Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005190.1 Corchorus capsularis cultivar CVL-1 contig05208, 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: 16917
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2807 original size:31 final size:30
Alignment explanation
Indices: 2772--2934 Score: 122
Period size: 31 Copynumber: 5.4 Consensus size: 30
2762 CGTGAGACAA
2772 GCCCTTATTTGAGCATTTTGACAAACGTTAG
1 GCCCTTATTTGAGCATTTT-ACAAACGTTAG
** **
2803 GCCCTTATTTG-GCCAAATT-CAAA-GATGGG
1 GCCCTTATTTGAG-CATTTTACAAACG-TTAG
*
2832 GCCCTTATTTGAGTATTTTGACAAACGTTAG
1 GCCCTTATTTGAGCATTTT-ACAAACGTTAG
** **
2863 GCCCTTATTTG-GCCAAATT-CAAA-GATGGG
1 GCCCTTATTTGAG-CATTTTACAAACG-TTAG
* *
2892 GCCCTTATTTAAGCATTTTAGCAAACGTTAA
1 GCCCTTATTTGAGCATTTTA-CAAACGTTAG
2923 GCCCTTATTTGA
1 GCCCTTATTTGA
2935 CCAAATAAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
28 2 0.02
29 40 0.40
30 4 0.04
31 51 0.52
32 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTACAAACGTTAG
Found at i:2835 original size:29 final size:29
Alignment explanation
Indices: 2802--2901 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
2792 ACAAACGTTA
2802 GGCCCTTATTTGGCCAAATTCAAAGATGG
1 GGCCCTTATTTGGCCAAATTCAAAGATGG
* ** **
2831 GGCCCTTATTTGAG-TATTTTGACAAACG-TTA
1 GGCCCTTATTTG-GCCAAATT--CAAA-GATGG
2862 GGCCCTTATTTGGCCAAATTCAAAGATGG
1 GGCCCTTATTTGGCCAAATTCAAAGATGG
2891 GGCCCTTATTT
1 GGCCCTTATTT
2902 AAGCATTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 1 0.02
29 31 0.56
30 2 0.04
31 20 0.36
32 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTCAAAGATGG
Found at i:2865 original size:60 final size:60
Alignment explanation
Indices: 2772--2940 Score: 286
Period size: 60 Copynumber: 2.8 Consensus size: 60
2762 CGTGAGACAA
2772 GCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
1 GCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
*
2832 GCCCTTATTTGAGTATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
1 GCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
* * *
2892 GCCCTTATTTAAGCATTTT-AGCAAACGTTAAGCCCTTATTTGACCAAAT
1 GCCCTTATTTGAGCATTTTGA-CAAACGTTAGGCCCTTATTTGGCCAAAT
2941 AAAAAGATCA
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
59 1 0.01
60 102 0.99
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGGG
Found at i:4722 original size:75 final size:74
Alignment explanation
Indices: 4630--4767 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 74
4620 AATATGCAAG
*
4630 TTTGGCAAATGGCACAAATCAGAACAACTTTTAAGAAGCGCAAATTTGCAGGGA-AAATTGTTTT
1 TTTGGCAAATAGCACAAATCA-AACAACTTTTAAGAAGCGCAAATTTGCAGGGATAAA-TGTTTT
4694 AAAGATAGGCA
64 AAAGATAGGCA
* * *
4705 TTTGGCAAATAAG-ACAAATTATATAACTTTTAAGAAGCGCAAATTTGCAGGGATAAATGTTTT
1 TTTGGCAAAT-AGCACAAATCAAACAACTTTTAAGAAGCGCAAATTTGCAGGGATAAATGTTTT
4768 GCAAGTACAG
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
74 36 0.63
75 20 0.35
76 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (74 bp):
TTTGGCAAATAGCACAAATCAAACAACTTTTAAGAAGCGCAAATTTGCAGGGATAAATGTTTTAA
AGATAGGCA
Found at i:5905 original size:179 final size:179
Alignment explanation
Indices: 5605--5962 Score: 689
Period size: 179 Copynumber: 2.0 Consensus size: 179
5595 TCTTGGGTTT
5605 TGTGCACCATTTAGCTTTTGCCATAGTAAATATATGTTACTTTTCCTCTGCAGATCTGCATTCAT
1 TGTGCACCATTTAGCTTTTGCCATAGTAAATATATGTTACTTTTCCTCTGCAGATCTGCATTCAT
*
5670 GCTAGATTAAACAGCACCTCTTGCACCATCTACCCACCGCAAACATCACGTCCCCTATTCAGGAA
66 GCTAGATTAAACAGCACCTCTTGCACCATCTACCCACCCCAAACATCACGTCCCCTATTCAGGAA
5735 TTTTTTGAGTATTAATCGTGACACATATTTAAAGCATAAAGAATTCTAA
131 TTTTTTGAGTATTAATCGTGACACATATTTAAAGCATAAAGAATTCTAA
* *
5784 TGTGCACCATTTAGCTTTTGTCATAGTAAATATATGTTACTTTTCCTCTGCAGTTCTGCATTCAT
1 TGTGCACCATTTAGCTTTTGCCATAGTAAATATATGTTACTTTTCCTCTGCAGATCTGCATTCAT
5849 GCTAGATTAAACAGCACCTCTTGCACCATCTACCCACCCCAAACATCACGTCCCCTATTCAGGAA
