Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013621.1 Corchorus capsularis cultivar CVL-1 contig13642, 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: 26093
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:2374 original size:13 final size:13
Alignment explanation
Indices: 2347--2385 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2337 TCAAAATTTG
2347 AAGGAAAATGAAAA
1 AAGGAAAA-GAAAA
2361 AAGGAAAAGAAAA
1 AAGGAAAAGAAAA
*
2374 AATGAAAA-AAAA
1 AAGGAAAAGAAAA
2386 TCAGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 4 0.17
13 12 0.50
14 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (13 bp):
AAGGAAAAGAAAA
Found at i:7630 original size:25 final size:25
Alignment explanation
Indices: 7596--7679 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
7586 AAAAAAAGTC
7596 ATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAGGTTTTGATAAA
** *
7621 ATGGTTTTCAAAA----AAGAGT--C
1 ATGGTTTTCAAAAGGTTTTGA-TAAA
7641 ATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAGGTTTTGATAAA
7666 ATGGTTTTCCAAAA
1 ATGGTTTT-CAAAA
7680 ATGATTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
20 13 0.29
21 2 0.04
22 1 0.02
23 1 0.02
24 2 0.04
25 21 0.47
26 5 0.11
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (25 bp):
ATGGTTTTCAAAAGGTTTTGATAAA
Found at i:7674 original size:45 final size:45
Alignment explanation
Indices: 7535--7680 Score: 231
Period size: 45 Copynumber: 3.2 Consensus size: 45
7525 GCAACGATGT
* *
7535 TTTTC-AAAAAGAGTTATGGTTTTTCAAAAGGTTTTGATGAAATGG
1 TTTTCAAAAAAGAGTCATGG-TTTTCAAAAGGTTTTGATAAAATGG
* *
7580 TTTTAAAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
1 TTTTCAAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
7625 TTTTCAAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
1 TTTTCAAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
*
7670 TTTTCCAAAAA
1 TTTTCAAAAAA
7681 TGATTTCAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 81 0.87
46 12 0.13
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (45 bp):
TTTTCAAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
Found at i:8349 original size:15 final size:14
Alignment explanation
Indices: 8329--8379 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
8319 AAATGCATGT
*
8329 AAAAAATGAAAGAA
1 AAAAAAAGAAAGAA
*
8343 AAAAAAAGAAAAGGA
1 AAAAAAAG-AAAGAA
*
8358 AAAAAAAGAGAGAA
1 AAAAAAAGAAAGAA
8372 AAAGAAAA
1 AAA-AAAA
8380 AAAATGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAGAA
Found at i:8371 original size:19 final size:17
Alignment explanation
Indices: 8337--8383 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
8327 GTAAAAAATG
8337 AAAG-AAAAAAAAAGAA
1 AAAGAAAAAAAAAAGAA
*
8353 AAGGAAAAAAAAGAGAGAA
1 AAAGAAAAAAAA-A-AGAA
8372 AAAGAAAAAAAA
1 AAAGAAAAAAAA
8384 TGATGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 7 0.27
18 1 0.04
19 15 0.58
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAAGAA
Found at i:9579 original size:35 final size:35
Alignment explanation
Indices: 9528--9774 Score: 309
Period size: 35 Copynumber: 7.0 Consensus size: 35
9518 GGCAGTCGTT
* *
9528 TTTCAAGTTGATCCAGGGCGGT-TATTCTTCAGTTTG
1 TTTC-AGTTGACCCAGGGCGGTCT-TTCTTCAGTTTA
*
9564 TTTCAGTTGACCCAGGGCGGT-TATTATTCAGTTTA
1 TTTCAGTTGACCCAGGGCGGTCT-TTCTTCAGTTTA
* *
9599 TTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTA
1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
**
9634 TTTCAGTTGACCCAGGGTAGTCTTTCTTCAGTTTA
1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
* *
