Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011409.1 Corchorus capsularis cultivar CVL-1 contig11430, whole genome shotgun sequence
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: 148047
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1028 original size:38 final size:38
Alignment explanation
Indices: 955--1028 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 38
945 AAATAAATAT
* *
955 ATAAATATAATACTCCCGCATTATTTTTAGTTTTTACCA
1 ATAAATATAATAATCCCACATTATTTTTAG-TTTTACCA
994 ATAAATA-AATAATCCCACATTAGTATTTTA-TTTTA
1 ATAAATATAATAATCCCACATTA-T-TTTTAGTTTTA
1029 TAGTAACCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 18 0.58
39 8 0.26
40 5 0.16
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (38 bp):
ATAAATATAATAATCCCACATTATTTTTAGTTTTACCA
Found at i:3279 original size:2 final size:2
Alignment explanation
Indices: 3274--3307 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3264 ATATATCACC
*
3274 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3308 CCTGATCAGT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4558 original size:22 final size:22
Alignment explanation
Indices: 4412--4883 Score: 179
Period size: 22 Copynumber: 21.6 Consensus size: 22
4402 CCAATCCCAT
*
4412 TATGAAATTTTGATAACTTTC-C
1 TATGAAATTTTGATAAC-CTCAC
* *
4434 TATGAAATTTTAATAA-AT-AC
1 TATGAAATTTTGATAACCTCAC
* * * ***
4454 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCAC
* ** *
4476 TAT-AATTTTTTTTAACCTTC-T
1 TATGAAATTTTGATAACC-TCAC
*
4497 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTCAC
* * * * *
4519 TAAGGAATTTCGAAAACCTCAA
1 TATGAAATTTTGATAACCTCAC
*
4541 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
4564 TATGAGATGTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
* *
4586 TATGATATATTGATAA--TCAC
1 TATGAAATTTTGATAACCTCAC
* * *
4606 GTTATGAAAATTTAAAAACCTC-C
1 --TATGAAATTTTGATAACCTCAC
* *
4629 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
4652 TCTGAAATTTTAATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* **
4674 TATGAAATTGTGATAACCTCGT
1 TATGAAATTTTGATAACCTCAC
*
4696 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* *
4719 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
4742 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAAC-CTCAC
* * * *
4764 TATGAAATCTTAATTA--TAAC
1 TATGAAATTTTGATAACCTCAC
* *
4784 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** * *
4805 TATGATTTTTTTATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
4827 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
*
4849 TATGAAATTTTGATTAACCTC-T
1 TATGAAATTTTGA-TAACCTCAC
4871 TATGAAATTTTGA
1 TATGAAATTTTGA
4884 AAACTAAATT
Statistics
Matches: 332, Mismatches: 90, Indels: 56
0.69 0.19 0.12
Matches are distributed among these distances:
19 13 0.04
20 16 0.05
21 23 0.07
22 206 0.62
23 69 0.21
24 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:4728 original size:23 final size:23
Alignment explanation
Indices: 4673--4757 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
4663 AATAATCACA
* * *
4673 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATTTTGATAAACCTCC
* * * *
4695 TTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
4718 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
4741 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
4758 CTTTCTTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 13 0.25
23 40 0.75
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:5073 original size:22 final size:22
Alignment explanation
Indices: 5048--5127 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
5038 AATCACATTT
5048 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
** *
5070 TGAAGTTTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
* * *
5092 T-AAAATTTTGTTGACCCCTTTA
1 TGAAAA-TTTGATAACCTCTTTA
5114 TG-AAATTCTGATAA
1 TGAAAATT-TGATAA
5128 TCATTATCTA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
21 4 0.09
22 40 0.91
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:5327 original size:22 final size:23
Alignment explanation
