Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011841.1 Corchorus capsularis cultivar CVL-1 contig11862, 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: 101085
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:13889 original size:19 final size:20
Alignment explanation
Indices: 13840--13889 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
13830 AACAGTCTAA
*
13840 CAGAGC-AAACTATAAGCAT
1 CAGAGCTAAACTAAAAGCAT
* *
13859 CAAAGCTATAAATAAAAGCAT
1 CAGAGCTA-AACTAAAAGCAT
13880 CAGAGCTAAA
1 CAGAGCTAAA
13890 AGATATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 17 0.68
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (20 bp):
CAGAGCTAAACTAAAAGCAT
Found at i:18271 original size:14 final size:14
Alignment explanation
Indices: 18254--18280 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18244 GATACTAATA
18254 TAAATGGACTAAAC
1 TAAATGGACTAAAC
18268 TAAATGGACTAAA
1 TAAATGGACTAAA
18281 GTTAATATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (14 bp):
TAAATGGACTAAAC
Found at i:21109 original size:22 final size:22
Alignment explanation
Indices: 21081--21126 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
21071 CCGAATGAAG
21081 TGATGTCTTATTTCGATGTGCT
1 TGATGTCTTATTTCGATGTGCT
*
21103 TGATGTCTTATTTTGATGTGCT
1 TGATGTCTTATTTCGATGTGCT
21125 TG
1 TG
21127 GTGCGTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.52
Consensus pattern (22 bp):
TGATGTCTTATTTCGATGTGCT
Found at i:29841 original size:2 final size:2
Alignment explanation
Indices: 29834--29867 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29824 CGATACATAA
29834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29868 TTACTAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34476 original size:25 final size:25
Alignment explanation
Indices: 34442--34496 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
34432 TGAGAACAAT
34442 TTCTCACATTCTTCATATTTTATTG
1 TTCTCACATTCTTCATATTTTATTG
*
34467 TTCTCACATTCTTCATATTTTATTT
1 TTCTCACATTCTTCATATTTTATTG
34492 TTCTC
1 TTCTC
34497 CATATTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.58
Consensus pattern (25 bp):
TTCTCACATTCTTCATATTTTATTG
Found at i:38633 original size:46 final size:46
Alignment explanation
Indices: 38580--38675 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
38570 CGTGCGGCTG
*
38580 TTTTATTTTATAAATT-TTTTAAAGCAAATTCAGTTAAGAAATCAAA
1 TTTTATTTTATAAATTCTTTT-AAGAAAATTCAGTTAAGAAATCAAA
*
38626 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAATAAATCAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
38672 TTTT
1 TTTT
38676 GTTGTGAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 43 0.91
47 4 0.09
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (46 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAA
Found at i:38807 original size:59 final size:59
Alignment explanation
Indices: 38710--38837 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
38700 GCAATGGAGT
* *
38710 AAAAT-TGAAGCATGTTAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAG
1 AAAATATGAAGCATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAAAAG
*
38768 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAAAAG
1 AAAATATGAAGCATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAAAAG
38827 AAAATATGAAG
1 AAAATATGAAG
38838 AATGAGAGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
58 5 0.08
59 61 0.92
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (59 bp):
AAAATATGAAGCATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAAAAG
Found at i:39104 original size:23 final size:23
Alignment explanation
Indices: 39074--39117 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
39064 TTCCCATTCA
39074 AGTGGGAAAGTGGTGGGAATGCC
1 AGTGGGAAAGTGGTGGGAATGCC
39097 AGTGGGAAAGTGGTGGGAATG
1 AGTGGGAAAGTGGTGGGAATG
39118 GCATTCCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.50, T:0.18
Consensus pattern (23 bp):
AGTGGGAAAGTGGTGGGAATGCC
Found at i:45641 original size:16 final size:16
Alignment explanation
Indices: 45620--45653 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
