Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007267.1 Corchorus capsularis cultivar CVL-1 contig07288, 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: 49238
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1656 original size:11 final size:11
Alignment explanation
Indices: 1623--1656 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1613 TTCTTGAATA
1623 TATTTTTATTT
1 TATTTTTATTT
* *
1634 CATTATTATTT
1 TATTTTTATTT
1645 TATTTTTATTT
1 TATTTTTATTT
1656 T
1 T
1657 TAACAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:4733 original size:156 final size:155
Alignment explanation
Indices: 4373--4733 Score: 358
Period size: 156 Copynumber: 2.3 Consensus size: 155
4363 CAGACTTCGT
* * * * ** * *
4373 ATGAAAAACTTATGCTAGTTTTTTAGTTAAGGACAGTTTGGGGTGTCAAACCTACTTCTCTATGC
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCTACTTCACCATGC
* *
4438 TAGAGAGATCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGGGATAATCTAAGTCTACTGGT
66 AAGAGAGATCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGAGATAATCTAAGTCTACT-GT
** *
4503 GGAAAATCAGCTTCTTTGGACTTAGA
130 GGAAAATCAGCTTCTTCAGACTTAAA
* * * * * *
4529 GTGAAAAACTTATGCTAATTTTTCATTTAAGGACAA-CTCAGGGAGAGAAACCTAGTTCACCAT-
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGA-GGTGAGAAACCTACTTCACCATG
* * * ** * *
4592 CAAGGGGAGCTCGGTTTTACTTGGAATTTTTTTCATAG-TCTCATGGAGATATTCTAAGTC-CCT
65 CAA-GAGAGATCGGTTTTACTTAGAATTTTTCCCATAGCT-TCATGGAGATAATCTAAGTCTACT
4655 -T-GACAAAGTTTCAGC-TCATTCAGACTTAAA
128 GTGGA-AAA---TCAGCTTC-TTCAGACTTAAA
4685 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
4734 GTCTAGTTTA
Statistics
Matches: 165, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
152 2 0.01
153 4 0.02
155 8 0.05
156 149 0.90
157 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (155 bp):
ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCTACTTCACCATGC
AAGAGAGATCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGAGATAATCTAAGTCTACTGTG
GAAAATCAGCTTCTTCAGACTTAAA
Found at i:11612 original size:28 final size:30
Alignment explanation
Indices: 11538--11612 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
11528 CTAGGTGAAA
* *
11538 ATTTATAATTTTGCCATGTCCTCTAAAAAG
1 ATTTACAATTTTGCCATGTACTCTAAAAAG
* *
11568 ATTTACAATTTTACCATGTACT-T-AAAAT
1 ATTTACAATTTTGCCATGTACTCTAAAAAG
* *
11596 ATTTGCAATTTGGCCAT
1 ATTTACAATTTTGCCAT
11613 CAACAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.47
29 1 0.03
30 19 0.50
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (30 bp):
ATTTACAATTTTGCCATGTACTCTAAAAAG
Found at i:22542 original size:31 final size:30
Alignment explanation
Indices: 22504--22582 Score: 122
Period size: 31 Copynumber: 2.6 Consensus size: 30
22494 CGTTGCTGTT
22504 TTTAGACTCAAATTGGTCAAATTTTGAAAGG
1 TTTAGACTCAAATTGGT-AAATTTTGAAAGG
* *
22535 TTTAGACTCAAATTAAGTAACTTTTGAAAGG
1 TTTAGACTCAAATT-GGTAAATTTTGAAAGG
22566 TTTAGACTCAAATTGGT
1 TTTAGACTCAAATTGGT
22583 GGCTAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.05
31 40 0.91
32 2 0.05
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTAGACTCAAATTGGTAAATTTTGAAAGG
Found at i:25093 original size:31 final size:31
Alignment explanation
Indices: 25053--25113 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
25043 AATAAGCCCC
* *
25053 TAACATTGCAAAATTGGCTCAAATCAGTCCA
1 TAACATTGCAAAATCGACTCAAATCAGTCCA
*
25084 TAACGTTGCAAAATCGACTCAAATCAGTCC
1 TAACATTGCAAAATCGACTCAAATCAGTCC
25114 CTAAAGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (31 bp):
TAACATTGCAAAATCGACTCAAATCAGTCCA
Found at i:30951 original size:22 final size:22
Alignment explanation
Indices: 30926--30968 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30916 CCATGGATCT
30926 CCGGGTTAGAGGGACATGAACA
1 CCGGGTTAGAGGGACATGAACA
30948 CCGGGTTAGAGGGACATGAAC
1 CCGGGTTAGAGGGACATGAAC
30969 GCTGGCGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.37, T:0.14
Consensus pattern (22 bp):
CCGGGTTAGAGGGACATGAACA
Found at i:31106 original size:11 final size:10
Alignment explanation
Indices: 31079--31139 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
31069 CGTTGAGGAG
*
