Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015216.1 Corchorus capsularis cultivar CVL-1 contig15237, 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: 13119
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:766 original size:17 final size:17
Alignment explanation
Indices: 752--784 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
742 ACAGCCTATC
752 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
769 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
785 GTACTATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:3755 original size:19 final size:18
Alignment explanation
Indices: 3717--3755 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3707 TTTTTCGGTT
* *
3717 TAAATTTATAATATATAA
1 TAAATTTATAATAGAAAA
3735 TAAATTATATAATAGAAAA
1 TAAATT-TATAATAGAAAA
3754 TA
1 TA
3756 GAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATTTATAATAGAAAA
Found at i:6982 original size:179 final size:181
Alignment explanation
Indices: 6630--6991 Score: 597
Period size: 179 Copynumber: 2.0 Consensus size: 181
6620 TTTACGAGAG
* *
6630 TTGTAGACCATGGAATTACCTTTAAATAGACACTTGAATCACCTTGATCGGTCAAATAGGAAAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAATAGGAAAAA
* * *
6695 AATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAGTGATTAAATAATAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAT
*
6760 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAAATGA
131 AAATTATAAAAGCATGAGGATCATTTAATAAATAATCCAAC-AAAAAAATGA
*
6812 TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAAT-TG-AAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAATAGGAAAAA
* *
6875 AA-AAAACAATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAGCAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAT
6938 AAATTATAAAAGCATGAGGATCATTTTAATAAATAATCCAACAAAAAAATGA
131 AAATTATAAAAGCATGAGGATCA-TTTAATAAATAATCCAACAAAAAAATGA
6990 TT
1 TT
6992 TGTTTTATGG
Statistics
Matches: 170, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
178 45 0.26
179 63 0.37
180 6 0.04
181 1 0.01
182 55 0.32
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (181 bp):
TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAATAGGAAAAA
AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAACAT
AAATTATAAAAGCATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
Found at i:7138 original size:619 final size:623
Alignment explanation
Indices: 6203--7427 Score: 1601
Period size: 619 Copynumber: 2.0 Consensus size: 623
6193 ACCTGACATT
* * *
6203 AAATTATCTTTCAATAGACACTTGAATCACCTTGATCCGACAAATAGAACAAAAAATACAAAAAT
1 AAATTACCTTTAAATAGACACCTGAATCACCTTGATCCGACAAATAGAACAAAAAATACAAAAAT
* ** * *
6268 AAAAACCGACATGTTAAATCGTCTAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAA
66 AAAAACCGAAACATTAAATCGTCCAACACATAATTGTAAAGGATTAAATAGCATAAAGCATAAAA
* * * *
6333 GTACGAGGGTCATTTGATAAATAATACAAGGAAAAAAATATTTGTTTATGAAGACCAAACATAAA
131 GCACGAGGATCATTTAATAAATAATACAAGCAAAAAAATATTTGTTTATGAAGACCAAACATAAA