Indices: 5298--5352 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5288 AAATTGAGAC
* *
5298 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
5319 TTTTGATAA-CTACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
5341 TTTTGATAACCT
1 TTTTGATAACCT
5353 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.28
22 19 0.66
23 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:5363 original size:22 final size:22
Alignment explanation
Indices: 5313--5363 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5303 TAACCTTCAT
*
5313 ATGAAATTTTGATAACTACACT
1 ATGAAATTTTGATAACTACACC
* *
5335 ATAAAATTTTGATAACCT-CCCC
1 ATGAAATTTTGATAA-CTACACC
5357 ATGAAAT
1 ATGAAAT
5364 ATTAGTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACACC
Found at i:5372 original size:22 final size:22
Alignment explanation
Indices: 5347--5389 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5337 AAAATTTTGA
*
5347 TAACCTCCCCATGAAATATTAG
1 TAACCTCCCAATGAAATATTAG
* *
5369 TAACTTCCTAATGAAATATTA
1 TAACCTCCCAATGAAATATTA
5390 TGAATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (22 bp):
TAACCTCCCAATGAAATATTAG
Found at i:5535 original size:22 final size:22
Alignment explanation
Indices: 5510--5755 Score: 134
Period size: 22 Copynumber: 11.3 Consensus size: 22
5500 AAATACATTT
*
5510 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
5532 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
5554 T-AAATTTTTGTTGACC-CTTTA
1 TGAAA-TTTTGATAACCTCTTTA
* * * * *
5575 AGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
*
5597 TGTAATTTTGATAACCTCGTTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
5619 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
5641 TGAAATTTTTATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
*
5663 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
5687 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
5709 TGAGA-TTAGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
5729 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
5749 TGAAATT
1 TGAAATT
5756 GAGACTTTTA
Statistics
Matches: 169, Mismatches: 40, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 39 0.23
22 91 0.54
23 2 0.01
24 4 0.02
25 11 0.07
26 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:5714 original size:463 final size:462
Alignment explanation
Indices: 5001--5903 Score: 1526
Period size: 463 Copynumber: 2.0 Consensus size: 462
4991 ATGAAATTTT
*
5001 GATAACCTCCCCAGAGATACCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTC
1 GATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTC
* * *
5066 TTTATGAAGTTTTGATAACCTTTTTATAAAATTTTGTTGACCCCTTTATGAAATTCTGATAATCA
66 TTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTTTAAGAAATTCTGATAATCA
5131 TTATCTAATTTTGATAACCCCGCTTTGAAATTTTGATAACAACACAATGAAATTTTGATAATCTT
131 TTATCTAATTTTGATAACCCCGCTTTGAAATTTTGATAACAACACAATGAAATTTTGATAATCTT
* * *
5196 CCTAAAAATTTTGATGATCTGATCTCTATGAAATTTCAATAATCACTCTATGAGATTGGATAACC
196 CCTAAAAATTTTGATAATCCGATCTCTATGAAATTTCAATAATCACTCTATGAGATTAGATAACC
*
5261 TTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTTATAACCTTCATATGAAATTTTGAT
261 TTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTTATAACCTTCATATGAAAATTTGAT
5326 AA-CTACACTATAAAATTTTGATAACCTCCCCATGAAATATTAGTAA-CTTCCTAATGAAATATT
326 AATC-ACACTATAAAATTTTGATAACCTCCCCATGAAATATTAGTAACCTT-CTAATGAAATATT
* *
5389 ATGAATTAAATAGTTATTTAATTCATATAGTTAATATTTAATATGTTTTTTTTTTTAAAAAAAGG
389 ATGAATTAAATAATTATTTAATTCATATAGTTAATATTTAATATATTTTTTTTTTTAAAAAAAGG
5454 GTAAAATTG
454 GTAAAATTG
*
5463 GATAACCTCCTCAGAAATACCACTATGAAATTTTTGTAAAT-ACATTTTGAAAATTTGATAACCT
1 GATAACCTCCCCAGAAATACCACTATGAAATTTTTGT-AATCACATTTTGAAAATTTGATAACCT
*
5527 CTTTATGAAATTTTGATAACCTCTTTATAAATTTTTGTTGA-CCCTTTAAGAAATTCTGATAATC
65 CTTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTTTAAGAAATTCTGATAAT-
* * * * *
5591 ACATTATGTAATTTTGATAACCTCGTTTTGAAATTTTGATAACAACACTATGAAATTTTTATAAT
129 -CATTATCTAATTTTGATAACCCCGCTTTGAAATTTTGATAACAACACAATGAAATTTTGATAAT
* *
5656 CTTCCTATAAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACTCTATGAGATTAGATA
193 CTTCCTAAAAATTTTGATAATCCGATCTCTATGAAATTTCAATAATCACTCTATGAGATTAGATA
