Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013307.1 Corchorus capsularis cultivar CVL-1 contig13328, 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: 16624
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:235 original size:13 final size:14
Alignment explanation
Indices: 212--249 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
202 TTACTCTAGT
*
212 TTATGACTTTGATA
1 TTATGATTTTGATA
226 -TATGATTTTGATA
1 TTATGATTTTGATA
239 TTAATGATTTT
1 TT-ATGATTTT
250 CTTGTATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 1 0.05
15 8 0.38
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (14 bp):
TTATGATTTTGATA
Found at i:3569 original size:18 final size:17
Alignment explanation
Indices: 3542--3577 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3532 CTTGTTTGCT
3542 ATAAAAAAATATAAATAA
1 ATAAAAAAATA-AAATAA
*
3560 ATAAATAAATAAAATAA
1 ATAAAAAAATAAAATAA
3577 A
1 A
3578 AATATTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAAAAATAAAATAA
Found at i:3960 original size:26 final size:26
Alignment explanation
Indices: 3927--3978 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3917 TTAATCAAAT
3927 AATTTTGAAGGTATGAGTTAACCCTC
1 AATTTTGAAGGTATGAGTTAACCCTC
3953 AATTTTGAAGGTATGAGTTAACCCTC
1 AATTTTGAAGGTATGAGTTAACCCTC
3979 GCCGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (26 bp):
AATTTTGAAGGTATGAGTTAACCCTC
Found at i:6405 original size:27 final size:28
Alignment explanation
Indices: 6365--6437 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
6355 TAAGATAGTA
6365 AAATTAC-GTATTTGCCCCTGTTAT-TG-C
1 AAATTACAGT-TTTGCCCCT-TTATGTGTC
*
6392 AAATTACCAG-TTTG-CCCTTTATGTGTT
1 AAATTA-CAGTTTTGCCCCTTTATGTGTC
6419 AAATTACAGTTTTGCCCCT
1 AAATTACAGTTTTGCCCCT
6438 AGAGGCTGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
25 4 0.10
26 9 0.23
27 20 0.51
28 5 0.13
29 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (28 bp):
AAATTACAGTTTTGCCCCTTTATGTGTC
Found at i:6672 original size:13 final size:14
Alignment explanation
Indices: 6649--6686 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
6639 TTACTCTAGT
*
6649 TTATGACTTTGATA
1 TTATGATTTTGATA
6663 -TATGATTTTGATA
1 TTATGATTTTGATA
6676 TTAATGATTTT
1 TT-ATGATTTT
6687 CTTGTATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 1 0.05
15 8 0.38
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (14 bp):
TTATGATTTTGATA
Found at i:6888 original size:14 final size:12
Alignment explanation
Indices: 6832--6888 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
6822 GAGGGACTTA
* *
6832 TTTTTATTACTG
1 TTTTTATAAATG
6844 TTTTTAATAAATTG
1 TTTTT-ATAAA-TG
6858 TTTTTATAAATG
1 TTTTTATAAATG
6870 ATTTTTATTAAGATG
1 -TTTTTA-TAA-ATG
6885 TTTT
1 TTTT
6889 GGGTGCATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.18
13 14 0.37
14 14 0.37
15 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (12 bp):
TTTTTATAAATG
Found at i:12793 original size:52 final size:52
Alignment explanation
Indices: 12728--12827 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
12718 TCTGCTGAAT
*
12728 TAAAGACAACCTATTATTTTCAAAGGAACCATAGACGATTTGTCAGCACCAC
1 TAAAGACAACCTATTATTTTCAAAGGAACCATAGACGATTTATCAGCACCAC
* *
12780 TAAAGAGAACCTATTATTTTCAAAGGAACCATAGACGTTTTATCAGCA
1 TAAAGACAACCTATTATTTTCAAAGGAACCATAGACGATTTATCAGCA
12828 ACACCAAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (52 bp):
TAAAGACAACCTATTATTTTCAAAGGAACCATAGACGATTTATCAGCACCAC
Done.