Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009797.1 Corchorus olitorius cultivar O-4 contig09829, 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: 1681
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Found at i:797 original size:75 final size:75
Alignment explanation
Indices: 671--822 Score: 225
Period size: 75 Copynumber: 2.0 Consensus size: 75
661 TTATCTGGAC
* * *
671 TGTGAGCAAAGGAATTGTGAGTTTTGATTAAAAGATGTTTCAAAATAAGTTTTAATCAAAGCAAT
1 TGTGAGCAAAGGAATAGTGAGTTTTAATCAAAAGATGTTTCAAAATAAGTTTTAATCAAAGCAAT
* *
736 GGTTTCGAGG
66 GATTTCAAGG
* *
746 TGTGAGCAAAGGAA-AGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAA
1 TGTGAGCAAAGGAATAG-TGAGTTTTAATCAAAAGATGTTTCAAAATAAGTTTTAATCAAAGCAA
810 TGATTTCAAGG
65 TGATTTCAAGG
821 TG
1 TG
823 ATTGAATCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 1 0.01
75 68 0.99
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (75 bp):
TGTGAGCAAAGGAATAGTGAGTTTTAATCAAAAGATGTTTCAAAATAAGTTTTAATCAAAGCAAT
GATTTCAAGG
Found at i:1253 original size:16 final size:16
Alignment explanation
Indices: 1210--1262 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1200 ATTCCCCGAT
1210 AAAAAAAG-AAAAA-A
1 AAAAAAAGTAAAAAGA
* *
1224 AAAGAGAG-AAAAAGA
1 AAAAAAAGTAAAAAGA
*
1239 GAAAAAAGTAAAAAGA
1 AAAAAAAGTAAAAAGA
1255 AAAAAAAG
1 AAAAAAAG
1263 AGCACTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 14 0.45
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAAAGTAAAAAGA
Done.