Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014763.1 Corchorus capsularis cultivar CVL-1 contig14784, 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: 19411
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:4666 original size:29 final size:31
Alignment explanation
Indices: 4607--4670 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
4597 AACTTTATGT
*
4607 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
4638 TTTCCAATTGTA-CCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
4667 TTTC
1 TTTC
4671 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.53
30 4 0.12
31 11 0.34
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:4887 original size:37 final size:37
Alignment explanation
Indices: 4798--4887 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
4788 GCTTTTTATT
* *
4798 TCCAATGTCCTATTTAATTTTACCTTTTGTCTTTGTT
1 TCCAACGTCCTATTTAATTTTACCTTTTGTCTTTGTC
**
4835 TCCAATCGTTGTATTTAATTTT-CCTTTTTGTCTTTGTC
1 TCCAA-CGTCCTATTTAATTTTACC-TTTTGTCTTTGTC
4873 TCCAACGTCCTATTT
1 TCCAACGTCCTATTT
4888 GGGCTTAGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 15 0.33
38 30 0.67
ACGTcount: A:0.16, C:0.21, G:0.09, T:0.54
Consensus pattern (37 bp):
TCCAACGTCCTATTTAATTTTACCTTTTGTCTTTGTC
Found at i:5053 original size:19 final size:20
Alignment explanation
Indices: 5026--5063 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5016 TACTATTATT
5026 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5046 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5064 ACTGTCAATA
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:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:5257 original size:22 final size:22
Alignment explanation
Indices: 5229--5390 Score: 121
Period size: 22 Copynumber: 7.3 Consensus size: 22
5219 TGTCTCTACG
*
5229 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
5251 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
5274 -GGTTATCAAAATTCCATAGTA
1 TGGTTATCAAAATTTCATAGGA
* *
5295 TGGTTACCAAACTTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
5318 -AGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
** * * *
5339 TCAGGTTATTGAAATTTCTTATGT
1 T--GGTTATCAAAATTTCATAGGA
** *
5363 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
5385 TGGTTA
1 TGGTTA
5391 ATTATCACAA
Statistics
Matches: 111, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.05
22 85 0.77
23 5 0.05
24 15 0.14
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:5480 original size:22 final size:22
Alignment explanation
Indices: 5455--5545 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
5445 AGATTATAAG
*
5455 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
5477 AATTTCATTAG-GAGGTT-ACTAA
1 AATTTCA-TAGTGAGGTTAAC-AA
* * * *
5499 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
* * *
5521 AATTTTATAGTGTGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
5543 AAT
1 AAT
5546 CACATATGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.07
22 48 0.86
23 4 0.07
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:5808 original size:66 final size:65
Alignment explanation
Indices: 5571--5842 Score: 211
Period size: 66 Copynumber: 4.2 Consensus size: 65
5561 TAAAAATCTC
* * * * *
5571 AATTTCATAAGGA-G-TACCAAAATTTCATAAA-AGGTTATC-AAATCTCATAGAGTGATTATCG
1 AATTTCATAAAGAGGTTATCAAAATTT-ATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATCA
5632 A
65 A
* * *
5633 AATTTCATAAAGATCAGATTATCAAAATTTATAGGAAGA--TTATCAAAATTTCATAGTGTTGTT
1 AATTTCATAAAG---AGGTTATCAAAATTTATA--AAGAGGTTATCAAAATTTCATAGAGTGGTT
5696 ATCAA
61 ATCAA
* * * * * * *
5701 AATTTCA-AAACGAGGTTATCAAAAGTATATAATGTGATTATCAAAATTTCATAGAGGGGTCAAC
1 AATTTCATAAA-GAGGTTATCAAAA-TTTATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATC
5765 AA
64 AA
* * * *
5767 AATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA-AAATGTGATTA-C
1 AATTTCATAAAGAGGTTATCAAAATTT-ATAAAGAGGTTATCAAAATTTCATAGA-GTGGTTATC
5830 AAA
64 -AA
5833 AATTTCATAA
1 AATTTCATAA
5843 TGGTATTTCT
Statistics
Matches: 165, Mismatches: 28, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
62 11 0.07
