Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008277.1 Corchorus capsularis cultivar CVL-1 contig08298, 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: 135408
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3495 original size:234 final size:234
Alignment explanation
Indices: 3052--3498 Score: 603
Period size: 234 Copynumber: 1.9 Consensus size: 234
3042 TTTAGCGGCG
* * * *
3052 TCTGTTGTGTAAAACGCCATTATTTAACGGTGTCTGAGGGATAAGACGCCGCTATTTGGTGGAGT
1 TCTGTTGTGTAAAACGCCACTATTTAACGGCGTCTGAGGGATAAGACACCGCTATTTGGTGGAGA
** *
3117 CAAAATGGGATCCCGGTAGCCACTCAACTGGGAGCCCGGTTGAAACCTACCATTTTGGTGTAGGG
66 CAAAATGGGATCCCGGTAGCCACTCAACTGGGAGCCCGGTTGAAACCTAAAATTTTGGGGTAGGG
* * * * *
3182 TCTGTCCTGACTGTGCGCCTAGTTGGACCCTAACCGGGCCCCCAGTTGGGCTTCCTAATTTCTAA
131 TCTGTCCTGACTGGGCGCCCAGTTGGACCCTAACCGGGCCCCCAGTTAGACTTCCGAATTTCTAA
*
3247 TTATTAATATTTTTTTATTTAATTTCTAGAATGGTGGCA
196 TGATTAATATTTTTTTATTTAATTTCTAGAATGGTGGCA
* * *
3286 TCTGTTTTGTCAAACGCCACTATTTAACGGCGTCTGAGGTAGT-AGACACCGCTATTTGGTGGAG
1 TCTGTTGTGTAAAACGCCACTATTTAACGGCGTCTGAGGGA-TAAGACACCGCTATTTGGTGGAG
* * *
3350 ACAAAATGGGATCCCGGTTGGCACTC-ACTTGGGAGCCCGGTTGAGACCTAAAATTTTGGGGTAG
65 ACAAAATGGGATCCCGGTAGCCACTCAAC-TGGGAGCCCGGTTGAAACCTAAAATTTTGGGGTAG
* * * * * * *
3414 GGTCTGTCCTGATTGGGCGCCCAGTTGGACCTTAACCGGGCTCCCATTTATATTTGTCGAATTTC
129 GGTCTGTCCTGACTGGGCGCCCAGTTGGACCCTAACCGGGCCCCCAGTTAGACTT-CCGAATTTC
3479 TAATGATTTAAT-TTTTTTTA
193 TAATGA-TTAATATTTTTTTA
3499 ATTTCTTATA
Statistics
Matches: 183, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
233 2 0.01
234 155 0.85
235 21 0.11
236 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (234 bp):
TCTGTTGTGTAAAACGCCACTATTTAACGGCGTCTGAGGGATAAGACACCGCTATTTGGTGGAGA
CAAAATGGGATCCCGGTAGCCACTCAACTGGGAGCCCGGTTGAAACCTAAAATTTTGGGGTAGGG
TCTGTCCTGACTGGGCGCCCAGTTGGACCCTAACCGGGCCCCCAGTTAGACTTCCGAATTTCTAA
TGATTAATATTTTTTTATTTAATTTCTAGAATGGTGGCA
Found at i:3691 original size:17 final size:16
Alignment explanation
Indices: 3669--3700 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3659 CCTAAACTTG
3669 TCGAATCGCAGTGTCAA
1 TCGAATCGCAG-GTCAA
3686 TCGAATCGCAGGTCA
1 TCGAATCGCAGGTCA
3701 TTCTCCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (16 bp):
TCGAATCGCAGGTCAA
Found at i:3764 original size:13 final size:13
Alignment explanation
Indices: 3746--3770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3736 CTCTTCCTTC
3746 CTTTTCTCCTTTA
1 CTTTTCTCCTTTA
3759 CTTTTCTCCTTT
1 CTTTTCTCCTTT
3771 CCTTCTCATT
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:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTTTCTCCTTTA
Found at i:5495 original size:27 final size:27
Alignment explanation
Indices: 5422--5511 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
5412 TCCGGCTCTC
*
5422 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
**** *
5449 CCCACTGT-TTTTCCAACAGTGGATCCT
1 CCCACT-TCGACCCCAGCAGTGGATCCT
*
5476 CCCATTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
5503 CCCACTTCG
1 CCCACTTCG
5512 CCTCGGGTCG
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 1 0.02
27 46 0.96
28 1 0.02
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.24
Consensus pattern (27 bp):
CCCACTTCGACCCCAGCAGTGGATCCT
Found at i:7573 original size:2 final size:2
Alignment explanation
Indices: 7566--7595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7556 AACAATTTTC
7566 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
7596 GCTACTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7833 original size:32 final size:32
Alignment explanation
Indices: 7787--7849 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
