Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011925.1 Corchorus capsularis cultivar CVL-1 contig11946, 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: 35616
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:502 original size:23 final size:23
Alignment explanation
Indices: 472--527 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
462 AAATCGAAAA
*
472 CGAACCCGAACCCGACCCGGGCC
1 CGAACCCGAACCCGACCCGAGCC
*
495 CGAACCCGAACCCGATCCGAGCC
1 CGAACCCGAACCCGACCCGAGCC
518 CGAACCCGAA
1 CGAACCCGAA
528 AATACCCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.48, G:0.23, T:0.02
Consensus pattern (23 bp):
CGAACCCGAACCCGACCCGAGCC
Found at i:514 original size:17 final size:17
Alignment explanation
Indices: 494--526 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
484 CGACCCGGGC
494 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
511 CCGAGCCCGAACCCGA
1 CCGAACCCGAACCCGA
527 AAATACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:543 original size:6 final size:6
Alignment explanation
Indices: 472--527 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
462 AAATCGAAAA
** * *
472 CGAACC CGAACC CG-ACC CGGGCC CGAACC CGAACC CG-ATC CGAGCC
1 CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC
518 CGAACC CGAA
1 CGAACC CGAA
528 AATACCCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 9 0.22
6 32 0.78
ACGTcount: A:0.27, C:0.48, G:0.23, T:0.02
Consensus pattern (6 bp):
CGAACC
Found at i:555 original size:31 final size:31
Alignment explanation
Indices: 517--613 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
507 CGATCCGAGC
517 CCGAACCCGAAAATACCCGAACCCGAAATAA
1 CCGAACCCGAAAATACCCGAACCCGAAATAA
548 CCGAACCCGAAAATACCCGAACCCG-AA-AA
1 CCGAACCCGAAAATACCCGAACCCGAAATAA
* * *
577 ---TACCCGAAAATACCCGAACCCGAAGTAC
1 CCGAACCCGAAAATACCCGAACCCGAAATAA
605 CCGAACCCG
1 CCGAACCCG
614 CCCAATTGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
26 21 0.37
27 1 0.02
28 1 0.02
29 2 0.04
30 2 0.04
31 30 0.53
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.06
Consensus pattern (31 bp):
CCGAACCCGAAAATACCCGAACCCGAAATAA
Found at i:565 original size:10 final size:10
Alignment explanation
Indices: 552--594 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
542 AAATAACCGA
552 ACCCGAAAAT
1 ACCCGAAAAT
562 ACCCG---A-
1 ACCCGAAAAT
568 ACCCGAAAAT
1 ACCCGAAAAT
578 ACCCGAAAAT
1 ACCCGAAAAT
588 ACCCGAA
1 ACCCGAA
595 CCCGAAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 5 0.17
7 1 0.03
9 1 0.03
10 22 0.76
ACGTcount: A:0.47, C:0.35, G:0.12, T:0.07
Consensus pattern (10 bp):
ACCCGAAAAT
Found at i:600 original size:16 final size:16
Alignment explanation
Indices: 516--584 Score: 122
Period size: 16 Copynumber: 4.4 Consensus size: 16
506 CCGATCCGAG
516 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
532 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
*
547 ACCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
563 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
579 CCCGAA
1 CCCGAA
585 AATACCCGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
15 14 0.28
16 36 0.72
ACGTcount: A:0.43, C:0.38, G:0.13, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:3660 original size:50 final size:46
Alignment explanation
Indices: 3574--3716 Score: 232
Period size: 46 Copynumber: 3.0 Consensus size: 46
3564 TGTTTCTTTC
*
3574 TTTTAAACAAGGTCTAATGTTTGAATAAACGAACTGGTATTCACCT
1 TTTTAAACAAGGTCTAATGTTTGAATAGACGAACTGGTATTCACCT
3620 TTTTAAACAAGGTCTAATGCTTGTTTGAATAGACGAACTGGTATTCACCT
1 TTTTAAACAAGGTCTAA----TGTTTGAATAGACGAACTGGTATTCACCT
*
3670 TTTTAAACAAGGTCTAATGTTTGAATAGACGAAATGGTATTCACCT
1 TTTTAAACAAGGTCTAATGTTTGAATAGACGAACTGGTATTCACCT
3716 T
1 T
3717 ATTCCCAGAG
Statistics
Matches: 91, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
46 46 0.51
50 45 0.49
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (46 bp):
TTTTAAACAAGGTCTAATGTTTGAATAGACGAACTGGTATTCACCT
Found at i:10256 original size:12 final size:12
Alignment explanation
Indices: 10239--10264 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10229 CACACAATCC
10239 CTTAGACTCAAT
1 CTTAGACTCAAT
10251 CTTAGACTCAAT
1 CTTAGACTCAAT
10263 CT
1 CT
10265 CCAAGTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
CTTAGACTCAAT
Found at i:23854 original size:8 final size:8
Alignment explanation
Indices: 23841--23870 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
23831 TGAATAGCAC
23841 ACTTTAAA
1 ACTTTAAA
23849 ACTTTAAA
1 ACTTTAAA
23857 ACTTTAAA
1 ACTTTAAA
23865 A-TTTAA
1 ACTTTAA
23871 CTAACTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
ACTTTAAA
Found at i:24157 original size:12 final size:13
Alignment explanation
Indices: 24140--24168 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
24130 ATCAGAAATA
24140 ATGGAGAGT-AAG
1 ATGGAGAGTGAAG
24152 ATGGAGAGTGAAG
1 ATGGAGAGTGAAG
24165 ATGG
1 ATGG
24169 CATGCAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (13 bp):
ATGGAGAGTGAAG
Found at i:28084 original size:21 final size:21
Alignment explanation
Indices: 28058--28099 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28048 TCAGGTCATA
* *
28058 TGATTCGGATATTTTCGGGTT
1 TGATTCGCAGATTTTCGGGTT
*
28079 TGATTCTCAGATTTTCGGGTT
1 TGATTCGCAGATTTTCGGGTT
28100 CGAATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.12, G:0.26, T:0.48
Consensus pattern (21 bp):
TGATTCGCAGATTTTCGGGTT
Found at i:29905 original size:51 final size:50
Alignment explanation
Indices: 29820--29920 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 50
29810 TACTAATAAG
* *
29820 TAAAGCAAAACCAGTAAAAACAGTAACATAGTCTCAAATTAACATTGTTT
1 TAAAGCAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTT
* *
29870 TAAAGCAAAACCAATAATAAACAATAACATTGTCTCAAGTTAACATTGTTT
1 TAAAGCAAAACCAATAA-AAACAATAACATAGTCTCAAATTAACATTGTTT
29921 CTAAGTTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 16 0.35
51 30 0.65
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (50 bp):
TAAAGCAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTT
Found at i:29915 original size:16 final size:17
Alignment explanation
Indices: 29894--29928 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29884 TAATAAACAA
29894 TAACATTGTCTC-AAGT
1 TAACATTGTCTCTAAGT
*
29910 TAACATTGTTTCTAAGT
1 TAACATTGTCTCTAAGT
29927 TA
1 TA
29929 GATAACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
TAACATTGTCTCTAAGT
Done.