Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023248.1 Corchorus olitorius cultivar O-4 contig23281, 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: 1819
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:354 original size:204 final size:204
Alignment explanation
Indices: 5--459 Score: 831
Period size: 204 Copynumber: 2.2 Consensus size: 204
1 GTTA
* *
5 GTAGTGAATAAGATACAACACA-TATTATTATATATATAAAACTATACAAAAAAAAAGTAGTTGA
1 GTAGTGAATAAGATACAACACATTACTATTATATATATAGAACTATACAAAAAAAAAGTAGTTGA
*
69 ACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAATAAAATTTCAAAATTATAAAA
66 ACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAA
134 GATATTAAAGATCCGATTTATTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACT
131 GATATTAAAGATCCGATTTATTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACT
199 AACAAAGTT
196 AACAAAGTT
* * *
208 GTAGTGAATAAGATATAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGA
1 GTAGTGAATAAGATACAACACATTACTATTATATATATAGAACTATACAAAAAAAAAGTAGTTGA
273 ACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAA
66 ACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAA
338 GATATTAAAGATCCGATTTATTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACT
131 GATATTAAAGATCCGATTTATTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACT
403 AACAAAGTT
196 AACAAAGTT
* *
412 GTGGTGAATAAGATACAACACATTACTATTATATATATAGAACAATAC
1 GTAGTGAATAAGATACAACACATTACTATTATATATATAGAACTATAC
460 GTCATGAATC
Statistics
Matches: 242, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
203 21 0.09
204 221 0.91
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (204 bp):
GTAGTGAATAAGATACAACACATTACTATTATATATATAGAACTATACAAAAAAAAAGTAGTTGA
ACATTAGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAA
GATATTAAAGATCCGATTTATTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACT
AACAAAGTT
Found at i:1281 original size:32 final size:32
Alignment explanation
Indices: 1240--1311 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1230 TTCAAAGAAC
* * **
1240 ATTTTGTCCTACTTTGTCAAAATTTGAGGGTT
1 ATTTTGTCCTACTATGTCAAAATTCGAGGACT
*
1272 ATTTTGTCCTTCTATGTCAAAATTCGAGGACT
1 ATTTTGTCCTACTATGTCAAAATTCGAGGACT
1304 ATTTTGTC
1 ATTTTGTC
1312 TATCAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (32 bp):
ATTTTGTCCTACTATGTCAAAATTCGAGGACT
Done.