Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015816.1 Corchorus capsularis cultivar CVL-1 contig15837, 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: 13721
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:1490 original size:6 final size:6
Alignment explanation
Indices: 1481--1507 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1471 AAAGCAAAGC
1481 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
1508 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:1519 original size:12 final size:13
Alignment explanation
Indices: 1504--1537 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1494 AATCTAAATC
*
1504 TAAAGCAGATT-A
1 TAAAGCAAATTAA
1516 TAAAGCAAATTAA
1 TAAAGCAAATTAA
1529 TAAAGCAAA
1 TAAAGCAAA
1538 CAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:2462 original size:10 final size:10
Alignment explanation
Indices: 2447--2471 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2437 GAGGACTCTA
2447 GAATTTTCTG
1 GAATTTTCTG
2457 GAATTTTCTG
1 GAATTTTCTG
2467 GAATT
1 GAATT
2472 GTGCAGGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:9001 original size:9 final size:8
Alignment explanation
Indices: 8983--9016 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
8973 GAATCGGTTA
8983 TGAATTTT
1 TGAATTTT
8991 TGAAGTTTT
1 TGAA-TTTT
9000 TGAATTTT
1 TGAATTTT
9008 TGAATTTT
1 TGAATTTT
9016 T
1 T
9017 CAAGAAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (8 bp):
TGAATTTT
Found at i:9005 original size:17 final size:16
Alignment explanation
Indices: 8983--9016 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
8973 GAATCGGTTA
8983 TGAATTTTTGAAGTTTT
1 TGAATTTTTGAA-TTTT
9000 TGAATTTTTGAATTTT
1 TGAATTTTTGAATTTT
9016 T
1 T
9017 CAAGAAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (16 bp):
TGAATTTTTGAATTTT
Found at i:10014 original size:33 final size:32
Alignment explanation
Indices: 9977--10083 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
9967 CGCCAAGCGA
* *
9977 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCA-GTCGCG
*
10010 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
* *
10043 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATCTCC-AGTCGCG
10076 TGGCCGGT
1 TGGCCGGT
10084 CACTAGTGCC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 63 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAGTCGCG
Found at i:11463 original size:80 final size:80
Alignment explanation
Indices: 11330--11493 Score: 319
Period size: 80 Copynumber: 2.0 Consensus size: 80
11320 GGGAGTATAG
*
11330 CTAAATCCGACAAATATTTAGCAGGTGGATATTGACTCTTATTTTCCTGATAGTTGTTAATTATT
1 CTAAATCCAACAAATATTTAGCAGGTGGATATTGACTCTTATTTTCCTGATAGTTGTTAATTATT
11395 TGTGTTTTTTATCTT
66 TGTGTTTTTTATCTT
11410 CTAAATCCAACAAATATTTAGCAGGTGGATATTGACTCTTATTTTCCTGATAGTTGTTAATTATT
1 CTAAATCCAACAAATATTTAGCAGGTGGATATTGACTCTTATTTTCCTGATAGTTGTTAATTATT
11475 TGTGTTTTTTATCTT
66 TGTGTTTTTTATCTT
11490 CTAA
1 CTAA
11494 CAGTTTGCTG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (80 bp):
CTAAATCCAACAAATATTTAGCAGGTGGATATTGACTCTTATTTTCCTGATAGTTGTTAATTATT
TGTGTTTTTTATCTT
Found at i:12290 original size:2 final size:2
Alignment explanation
Indices: 12283--12311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12273 TTTATTAATC
12283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12312 CTAGTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.