTTAGCGGCGTTTGTGGAAAA-GCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGT
56132479 GAG
127 GAG
* * *
56132482 AAAAGCGCGGCTAAATGTCT-TGGTCTTTAGTGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTT
1 AAAAGCGCCGCTAAATGTCTATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCAT
*
56132546 AGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
66 GGTCTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAG
56132584 TTAGCGACGC
Statistics
Matches: 209, Mismatches: 13, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
127 1 0.00
128 36 0.17
129 74 0.35
130 95 0.45
131 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (129 bp):
AAAAGCGCCGCTAAATGTCTATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCAT
GGTCTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAACGGCGTTTGTGAG
Found at i:56134256 original size:27 final size:28
Alignment explanation
Indices: 56134195--56134257 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
56134185 TAGTTATAAT
*
56134195 AATTCATAAAAAGTGATTAAATATAATTA
1 AATT-ATAAAAAGTGAATAAATATAATTA
*
56134224 AA-TATAAAAAGTGAATATAAT-TTA-TA
1 AATTATAAAAAGTGAATA-AATATAATTA
56134250 AATTATAA
1 AATTATAA
56134258 TTAATATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.13
27 20 0.67
28 4 0.13
29 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (28 bp):
AATTATAAAAAGTGAATAAATATAATTA
Found at i:56139402 original size:24 final size:23
Alignment explanation
Indices: 56139355--56139416 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
56139345 AATCGATTAA
** *
56139355 ATTAAATTATAATTTTTTATAAG
1 ATTAAATTATAATTTTAAAAAAG
*
56139378 ACTTAAAATATAATTTTAAAAAAG
1 A-TTAAATTATAATTTTAAAAAAG
*
56139402 ATTATATTATAATTT
1 ATTAAATTATAATTT
56139417 ATATTTTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (23 bp):
ATTAAATTATAATTTTAAAAAAG
Found at i:56154518 original size:19 final size:19
Alignment explanation
Indices: 56154472--56154518 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
56154462 TCATCAGCTA
56154472 TAGG-CAAATAGATAGCAT
1 TAGGACAAATAGATAGCAT
*
56154490 TAGGATAAATAGATAGCAT
1 TAGGACAAATAGATAGCAT
*
56154509 TATGACAAAT
1 TAGGACAAAT
56154519 TTCCAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (19 bp):
TAGGACAAATAGATAGCAT
Found at i:56158875 original size:4 final size:4
Alignment explanation
Indices: 56158868--56158897 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
56158858 TGCATGTTTG
56158868 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
56158898 GGAACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:56167573 original size:31 final size:29
Alignment explanation
Indices: 56167537--56167611 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
56167527 AATTAAATTA
56167537 AAATTAAAGTTT-TATGTATACATTTGAACC
1 AAATTAAAGTTTATATGTATA-A-TTGAACC
* *
56167567 ACAATTAAGGTTTCATATGTATAATTGTACC
1 A-AATTAAAGTTT-ATATGTATAATTGAACC
*
56167598 AAATTAAAATTTAT
1 AAATTAAAGTTTAT
56167612 TTATTGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.05
30 10 0.26
31 17 0.45
32 1 0.03
33 8 0.21
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (29 bp):
AAATTAAAGTTTATATGTATAATTGAACC
Found at i:56180360 original size:30 final size:31
Alignment explanation
Indices: 56180303--56180360 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
56180293 ATATTTCAAG
**
56180303 TCCCTGTATTTTTTGTTTATTTAAAATTTAA
1 TCCCTGTATTTTTTGTGGATTTAAAATTTAA
* *
56180334 TCCCTTTATTTTTT-TGGATTTGAAATT
1 TCCCTGTATTTTTTGTGGATTTAAAATT
56180361 CAGGTCTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 10 0.43
31 13 0.57
ACGTcount: A:0.22, C:0.10, G:0.09, T:0.59
Consensus pattern (31 bp):
TCCCTGTATTTTTTGTGGATTTAAAATTTAA
Found at i:56181922 original size:2 final size:2
Alignment explanation
Indices: 56181915--56181957 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
56181905 ATACCACCAA
56181915 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
56181957 A
1 A
56181958 ACTAAACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56186900 original size:205 final size:204
Alignment explanation
Indices: 56186436--56187114 Score: 975
Period size: 205 Copynumber: 3.3 Consensus size: 204
56186426 AGCAGTTAAC
*
56186436 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATCTTAAGGCATTCAACT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
* * * * **
56186501 TGCATTTTATATGGTACAATTATCCAAAAGAAATCAAGGCAGAGCAGTGGAACAAT-AAAATCAG
66 TACA-TTTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAAC-ATGAAAATCAG
*
56186565 CAGTTCAATGACAGAAATATTACTAATTTTTGAAACACAAAACACAA-ATGCAATTATACTTTCA
129 CAGTT-AATGACAGAAATATTACTAA-TTTTGATACACAAAACACAAGATGCAATTATACTTTCA
56186629 TCCACTCTGGTTTAT
192 TCCACTCTGG-TT-T
56186644 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
* * *
56186709 TACATCTTATATGGTACAACTATCCAAATGAAAACAAGGGAGAGCAGCAGAACATGAAAATTAGC
66 TACAT-TTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAGC
* *
56186774 AGTTAATGACAGAAATATTGCTAATTTTGATACACAAAACACAAGATGCAATAATAC-TTCAATC
130 AGTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTC-ATC
56186838 CACTCTGGTTT
194 CACTCTGGTTT
*
56186849 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAAAT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
*
56186914 TACATTATATATGGTA-AAATCATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGCAAATCAG
66 TACATT-TATATGGTACAAAT-ATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAG
* *
56186978 CAGTTAATGACGGAAATATTAATAA-TTT--T----AAAACACAAGATGCAATTATACTTTCATC
129 CAGTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTCATC
*
56187036 CATTCTGGTTT
194 CACTCTGGTTT
* * * *
56187047 ATACACAGTTTTCAAGCATTACAAGATAGAAACACCATACCATGCATCCTTATTAAGGCATTCAA
1 AT--ACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAA
56187112 CTT
64 CTT
56187115 TCTAATTTCT
Statistics
Matches: 435, Mismatches: 27, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
198 36 0.08
199 3 0.01
200 59 0.14
202 1 0.00
204 7 0.02
205 141 0.32
206 24 0.06
207 44 0.10
208 120 0.28
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (204 bp):
ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
TACATTTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAGCA
GTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTCATCCA
CTCTGGTTT
Found at i:56191963 original size:33 final size:33
Alignment explanation
Indices: 56191918--56191982 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
56191908 CAAAAACAGA
*
56191918 ACCAATACCAAAACAAAATACACTCTCTCATGT
1 ACCAATACCAAAACAAAATACACTCTCCCATGT
* *
56191951 ACCAATATCAAAACAAAATGCACTCTCCCATG
1 ACCAATACCAAAACAAAATACACTCTCCCATG
56191983 GATAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.31, G:0.05, T:0.20
Consensus pattern (33 bp):
ACCAATACCAAAACAAAATACACTCTCCCATGT
Found at i:56194445 original size:12 final size:12
Alignment explanation
Indices: 56194428--56194460 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
56194418 TCATTGTGTG
56194428 TGTTCTTTTTGT
1 TGTTCTTTTTGT
56194440 TGTTC-TTTTGT
1 TGTTCTTTTTGT
56194451 TGCTTCTTTT
1 TG-TTCTTTT
56194461 AGCATAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (12 bp):
TGTTCTTTTTGT
Found at i:56203213 original size:13 final size:13
Alignment explanation
Indices: 56203195--56203259 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
56203185 AGTTCTTCAT
56203195 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
56203208 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* * * *
56203221 TACTGTGGAAAAA
1 TGCTTTTGAAAAG
** *
56203234 TATTTTTGAGAAG
1 TGCTTTTGAAAAG
