Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012827.1 Corchorus olitorius cultivar O-4 contig12860, 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: 4426
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Found at i:383 original size:200 final size:196
Alignment explanation
Indices: 1--602 Score: 918
Period size: 199 Copynumber: 3.0 Consensus size: 196
*
1 ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
1 ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACA
66 TACCCCCATTTCATAATTAATTAAATACATTTAATATTAATA-AGTATTCCTTAAGGGGACACAT
66 TA-CCCCATTTCATAA-TAATTAAAT--ATTTAATATTAATACA-TATTCCTT-AGGGGACACAT
*
130 ATCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTT
125 GTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAC-GTGTATTGTATAATTTTT
195 CTTATAGGG
189 CTTATA-GG
204 ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACA
1 ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACA
269 TACCCCATTTCATAATAAATTAAATATTTAATATTAATACATATTCCCTTAGGGGACACATGTCA
66 TACCCCATTTCATAAT-AATTAAATATTTAATATTAATACATATT-CCTTAGGGGACACATGTCA
* ** *
334 ACCCTTAAACCTCGCACGTGCAGTCTATTAAACTCCACTGACAGTGTATTGCATAATTTTTCTTA
129 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAC-GTGTATTGTATAATTTTTCTTA
399 TAGG
193 TAGG
* * * * *
403 ACTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCAGATTAAGAAGTTGACACA
1 ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACA
* *
468 TACCCCATTTCATAACTAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACATATGTCA
66 TACCCCATTTCATAA-TAATTAAATATTTAATATTAATACATA-TTCCTTAGGGGACACATGTCA
*
533 ACCCTTAAACCCCGCACGTGAAGTCTGCTAAACTCCACTGACGATGTATTGTAGTGTAATTTTTC
129 ACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACG-TGTATTGTA---TAATTTTTC
598 TTATA
190 TTATA
603 ATAAACTTAT
Statistics
Matches: 371, Mismatches: 19, Indels: 19
0.91 0.05 0.05
Matches are distributed among these distances:
198 1 0.00
199 166 0.45
200 97 0.26
201 6 0.02
202 35 0.09
203 66 0.18
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (196 bp):
ATTATTATGCAATACACTGTCGGTGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTGACACA
TACCCCATTTCATAATAATTAAATATTTAATATTAATACATATTCCTTAGGGGACACATGTCAAC
CCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGTGTATTGTATAATTTTTCTTATAG
G
Found at i:3068 original size:12 final size:13
Alignment explanation
Indices: 3053--3081 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3043 TGAAAACGAA
3053 AGAAGAAGAAG-G
1 AGAAGAAGAAGAG
3065 AGAAGAAGAAGAG
1 AGAAGAAGAAGAG
3078 AGAA
1 AGAA
3082 ACCAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAGAG
Done.