Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013828.1 Corchorus olitorius cultivar O-4 contig13861, 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: 2581
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Found at i:2312 original size:154 final size:154
Alignment explanation
Indices: 2032--2578 Score: 800
Period size: 154 Copynumber: 3.6 Consensus size: 154
2022 ATTCTCCCCC
*
2032 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGAATTGACAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGAATTGCCAA
* ** * * *
2097 ATTGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAATT
66 ATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
2162 GAGCTAAAAACTTCACAATGGACT
131 GAGCTAAAAACTTCACAATGGACT
* * * * *
2186 AATCTCACCAAAGTGATTATAGTTAGGCAATAAACAATGGAAAGAAAGGAATTGAGG-TTTGCCA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-GGAATTGCCA
2250 AATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
65 AATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
*
2315 TGTGCTAAAAACTTACACAGA-GGACT
130 TGAGCTAAAAACTT-CACA-ATGGACT
* * *
2341 AATCTCACCTAAATGATTATAGTTAGGCCGTAAAGAATGG-AAGAAAAGCATTGGGAATTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGAATTGCCAA
* * *
2405 ATCGAAGACGATTCAAAACATCACTAATGGTCCCCGATAGGCCTAAAATATA-AAGTGTTCCAAA
66 ATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATA-ACAAGTGTTCCAAA
*
2469 TGAGCTAAAAACTTCACAGTGGACT
130 TGAGCTAAAAACTTCACAATGGACT
*
2494 AATCTCACCAAAATGATTATA-TTCAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCC
1 AATCTCACCAAAATGATTATAGTT-AGGCCATAAACAATGGAAAGAAAAGCATTG-GGAATTGCC
*
2557 AAATCGAAGACAATTCAAAACG
64 AAATCGAAGACGATTCAAAACG
2579 GAA
Statistics
Matches: 352, Mismatches: 32, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
152 2 0.01
153 45 0.13
154 255 0.72
155 49 0.14
156 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGAATTGCCAA
ATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAATGGACT
Done.