Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014854.1 Corchorus capsularis cultivar CVL-1 contig14875, 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: 29364
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2136 original size:20 final size:20
Alignment explanation
Indices: 2108--2149 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2098 ACCAGTAACC
*
2108 ATGGTAGCTACAACTTTGAA
1 ATGGCAGCTACAACTTTGAA
2128 ATGGCAGCTACAACTTTGAA
1 ATGGCAGCTACAACTTTGAA
2148 AT
1 AT
2150 ACCCAAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
ATGGCAGCTACAACTTTGAA
Found at i:11662 original size:76 final size:77
Alignment explanation
Indices: 11529--11678 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 77
11519 AACTACTCAA
*
11529 CGTAATTTGTGTTTTAAAAAGAAAAAAAAACCAACTTCTACAAAGTCTTTCTGCTTCTTCCTTCC
1 CGTAATTTGTGTTTTAAAAAGAAAAAAAAACCAACTTCTACAAAGTCTTTCTGCTTCTTCCATCC
11594 TCTTCCTCTACC
66 TCTTCCTCTACC
*
11606 CGTAATTTGTGTTTTAAAAAGAAAAAAAAA-CAACTTCTACAAAGTCTTTCTTCTTCTTCCATCC
1 CGTAATTTGTGTTTTAAAAAGAAAAAAAAACCAACTTCTACAAAGTCTTTCTGCTTCTTCCATCC
*
11670 TCTTTCTCT
66 TCTTCCTCT
11679 TCCTCTACCC
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 40 0.57
77 30 0.43
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (77 bp):
CGTAATTTGTGTTTTAAAAAGAAAAAAAAACCAACTTCTACAAAGTCTTTCTGCTTCTTCCATCC
TCTTCCTCTACC
Found at i:12391 original size:9 final size:9
Alignment explanation
Indices: 12377--12402 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12367 TTTTGTTGCA
12377 AAAAAAAAT
1 AAAAAAAAT
12386 AAAAAAAAT
1 AAAAAAAAT
12395 AAAAAAAA
1 AAAAAAAA
12403 ACTTAGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:14164 original size:40 final size:40
Alignment explanation
Indices: 14109--14190 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
14099 CAAGCTCTTG
14109 GAGCTTGTTTCAAGCCATAAATGGCCTTGTCCAATTTGCA
1 GAGCTTGTTTCAAGCCATAAATGGCCTTGTCCAATTTGCA
14149 GAGCTTGTTTCAAGCCATAAATGGCCTTGTCCAATTTGCA
1 GAGCTTGTTTCAAGCCATAAATGGCCTTGTCCAATTTGCA
14189 GA
1 GA
14191 CATAGTTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (40 bp):
GAGCTTGTTTCAAGCCATAAATGGCCTTGTCCAATTTGCA
Found at i:21601 original size:27 final size:27
Alignment explanation
Indices: 21563--21618 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
21553 TAAATTAGAA
21563 TCCTCATTGTCTTCTTCTTGTTACAGG
1 TCCTCATTGTCTTCTTCTTGTTACAGG
21590 TCCTCATTGTCTTCTTCTTGTTACAGG
1 TCCTCATTGTCTTCTTCTTGTTACAGG
21617 TC
1 TC
21619 AATGGAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.27, G:0.14, T:0.48
Consensus pattern (27 bp):
TCCTCATTGTCTTCTTCTTGTTACAGG
Found at i:22618 original size:58 final size:58
Alignment explanation
Indices: 22528--22640 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
22518 GGGAGTCCAA
22528 CAAGGTTTATTGCTTGCAAAGGAACGTGGTTCCCTTTAATTGTTGAATTGGATGCCGG
1 CAAGGTTTATTGCTTGCAAAGGAACGTGGTTCCCTTTAATTGTTGAATTGGATGCCGG
*
22586 CAAGGTTTATTGTTTGCAAAGGAACGTGGTTCCCTTTAATTGTTGAATTGGATGC
1 CAAGGTTTATTGCTTGCAAAGGAACGTGGTTCCCTTTAATTGTTGAATTGGATGC
22641 AGCAGTGGTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (58 bp):
CAAGGTTTATTGCTTGCAAAGGAACGTGGTTCCCTTTAATTGTTGAATTGGATGCCGG
Found at i:27637 original size:14 final size:15
Alignment explanation
Indices: 27618--27649 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
27608 GAATAAAAAT
27618 CGAAAAAACCGA-AC
1 CGAAAAAACCGACAC
27632 CGAAAAAACCGACAC
1 CGAAAAAACCGACAC
27647 CGA
1 CGA
27650 CCGACACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (15 bp):
CGAAAAAACCGACAC
Found at i:28316 original size:2 final size:2
Alignment explanation
Indices: 28309--28335 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28299 GTCTTTCAAG
28309 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 A
28336 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29322 original size:2 final size:2
Alignment explanation
Indices: 29315--29364 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29305 GAAAGGCCAC
29315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29357 TA TA TA TA
1 TA TA TA TA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.