56203247 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
56203260 ATTGGTTTAA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:56206937 original size:19 final size:20
Alignment explanation
Indices: 56206894--56206935 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56206884 ATTAAAGAGT
*
56206894 AAATTGATTTTTTTTGTTAA
1 AAATTGATTTTTATTGTTAA
56206914 AAATT-ATTTTCTATTGTTAA
1 AAATTGATTTT-TATTGTTAA
56206934 AA
1 AA
56206936 TTTGGTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
AAATTGATTTTTATTGTTAA
Found at i:56212751 original size:12 final size:12
Alignment explanation
Indices: 56212734--56212758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56212724 ATTTTATAAC
56212734 ATAAATATTGTT
1 ATAAATATTGTT
56212746 ATAAATATTGTT
1 ATAAATATTGTT
56212758 A
1 A
56212759 ATAGCCTCTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:56218715 original size:18 final size:19
Alignment explanation
Indices: 56218677--56218716 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
56218667 GCTTTGAGGA
56218677 TTTGGGTGTTTTAAATTTAT
1 TTTGGGTGTTTTAAA-TTAT
*
56218697 TTTGGGTTTTTTAAA-TAT
1 TTTGGGTGTTTTAAATTAT
56218715 TT
1 TT
56218717 GTCCAAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.62
Consensus pattern (19 bp):
TTTGGGTGTTTTAAATTAT
Found at i:56230424 original size:15 final size:16
Alignment explanation
Indices: 56230404--56230433 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56230394 AATGTTTAAA
56230404 ATATTTTTA-AATTTT
1 ATATTTTTACAATTTT
56230419 ATATTTTTACAATTT
1 ATATTTTTACAATTT
56230434 CTTGTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTTTACAATTTT
Found at i:56231683 original size:3 final size:3
Alignment explanation
Indices: 56231675--56231701 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56231665 GCATTTGAGG
56231675 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
56231702 GAACATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56232345 original size:14 final size:14
Alignment explanation
Indices: 56232326--56232353 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56232316 GCTCCCTGCT
56232326 TCATTGCATGCATG
1 TCATTGCATGCATG
56232340 TCATTGCATGCATG
1 TCATTGCATGCATG
56232354 AATGCATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TCATTGCATGCATG
Found at i:56233880 original size:33 final size:33
Alignment explanation
Indices: 56233843--56233918 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
56233833 GTTGTCAGCC
56233843 TCATCTTCATCGTCGTCATCAACAAATTCGCTA
1 TCATCTTCATCGTCGTCATCAACAAATTCGCTA
* * * *
56233876 TCATCTTCATTGTGGTCGTCAACGAATTCGCTA
1 TCATCTTCATCGTCGTCATCAACAAATTCGCTA
56233909 TCATCTTCAT
1 TCATCTTCAT
56233919 AATCATCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.37
Consensus pattern (33 bp):
TCATCTTCATCGTCGTCATCAACAAATTCGCTA
Found at i:56234243 original size:42 final size:42
Alignment explanation
Indices: 56234178--56234262 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
56234168 CCGAGACGGG
**
56234178 ATCAAACTGGCCATGCTTGCCTGAGCCCCTATTATTATCATC
1 ATCAAACTGGCCATGCTCACCTGAGCCCCTATTATTATCATC
*
56234220 ATCAAACTGGCCATGCTCACCTGAGCTCCTATTATTATCATC
1 ATCAAACTGGCCATGCTCACCTGAGCCCCTATTATTATCATC
56234262 A
1 A
56234263 CCACCATCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (42 bp):
ATCAAACTGGCCATGCTCACCTGAGCCCCTATTATTATCATC
Found at i:56237718 original size:280 final size:280
Alignment explanation
Indices: 56237217--56237739 Score: 1037
Period size: 280 Copynumber: 1.9 Consensus size: 280
56237207 AAAATACTTG
56237217 TTTCTAAGCAGCAAGACACCTCCAGTTAAGTTCTGCAAAATTGTTAGTACGCATGAGAAGTATAT
1 TTTCTAAGCAGCAAGACACCTCCAGTTAAGTTCTGCAAAATTGTTAGTACGCATGAGAAGTATAT
56237282 TCTTCTGTCTCTTTTGAAAGTGCAGCATATCTTAAATGATGAAGAGTCCAAAGAAAGACAAAAAA
66 TCTTCTGTCTCTTTTGAAAGTGCAGCATATCTTAAATGATGAAGAGTCCAAAGAAAGACAAAAAA
56237347 ATGTCATACACCAGTAAAAAAGATCACTTCAGTATGAATCAGGAATATGAATATGCAATTGCAAC
131 ATGTCATACACCAGTAAAAAAGATCACTTCAGTATGAATCAGGAATATGAATATGCAATTGCAAC
*
56237412 AAGGCAGAAGACTATGATCATGCAAAACACAAGATACCAAAGCCTATACACAAAAATATCACTTC
196 AAGGCAGAAGAATATGATCATGCAAAACACAAGATACCAAAGCCTATACACAAAAATATCACTTC
56237477 AGTAAAAAAATGTATGACAT
261 AGTAAAAAAATGTATGACAT
56237497 TTTCTAAGCAGCAAGACACCTCCAGTTAAGTTCTGCAAAATTGTTAGTACGCATGAGAAGTATAT
1 TTTCTAAGCAGCAAGACACCTCCAGTTAAGTTCTGCAAAATTGTTAGTACGCATGAGAAGTATAT
56237562 TCTTCTGTCTCTTTTGAAAGTGCAGCATATCTTAAATGATGAAGAGTCCAAAGAAAGACAAAAAA
66 TCTTCTGTCTCTTTTGAAAGTGCAGCATATCTTAAATGATGAAGAGTCCAAAGAAAGACAAAAAA
56237627 ATGTCATACACCAGTAAAAAAGATCACTTCAGTATGAATCAGGAATATGAATATGCAATTGCAAC
131 ATGTCATACACCAGTAAAAAAGATCACTTCAGTATGAATCAGGAATATGAATATGCAATTGCAAC
56237692 AAGGCAGAAGAATATGATCATGCAAAACACAAGATACCAAAGCCTATA
196 AAGGCAGAAGAATATGATCATGCAAAACACAAGATACCAAAGCCTATA
56237740 AGTTGTAAAA
Statistics
Matches: 242, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
280 242 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (280 bp):
TTTCTAAGCAGCAAGACACCTCCAGTTAAGTTCTGCAAAATTGTTAGTACGCATGAGAAGTATAT
TCTTCTGTCTCTTTTGAAAGTGCAGCATATCTTAAATGATGAAGAGTCCAAAGAAAGACAAAAAA
ATGTCATACACCAGTAAAAAAGATCACTTCAGTATGAATCAGGAATATGAATATGCAATTGCAAC
AAGGCAGAAGAATATGATCATGCAAAACACAAGATACCAAAGCCTATACACAAAAATATCACTTC
AGTAAAAAAATGTATGACAT
Found at i:56238960 original size:19 final size:19
Alignment explanation
Indices: 56238936--56238972 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56238926 CAGACGCATG
56238936 AATAACAAAAACTCGAACC
1 AATAACAAAAACTCGAACC
* *
56238955 AATAACATAATCTCGAAC
1 AATAACAAAAACTCGAAC
56238973 TACATTACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.24, G:0.05, T:0.16
Consensus pattern (19 bp):
AATAACAAAAACTCGAACC
Found at i:56240753 original size:29 final size:30
Alignment explanation
Indices: 56240703--56240771 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
56240693 TCACAAACTT
* *
56240703 AAAATTTAATCCTTATAATTTT-ATTTTTA
1 AAAATTTAATCCTTATAATTTTAAATTTCA
**
56240732 AAAATTTAATCTCTT-TGCTTTTCAAATTTCA
1 AAAATTTAATC-CTTATAATTTT-AAATTTCA
56240763 AAAATTTAA
1 AAAATTTAA
56240772 ATCCAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.48
30 3 0.09
31 14 0.42
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAATTTAATCCTTATAATTTTAAATTTCA
Found at i:56240875 original size:29 final size:29
Alignment explanation
Indices: 56240831--56240886 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
56240821 TTTAAACATT
*
56240831 TAAAAATTAGAAAGACTAAATTCTTAAAAA
1 TAAAAATTACAAAGACTAAATT-TTAAAAA
56240861 TAAAAA-TACAAAGACTAAATTTTAAA
1 TAAAAATTACAAAGACTAAATTTTAAA
56240887 TTTATAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 14 0.56
30 6 0.24
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (29 bp):
TAAAAATTACAAAGACTAAATTTTAAAAA
Found at i:56251412 original size:21 final size:21
Alignment explanation
Indices: 56251383--56251422 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56251373 ATATTTAATG
* *
56251383 TTTATTTTTTATTACTTTAAC
1 TTTAATTTTTATTAATTTAAC
*
56251404 TTTAATTTTTTTTAATTTA
1 TTTAATTTTTATTAATTTA
56251423 GCCCTTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTAATTTTTATTAATTTAAC
Found at i:56253737 original size:2 final size:2
Alignment explanation
Indices: 56253730--56253767 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56253720 TTACTTTACC
56253730 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
56253768 CCTATTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56255718 original size:16 final size:17
Alignment explanation
Indices: 56255688--56255733 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
56255678 GTGTATGTGT
*
56255688 ATATATATGTATATAAAA
1 ATATATAAGTATA-AAAA