31079 AAGAAGAAGAG
1 AAGAA-AAGAA
31090 AA-AAAAGAA
1 AAGAAAAGAA
31099 AAGGAAAAGAA
1 AA-GAAAAGAA
31110 AAGAGAAAGAAA
1 AAGA-AAAG-AA
31122 AAGAAAA-AA
1 AAGAAAAGAA
*
31131 AATAAAAGA
1 AAGAAAAGA
31140 GGGAAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
9 14 0.33
10 5 0.12
11 18 0.42
12 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AAGAAAAGAA
Found at i:31109 original size:18 final size:17
Alignment explanation
Indices: 31088--31130 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
31078 GAAGAAGAAG
*
31088 AGAAAAAAGAAAAGGAAA
1 AGAAAAAAG-AAAGAAAA
*
31106 AGAAAAGAGAAAGAAAA
1 AGAAAAAAGAAAGAAAA
31123 AGAAAAAA
1 AGAAAAAA
31131 AATAAAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGAAAGAAAA
Found at i:35264 original size:22 final size:20
Alignment explanation
Indices: 35239--35285 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
35229 CGTGGACTAC
35239 TCGAGCTCGACTCGAGAAAAAT
1 TCGAGCTCGACTCG-G-AAAAT
* *
35261 TCGAGTTCGGCTCGGAAAAT
1 TCGAGCTCGACTCGGAAAAT
35281 TCGAG
1 TCGAG
35286 TCAAGCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 1 0.04
22 12 0.52
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (20 bp):
TCGAGCTCGACTCGGAAAAT
Found at i:40378 original size:3 final size:3
Alignment explanation
Indices: 40370--40411 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
40360 AAACCCCATT
40370 TTC TTC TTC TTC TTC TTC TTTC TCTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC -TTC T-TC TTC TTC TTC TTC TTC T
40412 CCTCCTCCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:40399 original size:20 final size:19
Alignment explanation
Indices: 40369--40409 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
40359 GAAACCCCAT
40369 TTTCTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTCTTC
40388 TTTCTCTCTTCTTCTTCTTC
1 TTTCT-TCTTCTTCTTCTTC
40408 TT
1 TT
40410 CTCCTCCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTCTTCTTCTTCTTC
Found at i:40416 original size:3 final size:3
Alignment explanation
Indices: 40410--40438 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40400 TCTTCTTCTT
40410 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
40439 TCTTCTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:40446 original size:9 final size:9
Alignment explanation
Indices: 40370--40452 Score: 64
Period size: 9 Copynumber: 9.3 Consensus size: 9
40360 AAACCCCATT
*
40370 TTCTTCTTC
1 TTCTCCTTC
*
40379 TTCTTCTTC
1 TTCTCCTTC
40388 TTTCTCTCTTC
1 -TTCTC-CTTC
*
40399 TTCTTCTTC
1 TTCTCCTTC
40408 TTCTCC-TC
1 TTCTCCTTC
*
40416 --CTCCTCC
1 TTCTCCTTC
* *
40423 TCCTCCTCC
1 TTCTCCTTC
*
40432 TCCTCCTTC
1 TTCTCCTTC
40441 TTCTCCTTC
1 TTCTCCTTC
40450 TTC
1 TTC
40453 CTTACCGTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 2 0.03
9 44 0.70
10 8 0.13
11 4 0.06
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (9 bp):
TTCTCCTTC
Found at i:41388 original size:56 final size:56
Alignment explanation
Indices: 41302--41431 Score: 251
Period size: 56 Copynumber: 2.3 Consensus size: 56
41292 GTAATATAGA
*
41302 ATTGCAATTGATGGATCTGTAAAGAGCCATATTTGGATGAATGATTAATTTCATCC
1 ATTGCAATTGATGGATCTATAAAGAGCCATATTTGGATGAATGATTAATTTCATCC
41358 ATTGCAATTGATGGATCTATAAAGAGCCATATTTGGATGAATGATTAATTTCATCC
1 ATTGCAATTGATGGATCTATAAAGAGCCATATTTGGATGAATGATTAATTTCATCC
41414 ATTGCAATTGATGGATCT
1 ATTGCAATTGATGGATCT
41432 GAAATGCAGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (56 bp):
ATTGCAATTGATGGATCTATAAAGAGCCATATTTGGATGAATGATTAATTTCATCC
Found at i:47240 original size:5 final size:5
Alignment explanation
Indices: 47232--47256 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47222 AAAAAAATAA
47232 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
47257 CATGGGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:48434 original size:7 final size:7
Alignment explanation
Indices: 48424--48455 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
48414 CAAAAACAAA
48424 AAAAAAC
1 AAAAAAC
48431 AAAAAAC
1 AAAAAAC
48438 AAAAAAC
1 AAAAAAC
48445 AAAAAAC
1 AAAAAAC
48452 AAAA
1 AAAA
48456 TACGAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Done.