Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006225.1 Corchorus capsularis cultivar CVL-1 contig06244, 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: 12185
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:652 original size:21 final size:21
Alignment explanation
Indices: 628--676 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
618 TCTAAATAAG
*
628 TCTGATTTGAAT-TTGAAAACC
1 TCTGATTTAAATCTTGAAAA-C
649 TCTGA-TTAAATCTTGAAAAC
1 TCTGATTTAAATCTTGAAAAC
669 TCTTGATT
1 TC-TGATT
677 ACCAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTGATTTAAATCTTGAAAAC
Found at i:4760 original size:28 final size:28
Alignment explanation
Indices: 4691--4760 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
4681 AAGTGGACTT
* *
4691 AAAATAACCAAAACACCCCTTGAATGCA
1 AAAATGACCAAAATACCCCTTGAATGCA
**
4719 AAAATGACCAAAATACACCC-TGAATGTG
1 AAAATGACCAAAATAC-CCCTTGAATGCA
4747 AAAATGACCAAAAT
1 AAAATGACCAAAAT
4761 GCCCTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATACCCCTTGAATGCA
Found at i:5204 original size:20 final size:20
Alignment explanation
Indices: 5166--5204 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5156 AATATGAGTG
*
5166 TGCCCGGAGGTCTTATCAAA
1 TGCCCGGAGGACTTATCAAA
*
5186 TGCCCGGAGGACTTGTCAA
1 TGCCCGGAGGACTTATCAA
5205 TGCAAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (20 bp):
TGCCCGGAGGACTTATCAAA
Found at i:5551 original size:156 final size:159
Alignment explanation
Indices: 5262--5741 Score: 770
Period size: 156 Copynumber: 3.0 Consensus size: 159
5252 CATGAATCTT
5262 TGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATC
1 TGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATC
* *
5327 AGAATTAATACCCGGAGGTTTCTGAATTTGTACCCAGAGGACTTACCAATGCAAACTCTGAACTG
66 AGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTG
5392 ACACCTTCGATCAAGGATTTTAAA-GT-A
131 ACACCTTCGATCAAGGATTTTAAACGTAA
5419 TGAT-AAAAACTTGATGGAAA-GAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTAT
1 TGATGAAAAACTTGAT-GAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTAT
* *
5482 CAGAATCAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTCTGAATT
65 CAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATT
*
5547 GACACCTTCGATCAAGGATTTTAAACTTAAACA
130 GACACCTTCGATCAAGGATTTTAAACGT--A-A
* *
5580 TGAATCTTTGATGAAAAGTTGATGAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGG
1 TG-A----TGA--AAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGG
5645 ACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTC
59 ACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTC
5710 TGAATTGACACCTTCGATCAAGGATTTTAAAC
124 TGAATTGACACCTTCGATCAAGGATTTTAAAC
5742 TTAAATATGA
Statistics
Matches: 299, Mismatches: 9, Indels: 18
0.92 0.03 0.06
Matches are distributed among these distances:
156 140 0.47
157 9 0.03
161 3 0.01
162 1 0.00
166 1 0.00
167 1 0.00
168 4 0.01
169 140 0.47
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (159 bp):
TGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATC
AGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTG
ACACCTTCGATCAAGGATTTTAAACGTAA
Found at i:5718 original size:169 final size:169
Alignment explanation
Indices: 5419--5751 Score: 596
Period size: 169 Copynumber: 2.0 Consensus size: 169
5409 TTTTAAAGTA
*
5419 TGATAAAAACTTGATGGAAAGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
1 TGATAAAAACTTGATGGAAAGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
*
5484 GAATCAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCAAACTCTGAATTGA
66 GAATCAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTGA
5549 CACCTTCGATCAAGGATTTTAAACTTAAACATGAATCTT
131 CACCTTCGATCAAGGATTTTAAACTTAAACATGAATCTT
* *
5588 TGATGAAAAGTTGAT-GAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATC
1 TGATAAAAACTTGATGGAAA-GAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATC
*
5652 AGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTG
