Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014535.1 Corchorus capsularis cultivar CVL-1 contig14556, 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: 48057
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:148 original size:31 final size:31
Alignment explanation
Indices: 110--211 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
100 ACTAACACCT
*
110 GGCCCTTATTTGAGTATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTA
** * *
141 GGCCCTTATTTG-GCCAAATT--A-AAAGATCA
1 GGCCCTTATTTGAG-CATTTTCGATAACG-TTA
*
170 GACCCTTATTTGAGCATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTA
*
201 GGCTCTTATTT
1 GGCCCTTATTT
212 TGCCAAATTA
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 18 0.34
30 2 0.04
31 27 0.51
32 3 0.06
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (31 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTA
Found at i:272 original size:60 final size:60
Alignment explanation
Indices: 110--273 Score: 240
Period size: 60 Copynumber: 2.7 Consensus size: 60
100 ACTAACACCT
* *
110 GGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCA
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTTGCCAAATTAAAAGATCA
* * *
170 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTTGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTTGCCAAATTAAAAGATCA
* * *
230 GGCCCTTATTTGAGCATTTTGGCA-AACTTTAGACCCTTATTTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTTG
274 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTTGCCAAATTAAAAGATCA
Found at i:5094 original size:37 final size:37
Alignment explanation
Indices: 5040--5140 Score: 193
Period size: 37 Copynumber: 2.7 Consensus size: 37
5030 GAGTTAAGCA
*
5040 GCTCTCAGGTTCAAGCGGGTCGAATCCAGATTAGTCG
1 GCTCTCAGGTTCCAGCGGGTCGAATCCAGATTAGTCG
5077 GCTCTCAGGTTCCAGCGGGTCGAATCCAGATTAGTCG
1 GCTCTCAGGTTCCAGCGGGTCGAATCCAGATTAGTCG
5114 GCTCTCAGGTTCCAGCGGGTCGAATCC
1 GCTCTCAGGTTCCAGCGGGTCGAATCC
5141 GGGTTTCAGC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.24
Consensus pattern (37 bp):
GCTCTCAGGTTCCAGCGGGTCGAATCCAGATTAGTCG
Found at i:5150 original size:21 final size:21
Alignment explanation
Indices: 5121--5163 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5111 TCGGCTCTCA
5121 GGTTCCAGCGGGTCGAATCCG
1 GGTTCCAGCGGGTCGAATCCG
*
5142 GGTTTCAGCGGGTCGAATCCG
1 GGTTCCAGCGGGTCGAATCCG
5163 G
1 G
5164 ATTAGTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.21
Consensus pattern (21 bp):
GGTTCCAGCGGGTCGAATCCG
Found at i:9260 original size:2 final size:2
Alignment explanation
Indices: 9253--9291 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9243 TTCATTTTCT
9253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9292 GCAGGTGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13227 original size:13 final size:13
Alignment explanation
Indices: 13205--13236 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13195 TTTACCCTAT
*
13205 AAAAAGAGGGTCA
1 AAAAATAGGGTCA
13218 AAAAATAGGGTCA
1 AAAAATAGGGTCA
13231 AAAAAT
1 AAAAAT
13237 GAAAAACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (13 bp):
AAAAATAGGGTCA
Found at i:35135 original size:1 final size:1
Alignment explanation
Indices: 35129--35164 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
35119 TTCAAATGGT
35129 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35165 CTTCTAACCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36892 original size:2 final size:2
Alignment explanation
Indices: 36885--36909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36875 TATTATAAAG
36885 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36910 GTACCTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40449 original size:33 final size:35
Alignment explanation
Indices: 40392--40459 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
40382 TTCTTCAATA
40392 AAGAAGTGGAATTCAGATTCTTCTTCAAAAGGGAAG
1 AAGAAGTGGAATTCAGA-TCTTCTTCAAAAGGGAAG
**
40428 AAGAAGTGGAATTCAG-T-TTCTTGGAAAGGGAA
1 AAGAAGTGGAATTCAGATCTTCTTCAAAAGGGAA
40460 TTACTAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 1 0.03
36 16 0.53
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (35 bp):
AAGAAGTGGAATTCAGATCTTCTTCAAAAGGGAAG
Found at i:47069 original size:64 final size:60
Alignment explanation
Indices: 46946--47071 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 60
46936 CTGTTCTTCC
* *
46946 GAATTTGGTAATAGAGGATCAAGAGTTTGCTTATGACTTATTGATTCCCATTATTTATGA
1 GAATTTGGTAAAAGAGGATCAAGAGTTTGCTTATGACTTATTGATGCCCATTATTTATGA
47006 GAATTTGGTAAAAGAGGATCAAGAGTTTGCCACATTATGACTTATTGATGCCCATTATTTATGA
1 GAATTTGGTAAAAGAGGATCAAGAGTTTG---C-TTATGACTTATTGATGCCCATTATTTATGA
47070 GA
1 GA
47072 TGTTGTATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
60 28 0.47
63 1 0.02
64 31 0.52
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (60 bp):
GAATTTGGTAAAAGAGGATCAAGAGTTTGCTTATGACTTATTGATGCCCATTATTTATGA
Found at i:47525 original size:2 final size:2
Alignment explanation
Indices: 47518--47552 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47508 AGGACTCGAA
47518 AT AT AT 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 AT AT AT A
47553 AATTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.