56255706 AT-TATAAAGTATAAAAA
1 ATATAT-AAGTATAAAAA
56255723 ATATATAAGTA
1 ATATATAAGTA
56255734 GGTATACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (17 bp):
ATATATAAGTATAAAAA
Found at i:56255729 original size:18 final size:18
Alignment explanation
Indices: 56255696--56255730 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56255686 GTATATATAT
56255696 GTATATAAAAATTATAAA
1 GTATATAAAAATTATAAA
56255714 GTATA-AAAAATATATAA
1 GTATATAAAAAT-TATAA
56255731 GTAGGTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
GTATATAAAAATTATAAA
Found at i:56256008 original size:12 final size:12
Alignment explanation
Indices: 56255987--56256015 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
56255977 ATGAATGAAC
56255987 TAAT-ACAATAA
1 TAATAACAATAA
56255998 TAATAACAATAA
1 TAATAACAATAA
56256010 TAATAA
1 TAATAA
56256016 TAACTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (12 bp):
TAATAACAATAA
Found at i:56259874 original size:17 final size:17
Alignment explanation
Indices: 56259843--56259895 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
56259833 AAAATTTTAG
*
56259843 AAAATATATATAAAATCT
1 AAAATATATAAAAAAT-T
56259861 AAAA-ATATAAAAAATT
1 AAAATATATAAAAAATT
* *
56259877 -AAATTTATTAAAAATT
1 AAAATATATAAAAAATT
56259893 AAA
1 AAA
56259896 TCACATCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 12 0.40
18 4 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATATAAAAAATT
Found at i:56259879 original size:16 final size:16
Alignment explanation
Indices: 56259843--56259895 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
56259833 AAAATTTTAG
*
56259843 AAAATATATATAAAATCT
1 AAAA-ATATAAAAAAT-T
56259861 AAAAATATAAAAAATT
1 AAAAATATAAAAAATT
** *
56259877 AAATTTATTAAAAATT
1 AAAAATATAAAAAATT
56259893 AAA
1 AAA
56259896 TCACATCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 17 0.55
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATATAAAAAATT
Found at i:56260838 original size:2 final size:2
Alignment explanation
Indices: 56260831--56260857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56260821 ACTTTTCTGC
56260831 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56260858 AAGCTTGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56279817 original size:17 final size:18
Alignment explanation
Indices: 56279778--56279827 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
56279768 AAAAATGTAT
56279778 TTATAAAATATAAAAAAC
1 TTATAAAATATAAAAAAC
* * *
56279796 ATATAAATTGTAAAAAA-
1 TTATAAAATATAAAAAAC
*
56279813 TTATAAAAAATAAAA
1 TTATAAAATATAAAA
56279828 GTTACAAAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
TTATAAAATATAAAAAAC
Found at i:56285736 original size:50 final size:50
Alignment explanation
Indices: 56285659--56285765 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 50
56285649 GCATTAATAT
* * *
56285659 TTTCTATCAATTGTGCATATAATTTTGATTGGTATAATAATAAATTTAGC
1 TTTCAATCAATTGTGCATATAATTTTGATTGATATAATAACAAATTTAGC
*
56285709 TTTCAATCAATTGTGCATATAATTTTGATTGATATAATAACAAATTTAGT
1 TTTCAATCAATTGTGCATATAATTTTGATTGATATAATAACAAATTTAGC
56285759 TTTCAAT
1 TTTCAAT
56285766 GTTTATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (50 bp):
TTTCAATCAATTGTGCATATAATTTTGATTGATATAATAACAAATTTAGC
Found at i:56292504 original size:25 final size:25
Alignment explanation
Indices: 56292476--56292540 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
56292466 ACAAATAAAC
56292476 AAATAAAGGCTAAACGAAGGTGTTT
1 AAATAAAGGCTAAACGAAGGTGTTT
56292501 AAATAAAGGCTAAACGAAGGTGTTT
1 AAATAAAGGCTAAACGAAGGTGTTT
56292526 AAATAAAGGCTAAAC
1 AAATAAAGGCTAAAC
56292541 CTTTTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.22
Consensus pattern (25 bp):
AAATAAAGGCTAAACGAAGGTGTTT
Found at i:56292803 original size:31 final size:31
Alignment explanation
Indices: 56292745--56292803 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
56292735 GAAAAAAATT
* *
56292745 CTTATATGAGCATATCTAAAAATGTTTGATC
1 CTTATATGACCATATCTAAAAAGGTTTGATC
*
56292776 CTTATATGACCA-ATTCTTAAAAGGTTTG
1 CTTATATGACCATA-TCTAAAAAGGTTTG
56292804 GCTCAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (31 bp):
CTTATATGACCATATCTAAAAAGGTTTGATC
Found at i:56293270 original size:7 final size:7
Alignment explanation
Indices: 56293258--56293282 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56293248 TTCAGTAAGT
56293258 TTTTAAA
1 TTTTAAA
56293265 TTTTAAA
1 TTTTAAA
56293272 TTTTAAA
1 TTTTAAA
56293279 TTTT
1 TTTT
56293283 TTCTGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:56296392 original size:125 final size:125
Alignment explanation
Indices: 56296170--56296408 Score: 442
Period size: 125 Copynumber: 1.9 Consensus size: 125
56296160 GTCACTTTTC
56296170 CTTCTTATCTCTCTTCCCCTTTGCACTCCCTTTAGTTCTGGATTCATTTCAACTTACTTGCATGT
1 CTTCTTATCTCTCTTCCCCTTTGCACTCCCTTTAGTTCTGGATTCATTTCAACTTACTTGCATGT
56296235 GTTTATTTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCCATCTGTCTTCCCCTTTG
66 GTTTATTTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCCATCTGTCTTCCCCTTTG
* * *
56296295 CTTCTTATCTCTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGTATGT
1 CTTCTTATCTCTCTTCCCCTTTGCACTCCCTTTAGTTCTGGATTCATTTCAACTTACTTGCATGT
*
56296360 GTTTATTTATTCAGATTTTAAACCCAATTGAGTCACCAAGTCCATCTGT
66 GTTTATTTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCCATCTGT
56296409 GAAGAAGTGT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (125 bp):
CTTCTTATCTCTCTTCCCCTTTGCACTCCCTTTAGTTCTGGATTCATTTCAACTTACTTGCATGT
GTTTATTTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCCATCTGTCTTCCCCTTTG
Found at i:56301710 original size:5 final size:5
Alignment explanation
Indices: 56301700--56301724 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56301690 ATATCAACAT
56301700 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
56301725 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:56302726 original size:38 final size:38
Alignment explanation
Indices: 56302675--56302751 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
56302665 TTAGGTGCAT
56302675 TGGAATTTTAGAATCTCAATTTTACCGACACAAATAAA
1 TGGAATTTTAGAATCTCAATTTTACCGACACAAATAAA
56302713 TGGAATTTTAGAATCTCAATTTTACCGACACAAATAAA
1 TGGAATTTTAGAATCTCAATTTTACCGACACAAATAAA
56302751 T
1 T
56302752 TGTTAAGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (38 bp):
TGGAATTTTAGAATCTCAATTTTACCGACACAAATAAA
Found at i:56313177 original size:31 final size:31
Alignment explanation
Indices: 56313141--56313206 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
56313131 TTAGTCCCTG
*
56313141 AACTTGACAATTGTTCCCATATTGGGGCCTA
1 AACTTGACAATTGTTCCCACATTGGGGCCTA
* *
56313172 AACTTGACAATTGTTCCCACATTGTGGCCTG
1 AACTTGACAATTGTTCCCACATTGGGGCCTA
56313203 AACT
1 AACT
56313207 ATAAGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (31 bp):
AACTTGACAATTGTTCCCACATTGGGGCCTA
Found at i:56313658 original size:15 final size:15
Alignment explanation
Indices: 56313638--56313674 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
56313628 TCAAGTCTGC
56313638 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
* *
56313653 AAAAAAAGAAACAAG
1 AAAAAAAGAAAAAAA
56313668 AAAAAAA
1 AAAAAAA
56313675 CATTACCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:56313714 original size:4 final size:4
Alignment explanation
Indices: 56313698--56313734 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
56313688 CTTATGAGAC
*
56313698 CATA CATA TATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA C
56313735 CTTAGAGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:56314904 original size:2 final size:2
