Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008226.1 Corchorus capsularis cultivar CVL-1 contig08247, 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: 50584
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:39 original size:2 final size:2
Alignment explanation
Indices: 28--61 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
18 TATTGTTTCT
28 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62 TGGAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:412 original size:26 final size:27
Alignment explanation
Indices: 357--414 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
347 GTCATTGCTT
* * *
357 AAACTATTATAGTTTTTTTTTGCCACA
1 AAACTATTATAGTTTTATTCTACCACA
*
384 AAACTATTATAGTTTTATTCTACTA-A
1 AAACTATTATAGTTTTATTCTACCACA
410 AAACT
1 AAACT
415 CTATTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (27 bp):
AAACTATTATAGTTTTATTCTACCACA
Found at i:2090 original size:9 final size:8
Alignment explanation
Indices: 2032--2088 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
2022 ATACTTATGT
2032 GTGA-TTA
1 GTGATTTA
*
2039 GTGATATA
1 GTGATTTA
2047 GTGATTTA
1 GTGATTTA
2055 GTGACTTATA
1 GTGA-TT-TA
* *
2065 GTCTAATTA
1 GT-GATTTA
2074 GTGATTTA
1 GTGATTTA
2082 GTGATTT
1 GTGATTT
2089 TATGTAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
7 4 0.10
8 24 0.60
9 6 0.15
10 5 0.12
11 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.46
Consensus pattern (8 bp):
GTGATTTA
Found at i:2751 original size:34 final size:34
Alignment explanation
Indices: 2683--2749 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
2673 AAAGTATAAC
*
2683 AAGAGTCTCAAAAGAGATTTATTAATAAAAAAACA
1 AAGAGTCTCAAAAGAGATTTACTAAT-AAAAAACA
*
2718 AAGAGTCTACAAAAGAGGTTTACTAATAAAAA
1 AAGAGTCT-CAAAAGAGATTTACTAATAAAAA
2750 CAATTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.22
Consensus pattern (34 bp):
AAGAGTCTCAAAAGAGATTTACTAATAAAAAACA
Found at i:4453 original size:41 final size:41
Alignment explanation
Indices: 4415--4493 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
4405 TCTAATCCTA
4415 ACAAAAGTATTTATTATTTTTTAACAGTAATCAAAATCCAT
1 ACAAAAGTATTTATTATTTTTTAACAGTAATCAAAATCCAT
*
4456 TCAAAAGTATTTATTATTTTTTAACAGTAATCAAAATC
1 ACAAAAGTATTTATTATTTTTTAACAGTAATCAAAATC
4494 AAGAATCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (41 bp):
ACAAAAGTATTTATTATTTTTTAACAGTAATCAAAATCCAT
Found at i:4640 original size:68 final size:68
Alignment explanation
Indices: 4558--4691 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 68
4548 ATCGATTTAA
* * *
4558 TTGGTTTCATTGGGTCAATTTCACTTCTGAGTTAATTAATATGAGAACCATACCGGCACTATTTC
1 TTGGTTTCACTGGGTCAATTTCACATCTGAATTAATTAATATGAGAACCATACCGGCACTATTTC
4623 CAT
66 CAT
* ** *
4626 TTGGTTTTACTGGGTCAATTTCACATCTGAATTAATTAATATGAGAACCATATTGTCACTATTTC
1 TTGGTTTCACTGGGTCAATTTCACATCTGAATTAATTAATATGAGAACCATACCGGCACTATTTC
4691 C
66 C
4692 GTTTACCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (68 bp):
TTGGTTTCACTGGGTCAATTTCACATCTGAATTAATTAATATGAGAACCATACCGGCACTATTTC
CAT
Found at i:5328 original size:105 final size:106
Alignment explanation
Indices: 5147--5408 Score: 422
Period size: 107 Copynumber: 2.5 Consensus size: 106
5137 AATTTTTCTA
* **
5147 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
5210 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTAAAACAATAATTATTAATTATGAAATTT
* *
5250 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
5315 TTTCTAAAACCCTAAAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTAAAACAAT-AATTATTAATTATGAAATTT
5357 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
5409 AGACTAAACT
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 27 0.18
104 15 0.10
105 36 0.24
107 69 0.47
