Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013801.1 Corchorus olitorius cultivar O-4 contig13834, 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: 9718
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:571 original size:17 final size:17
Alignment explanation
Indices: 538--571 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
528 CAAAGGTATC
* *
538 TTTTTTCTTGCTTTCTA
1 TTTTTTCTGGCTCTCTA
555 TTTTTTCTGGCTCTCTA
1 TTTTTTCTGGCTCTCTA
572 CCTCTCCTTT
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:0.06, C:0.21, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTTTTCTGGCTCTCTA
Found at i:1472 original size:19 final size:19
Alignment explanation
Indices: 1448--1489 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1438 TCTTATGGTC
1448 TTGTGTACTTGGTGAATAT
1 TTGTGTACTTGGTGAATAT
1467 TTGTGTACTTGGTGAATAT
1 TTGTGTACTTGGTGAATAT
1486 TTGT
1 TTGT
1490 ACCTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.50
Consensus pattern (19 bp):
TTGTGTACTTGGTGAATAT
Found at i:2087 original size:28 final size:27
Alignment explanation
Indices: 2008--2088 Score: 110
Period size: 28 Copynumber: 3.0 Consensus size: 27
1998 AAATTAAAAG
2008 TGAACTT-AAAATGACCAAAATGCCCC
1 TGAACTTGAAAATGACCAAAATGCCCC
*
2034 TGAACTTGCAAATGACCAAAATGCCCC
1 TGAACTTGAAAATGACCAAAATGCCCC
** *
2061 TGGATTTTGAAAATGACCAAAACGCCCC
1 T-GAACTTGAAAATGACCAAAATGCCCC
2089 CTGGGTGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 7 0.15
27 19 0.40
28 22 0.46
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (27 bp):
TGAACTTGAAAATGACCAAAATGCCCC
Found at i:2534 original size:51 final size:50
Alignment explanation
Indices: 2362--2565 Score: 354
Period size: 50 Copynumber: 4.0 Consensus size: 50
2352 CTAATATTAT
* *
2362 AAGGACCGTCTTTCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTGA
1 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAA
*
2412 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTAAATCTTAA
1 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAA
*
2462 AAGGACCGTCTTCTGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAA
1 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-TTAA
2513 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTTAA
1 AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-TTAA
2564 AA
1 AA
2566 AAGGTAATGC
Statistics
Matches: 147, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 91 0.62
51 56 0.38
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (50 bp):
AAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAA
Found at i:2634 original size:48 final size:51
Alignment explanation
Indices: 2578--2941 Score: 325
Period size: 50 Copynumber: 7.3 Consensus size: 51
2568 GGTAATGCAC
2578 CGTATGGAAACGGA-TGT-GGC-T-TGGATGAAACCAAGGTTTGA-AA-TGACT
1 CGTATGGAAACGGAGT-TCGGCTTGTGGA-GAAACCAAGG-TTGATAATTGACT
* *
2626 CGTATGGAAAC-GAGTTCGGCTTGTGGAGAAACCTATGTTGATAATTGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAACCAAGGTTGATAATTGACT
* * *
2676 CGTATGGAAAC-GAGTTTGGCTTGTGGA-AAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAA-CCAAGGTTGATAATTGACT
* ***
2726 CGTATGGAAAC-GAGTTTGGCTTGTGGA-AAAGCCTTTGTTGATAATTGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAA-CCAAGGTTGATAATTGACT
* * *
2776 CGTATGGAAAC-GAGTTTGGCTTGTGGA-AAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAA-CCAAGGTTGATAATTGACT
* * * *
2826 CGTATGGAAAC-GAGTTTGGCTTGTGGA-AAAGCC-TGTGCTGATAACTGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAA-CCAAG-GTTGATAATTGACT
* * * * *
2876 CATATGGAAAC-GAGTTTGGCTTGTGGA-AAAGCCTATGTTGATAATCGACT
1 CGTATGGAAACGGAGTTCGGCTTGTGGAGAAA-CCAAGGTTGATAATTGACT
2926 CGTATGGAAAC-GAGTT
1 CGTATGGAAACGGAGTT
2942 TGACTTATGG
Statistics
Matches: 291, Mismatches: 16, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
47 3 0.01
48 19 0.07
49 14 0.05
50 255 0.88
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (51 bp):
CGTATGGAAACGGAGTTCGGCTTGTGGAGAAACCAAGGTTGATAATTGACT
Found at i:2685 original size:50 final size:50
Alignment explanation
Indices: 2621--2958 Score: 579
Period size: 50 Copynumber: 6.8 Consensus size: 50