Alignment explanation
Indices: 56314897--56314921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56314887 CCTGAAAATT
56314897 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
56314922 TTAATTTTTC
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:56316159 original size:35 final size:35
Alignment explanation
Indices: 56316118--56316232 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 35
56316108 TCTTAAATTA
56316118 AAATTAAAATATTAATGACATAAATCAAATGAGTC
1 AAATTAAAATATTAATGACATAAATCAAATGAGTC
* ** * * *
56316153 AAATT-AAATAATTCCAT--CGAT-TTTAAAATAAGTAA
1 AAATTAAAAT-ATT-AATGAC-ATAAATCAAATGAGT-C
56316188 AAGCATTAAAATATTAATGACATAAATCAAATGAGTC
1 AA--ATTAAAATATTAATGACATAAATCAAATGAGTC
56316225 AAATTAAA
1 AAATTAAA
56316233 TAATTCCATC
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
34 13 0.22
35 18 0.31
36 4 0.07
37 10 0.17
38 13 0.22
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.30
Consensus pattern (35 bp):
AAATTAAAATATTAATGACATAAATCAAATGAGTC
Found at i:56316196 original size:72 final size:72
Alignment explanation
Indices: 56316120--56316263 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
56316110 TTAAATTAAA
*
56316120 ATTAAAATATTAATGACATAAATCAAATGAGTCAAATTAAATAATTCCATCGATTTTAAAATAAG
1 ATTAAAATATTAATGACATAAATCAAATGAGTCAAATTAAATAATTCCATCGATTTCAAAATAAG
56316185 TAAAAGC
66 TAAAAGC
56316192 ATTAAAATATTAATGACATAAATCAAATGAGTCAAATTAAATAATTCCATCGATTTCAAAATAAG
1 ATTAAAATATTAATGACATAAATCAAATGAGTCAAATTAAATAATTCCATCGATTTCAAAATAAG
56316257 TAAAAGC
66 TAAAAGC
56316264 TAACGTTTTG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.30
Consensus pattern (72 bp):
ATTAAAATATTAATGACATAAATCAAATGAGTCAAATTAAATAATTCCATCGATTTCAAAATAAG
TAAAAGC
Found at i:56319397 original size:18 final size:18
Alignment explanation
Indices: 56319376--56319410 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56319366 GAACGAACAG
*
56319376 AAAAGAAAAACCGAAAGT
1 AAAAAAAAAACCGAAAGT
*
56319394 AAAAAAAAAAGCGAAAG
1 AAAAAAAAAACCGAAAG
56319411 ATGCAGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAACCGAAAGT
Found at i:56320320 original size:22 final size:21
Alignment explanation
Indices: 56320293--56320349 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
56320283 TACTCTAATT
56320293 AAATATTAAAATAATGTTAAA
1 AAATATTAAAATAATGTTAAA
* *
56320314 ATAATA-TAATATAAATTTTAAA
1 A-AATATTAAAAT-AATGTTAAA
*
56320336 AAA-ATAAAAATAAT
1 AAATATTAAAATAAT
56320350 ATGGGTGGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATATTAAAATAATGTTAAA
Found at i:56347293 original size:54 final size:51
Alignment explanation
Indices: 56347214--56347329 Score: 135
Period size: 55 Copynumber: 2.2 Consensus size: 51
56347204 ATAAAAAAAT
* * * *
56347214 AAAAAAAATTTGGGTGCTGGCCTATCACTGGCCGGCACCACCAGTACGAAAATGA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCAGCACCA-C--TACGAAAA-CA
* *
56347269 AAAAAAAATTTAGGTGTTGG-CTATCAATGGCCAGCACTACTACGAAAACA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCAGCACCACTACGAAAACA
56347319 AAAAAAAATTT
1 AAAAAAAATTT
56347330 CGTTTTCGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 12 0.22
51 8 0.15
53 1 0.02
54 16 0.29
55 18 0.33
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (51 bp):
AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCAGCACCACTACGAAAACA
Found at i:56347510 original size:53 final size:53
Alignment explanation
Indices: 56347437--56347541 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
56347427 TTTTTTTTTT
*
56347437 GTTTTCGTACAGGTGGTGCCGGCCATTGACAGGCCAACACCAAAAAAAAATTA
1 GTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAACACCAAAAAAAAATTA
* *
56347490 GTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCCAAAAAAAATT
1 GTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAACACCAAAAAAAAATT
56347542 TTCTTTTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (53 bp):
GTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAACACCAAAAAAAAATTA
Found at i:56347565 original size:60 final size:58
Alignment explanation
Indices: 56347327--56347599 Score: 227
Period size: 60 Copynumber: 4.9 Consensus size: 58
56347317 CAAAAAAAAA
* * * * *
56347327 TTTCGTTTTCGTACTGATGGTGTCGGCCATTGACAGGTCAGCACC--AAAAAA-TTTT
1 TTTCGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCAAAAAAAATTTTT
** * * * *
56347382 TTTCGTTTTCGTAC---TAATGCAG-CAATTGACAGGCCAACACC---AAAATTTTTT
1 TTTCGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCAAAAAAAATTTTT
* * *
56347433 TTTTGTTTTCGTACAGGTGGTGCCGGCCATTGACAGGCCAACACCAAAAAAAA-----
1 TTTCGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCAAAAAAAATTTTT
* *
56347486 ATTAGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCCAAAAAAAATTTTCT
1 TTTCGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCA-CCAAAAAAAATTTT-T
* * *
56347546 TTTCGTTTTCGTACTGGTGGTGCC-AGCCATTGATAAGCCAGCACCACAAAAAAA
1 TTTCGTTTTCGTACAGGTGGTGCCGA-CCATTGACAGGCCAGCACCA-AAAAAAA
56347600 ATGTAACACC
Statistics
Matches: 178, Mismatches: 23, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
50 4 0.02
51 33 0.19
52 4 0.02
53 39 0.22
54 15 0.08
55 32 0.18
58 4 0.02
59 4 0.02
60 43 0.24
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (58 bp):
TTTCGTTTTCGTACAGGTGGTGCCGACCATTGACAGGCCAGCACCAAAAAAAATTTTT
Found at i:56348308 original size:23 final size:23
Alignment explanation
Indices: 56348257--56348308 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
56348247 TTCACACCAA
*
56348257 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
*
56348280 AATTTGGGCAGCATATAA-ACAAC
1 AATTTGGACAGCATA-AATACAAC
*
56348303 AGTTTG
1 AATTTG
56348309 AGCAACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:56348367 original size:35 final size:34
Alignment explanation
Indices: 56348310--56348384 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
56348300 AACAGTTTGA
*
56348310 GCAACATTTTACACCAAAACTGGACAGCATATAT
1 GCAACATTTAACACCAAAACTGGACAGCATATAT
*
56348344 GCAACATTTAAGCATCAAAACTGGACAGCATATAT
1 GCAACATTTAA-CACCAAAACTGGACAGCATATAT
*
56348379 GTAACA
1 GCAACA
56348385 AATTGGGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 10 0.27
35 27 0.73
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (34 bp):
GCAACATTTAACACCAAAACTGGACAGCATATAT
Found at i:56348417 original size:47 final size:47
Alignment explanation
Indices: 56348348--56348437 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
56348338 ATATATGCAA
56348348 CATTTAAGCATCAAAACTGGACAGCATATATGTAACAAATTGGGCAG
1 CATTTAAGCATCAAAACTGGACAGCATATATGTAACAAATTGGGCAG
*
56348395 CATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
1 CATTTAAGCATCAAAACTGGACAGCATATATGTAACAAATTGG
56348438 TCCAACTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (47 bp):
CATTTAAGCATCAAAACTGGACAGCATATATGTAACAAATTGGGCAG
Found at i:56348419 original size:24 final size:24
Alignment explanation
Indices: 56348348--56348421 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
56348338 ATATATGCAA
*
56348348 CATTTAAGCATCAAAACTGGACAG
1 CATTTAAGCATCAAAATTGGACAG
* * * * *
56348372 CATATATGTAAC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGACAG
56348395 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGACAG
56348419 CAT
1 CAT
56348422 ATATGTAACA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (24 bp):
CATTTAAGCATCAAAATTGGACAG
Found at i:56348433 original size:24 final size:23
Alignment explanation
Indices: 56348365--56348437 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
56348355 GCATCAAAAC
56348365 TGGACAGCATATATGTAACAAAT
1 TGGACAGCATATATGTAACAAAT
* * * * *
56348388 TGGGCAGCATTTAAGCATCAAAAT
