Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008958.1 Corchorus capsularis cultivar CVL-1 contig08979, 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: 38868
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2423 original size:29 final size:30
Alignment explanation
Indices: 2363--2431 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
2353 TTTTCTGTTG
** *
2363 AAACTTGAAACGATTTTTGCTC-ATAAAAA
1 AAACTTGAAACGATTTTCACTCAAAAAAAA
2392 AAACTTGAAACGATTTTCAC-CAAAAAAGAA
1 AAACTTGAAACGATTTTCACTCAAAAAA-AA
2422 AAACTTGAAA
1 AAACTTGAAA
2432 AGAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 22 0.63
30 12 0.34
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (30 bp):
AAACTTGAAACGATTTTCACTCAAAAAAAA
Found at i:5246 original size:2 final size:2
Alignment explanation
Indices: 5239--5266 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5229 ATCCTCACAA
5239 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5267 ATACCTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:6521 original size:9 final size:9
Alignment explanation
Indices: 6507--6534 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6497 TGAAAACCCT
6507 AATTCCCAA
1 AATTCCCAA
6516 AATTCCCAA
1 AATTCCCAA
6525 AATTCCCAA
1 AATTCCCAA
6534 A
1 A
6535 CAAAAACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTCCCAA
Found at i:13519 original size:21 final size:21
Alignment explanation
Indices: 13495--13535 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13485 AAAATACATG
13495 GGCGGCTAGTCATAAAAACTA
1 GGCGGCTAGTCATAAAAACTA
13516 GGCGGCTAGTCATAAAAACT
1 GGCGGCTAGTCATAAAAACT
13536 GGGCAGCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
GGCGGCTAGTCATAAAAACTA
Found at i:17215 original size:15 final size:15
Alignment explanation
Indices: 17187--17228 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
17177 ATTCAAACAA
17187 AAATAAAA-AGAAAGT
1 AAATAAAAGA-AAAGT
17202 AAATAAAAGAAAAGT
1 AAATAAAAGAAAAGT
* *
17217 TAAGAAAAGAAA
1 AAATAAAAGAAA
17229 TTCTTAGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (15 bp):
AAATAAAAGAAAAGT
Found at i:26657 original size:5 final size:5
Alignment explanation
Indices: 26637--26670 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
26627 TTTCCTTCTT
26637 TTTTA TTCTT- TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTT
26671 TCTTGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.07
5 23 0.85
6 2 0.07
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:27018 original size:38 final size:35
Alignment explanation
Indices: 26947--27025 Score: 88
Period size: 38 Copynumber: 2.2 Consensus size: 35
26937 TTTTCTGGCC
*
26947 AAAA-AAAAACCTAACTTGTTTTAAACTTGGGCAGG
1 AAAAGAAAAACCTAACCTGTTTTAAACTTGGGCA-G
** *
26982 TAAAAGAAAATACCTAACCTGTTTTATGCTTTGGCAG
1 -AAAAGAAAA-ACCTAACCTGTTTTAAACTTGGGCAG
27019 AAAAGAA
1 AAAAGAA
27026 TTAATAGCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 11 0.30
37 5 0.14
38 21 0.57
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (35 bp):
AAAAGAAAAACCTAACCTGTTTTAAACTTGGGCAG
Found at i:27065 original size:2 final size:2
Alignment explanation
Indices: 27053--27091 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
27043 GTTGCAGTAC
*
27053 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27092 GTGTTAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:32070 original size:97 final size:97
Alignment explanation
Indices: 31904--32098 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
31894 TTTCTCCAAA
31904 AAAAAATGACAAATACTCGAAAGGTGCCAAACATATGGCATAAAGTATTTTTGTCTTTAAGGAGG
1 AAAAAATGACAAATACTCGAAAGGTGCCAAACATATGGCATAAAGTATTTTTGTCTTTAAGGAGG
31969 AAGTTAAGAAATCAAGAGTGTCAATTGAAGGT
66 AAGTTAAGAAATCAAGAGTGTCAATTGAAGGT
32001 AAAAAATGACAAATACTCGAAAGGTGCCAAACATATGGCATAAAGTATTTTTGTCTTTAAGGAGG
1 AAAAAATGACAAATACTCGAAAGGTGCCAAACATATGGCATAAAGTATTTTTGTCTTTAAGGAGG
*
32066 AAGTTCAGAAATCAAGAGTGTCAATTGAAGGT
66 AAGTTAAGAAATCAAGAGTGTCAATTGAAGGT
32098 A
1 A
32099 TTAGAACTGC
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (97 bp):
AAAAAATGACAAATACTCGAAAGGTGCCAAACATATGGCATAAAGTATTTTTGTCTTTAAGGAGG
AAGTTAAGAAATCAAGAGTGTCAATTGAAGGT
Found at i:38175 original size:19 final size:18
Alignment explanation
Indices: 38144--38179 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38134 TTGAAATAAT
38144 TCTTAAATGATCTTCAAA
1 TCTTAAATGATCTTCAAA
*
38162 TCTTCAAATTATCTTCAA
1 TCTT-AAATGATCTTCAA
38180 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTAAATGATCTTCAAA
Found at i:38733 original size:159 final size:160
Alignment explanation
Indices: 38462--38836 Score: 425
Period size: 161 Copynumber: 2.3 Consensus size: 160
38452 GATGAACTTT
* * * *
38462 TTGGATAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAGCCTCAACTTTGAGCATTTGT
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTTCAGCATTTGT
* * *
38527 GTGCAAAACATCGTTTTGAGGAACATGCTCATTCCAGTTGCG-TTTTTTGCGCAATGAGTGCTCA
66 GTGCAAAACATCGTTTTGAGCAAAATGCTCATTCCAGATGCGATTTTTTGCGCAATGAGTGCTCA
* ** * * *
38591 AATGTCATACGTCGGAGTGAGTTGAGCAGG
131 AAAGTCATACGTCAAAGTAAGATGAGCAAG
* * * *
38621 TTGGAAAGCCCTGTGCACAAACAAAGATTTCCCCGAAGTCCAAAACCTCAACTTATCATCATTT-
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTT-TCAGCATTTG
** * *
38685 TGTGCAAAACATCGTTCTT-AGCAAAACT-CTTTTTCCGGATGCGATTTTTTTGTGCAATGAGTG
65 TGTGCAAAACATCGTT-TTGAGCAAAA-TGCTCATTCCAGATGCGA-TTTTTTGCGCAATGAGTG
* **
38748 CTCAAAAGTCGTTTGTCAAAGTAAGATGAGCAAG
127 CTCAAAAGTCATACGTCAAAGTAAGATGAGCAAG
* * * * *
38782 ATGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTT
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTT
38837 GCGCCTATGT
Statistics
Matches: 179, Mismatches: 32, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
159 80 0.45
160 11 0.06
161 88 0.49
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (160 bp):
TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTTCAGCATTTGT
GTGCAAAACATCGTTTTGAGCAAAATGCTCATTCCAGATGCGATTTTTTGCGCAATGAGTGCTCA
AAAGTCATACGTCAAAGTAAGATGAGCAAG
Done.