Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011559.1 Corchorus capsularis cultivar CVL-1 contig11580, 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: 39883
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--45 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 AAAGTA
7 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46 AACTTCATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1336 original size:2 final size:2
Alignment explanation
Indices: 1329--1353 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1319 TGTGATTGAA
1329 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1354 ATCTTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2425 original size:54 final size:54
Alignment explanation
Indices: 2343--2506 Score: 328
Period size: 54 Copynumber: 3.0 Consensus size: 54
2333 TGCTTTAGAT
2343 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
1 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
2397 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
1 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
2451 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
1 GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
2505 GG
1 GG
2507 GTAACTTATT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (54 bp):
GGTATATCAATTTTATCAATAGTTGGATGTGTTGCTTATTGTTGGTGTAGCAAA
Found at i:2943 original size:24 final size:24
Alignment explanation
Indices: 2914--2961 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2904 CTTTCCACTA
2914 GTGAAAATACAATCATACACGATT
1 GTGAAAATACAATCATACACGATT
*
2938 GTGAAAATACAATCATACGCGATT
1 GTGAAAATACAATCATACACGATT
2962 CAACCTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (24 bp):
GTGAAAATACAATCATACACGATT
Found at i:6345 original size:110 final size:110
Alignment explanation
Indices: 6163--6380 Score: 409
Period size: 110 Copynumber: 2.0 Consensus size: 110
6153 AATCTACATT
**
6163 GATTTTGTGTGTCACTTGATTAATGTATGTGGTGACCCAAGAATGACTCAATGAGAATGATACCT
1 GATTTTGTGTGTCACTCAATTAATGTATGTGGTGACCCAAGAATGACTCAATGAGAATGATACCT
*
6228 CCGAAGACTTGCAAAAGAGAGAATCGTAAGGAAAAAATCCTCTCC
66 CCGAAGACTTGCAAAAGAGAGAATCATAAGGAAAAAATCCTCTCC
6273 GATTTTGTGTGTCACTCAATTAATGTATGTGGTGACCCAAGAATGACTCAATGAGAATGATACCT
1 GATTTTGTGTGTCACTCAATTAATGTATGTGGTGACCCAAGAATGACTCAATGAGAATGATACCT
6338 CCGAAGACTTGCAAAAGAGAGAATCATAAGGAAAAAATCCTCT
66 CCGAAGACTTGCAAAAGAGAGAATCATAAGGAAAAAATCCTCT
6381 ACCATAGTTG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (110 bp):
GATTTTGTGTGTCACTCAATTAATGTATGTGGTGACCCAAGAATGACTCAATGAGAATGATACCT
CCGAAGACTTGCAAAAGAGAGAATCATAAGGAAAAAATCCTCTCC
Found at i:11414 original size:13 final size:13
Alignment explanation
Indices: 11396--11422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11386 CTATCCGTAT
11396 CCATATAAAATCA
1 CCATATAAAATCA
11409 CCATATAAAATCA
1 CCATATAAAATCA
11422 C
1 C
11423 TATCTGTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (13 bp):
CCATATAAAATCA
Found at i:11450 original size:12 final size:12
Alignment explanation
Indices: 11433--11459 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11423 TATCTGTACC
11433 CGTATAAAATAT
1 CGTATAAAATAT
11445 CGTATAAAATAT
1 CGTATAAAATAT
11457 CGT
1 CGT
11460 TAACTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (12 bp):
CGTATAAAATAT
Found at i:12446 original size:16 final size:16
Alignment explanation
Indices: 12425--12480 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
12415 ATGGAGGGAG
12425 TAATTAATTAATATAT
1 TAATTAATTAATATAT
*
12441 TAATTAATGAATAT-T
1 TAATTAATTAATATAT
** *
12456 ATAAAAAATTAAGATAT
1 -TAATTAATTAATATAT
12473 TAATTAAT
1 TAATTAAT
12481 GGAATAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
TAATTAATTAATATAT
Found at i:14432 original size:19 final size:19
Alignment explanation
Indices: 14410--14448 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
14400 AAAAAAAAAA
14410 AAAAAAAAAAGAAGAAAGT
1 AAAAAAAAAAGAAGAAAGT
* *
14429 AAAAAAAGAAGAAGCAAGT
1 AAAAAAAAAAGAAGAAAGT
14448 A
1 A
14449 GCTAGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAAAGT
Found at i:16750 original size:13 final size:13
Alignment explanation
Indices: 16732--16759 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16722 TTATGTTATT
16732 AACACATGATAAC
1 AACACATGATAAC
16745 AACACATGATAAC
1 AACACATGATAAC
16758 AA
1 AA
16760 TAACAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (13 bp):
AACACATGATAAC
Found at i:24883 original size:2 final size:2
Alignment explanation
Indices: 24876--24905 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24866 TGTTATTGAG
24876 AT AT AT AT AT AT 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
24906 GATACTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27454 original size:2 final size:2
Alignment explanation
Indices: 27447--27471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27437 TCTTTCCCTC
27447 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27472 ATTTCGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29808 original size:21 final size:21
Alignment explanation
Indices: 29784--29823 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29774 AAGAGGGAGA
*
29784 GAAGAGAGAGAAAAAAAAAAC
1 GAAGAAAGAGAAAAAAAAAAC
* *
29805 GAAGAAAGGGGAAAAAAAA
1 GAAGAAAGAGAAAAAAAAA
29824 GTAAAGACAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (21 bp):
GAAGAAAGAGAAAAAAAAAAC
Found at i:30330 original size:18 final size:19
Alignment explanation
Indices: 30296--30331 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30286 TTCTCTTTAA
30296 TTTTTTTAAAAATTGTAAT
1 TTTTTTTAAAAATTGTAAT
*
30315 TTTTTTTTAAAA-TGTAA
1 TTTTTTTAAAAATTGTAA
30332 GTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTTTTAAAAATTGTAAT
Found at i:35096 original size:2 final size:2
Alignment explanation
Indices: 35089--35121 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35079 TCTTTCGCTC
35089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35122 GGGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39694 original size:28 final size:28
Alignment explanation
Indices: 39646--39699 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
39636 CGTGCTCTTC
* *
39646 AAAACGCCACTTAAAGTTGCGCATCATT
1 AAAACACCACTTAAAGCTGCGCATCATT
* *
39674 AAAACACCACTTAATGCTGCGTATCA
1 AAAACACCACTTAAAGCTGCGCATCA
39700 ATTGTTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAACACCACTTAAAGCTGCGCATCATT
Done.