* **
6398 AATTCTCTCTAAAATTCTCCACGAAACTCATTAATCAAATACAGCTTTCAGACCCTTGGCGAAAG
196 AATTCTCTCTAAAATCCTCCACGAAACTCATTAATCAAATACAGCTTTCAGACCCTTAACGAAAG
* * *
6463 TCGTAGATAACACAATCACCTTTCAACCGACACTTGAACAACCTCAATCGGACAAGTCGACCGAA
261 TCATAGATAACACAATAACCTTTCAACCGACACTTGAACAACCTCAATCAGACAAGTCGA-CGAA
* * *
6528 AA-TTATACAATATTAGATAGACCGACAATCGAGACCACAAAATTTTAGAAGCATTTTTTAGAAT
325 AATTTATACAATATCACATAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAAT
* * * * **
6592 CAAAACGTCAAAATTGGCTTTTGATTCCTTTAC-GAGAGTTGTAGACCATGGAATTACCTTTAAA
390 CAAAACATCAAAATTGGCTTTTGAGTCCTTCACGGA-ACTTGTAGACCATAAAATTACCTTTAAA
* * * **
6656 TAGACACTTGAATCACCTTGATCGGTCAAATAGGA-AAAAAATAAAAGAATTAAAGCCGAAACAT
454 TAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACAT
* * * **
6720 TCAATCGTCCAACCC-ATAATTGT-AAGTGATTAAATAATATAAATTATAAAAGTAT-GAGGATC
519 TCAATCGTCCAACCCAAAAATTGTGAAG-GACTAAATAACATAAAACATAAAAGTATAG-GGATC
*
6782 ATTTAATAAATAATCCAACAAAAAAAATGATTGTAGACCATG
582 ATTTAATAAATAAACCAACAAAAAAAATGATTGTAGACCATG
* * * *
6824 AAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAATTG-A-AAAAAA-A-AACAAT
1 AAATTACCTTTAAATAGACACCTGAATCACCTTGATCCGACAAATAGAACAAAAAATACAAAAAT
* * * * **
6885 TAAAGCCGAAACATTCAATCGTCCAACATATAATTGT-AAGGATTAAATAGCATAAATTATAAAA
66 AAAAACCGAAACATTAAATCGTCCAACACATAATTGTAAAGGATTAAATAGCATAAAGCATAAAA
* * *
6949 GCATGAGGATCATTTTAATAAATAATCCAA-CAAAAAAATGATTTGTTTTATGGAGACCAAACAT
131 GCACGAGGATCA-TTTAATAAATAATACAAGCAAAAAAAT-ATTTG-TTTATGAAGACCAAACAT
** * * *
7013 AAAAAATTCTCTCTTGAATCCTCCACGAAACTCATTAATCAAATTCGGCTTTCAGGCCCTTAACG
193 -AAAAATTCTCTCTAAAATCCTCCACGAAACTCATTAATCAAATACAGCTTTCAGACCCTTAACG
* * *
7078 AAAGTCATAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCAGACAAGTGGAC
257 AAAGTCATAGATAACACAATAACCTTTCAACCGACACTTGAACAACCTCAATCAGACAAGTCGAC
* * ** *
7143 TAAAATTTATACGATATCACATAGACCGGTAATCGAGACCACAAAATTTCAGAAGCATTTTTTTG
322 GAAAATTTATACAATATCACATAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAG
* * ** * * *
7208 AATGAAAACATTAAAATTGTTTTTTGAGTCCTTCATGGAACTTGTAGATCATAAAATTACCTTTT
387 AATCAAAACATCAAAATTGGCTTTTGAGTCCTTCACGGAACTTGTAGACCATAAAATTACCTTTA
*
7273 AATAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCTGAAAC
452 AATAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAAC
* *
7338 GTTCAATCGTCCAACCCAAAAATTGTGAAGGACTAAATAGCATAAAACATAAAAGTATAGGGATC
517 ATTCAATCGTCCAACCCAAAAATTGTGAAGGACTAAATAACATAAAACATAAAAGTATAGGGATC
* * *
7403 GTTTGATAAATAAACCAGCAAAAAA
582 ATTTAATAAATAAACCAACAAAAAA
7428 TGATTTGTTT
Statistics
Matches: 517, Mismatches: 77, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
616 42 0.08
617 53 0.10
618 23 0.04
619 253 0.49
620 45 0.09
621 97 0.19
622 4 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (623 bp):
AAATTACCTTTAAATAGACACCTGAATCACCTTGATCCGACAAATAGAACAAAAAATACAAAAAT
AAAAACCGAAACATTAAATCGTCCAACACATAATTGTAAAGGATTAAATAGCATAAAGCATAAAA