2611 AGGTTTGAAA
*
2621 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAGAAA-CCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGA-AAAGCCTATGTTGATAAT
2671 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
2721 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTTTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
2771 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
2821 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGCTGATAAC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
2871 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * *
2921 CGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
2959 AAAACATTCG
Statistics
Matches: 273, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 3 0.01
50 270 0.99
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:3706 original size:50 final size:50
Alignment explanation
Indices: 3560--3709 Score: 196
Period size: 50 Copynumber: 3.0 Consensus size: 50
3550 CTTAAATGCC
* **
3560 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAAT-GAAATGCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAA-GCAATTTTA
* * * *
3610 CTTTGAAAAGCAAATTTTGAT-TTTAGATTTACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGA-ACTCACAAATGGAAAGCAATTTTA
*
3660 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
3710 TTATAAAACT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
49 2 0.02
50 76 0.89
51 7 0.08
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:4315 original size:8 final size:8
Alignment explanation
Indices: 4302--4333 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
4292 TGATTTGATT
4302 TTTTTTTA
1 TTTTTTTA
4310 TTTTTTTGA
1 TTTTTTT-A
4319 TTTTTTTA
1 TTTTTTTA
4327 TTTTTTT
1 TTTTTTT
4334 TGATTGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:4315 original size:9 final size:9
Alignment explanation
Indices: 4301--4366 Score: 62
Period size: 9 Copynumber: 7.0 Consensus size: 9
4291 TTGATTTGAT
4301 TTTTTTTTA
1 TTTTTTTTA
*
4310 TTTTTTTGA
1 TTTTTTTTA
4319 -TTTTTTTA
1 TTTTTTTTA
4327 TTTTTTTTGA
1 TTTTTTTT-A
* *
4337 TTGATTGATTGA
1 TT--TT-TTTTA
4349 TTTTTTTTA
1 TTTTTTTTA
4358 TTTTTTTTA
1 TTTTTTTTA
4367 ATTGATTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 7 0.15
9 27 0.59
10 5 0.11
12 5 0.11
13 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4357 original size:31 final size:32
Alignment explanation
Indices: 4315--4382 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 32
4305 TTTTATTTTT
*
4315 TTGA-TTTTTTTATTTTTTTTGATTGA-TTGA
1 TTGATTTTTTTTATTTTTTTTAATTGATTTGA
4345 TTGATTTTTTTTATTTTTTTTAATTGATTTGA
1 TTGATTTTTTTTATTTTTTTTAATTGATTTGA
4377 TTGATT
1 TTGATT
4383 GATTTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 4 0.11
31 21 0.60
32 10 0.29
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (32 bp):
TTGATTTTTTTTATTTTTTTTAATTGATTTGA
Found at i:4365 original size:40 final size:39
Alignment explanation
Indices: 4309--4401 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
4299 ATTTTTTTTT
* **
4309 ATTTTTTTGATTTTTTTATTTTTTTTGATTGATTGATTG
1 ATTTTTTTGATTTTTTTAATTGATTTGATTGATTGATTG
*
4348 ATTTTTTTTATTTTTTTTAATTGATTTGATTGATTGA-T-
1 ATTTTTTTGA-TTTTTTTAATTGATTTGATTGATTGATTG
*
4386 -TTTTTTCGATTTTTTT
1 ATTTTTTTGATTTTTTT
4402 TCTTTTTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
36 7 0.15
37 7 0.15
39 10 0.21
40 23 0.49
ACGTcount: A:0.16, C:0.01, G:0.11, T:0.72
Consensus pattern (39 bp):
ATTTTTTTGATTTTTTTAATTGATTTGATTGATTGATTG
Found at i:4402 original size:40 final size:38
Alignment explanation
Indices: 4309--4402 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 38
4299 ATTTTTTTTT
**
4309 ATTTTTTTGATTTTTTTATTTTTTTTGATTGATTGATTG
1 ATTTTTTTGATTTTTTT-TTTTAATTGATTGATTGATTG
*
4348 A-TTTTTT--TTATTTTTTTTAATTGATTTGATTGATTG
1 ATTTTTTTGATTTTTTTTTTTAATTGA-TTGATTGATTG
4384 ATTTTTTTCGATTTTTTTT
1 ATTTTTTT-GATTTTTTTT
4403 CTTTTTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
35 8 0.17
36 18 0.39
37 6 0.13
38 6 0.13
39 1 0.02
40 7 0.15
ACGTcount: A:0.16, C:0.01, G:0.11, T:0.72
Consensus pattern (38 bp):
ATTTTTTTGATTTTTTTTTTTAATTGATTGATTGATTG
Done.