7777 GGATATACCT
*
7787 TTATATAGCGGCGTCTGAAGAACAAAACGCCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCCC
* *
7819 TTATCTAGCGGCGTCTAAAGAACAAGACGCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCC
7850 GCTATATTTA
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:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (32 bp):
TTATATAGCGGCGTCTAAAGAACAAAACGCCC
Found at i:8611 original size:44 final size:43
Alignment explanation
Indices: 8536--8633 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
8526 ATTAGGAGGT
* * * *
8536 TATCAAAA-TTCATATTGTGGTTATTAAAATTTCATAGGTAAGA
1 TATCAAAATTTCATAATGTAGTTATCAAAATTTCAT-GGGAAGA
* * * *
8579 TATCAAAATTTTATAATGTAGTTATCACAATTTCATGGGATGT
1 TATCAAAATTTCATAATGTAGTTATCAAAATTTCATGGGAAGA
8622 TATCAAAATTTC
1 TATCAAAATTTC
8634 TTAGGGAGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 23 0.51
44 22 0.49
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (43 bp):
TATCAAAATTTCATAATGTAGTTATCAAAATTTCATGGGAAGA
Found at i:8713 original size:22 final size:22
Alignment explanation
Indices: 8519--8883 Score: 186
Period size: 22 Copynumber: 16.5 Consensus size: 22
8509 TAATTTTTCC
* *
8519 AAATTTTATTAGGAGGTTATCA
1 AAATTTCATAAGGAGGTTATCA
** * *
8541 AAA-TTCATATTGTGGTTATTA
1 AAATTTCATAAGGAGGTTATCA
* *
8562 AAATTTCAT-AGGTAAGATATCA
1 AAATTTCATAAGG-AGGTTATCA
* *
8584 AAATTTTATAATGTA-GTTATCA
1 AAATTTCATAA-GGAGGTTATCA
* * *
8606 CAATTTCAT-GGGATGTTATCA
1 AAATTTCATAAGGAGGTTATCA
* * *
8627 AAATTTCTTAGGGAGGTTATTATAATA
1 AAATTTCATAAGGAGG---TTAT--CA
* * *
8654 AAATTTCACAGGGATGTTATCA
1 AAATTTCATAAGGAGGTTATCA
*
8676 AAATTTCATATGGAGGTTATCA
1 AAATTTCATAAGGAGGTTATCA
*
8698 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAGGAGGTTATCA
* * ** *
8720 GAATTCCATAAAAAGATTATCA
1 AAATTTCATAAGGAGGTTATCA
*
8742 AAATTTCACAAGGAGGTTA-CTA
1 AAATTTCATAAGGAGGTTATC-A
* **** *
8764 AAATATCATACTTTGGATATCA
1 AAATTTCATAAGGAGGTTATCA
** *
8786 AAATTTCATAAGGAGGCGAACA
1 AAATTTCATAAGGAGGTTATCA
* *
8808 AAATTTCATAGGGCA-ATTATCA
1 AAATTTCATAAGG-AGGTTATCA
* * *
8830 AAATTTTATATGGAGGTTATCG
1 AAATTTCATAAGGAGGTTATCA
* * *
8852 GAATTTTAT-AGTGTGGTTATCA
1 AAATTTCATAAG-GAGGTTATCA
*
8874 ATATTTCATA
1 AAATTTCATA
8884 GTGTGCTAAT
Statistics
Matches: 253, Mismatches: 73, Indels: 33
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.01
21 33 0.13
22 191 0.75
23 4 0.02
24 5 0.02
25 4 0.02
27 14 0.06
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
AAATTTCATAAGGAGGTTATCA
Found at i:9054 original size:22 final size:22
Alignment explanation
Indices: 8926--9224 Score: 79
Period size: 22 Copynumber: 14.0 Consensus size: 22
8916 GTGAGCTTAC
* * *
8926 CAAAATTGCA-AGTGTCGTTAC
1 CAAAATTTCATAGTGTGGTTAT
**
8947 CAAAATTTCATAGTGTAATTAT
1 CAAAATTTCATAGTGTGGTTAT
* * *
8969 CACAATTT--TAGAG-GCGTTAA
1 CAAAATTTCATAGTGTG-GTTAT
* *
8989 CAAAATTTCAT-GGGAAGGTTAT
1 CAAAATTTCATAGTG-TGGTTAT
* * * * *
9011 CGAAATTTTAGAAG-GAGATTAT
1 CAAAATTTCA-TAGTGTGGTTAT
9033 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGTGTGGTTAT
* * *
9055 -AAAATTTTATAATGTGG-TGT
1 CAAAATTTCATAGTGTGGTTAT
* * *
9075 ----GTTTCATAGGGAGATGTTAT
1 CAAAATTTCATAGTGTG--GTTAT
* * *
9095 CAAAACTTCATAGTATGGTTAC
1 CAAAATTTCATAGTGTGGTTAT
* **
9117 CGAAATTTCATTAG-AAGGTTAT
1 CAAAATTTCA-TAGTGTGGTTAT
* *
9139 CAAATTTTCATAGTGTGGTAAT
1 CAAAATTTCATAGTGTGGTTAT
* * * *
9161 TAAATTTTCATAAT-TAGTTTAT
1 CAAAATTTCATAGTGT-GGTTAT
* * *
9183 CAAAATTT-ATAGTGAGATTAA
1 CAAAATTTCATAGTGTGGTTAT
* **
9204 CAAGATTTGGTAGTGTGGTTA
1 CAAAATTTCATAGTGTGGTTA
9225 GGGAAGTTAT
Statistics
Matches: 198, Mismatches: 59, Indels: 41
0.66 0.20 0.14
Matches are distributed among these distances:
