Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006444.1 Corchorus capsularis cultivar CVL-1 contig06465, 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: 16356
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1247 original size:2 final size:2
Alignment explanation
Indices: 1240--1269 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1230 TTGCTAAAGG
1240 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
1270 TATTTTTAGT
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:4503 original size:22 final size:23
Alignment explanation
Indices: 4455--4509 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4445 CAATGAAATT
*
4455 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
4478 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
4500 TTGATAACCA
1 TTGATAACCA
4510 CGTTATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:4626 original size:23 final size:23
Alignment explanation
Indices: 4578--4684 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
4568 GATAGTCACA
*
4578 CTATGAAATTGTGAT-AATC-TC
1 CTATGAAATTTTGATAAATCTTC
4599 GCTATGAAATTTTGATAAATCTTC
1 -CTATGAAATTTTGATAAATCTTC
* * *
4623 CTATAAAATTTTGACAAATCTCC
1 CTATGAAATTTTGATAAATCTTC
* *
4646 CTATAAAATTTTGATAACT-TTC
1 CTATGAAATTTTGATAAATCTTC
* *
4668 TTATGAAATCTTGATAA
1 CTATGAAATTTTGATAA
4685 CTACAAATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 30 0.41
23 41 0.56
24 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTGATAAATCTTC
Found at i:4715 original size:20 final size:21
Alignment explanation
Indices: 4559--4848 Score: 110
Period size: 22 Copynumber: 13.6 Consensus size: 21
4549 AATCACACTC
** * *
4559 ATAAATTTTGATAGTCACACT
1 ATAAATTTTGATAACCTCCCT
* * *
4580 ATGAAATTGTGATAATCTCGCT
1 AT-AAATTTTGATAACCTCCCT
* *
4602 ATGAAATTTTGATAAATCTTCCT
1 AT-AAATTTTGAT-AACCTCCCT
* *
4625 ATAAAATTTTGACAAATCTCCCT
1 AT-AAATTTTGA-TAACCTCCCT
* * *
4648 ATAAAATTTTGATAACTTTCTT
1 AT-AAATTTTGATAACCTCCCT
*
4670 ATGAAATCTTGATAA-----CT
1 AT-AAATTTTGATAACCTCCCT
*
4687 ACAAATTTTGATAACCTCCCT
1 ATAAATTTTGATAACCTCCCT
* * **
4708 ATAATTTTTTTATAACCTCATT
1 ATAA-ATTTTGATAACCTCCCT
* *
4730 ATGAAATTTTGTTAATCTCCCT
1 AT-AAATTTTGATAACCTCCCT
**
4752 ATGAAATTTTGATAACC-CTGTT
1 AT-AAATTTTGATAACCTC-CCT
* ***
4774 ATGACATTTTGATAACCTTTAT
1 AT-AAATTTTGATAACCTCCCT
*
4796 ATCAAATTTTGATATCCTCCCT
1 AT-AAATTTTGATAACCTCCCT
* * *
4818 -GAAATTTTGATATCCTCTCT
1 ATAAATTTTGATAACCTCCCT
*
4838 -GAAATTTTGAT
1 ATAAATTTTGAT
4849 TACTCCATAA
Statistics
Matches: 210, Mismatches: 47, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
20 29 0.14
21 8 0.04
22 120 0.57
23 40 0.19
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (21 bp):
ATAAATTTTGATAACCTCCCT
Found at i:4979 original size:22 final size:22
Alignment explanation
Indices: 4954--5059 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
4944 AATCACATTT
4954 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
4976 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
4998 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
5020 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
5042 TGTAATTTTGATAACCTC
1 TGAAAATTTGATAACCTC
5060 GCTTTCAAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.08
22 56 0.86
23 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:5049 original size:44 final size:44
Alignment explanation
Indices: 4929--5079 Score: 142
Period size: 44 Copynumber: 3.4 Consensus size: 44
4919 AGAAATACAA
* * *
4929 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
4973 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * *
5017 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* *