64 2 0.01
65 17 0.10
66 85 0.52
67 21 0.13
68 28 0.17
69 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (65 bp):
AATTTCATAAAGAGGTTATCAAAATTTATAAAGAGGTTATCAAAATTTCATAGAGTGGTTATCAA
Found at i:5844 original size:22 final size:22
Alignment explanation
Indices: 5571--5844 Score: 138
Period size: 22 Copynumber: 12.5 Consensus size: 22
5561 TAAAAATCTC
* *
5571 AATTTCATAA-G-GAGTACCAA
1 AATTTCATAATGAGATTATCAA
* *
5591 AATTTCATAA-AAGGTTATC-A
1 AATTTCATAATGAGATTATCAA
* * *
5611 AATCTCATAGA-GTGATTATCGA
1 AATTTCATA-ATGAGATTATCAA
*
5633 AATTTCATAAAGATCAGATTATCAA
1 AATTTCAT--A-ATGAGATTATCAA
*
5658 AATTT-AT-AGGAAGATTATCAA
1 AATTTCATAATG-AGATTATCAA
* *
5679 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAATG-AGATTATCAA
* * *
5701 AATTTCAAAACGAGGTTATCAA
1 AATTTCATAATGAGATTATCAA
* *
5723 AAGTAT-ATAATGTGATTATCAA
1 AA-TTTCATAATGAGATTATCAA
* * * *
5745 AATTTCATAGA-GGGGTCAACAA
1 AATTTCATA-ATGAGATTATCAA
* * *
5767 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAATGAGATTATCAA
* *
5789 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAATGAGATTATCAA
* * *
5811 ATTTTCAAAATGTGATTA-CAAA
1 AATTTCATAATGAGATTATC-AA
5833 AATTTCATAATG
1 AATTTCATAATG
5845 GTATTTCTGG
Statistics
Matches: 195, Mismatches: 44, Indels: 28
0.73 0.16 0.10
Matches are distributed among these distances:
20 20 0.10
21 31 0.16
22 121 0.62
23 5 0.03
24 5 0.03
25 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTCATAATGAGATTATCAA
Found at i:6016 original size:44 final size:42
Alignment explanation
Indices: 5962--6104 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 42
5952 TCAGGAAGGA
* * *
5962 TATCACAATTTCATAATTTAGTTTTCAAAATTTCATAAGAGG-G-T
1 TATCAAAATTTCATAATGTAG--ATCAAAATTTCAT-AG-GGAGCT
6006 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGCT
1 TATCAAAATTTCATA--ATGTAGATCAAAATTTCATAGGGAGCT
* * ** *
6050 TAACAAAATTTCATAATAAGGT-TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAAT---GTAGATCAAAATTTCATAGGGAGCT
6094 TATCAAAATTT
1 TATCAAAATTT
6105 GTAGTTATCA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
42 4 0.05
43 3 0.04
44 69 0.83
45 2 0.02
46 5 0.06
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (42 bp):
TATCAAAATTTCATAATGTAGATCAAAATTTCATAGGGAGCT
Found at i:6159 original size:23 final size:23
Alignment explanation
Indices: 6131--6188 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6121 CATAAAAAAG
* * *
6131 TTATCAAAATTTTATTGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
6154 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
6177 TTATCAAAATTT
1 TTATCAAAATTT
6189 CATAACGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:6370 original size:45 final size:44
Alignment explanation
Indices: 6283--6389 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 44
6273 TTTTCGTAAC
* * *
6283 GTGGTTATCAATATATCATATGGAGGTTATCAACATCTCTTAGTG
1 GTGGTTATCAAAATTTCATATGGAGGTTATCAAAATCTCTTAG-G
* *
6328 TTGGTTATCAAAATTTCATATTGAGGTCT-TCAAAAT-TCCTTAGG
1 GTGGTTATCAAAATTTCATATGGAGGT-TATCAAAATCT-CTTAGG
* *
6372 GAGGTTAACAAAATTTCA
1 GTGGTTATCAAAATTTCA
6390 CAAGAAGGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 17 0.33
45 34 0.65
46 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (44 bp):
GTGGTTATCAAAATTTCATATGGAGGTTATCAAAATCTCTTAGG
Found at i:6479 original size:22 final size:22
Alignment explanation
Indices: 5986--6478 Score: 133
Period size: 22 Copynumber: 22.6 Consensus size: 22
5976 AATTTAGTTT
*
5986 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
6008 TCAAAATTTCAT-AGTATGTAGA
1 TCAAAATTTCATAAGAAGGT-TA
* * *
6030 TCAAAATTTCATAGGGAGCTTA
1 TCAAAATTTCATAAGAAGGTTA
* *
6052 ACAAAATTTCATAATAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
** * *
6074 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
*
6096 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
6112 TCAAGATTTCATAAAAAAGTTA
1 TCAAAATTTCATAAGAAGGTTA
* ** *
6134 TCAAAATTTTATTGGGAGGTTTA
1 TCAAAATTTCATAAGAAGG-TTA
* * *
6157 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAGAAG-GTTA
6180 TCAAAATTTCATAACG-AGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
* * *
