Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015194.1 Corchorus capsularis cultivar CVL-1 contig15215, 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: 22898
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:700 original size:16 final size:15
Alignment explanation
Indices: 681--804 Score: 81
Period size: 16 Copynumber: 7.9 Consensus size: 15
671 CCGCCTGAAT
681 CTGAACCCGAAAAAAC
1 CTGAACCCG-AAAAAC
* *
697 CTGAACCTGAAAAAG
1 CTGAACCCGAAAAAC
*
712 CTCAAACCCGAAAAAC
1 CT-GAACCCGAAAAAC
*
728 AC-GAACCCGAAAAAG
1 -CTGAACCCGAAAAAC
*
743 CTCAAACCCGAAAAAATC
1 CT-GAACCCG-AAAAA-C
*
761 C-GAACCCGAAAAAG
1 CTGAACCCGAAAAAC
*
775 CTCAAACCCGAAAAGAC
1 CT-GAACCCGAAAA-AC
* *
792 CCGAATCCGAAAA
1 CTGAACCCGAAAA
805 TTTATGAAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
14 2 0.02
15 23 0.28
16 49 0.59
17 8 0.10
18 1 0.01
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.06
Consensus pattern (15 bp):
CTGAACCCGAAAAAC
Found at i:734 original size:31 final size:31
Alignment explanation
Indices: 684--804 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 31
674 CCTGAATCTG
*
684 AACCCGAAAAAACCTGAACCTGAAAAAGCTCA
1 AACCCGAAAAAACC-GAACCCGAAAAAGCTCA
716 AACCCG-AAAAACACGAACCCGAAAAAGCTCA
1 AACCCGAAAAAAC-CGAACCCGAAAAAGCTCA
747 AACCCGAAAAAATCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAA-CCGAACCCGAAAAAGCTCA
* *
779 AACCCGAAAAGACCCGAATCCGAAAA
1 AACCCGAAAA-AACCGAACCCGAAAA
805 TTTATGAAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
31 28 0.34
32 52 0.63
33 2 0.02
ACGTcount: A:0.50, C:0.31, G:0.13, T:0.06
Consensus pattern (31 bp):
AACCCGAAAAAACCGAACCCGAAAAAGCTCA
Found at i:979 original size:15 final size:15
Alignment explanation
Indices: 942--996 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
932 TCTGGCCAAA
*
942 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCTG
958 AACCCAAATTAACCTG
1 -ACCCAAATTAACCTG
974 ACCCAAATTAACCTG
1 ACCCAAATTAACCTG
*
989 ACACAAAT
1 ACCCAAAT
997 CCAACCCGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 22 0.61
16 5 0.14
17 9 0.25
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:11223 original size:6 final size:6
Alignment explanation
Indices: 11181--11206 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11171 GTTGAGCAGC
11181 TTGAAG TTGAAG TTGAAG TTGAAG TT
1 TTGAAG TTGAAG TTGAAG TTGAAG TT
11207 CAATAGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (6 bp):
TTGAAG
Found at i:14046 original size:27 final size:27
Alignment explanation
Indices: 14016--14072 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
14006 GTTGGGAACC
*
14016 TTTAATTGATGTAATATGAATTGGTCT
1 TTTAATTGATATAATATGAATTGGTCT
14043 TTTAATTGATATAATATGAATTGGTCT
1 TTTAATTGATATAATATGAATTGGTCT
14070 TTT
1 TTT
14073 GTAATAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.51
Consensus pattern (27 bp):
TTTAATTGATATAATATGAATTGGTCT
Found at i:18201 original size:33 final size:32
Alignment explanation
Indices: 18128--18232 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 32
18118 TGCTTGATCA
* ** *
18128 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTGGTTTCATCACAAACAAC
*
18160 ATCCAAAACATATTTGGTTTCATCACAAACAAC
1 A-CCAAAACAGATTTGGTTTCATCACAAACAAC
* ** *
18193 ACCTAAAACAGATTTAGTGCCATCGCAAACAAC
1 ACC-AAAACAGATTTGGTTTCATCACAAACAAC
18226 ACTCAAA
1 AC-CAAA
18233 TTAGGTCTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
32 3 0.05
33 56 0.93
34 1 0.02
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (32 bp):
ACCAAAACAGATTTGGTTTCATCACAAACAAC
Found at i:22862 original size:2 final size:2
Alignment explanation
Indices: 22855--22898 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
22845 TGGCCTTGGG
22855 GA GA GA GA GA GA GA GA GA GA GA GA G- GA G- GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22895 GA GA
1 GA GA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.