Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010376.1 Corchorus capsularis cultivar CVL-1 contig10397, 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: 32121
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:23561 original size:90 final size:90
Alignment explanation
Indices: 23408--23591 Score: 341
Period size: 90 Copynumber: 2.0 Consensus size: 90
23398 CATTGAGCAA
23408 ATAAAATGAGCCTCATTTGAGGATTGCAGTGTAGATGTTTGCTTGCCCCATTTAAGAACTGTTTC
1 ATAAAATGAGCCTCATTTGAGGATTGCAGTGTAGATGTTTGCTTGCCCCATTTAAGAACTGTTTC
*
23473 TCACAAGATGTTGGAAACTAGAGTG
66 TCACAAGATGTTGGAAACAAGAGTG
* *
23498 ATAAAATGAGCCTCATTTGAGGATTGCAGTGTAGATGTTTGCTTGCCGCTTTTAAGAACTGTTTC
1 ATAAAATGAGCCTCATTTGAGGATTGCAGTGTAGATGTTTGCTTGCCCCATTTAAGAACTGTTTC
23563 TCACAAGATGTTGGAAACAAGAGTG
66 TCACAAGATGTTGGAAACAAGAGTG
23588 ATAA
1 ATAA
23592 CATTGATGCA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (90 bp):
ATAAAATGAGCCTCATTTGAGGATTGCAGTGTAGATGTTTGCTTGCCCCATTTAAGAACTGTTTC
TCACAAGATGTTGGAAACAAGAGTG
Found at i:29786 original size:17 final size:16
Alignment explanation
Indices: 29764--29821 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
29754 AAAGCTCAAA
29764 TCCGAAGAAATCCGAAT
1 TCCGAA-AAATCCGAAT
* *
29781 TCCGAAAAAACTCAAAT
1 TCCGAAAAATC-CGAAT
29798 T-CGAAAAAATCCGAA-
1 TCCG-AAAAATCCGAAT
29813 TCC-AAAAAT
1 TCCGAAAAAT
29822 TTATGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 10 0.29
17 17 0.50
ACGTcount: A:0.50, C:0.22, G:0.10, T:0.17
Consensus pattern (16 bp):
TCCGAAAAATCCGAAT
Found at i:29795 original size:33 final size:32
Alignment explanation
Indices: 29749--29820 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
29739 TCTGGTTAAC
* *
29749 CCGAAAAAGCTCAAATCCGAAGAAATCCGAATT
1 CCGAAAAAACTCAAATCCGAAAAAATCCGAA-T
*
29782 CCGAAAAAACTCAAATTCGAAAAAATCCGAAT
1 CCGAAAAAACTCAAATCCGAAAAAATCCGAAT
29814 CC-AAAAA
1 CCGAAAAA
29821 TTTATGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 5 0.14
32 3 0.08
33 28 0.78
ACGTcount: A:0.51, C:0.24, G:0.11, T:0.14
Consensus pattern (32 bp):
CCGAAAAAACTCAAATCCGAAAAAATCCGAAT
Found at i:29804 original size:16 final size:16
Alignment explanation
Indices: 29750--29806 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
29740 CTGGTTAACC
* *
29750 CGAAAAAGCTCAAATC
1 CGAAAAAACTCAAATT
* *
29766 CGAAGAAA-TCCGAATT
1 CGAAAAAACT-CAAATT
29782 CCGAAAAAACTCAAATT
1 -CGAAAAAACTCAAATT
29799 CGAAAAAA
1 CGAAAAAA
29807 TCCGAATCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.03
16 18 0.56
17 12 0.38
18 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.14
Consensus pattern (16 bp):
CGAAAAAACTCAAATT
Found at i:29989 original size:16 final size:16
Alignment explanation
Indices: 29958--30003 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
29948 TCTAGTCAAA
*
29958 ACCCAAACTCAACCTG
1 ACCCAAATTCAACCTG
*
29974 AACCCGAATT-AACCTG
1 -ACCCAAATTCAACCTG
29990 ACCCAAATTCAACC
1 ACCCAAATTCAACC
30004 CGAAACCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 7 0.28
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.15
Consensus pattern (16 bp):
ACCCAAATTCAACCTG
Found at i:30061 original size:20 final size:19
Alignment explanation
Indices: 30017--30062 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
30007 AACCGATTCA
30017 AGCCCGAACCCAATGACCC
1 AGCCCGAACCCAATGACCC
30036 AAGCCCGAACCCAACCTGACCC
1 -AGCCCGAACCCAA--TGACCC
30058 -GCCCG
1 AGCCCG
30063 TTTGCCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 18 0.75
22 6 0.25
ACGTcount: A:0.28, C:0.50, G:0.17, T:0.04
Consensus pattern (19 bp):
AGCCCGAACCCAATGACCC
Found at i:31525 original size:25 final size:25
Alignment explanation
Indices: 31497--31544 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
31487 TTTGGGTAAA
31497 TTTATTTATGTTAATATATATTTTT
1 TTTATTTATGTTAATATATATTTTT
*
31522 TTTATTTATGTTTATATATATTT
1 TTTATTTATGTTAATATATATTT
31545 ATATATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTATTTATGTTAATATATATTTTT
Done.