Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007542.1 Corchorus capsularis cultivar CVL-1 contig07563, 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: 26502
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2574 original size:31 final size:31
Alignment explanation
Indices: 2539--2705 Score: 111
Period size: 31 Copynumber: 5.5 Consensus size: 31
2529 TCCTTTTGTG
*
2539 CACGTGGCATGCCATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* **
2570 CACGTGGCTTGCCACGAATCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
2601 CA--T---ATG--ACGTGCCACTTTTTTGGCA
1 CACGTGGCATGCCACGTGTCAC-TTTTTGGTA
* * * *
2626 CACATGGCGTGCCATGTGTCACTTTTT-TTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
2656 TCCACGTGGCATACCACGTGTTACTTTTT--TA
1 --CACGTGGCATGCCACGTGTCACTTTTTGGTA
2687 TCTACGTGGCATGCCACGT
1 -C-ACGTGGCATGCCACGT
2706 CGAACACCGT
Statistics
Matches: 104, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
24 6 0.06
25 10 0.10
26 2 0.02
27 1 0.01
29 1 0.01
30 4 0.04
31 51 0.49
32 29 0.28
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:2636 original size:25 final size:25
Alignment explanation
Indices: 2592--2639 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2582 CACGAATCAC
* *
2592 TTTTTGGTACATATGACGTGCCACT
1 TTTTTGGCACACATGACGTGCCACT
*
2617 TTTTTGGCACACATGGCGTGCCA
1 TTTTTGGCACACATGACGTGCCA
2640 TGTGTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (25 bp):
TTTTTGGCACACATGACGTGCCACT
Found at i:4740 original size:20 final size:20
Alignment explanation
Indices: 4694--4740 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4684 CAAATAAATA
* *
4694 ATATATTAATTTTTTTATTT
1 ATATATTAATTTATATATTT
* *
4714 TTTTATTAATTTATATATTT
1 ATATATTAATTTATATATTT
4734 ATATATT
1 ATATATT
4741 TATGAATTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATATTAATTTATATATTT
Found at i:5072 original size:11 final size:11
Alignment explanation
Indices: 5056--5082 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5046 ACAGCTCTAA
5056 TAAAAGACTAC
1 TAAAAGACTAC
5067 TAAAAGACTAC
1 TAAAAGACTAC
5078 TAAAA
1 TAAAA
5083 TAAGGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.19
Consensus pattern (11 bp):
TAAAAGACTAC
Found at i:9067 original size:80 final size:76
Alignment explanation
Indices: 8934--9088 Score: 274
Period size: 80 Copynumber: 2.0 Consensus size: 76
8924 TCTTCATATA
8934 TATACTTGGAATTGAAGATTCAATTGCGAAGATTAATCAACAGCTATGACTTATATATATCAATA
1 TATACTTGGAATTGAAGATTCAATTGCGAAGATTAATCAACAGCTATGAC---T-TATATCAATA
8999 AGTGAATCTTTTTAT
62 AGTGAATCTTTTTAT
9014 TATACTTGGAATTGAAGATTCAATTGCGAAGATTAATCAACAGCTATGACTTATATCAATAAGTG
1 TATACTTGGAATTGAAGATTCAATTGCGAAGATTAATCAACAGCTATGACTTATATCAATAAGTG
9079 AATCTTTTTA
66 AATCTTTTTA
9089 ATAATAATAA
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
76 24 0.32
77 1 0.01
80 50 0.67
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (76 bp):
TATACTTGGAATTGAAGATTCAATTGCGAAGATTAATCAACAGCTATGACTTATATCAATAAGTG
AATCTTTTTAT
Found at i:14229 original size:28 final size:28
Alignment explanation
Indices: 14189--14263 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
14179 CCTCTTTATC
14189 ATATTTAGTCTATGCCTTTGTGCAAAAA
1 ATATTTAGTCTATGCCTTTGTGCAAAAA
14217 ATATTTAGTCTATGCCTTTGTGCAAAAA
1 ATATTTAGTCTATGCCTTTGTGCAAAAA
14245 ATATTTAGTCTATGCCTTT
1 ATATTTAGTCTATGCCTTT
14264 TGGTTTTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (28 bp):
ATATTTAGTCTATGCCTTTGTGCAAAAA
Found at i:15818 original size:16 final size:16
Alignment explanation
Indices: 15794--15828 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15784 GTATTAACGA
*
15794 AAAGCTTAGTATCTTC
1 AAAGCTTAGTATCTGC
*
15810 AAAGTTTAGTATCTGC
1 AAAGCTTAGTATCTGC
15826 AAA
1 AAA
15829 TTAAGTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (16 bp):
AAAGCTTAGTATCTGC
Found at i:20141 original size:15 final size:15
Alignment explanation
Indices: 20121--20152 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20111 AGTCCAATGG
20121 ATCCGTAAATCCCAA
1 ATCCGTAAATCCCAA
20136 ATCCGTAAATCCCAA
1 ATCCGTAAATCCCAA
20151 AT
1 AT
20153 TGGGTCGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.06, T:0.22
Consensus pattern (15 bp):
ATCCGTAAATCCCAA
Found at i:21748 original size:22 final size:24
Alignment explanation
Indices: 21720--21768 Score: 84
Period size: 22 Copynumber: 2.1 Consensus size: 24
21710 ATATATACAC
21720 TATTTTGCAAAAAAAA-AAA-AAA
1 TATTTTGCAAAAAAAATAAATAAA
21742 TATTTTGCAAAAAAAATAAATAAA
1 TATTTTGCAAAAAAAATAAATAAA
21766 TAT
1 TAT
21769 ATATACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 16 0.64
23 3 0.12
24 6 0.24
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
TATTTTGCAAAAAAAATAAATAAA
Done.