6202 TTACAATTTCAT-AG-TGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* *
6224 TCAAAATTTCA-GAG-TGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* * *
6246 -CTAACAA-TTCATATGGAGGTTT
1 TC-AA-AATTTCATAAGAAGGTTA
* * * *
6268 TTAAATTTTCGTAACG-TGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
* * * *
6290 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * * **
6312 TCAACATCTCTTAGTGTTGGTTA
1 TCAAAATTTCATA-AGAAGGTTA
*
6335 TCAAAATTTCATATTG-AGGTCT-
1 TCAAAATTTCATA-AGAAGGT-TA
* * * *
6357 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* *
6379 ACAAAATTTCACAAGAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
** * *
6401 AAAAAATTT-ATAAAAAGGTTC
1 TCAAAATTTCATAAGAAGGTTA
* *** *
6422 TCAAAATTCCAT-AGTATCATTG
1 TCAAAATTTCATAAG-AAGGTTA
* * *
6444 TTAATATTTCATACGAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
6466 TCAAAATTTCATA
1 TCAAAATTTCATA
6479 CTGTGATCAT
Statistics
Matches: 341, Mismatches: 101, Indels: 58
0.68 0.20 0.12
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 2 0.01
21 29 0.09
22 228 0.67
23 65 0.19
24 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGAAGGTTA
Found at i:6642 original size:2 final size:2
Alignment explanation
Indices: 6599--6624 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6589 CTAAAACTAG
6599 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
6625 ATTCTAATGA
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:9220 original size:2 final size:2
Alignment explanation
Indices: 9210--9239 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9200 CTTTTTTATG
*
9210 TA TA AA 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 TA
9240 AAATTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:14531 original size:40 final size:40
Alignment explanation
Indices: 14484--14724 Score: 214
Period size: 40 Copynumber: 5.7 Consensus size: 40
14474 AATCCCCAAT
* *
14484 TTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTTCCAGTT
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTCCAGTC
* * *
14524 TTTCCCTTCCTCATCGGAAGATGTTGTTTAGTTGTCTAAGTCTTTTC
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTT-TC-CAG-----TC
* * *
14571 TTGTTTTGCCCTTCCCCTTCGGAAGGTGTTGTTTAGTTTCCAATC
1 -----TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTCCAGTC
*
14616 TTGCCCTTCCTCATCAGAAGGTGTTGTTTAGTTTCCAGTC
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTCCAGTC
*
14656 TTGCCCTTCCTCATCGGAAGGTGTTGTCTAGTTTTCCCAGTC
1 TTGCCCTTCCTCATCGGAAGGTGTTGTTTAG-TTT-CCAGTC
* * * *
14698 -TGCGCTTCCCCGGTCGGAAGATGTTGT
1 TTGCCCTTCCTC-ATCGGAAGGTGTTGT
14725 CTACTTTTCT
Statistics
Matches: 165, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
40 95 0.58
41 14 0.08
42 21 0.13
45 2 0.01
47 1 0.01
50 1 0.01
51 2 0.01
52 29 0.18
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.41
Consensus pattern (40 bp):
TTGCCCTTCCTCATCGGAAGGTGTTGTTTAGTTTCCAGTC
Found at i:15973 original size:24 final size:25
Alignment explanation
Indices: 15935--15981 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
15925 GCCTAAAGAG
15935 ATTTCAAAATAGGCCATTCTGACAT
1 ATTTCAAAATAGGCCATTCTGACAT
* *
15960 ATTTC-AAATCGGCCATTGTGAC
1 ATTTCAAAATAGGCCATTCTGAC
15982 TGTACTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (25 bp):
ATTTCAAAATAGGCCATTCTGACAT
Found at i:18067 original size:85 final size:82
Alignment explanation
Indices: 17958--18113 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 82
17948 CCTTCTTTCT
* **
17958 ATTTGAGATTAAAAAACAACAAATAGAGAAAGAAAAAGAAATTAACGGAGAGAACGATAAGAATG
1 ATTTGAGATTAAAAAACAAAAAATAGAGAAAGAAAAA-AAA-TAACGGAGAGAA-GATAAGAACC
18023 AAGGAATGCGGTCTCTCCTG
63 AAGGAATGCGGTCTCTCCTG
* * * * *
18043 ATTTGAGATTAAAAAAGAAAAAATAGATAAAGAAAAAAAATGATGGAGGGAAGATAAGAACCAAG
1 ATTTGAGATTAAAAAACAAAAAATAGAGAAAGAAAAAAAATAACGGAGAGAAGATAAGAACCAAG
18108 GAATGC
66 GAATGC
18114 AGAGGTGGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 17 0.27
83 9 0.14
84 3 0.05
85 34 0.54
ACGTcount: A:0.53, C:0.08, G:0.22, T:0.17
Consensus pattern (82 bp):
ATTTGAGATTAAAAAACAAAAAATAGAGAAAGAAAAAAAATAACGGAGAGAAGATAAGAACCAAG
GAATGCGGTCTCTCCTG
Done.