Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015388.1 Corchorus capsularis cultivar CVL-1 contig15409, 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: 34388
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7066 original size:22 final size:21
Alignment explanation
Indices: 7041--7087 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7031 CCATACCGAC
*
7041 AACCGACCCGCTAACCCGAATA
1 AACCGACCC-CTAAACCGAATA
* *
7063 AACCGACTCTTAAACCGAATA
1 AACCGACCCCTAAACCGAATA
7084 AACC
1 AACC
7088 ACGAAACCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.40, C:0.36, G:0.11, T:0.13
Consensus pattern (21 bp):
AACCGACCCCTAAACCGAATA
Found at i:8073 original size:58 final size:58
Alignment explanation
Indices: 8001--8113 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
7991 CATCAGGTTC
* *
8001 TTATTTGAGCATTTTCGTAAACATTAAGG-CCTTATTTGACCAAATTAAAAGCATACCT
1 TTATTTGAGCATTTTCGTAAACATTAAGGTAC-TATTTAACCAAATTAAAAGCATACCT
* * * *
8059 TTATTTGAGTATTTTCGTATACATTAGGGTACTATTTAACTAAATTAAAAGCATA
1 TTATTTGAGCATTTTCGTAAACATTAAGGTACTATTTAACCAAATTAAAAGCATA
8114 AGACCCAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 47 0.98
59 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (58 bp):
TTATTTGAGCATTTTCGTAAACATTAAGGTACTATTTAACCAAATTAAAAGCATACCT
Found at i:8681 original size:24 final size:23
Alignment explanation
Indices: 8636--8682 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8626 GCAAGCAAAG
* *
8636 ATAGTATCTGATTTGGAGGTTTT
1 ATAGTATCCGATTTGGAAGTTTT
*
8659 ATAGTATCCGATTTTGATAGTTTT
1 ATAGTATCCGATTTGGA-AGTTTT
8683 TACGGGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.23, C:0.06, G:0.21, T:0.49
Consensus pattern (23 bp):
ATAGTATCCGATTTGGAAGTTTT
Found at i:15155 original size:40 final size:40
Alignment explanation
Indices: 15100--15179 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
15090 TCTTATGGAC
15100 TGCCTTCGGCCGAAACAGCAAAATGGGAAGGATCGAGTAG
1 TGCCTTCGGCCGAAACAGCAAAATGGGAAGGATCGAGTAG
15140 TGCCTTCGGCCGAAACAGCAAAATGGGAAGGATCGAGTAG
1 TGCCTTCGGCCGAAACAGCAAAATGGGAAGGATCGAGTAG
15180 CTCTGGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (40 bp):
TGCCTTCGGCCGAAACAGCAAAATGGGAAGGATCGAGTAG
Found at i:31082 original size:201 final size:198
Alignment explanation
Indices: 30666--31109 Score: 634
Period size: 201 Copynumber: 2.2 Consensus size: 198
30656 CATTATGATC
*
30666 AGATTCAGAAGACAAATGATTTAACTCCGACTG---ATGTGCAGGAAGTAGATCACCACCCTCCA
1 AGATTCAGAAGACAAATGGTTTAACT-CGACTGATCATGTGCAGGAAGTAGATCACCACCCTCCA
* *
30728 ATTTTACATCTGAAACATATATATTGAAAATCAATGTCAGGTTACAATAATCAAGTAATCAACTG
65 ATTTGACATCTGAAAAATATATATTGAAAATCAATGTCAGGTTACAATAATCAAGTAATCAACTG
**
30793 TTATAATAATATATAATAGGTTATAATGATATAAAACCTGATAAAGATCATATTACTTACTTTCT
130 CAATAATAATATATAATA-GTTATAATGATATAAAACCTGATAAAGATCATATTACTTACTTTCT
30858 TGAGG
194 TGAGG
*
30863 AGATTCAGAAGACAAATGGTTTAACTGCGACTGATCATGTGCAGGAAGTAGATCACCACCCTTCA
1 AGATTCAGAAGACAAATGGTTTAACT-CGACTGATCATGTGCAGGAAGTAGATCACCACCCTCCA
