Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022554.1 Corchorus olitorius cultivar O-4 contig22587, 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: 6920
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Found at i:1295 original size:104 final size:105
Alignment explanation
Indices: 1130--1338 Score: 339
Period size: 104 Copynumber: 2.0 Consensus size: 105
1120 TAAAAAAATT
*
1130 TAATGACTAAAAAGAATATTAATTAAAAAGTTATTATAATATAATACTAAGAATATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAGTTATTATAATATAACACTAAGAATATTTTAGAAAT
* *
1195 TTCCCAATTAAGATTTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAAATTTTGAGTTCGTGATTTTATATAGTA
* * **
1235 TAATGACTAATAAGAATATTAATTAAAAA-TTATTATACTATAACACTAAGGGTATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAGTTATTATAATATAACACTAAGAATATTTTAGAAAT
*
1299 TTCCTAATTAAAAATTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAAATTTTGAGTTCGTGATTTTATATAGTA
1339 GTAAGATAGT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 68 0.71
105 28 0.29
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (105 bp):
TAATGACTAAAAAGAATATTAATTAAAAAGTTATTATAATATAACACTAAGAATATTTTAGAAAT
TTCCCAATTAAAAATTTTGAGTTCGTGATTTTATATAGTA
Found at i:1359 original size:2 final size:2
Alignment explanation
Indices: 1352--1381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1342 AGATAGTAAG
1352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1382 CTTACTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4591 original size:204 final size:201
Alignment explanation
Indices: 4211--4620 Score: 757
Period size: 204 Copynumber: 2.0 Consensus size: 201
4201 GCTTAATAAC
4211 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
4276 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACACTAGTGGTTG
*
4341 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
4406 CGATTTA
195 CGATTTA
4413 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
4478 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACACTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACACTAGTGGT
4543 TGATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
4608 CCGATTTA
194 CCGATTTA
4616 TTTAT
1 TTTAT
4621 TATTAAGGAA
Statistics
Matches: 202, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
202 90 0.45
203 19 0.09
204 93 0.46
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACACTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:4779 original size:39 final size:40
Alignment explanation
Indices: 4725--4805 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
4715 ATACCTAAGA
4725 ATTTAATTAATGTAAGTATTTCAGTT-TT-TATAGTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATA-TATTAC
*
4764 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
4804 AT
1 AT
4806 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 25 0.64
40 10 0.26
41 4 0.10
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.