5061 CTTTCAAATTTTGATAATC
1 CTATGAAATTTTGATAATC
5080 TTCCCATAAA
Statistics
Matches: 82, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
43 5 0.06
44 77 0.94
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:5122 original size:25 final size:21
Alignment explanation
Indices: 5091--5144 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
5081 TCCCATAAAG
5091 TTTGATAATCTGATCTCTATGAAA
1 TTTGATAATC--A-CTCTATGAAA
*
5115 TTTCGATAATCACTCTATGAGA
1 TTT-GATAATCACTCTATGAAA
5137 TTTGATAA
1 TTTGATAA
5145 CCTTCTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 1 0.04
24 3 0.11
25 7 0.25
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (21 bp):
TTTGATAATCACTCTATGAAA
Found at i:5213 original size:22 final size:21
Alignment explanation
Indices: 5184--5323 Score: 70
Period size: 22 Copynumber: 6.4 Consensus size: 21
5174 AAACTGAGAC
5184 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
5205 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
* ** *
5227 TTTTGATAATCTCCCCATAAAA
1 TTTTGATAACCT-CATATGAAA
* *
5249 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
5271 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* * *
5293 TTCTT-ATAACATCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
5315 TTTTGATAA
1 TTTTGATAA
5324 TCTCTTTGAT
Statistics
Matches: 90, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
21 11 0.12
22 75 0.83
23 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:5430 original size:46 final size:44
Alignment explanation
Indices: 5371--5475 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 44
5361 ACCACCCTAA
**
5371 GAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGACACTAT
1 GAAATTTTGATAACCACA-CTAAGAAATTTTAATAA-C-GACACTAT
* **
5417 GAAATTTTGATAACCACACTATGAAATTTTGGTAACGACACTAT
1 GAAATTTTGATAACCACACTAAGAAATTTTAATAACGACACTAT
*
5461 GGAATTTTGATAACC
1 GAAATTTTGATAACC
5476 TCCTCATGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 22 0.42
45 1 0.02
46 28 0.54
47 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTAAGAAATTTTAATAACGACACTAT
Found at i:5438 original size:22 final size:22
Alignment explanation
Indices: 5359--5523 Score: 120
Period size: 22 Copynumber: 7.4 Consensus size: 22
5349 TTATGATAAT
* * **
5359 TAACCACCCTAAGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
5381 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
5403 TAACCTGACACTATGAAATTTTGA
1 TAACC--ACACTATGAAATTTTGA
*
5427 TAACCACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
* *
5449 TAACGACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
5471 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
* * *
5493 TAATCATC-TTATAAAATTTTTGA
1 TAACCA-CACTATGAAA-TTTTGA
5516 TAACCACA
1 TAACCACA
5524 TAGAGACAAG
Statistics
Matches: 115, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.02
22 83 0.72
23 11 0.10
24 18 0.16
25 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:5719 original size:19 final size:20
Alignment explanation
Indices: 5688--5725 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5678 TATTGACATT
5688 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5707 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5726 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:5942 original size:27 final size:30
Alignment explanation
Indices: 5908--5962 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5898 ATCTAAATTG
*
5908 AAATTTT-ATAAT-T-AATTTATAAATAAT
1 AAATTTTAATAATGTCAATTTAGAAATAAT
5935 AAATTTTAATAATGTCAATTTAGAAATA
1 AAATTTTAATAATGTCAATTTAGAAATA
5963 TAATTGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 5 0.21