5721 ACCTTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTTATAACCTTCATATGAAAATTT
258 ACCTTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTTATAACCTTCATATGAAAATTT
* * *
5786 GATAATCACACTATAAAATTTTGATAATCTCCTCATGAAATATTAGTAACCTTCTAATGAAATTT
323 GATAATCACACTATAAAATTTTGATAACCTCCCCATGAAATATTAGTAACCTTCTAATGAAATAT
*
5851 TATGAATTAAATAATTTTTTAATTCATATAGTTAATATTTAATATATTTTTTT
388 TATGAATTAAATAATTATTTAATTCATATAGTTAATATTTAATATATTTTTTT
5904 AAAAAAAGAG
Statistics
Matches: 413, Mismatches: 23, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
461 21 0.05
462 96 0.23
463 292 0.71
464 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (462 bp):
GATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTC
TTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTTTAAGAAATTCTGATAATCA
TTATCTAATTTTGATAACCCCGCTTTGAAATTTTGATAACAACACAATGAAATTTTGATAATCTT
CCTAAAAATTTTGATAATCCGATCTCTATGAAATTTCAATAATCACTCTATGAGATTAGATAACC
TTCTATCAAATTTTGGTACTCCTTATGAAATTGAGACTTTTATAACCTTCATATGAAAATTTGAT
AATCACACTATAAAATTTTGATAACCTCCCCATGAAATATTAGTAACCTTCTAATGAAATATTAT
GAATTAAATAATTATTTAATTCATATAGTTAATATTTAATATATTTTTTTTTTTAAAAAAAGGGT
AAAATTG
Found at i:8065 original size:26 final size:26
Alignment explanation
Indices: 8016--8065 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
8006 TGATTGAACA
*
8016 CAAAATTTGATAACAATCATACATTC
1 CAAAATTTGATAACAATCAAACATTC
*
8042 CAAAATTTGATCAA-AGTCAAACAT
1 CAAAATTTGAT-AACAATCAAACAT
8066 GGATGTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (26 bp):
CAAAATTTGATAACAATCAAACATTC
Found at i:11661 original size:18 final size:18
Alignment explanation
Indices: 11638--11681 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
11628 ATGGTGAAGC
11638 CTGCCGTGTGGGGAGGCT
1 CTGCCGTGTGGGGAGGCT
11656 CTGCCGTGTGGGGAGGCT
1 CTGCCGTGTGGGGAGGCT
*
11674 CCGCCGTG
1 CTGCCGTG
11682 GCTGAGCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.05, C:0.27, G:0.48, T:0.20
Consensus pattern (18 bp):
CTGCCGTGTGGGGAGGCT
Found at i:12410 original size:6 final size:6
Alignment explanation
Indices: 12388--12426 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
12378 ATCAATGGTG
* *
12388 TTGCGT TTGCAT TTGCTT TTGCTT TT-CTT TTGCTT TTGC
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTGC
12427 GTGATCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (6 bp):
TTGCTT
Found at i:22595 original size:13 final size:13
Alignment explanation
Indices: 22573--22602 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22563 CCTATTTCCC
22573 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
22586 TTTTTTTTTTTCT
1 TTTTTCTTTTTCT
22599 TTTT
1 TTTT
22603 CCTCCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:31623 original size:2 final size:2
Alignment explanation
Indices: 31618--31648 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31608 AAGAAGAAAG
31618 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31649 TAATAATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31661 original size:14 final size:14
Alignment explanation
Indices: 31644--31674 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31634 ATATATATAT
31644 TATATTAATAATAC
1 TATATTAATAATAC
31658 TATATTAATAATAC
1 TATATTAATAATAC
31672 TAT
1 TAT
31675 GGTCTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATTAATAATAC
Found at i:32585 original size:81 final size:81
Alignment explanation
Indices: 32450--32612 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
32440 GATTCCCATC
32450 GGTTTACTTCTAAGTTCTAACATTTCACACACTTAAAGGCTCCCTTCGTTAATCCCTTCTCATTC
1 GGTTTACTTCTAAGTTCTAACATTTCACACACTTAAAGGCTCCCTTCGTTAATCCCTTCTCATTC
32515 GGTGAGACAAAAAGCG
66 GGTGAGACAAAAAGCG
32531 GGTTTACTTCTAAGTTCTAACATTTCACACACTTAAAGGCTCCCTTCGTTAATCCCTTCTCATTC
1 GGTTTACTTCTAAGTTCTAACATTTCACACACTTAAAGGCTCCCTTCGTTAATCCCTTCTCATTC
32596 GGTGAGACAAAAAGCG
66 GGTGAGACAAAAAGCG
32612 G
1 G
32613 CTTAAAGCTA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (81 bp):
GGTTTACTTCTAAGTTCTAACATTTCACACACTTAAAGGCTCCCTTCGTTAATCCCTTCTCATTC
GGTGAGACAAAAAGCG
Found at i:53990 original size:12 final size:12
