Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005594.1 Corchorus capsularis cultivar CVL-1 contig05612, 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: 2104
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Found at i:135 original size:36 final size:33
Alignment explanation
Indices: 92--190 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 33
82 GATCAGTCAG
*
92 AAAGTAAAAAGGGTAATCAGAGTAATTAAGTTCCAA
1 AAAGTAAAAAGGGCAATC--AGTAATTAAGTT-CAA
*
128 AAAGTAAAAAAGGCAATCAGTAATTAAGTTCAA
1 AAAGTAAAAAGGGCAATCAGTAATTAAGTTCAA
* * *
161 TAAG-AAAAA--GAAATCAGTGATTAAGTTCAA
1 AAAGTAAAAAGGGCAATCAGTAATTAAGTTCAA
191 TAAGAAAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 19 0.33
32 5 0.09
33 6 0.10
34 12 0.21
36 16 0.28
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (33 bp):
AAAGTAAAAAGGGCAATCAGTAATTAAGTTCAA
Found at i:177 original size:30 final size:31
Alignment explanation
Indices: 112--197 Score: 111
Period size: 30 Copynumber: 2.7 Consensus size: 31
102 GGGTAATCAG
* *
112 AGTAATTAAGTTCCAAAAAGTAAAAAAGGCAATC
1 AGTAATTAAGTT-CAATAAG--AAAAAGGAAATC
146 AGTAATTAAGTTCAATAAGAAAAA-GAAATC
1 AGTAATTAAGTTCAATAAGAAAAAGGAAATC
*
176 AGTGATTAAGTTCAATAAGAAA
1 AGTAATTAAGTTCAATAAGAAA
198 GATATAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 26 0.53
31 5 0.10
33 6 0.12
34 12 0.24
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (31 bp):
AGTAATTAAGTTCAATAAGAAAAAGGAAATC
Found at i:240 original size:22 final size:21
Alignment explanation
Indices: 206--262 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
196 AAGATATAAT
206 TAGTAAA-AGGTAAAATGACAA
1 TAGTAAAGA-GTAAAATGACAA
* *
227 CTAGTAAAGAGTAAAGTGATAA
1 -TAGTAAAGAGTAAAATGACAA
249 TAAGTAAAGAGTAA
1 T-AGTAAAGAGTAA
263 TAGAAATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (21 bp):
TAGTAAAGAGTAAAATGACAA
Found at i:328 original size:55 final size:55
Alignment explanation
Indices: 258--673 Score: 638
Period size: 55 Copynumber: 7.6 Consensus size: 55
248 ATAAGTAAAG
* * *
258 AGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
313 AGTAGTAGTAATCAGTAAATCAATAATTAAGTAAAAAGGGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* *
368 AGTAATAGTAATCAGTAAATTAATAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * * *
423 AGTAGTAGTAATCAGTAAATCAGTAACTAAGTGAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * *
478 GGTAATAGTAATCCGTAAATCAGTAATTAAGCAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
533 AGTAATAATAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
588 GGTAATAGTAATCAGTAAATC-GATAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAG-TAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
643 GGTAATAGTAATCAGTAAATC-GATAATTAAG
1 AGTAATAGTAATCAGTAAATCAG-TAATTAAG
674 AGTTAAAATG
Statistics
Matches: 332, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
54 1 0.00
55 331 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (55 bp):
AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
Found at i:899 original size:7 final size:7
Alignment explanation
Indices: 887--988 Score: 88
Period size: 7 Copynumber: 15.1 Consensus size: 7
877 GGCATCTGAA
887 AGTAAAG
1 AGTAAAG
894 AGTAAAG
1 AGTAAAG
*
901 AGTAGAG
1 AGTAAAG
908 AGT--AG
1 AGTAAAG
913 AGTAAAG
1 AGTAAAG
**
920 AGTAATC
1 AGTAAAG
927 AGTAAAG
1 AGTAAAG
**
934 AAAAAATG
1 AGTAAA-G
*
942 -GTAAAA
1 AGTAAAG
948 AGTAAAG
1 AGTAAAG
955 AGTAAAG
1 AGTAAAG
962 AGT--AG
1 AGTAAAG
967 AGTAAAG
1 AGTAAAG
**
974 AGTAATC
1 AGTAAAG
981 AGTAAAG
1 AGTAAAG
988 A
1 A
989 AAAAATGGTA
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
5 10 0.14
7 63 0.85
8 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:946 original size:54 final size:54
Alignment explanation
Indices: 888--1004 Score: 216
Period size: 54 Copynumber: 2.2 Consensus size: 54
878 GCATCTGAAA
* *
888 GTAAAGAGTAAAGAGTAGAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
1 GTAAAAAGTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
942 GTAAAAAGTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
1 GTAAAAAGTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
996 GTAAAAAGT
1 GTAAAAAGT
1005 GAAGGGAAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.17
Consensus pattern (54 bp):
GTAAAAAGTAAAGAGTAAAGAGTAGAGTAAAGAGTAATCAGTAAAGAAAAAATG
Done.