Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011746.1 Corchorus capsularis cultivar CVL-1 contig11767, 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: 70572
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:12965 original size:1 final size:1
Alignment explanation
Indices: 12959--12999 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
12949 TCTGGAAGAC
12959 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13000 CCCTATTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23664 original size:14 final size:14
Alignment explanation
Indices: 23645--23673 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23635 TTATATATAG
23645 AGTACATTTCCAAT
1 AGTACATTTCCAAT
23659 AGTACATTTCCAAT
1 AGTACATTTCCAAT
23673 A
1 A
23674 AAATGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
AGTACATTTCCAAT
Found at i:24602 original size:29 final size:29
Alignment explanation
Indices: 24530--24610 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
24520 TTTTATTTGA
*
24530 GTTTGTTTTTAGTCGGTTT-GAGTCAATTT
1 GTTT-TTTTTAGTCAGTTTCGAGTCAATTT
*
24559 G-TTTTTTTAGTCAGTTTCGAGTCAGTTT
1 GTTTTTTTTAGTCAGTTTCGAGTCAATTT
*
24587 GTTTTTTTTAGCCAGTTTCGAGTC
1 GTTTTTTTTAGTCAGTTTCGAGTC
24611 TAGTCTCAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
27 13 0.28
28 12 0.26
29 22 0.47
ACGTcount: A:0.14, C:0.11, G:0.22, T:0.53
Consensus pattern (29 bp):
GTTTTTTTTAGTCAGTTTCGAGTCAATTT
Found at i:34869 original size:304 final size:304
Alignment explanation
Indices: 34315--34921 Score: 1160
Period size: 304 Copynumber: 2.0 Consensus size: 304
34305 CGTTTGAGCA
* * *
34315 ATAGTGCGTGCTTATCTTGCCTTGTATGTATCTAATTCAAACTAACTAGAATTTCCCGGCCGCGC
1 ATAGCGCGTGCTTATCTTGCCTTGTATGTATCTAATTCAAACTAACTAGAACTTCCCGGCCGCAC
*
34380 TTCGCGTGCGGCTGCTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAAATTTTG
66 TTCGCGTGCGGCTGCTTTATTTTATAAATTCGTTTAAGAAAATTCAGTTAAGAAATGAAATTTTG
34445 TTGTGAAATGATAACAAAACAAAGCAAGTGAGTAGAGAATTGAAGTATGGAAAAGACAAGAGAAT
131 TTGTGAAATGATAACAAAACAAAGCAAGTGAGTAGAGAATTGAAGTATGGAAAAGACAAGAGAAT
*
34510 AGAGAGACAATAGAATATGAAAAATAAGAAAATATGAAGAATGGGAGAAATTGTTCTTATTCATA
196 AGAGAGACAATAGAATATGAAAAATAAGAAAATATGAAGAAGGGGAGAAATTGTTCTTATTCATA
34575 TTATTCCATAACAAAGTGGCCTATTTATAGGCACATAGATACAC
261 TTATTCCATAACAAAGTGGCCTATTTATAGGCACATAGATACAC
34619 ATAGCGCGTGCTTATCTTGCCTTGTATGTATCTAATTCAAACTAACTAGAACTTCCCGGCCGCAC
1 ATAGCGCGTGCTTATCTTGCCTTGTATGTATCTAATTCAAACTAACTAGAACTTCCCGGCCGCAC
34684 TTCGCGTGCGGCTGCTTTATTTTATAAATTCGTTTAAGAAAATTCAGTTAAGAAATGAAATTTTG
66 TTCGCGTGCGGCTGCTTTATTTTATAAATTCGTTTAAGAAAATTCAGTTAAGAAATGAAATTTTG
34749 TTGTGAAATGATAACAAAACAAAGCAAGTGAGTAGAGAATTGAAGTATGGAAAAGACAAGAGAAT
131 TTGTGAAATGATAACAAAACAAAGCAAGTGAGTAGAGAATTGAAGTATGGAAAAGACAAGAGAAT
*
34814 AGAGAGACAATAGAATATGAAGAATAAGAAAATATGAAGAAGGGGAGAAATTGTTCTTATTCATA
196 AGAGAGACAATAGAATATGAAAAATAAGAAAATATGAAGAAGGGGAGAAATTGTTCTTATTCATA
34879 TTATTCCATAACAAAGTGGCCTATTTATAGGCACATAGATACA
261 TTATTCCATAACAAAGTGGCCTATTTATAGGCACATAGATACA
34922 TCACCATAAA
Statistics
Matches: 297, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
304 297 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (304 bp):
ATAGCGCGTGCTTATCTTGCCTTGTATGTATCTAATTCAAACTAACTAGAACTTCCCGGCCGCAC
TTCGCGTGCGGCTGCTTTATTTTATAAATTCGTTTAAGAAAATTCAGTTAAGAAATGAAATTTTG
TTGTGAAATGATAACAAAACAAAGCAAGTGAGTAGAGAATTGAAGTATGGAAAAGACAAGAGAAT
AGAGAGACAATAGAATATGAAAAATAAGAAAATATGAAGAAGGGGAGAAATTGTTCTTATTCATA
TTATTCCATAACAAAGTGGCCTATTTATAGGCACATAGATACAC
Found at i:35063 original size:11 final size:11
Alignment explanation
Indices: 35049--35081 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
35039 ATTCATAACA
35049 AATTTATAATT
1 AATTTATAATT
35060 AATTTATAATT
1 AATTTATAATT
35071 -ATTTGATAATT
1 AATTT-ATAATT
35082 TATTCTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:37356 original size:33 final size:33
Alignment explanation
Indices: 37314--37385 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
37304 TACACTGATT