Alignment explanation
Indices: 53973--53997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53963 AGATTCTTAC
53973 ATTGCAATTGAA
1 ATTGCAATTGAA
53985 ATTGCAATTGAA
1 ATTGCAATTGAA
53997 A
1 A
53998 CTTTCAAAAA
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:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
ATTGCAATTGAA
Found at i:55782 original size:16 final size:16
Alignment explanation
Indices: 55761--55791 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55751 AAATTAACAA
55761 ATTAATGGGATCCAAC
1 ATTAATGGGATCCAAC
55777 ATTAATGGGATCCAA
1 ATTAATGGGATCCAA
55792 AGGCAACAAG
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:0.16, G:0.19, T:0.26
Consensus pattern (16 bp):
ATTAATGGGATCCAAC
Found at i:57800 original size:29 final size:29
Alignment explanation
Indices: 57758--57814 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
57748 GAAAACTGTT
57758 ACAATGGCCCTGTGCCCTCCGCTTCTATC
1 ACAATGGCCCTGTGCCCTCCGCTTCTATC
* *
57787 ACAATGGCCTTGTGTCCTCCGCTTCTAT
1 ACAATGGCCCTGTGCCCTCCGCTTCTAT
57815 AACTCTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.37, G:0.18, T:0.32
Consensus pattern (29 bp):
ACAATGGCCCTGTGCCCTCCGCTTCTATC
Found at i:63996 original size:16 final size:16
Alignment explanation
Indices: 63975--64007 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
63965 GAAGAGTAGG
63975 AACCTTATTTGCTTGA
1 AACCTTATTTGCTTGA
63991 AACCTTATTTGCTTGA
1 AACCTTATTTGCTTGA
64007 A
1 A
64008 TTGCTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (16 bp):
AACCTTATTTGCTTGA
Found at i:74380 original size:63 final size:63
Alignment explanation
Indices: 74276--74403 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 63
74266 GAGAAACCAA
* *
74276 CTAACCAATGAGCACATTTTTTTCATTCTTTTTTGTTTTTGTCTCAATTATTGTTCTTTAGTG
1 CTAACCAATGAGCACATTTCTTTCATTCTTTTTTGTTTTTGTCTCAATTATTGTTCTTTACTG
*
74339 CTAATCAATGAGCACATTTCTTTCATTCTTTTTTGTTTTTGTCTCAATTATTGTTCTTTACTG
1 CTAACCAATGAGCACATTTCTTTCATTCTTTTTTGTTTTTGTCTCAATTATTGTTCTTTACTG
74402 CT
1 CT
74404 CTCTGACTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (63 bp):
CTAACCAATGAGCACATTTCTTTCATTCTTTTTTGTTTTTGTCTCAATTATTGTTCTTTACTG
Found at i:74895 original size:38 final size:38
Alignment explanation
Indices: 74821--74898 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 38
74811 GTTTCAATGT
* * * *
74821 ACAGCAAGATCGGGTGGAATGGTTGTCACCCAGTTTTG
1 ACAGCAAGATCAGGTGGAATAGCTGGCACCCAGTTTTG
* *
74859 ACAGCAAGATCAGGTGGAATAGCTGGCATCCTGTTTTG
1 ACAGCAAGATCAGGTGGAATAGCTGGCACCCAGTTTTG
74897 AC
1 AC
74899 CTATCAACCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (38 bp):
ACAGCAAGATCAGGTGGAATAGCTGGCACCCAGTTTTG
Found at i:77427 original size:12 final size:12
Alignment explanation
Indices: 77407--77436 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
77397 TGGATCCAGA
77407 TGATGATAGTAG
1 TGATGATAGTAG
*
77419 TGATTATAGTAG
1 TGATGATAGTAG
77431 TGATGA
1 TGATGA
77437 GGGAAGCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (12 bp):
TGATGATAGTAG
Found at i:78363 original size:70 final size:70
Alignment explanation
Indices: 78281--78513 Score: 281
Period size: 70 Copynumber: 3.2 Consensus size: 70
78271 TTGTTTAGGT
*
78281 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATT
78345 ATTTTA
65 ATTTTA
*
78351 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAT-CTT-T-A-TA
*
78416 TTATATTTTACCA
62 AT-TATTTT---A
* * * *
78429 TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATCA-AATATCCTTATAACT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAT-ATAATATCTTTATAATT
*
78493 ATTATA
65 ATTTTA
*
78499 TTTTACAATTTTACT
1 TTTTACTATTTTACT
78514 TTTTTAGTTA
Statistics
Matches: 142, Mismatches: 11, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
70 64 0.45
71 5 0.04
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 51 0.36
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:78512 original size:78 final size:77
Alignment explanation
Indices: 78281--78519 Score: 325
Period size: 78 Copynumber: 3.2 Consensus size: 77
78271 TTGTTTAGGT
*
78281 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAAT-ATAATAT-CTT-T-A-