66 GCTAGATTAAACAGCACCTCTTGCACCATCTACCCACCCCAAACATCACGTCCCCTATTCAGGAA
5914 TTTTTTGAGTATTAATCGTGACACATATTTAAAGCATAAAGAATTCTAA
131 TTTTTTGAGTATTAATCGTGACACATATTTAAAGCATAAAGAATTCTAA
5963 CTTCATTTTC
Statistics
Matches: 176, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 176 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (179 bp):
TGTGCACCATTTAGCTTTTGCCATAGTAAATATATGTTACTTTTCCTCTGCAGATCTGCATTCAT
GCTAGATTAAACAGCACCTCTTGCACCATCTACCCACCCCAAACATCACGTCCCCTATTCAGGAA
TTTTTTGAGTATTAATCGTGACACATATTTAAAGCATAAAGAATTCTAA
Found at i:6710 original size:28 final size:28
Alignment explanation
Indices: 6677--6732 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6667 TATCAAGGGT
*
6677 TTGGCCCTGGCTAATCCGGATTCGACCC
1 TTGGCCCTGACTAATCCGGATTCGACCC
6705 TTGGCCCTGACTAATCCGGATTCGACCC
1 TTGGCCCTGACTAATCCGGATTCGACCC
6733 GCGTCGCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.23, T:0.25
Consensus pattern (28 bp):
TTGGCCCTGACTAATCCGGATTCGACCC
Found at i:8571 original size:18 final size:18
Alignment explanation
Indices: 8548--8584 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8538 ACTCCCTGGC
8548 CCTTCTTCTTTGACTCTG
1 CCTTCTTCTTTGACTCTG
8566 CCTTCTTCTTTGACTCTG
1 CCTTCTTCTTTGACTCTG
8584 C
1 C
8585 ATTTTCTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.35, G:0.11, T:0.49
Consensus pattern (18 bp):
CCTTCTTCTTTGACTCTG
Found at i:10336 original size:34 final size:34
Alignment explanation
Indices: 10297--10365 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
10287 TAGTTCGGTA
10297 CCAGTATATATATAAAGTCGCATAGTCAACGTAC
1 CCAGTATATATATAAAGTCGCATAGTCAACGTAC
10331 CCAGTATATATATAAAGTCGCATAGTCAACGTAC
1 CCAGTATATATATAAAGTCGCATAGTCAACGTAC
10365 C
1 C
10366 GGCGTTGACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (34 bp):
CCAGTATATATATAAAGTCGCATAGTCAACGTAC
Found at i:12551 original size:30 final size:31
Alignment explanation
Indices: 12515--12578 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
12505 AGCCGAAACC
*
12515 GTTTCCTAGTTGGACATGAT-ATATAAGGTT
1 GTTTCCTAGTTGGACATCATGATATAAGGTT
12545 GTTTCCTAGTTGGACATCATGATATAAGGTT
1 GTTTCCTAGTTGGACATCATGATATAAGGTT
12576 GTT
1 GTT
12579 GTCTTCTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTCCTAGTTGGACATCATGATATAAGGTT
Found at i:13601 original size:10 final size:10
Alignment explanation
Indices: 13586--13625 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
13576 CTGTTCATCA
13586 TTTTTCTACT
1 TTTTTCTACT
*
13596 TTTTTCTAAACA
1 TTTTTCT--ACT
13608 TTTTTCTACT
1 TTTTTCTACT
13618 TTTTTCTA
1 TTTTTCTA
13626 AACAGATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 17 0.65
12 9 0.35
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTCTACT
Found at i:13612 original size:22 final size:22
Alignment explanation
Indices: 13584--13629 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13574 ATCTGTTCAT
13584 CATTTTTCTACTTTTTTCTAAA
1 CATTTTTCTACTTTTTTCTAAA
13606 CATTTTTCTACTTTTTTCTAAA
1 CATTTTTCTACTTTTTTCTAAA
13628 CA
1 CA
13630 GATTTAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (22 bp):
CATTTTTCTACTTTTTTCTAAA
Found at i:13963 original size:13 final size:12
Alignment explanation
Indices: 13940--14007 Score: 118
Period size: 12 Copynumber: 5.5 Consensus size: 12
13930 TAAATACAGG
13940 TATCGACGGATA
1 TATCGACGGATA
13952 TATCGAACGGATA
1 TATCG-ACGGATA
13965 TATCGACGGATA
1 TATCGACGGATA
13977 TATCGAACGGATA
1 TATCG-ACGGATA
13990 TATCGACGGATA
1 TATCGACGGATA
14002 TATCGA
1 TATCGA
14008 GGTATCGATG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
12 30 0.56
13 24 0.44
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:13974 original size:25 final size:25
Alignment explanation
Indices: 13940--14007 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
13930 TAAATACAGG
13940 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
13965 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
