Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005070.1 Corchorus capsularis cultivar CVL-1 contig05088, 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: 15858
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:528 original size:22 final size:22
Alignment explanation
Indices: 488--529 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
478 GTGTTGGTTA
**
488 TCAAAATTCCATATTAAGGTCT
1 TCAAAATTCCATAGGAAGGTCT
*
510 TCAAAATTCCTTAGGAAGGT
1 TCAAAATTCCATAGGAAGGT
530 TAACAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
TCAAAATTCCATAGGAAGGTCT
Found at i:1094 original size:60 final size:60
Alignment explanation
Indices: 1001--1163 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 60
991 GCTAATTGCT
* * * *
1001 CAAATAAGGGTCTAACGTT-TGCAAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * *
1061 CAAATTAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * *
1121 CAGATAAGGGCCTAACTTTATCGAAAATACTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1164 TGGTGTCAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
60 89 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:1270 original size:60 final size:60
Alignment explanation
Indices: 1193--1355 Score: 272
Period size: 60 Copynumber: 2.7 Consensus size: 60
1183 ACGTGAGACA
* * *
1193 GGCCCTTATTTGGGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATGG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
1253 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
1313 GGCCCTTGTTTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1356 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:1356 original size:31 final size:31
Alignment explanation
Indices: 1192--1359 Score: 136
Period size: 31 Copynumber: 5.5 Consensus size: 31
1182 CACGTGAGAC
*
1192 AGGCCCTTATTTGGGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** *
1223 AGGCCCTTATTTG-GCCAAATT--CAAA-GATG
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
1252 GGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
1283 AGGCCCTTATTTG-GTCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
* *
1312 GGGCCCTTGTTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
*
1343 AGACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
1360 ATTAGCCCTT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 37 0.36
30 4 0.04
31 53 0.51
32 5 0.05
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:3142 original size:16 final size:17
Alignment explanation
Indices: 3116--3152 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
3106 CATGATTAAA
3116 CTGTCCAAGTACTGTAT
1 CTGTCCAAGTACTGTAT
3133 CTGT-CAAGTACTGTAT
1 CTGTCCAAGTACTGTAT
3149 CTGT
1 CTGT
3153 TCCGACCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (17 bp):
CTGTCCAAGTACTGTAT
Found at i:13400 original size:13 final size:12
Alignment explanation
Indices: 13377--13419 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
13367 TAAATACAGG
13377 TATCGACGGATA
1 TATCGACGGATA
13389 TATCGAACGGATA
1 TATCG-ACGGATA
13402 TATCGACGGATA
1 TATCGACGGATA
13414 TATCGA
1 TATCGA
13420 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:14449 original size:10 final size:10
Alignment explanation
Indices: 14432--14477 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
14422 AATTTAATAT
14432 GGATATTTAC
1 GGATATTTAC
* *
14442 GAATATTTAT
1 GGATATTTAC
14452 GGATATTTAC
1 GGATATTTAC
14462 GGATATTTAC
1 GGATATTTAC
14472 GGATAT
1 GGATAT
14478 ATCGAGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (10 bp):
GGATATTTAC
Found at i:14605 original size:12 final size:12
Alignment explanation
Indices: 14588--14626 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
14578 GTACAGATAT
14588 CGGATATATCGA
1 CGGATATATCGA
14600 CGGATATATCGA
1 CGGATATATCGA
14612 -GG---TATCGA
1 CGGATATATCGA
14620 CGGATAT
1 CGGATAT
14627 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Done.