1 TGGACAGCATATATGTAAC-AAAT
56348412 TGGACAGCATATATGTAACAAAT
1 TGGACAGCATATATGTAACAAAT
56348435 TGG
1 TGG
56348438 TCCAACTCAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (23 bp):
TGGACAGCATATATGTAACAAAT
Found at i:56349842 original size:29 final size:30
Alignment explanation
Indices: 56349783--56349840 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56349773 TCCGAGCCTT
*
56349783 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
56349813 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
56349841 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:56350071 original size:13 final size:13
Alignment explanation
Indices: 56350053--56350083 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56350043 TTCCAGCAAC
56350053 TATGAATTTATTT
1 TATGAATTTATTT
56350066 TATGAATTTATTT
1 TATGAATTTATTT
*
56350079 GATGA
1 TATGA
56350084 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:56350253 original size:50 final size:50
Alignment explanation
Indices: 56350178--56350420 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
56350168 ATTTGGGTAA
56350178 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
56350228 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
56350278 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
56350328 AGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
56350378 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
56350421 TGTTATTATC
Statistics
Matches: 174, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 141 0.81
51 33 0.19
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:56352121 original size:43 final size:43
Alignment explanation
Indices: 56352055--56352182 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 43
56352045 AGCTCGTACA
*
56352055 ATGTCA-TCGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGTCACT-GTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
56352098 ATGTCACTGTCCCAGACAG-GGTCTTACACGTAATCAAATATCG
1 ATGTCACTGTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* * *
56352141 ATGCCGAC-GTCCCAGACGTGGTCTTACACGAAAACACATATC
1 ATGTC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATC
56352183 AGAATCTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.01
43 70 0.93
44 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGTCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:56353108 original size:28 final size:28
Alignment explanation
Indices: 56353068--56353124 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
56353058 TATGTTTGTT
56353068 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
56353096 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
56353124 T
1 T
56353125 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:56353335 original size:14 final size:15
Alignment explanation
Indices: 56353316--56353344 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56353306 TCACGAAACT
56353316 TTCACACAT-ATAAA
1 TTCACACATAATAAA
56353330 TTCACACATAATAAA
1 TTCACACATAATAAA
56353345 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:56353554 original size:53 final size:55
Alignment explanation
Indices: 56353492--56353644 Score: 140
Period size: 50 Copynumber: 2.8 Consensus size: 55
56353482 AAGAAAATTC
*
56353492 TTTTCGTTTTCGTACTGGTGGCGCCAGCCATTGATAGGTCAGCACCCAAAAA-AAA
1 TTTTAGTTTTCGTACTGGTGG-GCCAGCCATTGATAGGTCAGCACCCAAAAAGAAA
* * *
56353547 -TTT-GTTTTCGTACTGAT--GCCGGCAATTGATAGG-CTAGCACCCAAAAAGAAA
1 TTTTAGTTTTCGTACTGGTGGGCCAGCCATTGATAGGTC-AGCACCCAAAAAGAAA
* * * *
56353598 TTTTTAATTTTTGTACTAGTGGTGCCAACCATTGATAGGAT-AGCACC
1 -TTTTAGTTTTCGTACTGGTGG-GCCAGCCATTGATAGG-TCAGCACC
56353645 TAATTTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
49 1 0.01
50 26 0.33
51 3 0.04
53 16 0.21
54 13 0.17
57 19 0.24
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (55 bp):
TTTTAGTTTTCGTACTGGTGGGCCAGCCATTGATAGGTCAGCACCCAAAAAGAAA
Found at i:56353643 original size:107 final size:106
Alignment explanation
Indices: 56353434--56353644 Score: 241
Period size: 107 Copynumber: 2.0 Consensus size: 106
56353424 GGGCTGTTAC
* * * * **
56353434 AAAAAATTTTGTTTTCGTGCTGTTGCCGGCCATTGACAGGCCAACAAAAAGAAAATTCTTTTCGT
1 AAAAAAATTTGTTTTCGTACTGATGCCGGCAATTGACAGGCCAACAAAAAGAAAATTCTTTTAAT
* *
56353499 TTTCGTACTGGTGGCGCCAGCCATTGATAGGTCAGCACCCA
66 TTTCGTACTAGTGGCGCCAACCATTGATAGGTCAGCACCCA
* *
56353540 AAAAAAATTTGTTTTCGTACTGATGCCGGCAATTGATAGGCTAGCACCCAAAAAG-AAA-T-TTT
1 AAAAAAATTTGTTTTCGTACTGATGCCGGCAATTGACAGGC---CA-ACAAAAAGAAAATTCTTT
* *
56353602 TAATTTTTGTACTAGTGGTGCCAACCATTGATAGGAT-AGCACC
62 TAATTTTCGTACTAGTGGCGCCAACCATTGATAGG-TCAGCACC
56353645 TAATTTTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
106 36 0.41
107 38 0.43
108 2 0.02
109 5 0.06
110 7 0.08
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (106 bp):
AAAAAAATTTGTTTTCGTACTGATGCCGGCAATTGACAGGCCAACAAAAAGAAAATTCTTTTAAT
TTTCGTACTAGTGGCGCCAACCATTGATAGGTCAGCACCCA
Found at i:56353734 original size:53 final size:53
Alignment explanation
Indices: 56353648--56353937 Score: 272
Period size: 53 Copynumber: 5.4 Consensus size: 53
56353638 TAGCACCTAA
* *
56353648 TTTTTTTTT-GTTTTCGTACTAGATGTGCTGGCCATTGACAGGCCAGCACCAAATT
1 TTTTTTTTTCGTTTTCGTACT--A-GTGCCGACCATTGACAGGCCAGCACCAAATT
* * * *
56353703 TTTTTTTTTCGTTTTTGTACT-GCTACCGGCCATTGACAGGTCAGCACCAAAAAATGT
1 TTTTTTTTTCGTTTTCGTACTAG-TGCCGACCATTGACAGGCCAGCACC---AAAT-T
* * * *
56353760 TTTTTTTTT-GTTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCCAATT
1 TTTTTTTTTCGTTTTCGTAC---TAGTGCCGACCATTGACAGGCCAGCACCAAATT
* * * *
56353815 TTTTTTTTTCGTTTTCATACTAGTGCCGACCATTGATAGGTCAGCACCTAAA-A
1 TTTTTTTTTCGTTTTCGTACTAGTGCCGACCATTGACAGGCCAGCACC-AAATT
* *
56353868 TTTTTTTTTCGTTTTCGTACTAGTGCCCACCATTGACAGGCCAACACC-AA--
1 TTTTTTTTTCGTTTTCGTACTAGTGCCGACCATTGACAGGCCAGCACCAAATT
56353918 TTTTTTTTT-GTTTTCGTACT
1 TTTTTTTTTCGTTTTCGTACT
56353938 GGTGGTGTTG
Statistics
Matches: 199, Mismatches: 24, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
49 11 0.06
50 9 0.05
51 2 0.01
52 1 0.01
53 88 0.44
54 2 0.01
55 19 0.10
56 35 0.18
57 10 0.05
59 21 0.11
60 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (53 bp):
TTTTTTTTTCGTTTTCGTACTAGTGCCGACCATTGACAGGCCAGCACCAAATT
Found at i:56353801 original size:112 final size:106
Alignment explanation
Indices: 56353648--56353926 Score: 328
Period size: 112 Copynumber: 2.6 Consensus size: 106
56353638 TAGCACCTAA
* *
56353648 TTTTTTTTTGTTTTCGTACTAGATGTGCTGGCCATTGACAGGCCAGCACCAAATTTTTTTTTTTC
1 TTTTTTTTTGTTTTCGTACT-G-TGTGCCGACCATTGACAGGCCAGCACC-AATTTTTTTTTTTC
** *
56353713 GTTTTTGTACT-GCTACCGGCCATTGACAGGTCAGCACCAAAAAATGT
63 GTTTTCATACTAG-TACCGACCATTGACAGGTCAGCACC-AAAAA--T
* *
56353760 TTTTTTTTTGTTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCCAATTTTTTTTTTTC
1 TTTTTTTTTGTTTTCGTACT-GT-GTGCCGACCATTGACAGGCCAGCA-CCAATTTTTTTTTTTC
* * *
56353825 GTTTTCATACTAGTGCCGACCATTGATAGGTCAGCACCTAAAAT
63 GTTTTCATACTAGTACCGACCATTGACAGGTCAGCACCAAAAAT
* * * *
56353869 TTTTTTTTCGTTTTCGTACT-AGTGCCCACCATTGACAGGCCAACACCAATTTTTTTTT
1 TTTTTTTTTGTTTTCGTACTGTGTGCCGACCATTGACAGGCCAGCACCAATTTTTTTTT
56353927 GTTTTCGTAC
Statistics
Matches: 147, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
105 13 0.09
106 20 0.14
109 20 0.14
111 5 0.03
112 86 0.59
113 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.41
Consensus pattern (106 bp):
TTTTTTTTTGTTTTCGTACTGTGTGCCGACCATTGACAGGCCAGCACCAATTTTTTTTTTTCGTT
TTCATACTAGTACCGACCATTGACAGGTCAGCACCAAAAAT
Found at i:56353821 original size:165 final size:157
Alignment explanation
Indices: 56353605--56353944 Score: 364
