Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010593.1 Corchorus capsularis cultivar CVL-1 contig10614, 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: 39246
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5323 original size:16 final size:16
Alignment explanation
Indices: 5254--5331 Score: 70
Period size: 16 Copynumber: 4.8 Consensus size: 16
5244 TCTGAACCTG
*
5254 AACCCGAAAAAACCT-T
1 AACCCG-AAAAACCTCA
* *
5270 AATCCGAAAAAGCTCA
1 AACCCGAAAAACCTCA
**
5286 AACCTAAAAAAACC-CA
1 AACC-CGAAAAACCTCA
5302 AACCCGAAAAACCTCA
1 AACCCGAAAAACCTCA
5318 AACCCGAAAGAACC
1 AACCCGAAA-AACC
5332 CGAATCCTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.29
16 25 0.51
17 10 0.20
ACGTcount: A:0.53, C:0.32, G:0.08, T:0.08
Consensus pattern (16 bp):
AACCCGAAAAACCTCA
Found at i:5332 original size:32 final size:32
Alignment explanation
Indices: 5254--5332 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
5244 TCTGAACCTG
** * *
5254 AACCCGAAAAAACCTTAATCCGAAAAAGCTCA
1 AACCCGAAAAAACCCAAACCCGAAAAACCTCA
**
5286 AACCTAAAAAAACCCAAACCCGAAAAACCTCA
1 AACCCGAAAAAACCCAAACCCGAAAAACCTCA
*
5318 AACCCGAAAGAACCC
1 AACCCGAAAAAACCC
5333 GAATCCTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.52, C:0.33, G:0.08, T:0.08
Consensus pattern (32 bp):
AACCCGAAAAAACCCAAACCCGAAAAACCTCA
Found at i:5519 original size:32 final size:32
Alignment explanation
Indices: 5483--5567 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
5473 TGGCCAAAAT
* * *
5483 CCAAACAGAACCCGAACCCGAATTAACCTGAC
1 CCAAACACAACCCGAACCCGAATTAACATAAC
**
5515 CCAAATTCAACCCGAACCCGAATTAACATAAC
1 CCAAACACAACCCGAACCCGAATTAACATAAC
*
5547 CCAAATC-CAACCCAAACCCGA
1 CCAAA-CACAACCCGAACCCGA
5568 CTCAAGCCCG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.42, C:0.39, G:0.08, T:0.11
Consensus pattern (32 bp):
CCAAACACAACCCGAACCCGAATTAACATAAC
Found at i:5876 original size:37 final size:37
Alignment explanation
Indices: 5835--5909 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
5825 ATAGCCTATC
*
5835 ATTTAATTTCATATTTATAAGTA-AAAAAAAGAAGTTG
1 ATTTAATTTCATATTCATAAGTACAAAAAAA-AAGTTG
5872 ATTTAATTTCATATTCATAAGTAGCAAAAAAAAAGTTG
1 ATTTAATTTCATATTCATAAGTA-CAAAAAAAAAGTTG
5910 TATATGACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 22 0.63
38 6 0.17
39 7 0.20
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (37 bp):
ATTTAATTTCATATTCATAAGTACAAAAAAAAAGTTG
Found at i:7931 original size:5 final size:5
Alignment explanation
Indices: 7921--7950 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
7911 TTAAGACCAA
*
7921 GCCCG GCCCG GCCCG GCCCG GTCCG GCCCG
1 GCCCG GCCCG GCCCG GCCCG GCCCG GCCCG
7951 TATAGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.57, G:0.40, T:0.03
Consensus pattern (5 bp):
GCCCG
Found at i:13077 original size:26 final size:25
Alignment explanation
Indices: 13048--13114 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 25
13038 TGGCAATTCA
13048 TTTTCTCTATTTGGAAAAGCAAATCTT
1 TTTTCT-TATTTGGAAAAGCAAATC-T
* * *
13075 TTTTTTTACCTCGGAAAAGCAAATCT
1 TTTTCTTA-TTTGGAAAAGCAAATCT
* *
13101 GTTTCTTCTTTGGA
1 TTTTCTTATTTGGA
13115 TAATTATTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
