Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013251.1 Corchorus olitorius cultivar O-4 contig13284, 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: 6572
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:962 original size:281 final size:283
Alignment explanation
Indices: 453--1009 Score: 1073
Period size: 281 Copynumber: 2.0 Consensus size: 283
443 ATTCTCAATC
*
453 ATAATTTCAATCAAGATTGAACACAAGTTCTAGAAATAGATAATCATAGAAGCAATTAATAAATA
1 ATAATTTCAATCAAGATTGAACACAAGTTCTAGAAATAGATAATCATAAAAGCAATTAATAAATA
518 AGATCATATCACAAACTTCAATTATACCTAATTCTAAGAAATCAAACAACATGCTATAACTCAAT
66 AGATCATATCACAAACTTCAATTATACCTAATTCTAAGAAATCAAACAACATGCTATAACTCAAT
583 CAATAAATCAAACATTATTAAAATTCTAAGCATTCATCAATCATAATCAAATCAATTAATCAAAA
131 CAATAAATCAAACATTATTAAAATTCTAAGCATTCATCAATCATAATCAAATCAATTAATCAAAA
648 TATGCATGAAAAATTCAAAAGGTTTGAAAAATTCGAAA-TTTTATCATC-AAAATCAATTTTCGA
196 TATGCATGAAAAATTCAAAAGGTTTGAAAAATTCGAAATTTTTATCATCAAAAATCAATTTTCGA
711 AAATTTTGTCAAAAAAATGGAGA
261 AAATTTTGTCAAAAAAATGGAGA
734 ATAATTTCAATCAAGATTGAACACAAGTTCTAGAAATAGATAATCATAAAAGCAATTAATAAATA
1 ATAATTTCAATCAAGATTGAACACAAGTTCTAGAAATAGATAATCATAAAAGCAATTAATAAATA
799 AGATCATATCACAAACTTCAATTATACCTAATTCTAAGAAATCAAACAACATGCTATAACTCAAT
66 AGATCATATCACAAACTTCAATTATACCTAATTCTAAGAAATCAAACAACATGCTATAACTCAAT
864 CAATAAATCAAACATTATTAAAATTCTAAGCATTCATCAATCATAATCAAATCAATTAATCAAAA
131 CAATAAATCAAACATTATTAAAATTCTAAGCATTCATCAATCATAATCAAATCAATTAATCAAAA
*
929 TATGCATGAAAAATTCAAAAGGTTTGGAAAATTCGAAATTTTTATCATCAAAAAATCAATTTTCG
196 TATGCATGAAAAATTCAAAAGGTTTGAAAAATTCGAAATTTTTATCATC-AAAAATCAATTTTCG
994 AAAATTTTGTCAAAAA
260 AAAATTTTGTCAAAAA
1010 TTGGGGAAAA
Statistics
Matches: 271, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
281 231 0.85
282 10 0.04
284 30 0.11
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.29
Consensus pattern (283 bp):
ATAATTTCAATCAAGATTGAACACAAGTTCTAGAAATAGATAATCATAAAAGCAATTAATAAATA
AGATCATATCACAAACTTCAATTATACCTAATTCTAAGAAATCAAACAACATGCTATAACTCAAT
CAATAAATCAAACATTATTAAAATTCTAAGCATTCATCAATCATAATCAAATCAATTAATCAAAA
TATGCATGAAAAATTCAAAAGGTTTGAAAAATTCGAAATTTTTATCATCAAAAATCAATTTTCGA
AAATTTTGTCAAAAAAATGGAGA
Found at i:2345 original size:22 final size:22
Alignment explanation
Indices: 2320--2396 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
2310 TTGCCTTCTT
* *
2320 GTCGACACTTGCTTCTTCTTAA
1 GTCGACAATTGCTTCCTCTTAA
*
2342 GTCGATAATTGCTTCCTCTTAA
1 GTCGACAATTGCTTCCTCTTAA
* * **
2364 GTTGACTATTTTTTTCCTCTTTAA
1 GTCGAC-AATTGCTTCCTC-TTAA
2388 GTCGACAAT
1 GTCGACAAT
2397 CCCTTTGTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 23 0.53
23 11 0.26
24 9 0.21
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (22 bp):
GTCGACAATTGCTTCCTCTTAA
Done.