Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012146.1 Corchorus capsularis cultivar CVL-1 contig12167, 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: 34163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:171 original size:77 final size:74
Alignment explanation
Indices: 18--246 Score: 308
Period size: 77 Copynumber: 3.1 Consensus size: 74
8 TTTTATATAG
* * *
18 TTTTACTTAACTAAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTTTA-TA--ACTATTT
1 TTTTACTCAACT-AAAAACTCTATTTTTATATAATTAAATCTAATATCCTTTATTATTA-TATTT
79 TAT-TTTACTA
64 TATATTTACTA
89 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAATTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTT-T-ATTATTATATTT
154 TATAATTTACTA
64 TAT-ATTTACTA
166 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCC-TTATTACTTATATTTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTTATTA-TTATATTTT
*
230 ACCATTTTACTA
65 A-TA-TTTACTA
242 TTTTA
1 TTTTA
247 ATTAAAAAAC
Statistics
Matches: 143, Mismatches: 4, Indels: 17
0.87 0.02 0.10
Matches are distributed among these distances:
70 32 0.22
71 14 0.10
72 1 0.01
73 1 0.01
74 6 0.04
75 20 0.14
76 14 0.10
77 55 0.38
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (74 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTTATTATTATATTTTA
TATTTACTA
Found at i:10009 original size:14 final size:14
Alignment explanation
Indices: 9990--10020 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
9980 ACTCAGACTC
9990 TCAGAGAAAAATCT
1 TCAGAGAAAAATCT
10004 TCAGAGAAAAATCT
1 TCAGAGAAAAATCT
10018 TCA
1 TCA
10021 ACCAAGCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (14 bp):
TCAGAGAAAAATCT
Found at i:10140 original size:37 final size:37
Alignment explanation
Indices: 10090--10203 Score: 219
Period size: 37 Copynumber: 3.1 Consensus size: 37
10080 CAAGTTCTCA
10090 TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
1 TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
10127 TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
1 TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
*
10164 TTTGATATTTTTATATTATTAATCTTGTCAACCTTGT
1 TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
10201 TTT
1 TTT
10204 TACAAGTTTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.60
Consensus pattern (37 bp):
TTTGATATTTTTATTTTATTAATCTTGTCAACCTTGT
Found at i:15340 original size:2 final size:2
Alignment explanation
Indices: 15335--15371 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
15325 GATCAAGTAC
15335 TA 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 TA
15372 GATGGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32665 original size:12 final size:12
Alignment explanation
Indices: 32648--32702 Score: 101
Period size: 12 Copynumber: 4.5 Consensus size: 12
32638 TAAATACAGG
32648 TATCGACGGATA
1 TATCGACGGATA
32660 TATCGAACGGATA
1 TATCG-ACGGATA
32673 TATCGACGGATA
1 TATCGACGGATA
32685 TATCGACGGATA
1 TATCGACGGATA
32697 TATCGA
1 TATCGA
32703 GGTATCGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:32682 original size:25 final size:24
Alignment explanation
Indices: 32648--32702 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
32638 TAAATACAGG
32648 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
32673 TATCGACGGATATATCGACGGATA
1 TATCGACGGATATATCGACGGATA
32697 TATCGA
1 TATCGA
32703 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:33727 original size:10 final size:10
Alignment explanation
Indices: 33712--33747 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
33702 AATTTAATAT
33712 GGATATTTAC
1 GGATATTTAC
*
33722 GGATATTTAT
1 GGATATTTAC
33732 GGATATTTAC
1 GGATATTTAC
33742 GGATAT
1 GGATAT
33748 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:33734 original size:20 final size:20
Alignment explanation
Indices: 33709--33747 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
33699 TTTAATTTAA
33709 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
33729 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
33748 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Done.