13990 TATCGACGGATATATCGA
1 TATCGACGGATATATCGA
14008 GGTATCGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (25 bp):
TATCGACGGATATATCGAACGGATA
Found at i:14185 original size:10 final size:10
Alignment explanation
Indices: 14170--14195 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
14160 TGTAGACATT
14170 TTTTTTTTTA
1 TTTTTTTTTA
14180 TTTTTTTTTA
1 TTTTTTTTTA
14190 TTTTTT
1 TTTTTT
14196 GTACTGCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:15013 original size:10 final size:10
Alignment explanation
Indices: 14998--15033 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
14988 AATTTAATAT
14998 GGATATTTAC
1 GGATATTTAC
*
15008 GGATATTTAT
1 GGATATTTAC
15018 GGATATTTAC
1 GGATATTTAC
15028 GGATAT
1 GGATAT
15034 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:15020 original size:20 final size:20
Alignment explanation
Indices: 14995--15033 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14985 TTTAATTTAA
14995 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
15015 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
15034 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:16311 original size:157 final size:157
Alignment explanation
Indices: 16071--16533 Score: 847
Period size: 157 Copynumber: 3.0 Consensus size: 157
16061 GAATCCATGA
16071 GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
1 GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
16136 CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
66 CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
16201 ATAGGATTTTACGGTTAAAAGATTCAT
131 ATAGGATTTTACGGTTAAAAGATTCAT
16228 GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
1 GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
*
16293 CAATTTCACAATCTTAGCATCCCATCCCACTATTTCACAAAATATATCAAATTCTAGGTGAATAA
66 CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
16358 ATAGGATTTTACGGTTAAAAG----AT
131 ATAGGATTTTACGGTTAAAAGATTCAT
16381 -T--C---ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
1 GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
16440 CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
66 CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
16505 ATAGGATTTTACGGTTAAAAGATTCAT
131 ATAGGATTTTACGGTTAAAAGATTCAT
16532 GT
1 GT
16534 CATAGAATAT
Statistics
Matches: 299, Mismatches: 2, Indels: 15
0.95 0.01 0.05
Matches are distributed among these distances:
147 142 0.47
150 1 0.00
151 2 0.01
152 2 0.01
153 2 0.01
157 150 0.50
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (157 bp):
GTACCTGTATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCA
CAATTTCACAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAA
ATAGGATTTTACGGTTAAAAGATTCAT
Found at i:16400 original size:147 final size:147
Alignment explanation
Indices: 16236--16532 Score: 585
Period size: 147 Copynumber: 2.0 Consensus size: 147
16226 ATGTACCTGT
16236 ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCACAATTTCA
1 ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCACAATTTCA
*
16301 CAATCTTAGCATCCCATCCCACTATTTCACAAAATATATCAAATTCTAGGTGAATAAATAGGATT
66 CAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAAATAGGATT
16366 TTACGGTTAAAAGATTC
131 TTACGGTTAAAAGATTC
16383 ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCACAATTTCA
1 ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCACAATTTCA
16448 CAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAAATAGGATT
66 CAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAAATAGGATT
16513 TTACGGTTAAAAGATTC
131 TTACGGTTAAAAGATTC
16530 ATG
1 ATG
16533 TCATAGAATA
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (147 bp):
ATGACTTATCGATTGAATGAATAAATAAATAAACAAATATGAATTCCTTATAGATCACAATTTCA
CAATCTTAGCATCCCATCCCACCATTTCACAAAATATATCAAATTCTAGGTGAATAAATAGGATT
TTACGGTTAAAAGATTC
Done.