Period size: 165 Copynumber: 2.1 Consensus size: 157
56353595 AAATTTTTAA
* * * * * *
56353605 TTTTTGTACTAGTGGTGCCAACCATTGATAGGATAGCACCTAA-TTTTTTTTT-GTTTTCGTACT
1 TTTTCGTACTGGTGGTGCCAACCATTAACAGGATAGCACCCAATTTTTTTTTTCGTTTTCATACT
* * * * *
56353668 AGATGTGCTGGCCATTGACAGGCCAGCACC-AAATTTTTTTTTTTCGTTTTTGTACT-GCTACCG
66 --A-GTGCCGACCATTGACAGGCCAGCACCTAAA-ATTTTTTTTTCGTTTTCGTACTAG-TACCC
* * *
56353731 GCCATTGACAGGTCAGCACCAAAAAATGTTTTTTTTTTG
126 ACCATTGACAGGCCAACACC----AA---TTTTTTTTTG
* *
56353770 TTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCCAATTTTTTTTTTTCGTTTTCATAC
1 TTTTCGTACTGGTGGTGCCAACCATTAACAGGATAGCACCCAA-TTTTTTTTTTCGTTTTCATAC
* * *
56353835 TAGTGCCGACCATTGATAGGTCAGCACCTAAAATTTTTTTTTCGTTTTCGTACTAGTGCCCACCA
65 TAGTGCCGACCATTGACAGGCCAGCACCTAAAATTTTTTTTTCGTTTTCGTACTAGTACCCACCA
56353900 TTGACAGGCCAACACCAATTTTTTTTTG
130 TTGACAGGCCAACACCAATTTTTTTTTG
56353928 TTTTCGTACTGGTGGTG
1 TTTTCGTACTGGTGGTG
56353945 TTGGGCATTG
Statistics
Matches: 151, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
158 27 0.18
161 2 0.01
165 98 0.65
166 5 0.03
167 9 0.06
168 10 0.07
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (157 bp):
TTTTCGTACTGGTGGTGCCAACCATTAACAGGATAGCACCCAATTTTTTTTTTCGTTTTCATACT
AGTGCCGACCATTGACAGGCCAGCACCTAAAATTTTTTTTTCGTTTTCGTACTAGTACCCACCAT
TGACAGGCCAACACCAATTTTTTTTTG
Found at i:56354132 original size:104 final size:107
Alignment explanation
Indices: 56354002--56354200 Score: 242
Period size: 110 Copynumber: 1.9 Consensus size: 107
56353992 TTCGTACTGA
* * *
56354002 TGGTGCCAGTCATTAACAGACCAGCACC-TAA-TTTTTTTTTCA-TTTTCGTACCGGTGATGCCG
1 TGGTGCCAGTCATTAACAGACAAGCACCAAAACTTTTTTTTTCAGTTTTCGTACCGATGATGCCG
*
56354064 GCCATTAATAGGCCAGCACCCAAAAAAAATTTGTTTTCCTAC
66 GCCATTAACAGGCCAGCACCCAAAAAAAATTTGTTTTCCTAC
* * * * * *
56354106 TGGTGCCGGTCATTGACAGGCAAGCACCAAAAAAACTTTTTTTTTTAGTTTTCGTACTGATGGTG
1 TGGTGCCAGTCATTAACAGACAAGCACC---AAAACTTTTTTTTTCAGTTTTCGTACCGATGATG
* *
56354171 TCGGCCATTAACAGGCTAGCACCCAAAAAA
63 CCGGCCATTAACAGGCCAGCACCCAAAAAA
56354201 TTTTATTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
104 24 0.31
108 2 0.03
109 10 0.13
110 41 0.53
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (107 bp):
TGGTGCCAGTCATTAACAGACAAGCACCAAAACTTTTTTTTTCAGTTTTCGTACCGATGATGCCG
GCCATTAACAGGCCAGCACCCAAAAAAAATTTGTTTTCCTAC
Found at i:56354533 original size:56 final size:54
Alignment explanation
Indices: 56354367--56354575 Score: 174
Period size: 55 Copynumber: 3.8 Consensus size: 54
56354357 AAAAAATTTC
* * * *
56354367 TTTTTGTTTTTGTACTGGTGGTGCCGGCCATTGACAGGTCAGTATCCAAATTTTTT
1 TTTTTGTTTTTGTACTGGTTGTGCCGGCCATTGACA-GCCAGCA-CCCAATTTTTT
** * * * *
56354423 TTTTCATTTTCGTACTGG-TGCTGCCAGCCATTTACTAGCCTGCACCCTAA-TTTTT
1 TTTTTGTTTTTGTACTGGTTG-TGCCGGCCATTGAC-AGCCAGCACCC-AATTTTTT
**
56354478 TTTTTGTTTTTGTACTGGTTGTGTTGGCCATTGACAGACCAGCACCCAA--TTTT
1 TTTTTGTTTTTGTACTGGTTGTGCCGGCCATTGACAG-CCAGCACCCAATTTTTT
** * * *
56354531 TTTTCATTTTTGTGCTGGTGGTGCCGGCCATTGATAGGCCAGCAC
1 TTTTTGTTTTTGTACTGGTTGTGCCGGCCATTGACA-GCCAGCAC
56354576 AAGAAAAAAC
Statistics
Matches: 122, Mismatches: 25, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
53 40 0.33
54 5 0.04
55 41 0.34
56 35 0.29
57 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.42
Consensus pattern (54 bp):
TTTTTGTTTTTGTACTGGTTGTGCCGGCCATTGACAGCCAGCACCCAATTTTTT
Found at i:56354560 original size:53 final size:54
Alignment explanation
Indices: 56354373--56354575 Score: 212
Period size: 53 Copynumber: 3.7 Consensus size: 54
56354363 TTTCTTTTTG
* * *
56354373 TTTTTGTACTGGTGGTGCCGGCCATTGACAGGTCAGTATCCAAATTTTTTTTTTCA
1 TTTTTGTACTGGTGGTGCCGGCCATTGACAGGCCAGCA-CCCAA-TTTTTTTTTCA
* * * * * **
56354429 TTTTCGTACTGGTGCTGCCAGCCATTTACTA-GCCTGCACCCTAATTTTTTTTTTG
1 TTTTTGTACTGGTGGTGCCGGCCATTGAC-AGGCCAGCACCC-AATTTTTTTTTCA
* ** *
56354484 TTTTTGTACTGGTTGTGTTGGCCATTGACAGACCAGCACCCAA-TTTTTTTTCA
1 TTTTTGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAATTTTTTTTTCA
* *
56354537 TTTTTGTGCTGGTGGTGCCGGCCATTGATAGGCCAGCAC
1 TTTTTGTACTGGTGGTGCCGGCCATTGACAGGCCAGCAC
56354576 AAGAAAAAAC
Statistics
Matches: 117, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
53 41 0.35
54 3 0.03
55 41 0.35
56 31 0.26
57 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (54 bp):
TTTTTGTACTGGTGGTGCCGGCCATTGACAGGCCAGCACCCAATTTTTTTTTCA
Found at i:56354753 original size:56 final size:56
Alignment explanation
Indices: 56354641--56354807 Score: 160
Period size: 55 Copynumber: 3.0 Consensus size: 56
56354631 AAAAAATTTA
* * * * * * *
56354641 GTTTTAGTACTGGTGGTGCCGACCATTGACAAGTCGGCACCTAACA-TTTTTTTTTC
1 GTTTTA-TAATGGTGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTTTC
* *
56354697 GTTTTATAATGGTGGTGCCGGCCATTGATAGGCCAGCACCCAAAATTTTTTTTTTC
1 GTTTTATAATGGTGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTTTC
* * * * *
56354753 GTTTT-T-GTGTTGGTGCAGGCCGTTGACAGGCCAGCGCCAAAAAAGTTTTTTTTTT
1 GTTTTATAATGGTGGTGCCGGCCATTGACAGGCCAGCACC-AAAAA-TTTTTTTTTT
56354808 ATTTTCGTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
54 26 0.28
55 36 0.39
56 31 0.33
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (56 bp):
GTTTTATAATGGTGGTGCCGGCCATTGACAGGCCAGCACCAAAAATTTTTTTTTTC
Found at i:56354784 original size:54 final size:58
Alignment explanation
Indices: 56354687--56354807 Score: 151
Period size: 54 Copynumber: 2.2 Consensus size: 58
56354677 GCACCTAACA
* * *
56354687 TTTTTTTTTCGTTTTATAATGGTGGTGCCGGCCATTGATAGGCCAGCACC-CAAAA-T
1 TTTTTTTTTCGTTTTATAATGGTGGTGCAGGCCATTGACAGGCCAGCACCAAAAAAGT
* * * *
56354743 TTTTTTTTTCGTTTT-T-GTGTTGGTGCAGGCCGTTGACAGGCCAGCGCCAAAAAAGT
1 TTTTTTTTTCGTTTTATAATGGTGGTGCAGGCCATTGACAGGCCAGCACCAAAAAAGT
56354799 TTTTTTTTT
1 TTTTTTTTT
56354808 ATTTTCGTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 26 0.46
55 5 0.09
56 25 0.45
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.42
Consensus pattern (58 bp):
TTTTTTTTTCGTTTTATAATGGTGGTGCAGGCCATTGACAGGCCAGCACCAAAAAAGT
Found at i:56356407 original size:53 final size:50
Alignment explanation
Indices: 56356305--56356682 Score: 230
Period size: 53 Copynumber: 7.1 Consensus size: 50
56356295 AATAAATAAC
*
56356305 AAAAAAA-TTGGGTGCTGGCCTGTAAATGACCGACACCACCAGTACGAAAACGGA
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGACCG----CACCAGTACGAAAAC-GA
* * *
56356359 AAAAAAATTTTGGGTGCTGGCCTGTGAATGACCTGCACCAGTAAGAAAAAGA
1 AAAAAAA-TTTGGGTGCTGGCCTGTCAATGACC-GCACCAGTACGAAAACGA
*
56356411 AAAAAAATTT-GGTGCTAGCCTGTCAAT-AGCCGGCACCGCCAGTACGAAAAC-A
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGA-CC-GCA---CCAGTACGAAAACGA
* * * * *
56356463 TAAAAAATTTTGGGTGCTGGCCTGTCAATGGTCGGCACCAATACGAAAATGA
1 -AAAAAAATTTGGGTGCTGGCCTGTCAAT-GACCGCACCAGTACGAAAACGA
** * * * *
56356515 AAAAAAA-AAGGGTTCTGGCATGTCAA-AAGCCAGCACCACCAATACGAAAACGAAA
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGA-CC-G---CACCAGTACGAAAACG--A
* * * * * * *
56356570 AAAAAAATTTGAGCGATGGCCTATCAATGGCCGACACCATTACGAAAATGA
1 AAAAAAATTTGGGTGCTGGCCTGTCAATGACCG-CACCAGTACGAAAACGA
* *
56356621 AAAAAAATTTTGGGTGCTGGCCTGTTAATGGCCGGCACCACCAGTAC-AAAAGCGA
1 AAAAAAA-TTTGGGTGCTGGCCTGTCAATGACC-G---CACCAGTACGAAAA-CGA
56356676 AAAAAAA
1 AAAAAAA
56356683 GTTTCTTTTT
Statistics
Matches: 254, Mismatches: 44, Indels: 51
0.73 0.13 0.15
Matches are distributed among these distances:
49 2 0.01
50 36 0.14
51 28 0.11
52 31 0.12
53 63 0.25
54 30 0.12
55 27 0.11
56 36 0.14
57 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (50 bp):
AAAAAAATTTGGGTGCTGGCCTGTCAATGACCGCACCAGTACGAAAACGA
Found at i:56356511 original size:104 final size:105
Alignment explanation
Indices: 56356305--56356682 Score: 420