45610 TCAATACACA
*
45620 AAGCAGAAAAGCTTTG
1 AAGCAGAAAAGCTCTG
45636 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
45652 AA
1 AA
45654 ATATTTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.15
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:50977 original size:24 final size:25
Alignment explanation
Indices: 50929--50977 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
50919 GTCATTTCCT
* *
50929 TCAAACTTCAAAATTTTCAATTCTC
1 TCAAACTTCAAAACTTTCAAATCTC
*
50954 TCAACCTTC-AAACTTTCAAATCTC
1 TCAAACTTCAAAACTTTCAAATCTC
50978 AATCATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (25 bp):
TCAAACTTCAAAACTTTCAAATCTC
Found at i:51234 original size:3 final size:3
Alignment explanation
Indices: 51226--51260 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
51216 AAATCTTAAA
51226 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
51261 AGGCTGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52403 original size:17 final size:17
Alignment explanation
Indices: 52379--52424 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
52369 TTGATGTTTG
52379 AAAATTTGAAG-ATTGA
1 AAAATTTGAAGAATTGA
52395 AAGAATTTGAAAGAATTGA
1 AA-AATTTG-AAGAATTGA
*
52414 AAAGTTTGAAG
1 AAAATTTGAAG
52425 TTGGATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 8 0.31
19 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (17 bp):
AAAATTTGAAGAATTGA
Found at i:52421 original size:18 final size:16
Alignment explanation
Indices: 52376--52423 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
52366 TGATTGATGT
52376 TTGAAAATTTG-AAGA
1 TTGAAAATTTGAAAGA
52391 TTGAAAGAATTTGAAAGAA
1 TTG-AA-AATTTGAAAG-A
52410 TTGAAAAGTTTGAA
1 TTGAAAA-TTTGAA
52424 GTTGGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 8 0.29
18 11 0.39
19 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (16 bp):
TTGAAAATTTGAAAGA
Found at i:55915 original size:2 final size:2
Alignment explanation
Indices: 55908--55947 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
55898 GACTATCAAC
55908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55948 TACAAAAGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58063 original size:20 final size:18
Alignment explanation
Indices: 58039--58075 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
58029 TTAATGGAAA
58039 AAAAAAAAAGAGAGAATCT
1 AAAAAAAAAGA-AGAATCT
58058 AAAAAAAAAGAAGAATCT
1 AAAAAAAAAGAAGAATCT
58076 TTTACTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAGAAGAATCT
Found at i:65721 original size:2 final size:2
Alignment explanation
Indices: 65714--65739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65704 ACTTATAACG
65714 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
65740 CATACTGCAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:71486 original size:2 final size:2
Alignment explanation
Indices: 71479--71519 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
71469 CGCATTTAAA
* * *
71479 AT AT AT AT GT AT AT AT AC AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71520 GTGCCTAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:87686 original size:29 final size:29
Alignment explanation
Indices: 87651--87710 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
87641 AGGCACTGGG
87651 TATCAACATATATTATACTACTACTGATA
1 TATCAACATATATTATACTACTACTGATA
87680 TATCAACATATATTATACTACTACTGATA
1 TATCAACATATATTATACTACTACTGATA
87709 TA
1 TA
87711 AAACTGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (29 bp):
TATCAACATATATTATACTACTACTGATA
Found at i:87720 original size:26 final size:29
Alignment explanation
Indices: 87655--87721 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
87645 ACTGGGTATC
* *
87655 AACATATATTATACTACTACTGATATATC
1 AACATAGATTATACTACTACTGATATATA
*
87684 AACATATATTATACTACTACTGATATA-A
1 AACATAGATTATACTACTACTGATATATA
87712 AAC-T-GATTAT
1 AACATAGATTAT
87722 CCAGTGCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 5 0.14
27 1 0.03
28 3 0.08
29 27 0.75
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (29 bp):
AACATAGATTATACTACTACTGATATATA
