Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010421.1 Corchorus capsularis cultivar CVL-1 contig10442, 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: 13438
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:2802 original size:2 final size:2
Alignment explanation
Indices: 2790--2833 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
2780 GTATAATTAC
*
2790 TA TA T- TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2830 TA TA
1 TA TA
2834 CACACTATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3518 original size:106 final size:107
Alignment explanation
Indices: 3364--3567 Score: 331
Period size: 106 Copynumber: 1.9 Consensus size: 107
3354 TAAGAATATA
* *
3364 TTAATTTGGGGCTAAACTTAGTGACATCAGTTTTATATTTTAATTCTAAAACAT-TATAATAATA
1 TTAATTTGGGGCTAAACTTAGTGACATCAATTTTATATTTTAATTCTAAAAC-TCTAAAATAATA
*
3428 AATTATTAATTTTGGAATTTACCCTTTAAATTAAATTAAAATT
65 AATTATTAATTTTGGAATTTACCCTTAAAATTAAATTAAAATT
* * *
3471 TTAATTTGGGGTTAAATTTAGTGAC-TTAATTTTATATTTTAATTCTAAAACTCTAAAATAATAA
1 TTAATTTGGGGCTAAACTTAGTGACATCAATTTTATATTTTAATTCTAAAACTCTAAAATAATAA
3535 ATTATTAATTTTGGAATTTACCCTTAAAATTAA
66 ATTATTAATTTTGGAATTTACCCTTAAAATTAA
3568 TTTTGGGACT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 1 0.01
106 66 0.73
107 23 0.26
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (107 bp):
TTAATTTGGGGCTAAACTTAGTGACATCAATTTTATATTTTAATTCTAAAACTCTAAAATAATAA
ATTATTAATTTTGGAATTTACCCTTAAAATTAAATTAAAATT
Found at i:4778 original size:32 final size:32
Alignment explanation
Indices: 4737--4859 Score: 183
Period size: 32 Copynumber: 3.8 Consensus size: 32
4727 CATGGCTCAC
*
4737 GCCGTGGCACAACCGCCCTCCTGGGGCGGCAT
1 GCCGTGGCACAGCCGCCCTCCTGGGGCGGCAT
*
4769 GCCGTGGCACAGCCGCCCTCCTGGGCGCGACAT
1 GCCGTGGCACAGCCGCCCTCCTGGG-GCGGCAT
* *
4802 GCCGTGGCACAGCCTCCCTCCTGGGACGGCAT
1 GCCGTGGCACAGCCGCCCTCCTGGGGCGGCAT
* *
4834 GTCGTGGCACAGCCACCCTCCTGGGG
1 GCCGTGGCACAGCCGCCCTCCTGGGG
4860 TGACACGGTC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 52 0.63
33 30 0.37
ACGTcount: A:0.12, C:0.41, G:0.33, T:0.14
Consensus pattern (32 bp):
GCCGTGGCACAGCCGCCCTCCTGGGGCGGCAT
Found at i:4821 original size:65 final size:65
Alignment explanation
Indices: 4737--4858 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 65
4727 CATGGCTCAC
* *
4737 GCCGTGGCACAACCGCCCTCCTGGGGCGGCATGCCGTGGCACAGCCGCCCTCCTGGGCGCGACAT
1 GCCGTGGCACAACCGCCCTCCTGGGACGGCATGCCGTGGCACAGCCACCCTCCTGGGCGCGACAT
* * *
4802 GCCGTGGCACAGCCTCCCTCCTGGGACGGCATGTCGTGGCACAGCCACCCTCCTGGG
1 GCCGTGGCACAACCGCCCTCCTGGGACGGCATGCCGTGGCACAGCCACCCTCCTGGG
4859 GTGACACGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.12, C:0.41, G:0.33, T:0.14
Consensus pattern (65 bp):
GCCGTGGCACAACCGCCCTCCTGGGACGGCATGCCGTGGCACAGCCACCCTCCTGGGCGCGACAT
Found at i:8453 original size:31 final size:31
Alignment explanation
Indices: 8392--8455 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
8382 GTTGTGCCCA
*
8392 TGTACCAAAAAGTGACACATGTCACACCACG
1 TGTACCAAAAAGTGACACATGGCACACCACG
* **
8423 TGTACCAAAAAGTGACACGTGGCATGCCACG
1 TGTACCAAAAAGTGACACATGGCACACCACG
8454 TG
1 TG
8456 CACAAAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACATGGCACACCACG
Found at i:10413 original size:2 final size:2
Alignment explanation
Indices: 10401--10432 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10391 ATTCATTAAC
*
10401 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10433 GCCAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12975 original size:25 final size:25
Alignment explanation
Indices: 12941--12990 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12931 TTCAATTCAG
12941 GATACACCGTTACCCATTGTATCAA
1 GATACACCGTTACCCATTGTATCAA
12966 GATACACCGTTACCCATTGTATCAA
1 GATACACCGTTACCCATTGTATCAA
12991 TTCAGGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (25 bp):
GATACACCGTTACCCATTGTATCAA
Done.