Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013489.1 Corchorus capsularis cultivar CVL-1 contig13510, 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: 38690
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:486 original size:42 final size:42
Alignment explanation
Indices: 427--507 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
417 CACGTGCAAC
427 GCACGTGGAAGTGATGAAGACTAATTCCACTAAAAATTAGTT
1 GCACGTGGAAGTGATGAAGACTAATTCCACTAAAAATTAGTT
* *
469 GCACGTGGAAGTGATGAAGATTAGTTCCACTAAAAATTA
1 GCACGTGGAAGTGATGAAGACTAATTCCACTAAAAATTA
508 CACCATACGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (42 bp):
GCACGTGGAAGTGATGAAGACTAATTCCACTAAAAATTAGTT
Found at i:2613 original size:5 final size:5
Alignment explanation
Indices: 2603--2629 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2593 ATCGTGTTTA
2603 GTCGT GTCGT GTCGT GTCGT GTCGT GT
1 GTCGT GTCGT GTCGT GTCGT GTCGT GT
2630 ACACGACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.41, T:0.41
Consensus pattern (5 bp):
GTCGT
Found at i:5456 original size:70 final size:70
Alignment explanation
Indices: 5343--5552 Score: 402
Period size: 70 Copynumber: 3.0 Consensus size: 70
5333 GTCCATGAGC
5343 ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
1 ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
5408 AGGGG
66 AGGGG
* *
5413 ACGGTGAGCCTGGTGTGACCATCTAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACTACTCC
1 ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
5478 AGGGG
66 AGGGG
5483 ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
1 ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
5548 AGGGG
66 AGGGG
5553 TTAAGTCTTG
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 136 1.00
ACGTcount: A:0.16, C:0.22, G:0.37, T:0.25
Consensus pattern (70 bp):
ACGGTGAGCCTGGTGTGACCATCCAGGGCGTGCGATTGTGGAGTGTTCGTAGCTTGTACCACTCC
AGGGG
Found at i:6510 original size:22 final size:22
Alignment explanation
Indices: 6486--6610 Score: 103
Period size: 22 Copynumber: 5.7 Consensus size: 22
6476 TGAATATTTT
* *
6486 TATGAAATTTTGATAACTATCT
1 TATGAAATTTTGATAACTACCA
* * *
6508 TATTAAATTTTAATAACCACCA
1 TATGAAATTTTGATAACTACCA
*
6530 TATGAAATTTTGATAATTACC-
1 TATGAAATTTTGATAACTACCA
* *
6551 TATAAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCA
* * *
6573 TAAGAAACTTTGATAATCTAAC-
1 TATGAAATTTTGATAA-CTACCA
*
6595 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
6611 ACTTTGCTAT
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
21 16 0.20
22 62 0.78
23 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCA
Found at i:6585 original size:43 final size:44
Alignment explanation
Indices: 6489--6613 Score: 119
Period size: 44 Copynumber: 2.9 Consensus size: 44
6479 ATATTTTTAT
* * * * * * *
6489 GAAATTTTGATAA-CTATCTTATTAAATTTTAATAACCACCATAT
1 GAAACTTTGATAATCTAAC-TATAAAATTGTAATAAACTCCATAA
* * *
6533 GAAATTTTGATAAT-TACCTATAAAATTGTGATAAACTCCATAA
1 GAAACTTTGATAATCTAACTATAAAATTGTAATAAACTCCATAA
* *
6576 GAAACTTTGATAATCTAACTATGAAATTTTAATAAACT
1 GAAACTTTGATAATCTAACTATAAAATTGTAATAAACT
6614 TTGCTATGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 32 0.48
44 35 0.52
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (44 bp):
GAAACTTTGATAATCTAACTATAAAATTGTAATAAACTCCATAA
Found at i:7500 original size:2 final size:2
Alignment explanation
Indices: 7493--7520 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7483 AAACAATTAA
7493 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
7521 TACAATTTCA
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:12831 original size:32 final size:32
Alignment explanation
Indices: 12757--12831 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
12747 CTCAAACAAC
*
12757 AATTTTCGAGCAAACTACCACTTTTCATGCCA
1 AATTTTCGAGTAAACTACCACTTTTCATGCCA
*
12789 AATTTTCGAGTAAACTACTACTTTTCATGCCA
1 AATTTTCGAGTAAACTACCACTTTTCATGCCA
12821 AATTTTCGAGT
1 AATTTTCGAGT
12832 GAGGCCCACG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (32 bp):
AATTTTCGAGTAAACTACCACTTTTCATGCCA
Found at i:20792 original size:13 final size:13
Alignment explanation
Indices: 20774--20804 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20764 TAATTAACCT
20774 TTAAAAGTTAAAA
1 TTAAAAGTTAAAA
*
20787 TTAAAATTTAAAA
1 TTAAAAGTTAAAA
20800 TTAAA
1 TTAAA
20805 GAAGTGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
TTAAAAGTTAAAA
Found at i:24288 original size:14 final size:14
Alignment explanation
Indices: 24269--24295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24259 GATCTTATAA
24269 TTTTTTTTTTGAGT
1 TTTTTTTTTTGAGT
24283 TTTTTTTTTTGAG
1 TTTTTTTTTTGAG
24296 AAAATGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTTGAGT
Found at i:25002 original size:1 final size:1
Alignment explanation
Indices: 24996--25031 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
24986 CTTTGAGAGC
*
24996 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25032 GATGACTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:29446 original size:19 final size:20
Alignment explanation
Indices: 29424--29463 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29414 ATTTGGGAGA
*
29424 AAGGAA-ACCATTTACATCC
1 AAGGAATACCAATTACATCC
*
29443 AAGGAATACCAATTGCATCC
1 AAGGAATACCAATTACATCC
29463 A
1 A
29464 TATATGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (20 bp):
AAGGAATACCAATTACATCC
Done.