Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024185.1 Corchorus olitorius cultivar O-4 contig24218, 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: 25185
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1469 original size:22 final size:22
Alignment explanation
Indices: 1415--1585 Score: 108
Period size: 22 Copynumber: 7.8 Consensus size: 22
1405 TGAATATTTT
*
1415 TATGAAATTTTGATAACTACTGTCC
1 TATGAAATTTTGATAACTAC---AC
*
1440 TATTAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACTACAC
*
1462 TATGAAATTTTGATAATTTAC-C
1 TATGAAATTTTGATAA-CTACAC
* *
1484 TATGAAATTGTGATAAACTCCA-
1 TATGAAATTTTGAT-AACTACAC
*
1506 TA-GAAACTTTGATAACCTA-AC
1 TATGAAATTTTGATAA-CTACAC
* *
1527 TATGAAATATT-ATAAACATTC-C
1 TATGAAATTTTGAT-AAC-TACAC
*
1549 TATGAAATTTTG-TAACCTTCA-
1 TATGAAATTTTGATAA-CTACAC
*
1570 TATG-ATTTTTGATAAC
1 TATGAAATTTTGATAAC
1586 CTCCCTGAAG
Statistics
Matches: 118, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
20 10 0.08
21 28 0.24
22 56 0.47
23 5 0.04
25 19 0.16
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACAC
Found at i:1565 original size:43 final size:43
Alignment explanation
Indices: 1415--1566 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 43
1405 TGAATATTTT
** * *
1415 TATGAAATTTTGATAACTACTGTCCTATTAAATTTTGAT-AACTACAC
1 TATGAAATTTTGATAAC--CT-AACTATGAAATTGTGATAAACT-C-C
** *
1462 TATGAAATTTTGATAATTTACCTATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATAACCTAACTATGAAATTGTGATAAACTCC
*
1505 -ATAGAAACTTTGATAACCTAACTATGAAATAT-T-ATAAACATTCC
1 TAT-GAAATTTTGATAACCTAACTATGAAAT-TGTGATAAAC--TCC
1549 TATGAAATTTTG-TAACCT
1 TATGAAATTTTGATAACCT
1567 TCATATGATT
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
42 8 0.09
43 31 0.35
44 27 0.30
45 7 0.08
47 16 0.18
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTAACTATGAAATTGTGATAAACTCC
Found at i:1815 original size:6 final size:6
Alignment explanation
Indices: 1804--1831 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1794 ATTTGATAGT
1804 ATATAC ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
1832 TAAAGTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:3816 original size:27 final size:26
Alignment explanation
Indices: 3762--3822 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
3752 CTAAATTTCC
3762 ATTATTTTAATAATTCAATAATTAAAAT
1 ATTA-TTTAATAATTCAAT-ATTAAAAT
3790 ATTATTTAATAATGTCAAT-TTAGAAAT
1 ATTATTTAATAAT-TCAATATTA-AAAT
3817 A-TATTT
1 ATTATTT
3823 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 14 0.45
28 9 0.29
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTATTTAATAATTCAATATTAAAAT
Found at i:12570 original size:2 final size:2
Alignment explanation
Indices: 12563--12603 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
12553 AAACTTCACA
* *
12563 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12604 TTTGCATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:16333 original size:11 final size:11
Alignment explanation
Indices: 16290--16327 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16280 TTCCTATATA
*
16290 AAATAAATTAT
1 AAATTAATTAT
16301 CAAA-TAATTAT
1 -AAATTAATTAT
16312 AAATTAATTAT
1 AAATTAATTAT
16323 AAATT
1 AAATT
16328 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:17464 original size:28 final size:29
Alignment explanation
Indices: 17423--17478 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
17413 TGAAAATAAA
*
17423 AAAATTACG-GAAAAAAAGAATCCTAATT
1 AAAATTACGAAAAAAAAAGAATCCTAATT
17451 AAAATTACGAAAAAAAAAAGAATCCTAA
1 AAAATTACG-AAAAAAAAAGAATCCTAA
17479 ACCTAGTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
30 16 0.64
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.18
Consensus pattern (29 bp):
AAAATTACGAAAAAAAAAGAATCCTAATT
Found at i:22027 original size:437 final size:434
