Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014219.1 Corchorus capsularis cultivar CVL-1 contig14240, 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: 7900
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:2914 original size:31 final size:31
Alignment explanation
Indices: 2874--2934 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2864 ACTTTATGTT
*
2874 TTCCGATTGTACCCTTATT-TTTAAAACATAA
1 TTCCAATTGTACCCTT-TTCTTTAAAACATAA
2905 TTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTCCAATTGTACCCTTTTCTTTAAAACATA
2935 TTTCTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (31 bp):
TTCCAATTGTACCCTTTTCTTTAAAACATAA
Found at i:3792 original size:22 final size:22
Alignment explanation
Indices: 3683--3792 Score: 134
Period size: 22 Copynumber: 5.0 Consensus size: 22
3673 CTTGTCTCTA
3683 AGTGGTTATCAAAATTTCATA-
1 AGTGGTTATCAAAATTTCATAG
* *
3704 AGATGGTTATTATAATTTCAT-G
1 AG-TGGTTATCAAAATTTCATAG
*
3726 AGGAGGTTATCAAAATTTCATAG
1 A-GTGGTTATCAAAATTTCATAG
* *
3749 TGTGGTTACCAAAATTTCATAG
1 AGTGGTTATCAAAATTTCATAG
*
3771 AGTGGTTACCAAAATTTCATAG
1 AGTGGTTATCAAAATTTCATAG
3793 GATCAGGTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
21 2 0.03
22 72 0.95
23 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
AGTGGTTATCAAAATTTCATAG
Found at i:3920 original size:24 final size:22
Alignment explanation
Indices: 3886--3942 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
3876 AAGAGATTAT
*
3886 CAAAATGTCATAGTGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
3909 TAAGAATTTCATAGTGTGGTTAA
1 CAA-AATTTCATAGTGAGGTTAA
3932 CAAAATTTCAT
1 CAAAATTTCAT
3943 TAAATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.28
23 5 0.17
24 16 0.55
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:4114 original size:24 final size:21
Alignment explanation
Indices: 4096--4136 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
4086 CATAGAGACC
4096 AGATTATCAAAATTTATAGAA
1 AGATTATCAAAATTTATAGAA
4117 AGATTATCAAAATTTCATAG
1 AGATTATCAAAATTT-ATAG
4137 TGTTATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (21 bp):
AGATTATCAAAATTTATAGAA
Found at i:4166 original size:22 final size:23
Alignment explanation
Indices: 4036--4262 Score: 119
Period size: 22 Copynumber: 10.4 Consensus size: 23
4026 TAGGGAGTAC
*
4036 CAAAATTTGAT-AGA-AGGTTAT
1 CAAAATTTCATAAGAGAGGTTAT
* * *
4057 C-AAATCTCAT-AGAGTGATTATT
1 CAAAATTTCATAAGAGAGGTTA-T
* * *
4079 GAAAA-TTCATAGAGACCAGATTAT
1 CAAAATTTCATA-AGA-GAGGTTAT
* *
4103 CAAAATTT-AT-AGAAAGATTAT
1 CAAAATTTCATAAGAGAGGTTAT
*
4124 CAAAATTTCAT---AG-TGTTAT
1 CAAAATTTCATAAGAGAGGTTAT
*
4143 CAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAAGAGAGGTTAT
* *
4165 CAAAATTACATAATGTGA--TTAT
1 CAAAATTTCATAA-GAGAGGTTAT
* * * *
4187 CAGAATTTCAT-AGAGGGGTCAA
1 CAAAATTTCATAAGAGAGGTTAT
*
4209 CAAAATTTTATAA-AGAGGTTAT
1 CAAAATTTCATAAGAGAGGTTAT
*
4231 CAAAATTTCATAA-AGAGTTTAT
1 CAAAATTTCATAAGAGAGGTTAT
*
4253 CAAATTTTCA
1 CAAAATTTCA
4263 AAAAGTGATT
Statistics
Matches: 158, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
19 14 0.09
20 13 0.08
21 22 0.14
22 83 0.53
23 6 0.04
24 13 0.08
25 7 0.04
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAAGAGAGGTTAT
Found at i:4283 original size:22 final size:22
Alignment explanation
Indices: 4096--4284 Score: 102
Period size: 22 Copynumber: 8.8 Consensus size: 22
4086 CATAGAGACC
*
4096 AGATTATCAAAATTT-ATAGAA-
1 AGATTATCAAAATTTCA-AAAAG
*
4117 AGATTATCAAAATTTC--ATAG
1 AGATTATCAAAATTTCAAAAAG
* **
4137 TG-TTATCAAAATTTCAAAGCG
1 AGATTATCAAAATTTCAAAAAG
* * * *
4158 AGGTTATCAAAATTACATAATG
1 AGATTATCAAAATTTCAAAAAG
* * * *
4180 TGATTATCAGAATTTCATAGAG
1 AGATTATCAAAATTTCAAAAAG
* * * * * *
4202 GGGTCAACAAAATTTTATAAAG
1 AGATTATCAAAATTTCAAAAAG
* *
4224 AGGTTATCAAAATTTCATAAAG
1 AGATTATCAAAATTTCAAAAAG
* *
4246 AGTTTATCAAATTTTCAAAAAG
1 AGATTATCAAAATTTCAAAAAG
*
4268 TGATTA-CAAAAATTTCA
1 AGATTATC-AAAATTTCA
4285 TAGTGGTATT
Statistics
Matches: 129, Mismatches: 33, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
19 14 0.11
20 1 0.01
21 19 0.15
22 95 0.74
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (22 bp):
AGATTATCAAAATTTCAAAAAG
Found at i:4393 original size:20 final size:20
Alignment explanation
Indices: 4368--4440 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
