Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010396.1 Corchorus olitorius cultivar O-4 contig10428, 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: 2570
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:1536 original size:21 final size:21
Alignment explanation
Indices: 1510--1550 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1500 TTTAAACCCT
1510 ATTGGAGACAAGTGGTACTAA
1 ATTGGAGACAAGTGGTACTAA
***
1531 ATTGGATTTAAGTGGTACTA
1 ATTGGAGACAAGTGGTACTA
1551 GGGTTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (21 bp):
ATTGGAGACAAGTGGTACTAA
Found at i:2434 original size:398 final size:398
Alignment explanation
Indices: 1695--2476 Score: 1449
Period size: 398 Copynumber: 2.0 Consensus size: 398
1685 GTTTGTTCCT
1695 CAAGTAGGTCACGAGAAGAAAGGAGTACTCTAACAATTTGCTCTTATTAGGCCTATTGAAGCTAG
1 CAAGTAGGTCACGAGAAGAAAGGAGTACTCTAACAATTTGCTCTTATTAGGCCTATTGAAGCTAG
*
1760 ATAAAGGCATAATCTTGTGAGATTATTAAGAGAGTAGTGGATAGCCAATCCATAGGTTGAGTGCA
66 ATAAAGGCATAATCTTGTGAGATCATTAAGAGAGTAGTGGATAGCCAATCCATAGGTTGAGTGCA
1825 AACAGGAGAGCACAACAAAGGTAATTCACACACACACTTGTGAGAAATTTTTATTACTAACTTTT
131 AACAGGAGAGCACAACAAAGGTAATTCACACACACACTTGTGAGAAATTTTTATTACTAACTTTT
1890 CTTTGTGTGTAGGTACAATGGGAGATCAAAATCAAGCCAATGATGTGGCTACCTCGTTGCAAGCC
196 CTTTGTGTGTAGGTACAATGGGAGATCAAAATCAAGCCAATGATGTGGCTACCTCGTTGCAAGCC
1955 ATCATGCAACAATTAGGCACTATAACAACAAGATTAGAGGCCTTGGAGGTTCAAAATCAACAAGA
261 ATCATGCAACAATTAGGCACTATAACAACAAGATTAGAGGCCTTGGAGGTTCAAAATCAACAAGA
* * * *
2020 TCCACCACCCCAACAAAGGGAGAACAATGCCGCA-CAAGGCAATGAGCAAAGGGATCAACAACCT
326 ACCACAACCCCAACAAAGAGAGAACAATGCCGCACCAA-ACAATGAGCAAAGGGATCAACAACCT
2084 TAACATAGA
390 TAACATAGA
2093 CAAGTAGGTCACGAGAAGAAAGGAGTACTCTAACAATTTGCTCTTATTAGGCCTATTGAAGCTAG
1 CAAGTAGGTCACGAGAAGAAAGGAGTACTCTAACAATTTGCTCTTATTAGGCCTATTGAAGCTAG
2158 ATAAAGGCATAATCTTGTGAGATCATTAAGAGAGTAGTGGATAGCCAATCCATAGGTTGAGTGCA
66 ATAAAGGCATAATCTTGTGAGATCATTAAGAGAGTAGTGGATAGCCAATCCATAGGTTGAGTGCA
*
2223 AACAGGAGAGTACAACAAAGGTAATTCACACACACACTTGTGAGAAATTTTTATTACTAACTTTT
131 AACAGGAGAGCACAACAAAGGTAATTCACACACACACTTGTGAGAAATTTTTATTACTAACTTTT
2288 CTTTGTGTGTAGGTACAATGGGAGATCAAAATCAAGCCAATGATGTGGCTACCTCGTTGCAAGCC
196 CTTTGTGTGTAGGTACAATGGGAGATCAAAATCAAGCCAATGATGTGGCTACCTCGTTGCAAGCC
* *
2353 ATCATGCAACAATTAGGCACTATAACAACAAGATTAGATGCCTTGGAGGTTCGAAATCAACAAGA
261 ATCATGCAACAATTAGGCACTATAACAACAAGATTAGAGGCCTTGGAGGTTCAAAATCAACAAGA
* * *
2418 ACCACAACCTCAACAAAGAGAGAACAATGCCGCACCAAATAATGAGTAAAGGGATCAAC
326 ACCACAACCCCAACAAAGAGAGAACAATGCCGCACCAAACAATGAGCAAAGGGATCAAC
2477 CACAACAATA
Statistics
Matches: 372, Mismatches: 11, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
398 369 0.99
399 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (398 bp):
CAAGTAGGTCACGAGAAGAAAGGAGTACTCTAACAATTTGCTCTTATTAGGCCTATTGAAGCTAG
ATAAAGGCATAATCTTGTGAGATCATTAAGAGAGTAGTGGATAGCCAATCCATAGGTTGAGTGCA
AACAGGAGAGCACAACAAAGGTAATTCACACACACACTTGTGAGAAATTTTTATTACTAACTTTT
CTTTGTGTGTAGGTACAATGGGAGATCAAAATCAAGCCAATGATGTGGCTACCTCGTTGCAAGCC
ATCATGCAACAATTAGGCACTATAACAACAAGATTAGAGGCCTTGGAGGTTCAAAATCAACAAGA
ACCACAACCCCAACAAAGAGAGAACAATGCCGCACCAAACAATGAGCAAAGGGATCAACAACCTT
AACATAGA
Done.