Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010709.1 Corchorus olitorius cultivar O-4 contig10741, 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: 3743
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:3291 original size:154 final size:153
Alignment explanation
Indices: 3011--3743 Score: 1033
Period size: 154 Copynumber: 4.8 Consensus size: 153
3001 ATCACGAAGG
* *
3011 TCTCACCAAAATGATTATAGTTAGTCCATAAACAACGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
* *
3076 CGATGTCGAATCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
66 CGAAGTCGATTCAAAACGGATCTAATGGG-CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
*
3141 GCTAAAAACATCACGGTGGACATA
130 GCTAAAAACATCACAGTGGACATA
* * *
3165 TCTCACCAGAATGATTATAGTTAGTCCATAAACAATGGAAAGATAAGCTTTGAGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
* * * * * *
3230 CGAAATCGATTCAAAATGGATCTAATAGGCCTCGAAAGGCCCAAAATTACAATTTTTCCAAATGA
66 CGAAGTCGATTCAAAACGGATCTAATGGGCC-CGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
* *
3295 ACTAAAAACTTCACAGTGGACATA
130 GCTAAAAACATCACAGTGGACATA
* *
3319 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA-AAATAGATTTGTGGTTTGCCAAA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA-AGCTTTGAGGTTTGCCAAA
* * * * * *
3383 TCAAAATCGATTCAAAACGGAACTAAAGGGACCCGAAATGCCCAAAATAACAAGTGTTCCAAATA
65 TCGAAGTCGATTCAAAACGGATCTAATGGG-CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
*
3448 AGCTAAAAACTTCACAGTGGACATA
129 AGCTAAAAACATCACAGTGGACATA
* * *
3473 TCTCACCAAAATGATTATAGTTCGGCCATAAACATTGGGAAA-AAAAGTTTTAGAGGTTTG-CAA
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGAAAAGCTTT-GAGGTTTGCCAA
* * * *
3536 ATACGATGTCGATTCAAAATGGAACTAATGGGCCCGAAAGGACCAAAATAACAAGTGTTCCAAAT
64 AT-CGAAGTCGATTCAAAACGGATCTAATGGGCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
* *
3601 GAGTTAAAAACATAACAGTGGACATA
128 GAGCTAAAAACATCACAGTGGACATA
* *
3627 TCTCACCAAAATGATTATAGTTAGGCAATAAACAATAGAAAGAAAAGCTTTGAGGTTTGCCAAAT
1 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
3692 CGAAGTCGATTCAAAACGGAAT-TAATGGGCCCCGAAAGGCCCAAAATAACAA
66 CGAAGTCGATTCAAAACGG-ATCTAATGGG-CCCGAAAGGCCCAAAATAACAA
Statistics
Matches: 515, Mismatches: 54, Indels: 20
0.87 0.09 0.03
Matches are distributed among these distances:
153 40 0.08
154 434 0.84
155 41 0.08
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (153 bp):
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
CGAAGTCGATTCAAAACGGATCTAATGGGCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
CTAAAAACATCACAGTGGACATA
Done.