Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007459.1 Corchorus capsularis cultivar CVL-1 contig07480, 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: 41432
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Found at i:5280 original size:37 final size:37
Alignment explanation
Indices: 5230--5300 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
5220 ATATAATTAT
* *
5230 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
5267 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
5301 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:10571 original size:94 final size:93
Alignment explanation
Indices: 10464--10644 Score: 290
Period size: 94 Copynumber: 1.9 Consensus size: 93
10454 ATATGTTTCA
* ** * *
10464 TTTTTTAGGGTAAATCTTAAATTTTAAGACCAATTATTTTAGGGTTTTAGAAAAATAAGTTTGAA
1 TTTTTTAGGGTAAATCTCAAATGGTAAGACCAACTATCTTAGGGTTTTAGAAAAATAAGTTTGAA
*
10529 CACTTTTAAATAAGGTTTAGCCTATTTT
66 CACTTATAAATAAGGTTTAGCCTATTTT
*
10557 TTTTTTAAGGGTAAATCTCAAATGGTAAGACCCACTATCTTAGGGTTTTAGAAAAATAAGTTTGA
1 TTTTTT-AGGGTAAATCTCAAATGGTAAGACCAACTATCTTAGGGTTTTAGAAAAATAAGTTTGA
10622 ACACTTATAAATAAGGTTTAGCC
65 ACACTTATAAATAAGGTTTAGCC
10645 CCAAATATAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 6 0.08
94 74 0.93
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (93 bp):
TTTTTTAGGGTAAATCTCAAATGGTAAGACCAACTATCTTAGGGTTTTAGAAAAATAAGTTTGAA
CACTTATAAATAAGGTTTAGCCTATTTT
Found at i:11882 original size:33 final size:32
Alignment explanation
Indices: 11817--11891 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
11807 TTGTATTATT
11817 TTGGGA-TTTGGGTAGGGTTTCGAAACTGAAA
1 TTGGGATTTTGGGTAGGGTTTCGAAACTGAAA
* *
11848 TTGGGATTTTGGGTTAGGGTTTATGAAA-TTAAA
1 TTGGGATTTTGGG-TAGGGTTT-CGAAACTGAAA
*
11881 TTGGGCTTTTG
1 TTGGGATTTTG
11892 TTTTATGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.16
32 6 0.16
33 22 0.58
34 4 0.11
ACGTcount: A:0.23, C:0.04, G:0.33, T:0.40
Consensus pattern (32 bp):
TTGGGATTTTGGGTAGGGTTTCGAAACTGAAA
Found at i:13135 original size:12 final size:12
Alignment explanation
Indices: 13106--13149 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
13096 ATTTTATTAC
13106 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
13119 TGTTTTATAAAT
1 TGTTTTATAAAT
*
13131 GGTTTTAATAAAT
1 TGTTTT-ATAAAT
13144 TGTTTT
1 TGTTTT
13150 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:32787 original size:30 final size:31
Alignment explanation
Indices: 32746--32818 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
32736 GGCAAAAATG
* *
32746 CAATCCAGGATACACCGTTA-CGACTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
* * *
32776 CAATTTAGGATATAACGTTATCGAGTTGTGT
1 CAATTCAGGATACAACGTTATCGACTTGTGT
32807 CAATTCAGGATA
1 CAATTCAGGATA
32819 AAATCAGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
CAATTCAGGATACAACGTTATCGACTTGTGT
Found at i:33170 original size:69 final size:69
Alignment explanation
Indices: 33088--33227 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
33078 AACATGAACA
33088 AAAAAAAATGAACAAACTGAGACCGGAAAAACATCAGAAAACAGAAAATCCCAACCAAACAAAAC
