Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007943.1 Corchorus capsularis cultivar CVL-1 contig07964, 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: 15953
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1746 original size:27 final size:27
Alignment explanation
Indices: 1705--1779 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
1695 TTCTCAGAGG
1705 AGCAATATTAGTGGGAACAATCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
* *
1732 AGCAATATTATTGGGAACAACCTGGGA
1 AGCAATATTAGTGGGAACAATCTGGGA
1759 AGCAATATTAGTGGGAACAAT
1 AGCAATATTAGTGGGAACAAT
1780 GGAATTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.23
Consensus pattern (27 bp):
AGCAATATTAGTGGGAACAATCTGGGA
Found at i:4471 original size:15 final size:15
Alignment explanation
Indices: 4451--4479 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4441 CTTATCATCT
4451 TGTTGGATTTGAATC
1 TGTTGGATTTGAATC
4466 TGTTGGATTTGAAT
1 TGTTGGATTTGAAT
4480 TGGAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (15 bp):
TGTTGGATTTGAATC
Found at i:14876 original size:16 final size:15
Alignment explanation
Indices: 14848--14923 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 15
14838 TTTGACCCGT
14848 AACCCG-ATAGACCCGA
1 AACCCGAAT-GACCC-A
14864 AACCCGAATGACCCA
1 AACCCGAATGACCCA
* *
14879 AGACCGGAATAACCCA
1 A-ACCCGAATGACCCA
* *
14895 GACCC-AGATGACCAAA
1 AACCCGA-ATGACC-CA
14911 AACCCGAATGACC
1 AACCCGAATGACC
14924 AGAGAAAACT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
14 1 0.02
15 10 0.21
16 34 0.71
17 3 0.06
ACGTcount: A:0.41, C:0.36, G:0.17, T:0.07
Consensus pattern (15 bp):
AACCCGAATGACCCA
Found at i:15338 original size:8 final size:7
Alignment explanation
Indices: 15282--15338 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 7
15272 AAATCAAAGC
15282 AAAA-AA
1 AAAACAA
15288 AAAA-AA
1 AAAACAA
15294 AAAAC-A
1 AAAACAA
15300 AAAAC-A
1 AAAACAA
15306 AAAAC-A
1 AAAACAA
15312 AAAAC-A
1 AAAACAA
15318 AAAACAA
1 AAAACAA
15325 ACAAACAA
1 A-AAACAA
15333 GAAAAC
1 -AAAAC
15339 GAAATAGGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
6 34 0.72
7 2 0.04
8 10 0.21
9 1 0.02
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:15342 original size:6 final size:6
Alignment explanation
Indices: 15281--15325 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
15271 GAAATCAAAG
*
15281 CAAAAA -AAAAA AAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAA
15326 CAAACAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:15781 original size:33 final size:33
Alignment explanation
Indices: 15739--15826 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
15729 TTTTTACACT
* * *
15739 GAGCCTCCCCACTAGGACGGCTCAGCTACGGCG
1 GAGCCTCCCCACTAGGACGGCTCAACCACGGCA
15772 GAGCCTCCCCACTAGGGA-GGCTCAACCACGGCA
1 GAGCCTCCCCACTA-GGACGGCTCAACCACGGCA
* *
15805 GAGCCTCCCCACTGGGGCGGCT
1 GAGCCTCCCCACTAGGACGGCT
15827 TCACCATGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 43 0.90
34 3 0.06
ACGTcount: A:0.18, C:0.40, G:0.31, T:0.11
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTCAACCACGGCA
Done.