Found at i:88674 original size:27 final size:26
Alignment explanation
Indices: 88644--88704 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 26
88634 CTTCCATGCT
88644 ACCTAAATTGAAAATCAGTAGCATCCC
1 ACCTAAATTGAAAATCAGTAGCAT-CC
88671 ACCTAAATTGAAAATCAGTAGCATCC
1 ACCTAAATTGAAAATCAGTAGCATCC
88697 -CCTAAATT
1 ACCTAAATT
88705 ATTGAGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 8 0.24
26 2 0.06
27 24 0.71
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.25
Consensus pattern (26 bp):
ACCTAAATTGAAAATCAGTAGCATCC
Found at i:96845 original size:6 final size:6
Alignment explanation
Indices: 96834--96869 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
96824 TATATTTATT
96834 TATCTA TATC-- TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TAT
96870 ATAAAAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.15
5 5 0.19
6 18 0.67
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:96853 original size:16 final size:17
Alignment explanation
Indices: 96834--96869 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
96824 TATATTTATT
96834 TATCTATATCTAT-CTA
1 TATCTATATCTATACTA
96850 TATCTATATCTATACTA
1 TATCTATATCTATACTA
96867 TAT
1 TAT
96870 ATAAAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (17 bp):
TATCTATATCTATACTA
Found at i:96953 original size:30 final size:31
Alignment explanation
Indices: 96899--96963 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
96889 AACTTTATGT
* *
96899 TTTCCAATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCCATATTTTTAAAACATA
*
96930 TTTCCAATTGTATCCAT-TTTTTAAAACATA
1 TTTCCAATTGTACCCATATTTTTAAAACATA
96960 TTTC
1 TTTC
96964 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCATATTTTTAAAACATA
Found at i:97554 original size:38 final size:37
Alignment explanation
Indices: 97497--97588 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
97487 TGACTTTTTG
97497 TTTCCAACGTCTTATTTAATTTTGCCTTTTATCTTTA
1 TTTCCAACGTCTTATTTAATTTTGCCTTTTATCTTTA
* * *
97534 TTTCCAACCGT-TGTATTTAATTTTGCTTTTTGTCTTTG
1 TTTCCAA-CGTCT-TATTTAATTTTGCCTTTTATCTTTA
** *
97572 CCTCCAACGTCCTATTT
1 TTTCCAACGTCTTATTT
97589 GGGTTTAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
37 16 0.35
38 30 0.65
ACGTcount: A:0.16, C:0.22, G:0.09, T:0.53
Consensus pattern (37 bp):
TTTCCAACGTCTTATTTAATTTTGCCTTTTATCTTTA
Found at i:98359 original size:23 final size:23
Alignment explanation
Indices: 98173--98450 Score: 177
Period size: 22 Copynumber: 12.5 Consensus size: 23
98163 TTATGGAGTA
*
98173 ATCAAAATTTC--AGGGAGG-AT
1 ATCAAAATTTCATAGGGAGGTTT
* **
98193 ATTAAAATTTCATAGTTCA-GTTT
1 ATCAAAATTTCATAG-GGAGGTTT
* * *
98216 -TCAAAATTTTATA-AGAGGGTT
1 ATCAAAATTTCATAGGGAGGTTT
* * **
98237 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGTTT
**
98259 ATCAAAATTTCATAGGGA-AATT
1 ATCAAAATTTCATAGGGAGGTTT
* **
98281 AACAAAATTTCCATAATGAGG-TT
1 ATCAAAATTT-CATAGGGAGGTTT
** *
98304 ATCAAAAAATCATAGGGCGG-TT
1 ATCAAAATTTCATAGGGAGGTTT
*
98326 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGGTTT
* * *
98349 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAGGTTT
* *
98372 ATCAAAATTTCATAGGAAGATTT
1 ATCAAAATTTCATAGGGAGGTTT
*
98395 ATCAAAATTTCATAGCGAGG-TT
1 ATCAAAATTTCATAGGGAGGTTT
* * *
98417 ATCACAAA-TTCATAGTG-TGATT
1 ATCA-AAATTTCATAGGGAGGTTT
98439 ATCAAAATTTCA
1 ATCAAAATTTCA
98451 GAGTGCGATT
Statistics
Matches: 202, Mismatches: 43, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.05
21 7 0.03
22 100 0.50
23 84 0.42
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
ATCAAAATTTCATAGGGAGGTTT
Found at i:98517 original size:22 final size:23
Alignment explanation
Indices: 98492--98554 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
98482 TTTTAAATTT
*
98492 TCATAAT-ATGGTTATCAATATA
1 TCATAATGATGGTTATCAACATA
* *
98514 TCAT-ATGAAGGTTATCAACATC
1 TCATAATGATGGTTATCAACATA
* *
98536 TCATAGTGTTGGTTATCAA
1 TCATAATGATGGTTATCAA
98555 AATTTAATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 20 0.61
23 11 0.33
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (23 bp):
TCATAATGATGGTTATCAACATA
Done.