17 8 0.04
19 1 0.01
20 18 0.09
21 47 0.24
22 110 0.56
23 5 0.03
24 9 0.05
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGTGTGGTTAT
Found at i:9060 original size:21 final size:22
Alignment explanation
Indices: 9029--9072 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
9019 TAGAAGGAGA
*
9029 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAATGTGG
*
9051 TTAT-AAAATTTTATAATGTGG
1 TTATCAAAATTTCATAATGTGG
9072 T
1 T
9073 GTGTTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:9342 original size:22 final size:22
Alignment explanation
Indices: 9315--9379 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
9305 AAAATATTGT
9315 AGGAGGTTAACAAAATTTCATA
1 AGGAGGTTAACAAAATTTCATA
9337 AGGAGGGTATAA-AAAA-TTCATA
1 AGGA-GGT-TAACAAAATTTCATA
* *
9359 AGCAGGTTATCAAAATTTCAT
1 AGGAGGTTAACAAAATTTCAT
9380 CAGGTGGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 18 0.49
23 7 0.19
24 3 0.08
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (22 bp):
AGGAGGTTAACAAAATTTCATA
Found at i:13421 original size:34 final size:34
Alignment explanation
Indices: 13378--13461 Score: 115
Period size: 29 Copynumber: 2.6 Consensus size: 34
13368 CTCAAATACA
13378 GATTTCTAATCAATACAATTAGCCTTAACCAAAT
1 GATTTCTAATCAATACAATTAGCCTTAACCAAAT
*
13412 GATTTC---T-AATA-AATCAGCCTTAACCAAAT
1 GATTTCTAATCAATACAATTAGCCTTAACCAAAT
*
13441 AATTTCTAATCAATACAATTA
1 GATTTCTAATCAATACAATTA
13462 ATATGTTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
29 22 0.52
30 4 0.10
31 1 0.02
32 1 0.02
33 4 0.10
34 10 0.24
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (34 bp):
GATTTCTAATCAATACAATTAGCCTTAACCAAAT
Found at i:13838 original size:48 final size:48
Alignment explanation
Indices: 13767--13863 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
13757 AAGGTGGTTG
13767 AACTTTTAAGTGGTCTTGGAAAGTTGGGAAGAGAGAGAAGATTTGTTT
1 AACTTTTAAGTGGTCTTGGAAAGTTGGGAAGAGAGAGAAGATTTGTTT
*
13815 AACTTTTAGGTGGTCTTGGAAAGTTGGGAAGAGAGAGAAGATTTGTTT
1 AACTTTTAAGTGGTCTTGGAAAGTTGGGAAGAGAGAGAAGATTTGTTT
13863 A
1 A
13864 TTAATTGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (48 bp):
AACTTTTAAGTGGTCTTGGAAAGTTGGGAAGAGAGAGAAGATTTGTTT
Found at i:14685 original size:6 final size:6
Alignment explanation
Indices: 14674--14708 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
14664 GCAAAGCAAA
14674 CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTAAA
1 CTAAAT CTAAAT CTAAAT CTAAAT CTAAAT CTAAA
14709 GCAGATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
CTAAAT
Found at i:16279 original size:12 final size:12
Alignment explanation
Indices: 16244--16283 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 12
16234 TAAAAACACA
16244 TATAAAAATAGC
1 TATAAAAATAGC
16256 -A-AAAAATA--
1 TATAAAAATAGC
16264 TATAAAAATAGC
1 TATAAAAATAGC
16276 TATAAAAA
1 TATAAAAA
16284 CATGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.04
10 14 0.58
11 1 0.04
12 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (12 bp):
TATAAAAATAGC
Found at i:28821 original size:91 final size:91
Alignment explanation
Indices: 28666--28849 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
28656 ATGAAAAGTA
*
28666 ACAAACGCACTCTTAATTCCTGTTAATTTGTGTGCGATAAACAGAGCTTAAAGAAGAGAGAGTTC
1 ACAAACGCACTCTTAATTCCTGTCAATTTGTGTGCGATAAACAGAGCTTAAAGAAGAGAGAGTTC
28731 ATTGAAAGAGCAATACATGTGTTAGG
66 ATTGAAAGAGCAATACATGTGTTAGG
28757 ACAAACGCACTCTTAATTCCTGTCAATTTGTGTGCGATAAACAGAGCTTAAAGAAGAGAGAGTTC
1 ACAAACGCACTCTTAATTCCTGTCAATTTGTGTGCGATAAACAGAGCTTAAAGAAGAGAGAGTTC
28822 ATTGAAAGAGCAATACATGTGTTAGG
66 ATTGAAAGAGCAATACATGTGTTAGG
28848 AC
1 AC
28850 TTGGGCTCTC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (91 bp):
