Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008046.1 Corchorus capsularis cultivar CVL-1 contig08067, 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: 10683
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:117 original size:13 final size:14
Alignment explanation
Indices: 99--128 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
89 TGCGTCCCCC
99 TTTTC-TCTTTTTT
1 TTTTCTTCTTTTTT
112 TTTTCTTCTTTTTT
1 TTTTCTTCTTTTTT
126 TTT
1 TTT
129 AATTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:336 original size:27 final size:25
Alignment explanation
Indices: 283--383 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 25
273 TACCTTGGGA
* * *
283 GAGTCTCCCTTAGCACGTAGCAAGT
1 GAGTCTCCCCTAGCGCGCAGCAAGT
* *
308 GATTCTCCCCTAACGCGCGCAGCACGT
1 GAGTCTCCCCT-A-GCGCGCAGCAAGT
* * *
335 GAGTCTCTCCTAGCGCGCAACAGGT
1 GAGTCTCCCCTAGCGCGCAGCAAGT
360 GAGTCTCCCCTGAG-GCGCAGCAAG
1 GAGTCTCCCCT-AGCGCGCAGCAAG
384 AGAGCGCTCC
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
25 38 0.62
26 4 0.07
27 19 0.31
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.19
Consensus pattern (25 bp):
GAGTCTCCCCTAGCGCGCAGCAAGT
Found at i:1608 original size:36 final size:36
Alignment explanation
Indices: 1519--1609 Score: 128
Period size: 36 Copynumber: 2.5 Consensus size: 36
1509 TTATGTATTA
* * *
1519 GGCGACTTAGGCCAGCGACGTTATAGCCAAACATTG
1 GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
* * *
1555 GGCAACCAAGGCCAGCGGCGTTATAGCCAAGCATCG
1 GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
1591 GGCGACTAAGGCCAGCGGC
1 GGCGACTAAGGCCAGCGGC
1610 ATTACAACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
Found at i:3542 original size:17 final size:17
Alignment explanation
Indices: 3431--3531 Score: 134
Period size: 17 Copynumber: 6.1 Consensus size: 17
3421 TGGTGAGCTC
3431 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
3447 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
*
3463 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
3480 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
3497 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
3514 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
3531 A
1 A
3532 TTGGGTGAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
16 21 0.30
17 50 0.70
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.34
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:7267 original size:15 final size:17
Alignment explanation
Indices: 7236--7280 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
7226 TCCGAACCTG
7236 AACCCGAAAAAACTC-A
1 AACCCGAAAAAACTCAA
7252 AACCCGAAAAAA-TCAA
1 AACCCGAAAAAACTCAA
*
7268 AACCCGAGAAAAC
1 AACCCGAAAAAAC
7281 ATGAACCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.58, C:0.29, G:0.09, T:0.04
Consensus pattern (17 bp):
AACCCGAAAAAACTCAA
Found at i:7535 original size:16 final size:16
Alignment explanation
Indices: 7491--7593 Score: 95
Period size: 16 Copynumber: 6.4 Consensus size: 16
7481 CCAATCCGAG
*
7491 CCCGAACCCGAATTAA
1 CCCGAACCCAAATTAA
* *
7507 CCTG-ACCCAAAATTGA
1 CCCGAACCC-AAATTAA
7523 CCCGAACCCAAATTAA
1 CCCGAACCCAAATTAA
*
7539 -CCTAACCCAAATTTAA
1 CCCGAACCCAAA-TTAA
* *
7555 CCCGAACCCCAATCAA
1 CCCGAACCCAAATTAA
7571 CCCG-ACCCAAAATTTAA
1 CCCGAACCC-AAA-TTAA
7588 CCCGAA
1 CCCGAA
7594 ACCGACTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
15 18 0.26
16 30 0.43
17 20 0.29
18 1 0.01
ACGTcount: A:0.40, C:0.38, G:0.08, T:0.15
Consensus pattern (16 bp):
CCCGAACCCAAATTAA
Found at i:7537 original size:32 final size:32
Alignment explanation
Indices: 7491--7593 Score: 134
Period size: 32 Copynumber: 3.2 Consensus size: 32
7481 CCAATCCGAG
* *
7491 CCCGAACCCGAATTAACCTGACCCAAAATTGA
1 CCCGAACCCAAATTAACCTGACCCAAAATTAA
* *
7523 CCCGAACCCAAATTAACCTAACCCAAATTTAA
1 CCCGAACCCAAATTAACCTGACCCAAAATTAA
* * *
7555 CCCGAACCCCAATCAACCCGACCCAAAATTTAA
1 CCCGAACCCAAATTAACCTGACCCAAAA-TTAA
7588 CCCGAA
1 CCCGAA
7594 ACCGACTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
32 51 0.84
33 10 0.16
ACGTcount: A:0.40, C:0.38, G:0.08, T:0.15
Consensus pattern (32 bp):
CCCGAACCCAAATTAACCTGACCCAAAATTAA
Found at i:7547 original size:15 final size:15
Alignment explanation
Indices: 7495--7556 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
7485 TCCGAGCCCG
*
7495 AACCCGAATTAACCT
1 AACCCAAATTAACCT
* * *
7510 GACCCAAAATTGACCCG
1 AACCC-AAATT-AACCT
7527 AACCCAAATTAACCT
1 AACCCAAATTAACCT
7542 AACCCAAATTTAACC
1 AACCCAAA-TTAACC
7557 CGAACCCCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 15 0.41
16 15 0.41
17 7 0.19
ACGTcount: A:0.42, C:0.34, G:0.06, T:0.18
Consensus pattern (15 bp):
AACCCAAATTAACCT
Found at i:8724 original size:73 final size:73
Alignment explanation
Indices: 8605--8751 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
8595 GTTCAAAGAT
8605 GGCCTAAAACTTCATTCTTTCACAAAGATGGCATTGCCTGATCAAGCACTTGAAGTTTATTGATC
1 GGCCTAAAACTTCATTCTTTCACAAAGATGGCATTGCCTGATCAAGCACTTGAAGTTTATTGATC
8670 CACTACTA
66 CACTACTA
8678 GGCCTAAAACTTCATTCTTTCACAAAGATGGCATTGCCTGATCAAGCACTTGAAGTTTATTGATC
1 GGCCTAAAACTTCATTCTTTCACAAAGATGGCATTGCCTGATCAAGCACTTGAAGTTTATTGATC
8743 CACTACTA
66 CACTACTA
8751 G
1 G
8752 CTGGTGGTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (73 bp):
GGCCTAAAACTTCATTCTTTCACAAAGATGGCATTGCCTGATCAAGCACTTGAAGTTTATTGATC
CACTACTA
Found at i:10075 original size:14 final size:13
Alignment explanation
Indices: 10045--10082 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
10035 ACAAATGAGG
10045 AAAGATGAAA-G-
1 AAAGATGAAAGGC
10056 AAAGATGAAAGGC
1 AAAGATGAAAGGC
10069 AAAAGATGAAAGGC
1 -AAAGATGAAAGGC
10083 GTGTAATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 1 0.04
14 13 0.54
ACGTcount: A:0.58, C:0.05, G:0.29, T:0.08
Consensus pattern (13 bp):
AAAGATGAAAGGC
Done.