Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024192.1 Corchorus olitorius cultivar O-4 contig24225, 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: 3975
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:359 original size:31 final size:31
Alignment explanation
Indices: 323--415 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
313 ACTAAATACT
*
323 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
*
354 AAAAAAATTCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
385 -AAAAAATCCCTTATGTTTTT-TTTT-GGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
413 AAA
1 AAA
416 TTAGTCCCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 4 0.07
29 6 0.10
30 19 0.33
31 29 0.50
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:601 original size:29 final size:30
Alignment explanation
Indices: 565--632 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
555 TTTGAAACGC
* *
565 AAGGGATTAATTTGTCCCGAAA-AAAACAT
1 AAGGGATTAATTTGTCACAAAACAAAACAT
*
594 AAGGGATTATTTTGTCACAAAAGCAAAACAT
1 AAGGGATTAATTTGTCACAAAA-CAAAACAT
625 AAGGGATT
1 AAGGGATT
633 TTTCTGGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (30 bp):
AAGGGATTAATTTGTCACAAAACAAAACAT
Found at i:1637 original size:16 final size:18
Alignment explanation
Indices: 1600--1637 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1590 GTTTGCTTGG
1600 ATTTTTCTCTTTTAAGTT
1 ATTTTTCTCTTTTAAGTT
1618 -TTTTTCT-TTTTAA-TT
1 ATTTTTCTCTTTTAAGTT
1633 ATTTT
1 ATTTT
1638 AAAATATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.11
16 10 0.53
17 7 0.37
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTCTCTTTTAAGTT
Found at i:1720 original size:79 final size:80
Alignment explanation
Indices: 1615--1773 Score: 284
Period size: 79 Copynumber: 2.0 Consensus size: 80
1605 TCTCTTTTAA
*
1615 GTTTTTTTCTTTTTAATTATTTTAAAATATGACAATAGGAGG-ATCAACTTACACTTGGTGTAAA
1 GTTTTTTTCTTTTTAATTATTTTAAAATATGACAATAGAAGGAATCAACTTACACTTGGTGTAAA
1679 ACAACTTTATATATC
66 ACAACTTTATATATC
*
1694 GTTTTTTTCTTTTTAATTATTTTAAAATATGACAATAGAAGGAATCGACTTACACTTGGTGTAAA
1 GTTTTTTTCTTTTTAATTATTTTAAAATATGACAATAGAAGGAATCAACTTACACTTGGTGTAAA
*
1759 ACAATTTTATATATC
66 ACAACTTTATATATC
1774 TTTATAGATC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 41 0.54
80 35 0.46
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (80 bp):
GTTTTTTTCTTTTTAATTATTTTAAAATATGACAATAGAAGGAATCAACTTACACTTGGTGTAAA
ACAACTTTATATATC
Found at i:2140 original size:22 final size:22
Alignment explanation
Indices: 2115--2179 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
2105 TACATTAATT
2115 AAATTTAATACTATAATAACTG
1 AAATTTAATACTATAATAACTG
* *
2137 AAA--TACTTAC-AT--TAA-TT
1 AAATTTA-ATACTATAATAACTG
2154 AAATTTAATACTATAATAACTG
1 AAATTTAATACTATAATAACTG
2176 AAAT
1 AAAT
2180 ACTTACATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 4 0.12
20 4 0.12
21 6 0.19
22 8 0.25
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (22 bp):
AAATTTAATACTATAATAACTG
Found at i:2141 original size:39 final size:39
Alignment explanation
Indices: 2087--2197 Score: 204
Period size: 39 Copynumber: 2.8 Consensus size: 39
2077 ATGTAATATA
* *
2087 TATAGTAACTAAAATACTTACATTAATTAAATTTAATAC
1 TATAATAACTGAAATACTTACATTAATTAAATTTAATAC
2126 TATAATAACTGAAATACTTACATTAATTAAATTTAATAC