Period size: 106 Copynumber: 3.6 Consensus size: 105
56356295 AATAAATAAC
* *
56356305 AAAAAAATTGGGTGCTGGCCTGTAAAT-GACCGACACCACCAGTACGAAAACGGAAAAAAAATTT
1 AAAAAAATTGGGTGCTGGCCTGTCAATAG-CCGGCACCACCAGTACGAAAAC-GAAAAAAAATTT
* * * * * *
56356369 TGGGTGCTGGCCTGTGAATGACCTGCACCAGTAAGAAAAAGA
64 TGGGTGCTGGCCTGTCAATGGCCGGCACCAATACGAAAATGA
* * * *
56356411 AAAAAAATTTGGTGCTAGCCTGTCAATAGCCGGCACCGCCAGTACGAAAAC-ATAAAAAATTTTG
1 AAAAAAATTGGGTGCTGGCCTGTCAATAGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTTG
*
56356475 GGTGCTGGCCTGTCAATGGTCGGCACCAATACGAAAATGA
66 GGTGCTGGCCTGTCAATGGCCGGCACCAATACGAAAATGA
** * * * * * *
56356515 AAAAAAAAAGGGTTCTGGCATGTCAAAAGCCAGCACCACCAATACGAAAACGAAAAAAAAAATTT
1 AAAAAAATTGGGTGCTGGCCTGTCAATAGCCGGCACCACCAGTACGAAAACG-AAAAAAAATTTT
* * * * * *
56356580 GAGCGATGGCCTATCAATGGCCGACACCATTACGAAAATGA
65 GGGTGCTGGCCTGTCAATGGCCGGCACCAATACGAAAATGA
* *
56356621 AAAAAAATTTTGGGTGCTGGCCTGTTAATGGCCGGCACCACCAGTAC-AAAAGCGAAAAAAAA
1 AAAAAAA--TTGGGTGCTGGCCTGTCAATAGCCGGCACCACCAGTACGAAAA-CGAAAAAAAA
56356683 GTTTCTTTTT
Statistics
Matches: 225, Mismatches: 41, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
104 86 0.38
106 95 0.42
107 13 0.06
108 31 0.14
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (105 bp):
AAAAAAATTGGGTGCTGGCCTGTCAATAGCCGGCACCACCAGTACGAAAACGAAAAAAAATTTTG
GGTGCTGGCCTGTCAATGGCCGGCACCAATACGAAAATGA
Found at i:56358398 original size:17 final size:17
Alignment explanation
Indices: 56358373--56358409 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
56358363 TAACTTTGTT
*
56358373 AATCGCTTTAATTATGA
1 AATCCCTTTAATTATGA
*
56358390 AATCCCTTTAATTATTA
1 AATCCCTTTAATTATGA
56358407 AAT
1 AAT
56358410 TAGTTGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (17 bp):
AATCCCTTTAATTATGA
Found at i:56365184 original size:14 final size:14
Alignment explanation
Indices: 56365143--56365185 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
56365133 CAGCCAAATA
*
56365143 AATTAATTGATTTTT
1 AATTAATTGA-ATTT
* *
56365158 AATTAAATAAATTT
1 AATTAATTGAATTT
56365172 AATTAATTGAATTT
1 AATTAATTGAATTT
56365186 TATAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTAATTGAATTT
Found at i:56375084 original size:19 final size:19
Alignment explanation
Indices: 56375062--56375099 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56375052 ATCAGTCCGT
56375062 ATTGATTCTCAAATCGATC
1 ATTGATTCTCAAATCGATC
56375081 ATTGATTCTCAAATCGATC
1 ATTGATTCTCAAATCGATC
56375100 GATTCAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
ATTGATTCTCAAATCGATC
Found at i:56380551 original size:3 final size:3
Alignment explanation
Indices: 56380543--56380587 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
56380533 TTAAAAAATA
56380543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56380588 GTAATTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56381351 original size:23 final size:24
Alignment explanation
Indices: 56381316--56381360 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
56381306 GACTTGTAGG
*
56381316 TATTATTTGATAAA-ATTTCTAGA
1 TATTATTTCATAAACATTTCTAGA
*
56381339 TATTTTTTCATAAACATTTCTA
1 TATTATTTCATAAACATTTCTA
56381361 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (24 bp):
TATTATTTCATAAACATTTCTAGA
Found at i:56387470 original size:72 final size:72
Alignment explanation
Indices: 56387336--56387472 Score: 161
Period size: 72 Copynumber: 1.9 Consensus size: 72
56387326 AAGTGGTTGT
* * * * ** *
56387336 TTTCTTTTCTTTTGAATGGCAACATGTTGTGCTGGTTTGATATGATTATTATTTCCTGAAGGTGG
1 TTTCTTTTCTTTTGAAAGGCAACATCTTCTGCTGGTTAGATACAATTATTATTTCCTAAAGGTGG
56387401 TTCTCTC
66 TTCTCTC
* *
56387408 TTTCTTTTCTTTTGAAAGGTAACATCTTCTGCTGGTTCAG-TACAATTGTTATTCTCC-AAAGGT
1 TTTCTTTTCTTTTGAAAGGCAACATCTTCTGCTGGTT-AGATACAATTATTATT-TCCTAAAGGT
56387471 GG
64 GG
56387473 GTTTCGTCCA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
72 50 0.93
73 4 0.07
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (72 bp):
TTTCTTTTCTTTTGAAAGGCAACATCTTCTGCTGGTTAGATACAATTATTATTTCCTAAAGGTGG
TTCTCTC
Found at i:56404169 original size:12 final size:12
Alignment explanation
Indices: 56404152--56404176 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56404142 TACCCTCTGT
56404152 AAAATTTAAACC
1 AAAATTTAAACC
56404164 AAAATTTAAACC
1 AAAATTTAAACC
56404176 A
1 A
56404177 TTTGATAAAT
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTTAAACC
Found at i:56430059 original size:30 final size:31
Alignment explanation
Indices: 56430018--56430100 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
56430008 GGCCCATATT
56430018 TATTTTAAAAAT-TTTAAAAATTAAAAAATA
1 TATTTTAAAAATATTTAAAAATTAAAAAATA
* *
56430048 TATTTTCAAAATATTTTAAAATTAAAAAA-A
1 TATTTTAAAAATATTTAAAAATTAAAAAATA
*
56430078 -ATTTAAAAAAGTATTTTAAAAAT
1 TATTTTAAAAA-TA-TTTAAAAAT
56430101 ATTTTAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.18
30 14 0.31
31 23 0.51
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAATA
Found at i:56430063 original size:11 final size:10
Alignment explanation
Indices: 56430018--56430137 Score: 61
Period size: 11 Copynumber: 11.7 Consensus size: 10
56430008 GGCCCATATT
56430018 TATTTTAAAA
1 TATTTTAAAA
56430028 -ATTTTAAAA
1 TATTTTAAAA
**
56430037 -ATTAAAAAATA
1 TATT-TTAAA-A
56430048 TATTTTCAAAA
1 TATTTT-AAAA
56430059 TATTTT-AAA
1 TATTTTAAAA
**
56430068 -ATTAAAAAA
1 TATTTTAAAA
* *
56430077 AATTTAAAAAA
1 TATTT-TAAAA
56430088 GTATTTTAAAAA
1 -TATTTT-AAAA
56430100 TATTTTAAAA
1 TATTTTAAAA
**
56430110 -ATTAAAAAA
1 TATTTTAAAA
56430119 GTATTTTAAAAA
1 -TATTTT-AAAA
56430131 TATTTTA
1 TATTTTA
56430138 CAATTTTAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 25 0.29
10 11 0.13
11 28 0.33
12 18 0.21
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:56430078 original size:41 final size:42
Alignment explanation
Indices: 56430018--56430183 Score: 148
Period size: 41 Copynumber: 4.0 Consensus size: 42
56430008 GGCCCATATT
** *
56430018 TATTTTAAAAATT-TTAAAAA-TTAAAAAATATATTTTCAAAA
1 TATTTTAAAAATTAAAAAAAATTTAAAAAA-ATATTTTAAAAA
*
56430059 TATTTT-AAAATTAAAAAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTAAAAAAAATTTAAAAAAATATTTTAAAAA
* * *
56430100 TATTTTAAAAATTAAAAAAGTATTT-TAAAAATATTTT-ACAA
1 TATTTTAAAAATTAAAAAA-AATTTAAAAAAATATTTTAAAAA
* *
56430141 T-TTTAAAAAAAATAAAAAAAAGTATGT-AAAAAATATTTTAAAA
1 TATTT-TAAAAATTAAAAAAAA-T-T-TAAAAAAATATTTTAAAA
56430184 TTAAAAAAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
40 10 0.10
41 44 0.43
42 31 0.30
43 16 0.16
44 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (42 bp):
TATTTTAAAAATTAAAAAAAATTTAAAAAAATATTTTAAAAA
Found at i:56430098 original size:20 final size:19
Alignment explanation
Indices: 56430055--56430131 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
56430045 ATATATTTTC
56430055 AAAATATTTT-AAAATTAA
1 AAAATATTTTAAAAATTAA
* * *
56430073 AAAAAATTTAAAAAAGTATTTTA
1 AAAATATTT-TAAAA--A-TTAA
56430096 AAAATATTTTAAAAATTAA
1 AAAATATTTTAAAAATTAA
56430115 AAAAGTATTTTAAAAAT
1 AAAA-TATTTTAAAAAT
56430132 ATTTTACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
18 8 0.17
19 7 0.15
20 16 0.34
22 5 0.11
23 11 0.23
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAATATTTTAAAAATTAA
Found at i:56430100 original size:31 final size:31
Alignment explanation
Indices: 56430028--56430131 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
56430018 TATTTTAAAA
**
56430028 ATTTTAAAAATTAAAAAATATATTTTCAAAA-T
1 ATTTTAAAAATTAAAAAA-A-ATTTAAAAAAGT
56430060 ATTTT-AAAATTAAAAAAAATTTAAAAAAGT
1 ATTTTAAAAATTAAAAAAAATTTAAAAAAGT
***
56430090 ATTTTAAAAATATTTTAAAAA-TTAAAAAAGT
