Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013641.1 Corchorus capsularis cultivar CVL-1 contig13662, 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: 13018
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Found at i:620 original size:332 final size:333
Alignment explanation
Indices: 1--657 Score: 921
Period size: 332 Copynumber: 2.0 Consensus size: 333
* *
1 GAAGCGTTGGAAGCCTTTCAATCTTTTTGACGTTGAGTTATATATTTTTTTTAAGTATTGTAGCC
1 GAAGCGTTCGAAGCCTTTCAATCTTTTTGACGTTGAGTTATATATTTTTTATAAGTATTGTAGCC
* *
66 AAAAACTAAGGAGAAAATTTTTGGCTAAAATTTTGCAAAATTTTGGCCGAAATCGTGTACTAATC
66 AAAAACTAAGGAGAAAATTTTTGGCTAAAATTTTGCAAAATTTTGACCGAAATCGTGTACTAACC
* * * **
131 ATCACGGGTTTTTGGCTAAAAACGGATTCCGGGTCCCCGACTCAGTTTTGCATGATTTTTGACAC
131 ATCACGAGTTTTTGACTAAAAACGGATTCAGGGTCCCCGACTCAACTTTGCATGATTTTTGACAC
* * * *
196 AAAGACTCCTTGAAATATTTATATTCAACTATCGAAATCTAAGCCACATTGGATTTAAGGATTTG
196 AAAGACTCATTGAAATATCTATATTCAACTAACGAAATCTAAGCCACATTGGAATTAAGGATTTG
261 TTTTACAAGCATCCCAATCCGGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATAGGAAAAA
261 TTTTACAAGCATCCCAATCCGGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAA
325 CGACATTA
326 CGACATTA
* *
333 GAAGCGTTCGAAGCCTTTCAATCTTTTTGGCGTTGAGTTATATATTTTTTATGAGTATTGTAGCC
1 GAAGCGTTCGAAGCCTTTCAATCTTTTTGACGTTGAGTTATATATTTTTTATAAGTATTGTAGCC
* * * **
398 AAAAACTGAGGAG-AAATTTTTCGGGTCATTTTTTGCAAAA-TTTGAACCGAAATCGTGTACTAA
66 AAAAACTAAGGAGAAAATTTTT-GGCTAAAATTTTGCAAAATTTTG-ACCGAAATCGTGTACTAA
* *
461 CCATCAC-AGTTTTTTATTAAAAACGCG-TTCTAGGG-CCCCGACTCAACTTTGCATGATTTTTG
129 CCATCACGAGTTTTTGACTAAAAACG-GATTC-AGGGTCCCCGACTCAACTTTGCATGATTTTTG
* * * * * *
523 GCACGAAGACTCATTGAAATATCTATATTCATCTAACTAAATCTCATCCACATTGGAATTAAGGA
192 ACACAAAGACTCATTGAAATATCTATATTCAACTAACGAAATCTAAGCCACATTGGAATTAAGGA
* ** ** *
588 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAGAAAAATAGG
257 TTTG-TTTTACAAGCATCCCAATCCGGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGG
653 AAAAA
321 AAAAA
658 AGATATTAAT
Statistics
Matches: 285, Mismatches: 34, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
331 113 0.40
332 156 0.55
333 16 0.06
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (333 bp):
GAAGCGTTCGAAGCCTTTCAATCTTTTTGACGTTGAGTTATATATTTTTTATAAGTATTGTAGCC
AAAAACTAAGGAGAAAATTTTTGGCTAAAATTTTGCAAAATTTTGACCGAAATCGTGTACTAACC
ATCACGAGTTTTTGACTAAAAACGGATTCAGGGTCCCCGACTCAACTTTGCATGATTTTTGACAC
AAAGACTCATTGAAATATCTATATTCAACTAACGAAATCTAAGCCACATTGGAATTAAGGATTTG
TTTTACAAGCATCCCAATCCGGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAA
CGACATTA
Found at i:1079 original size:16 final size:16
Alignment explanation
Indices: 1046--1079 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1036 TTAATTTTAA
*
1046 TTAGTTTAATTACCTT
1 TTAGTTTAAATACCTT
*
1062 TTAGTTTAAATACGTT
1 TTAGTTTAAATACCTT
1078 TT
1 TT
1080 CTACGTGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (16 bp):
TTAGTTTAAATACCTT
Found at i:1332 original size:45 final size:45
Alignment explanation
Indices: 1283--1376 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
1273 TATCGACAAG
* *
1283 AAGAAACAACTAGCATAAAATAACTTCATTAGCATGAGTCATGCC
1 AAGAAACAACTACCATAAAATAACTTCATTAGCATGAATCATGCC
* *
1328 AAGAAACAACTACCATAAATTAACTTTATTAGCATGAATCATGCC
1 AAGAAACAACTACCATAAAATAACTTCATTAGCATGAATCATGCC
1373 AAGA
1 AAGA
1377 TCCATGAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (45 bp):
AAGAAACAACTACCATAAAATAACTTCATTAGCATGAATCATGCC
Done.