Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002172.1 Corchorus olitorius cultivar O-4 contig02172, 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: 5986
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:656 original size:67 final size:67
Alignment explanation
Indices: 548--681 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
538 CCGCCAATGT
*
548 ATCAAATAATTACCCTTGAAATTATTATATATTTTTTTTAATATGATACACTGGATAAGCCTACT
1 ATCAAATAATTACCCTTGAAATTATTATATATATTTTTTAATATGATACACTGGATAAGCCTACT
613 AA
66 AA
615 ATCAAATAATTACCCTTGAAATTATTATATATATTTTTTAATATGATACACTGGATAAGCCTACT
1 ATCAAATAATTACCCTTGAAATTATTATATATATTTTTTAATATGATACACTGGATAAGCCTACT
680 AA
66 AA
682 CTAAGTACTG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (67 bp):
ATCAAATAATTACCCTTGAAATTATTATATATATTTTTTAATATGATACACTGGATAAGCCTACT
AA
Found at i:2064 original size:10 final size:10
Alignment explanation
Indices: 2049--2079 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2039 GAAGAGATTT
2049 GGAAAACAGA
1 GGAAAACAGA
*
2059 GGAAAACAGG
1 GGAAAACAGA
2069 GGAAAACAGA
1 GGAAAACAGA
2079 G
1 G
2080 TATGTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.35, T:0.00
Consensus pattern (10 bp):
GGAAAACAGA
Found at i:2710 original size:19 final size:21
Alignment explanation
Indices: 2686--2730 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2676 CTATTGCCCC
2686 TTTCAC-C-CAAAACCTTCTT
1 TTTCACTCTCAAAACCTTCTT
*
2705 TTTCACTCTCAAAACCTTGTT
1 TTTCACTCTCAAAACCTTCTT
2726 TTTCA
1 TTTCA
2731 ATCAACAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTCACTCTCAAAACCTTCTT
Found at i:2739 original size:22 final size:21
Alignment explanation
Indices: 2693--2739 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2683 CCCTTTCACC
* *
2693 CAAAACCTTCTTTTTCACTCT
1 CAAAACCTTCTTTTTCAATCA
*
2714 CAAAACCTTGTTTTTCAATCAA
1 CAAAACCTTCTTTTTCAATC-A
2736 CAAA
1 CAAA
2740 GCTACAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (21 bp):
CAAAACCTTCTTTTTCAATCA
Found at i:5124 original size:20 final size:20
Alignment explanation
Indices: 5099--5139 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5089 TTGTAAGACA
5099 TTTTTTTTTT-CTCCCCCAC
1 TTTTTTTTTTCCTCCCCCAC
5118 TTTTTTTTTTCCTCCCCCAC
1 TTTTTTTTTTCCTCCCCCAC
5138 TT
1 TT
5140 ATTAGCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTTTTTCCTCCCCCAC
Found at i:5303 original size:20 final size:20
Alignment explanation
Indices: 5278--5321 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5268 GTTGTATTCT
* *
5278 GTATTATTATTGACCATCTG
1 GTATTATTATTAACCATATG
5298 GTATTATTATTAACCATATG
1 GTATTATTATTAACCATATG
5318 GTAT
1 GTAT
5322 CCTATAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
GTATTATTATTAACCATATG
Done.