Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007460.1 Corchorus capsularis cultivar CVL-1 contig07481, 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: 25762
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:488 original size:21 final size:21
Alignment explanation
Indices: 464--505 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
454 ATACATGGTA
*
464 TTATAGATTTGCTTAGTCATC
1 TTATAGATTTGCTTACTCATC
*
485 TTATAGCTTTGCTTACTCATC
1 TTATAGATTTGCTTACTCATC
506 ACTTAGCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (21 bp):
TTATAGATTTGCTTACTCATC
Found at i:512 original size:21 final size:21
Alignment explanation
Indices: 465--526 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
455 TACATGGTAT
* * *
465 TATAGATTTGCTTAGTCATCT
1 TATAGCTTTGCTTACTCATCC
486 TATAGCTTTGCTTACTCATCAC
1 TATAGCTTTGCTTACTCATC-C
* *
508 T-TAGCCTAGCTTACTCATC
1 TATAGCTTTGCTTACTCATC
527 TAGCCTAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (21 bp):
TATAGCTTTGCTTACTCATCC
Found at i:532 original size:18 final size:20
Alignment explanation
Indices: 495--533 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
485 TTATAGCTTT
495 GCTTACTCATCACTTAGCCTA
1 GCTTACTCAT-ACTTAGCCTA
516 GCTTACTCAT-C-TAGCCTA
1 GCTTACTCATACTTAGCCTA
534 ACATGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
21 10 0.56
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (20 bp):
GCTTACTCATACTTAGCCTA
Found at i:1576 original size:21 final size:21
Alignment explanation
Indices: 1551--1592 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1541 ATGCATGATA
*
1551 TTATAGCTTTACTTAGTCATC
1 TTATAGCTTTACTTACTCATC
*
1572 TTATAGCTTTGCTTACTCATC
1 TTATAGCTTTACTTACTCATC
1593 ACTTAGCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (21 bp):
TTATAGCTTTACTTACTCATC
Found at i:1619 original size:18 final size:20
Alignment explanation
Indices: 1582--1620 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1572 TTATAGCTTT
1582 GCTTACTCATCACTTAGCCTA
1 GCTTACTCAT-ACTTAGCCTA
1603 GCTTACTCAT-C-TAGCCTA
1 GCTTACTCATACTTAGCCTA
1621 ACATGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
21 10 0.56
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (20 bp):
GCTTACTCATACTTAGCCTA
Found at i:5221 original size:22 final size:21
Alignment explanation
Indices: 5196--5236 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5186 GAAGTTAACA
*
5196 TGGTTCAATCCAGCAAGCGCGG
1 TGGTTCAAGCCA-CAAGCGCGG
*
5218 TGGTTCTAGCCACAAGCGC
1 TGGTTCAAGCCACAAGCGC
5237 AAGAAAGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (21 bp):
TGGTTCAAGCCACAAGCGCGG
Found at i:8698 original size:2 final size:2
Alignment explanation
Indices: 8691--8718 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8681 TACATAGCAC
8691 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
8719 CTAAAGGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10583 original size:16 final size:16
Alignment explanation
Indices: 10562--10593 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10552 CTGTTAAACT
10562 TCCACCAAAAAAAAAA
1 TCCACCAAAAAAAAAA
10578 TCCACCAAAAAAAAAA
1 TCCACCAAAAAAAAAA
10594 ACACACTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (16 bp):
TCCACCAAAAAAAAAA
Found at i:12064 original size:110 final size:110
Alignment explanation
Indices: 11871--12082 Score: 424
Period size: 110 Copynumber: 1.9 Consensus size: 110
11861 TTTATTTAGC
11871 TTAAATTAAGTTGTTAATGGAATGTGGTTGCATAGCATTGCATTTTTAAAGCATGTTGGAATGTT
1 TTAAATTAAGTTGTTAATGGAATGTGGTTGCATAGCATTGCATTTTTAAAGCATGTTGGAATGTT
11936 TAACCATGCAACTGGATGTAAGATATTGGTGTATATGGAATGTGG
66 TAACCATGCAACTGGATGTAAGATATTGGTGTATATGGAATGTGG
11981 TTAAATTAAGTTGTTAATGGAATGTGGTTGCATAGCATTGCATTTTTAAAGCATGTTGGAATGTT
1 TTAAATTAAGTTGTTAATGGAATGTGGTTGCATAGCATTGCATTTTTAAAGCATGTTGGAATGTT
12046 TAACCATGCAACTGGATGTAAGATATTGGTGTATATG
66 TAACCATGCAACTGGATGTAAGATATTGGTGTATATG
12083 TATCCTTGCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (110 bp):
TTAAATTAAGTTGTTAATGGAATGTGGTTGCATAGCATTGCATTTTTAAAGCATGTTGGAATGTT
TAACCATGCAACTGGATGTAAGATATTGGTGTATATGGAATGTGG
Found at i:16312 original size:7 final size:7
Alignment explanation
Indices: 16302--16327 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16292 AAAAACCTCA
16302 CCTCAAG
1 CCTCAAG
16309 CCTCAAG
1 CCTCAAG
16316 CCTCAAG
1 CCTCAAG
16323 CCTCA
1 CCTCA
16328 TGCAATGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (7 bp):
CCTCAAG
Found at i:22690 original size:21 final size:21
Alignment explanation
Indices: 22656--22719 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
22646 TCGGTGAGAG
22656 TAAAA-TTGTTTACTGTAC-GTA
1 TAAAATTTG-TTACTGTACAG-A
* *
22677 TTAGATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
22698 TAAAATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
22719 T
1 T
22720 GAGAATATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (21 bp):
TAAAATTTGTTACTGTACAGA
Found at i:23710 original size:41 final size:41
Alignment explanation
Indices: 23653--23845 Score: 214
Period size: 41 Copynumber: 4.7 Consensus size: 41
23643 AAATATATTG
*
23653 AAAATTACCT-TTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTA-CTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
23694 AAAATTACTACTGACACTAGAAGTTGTCACCTTGGTAAATT
1 AAAATTACTATTGACACCAGAAGTTGTCACTTTGGTAAATT
23735 AAAATTACCT-TTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTA-CTATTGACACCAGAAGTTGTCACTTTGGTAAATT
* * ***
23776 AAAATTA-AATTAGACACCAGAAG-TGTTACTCCAGTAAATT
1 AAAATTACTATT-GACACCAGAAGTTGTCACTTTGGTAAATT
* * * *
23816 ATAATTACTGTTGACACTAGAAATTGTCAC
1 AAAATTACTATTGACACCAGAAGTTGTCAC
23846 CTTGAATTAC
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.25
41 94 0.73
42 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAATTACTATTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:24961 original size:10 final size:10
Alignment explanation
Indices: 24948--24981 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
24938 AGTTATATCG
24948 AAAAATATAA
1 AAAAATATAA
*
24958 AAAAAT-TCA
1 AAAAATATAA
24967 AAAAATATAA
1 AAAAATATAA
24977 AAAAA
1 AAAAA
24982 AAATTTCGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATATAA
Done.