4358 TTATGGAGTA
4368 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
4388 ATCAAAA-TTCAGGGAAGAT
1 ATCAAAATTTCAAGGAGGAT
* *
4407 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCA-A-GGAGGAT
4429 ATCAAAATTTCA
1 ATCAAAATTTCA
4441 TAGTTTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 17 0.39
20 11 0.25
22 16 0.36
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:4434 original size:22 final size:22
Alignment explanation
Indices: 4406--4966 Score: 194
Period size: 22 Copynumber: 25.7 Consensus size: 22
4396 TCAGGGAAGA
4406 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
4428 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4450 TTTCAAAATTTCACAAG-AGGAT
1 TATCAAAATTTCATATGAAGG-T
* *
4472 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
4493 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
4516 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
4538 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
4560 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
4576 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
4598 TATGAAAATTTTATAGGGAGATT
1 TATCAAAATTTCATATGAAG-GT
* * *
4621 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
4644 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
4666 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4688 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
4710 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
4732 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
4754 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
4776 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
4799 CATCAAAATTTCATTAGGAA-GT
1 TATCAAAATTTCA-TATGAAGGT
4821 TATCAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
4843 CT-TCAAAATTCCGTAGGGAA-GT
1 -TATCAAAATTTCATA-TGAAGGT
* * *
4865 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
4887 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
4908 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
4930 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
4952 TATCAAAATTTCATA
1 TATCAAAATTTCATA
4967 ATGGGATTAT
Statistics
Matches: 406, Mismatches: 96, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
20 3 0.01
21 35 0.09
22 284 0.70
23 68 0.17
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:4461 original size:44 final size:44
Alignment explanation
Indices: 4406--4966 Score: 236
Period size: 44 Copynumber: 12.8 Consensus size: 44
4396 TCAGGGAAGA
*
4406 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * *
4450 TTTCAAAATTTCACAAG-AGGATTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGT-T-TAGT
* * * * *
4495 -ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGAT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAG-T
** *
4538 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G--TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * * **
4576 TATCAAGATTTCATAAGAAAGTTATGAAAATTTTATAG-GGAGATT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAG--T
* * **
4621 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTTA-GT
* * * * *
4666 TATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTTTAG-T
* * * *** *
4710 TA-CTAACAA-TTCATATGG-AGGTTTTTAAATTTTCATAACGTGGT
1 TATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * *
4754 TATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGT-TTAGT
* * *
4799 CATCAAAATTTCATTAGGAA-GTTATCAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTTTA-GT
* * * * *
4843 CT-TCAAAATTCCGTAGGGAA-GTTAACCAAATTTCATAAG--AAGGT
1 -TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCAT-AGTTTA-GT
** ** * * * * *
4887 TAAAAAAATTT-ATAAAAAGGTTCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
*
4930 TATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
4967 ATGGGATTAT
Statistics
Matches: 388, Mismatches: 90, Indels: 78
0.70 0.16 0.14
Matches are distributed among these distances:
38 24 0.06
39 4 0.01
41 4 0.01
42 6 0.02
43 39 0.10
44 213 0.55
45 73 0.19
46 24 0.06
47 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:4623 original size:23 final size:23
Alignment explanation
Indices: 4575--4659 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
4565 AAATTTGTAG
* * * *
4575 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
