Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011205.1 Corchorus capsularis cultivar CVL-1 contig11226, 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: 14510
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:286 original size:2 final size:2
Alignment explanation
Indices: 279--308 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
269 AAGTTTTGTA
279 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
309 GGGTAAAATG
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:381 original size:20 final size:22
Alignment explanation
Indices: 352--424 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
342 TTTTAGTCAT
352 TATATATATAAATA-ATATGAAA
1 TATATATA-AAATATATATGAAA
*
374 TATTTATAAAATATATATGAAA
1 TATATATAAAATATATATGAAA
* **
396 T-TACA-AATTTATATAT-AAA
1 TATATATAAAATATATATGAAA
415 -ATATATAAAA
1 TATATATAAAA
425 GCTCGATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
19 6 0.15
20 11 0.28
21 7 0.17
22 16 0.40
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (22 bp):
TATATATAAAATATATATGAAA
Found at i:396 original size:11 final size:11
Alignment explanation
Indices: 353--396 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
343 TTTAGTCATT
353 ATATATAT-AA
1 ATATATATGAA
363 ATA-ATATGAA
1 ATATATATGAA
* *
373 ATATTTATAAA
1 ATATATATGAA
384 ATATATATGAA
1 ATATATATGAA
395 AT
1 AT
397 TACAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 4 0.14
10 8 0.29
11 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
ATATATATGAA
Found at i:1349 original size:89 final size:89
Alignment explanation
Indices: 1183--1356 Score: 233
Period size: 89 Copynumber: 2.0 Consensus size: 89
1173 TCTGTGGACA
* * * * *
1183 TTTACGAAAAATAGTACTTTTTTAAATTGCATATTGCGGCGTTTCAACGCCACTATTTTGGGGCG
1 TTTACCAAAAATAATACTTTTTTAAATTGCAGATTACGGCATTTCAACGCCACTATTTTGGGGCG
** *
1248 TATAGATGCCGCTATCTGCAGAAG
66 TATAGACACCGCTATATGCAGAAG
* *
1272 TTTACCAAAAATAATACTTTTTTAAATTGCAGATTACGGCATTTCGACGCCACTA-TTTGAGGGT
1 TTTACCAAAAATAATACTTTTTTAAATTGCAGATTACGGCATTTCAACGCCACTATTTTG-GGGC
*
1336 GTCTAGACACCGCTATATGCA
65 GTATAGACACCGCTATATGCA
1357 ATTTAATACT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
88 4 0.05
89 69 0.95
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (89 bp):
TTTACCAAAAATAATACTTTTTTAAATTGCAGATTACGGCATTTCAACGCCACTATTTTGGGGCG
TATAGACACCGCTATATGCAGAAG
Found at i:1499 original size:32 final size:32
Alignment explanation
Indices: 1439--1583 Score: 184
Period size: 32 Copynumber: 4.5 Consensus size: 32
1429 TAAAAGCTAT
* *
1439 TAAATATAGCGGCGTTTGGTTCTTTAGACGCCGC
1 TAAATA-AG-GGCGTTTGCTTCTATAGACGCCGC
*
1473 TAAATAAGGGTGTTTGCTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTGCTTCTATAGACGCCGC
*
1505 TAAATAGGGGCGTTT-CGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTGC-TTCTATAGACGCCGC
* * *
1537 TAAATAAGGGCGTTTGGTTCTGTAGATGCCGC
1 TAAATAAGGGCGTTTGCTTCTATAGACGCCGC
*
1569 TAAATAAGGTCGTTT
1 TAAATAAGGGCGTTT
1584 TCTTTTCATA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
31 1 0.01
32 90 0.91
33 2 0.02
34 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTGCTTCTATAGACGCCGC
Found at i:3381 original size:2 final size:2
Alignment explanation
Indices: 3374--3406 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3364 ACCTTTTTGA
3374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3407 AGGAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5622 original size:16 final size:16
Alignment explanation
Indices: 5601--5655 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
5591 CCGAACCCCA
5601 AAAAAACTTGAACCCG
1 AAAAAACTTGAACCCG
*
5617 AAAAAA-TCAGAACCCG
1 AAAAAACT-TGAACCCG
* *
5633 AAAAATC-TGAAATCCG
1 AAAAAACTTG-AACCCG
5649 AAAAAAC
1 AAAAAAC
5656 CCGAACCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 29 0.94
ACGTcount: A:0.56, C:0.22, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAACTTGAACCCG
Found at i:5636 original size:15 final size:15
Alignment explanation
Indices: 5610--5653 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
5600 AAAAAAACTT
5610 GAACCCGAAAAAATCA
1 GAACCCG-AAAAATCA
*
5626 GAACCCGAAAAATCT
1 GAACCCGAAAAATCA
*
5641 GAAATCCGAAAAA
1 G-AACCCGAAAAA
5654 ACCCGAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.55, C:0.23, G:0.14, T:0.09
Consensus pattern (15 bp):
GAACCCGAAAAATCA
Found at i:5945 original size:32 final size:32
Alignment explanation
Indices: 5904--5974 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
5894 AATTGTCTCG
5904 AACCCGAATCAACCAGACCCAAATTTAACCCA
1 AACCCGAATCAACCAGACCCAAATTTAACCCA
* * *
5936 AACCCGAATCAACCCGACCTAAATTTAACCCG
1 AACCCGAATCAACCAGACCCAAATTTAACCCA
5968 AACCCGA
1 AACCCGA
5975 CTTAAGCCCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.41, C:0.38, G:0.08, T:0.13
Consensus pattern (32 bp):
AACCCGAATCAACCAGACCCAAATTTAACCCA
Found at i:13807 original size:19 final size:19
Alignment explanation
Indices: 13775--13814 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13765 TTGCACATCT
*
13775 TCTCTTTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAG
* *
13794 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCCCCCACTAAG
13813 TC
1 TC
13815 AAGATGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.47, G:0.05, T:0.35
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAG
Found at i:14507 original size:2 final size:2
Alignment explanation
Indices: 14457--14487 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14447 GATGGTAATA
14457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14488 ATAGAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.