9669 TTTCAGTTGACCCATGGCGGTCTTACTTCAGTTTA
1 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
*** *
9704 TTTCAGTTGACCCAGGTTAGTCTTTCTTCAAATTTA
1 TTTCAGTTGACCCAGGGCGGTCTTTCTTC-AGTTTA
*
9740 TTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTT
1 TTTCAGTTGACCCAGGGCGGTC-TTTCTTCAGTTT
9775 TACTCGATTG
Statistics
Matches: 186, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
35 146 0.78
36 33 0.18
37 7 0.04
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (35 bp):
TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
Found at i:9715 original size:105 final size:107
Alignment explanation
Indices: 9528--9774 Score: 342
Period size: 105 Copynumber: 2.3 Consensus size: 107
9518 GGCAGTCGTT
* * * *
9528 TTTCAAGTTGATCCAGGGCGGT-TATTCTTCAGTTTGTTTCAGTTGACCCAGGGCGGTTATTATT
1 TTTC-AGTTGACCCAGGGAGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTTATTATT
* * *
9592 CAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTC-AGTTTA
65 CAGTTTATTTCAGTTGACCCAGGGTAGTCTTTCTTCAAATTTA
* *
9634 TTTCAGTTGACCCAGGGTA-GTC-TTTCTTCAGTTTATTTCAGTTGACCCATGGCGG-TCTTACT
1 TTTCAGTTGACCCAGGG-AGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTTATTA-T
*
9696 TCAGTTTATTTCAGTTGACCCAGGTTAGTCTTTCTTCAAATTTA
64 TCAGTTTATTTCAGTTGACCCAGGGTAGTCTTTCTTCAAATTTA
9740 TTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTT
1 TTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTT
9775 TACTCGATTG
Statistics
Matches: 125, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
104 4 0.03
105 80 0.64
106 29 0.23
107 12 0.10
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (107 bp):
TTTCAGTTGACCCAGGGAGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTTATTATTC
AGTTTATTTCAGTTGACCCAGGGTAGTCTTTCTTCAAATTTA
Found at i:12495 original size:2 final size:2
Alignment explanation
Indices: 12488--12519 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12478 TGATTAATTA
*
12488 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12520 GAAGGTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13680 original size:13 final size:14
Alignment explanation
Indices: 13653--13681 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13643 TCAAAATTTG
13653 AAGGAAAATGAAAA
1 AAGGAAAATGAAAA
13667 AAGGAAAA-GAAAA
1 AAGGAAAATGAAAA
13680 AA
1 AA
13682 ATGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (14 bp):
AAGGAAAATGAAAA
Found at i:13757 original size:15 final size:14
Alignment explanation
Indices: 13715--13756 Score: 75
Period size: 14 Copynumber: 2.9 Consensus size: 14
13705 AAGATGTAAT
13715 AAAAAGTGTTTTTTC
1 AAAAA-TGTTTTTTC
13730 AAAAATGTTTTTTC
1 AAAAATGTTTTTTC
13744 AAAAATGTTTTTT
1 AAAAATGTTTTTT
13757 TATTGTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (14 bp):
AAAAATGTTTTTTC
Found at i:14938 original size:22 final size:21
Alignment explanation
Indices: 14898--14938 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14888 CGGCTCGAAT
*
14898 TTTCCGAGTCGAACTCGAAAA
1 TTTCCGAGTCGAACCCGAAAA
*
14919 TTTCTCGAGTCGAGCCCGAA
1 TTTC-CGAGTCGAACCCGAA
14939 CAGTTCACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
TTTCCGAGTCGAACCCGAAAA
Found at i:24833 original size:19 final size:19
Alignment explanation
Indices: 24787--24833 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
24777 TTTATATGTG
*
24787 TGTGATGGCCCAACACCAA
1 TGTGATGGGCCAACACCAA
24806 TGTGATGGGCCAACACCAA
1 TGTGATGGGCCAACACCAA
24825 TGTGATGGG
1 TGTGATGGG
24834 TTTCTATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (19 bp):
TGTGATGGGCCAACACCAA
Done.