Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017280.1 Corchorus olitorius cultivar O-4 contig17313, 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: 2617
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Found at i:721 original size:32 final size:31
Alignment explanation
Indices: 614--755 Score: 119
Period size: 31 Copynumber: 4.6 Consensus size: 31
604 AGAGGATAAG
* * ***
614 CAAGTAATTTAGGATATAACGTTTTCTG-CCG
1 CAAGCAATTAAGGATATAACGTTTTC-GATTT
* ***
645 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
**
674 CAAGCAATTAAGGATATAACGGTTTTTTATTT
1 CAAGCAATTAAGGATATAAC-GTTTTCGATTT
* * *
706 TAAGCAATTAGGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
737 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
756 TCAGTTAGGG
Statistics
Matches: 88, Mismatches: 19, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
29 20 0.23
30 4 0.05
31 46 0.52
32 18 0.20
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:948 original size:29 final size:31
Alignment explanation
Indices: 874--940 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
864 CCTAATGGAC
874 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
905 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
934 TATATCC
1 TATATCC
941 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:2460 original size:67 final size:68
Alignment explanation
Indices: 2210--2615 Score: 484
Period size: 67 Copynumber: 6.0 Consensus size: 68
2200 CTATTTCTAG
* * * *
2210 AAATACCCTTTCGGTCGAAGGGTCATTTTCGTATTTTTGGACTTAAGTTTAGTATTTTCTTTTTC
1 AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
2275 CAA
66 CAA
* * * *
2278 AAACACCCTTTCGGTC-AAAGGGTCGGTTTT-GTCTTTTTGCCTTTAAGTTTAGTATTTTC-ATT
1 AAATACCCTTTCGGTCGAAA-GGTC-ATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTT
2340 TCCAA
64 TCCAA
* * * * ** * * *
2345 GAATGCCCTTTCGGTC-AAAGGCCATTTTTGTCTTTTCACATCTAAGTTTTG-GTTTTCTTTTTC
1 AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
2408 CAA
66 CAA
* * * *
2411 AAATACCCTTTCGGTCGAAGGGTCATTTTCGCCTTTTTGCATTTAAGTTTTG-GTTTTCTTTTTC
1 AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
2475 CAA
66 CAA
* * *
2478 AAATACCCTTTCGGTCGAAAGGTCATTTTCGCCTTTTTGCATTTAAGTTTTG-GTTTTCTTTTTC
1 AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
*
2542 AAA
66 CAA
* * * *
2545 AAACACCCTTTCGGTCGAAAGATCATTTTCATCTTTTTGCATTTAAGTTTAGTATTTTCTATTTC
1 AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
2610 CAA
66 CAA
2613 AAA
1 AAA
2616 CA
Statistics
Matches: 293, Mismatches: 39, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
65 9 0.03
66 41 0.14
67 180 0.61
68 59 0.20
69 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.45
Consensus pattern (68 bp):
AAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTTTAGTATTTTCTTTTTC
CAA
Found at i:2559 original size:134 final size:135
Alignment explanation
Indices: 2194--2615 Score: 537
Period size: 134 Copynumber: 3.1 Consensus size: 135
2184 AGTAGAGTTT
* * * * * * *
2194 TATTTGCTATTTCTAGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTATTTTTGGACTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTT
* * * * *
2259 TAGTATTTTCTTTTTCCAAAAACACCCTTTCGGTCAAAGGGTCGGTTTT-GTCTTTTTGCCTTTA
66 TTG-GTTTTCTTTTTCCAAAAACACCCTTTCGGTCGAAGGGTC-ATTTTCGTCTTTTTGCATTTA
2323 AGTTTAG
129 AGTTTAG
* * * * ** *
2330 TATTTTC-ATTTCCAAGAATGCCCTTTCGGTC-AAAGGCCATTTTTGTCTTTTCACATCTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTT
* *
2393 TTGGTTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGCCTTTTTGCATTTAAG
66 TTGGTTTTCTTTTTCCAAAAACACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
*
2458 TTTTG
131 TTTAG
* * *
2463 -GTTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCGCCTTTTTGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTT
* * * *
2527 TTGGTTTTCTTTTTCAAAAAACACCCTTTCGGTCGAAAGATCATTTTCATCTTTTTGCATTTAAG
66 TTGGTTTTCTTTTTCCAAAAACACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
2592 TTTAG
131 TTTAG
2597 TATTTTCTATTTCCAAAAA
1 TATTTTCTATTTCCAAAAA
2616 CA
Statistics
Matches: 241, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
132 9 0.04
133 76 0.32
134 114 0.47
135 36 0.15
136 6 0.02
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (135 bp):
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAAGGTCATTTTCGTCTTTTTGCATTTAAGTT
TTGGTTTTCTTTTTCCAAAAACACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
TTTAG
Done.