Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013240.1 Corchorus capsularis cultivar CVL-1 contig13261, 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: 23893
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1455 original size:33 final size:34
Alignment explanation
Indices: 1407--1480 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
1397 GCAAAGTTTT
1407 TAAC-CAAATGGAGAAAATGGCCATTCACAATCC
1 TAACACAAATGGAGAAAATGGCCATTCACAATCC
*
1440 TAACACAAAT-GAGAAAATGGCCATTCTCAATCC
1 TAACACAAATGGAGAAAATGGCCATTCACAATCC
1473 TAACACAA
1 TAACACAA
1481 GCAAGAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 34 0.87
34 5 0.13
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (34 bp):
TAACACAAATGGAGAAAATGGCCATTCACAATCC
Found at i:1488 original size:33 final size:33
Alignment explanation
Indices: 1418--1489 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
1408 AACCAAATGG
**
1418 AGAAAATGGCCATTCACAATCCTAACACAAATG
1 AGAAAATGGCCATTCACAATCCTAACACAAACA
* *
1451 AGAAAATGGCCATTCTCAATCCTAACACAAGCA
1 AGAAAATGGCCATTCACAATCCTAACACAAACA
1484 AGAAAA
1 AGAAAA
1490 GCATATTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.17
Consensus pattern (33 bp):
AGAAAATGGCCATTCACAATCCTAACACAAACA
Found at i:18311 original size:6 final size:7
Alignment explanation
Indices: 18294--18320 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
18284 TTCAGAGCCA
18294 AAAAAAT
1 AAAAAAT
18301 AAAAAAT
1 AAAAAAT
18308 AAAAAAT
1 AAAAAAT
18315 AAAAAA
1 AAAAAA
18321 AGAAGAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:20607 original size:14 final size:14
Alignment explanation
Indices: 20588--20622 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
20578 GGTTTCTTCC
20588 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCTT
20602 TTCTTTCCTTTTCTT
1 TTCTTT-CTTTTCTT
20617 TT-TTTC
1 TTCTTTC
20623 CGGGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 9 0.45
15 10 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:22492 original size:24 final size:24
Alignment explanation
Indices: 22465--22548 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
22455 CTTCCGATGC
* *
22465 TGCTCCTGCACCGCCTGCCGATGA
1 TGCTCCTGCACCACCTGCCAATGA
22489 TGCTCCTGCACCACCTGCCAATGA
1 TGCTCCTGCACCACCTGCCAATGA
* *
22513 TACTCCTGCGCCACCTGCCAATGA
1 TGCTCCTGCACCACCTGCCAATGA
*
22537 TGCACCTGCACC
1 TGCTCCTGCACC
22549 GCCATGCTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.18, C:0.43, G:0.19, T:0.20
Consensus pattern (24 bp):
TGCTCCTGCACCACCTGCCAATGA
Found at i:22626 original size:46 final size:46
Alignment explanation
Indices: 22559--22652 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
22549 GCCATGCTAA
22559 GCACTGCTGAAGATGCACCGCCATGCTAAGCAACTAGGGATATAGT
1 GCACTGCTGAAGATGCACCGCCATGCTAAGCAACTAGGGATATAGT
22605 GCACTGCTGAAGATGCACCGCCATGCTAAGCAACTAGGGATATAGT
1 GCACTGCTGAAGATGCACCGCCATGCTAAGCAACTAGGGATATAGT
22651 GC
1 GC
22653 TTTTAATTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (46 bp):
GCACTGCTGAAGATGCACCGCCATGCTAAGCAACTAGGGATATAGT
Found at i:22865 original size:33 final size:33
Alignment explanation
Indices: 22823--22923 Score: 202
Period size: 33 Copynumber: 3.1 Consensus size: 33
22813 TGCTTTCCCA
22823 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
1 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
22856 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
1 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
22889 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
1 TTCTTTTTCCCTAATCATCCCCTAATTACACAG
22922 TT
1 TT
22924 GGAAATTTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.24, C:0.33, G:0.03, T:0.41
Consensus pattern (33 bp):
TTCTTTTTCCCTAATCATCCCCTAATTACACAG
Found at i:23867 original size:31 final size:31
Alignment explanation
Indices: 23812--23892 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
23802 TTTTGTGCAC
* **
23812 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACCTTTTGAAACAT
**
23843 GTGGCATGCCACGTGTCACCTTTTGGTACAT
1 GTGGCATGCCACGTGTCACCTTTTGAAACAT
* * *
23874 GTGGCGTGACATGTGTCAC
1 GTGGCATGCCACGTGTCAC
23893 T
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACCTTTTGAAACAT
Done.