ACAAACGCACTCTTAATTCCTGTCAATTTGTGTGCGATAAACAGAGCTTAAAGAAGAGAGAGTTC
ATTGAAAGAGCAATACATGTGTTAGG
Found at i:36931 original size:7 final size:7
Alignment explanation
Indices: 36910--36942 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
36900 AAAATTCCAA
36910 AAAAATC
1 AAAAATC
36917 -AAAATC
1 AAAAATC
*
36923 AAAATTC
1 AAAAATC
36930 AAAAATC
1 AAAAATC
36937 AAAAAT
1 AAAAAT
36943 TTTTCATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATC
Found at i:37012 original size:52 final size:52
Alignment explanation
Indices: 36947--37073 Score: 200
Period size: 52 Copynumber: 2.4 Consensus size: 52
36937 AAAAATTTTT
*
36947 CATCAAGTTTTCAAAGCATTCAATTTAGCCCTTTTCAAATTGGGAAAGTTCC
1 CATCAAGTTTTCAAAACATTCAATTTAGCCCTTTTCAAATTGGGAAAGTTCC
* ** **
36999 CATTAAGTTTTCAAAATGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
1 CATCAAGTTTTCAAAACATTCAATTTAGCCCTTTTCAAATTGGGAAAGTTCC
37051 CATCAAGTTTTCAAAACATTCAA
1 CATCAAGTTTTCAAAACATTCAA
37074 ACGGCATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (52 bp):
CATCAAGTTTTCAAAACATTCAATTTAGCCCTTTTCAAATTGGGAAAGTTCC
Found at i:42642 original size:27 final size:26
Alignment explanation
Indices: 42580--42642 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
42570 CTAAACTTAC
*
42580 TAAAATTAGTTCTAGAAAAAAACATAA
1 TAAAA-TAGTTCTAGAAAAAAAAATAA
* * *
42607 TAAAGTAGTTCTGGCAAAAAAAAATGA
1 TAAAATAGTTCTAG-AAAAAAAAATAA
42634 TAAAATAGT
1 TAAAATAGT
42643 CTGTTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.25
Consensus pattern (26 bp):
TAAAATAGTTCTAGAAAAAAAAATAA
Found at i:43166 original size:21 final size:21
Alignment explanation
Indices: 43127--43166 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43117 AGGGGGTTGT
*
43127 TAAATACCGCCCTAGTTTTGC
1 TAAATACCGCCCTACTTTTGC
43148 TAAATACCGCCGC-ACTTTT
1 TAAATACCGCC-CTACTTTT
43167 TACACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAATACCGCCCTACTTTTGC
Found at i:43185 original size:15 final size:16
Alignment explanation
Indices: 43164--43208 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
43154 CCGCCGCACT
*
43164 TTTTACACTTTTGCCC
1 TTTTACACTTTTACCC
43180 -TTTACA-TTTTACCC
1 TTTTACACTTTTACCC
43194 TTTTTACACTTTTAC
1 -TTTTACACTTTTAC
43209 ACTGAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 6 0.24
17 6 0.24
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTACACTTTTACCC
Found at i:43490 original size:32 final size:34
Alignment explanation
Indices: 43401--43478 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
43391 CTTATTCATA
*
43401 GTGAAGCCGCCCCAGTGGGGCGGCCTGCCCAATG
1 GTGAAGCCGCCCAAGTGGGGCGGCCTGCCCAATG
*
43435 GTGAAGCCGCCCAAGTAGGGCGGCCTGCCC-ATG
1 GTGAAGCCGCCCAAGTGGGGCGGCCTGCCCAATG
43468 GT-AAGCCGCCC
1 GTGAAGCCGCCC
43479 TCTTGGGGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 9 0.21
33 5 0.12
34 28 0.67
ACGTcount: A:0.17, C:0.36, G:0.36, T:0.12
Consensus pattern (34 bp):
GTGAAGCCGCCCAAGTGGGGCGGCCTGCCCAATG
Found at i:53260 original size:6 final size:6
Alignment explanation
Indices: 53249--53276 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53239 ATTATCTTAA
53249 CATTGT CATTGT CATTGT CATTGT CATT
1 CATTGT CATTGT CATTGT CATTGT CATT
53277 ATTAACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (6 bp):
CATTGT
Found at i:57503 original size:16 final size:16
Alignment explanation
Indices: 57482--57524 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
57472 TTAAAAATTT
57482 CATAAACATTTCATCC
1 CATAAACATTTCATCC
57498 CATAAACATTTCATCC
1 CATAAACATTTCATCC
*
57514 CATAAAAATTT
1 CATAAACATTT
57525 TCTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.33