4597 TTATGAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGAAGAT
4620 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
4643 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
4660 CGAGGTTATC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 15 0.28
23 38 0.72
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:7090 original size:22 final size:22
Alignment explanation
Indices: 7065--7368 Score: 136
Period size: 22 Copynumber: 13.9 Consensus size: 22
7055 TATTATCCCG
7065 ATGAAATTTTGATAACCAT-ATT
1 ATGAAATTTTGATAACC-TCATT
* *
7087 ATGAAATTTTTATAACCTCCTT
1 ATGAAATTTTGATAACCTCATT
* * *
7109 AAGAAATTTTGGTAACCATACACT
1 ATGAAATTTTGATAACC-T-CATT
* * **
7133 GTGAACTTTTGATAACCTCCGT
1 ATGAAATTTTGATAACCTCATT
* * *
7155 ATGAAATTTCGATGACCTCTTT
1 ATGAAATTTTGATAACCTCATT
* **
7177 ATGAAATTTTGATAACCACCCT
1 ATGAAATTTTGATAACCTCATT
* * * * *
7199 ATAAAATCTTAATAACATCCTT
1 ATGAAATTTTGATAACCTCATT
* *
7221 ACGAAATTTTGTTAACCTC--T
1 ATGAAATTTTGATAACCTCATT
* * *
7241 ATGAAA-TTTGTTAACTTTC-GT
1 ATGAAATTTTGATAAC-CTCATT
* * * **
7262 ATGGAATTTTGATATCCACGGT
1 ATGAAATTTTGATAACCTCATT
* *
7284 -T-AAATTTTGATAATCTCACT
1 ATGAAATTTTGATAACCTCATT
* * *
7304 ATGAAATTTTGATAATCTCCTC
1 ATGAAATTTTGATAACCTCATT
* * * *
7326 ATGAATTTTTTTTATAACCACACT
1 ATGAA--ATTTTGATAACCTCATT
**
7350 ATGAAATTCGGATAACCTC
1 ATGAAATTTTGATAACCTC
7369 CCTAGTCTTT
Statistics
Matches: 207, Mismatches: 64, Indels: 22
0.71 0.22 0.08
Matches are distributed among these distances:
19 9 0.04
20 21 0.10
21 10 0.05
22 135 0.65
23 2 0.01
24 30 0.14
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCATT
Found at i:7163 original size:46 final size:44
Alignment explanation
Indices: 7029--7369 Score: 177
Period size: 44 Copynumber: 7.8 Consensus size: 44
7019 TCATTTCATC
* * *
7029 TTGATAACCTTCCTATGAAATTTTGATATTATC-CCG-ATGAAATT
1 TTGATAACCATACTATGAAATTTTGATA--ACCTCCGTATGAAATT
* * * *
7073 TTGATAACCATATTATGAAATTTTTATAACCTCCTTAAGAAATT
1 TTGATAACCATACTATGAAATTTTGATAACCTCCGTATGAAATT
* * *
7117 TTGGTAACCATACACTGTGAACTTTTGATAACCTCCGTATGAAATT
1 TTGATAACCAT--ACTATGAAATTTTGATAACCTCCGTATGAAATT
* * * * * *
7163 TCGATGACC-T-CTTTATGAAATTTTGATAACCACCCTATAAAATC
1 TTGATAACCATAC--TATGAAATTTTGATAACCTCCGTATGAAATT
* * * *
7207 TTAATAA-CATCCTTACGAAATTTTGTTAACCT-C-TATGAAA-T
1 TTGATAACCATAC-TATGAAATTTTGATAACCTCCGTATGAAATT
* * * * * * *
7248 TTGTTAA-CTTTCGTATGGAATTTTGATATCCACGGT-T-AAATT
1 TTGATAACCATAC-TATGAAATTTTGATAACCTCCGTATGAAATT
* * *
7290 TTGATAATC-TCACTATGAAATTTTGATAATCTCC-TCATGAATTTTT
1 TTGATAACCAT-ACTATGAAATTTTGATAACCTCCGT-ATGAA--ATT
* * **
7336 TTTATAACCACACTATGAAATTCGGATAACCTCC
1 TTGATAACCATACTATGAAATTTTGATAACCTCC
7370 CTAGTCTTTA
Statistics
Matches: 222, Mismatches: 56, Indels: 36
0.71 0.18 0.11
Matches are distributed among these distances:
41 26 0.12
42 34 0.15
43 8 0.04
44 90 0.41
45 2 0.01
46 62 0.28
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (44 bp):
TTGATAACCATACTATGAAATTTTGATAACCTCCGTATGAAATT
Found at i:7430 original size:22 final size:22
Alignment explanation
Indices: 7404--7481 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
7394 CCTCCCAATG
7404 TTTTGGTAACCATACTATAAAA
1 TTTTGGTAACCATACTATAAAA
* *
7426 TTTTGATAACC-TCCCTATAAAA
1 TTTTGGTAACCAT-ACTATAAAA
* * * *
7448 TTTTTGTAACCACACCATGAAA
1 TTTTGGTAACCATACTATAAAA
*
7470 TTTTAGTAACCA
1 TTTTGGTAACCA
7482 AAATATGAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (22 bp):
TTTTGGTAACCATACTATAAAA
Found at i:7489 original size:22 final size:22
Alignment explanation
Indices: 7445--7493 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7435 CCTCCCTATA
* * *
7445 AAATTTTTGTAACCACACCATG
1 AAATTTTAGTAACCAAAACATG
*
7467 AAATTTTAGTAACCAAAATATG
1 AAATTTTAGTAACCAAAACATG
7489 AAATT
1 AAATT
7494 GTGATAATTT
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:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (22 bp):
AAATTTTAGTAACCAAAACATG
Found at i:7644 original size:18 final size:18
Alignment explanation
Indices: 7614--7648 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7604 TTTCAATTCG
7614 TGTCAATTAGGGGCAAAC
1 TGTCAATTAGGGGCAAAC
7632 TGTCTAATT-GGGGCAAA
1 TGTC-AATTAGGGGCAAA
7649 ATGTTTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (18 bp):
TGTCAATTAGGGGCAAAC
Done.