Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007219.1 Corchorus olitorius cultivar O-4 contig07244, 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: 2271
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1291 original size:36 final size:35
Alignment explanation
Indices: 1244--1312 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
1234 TTCAATAACC
* *
1244 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATC-TATTTCTTA
*
1280 TTACATTTTTTGTAATTTTGATTATCTATTTCT
1 TTACATCTTTTGTAATTTTGATTATCTATTTCT
1313 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 7 0.23
36 23 0.77
ACGTcount: A:0.20, C:0.10, G:0.09, T:0.61
Consensus pattern (35 bp):
TTACATCTTTTGTAATTTTGATTATCTATTTCTTA
Found at i:2222 original size:202 final size:202
Alignment explanation
Indices: 1825--2233 Score: 732
Period size: 202 Copynumber: 2.0 Consensus size: 202
1815 GCTTAATAAC
* *
1825 TTTATCAATGGTGAATGATATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATCGTGAATGATATAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1890 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
*
1955 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATCAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATCAAAGATC
2020 CGATTTA
196 CGATTTA
* *
2027 TTTATCAATCGTGAATGTTATAAATTTTTTAAGTGTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATCGTGAATGATATAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
2092 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTA-T-TATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
*
2157 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTC-AAATTATAAAAGACAT-TAAGA
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATCAAAGA
2220 TCCGATTTA
194 TCCGATTTA
2229 TTTAT
1 TTTAT
2234 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
202 96 0.48
203 16 0.08
204 87 0.44
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (202 bp):
TTTATCAATCGTGAATGATATAAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATCAAAGATC
CGATTTA
Done.