Consensus pattern (16 bp):
CATAAACATTTCATCC
Found at i:57534 original size:13 final size:13
Alignment explanation
Indices: 57516--57540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57506 TTTCATCCCA
57516 TAAAAATTTTCTT
1 TAAAAATTTTCTT
57529 TAAAAATTTTCT
1 TAAAAATTTTCT
57541 AATCTATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAAATTTTCTT
Found at i:60108 original size:22 final size:22
Alignment explanation
Indices: 60080--60124 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
60070 ATATTATTAG
60080 AGCTACTATATACAAAAAGACC
1 AGCTACTATATACAAAAAGACC
*
60102 AGCTACTATATGCAAAAAGACC
1 AGCTACTATATACAAAAAGACC
60124 A
1 A
60125 ATAATTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (22 bp):
AGCTACTATATACAAAAAGACC
Found at i:66902 original size:19 final size:20
Alignment explanation
Indices: 66859--66907 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
66849 TTCTCATCAG
66859 TCTTCTCCA--CTCTTACAC
1 TCTTCTCCATTCTCTTACAC
*
66877 TCTTTCTCCATTCTCTTTCA-
1 TC-TTCTCCATTCTCTTACAC
*
66897 TCTTCTACATT
1 TCTTCTCCATT
66908 TTTCTATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 2 0.08
21 7 0.27
ACGTcount: A:0.14, C:0.37, G:0.00, T:0.49
Consensus pattern (20 bp):
TCTTCTCCATTCTCTTACAC
Found at i:68643 original size:24 final size:23
Alignment explanation
Indices: 68616--68685 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 23
68606 TACTAGAGAT
68616 AATCAGAATGTAGTTCCATTAGGC
1 AATCAGAATGTAGTT-CATTAGGC
* *
68640 AATC---ATTTAGTT-ATTAGAGAT
1 AATCAGAATGTAGTTCATTAG-G-C
68661 AATCAGAATGTAGTTCAATTAGGC
1 AATCAGAATGTAGTTC-ATTAGGC
68685 A
1 A
68686 TAATCAGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 11 0.31
24 12 0.34
25 1 0.03
26 5 0.14
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (23 bp):
AATCAGAATGTAGTTCATTAGGC
Found at i:68659 original size:45 final size:45
Alignment explanation
Indices: 68595--68685 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
68585 AAATTTGCTT
*
68595 AATCATTTAGTTACTAGAGATAATCAGAATGTAGTTCCATTAGGC
1 AATCATTTAGTTACTAGAGATAATCAGAATGTAGTTCAATTAGGC
*
68640 AATCATTTAGTTATTAGAGATAATCAGAATGTAGTTCAATTAGGC
1 AATCATTTAGTTACTAGAGATAATCAGAATGTAGTTCAATTAGGC
68685 A
1 A
68686 TAATCAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (45 bp):
AATCATTTAGTTACTAGAGATAATCAGAATGTAGTTCAATTAGGC
Found at i:68664 original size:21 final size:21
Alignment explanation
Indices: 68594--68665 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
68584 AAAATTTGCT
*
68594 TAATCATTTAGTTACTAGAGA
1 TAATCATTTAGTTATTAGAGA
*
68615 TAATCAGAATGTAGTTCCATTAG-G-
1 TAATC---ATTTAGTT--ATTAGAGA
*
68639 CAATCATTTAGTTATTAGAGA
1 TAATCATTTAGTTATTAGAGA
68660 TAATCA
1 TAATCA
68666 GAATGTAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
19 5 0.13
20 1 0.03
21 17 0.44
24 11 0.28
25 1 0.03
26 4 0.10
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
TAATCATTTAGTTATTAGAGA
Found at i:68682 original size:26 final size:24
Alignment explanation
Indices: 68613--68692 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 24
68603 AGTTACTAGA
68613 GATAATCAGAATGTAGTTCCATTAG
1 GATAATCAGAATGTAGTT-CATTAG
* *
68638 G-CAATC---ATTTAGTT-ATTAG
1 GATAATCAGAATGTAGTTCATTAG
68657 AGATAATCAGAATGTAGTTCAATTAG
1 -GATAATCAGAATGTAGTTC-ATTAG
68683 GCATAATCAG
1 G-ATAATCAG
68693 CTTGCAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
19 5 0.12
20 1 0.02
21 11 0.26
24 11 0.26
25 2 0.05
26 13 0.30
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (24 bp):
GATAATCAGAATGTAGTTCATTAG
Found at i:73024 original size:13 final size:13
Alignment explanation
Indices: 73006--73044 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
