Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011943.1 Corchorus capsularis cultivar CVL-1 contig11964, 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: 15039
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Found at i:209 original size:85 final size:85
Alignment explanation
Indices: 109--339 Score: 417
Period size: 85 Copynumber: 2.7 Consensus size: 85
99 AAAATAATAA
* *
109 AATTTGTAAAAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATGTTTTAAGA
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
*
174 AATAAAAATTATAAAGATTT
66 AATAAAAATGATAAAGATTT
*
194 AATTTGTAAATAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
259 AATAAAAATGATAAAGATTT
66 AATAAAAATGATAAAGATTT
*
279 AATTTGTAAAGAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTT
1 AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTT
340 TAGATTTAAT
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 141 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (85 bp):
AATTTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
AATAAAAATGATAAAGATTT
Found at i:3424 original size:17 final size:17
Alignment explanation
Indices: 3402--3435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3392 AATGAAAAGG
* *
3402 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
3419 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
3436 GGATGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Found at i:3899 original size:21 final size:21
Alignment explanation
Indices: 3860--3901 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3850 TCAGCAAAAG
*
3860 AAAAAAGAAAATCAAGTGAAA
1 AAAAAAGAAAATAAAGTGAAA
3881 AAAAAAGAAAA-AAATGTGAAA
1 AAAAAAGAAAATAAA-GTGAAA
3902 GAAATGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (21 bp):
AAAAAAGAAAATAAAGTGAAA
Found at i:5679 original size:22 final size:22
Alignment explanation
Indices: 5653--5700 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5643 AGACAGTAGC
*
5653 CAAGAATGGGTA-AAGAAGAAGT
1 CAAGAAAGGGTAGAAGAAG-AGT
*
5675 CAAGAAAGGGTAGATGAAGAGT
1 CAAGAAAGGGTAGAAGAAGAGT
5697 CAAG
1 CAAG
5701 TTAAGGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.48, C:0.06, G:0.33, T:0.12
Consensus pattern (22 bp):
CAAGAAAGGGTAGAAGAAGAGT
Found at i:5856 original size:35 final size:35
Alignment explanation
Indices: 5810--6405 Score: 937
Period size: 35 Copynumber: 17.1 Consensus size: 35
5800 CTGTGCGGTC
* *
5810 TTTCAGGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
5845 TTTCAAGAAGTTTT-AGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
5879 TTCCAAGAAGTTTCCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
5914 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
5949 TATCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
5984 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
6019 TTCCAAGAAGTTTTCAGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
6054 TATCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
6089 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
6124 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
6159 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
6194 TTCCAAGAAGTTTCCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
6229 TTCCAAGAAGTTTCCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
6264 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
6299 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * * *
6334 TTCCAAGAAGTTTTTAGAGGTCACAGTTGATCGCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
6369 TTTTC-A-TAGTTTTTAGAGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
6403 TTT
1 TTT
6406 TCAGTATTTT
Statistics
Matches: 527, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
33 3 0.01
34 55 0.10
35 466 0.88
36 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:6433 original size:35 final size:35
Alignment explanation
Indices: 6358--6650 Score: 410
Period size: 35 Copynumber: 8.4 Consensus size: 35
6348 TAGAGGTCAC
** *
6358 AGTTGATCGCATTTTCA-TAGTTTTTAGA-GGTCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCA-ACGATCAG
* *
6392 AGTTGATCTCATTTTCAGTATTTTCCAACGATCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
*
6427 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAA
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
** *
6462 AGTTGATATCATTTTCAGTATTTTCCAACGATCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
6497 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
* * *
6532 AGTTGATCGCATTTTTAGTATTTTCCAACGATCAA
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
6567 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
* * *
6602 AGATGATCACATTTTCAGTAGTTTCCAACAATCAG
1 AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
* *
6637 AGGTGATCTCATTT
1 AGTTGATCGCATTT
6651 CAAGAAATTC
Statistics
Matches: 231, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
34 17 0.07
35 214 0.93
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.37
Consensus pattern (35 bp):
AGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
Found at i:8766 original size:74 final size:74
Alignment explanation
Indices: 8635--8784 Score: 255
Period size: 74 Copynumber: 2.0 Consensus size: 74
8625 AGGGAAATTC
* *
8635 GTAATTACGAAAAAGGGTAGAAGGAAAAGGAATTGGGGAAACTCATAAAGGGACTTTTTAGTCAT
1 GTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGACTTTTTAGTCAC
8700 CCAAAAAGT
66 CCAAAAAGT
* *
8709 GTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCAC
1 GTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGACTTTTTAGTCAC
*
8774 CCGAAAAGT
66 CCAAAAAGT
8783 GT
1 GT
8785 GAAAAGACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (74 bp):
GTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAAAGGGACTTTTTAGTCAC
CCAAAAAGT
Found at i:10478 original size:11 final size:11
Alignment explanation
Indices: 10449--10478 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10439 TTATTCATTT
*
10449 TTAATTAACTA
1 TTAATTAGCTA
10460 TTAATTAGCTA
1 TTAATTAGCTA
10471 TTAATTAG
1 TTAATTAG
10479 ATATAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (11 bp):
TTAATTAGCTA
Found at i:13248 original size:15 final size:14
Alignment explanation
Indices: 13230--13259 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
13220 TTTTCTAATA
13230 TTTATTTATTATATT
1 TTTATTTATT-TATT
13245 TTTATTTATTTATT
1 TTTATTTATTTATT
13259 T
1 T
13260 AGTTTGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:13345 original size:11 final size:11
Alignment explanation
Indices: 13302--13339 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13292 TTCCTATATA
*
13302 AAATAAATTAT
1 AAATTAATTAT
13313 CAAA-TAATTAT
1 -AAATTAATTAT
13324 AAATTAATTAT
1 AAATTAATTAT
13335 AAATT
1 AAATT
13340 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:13700 original size:27 final size:27
Alignment explanation
Indices: 13669--13785 Score: 74
Period size: 27 Copynumber: 4.3 Consensus size: 27
13659 TAACTGAATT
13669 TTTCTTAAAAGAATTTATAAAATAAAA
1 TTTCTTAAAAGAATTTATAAAATAAAA
** * * *
13696 TTTCTTAACTGAATTTTCTTAAA-AGAA
1 TTTCTTAAAAGAA-TTTATAAAATAAAA
* * * * * * * *
13723 TTTATAAAATAAAATTTCTTAACTGAAT
1 TTTCTTAAA-AGAATTTATAAAATAAAA
*
13751 TTTCTTAAAAGAATTTATAAAATAAAT
1 TTTCTTAAAAGAATTTATAAAATAAAA
*
13778 TTTTTTAA
1 TTTCTTAA
13786 CTGAATTTTC
Statistics
Matches: 65, Mismatches: 22, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
27 48 0.74
28 17 0.26
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTCTTAAAAGAATTTATAAAATAAAA
Found at i:13725 original size:41 final size:41
Alignment explanation
Indices: 13653--13818 Score: 305
Period size: 41 Copynumber: 4.0 Consensus size: 41
13643 GCAAAATTTC
13653 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
13695 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
13736 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
* *
13777 TTTTTTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
13818 A
1 A
13819 CAGTCGCACG
Statistics
Matches: 121, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
41 107 0.88
42 14 0.12
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (41 bp):
ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
Found at i:14635 original size:2 final size:2
Alignment explanation
Indices: 14628--14672 Score: 63
Period size: 2 Copynumber: 21.0 Consensus size: 2
14618 ATTGTTTTAA
14628 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT GAT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT -AT
14671 AT
1 AT
14673 TAAAATTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 34 0.85
3 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Done.