29 1 0.04
30 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTTAATAATGTCAATTTAGAAATAAT
Found at i:7069 original size:29 final size:31
Alignment explanation
Indices: 7037--7097 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
7027 ATTTAGAAAT
* *
7037 ATAT-TTTTTAAAA-AAGGGTACAATTGGAA
1 ATATGTTTTAAAAATAAGGGTACAATCGGAA
*
7066 ATATGTTTTAAAAATAATGGTACAATCGGAA
1 ATATGTTTTAAAAATAAGGGTACAATCGGAA
7097 A
1 A
7098 ACACAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 8 0.30
31 15 0.56
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (31 bp):
ATATGTTTTAAAAATAAGGGTACAATCGGAA
Found at i:8052 original size:49 final size:49
Alignment explanation
Indices: 7838--8062 Score: 246
Period size: 49 Copynumber: 4.6 Consensus size: 49
7828 CTTTGCCCGA
* * *
7838 AAGGGCATTTCGGGAACAA-CAAGTAAGAGAATT-GTGCCTTCTGTCCGGG
1 AAGGGCATTTTGGGAAAAAGCAAGTAA-A-AATTAGTGCCTTCCGTCCGGG
* * *
7887 AAGGGCGTTTTAGGAAAAA-C-AGATAAAAATTAGTGCCTTCCGTCCGAG
1 AAGGGCATTTTGGGAAAAAGCAAG-TAAAAATTAGTGCCTTCCGTCCGGG
* ** * *
7935 AAGGGCATTTTGGGACAAAGCTAAG-AAAAACAAGTGCCTTCCATCTGGG
1 AAGGGCATTTTGGGAAAAAGC-AAGTAAAAATTAGTGCCTTCCGTCCGGG
*
7984 AAGGGCGTTTTAGGG-AAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
1 AAGGGCATTTT-GGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
*
8033 AAGGGCATTTTGGGAAAAAGCAGGTAAAAA
1 AAGGGCATTTTGGGAAAAAGCAAGTAAAAA
8063 CTGAAAATTG
Statistics
Matches: 146, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
47 4 0.03
48 39 0.27
49 98 0.67
50 3 0.02
51 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (49 bp):
AAGGGCATTTTGGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGGG
Found at i:10876 original size:2 final size:2
Alignment explanation
Indices: 10869--10898 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10859 TATAAGTGCA
10869 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
10899 TACTAATGAA
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:11379 original size:22 final size:22
Alignment explanation
Indices: 11354--11402 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11344 GAATTTCGAG
* ** *
11354 AACCTTTTTATAATTTTTTTTT
1 AACCTTCTTATAAAATTTTGTT
11376 AACCTTCTTATAAAATTTTGTT
1 AACCTTCTTATAAAATTTTGTT
11398 AACCT
1 AACCT
11403 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.55
Consensus pattern (22 bp):
AACCTTCTTATAAAATTTTGTT
Found at i:11507 original size:22 final size:23
Alignment explanation
Indices: 11388--11667 Score: 110
Period size: 22 Copynumber: 12.6 Consensus size: 23
11378 CCTTCTTATA
* * *
11388 AAATTTTGTTAACCT-CCCTAAG
1 AAATTTTGATAACCTACCATATG
* *
11410 GAATTTTGA-AGACCT-CAATATG
1 AAATTTTGATA-ACCTACCATATG
* *
11432 AAATTTTGATAACTTCCCA-ATG
1 AAATTTTGATAACCTACCATATG
*
11454 AAATTTTGATAA-CTAACACTATG
1 AAATTTTGATAACCTACCA-TATG
* *
11477 AGATGTTGATAACCT-CCATATG
1 AAATTTTGATAACCTACCATATG
* * **
11499 ATATATTGATAACC-ACGTTATG
1 AAATTTTGATAACCTACCATATG
* * * *
11521 AAAATTTAAAAACCT-CCATGTG
1 AAATTTTGATAACCTACCATATG
* *
11543 -AATTGTT-AGTAATC-A-CACTCTG
1 AAATT-TTGA-TAACCTACCA-TATG
*
11565 AAATTTTGATAATC-A-CACTATG
1 AAATTTTGATAACCTACCA-TATG
*
11587 AAATTGTGATAACCT-CGC-TATG
1 AAATTTTGATAACCTAC-CATATG
* * *
11609 AAATTTTGATAAATCTTCC-TATA
1 AAATTTTGAT-AACCTACCATATG
* *
11632 AAATTTTGATAAACCT-CCCTATA
1 AAATTTTGAT-AACCTACCATATG
11655 AAATTTTGATAAC
1 AAATTTTGATAAC
11668 TTTCTCATGG
Statistics
Matches: 201, Mismatches: 37, Indels: 40
0.72 0.13 0.14
Matches are distributed among these distances:
21 10 0.05
22 127 0.63
23 60 0.30
24 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
AAATTTTGATAACCTACCATATG
Found at i:11635 original size:23 final size:23