72996 TCTTTGGGTT
*
73006 ACATTAGCTGATA
1 ACATTAACTGATA
*
73019 ACATTAATTGATA
1 ACATTAACTGATA
*
73032 ACATTAATTGATA
1 ACATTAACTGATA
73045 GGATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (13 bp):
ACATTAACTGATA
Found at i:73574 original size:4 final size:4
Alignment explanation
Indices: 73565--73592 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
73555 ATAAGTATAG
73565 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
73593 TATGAGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:76450 original size:15 final size:16
Alignment explanation
Indices: 76430--76460 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
76420 CCACTTCTGG
76430 GTTTCTTCACT-TTGC
1 GTTTCTTCACTCTTGC
76445 GTTTCTTCACTCTTGC
1 GTTTCTTCACTCTTGC
76461 CATCATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.06, C:0.29, G:0.13, T:0.52
Consensus pattern (16 bp):
GTTTCTTCACTCTTGC
Found at i:76701 original size:52 final size:52
Alignment explanation
Indices: 76623--76727 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
76613 TCAATCTGTC
76623 TTTTCCCTACAACTCTCATTCTACCTGCATTGAATGCATTAATTTATTTAAT
1 TTTTCCCTACAACTCTCATTCTACCTGCATTGAATGCATTAATTTATTTAAT
76675 TTTTCCCTACAACTCTCATTCTACCTGCATTGAATGCATTAATTTATTTAAT
1 TTTTCCCTACAACTCTCATTCTACCTGCATTGAATGCATTAATTTATTTAAT
76727 T
1 T
76728 ATGTTAATTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.45
Consensus pattern (52 bp):
TTTTCCCTACAACTCTCATTCTACCTGCATTGAATGCATTAATTTATTTAAT
Found at i:78037 original size:24 final size:24
Alignment explanation
Indices: 78000--78054 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
77990 GGGATTGAGA
* *
78000 TTCCAAATCGGGTAAATTAGCCTC
1 TTCCAAAACAGGTAAATTAGCCTC
*
78024 TTCCAAAACAGGTAGATTAGCCTC
1 TTCCAAAACAGGTAAATTAGCCTC
*
78048 CTCCAAA
1 TTCCAAA
78055 TGTTGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (24 bp):
TTCCAAAACAGGTAAATTAGCCTC
Found at i:91455 original size:13 final size:13
Alignment explanation
Indices: 91437--91463 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
91427 CATCAGCCTT
91437 GGATAATGGAGAG
1 GGATAATGGAGAG
91450 GGATAATGGAGAG
1 GGATAATGGAGAG
91463 G
1 G
91464 AACCCCAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (13 bp):
GGATAATGGAGAG
Found at i:92058 original size:2 final size:2
Alignment explanation
Indices: 92051--92085 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
92041 GGAAAACTTT
92051 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92086 TAATAAGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92070 original size:13 final size:13
Alignment explanation
Indices: 92052--92090 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
92042 GAAAACTTTT
92052 ATATATATATATA
1 ATATATATATATA
92065 ATATATATATAT-
1 ATATATATATATA
92077 ATAT-TATAT-TA
1 ATATATATATATA
92088 ATA
1 ATA
92091 AGTAGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
12 4 0.16
13 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATATATA
Found at i:92071 original size:15 final size:15
Alignment explanation
Indices: 92051--92085 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
92041 GGAAAACTTT
92051 TATATATATATATAA
1 TATATATATATATAA
*
92066 TATATATATATATAT
1 TATATATATATATAA
92081 TATAT
1 TATAT
92086 TAATAAGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:92073 original size:17 final size:17
Alignment explanation
Indices: 92051--92085 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
92041 GGAAAACTTT
92051 TATATATATATATAATA
1 TATATATATATATAATA
*
92068 TATATATATATATTATA
1 TATATATATATATAATA
92085 T
1 T
92086 TAATAAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATATATAATA
Found at i:92128 original size:31 final size:31
Alignment explanation
Indices: 92090--92153 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
92080 TTATATTAAT
* **
92090 AAGTAGTTTAATTTGATAATAATTCAAAAAA
1 AAGTAGTTTAATTTGATAAGAAGACAAAAAA
92121 AAGTAGTTTAATTTGATAAGAAGACAAAAAA
1 AAGTAGTTTAATTTGATAAGAAGACAAAAAA
92152 AA
1 AA
92154 TAGATAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (31 bp):
AAGTAGTTTAATTTGATAAGAAGACAAAAAA
Found at i:93400 original size:20 final size:21
Alignment explanation
Indices: 93361--93402 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
93351 TTACAAAGAA
93361 AACTCACAATCGCATGAGAGT
1 AACTCACAATCGCATGAGAGT
* *
93382 AACTCACATTC-CGTGAGAGT
1 AACTCACAATCGCATGAGAGT
93402 A
1 A
93403 GAACCCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
AACTCACAATCGCATGAGAGT
Found at i:122531 original size:15 final size:15
Alignment explanation
Indices: 122500--122628 Score: 92
Period size: 15 Copynumber: 8.5 Consensus size: 15
122490 TATAAAAGTA
*
122500 AATATATATTTATTAT
1 AATATATA-TAATTAT
122516 AATATATATAATTAT
1 AATATATATAATTAT
* *
122531 AATTATAATTTATATAAT
1 AA-TAT-ATATA-ATTAT
122549 AAATATATATAA--AGT
1 -AATATATATAATTA-T
122564 AA-ATATATAATTACT
1 AATATATATAATTA-T
*
122579 -TTATATAT-ATTAT
1 AATATATATAATTAT
*
122592 -ATATATATAAAGTA-
1 AATATATAT-AATTAT
122606 AATATATATAATTAT
1 AATATATATAATTAT
122621 AATATATA
1 AATATATA
122629 ATTTATATTT
Statistics
Matches: 92, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
13 16 0.17
14 11 0.12
15 36 0.39
16 12 0.13
17 8 0.09
18 7 0.08
19 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATATATAATTAT
Found at i:122546 original size:41 final size:42
Alignment explanation
Indices: 122501--122644 Score: 127
Period size: 43 Copynumber: 3.3 Consensus size: 42
122491 ATAAAAGTAA
*
122501 ATATATATTTATTAT-AATATATATAATTATAATTATAATTT
1 ATATATATATATTATAAATATATATAATTATAATTATAATTT
*
122542 ATATAATAAATATATATAAAGTAAATATATAATTACT--TTATATATATT
1 ATAT-ATATATAT-TATAAA-T--ATATATAATTA-TAATTATA-AT-TT
*
122590 ATATATATATA-AAGTAAATATATATAATTATAATATATAATTT
1 ATATATATATATTA-TAAATATATATAATTATAAT-TATAATTT
*
122633 ATATTTAT-TATT
1 ATATATATATATT
122645 TTTAAAAATA
Statistics
Matches: 83, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
41 4 0.05
42 9 0.11
43 23 0.28
44 5 0.06
45 7 0.08
46 9 0.11
47 19 0.23
48 7 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (42 bp):
ATATATATATATTATAAATATATATAATTATAATTATAATTT
Found at i:122559 original size:28 final size:28
Alignment explanation
Indices: 122513--122628 Score: 105
Period size: 30 Copynumber: 4.1 Consensus size: 28
122503 ATATATTTAT
* *
122513 TATAATATATATAATTATAATTATAATTTA
1 TATAATAAATAT-A-TATAATTATAATATA
122543 TATAATAAATATATATAA--AGTAA-ATA
1 TATAATAAATATATATAATTA-TAATATA
* * *
122569 TATAATTACTTTATATATATTAT-ATATA
1 TATAATAAATATATATA-ATTATAATATA
122597 TATAAAGTAAATATATATAATTATAATATA
1 TAT-AA-TAAATATATATAATTATAATATA
122627 TA
1 TA
122629 ATTTATATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
26 17 0.24
27 5 0.07
28 12 0.17
29 9 0.13
30 27 0.39
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (28 bp):
TATAATAAATATATATAATTATAATATA
Found at i:122629 original size:13 final size:13
Alignment explanation
Indices: 122519--122631 Score: 78
Period size: 13 Copynumber: 8.8 Consensus size: 13
122509 TTATTATAAT
122519 ATATATAATTATA
1 ATATATAATTATA
122532 AT-TATAATT-T-
1 ATATATAATTATA
*
122542 ATATAATAAATAT-
1 ATAT-ATAATTATA
*
122555 ATATA-AAGTA-A
1 ATATATAATTATA
122566 ATATATAATTACT-
1 ATATATAATTA-TA
*
122579 TTATATATATTATA
1 ATATATA-ATTATA
* *
122593 TATATATAAAGTAAA
1 -ATATAT-AATTATA
