Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008982.1 Corchorus capsularis cultivar CVL-1 contig09003, 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: 43722
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--73 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1 A
2 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
44 TC TC 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 TC TC
74 ATTTACCTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5497 original size:19 final size:21
Alignment explanation
Indices: 5461--5502 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5451 TTTCTTCTTT
5461 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
5481 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
5501 TT
1 TT
5503 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:7455 original size:21 final size:22
Alignment explanation
Indices: 7406--7456 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
7396 GCGGCGCGAG
7406 CGGGGAGGCACCCTTGACAAGAA
1 CGGGGA-GCACCCTTGACAAGAA
* **
7429 CAGGGAGC-CCCTTGACGTGAA
1 CGGGGAGCACCCTTGACAAGAA
7450 CGGGGAG
1 CGGGGAG
7457 GTCACCTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 2 0.08
23 5 0.21
ACGTcount: A:0.25, C:0.25, G:0.39, T:0.10
Consensus pattern (22 bp):
CGGGGAGCACCCTTGACAAGAA
Found at i:11829 original size:24 final size:24
Alignment explanation
Indices: 11797--11845 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
11787 GTGGAGGATG
*
11797 TGATGGGCTAGTAGCCCCAATAAT
1 TGATGGGCTAGTAGCCCCAAAAAT
11821 TGATGGGCTAGTAGCCCCAAAAAT
1 TGATGGGCTAGTAGCCCCAAAAAT
11845 T
1 T
11846 TAAGACTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (24 bp):
TGATGGGCTAGTAGCCCCAAAAAT
Found at i:13698 original size:19 final size:21
Alignment explanation
Indices: 13662--13705 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
13652 TTTCTTCTAT
13662 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
13682 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
13702 TTTA
1 TTTA
13706 TAGTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:14777 original size:157 final size:156
Alignment explanation
Indices: 14511--14869 Score: 381
Period size: 157 Copynumber: 2.3 Consensus size: 156
14501 CAAACTGGAC
* * * *
14511 TTCACACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCTAAGTCTGATTGAG
1 TTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCGAAGTCTCAATGAG
* * *
14576 CTGAAACTTTGCCAAGGGACTTAGATTCTCTCCACAAGAATATGGAAAAAAATTCTAAGTAAAAC
66 CTGAAACTTTGCCAAGGGACTTAGATTATCCCCAAAAGAATATGGAAAAAAA-TCTAAGTAAAAC
* * * *
14641 CGAGCTCCCCTTG-ATGGTGAACTAGGT
130 CGAACT-CCCTAGCATAGAGAACTAGGT
* * *
14668 TTCTCTCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCGAAGTC-CAATGAA
1 TTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCGAAGTCTCAATG-A
* * *
14732 GCTG-AA-TTT-CCACCAGTAGG-CTTATATTATCCCCATAAAG-CTATGGGAAAAAATCTAAGT
65 GCTGAAACTTTGCCA--AG--GGACTTAGATTATCCCCA-AAAGAATATGGAAAAAAATCTAAGT
* * * *
14792 AAAACTGAACTCTCTAGCATAGAGAAGTTGGT
125 AAAACCGAACTCCCTAGCATAGAGAACTAGGT
* * *
14824 TTGACACCCCAAACTGTCCTTAACTGAAAAACAAGCATAAGTTTTT
1 TTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTT
14870 CATCCTAAGT
Statistics
Matches: 168, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
154 3 0.02
155 7 0.04
156 73 0.43
157 80 0.48
158 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (156 bp):
TTCACACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTATTCGAAGTCTCAATGAG
CTGAAACTTTGCCAAGGGACTTAGATTATCCCCAAAAGAATATGGAAAAAAATCTAAGTAAAACC
GAACTCCCTAGCATAGAGAACTAGGT
Found at i:19526 original size:29 final size:30
Alignment explanation
Indices: 19472--19530 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
19462 ATGAAACTAG
*
19472 CAACTCATACCCCCCTAACATCAATAAAGC
1 CAACTCATACCCCCCTAACATAAATAAAGC
* *
19502 CAACTCAT-GCCCCCTAGCATAAATAAAGC
1 CAACTCATACCCCCCTAACATAAATAAAGC
19531 ATAATATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.39, C:0.37, G:0.07, T:0.17
Consensus pattern (30 bp):
CAACTCATACCCCCCTAACATAAATAAAGC
Found at i:19654 original size:15 final size:15
Alignment explanation
Indices: 19634--19670 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19624 TTTGTTTTAT
