Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012585.1 Corchorus olitorius cultivar O-4 contig12618, 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: 12095
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3422 original size:23 final size:23
Alignment explanation
Indices: 3379--3422 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3369 AGTTTTTTTT
*
3379 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
3402 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
3423 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:10051 original size:25 final size:27
Alignment explanation
Indices: 10000--10065 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
9990 AAAAGTACAC
*
10000 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGG-ATAATTT
*
10028 AAAATATTTTTTAATAATGG-TAATTT
1 AAAATATATTTTAATAATGGATAATTT
10054 AGAAATATATTT
1 A-AAATATATTT
10066 GGAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 23 0.70
28 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGATAATTT
Found at i:11053 original size:351 final size:351
Alignment explanation
Indices: 10410--11098 Score: 1017
Period size: 351 Copynumber: 2.0 Consensus size: 351
10400 TCTAAGTCAG
* * * **
10410 ATGTCTTGAAGTCTAAATCTAATATTCATAGATCCAATTTGTTAATATGGAAGCCCAAAGAAGGA
1 ATGTCTTAAAATCTAAATCTAATATTCATAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGA
* * * *
10475 GTTCAAGACTAATCAGTTATTATGATGCAGTAATGATTCAACTCTGATGGAACATTGTTAAAACA
66 GTTCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAACTCTGATGCAACATTATTAAAACA
* *
10540 TATTCAAATGAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTC
131 TATTCAAAAGAGGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTC
10605 AGAAAAATGCAAATGAGATACAGTTGGAAAGGAAATTCCAAGATCTACAACTTTTATGTTTACCT
196 AGAAAAATGCAAATGAGATACAGTTGGAAAGGAAATTCCAAGATCTACAACTTTTATGTTTACCT
* * * ** ** *
10670 TAAGACTTAATTCTGCAGTTTCGGTGGATGATTTTGCCCTTGAAGTTTCTAGATAGAATTGATCT
261 CAAGACCTAATTCTACAGTTTCAATGGATGATTTTGCCCTTGAAAATTCTAGACAGAATTGATCT
10735 TCTCCTAAACCGATTTGGAGAGCCAA
326 TCTCCTAAACCGATTTGGAGAGCCAA
* * *
10761 ATGTCTTAAAATCTAAATCTGATATTCTTAGACCCAATTCATTAATATGGAAGCCTAAAGAAGGA
1 ATGTCTTAAAATCTAAATCTAATATTCATAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGA
* * *
10826 G-TCTAAGTCCAATCAGTAATTATGATGCAGTAATGATTC-AGTCCTGATGCAACATTATTAAAT
66 GTTC-AAGACCAATCAGTAATTATGATGCAGTAATGATTCAACT-CTGATGCAACATTATTAAAA
* * *
10889 CCTATTCAAAAGAGGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAATTTTTTATCTAGAGC
129 CATATTCAAAAGAGGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTAGAGC
* *
10954 TCAGAAAAATGCAAATGAGATACCGTTGGAAA-GAGGATTCCAAGATCTACAACTTTTATGTTTA
194 TCAGAAAAATGCAAATGAGATACAGTTGGAAAGGA-AATTCCAAGATCTACAACTTTTATGTTTA
* * *
11018 TCTCGAGACCTAATTCTACAG-TTCTAATGGATGATTTTGCCCTTGAAAATTCTGGACAGAATTG
258 CCTCAAGACCTAATTCTACAGTTTC-AATGGATGATTTTGCCCTTGAAAATTCTAGACAGAATTG
11082 ATCTTCTCCTAAACCGA
322 ATCTTCTCCTAAACCGA
11099 CTGGGAGAAT
Statistics
Matches: 301, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
350 9 0.03
351 292 0.97
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (351 bp):
ATGTCTTAAAATCTAAATCTAATATTCATAGACCCAATTCATTAATATGGAAGCCCAAAGAAGGA
GTTCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAACTCTGATGCAACATTATTAAAACA
TATTCAAAAGAGGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTAGAGCTC
AGAAAAATGCAAATGAGATACAGTTGGAAAGGAAATTCCAAGATCTACAACTTTTATGTTTACCT
CAAGACCTAATTCTACAGTTTCAATGGATGATTTTGCCCTTGAAAATTCTAGACAGAATTGATCT
TCTCCTAAACCGATTTGGAGAGCCAA
Done.