25 4 0.13
26 8 0.26
27 19 0.61
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (25 bp):
TTTTCTTATTTGGAAAAGCAAATCT
Found at i:13496 original size:12 final size:12
Alignment explanation
Indices: 13479--13504 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13469 TTGTTGGATT
13479 GACAGTATATAG
1 GACAGTATATAG
13491 GACAGTATATAG
1 GACAGTATATAG
13503 GA
1 GA
13505 GTCATAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.27, T:0.23
Consensus pattern (12 bp):
GACAGTATATAG
Found at i:13696 original size:31 final size:31
Alignment explanation
Indices: 13658--13719 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
13648 AGTTTTATAA
* *
13658 AACTTTTGAAACGCCTATTGTATCCTTATTT
1 AACTTTTGAAACACCTATTATATCCTTATTT
13689 AACTTTTGAAACACCTATTATATCCTTATTT
1 AACTTTTGAAACACCTATTATATCCTTATTT
13720 GTCTAACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATATCCTTATTT
Found at i:18748 original size:30 final size:30
Alignment explanation
Indices: 18722--18778 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
18712 GAGCATTATT
* *
18722 GAAATGATATAGAAATGATTATGCATTAAA
1 GAAATGACAAAGAAATGATTATGCATTAAA
*
18752 GACATGACAAAGAAATGATTATGCATT
1 GAAATGACAAAGAAATGATTATGCATT
18779 CCCAGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (30 bp):
GAAATGACAAAGAAATGATTATGCATTAAA
Found at i:21887 original size:19 final size:19
Alignment explanation
Indices: 21863--21899 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21853 TGTTTAGTAC
21863 ACCGTTTCACCATCGTTTG
1 ACCGTTTCACCATCGTTTG
*
21882 ACCGTTTCATCATCGTTT
1 ACCGTTTCACCATCGTTT
21900 TGGGTCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.41
Consensus pattern (19 bp):
ACCGTTTCACCATCGTTTG
Found at i:30393 original size:56 final size:56
Alignment explanation
Indices: 30305--30410 Score: 176
Period size: 56 Copynumber: 1.9 Consensus size: 56
30295 TAATTTAATC
*
30305 TCTCAAGCTCTTAGGGGACACCAAGTTATTAATTTGTGTCAATTTAGGAATGGCCA
1 TCTCAAGCTCTAAGGGGACACCAAGTTATTAATTTGTGTCAATTTAGGAATGGCCA
* * *
30361 TCTCAAGCTCTAAGGGGACACCAAGTTGTTAATTTGTGTCACTTTTGGAA
1 TCTCAAGCTCTAAGGGGACACCAAGTTATTAATTTGTGTCAATTTAGGAA
30411 GGGGCATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (56 bp):
TCTCAAGCTCTAAGGGGACACCAAGTTATTAATTTGTGTCAATTTAGGAATGGCCA
Found at i:32572 original size:18 final size:18
Alignment explanation
Indices: 32549--32584 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32539 CATTAATGGG
*
32549 AAATAATAATTAATTATT
1 AAATAAAAATTAATTATT
*
32567 AAATAAAAATTTATTATT
1 AAATAAAAATTAATTATT
32585 TATTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAAAAATTAATTATT
Found at i:33760 original size:13 final size:13
Alignment explanation
Indices: 33750--33784 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
33740 TCAATTTTGG
*
33750 CTCTTTTTTTTTT
1 CTCTTTTTTTTCT
*
33763 CTTTTTTTTTTCT
1 CTCTTTTTTTTCT
33776 CTCTTTTTT
1 CTCTTTTTT
33785 CTTTTGGACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
CTCTTTTTTTTCT
Found at i:33765 original size:11 final size:11
Alignment explanation
Indices: 33751--33789 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