Alignment explanation
Indices: 21263--22287 Score: 1286
Period size: 437 Copynumber: 2.3 Consensus size: 434
21253 AACGCGTTGC
* *
21263 CTTTTATTTTTGTATTTTTTTTCTATTTGTCCGGTTAAGTTAATTCAAGTGTCTATTAAAAAGGT
1 CTTTTATTTTT-TATTTTTGTTCTATTTGTCCGATTAAGTTAATTCAAGTGTCTATT-AAAAGGT
* * ** * ** **
21328 AATTTCATGATCTACAATTTTTATTCAGAACTCAAAAGTCAATTTAAATATTTTGATTCTAAAAA
64 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAG-CAATTTTTATATTTCAATTCTAAAAA
* * ** *
21393 ATGCTTTCGAAATTTTGTGGTTTTGATTGTCGGTTAATTTAATATCATATAATTTTTCATCCACA
128 ATGCTTCCGAAATTTTGTCGTTTCAATTGTCGGTTAATTTAATACCATATAATTTTTCATCCACA
* * * * * * *
21458 TGTCCGATTGAAGTTATTGAAGTATCGTTTAAAAGGTTATTGCATAATTTACGACTTTCATGAAG
193 TGTCCAATTAAAGTTATTCAAGTATCGGTTAAAAGATTATTGCATAATCTACGACTTCCATGAAG
* *
21523 GACCCGAAAGCTAAATTTGATCTACGAGTTTCGTGAAAGGTTCAAAAGGGAATTTTCATGATTCA
258 AACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAAGGTTCAAAAGGGAATTTTCATGATTCA
* * * * *
21588 AGATCTCCATTAATAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTAC
323 AGATCCCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTAC
*
21653 TTTATACTACTTATTCCTTTACAAATTCTATCTTAATCTAATGTTTAA-A
388 TTTATACTACTTAGTCCTTTACAAATTCTATCTTAATC-AA--TTTAACA
* *
21702 -TTTTATTTTTTATTTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAA
1 CTTTTATTTTTTATTTTTGTTCTATTTGTCCGATTAAGTTAATTCAAGTGTCTATTAAAAGGTAA
* *
21766 TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAAT
66 TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATATTTCAATTCTAAAAAAT
* * *
21831 GCTTCCTAAA-TTTGTTCGTTTCAATTGTTGGTCT-ATTTAATACCCCATATAATTTTTGATCCA
130 GCTTCCGAAATTTTG-TCGTTTCAATTGTCGGT-TAATTTAATA--CCATATAATTTTTCATCCA
* *
21894 CATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGATTATTGTATAATCTACGACTTCCATGA
191 CATGTCCAATTAAAGTTATTCAAGTATCGGTTAAAAGATTATTGCATAATCTACGACTTCCATGA
* * * * * * *
21959 AGAACCCGAAA-TTTAATTTGATCTATGAGTTTTATGAAGGGTTCAAAAGGGAATTTTTATGTTT
256 AGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAAGGTTCAAAAGGGAATTTTCATGATT
* *
22023 CAAGATCCCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCATCCTCATACTTTTCT
321 CAAGATCCCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCT
* * * *
22088 ATTTTATGCTACTTAGTCCTTTCCAAATTCTATCTTACTCAATTTAACA
386 ACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCAATTTAACA
* * * * *
22137 CTTCATTTTTTTTTATTTTCTTTGCTCTATTTGTCCAATTAAGATAATTCAGGTGTCTATTAAAA
1 CTT--TTATTTTTTA--TT-TTTGTTCTATTTGTCCGATTAAGTTAATTCAAGTGTCTATTAAAA
* * *
22202 GGTAATTTTATGATCTACAACTTTCATGAAAGATTCAAAAGCTAATTTTTATATTTCAATTCTAA
61 GGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATATTTCAATTCTAA
* **
22267 AAAATACTTTTGAAATTTTGT
125 AAAATGCTTCCGAAATTTTGT
22288 GATTTCGGTT
Statistics
Matches: 504, Mismatches: 69, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
434 5 0.01
435 6 0.01
436 94 0.19
437 180 0.36
438 102 0.20
440 2 0.00
441 111 0.22
442 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (434 bp):
CTTTTATTTTTTATTTTTGTTCTATTTGTCCGATTAAGTTAATTCAAGTGTCTATTAAAAGGTAA
TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAATTTTTATATTTCAATTCTAAAAAATG
CTTCCGAAATTTTGTCGTTTCAATTGTCGGTTAATTTAATACCATATAATTTTTCATCCACATGT
CCAATTAAAGTTATTCAAGTATCGGTTAAAAGATTATTGCATAATCTACGACTTCCATGAAGAAC
CCGAAAGCTAAATTTGATCTACGAGTTTCATGAAAGGTTCAAAAGGGAATTTTCATGATTCAAGA
TCCCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTT
ATACTACTTAGTCCTTTACAAATTCTATCTTAATCAATTTAACA
Found at i:24799 original size:7 final size:7
Alignment explanation
Indices: 24789--24813 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
24779 ACTTCAAAGT
24789 TGAGCAA
1 TGAGCAA
24796 TGAGCAA
1 TGAGCAA
24803 TGAGCAA
1 TGAGCAA
24810 TGAG
1 TGAG
24814 ATTGTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (7 bp):
TGAGCAA
Done.