Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013643.1 Corchorus capsularis cultivar CVL-1 contig13664, 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: 10599
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Found at i:194 original size:31 final size:30
Alignment explanation
Indices: 159--295 Score: 141
Period size: 31 Copynumber: 4.5 Consensus size: 30
149 CCCTAACTGA
*
159 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-AATCAAAAACG
*
190 TTATATCCTTAATTGCTCGAAATCAAAAACG
1 TTATATCCTTAATTGCTTG-AATCAAAAACG
* **** *
221 TTATATCCTTAATTGCTTG-TTTTGTAACA
1 TTATATCCTTAATTGCTTGAATCAAAAACG
* *
250 TTATATCCTTAATTGCTTGCAGCAACAAACG
1 TTATATCCTTAATTGCTTGAATCAA-AAACG
*
281 TTATATCCTAAATTG
1 TTATATCCTTAATTG
296 AGTATTTGAC
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
29 23 0.26
31 64 0.74
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (30 bp):
TTATATCCTTAATTGCTTGAATCAAAAACG
Found at i:350 original size:3 final size:3
Alignment explanation
Indices: 344--404 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
334 TTCGTAGTAG
344 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
392 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
405 CCTAATTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1455 original size:31 final size:31
Alignment explanation
Indices: 1376--1455 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
1366 TTACAAAAGA
*
1376 AGCAATTAAGGATATAACGTTTTCGATTTCG
1 AGCAATTAAGGATATAATGTTTTCGATTTCG
*
1407 AGCAATTAAGGATATAATGTTTTCTATTTCG
1 AGCAATTAAGGATATAATGTTTTCGATTTCG
1438 AGCAATTAAGGATATAAT
1 AGCAATTAAGGATATAAT
1456 CAATTAAGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (31 bp):
AGCAATTAAGGATATAATGTTTTCGATTTCG
Found at i:1639 original size:29 final size:31
Alignment explanation
Indices: 1573--1639 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1563 TCTAACGGAC
*
1573 TATATCCTTATTTGCTCGATTTTCGTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
*
1604 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
1633 TATATCC
1 TATATCC
1640 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGATTTTCGTAACGT
Found at i:9660 original size:18 final size:18
Alignment explanation
Indices: 9639--9675 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9629 GGAAATACTA
9639 GCTTATATGGAACTTTAG
1 GCTTATATGGAACTTTAG
9657 GCTTATATGGAACTTTAG
1 GCTTATATGGAACTTTAG
9675 G
1 G
9676 ACATATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (18 bp):
GCTTATATGGAACTTTAG
Found at i:10204 original size:23 final size:23
Alignment explanation
Indices: 10164--10207 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10154 TAAAATAGTT
*
10164 ATAAAAATATTGAATTCAATTAA
1 ATAAAAATAGTGAATTCAATTAA
**
10187 ATAAAAATAGTGTTTTCAATT
1 ATAAAAATAGTGAATTCAATT
10208 GCAAAAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (23 bp):
ATAAAAATAGTGAATTCAATTAA
Found at i:10445 original size:78 final size:78
Alignment explanation
Indices: 10363--10592 Score: 363
Period size: 78 Copynumber: 2.9 Consensus size: 78
10353 TTGTTTAGAT
* * *
10363 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
10427 ATTTTATTTTACCA
65 ATTATATTTTACCA
*
10441 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAGTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
10506 TTATATTTTACCA
66 TTATATTTTACCA
* * * *
10519 TTTTACTATTTTATTCAACTAAAAACTCTATTTTTATATAATTACATCTATTAACCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
10584 TTATATTTT
66 TTATATTTT
10593 GATATTT
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 139 0.99
79 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Done.