Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012864.1 Corchorus capsularis cultivar CVL-1 contig12885, 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: 30931
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4910 original size:14 final size:15
Alignment explanation
Indices: 4879--4912 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4869 TTGTGCAAAA
*
4879 AAATAATATATAAGG
1 AAATAAGATATAAGG
4894 AAATAAGATAT-AGG
1 AAATAAGATATAAGG
4908 AAATA
1 AAATA
4913 CTAGCGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (15 bp):
AAATAAGATATAAGG
Found at i:10727 original size:2 final size:2
Alignment explanation
Indices: 10720--10744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10710 TATTATTACA
10720 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 A
10745 ATTATGAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13828 original size:16 final size:15
Alignment explanation
Indices: 13790--13831 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
13780 GTGCTAAAAG
*
13790 AAGTACTGAATTTTT
1 AAGTACTGAATTTAT
13805 AA-TACTGAATCTTAT
1 AAGTACTGAAT-TTAT
13820 AAGTACTGAATT
1 AAGTACTGAATT
13832 CAAACTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (15 bp):
AAGTACTGAATTTAT
Found at i:14982 original size:11 final size:11
Alignment explanation
Indices: 14952--14994 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
14942 ATTTAGTAAT
*
14952 AACGCACGTAC
1 AACGCACGTGC
*
14963 AACGTACGTGC
1 AACGCACGTGC
*
14974 AATGCACGTGC
1 AACGCACGTGC
14985 AACGCACGTG
1 AACGCACGTG
14995 AAGTGAATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (11 bp):
AACGCACGTGC
Found at i:18278 original size:14 final size:14
Alignment explanation
Indices: 18259--18287 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18249 GAAGAGAATT
18259 TAGGGATACACATA
1 TAGGGATACACATA
18273 TAGGGATACACATA
1 TAGGGATACACATA
18287 T
1 T
18288 TATATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
TAGGGATACACATA
Found at i:20115 original size:174 final size:176
Alignment explanation
Indices: 19808--20161 Score: 550
Period size: 174 Copynumber: 2.0 Consensus size: 176
19798 TTCAAGGAAC
** * *
19808 TGCAAAAACATCACCGGAGAAAGTTGGCATTTTAAAAGCAAAAAACAAAAAAAAGGAAGAAAAAT
1 TGCAAAAACATCACAAGAGAAAGTTGGCACTTTAAAAGC---AAACAAAAAAAAGGAAGAAAAAA
* * * *
19873 ACCAAAGTGAAAAATGAAAAAGTTAATAGGGACATGATCGGAAAGATGAGAAGAAGAGAGGAGAA
63 ACCAAAGTGAAAAATGAAAAAGTCAACAGGGACATGATCAGAAAGATGAGAAGAAAAGAGGAGAA
19938 ACATAGTAAGTGTTTGGAGAAAACAAAAGTTTAAAAAGGAAAGATTTTT
128 ACATAGTAAGTGTTTGGAGAAAACAAAAGTTTAAAAAGGAAAGATTTTT
*
19987 TGCAAAAACATCACAAGAGAAAGTTGGCACTTTAAAAGC-CA-AAAAAAAAGGAAGAAAAAAACC
1 TGCAAAAACATCACAAGAGAAAGTTGGCACTTTAAAAGCAAACAAAAAAAAGGAAGAAAAAAACC
* * *
20050 AAAGTGAAAAATGAAAAAGTCAACAGGGACATGATCAGAAAGATGAGAGGAAAATAGGTGAAACA
66 AAAGTGAAAAATGAAAAAGTCAACAGGGACATGATCAGAAAGATGAGAAGAAAAGAGGAGAAACA
*
20115 TAGTAAGTGTTTGGAGAAAACAAAAGTTTAAAAGGGAAAGATTTTT
131 TAGTAAGTGTTTGGAGAAAACAAAAGTTTAAAAAGGAAAGATTTTT
20161 T
1 T
20162 TGTGTATATA
Statistics
Matches: 162, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
174 125 0.77
175 1 0.01
179 36 0.22
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.17
Consensus pattern (176 bp):
TGCAAAAACATCACAAGAGAAAGTTGGCACTTTAAAAGCAAACAAAAAAAAGGAAGAAAAAAACC
AAAGTGAAAAATGAAAAAGTCAACAGGGACATGATCAGAAAGATGAGAAGAAAAGAGGAGAAACA
TAGTAAGTGTTTGGAGAAAACAAAAGTTTAAAAAGGAAAGATTTTT
Found at i:20391 original size:5 final size:5
Alignment explanation
Indices: 20378--20421 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
20368 CTTTAAAAGG
* * *
20378 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC AGAAC AGAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
20422 TGAAGAAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.80, C:0.16, G:0.05, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:22245 original size:38 final size:39
Alignment explanation
Indices: 22170--22246 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
22160 CCTACTCGAT
* *
22170 TGTGATTGTTCAAATATTAAAGAATCTACAACCCAAATA
1 TGTGATTGTTCAAATATTAAAGAATCCACAACACAAATA
* *
22209 TGTGA-TGTTCAAATATTAATGAGTCCA-AAGCACAAATA
1 TGTGATTGTTCAAATATTAAAGAATCCACAA-CACAAATA
22247 CCACCAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.06
38 26 0.79
39 5 0.15
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (39 bp):
TGTGATTGTTCAAATATTAAAGAATCCACAACACAAATA
Found at i:23139 original size:52 final size:52
Alignment explanation
Indices: 23072--23212 Score: 219
Period size: 52 Copynumber: 2.7 Consensus size: 52
23062 AAAATGAATC
* *
23072 TAACATAGTTGTTTATGATGGTGAAAATAAGTAATTCCCGTTAAAACAAATA
1 TAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCATTAAAACAAATA
* * *
23124 TAACTTAGTTGTTTATCATGGTGAAAATAAGTAATTCCCATTAAAACGAATC
1 TAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCATTAAAACAAATA
* *
23176 TAACATAGTTGTTTATCAAGGTGAAAGTAAGTAATTC
1 TAACATAGTTGTTTATCATGGTGAAAATAAGTAATTC
23213 TCATATATGT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (52 bp):
TAACATAGTTGTTTATCATGGTGAAAATAAGTAATTCCCATTAAAACAAATA
Found at i:25139 original size:15 final size:15
Alignment explanation
Indices: 25121--25155 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25111 TGAGGACGAC
*
25121 GAAGGAGAAGAAGCA
1 GAAGAAGAAGAAGCA
*
25136 GAAGAAGAAGAAGCG
1 GAAGAAGAAGAAGCA
25151 GAAGA
1 GAAGA
25156 GTTATTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.40, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGCA
Found at i:30864 original size:2 final size:2
Alignment explanation
Indices: 30857--30891 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30847 CTTTATAACC
30857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30892 AAGACTGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.