Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008608.1 Corchorus capsularis cultivar CVL-1 contig08629, 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: 11840
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Found at i:1375 original size:17 final size:17
Alignment explanation
Indices: 1353--1480 Score: 118
Period size: 17 Copynumber: 7.7 Consensus size: 17
1343 GTTCCTACCC
* *
1353 TACTCACCCAATACAAA
1 TACTCACCTAGTACAAA
*
1370 TACTCACCTGGTACAAA
1 TACTCACCTAGTACAAA
*
1387 TACTCACCTGGTACAAA
1 TACTCACCTAGTACAAA
*
1404 CACTCACCTAGTACAAA
1 TACTCACCTAGTACAAA
* * *
1421 CACTCACCTGGTGC-AA
1 TACTCACCTAGTACAAA
* * * *
1437 CACTCACCTGGT-GAGA
1 TACTCACCTAGTACAAA
*
1453 TACTCACCCAGTAC-AA
1 TACTCACCTAGTACAAA
1469 TACTCACCTAGT
1 TACTCACCTAGT
1481 GAGGTCACCA
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
16 36 0.38
17 58 0.62
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.21
Consensus pattern (17 bp):
TACTCACCTAGTACAAA
Found at i:1449 original size:16 final size:17
Alignment explanation
Indices: 1364--1448 Score: 127
Period size: 17 Copynumber: 5.1 Consensus size: 17
1354 ACTCACCCAA
*
1364 TACAAATACTCACCTGG
1 TACAAACACTCACCTGG
*
1381 TACAAATACTCACCTGG
1 TACAAACACTCACCTGG
*
1398 TACAAACACTCACCTAG
1 TACAAACACTCACCTGG
1415 TACAAACACTCACCTGG
1 TACAAACACTCACCTGG
*
1432 TGC-AACACTCACCTGG
1 TACAAACACTCACCTGG
1448 T
1 T
1449 GAGATACTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
16 14 0.22
17 50 0.78
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (17 bp):
TACAAACACTCACCTGG
Found at i:8482 original size:26 final size:26
Alignment explanation
Indices: 8414--8550 Score: 159
Period size: 28 Copynumber: 5.0 Consensus size: 26
8404 CTAAAGGAGG
*
8414 CCCAGCAGCGCGCCAGGGGAGACT-T
1 CCCAGCAGCGCGCCAGGGGAGACTCC
*
8439 CCCAGCTGCACGCGCCAGGGGAGACTCC
1 CCCAGCAG--CGCGCCAGGGGAGACTCC
*
8467 CCCAGCAGCGCACCAGGGGAGACTCC
1 CCCAGCAGCGCGCCAGGGGAGACTCC
8493 CCCAGCAGCGCGTGCGCCAGGGGAGACTCC
1 CCCAGCA--GC--GCGCCAGGGGAGACTCC
*
8523 CCCAGCAACGCGCGCCAGGGGAGGCTCC
1 CCCAGC-A-GCGCGCCAGGGGAGACTCC
8551 TGCGCTCCAG
Statistics
Matches: 98, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.07
26 24 0.24
27 16 0.16
28 25 0.26
30 25 0.26
31 1 0.01
ACGTcount: A:0.19, C:0.41, G:0.34, T:0.06
Consensus pattern (26 bp):
CCCAGCAGCGCGCCAGGGGAGACTCC
Found at i:8528 original size:56 final size:54
Alignment explanation
Indices: 8414--8550 Score: 186
Period size: 53 Copynumber: 2.5 Consensus size: 54
8404 CTAAAGGAGG
* *
8414 CCCAGCAGCGCGCCAGGGGAGACT-TCCCAGCTGCACGCGCCAGGGGAGACTCC
1 CCCAGCAGCGCGCCAGGGGAGACTCCCCCAGCAGCACGCGCCAGGGGAGACTCC
* *
8467 CCCAGCAGCGCACCAGGGGAGACTCCCCCAGCAGCGCGTGCGCCAGGGGAGACTCC
1 CCCAGCAGCGCGCCAGGGGAGACTCCCCCAGCAGCAC--GCGCCAGGGGAGACTCC
*
8523 CCCAGCAACGCGCGCCAGGGGAGGCTCC
1 CCCAGC-A-GCGCGCCAGGGGAGACTCC
8551 TGCGCTCCAG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
53 23 0.32
54 9 0.12
56 23 0.32
57 1 0.01
58 17 0.23
ACGTcount: A:0.19, C:0.41, G:0.34, T:0.06
Consensus pattern (54 bp):
CCCAGCAGCGCGCCAGGGGAGACTCCCCCAGCAGCACGCGCCAGGGGAGACTCC
Found at i:8550 original size:28 final size:27
Alignment explanation
Indices: 8414--8550 Score: 163
Period size: 30 Copynumber: 5.0 Consensus size: 27
8404 CTAAAGGAGG
*
8414 CCCAGCA-GCGCGCCAGGGGAGACT-T
1 CCCAGCACGCGCGCCAGGGGAGACTCC
* *
8439 CCCAGCTGCACGCGCCAGGGGAGACTCC
1 CCCAGC-ACGCGCGCCAGGGGAGACTCC
*
8467 CCCAGCA-GCGCACCAGGGGAGACTCC
1 CCCAGCACGCGCGCCAGGGGAGACTCC
8493 CCCAGCAGCGCGTGCGCCAGGGGAGACTCC
1 CCCAGCA-CGC--GCGCCAGGGGAGACTCC
*
8523 CCCAGCAACGCGCGCCAGGGGAGGCTCC
1 CCCAGC-ACGCGCGCCAGGGGAGACTCC
8551 TGCGCTCCAG
Statistics
Matches: 96, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.06
26 24 0.25
27 16 0.17
28 24 0.25
30 25 0.26
31 1 0.01
ACGTcount: A:0.19, C:0.41, G:0.34, T:0.06
Consensus pattern (27 bp):
CCCAGCACGCGCGCCAGGGGAGACTCC
Found at i:8560 original size:20 final size:20
Alignment explanation
Indices: 8532--8570 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8522 CCCCAGCAAC
8532 GCGCGCCAGGGGAGGCTCCT
1 GCGCGCCAGGGGAGGCTCCT
*
8552 GCGCTCCAGGGGAGGCTCC
1 GCGCGCCAGGGGAGGCTCC
8571 CCTAGTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.36, G:0.44, T:0.10
Consensus pattern (20 bp):
GCGCGCCAGGGGAGGCTCCT
Done.