Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007498.1 Corchorus olitorius cultivar O-4 contig07523, 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, 642
Length: 1071
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Found at i:705 original size:324 final size:325
Alignment explanation
Indices: 100--747 Score: 1018
Period size: 324 Copynumber: 2.0 Consensus size: 325
90 TTATCCATGA
*
100 CTTGTCTTCAATTAAAGCTCCAATCTTCAATCCTTGCTTCTTGAAATAAATCTTCAATGGTCTTC
1 CTTGTCTTCAATTAAAGCTCCAATCTTCAATCCTTGCCTCTTGAAATAAATCTTCAATGGTCTTC
165 AAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCAA
66 AAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCAA
* * *
230 AATTGCTTTGCTAAAATCTGTGTAAAAAGTCATAAAAATAGCTCCAAAAGTAGTGAAAATTATCA
131 AATTGCTTTGCTAAAATCTGTGTAAAAAGTCATAAAAATAGCTACAAAAGTAGTGAAAAATAACA
* * * *
295 AATTATCAATTTCACATCTCATAAAGACTCAAATCACAAATATTAACAAAATAACATATATTTAA
196 AATTATCAATTTCACATCACATAAAGACTAAAAACACAAATATTAACAAAATAACATATAATTAA
* * *
360 GCATAAATTGATCCTAAAACATAATAAAATAGCCATAAAAATAGGGT-TGTTTTTGGCTCGATCA
261 GCATAAATGGATCCTAAAACATAATAAAATAGCCATAAAAATAGGGTCT-TTTTTAGCTCAATCA
424 G
325 G
*
425 CTTGTCTTCAA-TAAAGCTCCAATTCTTCAATTCTT-CCTCTTGAAATAAATCTTCAATGGTCTT
1 CTTGTCTTCAATTAAAGCTCCAA-TCTTCAATCCTTGCCTCTTGAAATAAATCTTCAATGGTCTT
488 CAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCA
65 CAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCA
* *
553 AAATTGCTTTGCTCAAATCTGTGTAAAAAGTCATCAAAATAGCTACAGAAA-TAGTGAAAAATAA
130 AAATTGCTTTGCTAAAATCTGTGTAAAAAGTCATAAAAATAGCTACA-AAAGTAGTGAAAAATAA
* * * * * *
617 CAATTTCTCATTTTCACATCACTTAAAGACTAAAAACACAAATATTAATAAAATATCATATAATT
194 CAAATTATCAATTTCACATCACATAAAGACTAAAAACACAAATATTAACAAAATAACATATAATT
* * *
682 AAGCATAAATGGGT-CTAAAAACATAGTAAAATAGGCATAAAAATAGGGTCTTTTTTAGCTCAAT
259 AAGCATAAATGGATCCT-AAAACATAATAAAATAGCCATAAAAATAGGGTCTTTTTTAGCTCAAT
746 CA
323 CA
748 TATTTTCCCC
Statistics
Matches: 296, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
323 2 0.01
324 268 0.91
325 26 0.09
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (325 bp):
CTTGTCTTCAATTAAAGCTCCAATCTTCAATCCTTGCCTCTTGAAATAAATCTTCAATGGTCTTC
AAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCAA
AATTGCTTTGCTAAAATCTGTGTAAAAAGTCATAAAAATAGCTACAAAAGTAGTGAAAAATAACA
AATTATCAATTTCACATCACATAAAGACTAAAAACACAAATATTAACAAAATAACATATAATTAA
GCATAAATGGATCCTAAAACATAATAAAATAGCCATAAAAATAGGGTCTTTTTTAGCTCAATCAG
Done.