Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007114.1 Corchorus capsularis cultivar CVL-1 contig07135, 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: 32529
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Found at i:573 original size:20 final size:20
Alignment explanation
Indices: 548--587 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
538 ACTGATTTGT
* *
548 GTTTGTTTTGGCTATGGTGG
1 GTTTGTCTTGACTATGGTGG
*
568 GTTTGTCTTGACTTTGGTGG
1 GTTTGTCTTGACTATGGTGG
588 CTCCTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.07, G:0.38, T:0.50
Consensus pattern (20 bp):
GTTTGTCTTGACTATGGTGG
Found at i:2550 original size:27 final size:26
Alignment explanation
Indices: 2503--2556 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2493 TTAGGGTTTC
*
2503 TTTTATATTTTATTATTATTATTATAA
1 TTTTATATTTTATTATAATTATT-TAA
*
2530 TTTTTTATTTT-TTAATAATTATTTAA
1 TTTTATATTTTATT-ATAATTATTTAA
2556 T
1 T
2557 AAATACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTATATTTTATTATAATTATTTAA
Found at i:2558 original size:29 final size:29
Alignment explanation
Indices: 2503--2558 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2493 TTAGGGTTTC
* *
2503 TTTTATATTTTATTATTATTATTATAATT
1 TTTTATATTTTATAATTATTATAATAATT
*
2532 TTTTATTTTTTAATAATTATT-TAATAA
1 TTTTATATTTT-ATAATTATTATAATAA
2559 ATACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATATTTTATAATTATTATAATAATT
Found at i:3103 original size:31 final size:31
Alignment explanation
Indices: 3062--3140 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
3052 CTAATGCGTA
* *
3062 ATTTGCCCCCTGAACTTTGCAAATTTGGGAC
1 ATTTGTCCCCTGAACTTTGCAAATTCGGGAC
* *
3093 ATTTGTCCCCTTAACGTTGCAAATTCGGGAC
1 ATTTGTCCCCTGAACTTTGCAAATTCGGGAC
* *
3124 ACTTTGTCTCTTGAACT
1 A-TTTGTCCCCTGAACT
3141 AAAAATTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 28 0.72
32 11 0.28
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (31 bp):
ATTTGTCCCCTGAACTTTGCAAATTCGGGAC
Found at i:3263 original size:32 final size:32
Alignment explanation
Indices: 3227--3287 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3217 CTGCTAACAT
*
3227 GGACATGTCACGTCAACAATAAAAGCTGACAC
1 GGACATGGCACGTCAACAATAAAAGCTGACAC
* *
3259 GGACATGGCACGTCAATAGTAAAAGCTGA
1 GGACATGGCACGTCAACAATAAAAGCTGA
3288 TGTGACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (32 bp):
GGACATGGCACGTCAACAATAAAAGCTGACAC
Found at i:4162 original size:11 final size:11
Alignment explanation
Indices: 4146--4209 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
4136 ATGCTAAAGC
4146 CTTATGAAGAA
1 CTTATGAAGAA
4157 CTTAT---GAA
1 CTTATGAAGAA
4165 CTTATGAAGAA
1 CTTATGAAGAA
4176 CTTAT---GAA
1 CTTATGAAGAA
*
4184 CTTATGTAATCAA
1 CTTATG-AA-GAA
4197 CTTATGAAGAA
1 CTTATGAAGAA
4208 CT
1 CT
4210 CCTACTGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
8 16 0.37
11 17 0.40
12 2 0.05
13 8 0.19
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (11 bp):
CTTATGAAGAA
Found at i:4170 original size:19 final size:19
Alignment explanation
Indices: 4146--4204 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 19
4136 ATGCTAAAGC
4146 CTTATGAAGAACTTATGAA
1 CTTATGAAGAACTTATGAA
4165 CTTATGAAGAACTTATGAA
1 CTTATGAAGAACTTATGAA
*
4184 CTTATGTAATCAACTTATGAA
1 CTTATG-AA-GAACTTATGAA
4205 GAACTCCTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
19 25 0.68
20 2 0.05
21 10 0.27
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (19 bp):
CTTATGAAGAACTTATGAA
Found at i:30892 original size:36 final size:34
Alignment explanation
Indices: 30844--30913 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 34
30834 AATCGCAAAA
** *
30844 TTTTTTTTTAGAAAATTCGGAAAAAAGGAAAAACT
1 TTTTTTTTTAGAAAAAACGGAAAAAA-CAAAAACT
30879 TTTTTTTTATAGAAAAAACGGAAAAAACAAAAACT
1 TTTTTTTT-TAGAAAAAACGGAAAAAACAAAAACT
30914 AATTATTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (34 bp):
TTTTTTTTTAGAAAAAACGGAAAAAACAAAAACT
Found at i:30904 original size:35 final size:35
Alignment explanation
Indices: 30844--30913 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
30834 AATCGCAAAA
** **
30844 TTTTTTTTTAGAAAATTCGGAAAAAAGGAAAAACT
1 TTTTTTTTTAGAAAAAACGGAAAAAAACAAAAACT
30879 TTTTTTTTATAGAAAAAACGG-AAAAAACAAAAACT
1 TTTTTTTT-TAGAAAAAACGGAAAAAAACAAAAACT
30914 AATTATTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (35 bp):
TTTTTTTTTAGAAAAAACGGAAAAAAACAAAAACT
Done.