Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011641.1 Corchorus capsularis cultivar CVL-1 contig11662, 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: 12776
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2351 original size:27 final size:26
Alignment explanation
Indices: 2321--2410 Score: 128
Period size: 26 Copynumber: 3.5 Consensus size: 26
2311 TGCACATCAA
*
2321 GGGGAGTCTCCCCTAGGCGCGTTGCTG
1 GGGGAGCCTCCCCT-GGCGCGTTGCTG
2348 GGGGAGCCTCCCCTGGCGCGTTGCTG
1 GGGGAGCCTCCCCTGGCGCGTTGCTG
* * *
2374 GGGGAGCCTCCCCTGGTGCGCTGC-C
1 GGGGAGCCTCCCCTGGCGCGTTGCTG
2399 GGGGAGCCTCCC
1 GGGGAGCCTCCC
2411 TTGGTGCGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 12 0.20
26 34 0.58
27 13 0.22
ACGTcount: A:0.06, C:0.36, G:0.41, T:0.18
Consensus pattern (26 bp):
GGGGAGCCTCCCCTGGCGCGTTGCTG
Found at i:2408 original size:25 final size:26
Alignment explanation
Indices: 2321--2422 Score: 116
Period size: 26 Copynumber: 3.9 Consensus size: 26
2311 TGCACATCAA
* * *
2321 GGGGAGTCTCCCCTAGGCGCGTTGCTG
1 GGGGAGCCTCCCCT-GGCGCGCTGCTC
* *
2348 GGGGAGCCTCCCCTGGCGCGTTGCTG
1 GGGGAGCCTCCCCTGGCGCGCTGCTC
*
2374 GGGGAGCCTCCCCTGGTGCGCTGC-C
1 GGGGAGCCTCCCCTGGCGCGCTGCTC
* *
2399 GGGGAGCCTCCCTTGGTGCGCTGC
1 GGGGAGCCTCCCCTGGCGCGCTGC
2423 CAGACTTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 23 0.33
26 34 0.49
27 13 0.19
ACGTcount: A:0.05, C:0.34, G:0.41, T:0.20
Consensus pattern (26 bp):
GGGGAGCCTCCCCTGGCGCGCTGCTC
Found at i:3448 original size:23 final size:23
Alignment explanation
Indices: 3392--3467 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 23
3382 CCCTTGGCGC
3392 GCGCTGCTGGGGGAGCCTCCCCTGG
1 GCGC-GCTGGGGGAGCCTCCCCT-G
3417 CGCGCCGCTGGGGGAGCCTCCCCTG
1 -GCG-CGCTGGGGGAGCCTCCCCTG
* *
3442 GCGCGCTGCTGGG-GCCTCCTCTG
1 GCGCGCTG-GGGGAGCCTCCCCTG
3465 GCG
1 GCG
3468 TCGTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
23 17 0.37
24 6 0.13
25 1 0.02
26 21 0.46
27 1 0.02
ACGTcount: A:0.03, C:0.39, G:0.42, T:0.16
Consensus pattern (23 bp):
GCGCGCTGGGGGAGCCTCCCCTG
Found at i:3462 original size:26 final size:26
Alignment explanation
Indices: 3347--3455 Score: 137
Period size: 26 Copynumber: 4.1 Consensus size: 26
3337 TGCTTCCCTA
* * * *
3347 GGGAGGCCTCCTCTGGCTCGTTACTGG
1 GGGA-GCCTCCCCTGGCGCGCTGCTGG
*
3374 GGGAGCCTCCCTTGGCGCGCGCTGCTGG
1 GGGAGCCTCCCCT-G-GCGCGCTGCTGG
*
3402 GGGAGCCTCCCCTGGCGCGCCGCTGG
1 GGGAGCCTCCCCTGGCGCGCTGCTGG
3428 GGGAGCCTCCCCTGGCGCGCTGCTGG
1 GGGAGCCTCCCCTGGCGCGCTGCTGG
3454 GG
1 GG
3456 CCTCCTCTGG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 45 0.62
27 6 0.08
28 21 0.29
ACGTcount: A:0.05, C:0.36, G:0.42, T:0.17
Consensus pattern (26 bp):
GGGAGCCTCCCCTGGCGCGCTGCTGG
Found at i:7427 original size:18 final size:18
Alignment explanation
Indices: 7404--7440 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
7394 TATTATTTAA
7404 TTTTCATTAAACTTACCT
1 TTTTCATTAAACTTACCT
*
7422 TTTTCATTAGACTTACCT
1 TTTTCATTAAACTTACCT
7440 T
1 T
7441 CGGCATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTCATTAAACTTACCT
Found at i:7896 original size:18 final size:17
Alignment explanation
Indices: 7869--7902 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
7859 ACTCAAACTC
7869 AAACTAACTGACTCAAA
1 AAACTAACTGACTCAAA
7886 AAACTTAACTGACTCAA
1 AAAC-TAACTGACTCAA
7903 CTGACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
AAACTAACTGACTCAAA
Found at i:7930 original size:27 final size:27
Alignment explanation
Indices: 7874--7930 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
7864 AACTCAAACT
* * *
7874 AACTGACTCAAAAAACTTAACTGACTC
1 AACTGACTAAAAAAACTTAACTAACCC
*
7901 AACTGACTAAAAAAAC-TGACTAAACCC
1 AACTGACTAAAAAAACTTAACT-AACCC
7928 AAC
1 AAC
7931 AGGTCAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.18
Consensus pattern (27 bp):
AACTGACTAAAAAAACTTAACTAACCC
Found at i:12673 original size:12 final size:12
Alignment explanation
Indices: 12656--12683 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12646 CAACTAATTG
12656 ATTTTATTTGTA
1 ATTTTATTTGTA
12668 ATTTTATTTGTA
1 ATTTTATTTGTA
12680 ATTT
1 ATTT
12684 GTAATAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
ATTTTATTTGTA
Found at i:12699 original size:21 final size:21
Alignment explanation
Indices: 12650--12703 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
12640 GCAAATCAAC
12650 TAATTGATTT-T-ATTTGTAA
1 TAATTGATTTGTAATTTGTAA
*
12669 T--TTTATTTGTAATTTGTAA
1 TAATTGATTTGTAATTTGTAA
12688 TAATTGATTTGTAATT
1 TAATTGATTTGTAATT
12704 GATTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 1 0.03
19 10 0.34
21 12 0.41
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TAATTGATTTGTAATTTGTAA
Found at i:12714 original size:10 final size:11
Alignment explanation
Indices: 12688--12716 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12678 TAATTTGTAA
12688 TAATTGATTTG
1 TAATTGATTTG
12699 TAATTGATTT-
1 TAATTGATTTG
12709 TAATTGAT
1 TAATTGAT
12717 CAAAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (11 bp):
TAATTGATTTG
Done.