Alignment explanation
Indices: 11565--11666 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
11555 TCACACTCTG
* * * *
11565 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
11587 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
11609 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
11632 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
11655 AAATTTTGATAA
1 AAATTTTGATAA
11667 CTTTCTCATG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 27 0.40
23 41 0.60
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:11743 original size:22 final size:22
Alignment explanation
Indices: 11693--11811 Score: 91
Period size: 22 Copynumber: 5.4 Consensus size: 22
11683 TGATAACTAC
* **
11693 AAATTGTGATAACCTCCCTATG
1 AAATTTTGATAACCTCATTATG
** *
11715 ATTTTTTGATAACCTCATTAAG
1 AAATTTTGATAACCTCATTATG
* *
11737 AAATTTTGTTAATCTCCA-TATG
1 AAATTTTGATAACCT-CATTATG
* * *
11759 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCATTATG
11781 AAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CCTCATTATG
11803 AAATTTTGA
1 AAATTTTGA
11812 AAACTTTTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
21 2 0.03
22 68 0.92
23 4 0.05
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:12138 original size:31 final size:31
Alignment explanation
Indices: 12100--12164 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
12090 AACTGAACTA
*
12100 ACTCAAACATTCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
12131 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
12162 ACT
1 ACT
12165 GATAACCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:12814 original size:122 final size:118
Alignment explanation
Indices: 12619--12858 Score: 345
Period size: 122 Copynumber: 2.0 Consensus size: 118
12609 CAATTTGACA
* * * *
12619 AACTTATAATTCGGTCTAAATTGAAATTTTTACTTAATTTTTAAATAATAAATAATAATGTGAAT
1 AACTTATAATTCGATCTAAAATGAAATTTTTAATTAATTTTTAAATAATAAATAATAATGTCAAT
* * *
12684 TTAGAAATATATTTGGAAAAAAGGGTGCAATCAGAAAACATAAAGTTTCCCAT
66 TTAGAAATATAATTGAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCCCAT
* *
12737 AACTTATAATTTGATCTAAAATGAAATTTTATAATTAATTTTTAAGTAATAAATTTTAATAATGT
1 AACTTATAATTCGATCTAAAATGAAATTTT-TAATTAATTTTTAAATAATAAA---TAATAATGT
* *
12802 CAATTTAGAAATATAATTGAAAAAAAGGGTACAATCGGAAAACATAAAGTTTTCCAT
62 CAATTTAGAAATATAATTGAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCCCAT
12859 TATTCGTACT
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 27 0.25
119 20 0.19
122 60 0.56
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (118 bp):
AACTTATAATTCGATCTAAAATGAAATTTTTAATTAATTTTTAAATAATAAATAATAATGTCAAT
TTAGAAATATAATTGAAAAAAAGGGTACAATCAGAAAACATAAAGTTTCCCAT
Found at i:13930 original size:32 final size:32
Alignment explanation
Indices: 13894--13961 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
13884 TTAGTAATGG
*
13894 CAATTTAGAAATATGTTTTTTAAAA-AAGGATA
1 CAATTTAGAAATATG-TTTTAAAAATAAGGATA
* *
13926 CAA-TTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAAAAATAAGGATA
13957 CAATT
1 CAATT
13962 GGAAAACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 8 0.26
31 19 0.61
32 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTTAAAAATAAGGATA
Found at i:13936 original size:31 final size:31
Alignment explanation
Indices: 13901--13966 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
13891 TGGCAATTTA
*
13901 GAAATATGTTTTTTAAAA-AAGGATACAATTG
1 GAAATATG-TTTTAAAAATAAGGATACAATTG
*
13932 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGATACAATTG
13963 GAAA
1 GAAA
13967 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGATACAATTG
Done.