Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009703.1 Corchorus capsularis cultivar CVL-1 contig09724, 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: 17652
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Found at i:1244 original size:24 final size:23
Alignment explanation
Indices: 1212--1263 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
1202 CCAATTTCTT
*
1212 AAAAAAAAGGAAGATAATTCTTAA
1 AAAAAAAAGGAAGATAAAT-TTAA
1236 AAAAAAAAGGAAGATAAATTTAA
1 AAAAAAAAGGAAGATAAATTTAA
1259 AAAAA
1 AAAAA
1264 CGGGCATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (23 bp):
AAAAAAAAGGAAGATAAATTTAA
Found at i:7410 original size:64 final size:64
Alignment explanation
Indices: 7309--7429 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
7299 GCAACCTGAT
7309 TTCAATATGCTCATAGAGATAGATGCTCCATAAGCTTT-AGCTCTTTCCCCTTCACTAAATGGAA
1 TTCAATATGCTCATAGAGATAGATGCTCCATAAGCTTTGA-CTCTTTCCCCTTCACTAAATGGAA
7373 TTCAATATGCTCATAGAGATAGATGCTCCATAAGCTTTGACTCTTTCCCCTTCACTA
1 TTCAATATGCTCATAGAGATAGATGCTCCATAAGCTTTGACTCTTTCCCCTTCACTA
7430 GATTTCCATT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 55 0.98
65 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (64 bp):
TTCAATATGCTCATAGAGATAGATGCTCCATAAGCTTTGACTCTTTCCCCTTCACTAAATGGAA
Found at i:12053 original size:25 final size:25
Alignment explanation
Indices: 12022--12079 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
12012 GTGTTTTCTC
*
12022 AACGCAAGCACAGGCTCGTTTGCCA
1 AACGCAAGCACAGACTCGTTTGCCA
*
12047 AATGCAAGCACAGACTCGTTTGCCA
1 AACGCAAGCACAGACTCGTTTGCCA
12072 AACGCAAG
1 AACGCAAG
12080 AACATAAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (25 bp):
AACGCAAGCACAGACTCGTTTGCCA
Found at i:12091 original size:25 final size:25
Alignment explanation
Indices: 12038--12092 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
12028 AGCACAGGCT
* * **
12038 CGTTTGCCAAATGCAAGCACAGACT
1 CGTTTGCCAAACGCAAGAACAGAAG
*
12063 CGTTTGCCAAACGCAAGAACATAAG
1 CGTTTGCCAAACGCAAGAACAGAAG
12088 CGTTT
1 CGTTT
12093 ACCCACTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (25 bp):
CGTTTGCCAAACGCAAGAACAGAAG
Found at i:14177 original size:56 final size:56
Alignment explanation
Indices: 14091--14199 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
14081 TATATATGCA
* *
14091 TATAAGGTACCAATAACTAAATTAATCATCAAGAAAAGGTTCATGGTTGAATTTTG
1 TATAAGGTACCAAAAACTAAATTAATCATCAAGAAAAGGTTCATGATTGAATTTTG
* *
14147 TATAAGGTACCAAAAACTAAATTAGTCATCAAGATAAGGTTCATGATTGAATT
1 TATAAGGTACCAAAAACTAAATTAATCATCAAGAAAAGGTTCATGATTGAATT
14200 AAGTATAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (56 bp):
TATAAGGTACCAAAAACTAAATTAATCATCAAGAAAAGGTTCATGATTGAATTTTG
Found at i:15400 original size:79 final size:80
Alignment explanation
Indices: 15268--15437 Score: 279
Period size: 79 Copynumber: 2.1 Consensus size: 80
15258 AAGTACCATA
*
15268 TTGTTAATTTTTAATTTTTAAATTACAAGACACAGGGCACTCACTACGTGAGTGGTTTATAACAA
1 TTGTTACTTTTTAATTTTTAAATTACAAGACACAGGGCACTCACTACGTGAGTGGTTTATAACAA
15333 TTTTATTTCAATAGG
66 TTTTATTTCAATAGG
* *
15348 TTGTTACTTTTTAA-TTTTAAATTATAAGACACAGGGCACTCACTACGTGAGTGGTTTATAACAG
1 TTGTTACTTTTTAATTTTTAAATTACAAGACACAGGGCACTCACTACGTGAGTGGTTTATAACAA
*
15412 TTTTTTTTCAATAGG
66 TTTTATTTCAATAGG
* *
15427 TAGTTTCTTTT
1 TTGTTACTTTT
15438 AAATGATATA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 71 0.85
80 13 0.15
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (80 bp):
TTGTTACTTTTTAATTTTTAAATTACAAGACACAGGGCACTCACTACGTGAGTGGTTTATAACAA
TTTTATTTCAATAGG
Found at i:15469 original size:13 final size:13
Alignment explanation
Indices: 15453--15483 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
15443 ATATAAATAA
15453 ATTTAAATATTAT
1 ATTTAAATATTAT
15466 ATTTAAATATTAT
1 ATTTAAATATTAT
15479 ATTTA
1 ATTTA
15484 TCTTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAAATATTAT
Found at i:15544 original size:29 final size:30
Alignment explanation
Indices: 15487--15549 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
15477 ATATTTATCT
* *
15487 TATAATGGGTAGTTTTTTTTTTCTAAAATTGG
1 TATAATGGGTAG--TTTTTTATCTAAAATGGG
15519 TATAATGGGTAG-TTTTTATCTAAAATGGG
1 TATAATGGGTAGTTTTTTATCTAAAATGGG
15548 TA
1 TA
15550 GTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.59
32 12 0.41
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.48
Consensus pattern (30 bp):
TATAATGGGTAGTTTTTTATCTAAAATGGG
Done.