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTAAAACAATAATTATTAATTATGAAATTT
Found at i:7083 original size:60 final size:54
Alignment explanation
Indices: 6962--7117 Score: 177
Period size: 54 Copynumber: 2.8 Consensus size: 54
6952 AGTCAAATTA
* *
6962 TCATCAATTCGAGATCAAGTCATCAAGACCCACGAATCAAATCAAATTACTCCC
1 TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAATAACTCCC
* *
7016 TCATCAATTCGAGATCAAGTCATCAAAGACCCTCGAATCAGATCAAATCAAATTCCC
1 TCATCAATTCGAGATCAAGTCATC-AAGACCCTCGAATCAAATCAAAT--AACTCCC
* ** * *
7073 AAGTCATCAATTCAAGATCAAGTTGTCAAGACCCTTGAATTAAAT
1 ---TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAAT
7118 TATCAATTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
54 24 0.28
55 21 0.24
57 5 0.06
59 15 0.17
60 21 0.24
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (54 bp):
TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAATAACTCCC
Found at i:9089 original size:65 final size:67
Alignment explanation
Indices: 8972--9116 Score: 224
Period size: 65 Copynumber: 2.2 Consensus size: 67
8962 CCCAAAAAAA
* *
8972 AAAAAAAAAAAGGGAAGCTCGCTAAGTTGAAAATCCTGACAAAGGACGGCTTAGGCAAAAGTTAT
1 AAAAAAAAAAAGGG-AGCTCGCTAAGTTGAAAATCCTGACAAAGGACGGCTTAGGCAAAACTTAG
9037 AGC
65 AGC
9040 AAAAAAAAAAA-GG-GCTCAGCTAAGTTGAAAATCCTG-CAAAGGACGGCTTAGGCAAAACTTAG
1 AAAAAAAAAAAGGGAGCTC-GCTAAGTTGAAAATCCTGACAAAGGACGGCTTAGGCAAAACTTAG
9102 AGC
65 AGC
9105 ACAAAAAAAAAA
1 A-AAAAAAAAAA
9117 AGTGAACTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
65 32 0.44
66 28 0.38
67 2 0.03
68 11 0.15
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.14
Consensus pattern (67 bp):
AAAAAAAAAAAGGGAGCTCGCTAAGTTGAAAATCCTGACAAAGGACGGCTTAGGCAAAACTTAGA
GC
Found at i:11579 original size:64 final size:66
Alignment explanation
Indices: 11472--11614 Score: 220
Period size: 64 Copynumber: 2.2 Consensus size: 66
11462 TAGTTCATCA
* *
11472 TTTTTTTTTGTGCTCTAAGTTTTGCCTAAAAGTCGTCCTTTGCAGGATTTTCAACTTAGCGA-G-
1 TTTTTTTTTG-GCTCTAACTTTTGCCT-AAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGGT
11535 CTT
64 CTT
11538 TTTTCTTTTTGGCTCTAACTTTTGCCT-AAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGGTC
1 TTTT-TTTTTGGCTCTAACTTTTGCCTAAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGGTC
11602 TT
65 TT
11604 TTTTTTTTTGG
1 TTTTTTTTTGG
11615 GTTGACTGAA
Statistics
Matches: 72, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
64 32 0.44
65 8 0.11
66 26 0.36
67 6 0.08
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (66 bp):
TTTTTTTTTGGCTCTAACTTTTGCCTAAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGGTCT
T
Found at i:13876 original size:16 final size:16
Alignment explanation
Indices: 13855--13889 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
13845 ATCTGAAATA
13855 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
13871 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
13887 CTT
1 CTT
13890 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:21652 original size:2 final size:2
Alignment explanation
Indices: 21645--21685 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
21635 TGAATTGAAG
21645 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21686 GTTGCTAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39464 original size:31 final size:31
Alignment explanation
Indices: 39420--39522 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
39410 ACGGTGTCCG
* *
39420 ACGTGGCATGCCACGTGTTCCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
39451 ATGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* ** * *
39482 ACATTTCACACCACGTGTACAAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
39513 ACGTGGCACG
1 ACGTGGCACG
39523 TCACATGACA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Done.