1 AAAAAAAATGAACAAACTGAGACCGGAAAAACATCAGAAAACAGAAAATCCCAACCAAACAAAAC
33153 CAAT
66 CAAT
*
33157 AAAAAAAATGAACAAACTGAGACCGGAAAAACATCAGAAAACAGAAAATCCCAACCAAACCAAAC
1 AAAAAAAATGAACAAACTGAGACCGGAAAAACATCAGAAAACAGAAAATCCCAACCAAACAAAAC
33222 CAAT
66 CAAT
33226 AA
1 AA
33228 GGCTACTGCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.61, C:0.22, G:0.10, T:0.07
Consensus pattern (69 bp):
AAAAAAAATGAACAAACTGAGACCGGAAAAACATCAGAAAACAGAAAATCCCAACCAAACAAAAC
CAAT
Found at i:34219 original size:25 final size:24
Alignment explanation
Indices: 34196--34247 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
34186 TTTCAAATAA
34196 ATTTAT-TTTTATTTATTTTTAAT
1 ATTTATATTTTATTTATTTTTAAT
34219 ATTTATCATTTTATTTA-TTTTAA-
1 ATTTAT-ATTTTATTTATTTTTAAT
34242 ATTTAT
1 ATTTAT
34248 TTATTGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.44
24 6 0.22
25 9 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTTATATTTTATTTATTTTTAAT
Found at i:40348 original size:325 final size:324
Alignment explanation
Indices: 39758--40409 Score: 1153
Period size: 325 Copynumber: 2.0 Consensus size: 324
39748 GAGAGCATTG
39758 TTGGTAACATTCCTAACCTTGAATTAGCATAACTTACATACAGGTGCCAACAATATGAAGTATTG
1 TTGGTAACATTCCTAACCTTGAATTAGCATAACTTACATACAGGTGCCAACAATATGAAGTATTG
*
39823 GAGCCTCCATCACAATTAGCAATTCAGTCGGCAACCAATGCCTCGTCGTTTGGTAAGACTTGGTG
66 GAGCCTCCATCACAATTAGCAATTCAGCCGGCAACCAATGCCTCGTCGTTTGGTAAGACTTGGTG
*
39888 CATGGACTCCAGCGCCTCACATCATGACATGGCTGATCTTAATAATCTCTCGATCTCCTCTAAAT
131 CATGGACTCCAGCGCCTCACATCATGACATGGCTGATCTTAACAATCTCTCGATCTCCTCTAAAT
*
39953 ATGATGGCAATGAGGCAATTCAAATAGGAGATGGAACAAGTTTGTTGATTACTCACACAGGAACT
196 ATGATGGCAACGAGGCAATTCAAATAGGAGATGGAACAAGTTTGTTGATTACTCACACAGGAACT
*
40018 TGTTTCTTCTGATCATTCCTTCAAGCTAAATGAAGTATTATGTGTTCCTAAAATAGCATAGAATC
261 TGTTTCTTCTGATCATTCCTTCAAGCTAAATGAAGTATTATGTGTTCCTAAAATA-CACAGAATC
40083 TTGGTAACATTCCTAACCTTGAATTAGCATAACTTACATACAGGTGCCAACAATATGAAGTATTG
1 TTGGTAACATTCCTAACCTTGAATTAGCATAACTTACATACAGGTGCCAACAATATGAAGTATTG
* *
40148 GATCCTCCATCACAATTAGCAATTCAGCCGGCAACCAATGCCTCGTCTTTTGGTAAGACTTGGTG
66 GAGCCTCCATCACAATTAGCAATTCAGCCGGCAACCAATGCCTCGTCGTTTGGTAAGACTTGGTG
* * *
40213 CATGGACTCC-GACGTCTCACATCATGTCATGGCTGATCTTAACAATCTCTCGATCTCCTCTGAA
131 CATGGACTCCAG-CGCCTCACATCATGACATGGCTGATCTTAACAATCTCTCGATCTCCTCTAAA
* * * *
40277 TATGATGGCACCGAGGCAATTCAAATCGGAGATGGAACAGGTTTGTTGATTACTCACACATGAAC
195 TATGATGGCAACGAGGCAATTCAAATAGGAGATGGAACAAGTTTGTTGATTACTCACACAGGAAC
*
40342 TTGTTTCTTCTTATCATTCCTTCAAGCTAAATGAAGTATTATGTGTTCCTAAAATACACAGAATC
260 TTGTTTCTTCTGATCATTCCTTCAAGCTAAATGAAGTATTATGTGTTCCTAAAATACACAGAATC
40407 TTG
1 TTG
40410 TCTCAGTTAT
Statistics
Matches: 312, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
324 12 0.04
325 300 0.96
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (324 bp):
TTGGTAACATTCCTAACCTTGAATTAGCATAACTTACATACAGGTGCCAACAATATGAAGTATTG
GAGCCTCCATCACAATTAGCAATTCAGCCGGCAACCAATGCCTCGTCGTTTGGTAAGACTTGGTG
CATGGACTCCAGCGCCTCACATCATGACATGGCTGATCTTAACAATCTCTCGATCTCCTCTAAAT
ATGATGGCAACGAGGCAATTCAAATAGGAGATGGAACAAGTTTGTTGATTACTCACACAGGAACT
TGTTTCTTCTGATCATTCCTTCAAGCTAAATGAAGTATTATGTGTTCCTAAAATACACAGAATC
Done.