33741 CAATTTTGGC
33751 TCTTTTTTTTT
1 TCTTTTTTTTT
33762 TCTTTTTTTTT
1 TCTTTTTTTTT
* *
33773 TCTCTCTTTTT
1 TCTTTTTTTTT
33784 TCTTTT
1 TCTTTT
33790 GGACCAGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:37768 original size:33 final size:33
Alignment explanation
Indices: 37726--37789 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
37716 TGGGTAGTTG
* *
37726 ATGACGTAGAAATGCTTTTTATTTCTCCTTTAT
1 ATGACGTAGAAATGCCTTATATTTCTCCTTTAT
*
37759 ATGACGTAGAAATGCCTTATGTTTCTCCTTT
1 ATGACGTAGAAATGCCTTATATTTCTCCTTT
37790 GTTTGAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (33 bp):
ATGACGTAGAAATGCCTTATATTTCTCCTTTAT
Found at i:37908 original size:2 final size:2
Alignment explanation
Indices: 37895--37948 Score: 56
Period size: 2 Copynumber: 25.0 Consensus size: 2
37885 GAATTTTGAC
37895 AT AT AT AGT AT AT ACT AGT AT AT AGT AT AT -T AT AT AT AT AT AT
1 AT AT AT A-T AT AT A-T A-T AT AT A-T AT AT AT AT AT AT AT AT AT
37938 AT AT AGT AT AT
1 AT AT A-T AT AT
37949 CCCGAATTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
1 1 0.02
2 35 0.76
3 10 0.22
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:37908 original size:7 final size:6
Alignment explanation
Indices: 37895--37948 Score: 56
Period size: 7 Copynumber: 8.3 Consensus size: 6
37885 GAATTTTGAC
37895 ATATAT AGTATAT ACTAGTAT ATAGTAT AT-TAT ATATAT ATATAT ATAGTAT
1 ATATAT A-TATAT A-TA-TAT ATA-TAT ATATAT ATATAT ATATAT ATA-TAT
37947 AT
1 AT
37949 CCCGAATTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.12
6 13 0.30
7 21 0.49
8 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:37915 original size:10 final size:9
Alignment explanation
Indices: 37895--37948 Score: 64
Period size: 8 Copynumber: 6.4 Consensus size: 9
37885 GAATTTTGAC
37895 ATATATAGT
1 ATATATAGT
37904 ATATACTAG-
1 ATATA-TAGT
37913 -TATATAGT
1 ATATATAGT
37921 ATAT-TA-T
1 ATATATAGT
37928 ATATATA-T
1 ATATATAGT
37936 ATATATAGT
1 ATATATAGT
37945 ATAT
1 ATAT
37949 CCCGAATTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 8 0.20
8 16 0.40
9 13 0.32
10 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (9 bp):
ATATATAGT
Found at i:37918 original size:17 final size:16
Alignment explanation
Indices: 37896--37948 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
37886 AATTTTGACA
37896 TATATAGTATATACTAG
1 TATATAGTATATA-TAG
37913 TATATAGTATATTATA-
1 TATATAGTATA-TATAG
37929 TATATA-TATATATAG
1 TATATAGTATATATAG
37944 TATAT
1 TATAT
37949 CCCGAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.12
15 9 0.26
16 6 0.18
17 13 0.38
18 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (16 bp):
TATATAGTATATATAG
Found at i:37924 original size:24 final size:23
Alignment explanation
Indices: 37895--37948 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 23
37885 GAATTTTGAC
37895 ATATATAGTATATACTAGTATATAGT
1 ATATATA-TATATA-TA-TATATAGT
37921 ATATTATATATATATATATATAGT
1 ATA-TATATATATATATATATAGT
37945 ATAT
1 ATAT
37949 CCCGAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.04
24 11 0.41
25 2 0.07
26 9 0.33
27 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (23 bp):
ATATATATATATATATATATAGT
Done.