* * *
37314 CTCCCCACTA-GGACGTCTCAGCCACGGTGGAGC
1 CTCCCCACTAGGGA-GGCTCAACCACGCTGGAGC
37347 CTCCCCACTAGGGAGGCTCAACCACGCTGGAGC
1 CTCCCCACTAGGGAGGCTCAACCACGCTGGAGC
37380 CTCCCC
1 CTCCCC
37386 TCTGGGGCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 32 0.91
34 3 0.09
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (33 bp):
CTCCCCACTAGGGAGGCTCAACCACGCTGGAGC
Found at i:47475 original size:22 final size:24
Alignment explanation
Indices: 47438--47483 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
47428 AAAGAAGGAA
47438 AAAAGAAAAAATGTGAGAAAAAGG
1 AAAAGAAAAAATGTGAGAAAAAGG
*
47462 AAAA-AAAAAA-GTGATAAAAAGG
1 AAAAGAAAAAATGTGAGAAAAAGG
47484 GGAGGAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 6 0.29
24 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAAATGTGAGAAAAAGG
Found at i:50308 original size:16 final size:16
Alignment explanation
Indices: 50289--50333 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
50279 CACACACATG
**
50289 TTAAAACACGTAAAGC
1 TTAAAACAAATAAAGC
50305 TTAAAACAAATAAAGC
1 TTAAAACAAATAAAGC
50321 TTAAAACAAATAA
1 TTAAAACAAATAA
50334 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (16 bp):
TTAAAACAAATAAAGC
Found at i:51027 original size:1 final size:1
Alignment explanation
Indices: 51021--51051 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
51011 AAGGTACCTC
51021 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
51052 AAGTATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55688 original size:9 final size:9
Alignment explanation
Indices: 55676--55715 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
55666 CTAAATGCCT
55676 CAAATCTCC
1 CAAATCTCC
55685 CAAATCTCC
1 CAAATCTCC
*
55694 CAACTCTCC
1 CAAATCTCC
*
55703 CATATCTCC
1 CAAATCTCC
55712 CAAA
1 CAAA
55716 AGTCCAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.23
Consensus pattern (9 bp):
CAAATCTCC
Found at i:58079 original size:25 final size:25
Alignment explanation
Indices: 58044--58105 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 25
58034 CACAAATTGT
*
58044 TTTTTTCTTTTGGATCTAAACGCAAG
1 TTTTTT-TTTTAGATCTAAACGCAAG
58070 TTTTTTTTTTAGATCTAAACGCAAG
1 TTTTTTTTTTAGATCTAAACGCAAG
58095 TTGTTTTTTTT
1 TT-TTTTTTTT
58106 CTTTTGGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (25 bp):
TTTTTTTTTTAGATCTAAACGCAAG
Found at i:58105 original size:31 final size:31
Alignment explanation
Indices: 58029--58131 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
58019 AATGGTTATC
* *
58029 CTAAACACAAATTG-TTTTTTTCTTTTGGAT
1 CTAAACACAAGTTGTTTTTTTTCTTTTAGAT
*
58059 CTAAACGCAA---G--TTTTTT-TTTTAGAT
1 CTAAACACAAGTTGTTTTTTTTCTTTTAGAT
* *
58084 CTAAACGCAAGTTGTTTTTTTTCTTTTGGAT
1 CTAAACACAAGTTGTTTTTTTTCTTTTAGAT
**
58115 CTATTCACAAGTTGTTT
1 CTAAACACAAGTTGTTT
58132 GTTGTTGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 17 0.28
26 6 0.10
27 1 0.02
28 1 0.02
30 15 0.25
31 21 0.34
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.50
Consensus pattern (31 bp):
CTAAACACAAGTTGTTTTTTTTCTTTTAGAT
Found at i:62826 original size:44 final size:44
Alignment explanation
Indices: 62776--62867 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
62766 CTCCACGCGA
62776 CCTCTCCGAAAAGGCTAGATGACTAAAAAGTTTCCAACAGTCTT
1 CCTCTCCGAAAAGGCTAGATGACTAAAAAGTTTCCAACAGTCTT
62820 CCTCTCCGAAAAGGCTAGATGACTAAAAAGTTTCCAACAGTCTT
1 CCTCTCCGAAAAGGCTAGATGACTAAAAAGTTTCCAACAGTCTT
62864 CCTC
1 CCTC
62868 GGACAAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (44 bp):
CCTCTCCGAAAAGGCTAGATGACTAAAAAGTTTCCAACAGTCTT
Found at i:69124 original size:33 final size:33
Alignment explanation
Indices: 69087--69150 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
69077 TAAAAAAACA
*
69087 CAGGCATGCATAGGCACCTAAATTAGCAATGTG
1 CAGGCATGCATAGACACCTAAATTAGCAATGTG
69120 CAGGCATGCATAGACACCTAAATTAGCAATG
1 CAGGCATGCATAGACACCTAAATTAGCAATG
69151 CATGAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (33 bp):
CAGGCATGCATAGACACCTAAATTAGCAATGTG
Done.