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCA-AATATCCTTATAAC
*
78340 TAAT-TATTTT--A
64 TATTATATTTTACA
*
78351 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCAAATATCCTTATAACTA
78416 TTATATTTTACCA
66 TTATATTTTA-CA
* *
78429 TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATCAAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCAAATATCCTTATAACTA
78494 TTATATTTTACAA
66 TTATATTTTAC-A
*
78507 TTTTACTTTTTTA
1 TTTTACTATTTTA
78520 GTTAAAAAAA
Statistics
Matches: 151, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
70 48 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 86 0.57
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCAAATATCCTTATAACTA
TTATATTTTACA
Found at i:81195 original size:75 final size:75
Alignment explanation
Indices: 81107--81257 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
81097 TTATATGCTG
81107 TAGGCTAATGTTGCATATATCTCGATGGAATTGTGTGCTTTTAGTTTATGTTTTGCTTGAATTTG
1 TAGGCTAATGTTGCATATATCTCGATGGAATTGTGTGCTTTTAGTTTATGTTTTGCTTGAATTTG
81172 ATTGAGATTA
66 ATTGAGATTA
*
81182 TAGGCTAATGTTGCATATATCTCGATGGAATTGTGTGCTTTTTGTTTATGTTTTGCTTGAATTTG
1 TAGGCTAATGTTGCATATATCTCGATGGAATTGTGTGCTTTTAGTTTATGTTTTGCTTGAATTTG
81247 ATTGAGATTA
66 ATTGAGATTA
81257 T
1 T
81258 TGTATCATGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.48
Consensus pattern (75 bp):
TAGGCTAATGTTGCATATATCTCGATGGAATTGTGTGCTTTTAGTTTATGTTTTGCTTGAATTTG
ATTGAGATTA
Found at i:82155 original size:19 final size:19
Alignment explanation
Indices: 82131--82188 Score: 116
Period size: 19 Copynumber: 3.1 Consensus size: 19
82121 TTATATCTTT
82131 TACTGTTTTGGGTTATGGA
1 TACTGTTTTGGGTTATGGA
82150 TACTGTTTTGGGTTATGGA
1 TACTGTTTTGGGTTATGGA
82169 TACTGTTTTGGGTTATGGA
1 TACTGTTTTGGGTTATGGA
82188 T
1 T
82189 GAGAACGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.16, C:0.05, G:0.31, T:0.48
Consensus pattern (19 bp):
TACTGTTTTGGGTTATGGA
Found at i:85496 original size:24 final size:23
Alignment explanation
Indices: 85469--85513 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
85459 AGCAGTCCTT
85469 GAGAAGAAAAAAATAAAATAAAAA
1 GAGAAGAAAAAAAT-AAATAAAAA
*
85493 GAGAAGAAGAAAATAAATAAA
1 GAGAAGAAAAAAATAAATAAA
85514 TCTATACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (23 bp):
GAGAAGAAAAAAATAAATAAAAA
Found at i:85790 original size:109 final size:108
Alignment explanation
Indices: 85618--85912 Score: 428
Period size: 109 Copynumber: 2.6 Consensus size: 108
85608 ACTATTATAG
* *
85618 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATTTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAA-TTAATATCTTTATAATTACTT
* *
85683 TATTTTTACCAAAAAATTTGGTTATACTAAAATTTTTTCCAATATACAA
60 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCCAATAAACAA
85732 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TAATATCTTTATAATTACTTTATTT
* *
85797 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATAAACAA
65 TTACCAAAAAATTTGGATATACTAAAATTTTTTCCAATAAACAA
* **
85841 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATATAATTTTTTTATT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATT-AATATCTT-TATAATTACTTTATT
85906 TTTACCA
64 TTTACCA
85913 TTTTAATTTA
Statistics
Matches: 169, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
108 2 0.01
109 121 0.72
110 23 0.14
111 2 0.01
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTAATATCTTTATAATTACTTTATTTT
TACCAAAAAATTTGGATATACTAAAATTTTTTCCAATAAACAA
Found at i:85842 original size:17 final size:18
Alignment explanation
Indices: 85822--85855 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85812 GATATATTAA
85822 AATTTT-TTCTAATAAAC
1 AATTTTATTCTAATAAAC
*
85839 AATTTTATTCTACTAAA
1 AATTTTATTCTAATAAA
85856 AACTCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTATTCTAATAAAC
Found at i:87694 original size:48 final size:46
Alignment explanation
Indices: 87631--87814 Score: 156
Period size: 48 Copynumber: 3.8 Consensus size: 46
87621 GTTTTTGGTC
* * * *
87631 ATTTTGATCAATTTTTATCACTTTGGATCATGATGATTAACCTTTAGT
1 ATTTTGGTCAATTTTTATCACTTCGG-TCGTGATGGTTAACCTTTA-T
* * *