GCACGAGGATCATTTAATAAATAATACAAGCAAAAAAATATTTGTTTATGAAGACCAAACATAAA
AATTCTCTCTAAAATCCTCCACGAAACTCATTAATCAAATACAGCTTTCAGACCCTTAACGAAAG
TCATAGATAACACAATAACCTTTCAACCGACACTTGAACAACCTCAATCAGACAAGTCGACGAAA
ATTTATACAATATCACATAGACCGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTAGAATC
AAAACATCAAAATTGGCTTTTGAGTCCTTCACGGAACTTGTAGACCATAAAATTACCTTTAAATA
GACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAATAAAAGAATTAAAGCCGAAACATTC
AATCGTCCAACCCAAAAATTGTGAAGGACTAAATAACATAAAACATAAAAGTATAGGGATCATTT
AATAAATAAACCAACAAAAAAAATGATTGTAGACCATG
Found at i:7790 original size:24 final size:24
Alignment explanation
Indices: 7758--7811 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
7748 AGAGAAACAA
*
7758 TTGTTGTTGTTGTTGAAACTG-TTG
1 TTGTTGTTGCTGTTGAAA-TGCTTG
7782 TTGTTGTTGCTGTTGAAATGCTTG
1 TTGTTGTTGCTGTTGAAATGCTTG
7806 TTGTTG
1 TTGTTG
7812 CTGTGGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.11, C:0.06, G:0.30, T:0.54
Consensus pattern (24 bp):
TTGTTGTTGCTGTTGAAATGCTTG
Found at i:7806 original size:21 final size:22
Alignment explanation
Indices: 7758--7821 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
7748 AGAGAAACAA
* *
7758 TTGTTGTTGTTGTTGAAACTGTTG
1 TTGTTGTTGCTGTTGAAA-TG-TC
7782 TTGTTGTTGCTGTTGAAATG-C
1 TTGTTGTTGCTGTTGAAATGTC
*
7803 TTGTTGTTGCTGTGGAAAT
1 TTGTTGTTGCTGTTGAAAT
7822 TGTAACTGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.49
23 2 0.05
24 17 0.46
ACGTcount: A:0.14, C:0.06, G:0.30, T:0.50
Consensus pattern (22 bp):
TTGTTGTTGCTGTTGAAATGTC
Found at i:9971 original size:29 final size:29
Alignment explanation
Indices: 9929--10018 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
9919 TCGTTTGGCA
* *
9929 TTTTGTTTTATTTT-TTCTTAATTTTTTTT
1 TTTTGTTTCATTTTCGT-TTAATTTTTTTT
* *
9958 TTTTGTTTCGTTTTCGTTTAGTTTTTTTT
1 TTTTGTTTCATTTTCGTTTAATTTTTTTT
**
9987 TTTT-TTTTTTTTTGCGTTGTCAATTTTTTTT
1 TTTTGTTTCATTTT-CGTT-T-AATTTTTTTT
10018 T
1 T
10019 AAAACAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
28 7 0.14
29 31 0.62
30 2 0.04
31 10 0.20
ACGTcount: A:0.07, C:0.06, G:0.09, T:0.79
Consensus pattern (29 bp):
TTTTGTTTCATTTTCGTTTAATTTTTTTT
Found at i:11170 original size:16 final size:16
Alignment explanation
Indices: 11114--11172 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
11104 CGGGCTCGGG
*
11114 TCGGGTTCGGGT-TGTC
1 TCGGGTTCGGGTAT-TT
* *
11130 TCCGGTTCAGGTATTT
1 TCGGGTTCGGGTATTT
11146 TCGGGTTCGGGTAATTT
1 TCGGGTTCGGGT-ATTT
11163 T-GGGTTCGGG
1 TCGGGTTCGGG
11173 CGGGTTCAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 30 0.83
17 6 0.17
ACGTcount: A:0.07, C:0.15, G:0.39, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTATTT
Found at i:12739 original size:2 final size:2
Alignment explanation
Indices: 12732--12768 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12722 CTTCTTTTAT
12732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12769 ACACACAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.