Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022100.1 Corchorus olitorius cultivar O-4 contig22133, 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: 2854
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Found at i:974 original size:36 final size:36
Alignment explanation
Indices: 927--996 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
917 TTCAATAATC
* *
927 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
963 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
997 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1852 original size:205 final size:201
Alignment explanation
Indices: 1485--1895 Score: 725
Period size: 205 Copynumber: 2.0 Consensus size: 201
1475 GCTTAATAAC
* *
1485 TTTATCAATGGTGAATGTTATTAACTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAACTTTTTAAGTCTAAAATTACTAACAAAGTTATAGTGAATAA
*
1550 GATACAACACATAATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATAACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
1615 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
1680 CGATTTA
195 CGATTTA
1687 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAAATTACTAACAAAGTTATAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAACTTTTTAAGTCTAAAATTACTAACAAAGTTATAGTGAATAA
* *
1751 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAAATTAGTTGAACATTAGTG
66 GATACAACACATAACTATTATATATA-A-AACTATACC--AAAAAAAAGTAGTTGAACATTAGTG
1816 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
127 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
1881 ATCCGATTTA
192 ATCCGATTTA
1891 TTTAT
1 TTTAT
1896 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
201 62 0.31
202 25 0.12
203 9 0.05
204 18 0.09
205 86 0.43
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAACTTTTTAAGTCTAAAATTACTAACAAAGTTATAGTGAATAA
GATACAACACATAACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Done.