30928 ATTTGACATCTGAAAAATATATATTGAAAATCAATGTCAGATTAGGGTTACAATAATCAAGTAAT
65 ATTTGACATCTGAAAAATATATATTGAAAATCAATGTC-----A-GGTTACAATAATCAAGTAAT
* * * *
30993 TAA-T-CAACT-GTTATA-ATAATA-TTATAATGATATAAAACCTGATAAAGATCATTTTACTTA
124 CAACTGCAA-TAATAATATATAATAGTTATAATGATATAAAACCTGATAAAGATCATATTACTTA
*
31053 CTTTTTTGAGG
188 CTTTCTTGAGG
31064 AGATTCAGAAGACAAATGGTTTAACTCTGACTGATCATGTGCAGGA
1 AGATTCAGAAGACAAATGGTTTAACTC-GACTGATCATGTGCAGGA
31110 GGTAATGATA
Statistics
Matches: 224, Mismatches: 12, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
197 31 0.14
200 65 0.29
201 92 0.41
203 6 0.03
204 5 0.02
205 3 0.01
206 22 0.10
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
AGATTCAGAAGACAAATGGTTTAACTCGACTGATCATGTGCAGGAAGTAGATCACCACCCTCCAA
TTTGACATCTGAAAAATATATATTGAAAATCAATGTCAGGTTACAATAATCAAGTAATCAACTGC
AATAATAATATATAATAGTTATAATGATATAAAACCTGATAAAGATCATATTACTTACTTTCTTG
AGG
Found at i:32669 original size:29 final size:30
Alignment explanation
Indices: 32636--32733 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 30
32626 ACCTCCTGAA
**
32636 TCTTTTGCAGGTGGAA-ATTTCAACTTCCT
1 TCTTTTGCAACTGGAAGATTTCAACTTCCT
* *
32665 TCTTTTGGAACTTGAAGATTTCAACTTCCT
1 TCTTTTGCAACTGGAAGATTTCAACTTCCT
*
32695 TCTTTTAG-AACTTGAAGATTTCAAGTACTTCCT
1 TCTTTT-GCAACTGGAAGATTTC-A--ACTTCCT
32728 TCTTTT
1 TCTTTT
32734 AGACCTTGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
29 12 0.20
30 33 0.55
31 2 0.03
33 13 0.22
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.45
Consensus pattern (30 bp):
TCTTTTGCAACTGGAAGATTTCAACTTCCT
Found at i:32730 original size:33 final size:30
Alignment explanation
Indices: 32652--32747 Score: 147
Period size: 30 Copynumber: 3.1 Consensus size: 30
32642 GCAGGTGGAA
*
32652 ATTTCAACTTCCTTCTTTTGGAACTTGAAG
1 ATTTCAACTTCCTTCTTTTAGAACTTGAAG
32682 ATTTCAACTTCCTTCTTTTAGAACTTGAAG
1 ATTTCAACTTCCTTCTTTTAGAACTTGAAG
*
32712 ATTTCAAGTACTTCCTTCTTTTAGACCTTGAAG
1 ATTTC-A--ACTTCCTTCTTTTAGAACTTGAAG
32745 ATT
1 ATT
32748 CCTGATTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 34 0.56
31 1 0.02
33 26 0.43
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (30 bp):
ATTTCAACTTCCTTCTTTTAGAACTTGAAG
Found at i:33467 original size:20 final size:17
Alignment explanation
Indices: 33422--33458 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
33412 TCTCCCACAC
33422 TCATCTTCTCTTTTCTT
1 TCATCTTCTCTTTTCTT
33439 TCA-C-TCTCTGTTTCTT
1 TCATCTTCTCT-TTTCTT
33455 TCAT
1 TCAT
33459 GTCTTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.28
16 10 0.56
17 3 0.17
ACGTcount: A:0.08, C:0.30, G:0.03, T:0.59
Consensus pattern (17 bp):
TCATCTTCTCTTTTCTT
Found at i:33647 original size:20 final size:20
Alignment explanation
Indices: 33610--33647 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33600 TGTCCAGAGA
*
33610 TTTCCTTTTATAGGAAAACG
1 TTTCCTTTTATAGAAAAACG
33630 TTTCCTTTCT-TAGAAAAA
1 TTTCCTTT-TATAGAAAAA
33648 TTGCGAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTCCTTTTATAGAAAAACG
Done.