19634 TAGTATAAAATATAA
1 TAGTATAAAATATAA
*
19649 TAGTATAAACTATAA
1 TAGTATAAAATATAA
19664 TAGTATA
1 TAGTATA
19671 TAGTTCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (15 bp):
TAGTATAAAATATAA
Found at i:26561 original size:38 final size:37
Alignment explanation
Indices: 26494--26569 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
26484 GATTATTGCA
* * *
26494 TGATCTACGACTTTCATGGAGGGGGCGAAAGCTAAATT
1 TGATCTACGACTTTCATGAAGGGCGCGAAA-ATAAATT
* *
26532 TGATTTACGACTTTCATGAAGGGCTCGAAAATAAATT
1 TGATCTACGACTTTCATGAAGGGCGCGAAAATAAATT
26569 T
1 T
26570 TTATGTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (37 bp):
TGATCTACGACTTTCATGAAGGGCGCGAAAATAAATT
Found at i:26654 original size:427 final size:427
Alignment explanation
Indices: 25854--26681 Score: 1120
Period size: 427 Copynumber: 1.9 Consensus size: 427
25844 TTTTGTTCTG
* * * *
25854 TTTGTCCGATTAAGGTGATTCATGTGTCTATTAGAAGGTAATCTCATGATCTACAACTTTCGTGA
1 TTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGATAATCTCATGATCTACAAATTTCATGA
* * * * *
25919 AGGACTCAAAAGCCAGTTTTAATGTTTCAATTCAAAAAAATGCTTCTGAAATTTAGTGGTTTTGA
66 AGAACTCAAAAGCCAATTTTAATGTTTCAATTCAAAAAAATACTTCTAAAATTTAGTGGTTTCGA
* * * * *** * * *
25984 TTGCCGGTCTATTTAATATCATATAATTTTCAATCCGTGTGTCCGGTTAAAGTTATTCAGGTGCC
131 TTACCAGTCTATTTAATACCAAATAATTTTCAATCCACATGTCCGATTAAAATTATTCAAGTGCC
*
26049 GGTTAAAAGTTTATTGCATGATATACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATATACG
196 GGTTAAAAGATTATTGCATGATATACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATATACG
* * * * *
26114 AGTTTCATAAATGGCTCAAAACAGAATTTTCATGTTTCAAGATTTCCATCGACAAACATTTTCTT
261 ACTTTCATAAAGGGCTCAAAACAGAATTTTCATGTTTCAAGATCTCCACCAACAAACATTTTCTT
* * * *
26179 ATTTGGATTATTTATCGAATGATCATCATATTTTTTTACTTCATACTACTTAGTCCTTTACTAAT
326 ATTTGGATTATTTATCAAATGACCATCACATTTTTCTACTTCATACTACTTAGTCCTTTACTAAT
26244 TCTATCTTAATTTAACGTTTCAGCTTTATTTTTTTTA
391 TCTATCTTAATTTAACGTTTCAGCTTTATTTTTTTTA
* * *
26281 TTTGTCCTATTAAGGTGATTTA-GATGTCTATTAAAAGATAATTTCATGATCTACAAATTTCATG
1 TTTGTCCGATTAAGGTGATTCATG-TGTCTATTAAAAGATAATCTCATGATCTACAAATTTCATG
* * * * * *
26345 AAGAAGTCAAAAGTCAATTTTTATGTTTCAATTCTAAAAAATACTTTTAAAATTTTGTGGTTTCG
65 AAGAACTCAAAAGCCAATTTTAATGTTTCAATTCAAAAAAATACTTCTAAAATTTAGTGGTTTCG
* * * **
26410 ATTATCAGTCTATTTAATACCAAATAATTTTTAATCTACATGTCCGATTAAAATTATTCAAGTTT
130 ATTACCAGTCTATTTAATACCAAATAATTTTCAATCCACATGTCCGATTAAAATTATTCAAGTGC
* * *** *
26475 CGGTTAAAAGATTATTGCATGATCTACGACTTTCATGGAGGGGGCGAAAGCTAAATTTGATTTAC
195 CGGTTAAAAGATTATTGCATGATATACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATATAC
* * *
26540 GACTTTCATGAAGGGCTCGAAAATA-AATTTTTATGTTTCAAGATCTCCACCAACAAACATTTTC
260 GACTTTCATAAAGGGCTC-AAAACAGAATTTTCATGTTTCAAGATCTCCACCAACAAACATTTTC
* * * *
26604 TTATTTGGATTATTTATCAAATGACCCTCACATTTTTCTATTTTATACTACTTAGTCCTTTACTG
324 TTATTTGGATTATTTATCAAATGACCATCACATTTTTCTACTTCATACTACTTAGTCCTTTACTA
26669 ATTCTATCTTAAT
389 ATTCTATCTTAAT
26682 CGATTTAAAG
Statistics
Matches: 343, Mismatches: 56, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
426 1 0.00
427 337 0.98
428 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (427 bp):
TTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGATAATCTCATGATCTACAAATTTCATGA
AGAACTCAAAAGCCAATTTTAATGTTTCAATTCAAAAAAATACTTCTAAAATTTAGTGGTTTCGA
TTACCAGTCTATTTAATACCAAATAATTTTCAATCCACATGTCCGATTAAAATTATTCAAGTGCC
GGTTAAAAGATTATTGCATGATATACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATATACG
ACTTTCATAAAGGGCTCAAAACAGAATTTTCATGTTTCAAGATCTCCACCAACAAACATTTTCTT
ATTTGGATTATTTATCAAATGACCATCACATTTTTCTACTTCATACTACTTAGTCCTTTACTAAT
TCTATCTTAATTTAACGTTTCAGCTTTATTTTTTTTA
Found at i:39532 original size:2 final size:2
Alignment explanation
Indices: 39525--39554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39515 TTATTATTGG
39525 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
39555 GGATCAAAAA
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:40821 original size:3 final size:3
Alignment explanation
Indices: 40813--40837 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40803 TGATGAATAT
40813 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
40838 CAAAGGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Done.