1 TATAATAACTGAAATACTTACATTAATTAAATTTAATAC
2165 TATAATAACTGAAATACTTACATTAATTAAATT
1 TATAATAACTGAAATACTTACATTAATTAAATT
2198 CTTAGGTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (39 bp):
TATAATAACTGAAATACTTACATTAATTAAATTTAATAC
Found at i:2143 original size:17 final size:17
Alignment explanation
Indices: 2121--2182 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
2111 AATTAAATTT
2121 AATACTATAATAACTGA
1 AATACTATAATAACTGA
* **
2138 AATACTTACATTAATTAAATTT
1 AATAC-T--A-TAA-TAACTGA
2160 AATACTATAATAACTGA
1 AATACTATAATAACTGA
2177 AATACT
1 AATACT
2183 TACATTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
17 15 0.44
18 4 0.12
19 1 0.03
20 1 0.03
21 4 0.12
22 9 0.26
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.35
Consensus pattern (17 bp):
AATACTATAATAACTGA
Found at i:3217 original size:13 final size:13
Alignment explanation
Indices: 3199--3254 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
3189 GCAAGCGCCA
3199 GGCCAGGCGCGCG
1 GGCCAGGCGCGCG
**
3212 GGCCA-GCGCTTG
1 GGCCAGGCGCGCG
* *
3224 GCCCAGGCGC-CA
1 GGCCAGGCGCGCG
*
3236 GGCCTGGCGCGCG
1 GGCCAGGCGCGCG
3249 GGCCAG
1 GGCCAG
3255 AGCTTGGCCC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 17 0.53
13 15 0.47
ACGTcount: A:0.09, C:0.39, G:0.46, T:0.05
Consensus pattern (13 bp):
GGCCAGGCGCGCG
Found at i:3245 original size:37 final size:37
Alignment explanation
Indices: 3193--3265 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
3183 GGGCCAGCAA
*
3193 GCGCCAGGCCAGGCGCGCGGGCCAGCGCTTGGCCCAG
1 GCGCCAGGCCAGGCGCGCGGGCCAGAGCTTGGCCCAG
*
3230 GCGCCAGGCCTGGCGCGCGGGCCAGAGCTTGGCCCA
1 GCGCCAGGCCAGGCGCGCGGGCCAGAGCTTGGCCCA
3266 AGCTTGGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.11, C:0.40, G:0.42, T:0.07
Consensus pattern (37 bp):
GCGCCAGGCCAGGCGCGCGGGCCAGAGCTTGGCCCAG
Found at i:3352 original size:11 final size:11
Alignment explanation
Indices: 3336--3360 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3326 ATTTTGGAAT
3336 AAAGAAAAGGA
1 AAAGAAAAGGA
3347 AAAGAAAAGGA
1 AAAGAAAAGGA
3358 AAA
1 AAA
3361 AGAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGGA
Found at i:3379 original size:21 final size:21
Alignment explanation
Indices: 3346--3396 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3336 AAAGAAAAGG
3346 AAAAGAAAAGGAAAAAGAATT
1 AAAAGAAAAGGAAAAAGAATT
*
3367 AAAA-AAAAGGGAAAAAGAAAAT
1 AAAAGAAAA-GGAAAAAG-AATT
3389 AAAAGAAA
1 AAAAGAAA
3397 TAAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 7 0.27
23 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAGAAAAGGAAAAAGAATT
Found at i:3561 original size:84 final size:84
Alignment explanation
Indices: 3462--3631 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
3452 ACAATTTTAC
3462 CCTTGGATGGGTAAAATTACTAAATCACCCTTAATATGTTAAATTACGAAATTTACCTTTTGAAG
1 CCTTGGATGGGTAAAATTACTAAATCACCCTTAATATGTTAAATTACGAAATTTACCTTTTGAAG
3527 AGGAATTCAAAGAATTAAA
66 AGGAATTCAAAGAATTAAA
3546 CCTTGGATGGGTAAAATTACTAAATCACCCTTAATATGTTAAATTACGAAATTTACCTTTTGAAG
1 CCTTGGATGGGTAAAATTACTAAATCACCCTTAATATGTTAAATTACGAAATTTACCTTTTGAAG
3611 AGGAATTCAAAGAATTAAA
66 AGGAATTCAAAGAATTAAA
3630 CC
1 CC
3632 ACATCGGTTG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (84 bp):
CCTTGGATGGGTAAAATTACTAAATCACCCTTAATATGTTAAATTACGAAATTTACCTTTTGAAG
AGGAATTCAAAGAATTAAA
Done.