Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008230.1 Corchorus capsularis cultivar CVL-1 contig08251, 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: 21582
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Found at i:5827 original size:53 final size:53
Alignment explanation
Indices: 5770--5876 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
5760 ATTCCAACCG
5770 CAAAGTTAATATTGAATTTGCAAATACATCAAATTATAAACAACAAAGATATA
1 CAAAGTTAATATTGAATTTGCAAATACATCAAATTATAAACAACAAAGATATA
5823 CAAAGTTAATATTGAATTTGCAAATACATCAAATTATAAACAACAAAGATATA
1 CAAAGTTAATATTGAATTTGCAAATACATCAAATTATAAACAACAAAGATATA
5876 C
1 C
5877 GAGTTGAGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (53 bp):
CAAAGTTAATATTGAATTTGCAAATACATCAAATTATAAACAACAAAGATATA
Found at i:7351 original size:22 final size:24
Alignment explanation
Indices: 7297--7351 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
7287 ATTTGGGGTA
7297 CTATTTGC--ATGGTTTTTTTTGT
1 CTATTTGCGTATGGTTTTTTTTGT
*
7319 CTTTTTGCGTATGGTTTTTTTTGT
1 CTATTTGCGTATGGTTTTTTTTGT
7343 -TATTT-CGTA
1 CTATTTGCGTA
7352 GAACTCTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.38
23 4 0.14
24 14 0.48
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (24 bp):
CTATTTGCGTATGGTTTTTTTTGT
Found at i:7513 original size:41 final size:41
Alignment explanation
Indices: 7455--7539 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
7445 GTTCATGTTT
*
7455 TTTCTTTTTATCTCACCTAGGGTTTA-ATGTGTTTTTTTAGGG
1 TTTCTTTTTATCTCACCTAGGGTTTATAT-TG-TTTGTTAGGG
7497 TTTC-TTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
1 TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
7537 TTT
1 TTT
7540 GTGTTTCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 12 0.29
41 23 0.56
42 6 0.15
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.55
Consensus pattern (41 bp):
TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
Found at i:7774 original size:21 final size:21
Alignment explanation
Indices: 7741--7781 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7731 TTAGTTGGGG
** *
7741 TTTGCTATTTACCGTCCCCCT
1 TTTGCTAAATACCGCCCCCCT
7762 TTTGCTAAATACCGCCCCCC
1 TTTGCTAAATACCGCCCCCC
7782 CCCCCCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.41, G:0.10, T:0.34
Consensus pattern (21 bp):
TTTGCTAAATACCGCCCCCCT
Found at i:8116 original size:26 final size:26
Alignment explanation
Indices: 8087--8154 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
8077 TATTTAGTTT
8087 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
8113 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
8139 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
8155 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:8154 original size:15 final size:13
Alignment explanation
Indices: 8057--8148 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 13
8047 TATGATTAGT
*
8057 TTTAATTAGTTAA
1 TTTAATTAGTTTA
*
8070 TTAAAATTA-TTTA
1 TT-TAATTAGTTTA
8083 GTTT-ATTAGTTTA
1 -TTTAATTAGTTTA
8096 TGTTTAATTAG--TA
1 --TTTAATTAGTTTA
*
8109 TCTAATTAGTTTA
1 TTTAATTAGTTTA
8122 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
8135 TTTAATTAGTTTA
1 TTTAATTAGTTTA
8148 T
1 T
8149 GATTAAAATG
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
11 16 0.25
12 5 0.08
13 18 0.29
14 12 0.19
15 12 0.19
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:8215 original size:25 final size:23
Alignment explanation
Indices: 8163--8215 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
8153 AAAATGAAGG
*
8163 AAAATGAATTTGAAGATTTGTTA
1 AAAATGAATTTGAAGAGTTGTTA
8186 AAAATGAACTTTGAAGAAGTTGTTA
1 AAAATGAA-TTTGAAG-AGTTGTTA
*
8211 GAAAT
1 AAAAT
8216 TAAGTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 8 0.31
24 7 0.27
25 11 0.42
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (23 bp):
AAAATGAATTTGAAGAGTTGTTA
Found at i:8334 original size:21 final size:21
Alignment explanation
Indices: 8293--8336 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8283 CAAAAGTGTA
**
8293 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTAAATAGC
8314 AAAAGGGGGGCGGTAAATAGC
1 AAAAGGGGGGCGGTAAATAGC
8335 AA
1 AA
8337 TCCAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.41, T:0.14
Consensus pattern (21 bp):
AAAAGGGGGGCGGTAAATAGC
Found at i:18774 original size:46 final size:46
Alignment explanation
Indices: 18707--18797 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
18697 TGGATTGCTT
18707 GCAATCCATGAGTAGCTAAACTTTTATACTTCTTTTCCTTAGGTAA
1 GCAATCCATGAGTAGCTAAACTTTTATACTTCTTTTCCTTAGGTAA
18753 GCAATCCATGAGTAGCTAAACTTTTATACTTCTTTTCCTTAGGTA
1 GCAATCCATGAGTAGCTAAACTTTTATACTTCTTTTCCTTAGGTA
18798 CTTTTGATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (46 bp):
GCAATCCATGAGTAGCTAAACTTTTATACTTCTTTTCCTTAGGTAA
Done.