87679 ATTTTGGTTAATTTTT-TCCAGCTTCGGTTCGTGATGGTTAGCTTTTAT
1 ATTTTGGTCAATTTTTAT-CA-CTTCGG-TCGTGATGGTTAACCTTTAT
* *
87727 CATTTTGGTCAATTTTGACCACATTCGGTCGTGATGGTTAACCTTTAAT
1 -ATTTTGGTCAATTTTTATCAC-TTCGGTCGTGATGGTTAACCTTT-AT
* **
87776 ATTTTGGTCGATTTTGATATC-CTTCAATCGTGATGGTTA
1 ATTTTGGTCAATTTT--TATCACTTCGGTCGTGATGGTTA
87815 GTCTTAAGTA
Statistics
Matches: 110, Mismatches: 18, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
47 1 0.01
48 63 0.57
49 44 0.40
50 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (46 bp):
ATTTTGGTCAATTTTTATCACTTCGGTCGTGATGGTTAACCTTTAT
Found at i:87732 original size:49 final size:48
Alignment explanation
Indices: 87661--87792 Score: 151
Period size: 49 Copynumber: 2.7 Consensus size: 48
87651 CTTTGGATCA
* * * **
87661 TGATGATTAACCTTTAGTATTTTGGTTAATTTTTTCCAGC-TTCGGTTCG
1 TGATGGTTAACCTTTAATATTTTGGTCAATTTTGACCA-CATTCGG-TCG
* *
87710 TGATGGTT-AGCTTTTATCATTTTGGTCAATTTTGACCACATTCGGTCG
1 TGATGGTTAACCTTTAAT-ATTTTGGTCAATTTTGACCACATTCGGTCG
*
87758 TGATGGTTAACCTTTAATATTTTGGTCGATTTTGA
1 TGATGGTTAACCTTTAATATTTTGGTCAATTTTGA
87793 TATCCTTCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
48 34 0.49
49 36 0.51
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.47
Consensus pattern (48 bp):
TGATGGTTAACCTTTAATATTTTGGTCAATTTTGACCACATTCGGTCG
Found at i:88123 original size:48 final size:48
Alignment explanation
Indices: 88031--88131 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 48
88021 AACCTTGGAT
* * * *
88031 ATTTTGGATACCTAAGATCGTGGTAGTTAATCTTTGACATTTTGATCA
1 ATTTTGGACACCTAAGATCGTGATAGTTAATCTTTGACACTTTGACCA
* * **
88079 ATTTTGGACACCTTATG-TCGTGATAGTTAATTTTTGTTACTTTGACCA
1 ATTTTGGACACC-TAAGATCGTGATAGTTAATCTTTGACACTTTGACCA
88127 ATTTT
1 ATTTT
88132 AATCAGCTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 41 0.93
49 3 0.07
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.46
Consensus pattern (48 bp):
ATTTTGGACACCTAAGATCGTGATAGTTAATCTTTGACACTTTGACCA
Found at i:88207 original size:39 final size:38
Alignment explanation
Indices: 88127--88208 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
88117 ACTTTGACCA
* *
88127 ATTTTAATCAGCTTGGATTGTGATAGTTAGCTTTAGTC
1 ATTTTAATCAGCTTAGATTGTGATAGTTAGCTTTAGAC
* *
88165 ATTTTAATCATCTTAAGTTTGTGATAGTTAGCGTTT-GAC
1 ATTTTAATCAGCTT-AGATTGTGATAGTTAGC-TTTAGAC
88204 ATTTT
1 ATTTT
88209 GGCCACATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 13 0.34
39 22 0.58
40 3 0.08
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (38 bp):
ATTTTAATCAGCTTAGATTGTGATAGTTAGCTTTAGAC
Found at i:89438 original size:2 final size:2
Alignment explanation
Indices: 89431--89456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89421 CATAATTCGT
89431 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
89457 ACGAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90165 original size:32 final size:32
Alignment explanation
Indices: 90115--90206 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 32
90105 GTCATGTCGT
* **
90115 TGTCAGACCAAAAT-GATGATGTGGTATTACCA
1 TGTCAGACC-AAATCGATGACGTGACATTACCA
* **
90147 TGTCGGACCAAATCGATGACGTGACATTGTCA
1 TGTCAGACCAAATCGATGACGTGACATTACCA
* *
90179 TGTCAGACCAAACCGATGACATGACATT
1 TGTCAGACCAAATCGATGACGTGACATT
90207 GGCACGTTGG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.08
32 46 0.92
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (32 bp):
TGTCAGACCAAATCGATGACGTGACATTACCA
Found at i:90207 original size:32 final size:32
Alignment explanation
Indices: 90145--90207 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
90135 GTGGTATTAC
* * *
90145 CATGTCGGACCAAATCGATGACGTGACATTGT
1 CATGTCAGACCAAACCGATGACATGACATTGT
90177 CATGTCAGACCAAACCGATGACATGACATTG
1 CATGTCAGACCAAACCGATGACATGACATTG
90208 GCACGTTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (32 bp):
CATGTCAGACCAAACCGATGACATGACATTGT
Found at i:95815 original size:2 final size:2
Alignment explanation
Indices: 95810--95836 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95800 TACTAGTGTG
95810 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
95837 TCATTTTTAA