1 ATTTTAAAAAT-TAAAAAAAATTTAAAAAAGT
56430121 ATTTTAAAAAT
1 ATTTTAAAAAT
56430132 ATTTTACAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 8 0.12
30 7 0.11
31 38 0.59
32 11 0.17
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
ATTTTAAAAATTAAAAAAAATTTAAAAAAGT
Found at i:56430132 original size:31 final size:32
Alignment explanation
Indices: 56430074--56430150 Score: 129
Period size: 31 Copynumber: 2.4 Consensus size: 32
56430064 TAAAATTAAA
56430074 AAAAATTTAAAAAAGTATTTTAAAAATATTTT
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTT
56430106 AAAAA-TTAAAAAAGTATTTTAAAAATATTTT
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTT
* *
56430137 ACAATTTTAAAAAA
1 AAAAATTTAAAAAA
56430151 AATAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTT
Found at i:56430160 original size:43 final size:40
Alignment explanation
Indices: 56430113--56430196 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 40
56430103 TTTAAAAATT
* * *
56430113 AAAAAAGTATTTTAAAAATATTTTACAATTTTAAAAAAAATAA
1 AAAAAAGTATGTAAAAAATATTTTA-AA-ATT-AAAAAAATAA
56430156 AAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATAA
1 AAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATAA
56430196 A
1 A
56430197 TATATTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 11 0.29
41 2 0.05
42 2 0.05
43 23 0.61
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (40 bp):
AAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATAA
Found at i:56432107 original size:38 final size:38
Alignment explanation
Indices: 56432020--56432098 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
56432010 AGCACACATC
*
56432020 AAATATAAATTACTTATACAATAGAAACAAAGGTGTTT
1 AAATATAAATTACTTATACAATAGAAACAAAGGTATTT
56432058 AAATATAAATTACTTATACAATAGAAACAAAGGTATTT
1 AAATATAAATTACTTATACAATAGAAACAAAGGTATTT
56432096 AAA
1 AAA
56432099 ATTTAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (38 bp):
AAATATAAATTACTTATACAATAGAAACAAAGGTATTT
Found at i:56441127 original size:18 final size:16
Alignment explanation
Indices: 56441104--56441137 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
56441094 TGAGAATGTT
*
56441104 AAAATTTTAAAATATAA
1 AAAAATTTAAAAT-TAA
56441121 AAAAATTTAAAATTAA
1 AAAAATTTAAAATTAA
56441137 A
1 A
56441138 TAATAACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTTAAAATTAA
Found at i:56441793 original size:22 final size:22
Alignment explanation
Indices: 56441765--56441812 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
56441755 CAAAAACATT
*
56441765 TATTATTTGTTATT-AAATTATA
1 TATTATTTATTATTAAAATT-TA
*
56441787 TATTATTTATTTTTAAAATTTA
1 TATTATTTATTATTAAAATTTA
56441809 TATT
1 TATT
56441813 TGTCAAACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATTTATTATTAAAATTTA
Found at i:56442282 original size:25 final size:24
Alignment explanation
Indices: 56442254--56442302 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
56442244 AAAGTATTCT
56442254 AATTTAATAAATTTTATTTATTTGA
1 AATTTAAT-AATTTTATTTATTTGA
**
56442279 AATTTAATTTTTTTATTTATTTGA
1 AATTTAATAATTTTATTTATTTGA
56442303 TATGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
AATTTAATAATTTTATTTATTTGA
Found at i:56442292 original size:24 final size:24
Alignment explanation
Indices: 56442265--56442313 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
56442255 ATTTAATAAA
*
56442265 TTTTATTTATTTGAAATTTAATTT
1 TTTTATTTATTTGAAATGTAATTT
*
56442289 TTTTATTTATTTGATATGTAATTT
1 TTTTATTTATTTGAAATGTAATTT
56442313 T
1 T
56442314 GATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTTATTTATTTGAAATGTAATTT
Found at i:56442311 original size:29 final size:29
Alignment explanation
Indices: 56442266--56442323 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
56442256 TTTAATAAAT
*
56442266 TTTATTTATTTGAAA-TTTAATTTTTTTA
1 TTTATTTATATGAAATTTTAATTTTTTTA
* *
56442294 TTTATTTGATATGTAATTTTGATTTTTTTA
1 TTTATTT-ATATGAAATTTTAATTTTTTTA
56442324 GGTACTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 6 0.24
30 12 0.48
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTATTTATATGAAATTTTAATTTTTTTA
Found at i:56443312 original size:43 final size:43
Alignment explanation
Indices: 56443226--56443311 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
56443216 ATCACGAGAC
*
56443226 TAAAACTTTAATTTCACAAACTATATGATTTTAGGTAATTTTT
1 TAAAACTTTAATTTCACAAACTATATAATTTTAGGTAATTTTT
* *
56443269 TAAAAC-TTAATTTCATAAACTATGTAATTTTAGGTAATTTTT
1 TAAAACTTTAATTTCACAAACTATATAATTTTAGGTAATTTTT
56443311 T
1 T
56443312 TTGTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 34 0.85
43 6 0.15
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (43 bp):
TAAAACTTTAATTTCACAAACTATATAATTTTAGGTAATTTTT
Found at i:56451539 original size:58 final size:58
Alignment explanation
Indices: 56451465--56451601 Score: 161
Period size: 59 Copynumber: 2.3 Consensus size: 58
56451455 ATTTGGGGCT
* ** *
56451465 TGAACTTGGTAATTTTTTTAATATTA-AGGTTTGAA-TTTTTTTTATTTAAGTTAAGCTC
1 TGAACTTGGTAATTTTTCT-ATATTAGA-GCCTGAACTTTTTTTTATTTAAGTTAAGCCC
* *
56451523 TGAACTTGGTAATTTTTCTATATTGGAGCCTGAACGTTTTTTTTATTTAAGTTAGGCCC
1 TGAACTTGGTAATTTTTCTATATTAGAGCCTGAAC-TTTTTTTTATTTAAGTTAAGCCC
* *
56451582 TGAACTTGGTAGTTGTTCTA
1 TGAACTTGGTAATTTTTCTA
56451602 ACATTGTGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 10 0.15
58 19 0.28
59 39 0.57
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (58 bp):
TGAACTTGGTAATTTTTCTATATTAGAGCCTGAACTTTTTTTTATTTAAGTTAAGCCC
Found at i:56462150 original size:13 final size:13
Alignment explanation
Indices: 56462132--56462156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56462122 TTGACCTCAG
56462132 TTTAATTGATTAA
1 TTTAATTGATTAA
56462145 TTTAATTGATTA
1 TTTAATTGATTA
56462157 TTGAATTTTA
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:0.08, T:0.56
Consensus pattern (13 bp):
TTTAATTGATTAA
Found at i:56476070 original size:24 final size:22
Alignment explanation
Indices: 56476035--56476078 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
56476025 TTAATTATAT
*
56476035 TTTTTATTTATTAATTGTTTTTA
1 TTTTTATCTATTAATT-TTTTTA
*
56476058 TTTTTATACTATTTATTTTTT
1 TTTTTAT-CTATTAATTTTTT
56476079 AGAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTATCTATTAATTTTTTTA
Found at i:56484495 original size:14 final size:14
Alignment explanation
Indices: 56484471--56484511 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
56484461 AGGCAAAGTG
*
56484471 AAAGGAAAAA-GAA
1 AAAGAAAAAAGGAA
56484484 AAACGAAAAAAGGAA
1 AAA-GAAAAAAGGAA
56484499 AAAG-AAAAAGGAA
1 AAAGAAAAAAGGAA
56484512 GTGACCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 12 0.48
14 7 0.28
15 6 0.24
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGGAA
Found at i:56487326 original size:15 final size:15
Alignment explanation
Indices: 56487308--56487354 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
56487298 AAATTTGGAA
*
56487308 TTTAGTTTTTGTATT
1 TTTAGTTTTTTTATT
**
56487323 TTTA-TTTTTTTAAAA
1 TTTAGTTTTTTT-ATT
56487338 TTTAGTTTTTTTATT
1 TTTAGTTTTTTTATT
56487353 TT
1 TT
56487355 AGATTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTAGTTTTTTTATT
Found at i:56487327 original size:30 final size:30
Alignment explanation
Indices: 56487291--56487354 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
56487281 TAGTTGTATT
**
56487291 TTTTTATAAATTTGGAATTTAGTTTTTGTA
1 TTTTTATAAATTTAAAATTTAGTTTTTGTA
*** *
56487321 TTTTTATTTTTTTAAAATTTAGTTTTTTTA
1 TTTTTATAAATTTAAAATTTAGTTTTTGTA
56487351 TTTT
1 TTTT
56487355 AGATTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (30 bp):
TTTTTATAAATTTAAAATTTAGTTTTTGTA
Done.