Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015698.1 Corchorus capsularis cultivar CVL-1 contig15719, 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: 21875
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:4196 original size:21 final size:20
Alignment explanation
Indices: 4172--4215 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4162 GAATTCTGGA
4172 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCG-CCCATTT
**
4193 TTGCTATTCACCGCCCATTT
1 TTGCTAAACACCGCCCATTT
4213 TTG
1 TTG
4216 ACGCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.36
Consensus pattern (20 bp):
TTGCTAAACACCGCCCATTT
Found at i:4482 original size:32 final size:32
Alignment explanation
Indices: 4428--4595 Score: 140
Period size: 32 Copynumber: 5.2 Consensus size: 32
4418 TACCGTGGCG
* *
4428 AAGCCGCCCCACTTGGGAGGCTTCGCCACGGC
1 AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
* *
4460 AAGCCGCCCTCA-TGGGGCGGCTTCACCATGGGC
1 AAGCCGCCC-CACTGGGGCGGCTTCGCCA-CGGC
* * * * **
4493 AGGCCGCCCCACTGGGGCAGCTTCCCCATGAA
1 AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
* * *
4525 AAGGTCGCCCCACTGGGGCGGCTTAGCCAGGGC
1 AA-GCCGCCCCACTGGGGCGGCTTCGCCACGGC
* * **
4558 AGGCCGTCCCGGTGGGGCGGCTTCGCCACGGC
1 AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
*
4590 AGGCCG
1 AAGCCG
4596 TCCCGGTGGG
Statistics
Matches: 107, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
32 56 0.52
33 51 0.48
ACGTcount: A:0.14, C:0.38, G:0.36, T:0.12
Consensus pattern (32 bp):
AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
Found at i:4596 original size:32 final size:32
Alignment explanation
Indices: 4538--4611 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
4528 GTCGCCCCAC
*
4538 TGGGGCGGCTTAGCCAGGGCAGGCCGTCCCGG
1 TGGGGCGGCTTAGCCACGGCAGGCCGTCCCGG
*
4570 TGGGGCGGCTTCGCCACGGCAGGCCGTCCCGG
1 TGGGGCGGCTTAGCCACGGCAGGCCGTCCCGG
*
4602 TGGGGTGGCT
1 TGGGGCGGCT
4612 CGGCTAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.07, C:0.31, G:0.47, T:0.15
Consensus pattern (32 bp):
TGGGGCGGCTTAGCCACGGCAGGCCGTCCCGG
Found at i:4787 original size:21 final size:21
Alignment explanation
Indices: 4763--4806 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4753 AAAAAGTGTA
4763 AAAAAT-GGGACGGTATTTAGC
1 AAAAATAGGG-CGGTATTTAGC
*
4784 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
4805 AA
1 AA
4807 CCCCCTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAGC
Found at i:7070 original size:5 final size:5
Alignment explanation
Indices: 7060--7105 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
7050 CCAAACCCTA
*
7060 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT AATACT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT A
7106 ATAGTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 2 0.05
5 34 0.92
6 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:7756 original size:19 final size:20
Alignment explanation
Indices: 7728--7765 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7718 GTTAGATTTA
7728 TTACTATACAGAT-AAAATG
1 TTACTATACAGATGAAAATG
*
7747 TTACTGTACAGATGAAAAT
1 TTACTATACAGATGAAAAT
7766 ATTCTCGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
TTACTATACAGATGAAAATG
Found at i:14341 original size:73 final size:75
Alignment explanation
Indices: 14222--14368 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 75
14212 TCGATTCATG
* * *
14222 ACTTCAAAGTCATAAGCAAGCCTCTCCAGAGAATAACAAGCATAATCAGATAA-ATTCCC-TTTC
1 ACTTCAAAATCATAAGCAAACCTCTCCAGAGAATAACAACCATAATCAGATAACATTCCCTTTTC
*
14285 ATGAAAAGCA
66 ATAAAAAGCA
*
14295 ACTTCAAAATCATAAGCAAACCTCTTCAGAGAATAACAACCATAATCAGATAACGATTCCCTTTT
1 ACTTCAAAATCATAAGCAAACCTCTCCAGAGAATAACAACCATAATCAGATAAC-ATTCCCTTTT
14360 CATAAAAAG
65 CATAAAAAG
14369 AAAAGGAGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 49 0.74
75 6 0.09
76 11 0.17
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (75 bp):
ACTTCAAAATCATAAGCAAACCTCTCCAGAGAATAACAACCATAATCAGATAACATTCCCTTTTC
ATAAAAAGCA
Found at i:21293 original size:17 final size:17
Alignment explanation
Indices: 21261--21294 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21251 CAACAAAAAT
**
21261 AAAACAAAAATGAAACA
1 AAAACAAAAAAAAAACA
21278 AAAACAAAAAAAAAACA
1 AAAACAAAAAAAAAACA
21295 TGTATATATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.12, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAACAAAAAAAAAACA
Found at i:21294 original size:11 final size:11
Alignment explanation
Indices: 21252--21291 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
21242 TTGACAACCC
21252 AACAAAAATAA
1 AACAAAAATAA
*
21263 AACAAAAATGA
1 AACAAAAATAA
*
21274 AACAAAAACAA
1 AACAAAAATAA
21285 AA-AAAAA
1 AACAAAAA
21292 ACATGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (11 bp):
AACAAAAATAA
Done.