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:96753 original size:30 final size:29
Alignment explanation
Indices: 96684--96757 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
96674 GTAGCGTTTA
*
96684 GACGTTTTGTCCCCC-GAACTTCAATCTTG
1 GACGTTTT-ACCCCCTGAACTTCAATCTTG
* *
96713 GACATTTTACCCCCTGAACTTCAATTTTGG
1 GACGTTTTACCCCCTGAACTTCAATCTT-G
96743 GACGTTTTACCCCCT
1 GACGTTTTACCCCCT
96758 CAATTTAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 5 0.13
29 19 0.49
30 15 0.38
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (29 bp):
GACGTTTTACCCCCTGAACTTCAATCTTG
Found at i:96982 original size:29 final size:30
Alignment explanation
Indices: 96913--96986 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
96903 GTTAGGCTGA
96913 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
* * * *
96943 ATGGGGTAAAATGT-CCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
96972 -GGGAGGCAAAACGTC
1 AGGG-GGCAAAACGTC
96987 TAAACGCTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.06
29 22 0.63
30 11 0.31
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:98431 original size:20 final size:21
Alignment explanation
Indices: 98408--98446 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
98398 TCTGAGTTCG
*
98408 AGTTTGAATC-GAGAGTCTCA
1 AGTTCGAATCTGAGAGTCTCA
98428 AGTTCGAATCTGAGAGTCT
1 AGTTCGAATCTGAGAGTCT
98447 TGAGTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (21 bp):
AGTTCGAATCTGAGAGTCTCA
Found at i:98452 original size:21 final size:21
Alignment explanation
Indices: 98401--98462 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
98391 TTGAAAGTCT
*
98401 GAGT-TCGAGTTTGAATC-GA
1 GAGTCTCGAGTTCGAATCTGA
*
98420 GAGTCTCAAGTTCGAATCTGA
1 GAGTCTCGAGTTCGAATCTGA
* *
98441 GAGTCTTGAGTTCAAATTCTGA
1 GAGTCTCGAGTTCGAA-TCTGA
98463 AACAGACGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 15 0.43
22 5 0.14
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (21 bp):
GAGTCTCGAGTTCGAATCTGA
Found at i:108826 original size:2 final size:2
Alignment explanation
Indices: 108819--108846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108809 AAACATTAAT
108819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108847 GAGTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114165 original size:115 final size:115
Alignment explanation
Indices: 114023--114330 Score: 564
Period size: 115 Copynumber: 2.7 Consensus size: 115
114013 TTCAATTTAA
114023 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGATTGAGTTTGATCTGGTGT
1 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGATTGAGTTTGATCTGGTGT
*
114088 TTTTAGCGCCAAGCTAATTCTTCACTTTAATTTCCTTCGATTTCATTGTT
66 TTTTAGCGCCAAGCTAATTCTTCAATTTAATTTCCTTCGATTTCATTGTT
114138 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGATTGAGTTTGATCTGGTGT
1 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGATTGAGTTTGATCTGGTGT
*
114203 TTTTAGCGCCAAGCTATTTCTTCAATTTAATTTCCTTCGATTTCATTGTT
66 TTTTAGCGCCAAGCTAATTCTTCAATTTAATTTCCTTCGATTTCATTGTT
*
114253 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTTATCT-AGCTTTGATCTGGT
1 TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGAT-TGAG-TTTGATCTGGT
114317 GTTTTTAGCGCCAA
64 GTTTTTAGCGCCAA
114331 TCTTTGATCT
Statistics
Matches: 188, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
115 162 0.86
116 26 0.14
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (115 bp):
TTTCCTTCGATTTCAAGATTTAATTTCGTTTTTAGGTTAGTATTTGATTGAGTTTGATCTGGTGT
TTTTAGCGCCAAGCTAATTCTTCAATTTAATTTCCTTCGATTTCATTGTT
Found at i:119525 original size:28 final size:28
Alignment explanation
Indices: 119489--119550 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
119479 AATTCACTAA
*
119489 TTAAGTATGCAGAATCATTCAAATATAG
1 TTAATTATGCAGAATCATTCAAATATAG
119517 TTAATTATGCAGAATCATTCAAATATAG
1 TTAATTATGCAGAATCATTCAAATATAG
*
119545 ATAATT
1 TTAATT
119551 TATACTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (28 bp):
TTAATTATGCAGAATCATTCAAATATAG
Found at i:124998 original size:140 final size:139
Alignment explanation
Indices: 124742--125000 Score: 376
Period size: 140 Copynumber: 1.9 Consensus size: 139
