Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008204.1 Corchorus capsularis cultivar CVL-1 contig08225, 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: 34438
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:13463 original size:19 final size:20
Alignment explanation
Indices: 13431--13468 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
13421 TGTATCATTT
**
13431 TATTTATTTTATTA-TATAA
1 TATTTATTAAATTAGTATAA
13450 TATTTATTAAATTAGTATA
1 TATTTATTAAATTAGTATA
13469 TACATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTTATTAAATTAGTATAA
Found at i:15570 original size:84 final size:84
Alignment explanation
Indices: 15468--15636 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
15458 TACATAATAT
15468 ATCCATATTTATGAATACCTTATACTTTGTTTGTGATTGATTAATTACTAGTATAACGTTGATTA
1 ATCCATATTTATGAATACCTTATACTTTGTTTGTGATTGATTAATTACTAGTATAACGTTGATTA
15533 ATATATACGTATTTTTTAA
66 ATATATACGTATTTTTTAA
15552 ATCCATATTTATGAATACCTTATACTTTGTTTGTGATTGATTAATTACTAGTATAACGTTGATTA
1 ATCCATATTTATGAATACCTTATACTTTGTTTGTGATTGATTAATTACTAGTATAACGTTGATTA
15617 ATATATACGTATTTTTTAA
66 ATATATACGTATTTTTTAA
15636 A
1 A
15637 GGAATGATTT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (84 bp):
ATCCATATTTATGAATACCTTATACTTTGTTTGTGATTGATTAATTACTAGTATAACGTTGATTA
ATATATACGTATTTTTTAA
Found at i:15763 original size:33 final size:33
Alignment explanation
Indices: 15717--15791 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
15707 TTGTTGGATA
*
15717 TTTAGTAGCACGTACCCTAAGTAGTGGGGGGTG
1 TTTAGTAGTACGTACCCTAAGTAGTGGGGGGTG
15750 TTTAGTAGTACGTACCCTAAGTAGTGGGGGGTG
1 TTTAGTAGTACGTACCCTAAGTAGTGGGGGGTG
15783 --TAGTAGTAC
1 TTTAGTAGTAC
15792 TTGTAGTCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 9 0.22
33 32 0.78
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (33 bp):
TTTAGTAGTACGTACCCTAAGTAGTGGGGGGTG
Found at i:16241 original size:24 final size:26
Alignment explanation
Indices: 16190--16241 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
16180 TATCCTTTTT
* * *
16190 ATATTTCACAATTTATATTTTGATTA
1 ATATTTCACAATTTATATATTAAATA
16216 ATATTT-AC-ATTTATATATTAAATA
1 ATATTTCACAATTTATATATTAAATA
16240 AT
1 AT
16242 TACAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 2 0.09
26 6 0.26
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATTTCACAATTTATATATTAAATA
Found at i:17578 original size:2 final size:2
Alignment explanation
Indices: 17571--17609 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
17561 AGTTTTTATT
17571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
17610 AAATGAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23898 original size:29 final size:29
Alignment explanation
Indices: 23833--23913 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
23823 GCTTAATACC
* **
23833 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA
*
23864 CAAATTGGCCCCTTAACTTTTTTTTTGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGGA
23893 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
23914 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 28 0.61
30 1 0.02
31 17 0.37
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGGA
Found at i:24674 original size:31 final size:28
Alignment explanation
Indices: 24605--24684 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
24595 TCTCGTTTTT
*
24605 AAAAGTTAAGGGGCCAATTTGTCTCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
24633 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
* *
24661 ATGGATAGTTAAGGGGCTAATTTG
1 A---AAAGTTAAGGGGCCAATTTG
24685 GGTATTAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.61
31 18 0.39
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAA
Found at i:25738 original size:19 final size:19
Alignment explanation
Indices: 25714--25769 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
25704 TTCTATTTAA
25714 TTCAAAATAAGTGCAACAT
1 TTCAAAATAAGTGCAACAT
* *
25733 TTCAAAAT--TTGCAGTCA-
1 TTCAAAATAAGTGCA-ACAT
*
25750 TTCAAATTAAGTGCAACAT
1 TTCAAAATAAGTGCAACAT
25769 T
1 T
25770 ATAAACCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (19 bp):
TTCAAAATAAGTGCAACAT
Done.