122608 TATATATAATTATA
1 -ATATATAATTATA
122622 ATATATAATT
1 ATATATAATT
122632 TATATTTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.03
11 11 0.14
12 17 0.21
13 24 0.30
14 9 0.11
15 16 0.20
16 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:122629 original size:28 final size:27
Alignment explanation
Indices: 122490--122629 Score: 100
Period size: 28 Copynumber: 5.3 Consensus size: 27
122480 ATAATAAAGT
*
122490 TATA-AAAGTAAATATATATTTATTATAA
1 TATATAAA-TAAATATATA-TAATTATAA
122518 TATAT--AT--A-AT-TATAATTATAA
1 TATATAAATAAATATATATAATTATAA
* *
122539 TTTATATAATAAATATATATAAAGTA-AA
1 TATATA-AATAAATATATAT-AATTATAA
* * *
122567 TATAT-AATTACTTTATATATATTATATA
1 TATATAAATAAATATATATA-ATTATA-A
122595 TATATAAAGTAAATATATATAATTATAA
1 TATATAAA-TAAATATATATAATTATAA
122623 TATATAA
1 TATATAA
122630 TTTATATTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
21 12 0.14
22 2 0.02
23 2 0.02
24 3 0.03
25 1 0.01
26 15 0.17
27 4 0.05
28 27 0.31
29 12 0.14
30 9 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (27 bp):
TATATAAATAAATATATATAATTATAA
Found at i:125621 original size:12 final size:11
Alignment explanation
Indices: 125583--125625 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
125573 CCGGCCCGAA
125583 ATATATATATT
1 ATATATATATT
*
125594 ATGTATATTATT
1 ATATATA-TATT
125606 ATATATATATT
1 ATATATATATT
125617 A-ATATATAT
1 ATATATATAT
125626 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
12 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:135230 original size:17 final size:17
Alignment explanation
Indices: 135184--135231 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
135174 TCACTTCTAA
135184 TTAATATTCA-TTATTAT
1 TTAATATT-ATTTATTAT
* *
135201 TTAATTTTTATTTTTTAT
1 TTAA-TATTATTTATTAT
135219 TTAATATTATTTA
1 TTAATATTATTTA
135232 ATTAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATATTATTTATTAT
Found at i:135316 original size:72 final size:71
Alignment explanation
Indices: 135225--135408 Score: 217
Period size: 80 Copynumber: 2.5 Consensus size: 71
135215 TTATTTAATA
* *
135225 TTATTTAATTAAATATAATATCTTTATAATTATTTT-ATTTTACTATTTTACTCAACTAAAAACT
1 TTATATAATTAAATCTAATATCTTTATAATTATTTTCATTTTACTATTTTACTCAACTAAAAACT
*
135289 CATTTTTT
66 CA--ATTT
*
135297 TTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACCATTTTACTATTTTACTCAACT
1 TTATATAATTAAATCTAATAT-CTT-T-A-TAAT-TATTTT--CATTTTACTATTTTACTCAACT
135362 AAAAACTCAATTT
59 AAAAACTCAATTT
* * *
135375 TTACATAATTAAATCTAATATCCTTATAACTATT
1 TTATATAATTAAATCTAATATCTTTATAATTATT
Statistics
Matches: 96, Mismatches: 8, Indels: 15
0.81 0.07 0.13
Matches are distributed among these distances:
72 19 0.20
73 7 0.07
74 3 0.03
75 2 0.02
76 4 0.04
77 8 0.08
78 23 0.24
80 30 0.31
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (71 bp):
TTATATAATTAAATCTAATATCTTTATAATTATTTTCATTTTACTATTTTACTCAACTAAAAACT
CAATTT
Found at i:135407 original size:78 final size:79
Alignment explanation
Indices: 135261--135408 Score: 262
Period size: 78 Copynumber: 1.9 Consensus size: 79
135251 TAATTATTTT
* *
135261 ATTTTACTATTTTACTCAACTAAAAACTCATTTTTTTTATATAATTAAATCTAATATCCTTATAA
1 ATTTTACTATTTTACTCAACTAAAAACTCA-TATTTTTACATAATTAAATCTAATATCCTTATAA
135326 CTATTATATTTTACC
65 CTATTATATTTTACC
135341 ATTTTACTATTTTACTCAACTAAAAACTCA-ATTTTTACATAATTAAATCTAATATCCTTATAAC
1 ATTTTACTATTTTACTCAACTAAAAACTCATATTTTTACATAATTAAATCTAATATCCTTATAAC
135405 TATT
66 TATT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
78 36 0.55
80 30 0.45
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (79 bp):
ATTTTACTATTTTACTCAACTAAAAACTCATATTTTTACATAATTAAATCTAATATCCTTATAAC
TATTATATTTTACC
Done.