124732 TAATATAACC
* * * **
124742 ATAAGAATATCATCTGGCAATTTACTGATTCTATCTTCCTCATTACCAGCCGACTACAAGAACAA
1 ATAAAAATATCATCTAGCAATTCACTGATTCTATCCCCCTCATTACCAGCCGACTACAAGAACAA
* * *
124807 ATTCATTAATTAAGTATGCAGAATCATTAAAATATGAATAACTTATACTAGTAATCAACTAATCA
66 ATGCACTAATTAAGTATGCAGAATCATTAAAATAAGAATAACTTATACTAGTAATCAACTAATCA
124872 TAAATTATA
131 TAAATTATA
* *
124881 ATAAAAATATCATCTAGCAATTCACTGATTCTATCCCCCTGATTATCAGCCGACTACCAAGAACA
1 ATAAAAATATCATCTAGCAATTCACTGATTCTATCCCCCTCATTACCAGCCGACTA-CAAGAACA
* * *
124946 AGTGCACTAATTAAGTATGCAGAATCATTCAAATACAG-ATAAGTTATACTAGTAA
65 AATGCACTAATTAAGTATGCAGAATCATTAAAATA-AGAATAACTTATACTAGTAA
125001 CCATAAATTA
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
139 49 0.47
140 55 0.52
141 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (139 bp):
ATAAAAATATCATCTAGCAATTCACTGATTCTATCCCCCTCATTACCAGCCGACTACAAGAACAA
ATGCACTAATTAAGTATGCAGAATCATTAAAATAAGAATAACTTATACTAGTAATCAACTAATCA
TAAATTATA
Found at i:126891 original size:21 final size:21
Alignment explanation
Indices: 126866--126948 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 21
126856 TATCTTAGAT
126866 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
126887 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
*
126908 AT-A-AATCATGAGTTTAAAATAA
1 ATAATAAT-AT-A-TTTTAAATAA
126930 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
126949 TTACTAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
18 3 0.06
19 2 0.04
20 2 0.04
21 15 0.30
22 10 0.20
23 12 0.24
24 3 0.06
25 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:126905 original size:18 final size:20
Alignment explanation
Indices: 126884--126936 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 20
126874 TATTATTAAA
126884 TAAATAATAAATAT-A-TTT
1 TAAATAATAAATATGAGTTT
126902 TAAATAATAAATCATGAGTTT
1 TAAATAATAAAT-ATGAGTTT
*
126923 AAAATAAATAAATA
1 TAAAT-AATAAATA
126937 ATATATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.40
19 2 0.07
20 1 0.03
21 8 0.27
22 7 0.23
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
TAAATAATAAATATGAGTTT
Found at i:132321 original size:2 final size:2
Alignment explanation
Indices: 132314--132344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
132304 TGCTTTGATG
132314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
132345 GTAATAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:132429 original size:31 final size:29
Alignment explanation
Indices: 132394--132489 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 29
132384 TTGGTGAAGC
132394 ACTTAATATATTTAAATTCAATATTTTGAGG
1 ACTTAATATATTTAAATT-AAT-TTTTGAGG
** * * *
132425 ACTTAATCGATTTCAATTGAATTGTTGGAGA
1 ACTTAATATATTTAAATT-AATT-TTTGAGG
*
132456 ACTTAATATAATTAAATTAGATCTTTTGAGG
1 ACTTAATATATTTAAATTA-AT-TTTTGAGG
132487 ACT
1 ACT
132490 CGATTCGGAT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
30 2 0.04
31 47 0.94
32 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (29 bp):
ACTTAATATATTTAAATTAATTTTTGAGG
Found at i:137249 original size:31 final size:32
Alignment explanation
Indices: 137165--137250 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 32
137155 TTTGTTTTTT
*
137165 TTTTCAACTAATATCTCTCTCTCTTTTTTTGGCAG
1 TTTTC-ACTAATATCTCT-T-TCTTTTTTTGGCAA
137200 TATTTCACTAATATCTCTTT-TTTTTTTGGCAA
1 T-TTTCACTAATATCTCTTTCTTTTTTTGGCAA
137232 TTTTCACTAATATCTCTTT
1 TTTTCACTAATATCTCTTT
137251 AGTAAGTAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
31 18 0.37
32 12 0.24
33 1 0.02
34 1 0.02
35 13 0.27
36 4 0.08
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTTCACTAATATCTCTTTCTTTTTTTGGCAA
Found at i:137472 original size:23 final size:24
Alignment explanation
Indices: 137416--137474 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
137406 AGCATGTAAG
137416 CTTATTAGTTTTTTTACTCTTTTTA
1 CTTATT-GTTTTTTTACTCTTTTTA
*
137441 -TTCACTGTTTTTTT-C-CTTTTTAA
1 CTT-ATTGTTTTTTTACTCTTTTT-A
137464 CTTATTGTTTT
1 CTTATTGTTTT
137475 AAATCACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 12 0.41
25 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (24 bp):
CTTATTGTTTTTTTACTCTTTTTA
Done.