65 AGAATCAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTG
*
5717 ACACCTTCGATCAAGGATTTTAAACTTAAATATGA
130 ACACCTTCGATCAAGGATTTTAAACTTAAACATGA
5752 TTAAAACTCG
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
168 4 0.03
169 153 0.97
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (169 bp):
TGATAAAAACTTGATGGAAAGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCA
GAATCAATACCCGGAGGTTTCTGAATTTGTGCCCAGAGGACTTACCAATGCAAACTCTGAATTGA
CACCTTCGATCAAGGATTTTAAACTTAAACATGAATCTT
Found at i:7077 original size:6 final size:7
Alignment explanation
Indices: 7061--7120 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
7051 TATTCTTTTC
*
7061 TTTTCTT
1 TTTTCAT
*
7068 TTTTTAT
1 TTTTCAT
7075 TTTTCATT
1 TTTTCA-T
7083 TTTTCAT
1 TTTTCAT
7090 TTTTCAT
1 TTTTCAT
**
7097 CATT--T
1 TTTTCAT
7102 TTTTCATT
1 TTTTCA-T
7110 TTTTCAT
1 TTTTCAT
7117 TTTT
1 TTTT
7121 TTCATGGCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 3 0.07
7 25 0.60
8 14 0.33
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:7077 original size:8 final size:8
Alignment explanation
Indices: 7061--7121 Score: 72
Period size: 8 Copynumber: 7.5 Consensus size: 8
7051 TATTCTTTTC
7061 TTTTC-TT
1 TTTTCATT
*
7068 TTTTTA-T
1 TTTTCATT
7075 TTTTCATT
1 TTTTCATT
7083 TTTTCATT
1 TTTTCATT
7091 TTTCATCATTT
1 TTT--TCA-TT
7102 TTTTCATT
1 TTTTCATT
7110 TTTTCATT
1 TTTTCATT
7118 TTTT
1 TTTT
7122 TCATGGCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
7 10 0.21
8 26 0.55
9 3 0.06
10 3 0.06
11 5 0.11
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:7086 original size:9 final size:9
Alignment explanation
Indices: 7074--7125 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
7064 TCTTTTTTTA
7074 TTTTTCA-T
1 TTTTTCATT
7082 TTTTTCATT
1 TTTTTCATT
*
7091 TTTCATCATT
1 TTT-TTCATT
7101 TTTTTCA-T
1 TTTTTCATT
7109 TTTTTCATT
1 TTTTTCATT
7118 TTTTTCAT
1 TTTTTCAT
7126 GGCACTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 15 0.38
9 16 0.41
10 8 0.21
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:7105 original size:19 final size:17
Alignment explanation
Indices: 7061--7125 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
7051 TATTCTTTTC
7061 TTTTC-TTTTTTT-A-T
1 TTTTCATTTTTTTCATT
7075 TTTTCA-TTTTTTCATT
1 TTTTCATTTTTTTCATT
7091 TTTCATCATTTTTTTCATT
1 TTT--TCATTTTTTTCATT
7110 TTTTCATTTTTTTCAT
1 TTTTCATTTTTTTCAT
7126 GGCACTTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 4 0.09
17 13 0.29
18 3 0.07
19 13 0.29
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCATTTTTTTCATT
Found at i:7441 original size:11 final size:11
Alignment explanation
Indices: 7425--7490 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
7415 TCACTTCATC
7425 ATTTTTTATTG
1 ATTTTTTATTG
7436 ATTTTTTATT-
1 ATTTTTTATTG
7446 -TGTTTTTA---
1 AT-TTTTTATTG
7454 ATTTTTTATTTG
1 ATTTTTTA-TTG
7466 ATTTTTTTGATTG
1 A-TTTTTT-ATTG
*
7479 ATTTTTTTTTG
1 ATTTTTTATTG
7490 A
1 A
7491 AAATTCTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 6 0.13
11 14 0.30
12 7 0.15
13 10 0.22
14 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (11 bp):
ATTTTTTATTG
Found at i:7457 original size:18 final size:19
Alignment explanation
Indices: 7436--7471 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
7426 TTTTTTATTG
7436 ATTTTTTATTTG-TTTTTA
1 ATTTTTTATTTGATTTTTA
7454 ATTTTTTATTTGATTTTT
1 ATTTTTTATTTGATTTTT
7472 TTGATTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (19 bp):
ATTTTTTATTTGATTTTTA
Found at i:7779 original size:14 final size:14
Alignment explanation
Indices: 7762--7824 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
7752 ACGGGTTTCG
7762 AAAACCATTTTTTA
1 AAAACCATTTTTTA
**
7776 AAAA-CATTTTAGA
1 AAAACCATTTTTTA
* *
7789 AAAAACATTTTTTG
1 AAAACCATTTTTTA
* *
7803 AAAATCATTTTTTG
1 AAAACCATTTTTTA
7817 AAAACCAT
1 AAAACCAT
7825 GACTCTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
13 11 0.27
14 30 0.73
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAACCATTTTTTA
Done.