Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011623.1 Corchorus olitorius cultivar O-4 contig11656, 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: 2015
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Found at i:350 original size:154 final size:154
Alignment explanation
Indices: 1--1197 Score: 1897
Period size: 154 Copynumber: 7.8 Consensus size: 154
* * **
1 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGTCACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* **
66 CCGATA-GCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATTGTGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
130 -AAATGATTATAGTTAGGCCATAA
131 AAAATGATTATAGTTAGGCCATAA
* * * * *
153 ACGATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* * *
218 ACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAATGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
283 AAAATGATTATAGTTAGGCCATAA
131 AAAATGATTATAGTTAGGCCATAA
* * ** *
307 ACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCCAAGACGATTCAAAACGTCACTAAAGGGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* ** *
372 CCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACAACACACTGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
437 AAAATGATTATAGTTAGG-CATAA
131 AAAATGATTATAGTTAGGCCATAA
* * *
460 ACAATAGAAAAAAAAACATTGAG-GATTGCC-AATCGAAGACGATTCAAAACGGAACTAATGGGC
1 ACAATGGAAAGAAAAGCATTGAGAG-TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
* *
523 CCCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAACCTCAC
65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
587 C-AAATGATTATAGTTAGGCCATAA
130 CAAAATGATTATAGTTAGGCCATAA
* * **
611 ACAATGGAACGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
676 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
741 AAAATGATTATAGTTAGGCCATAA
131 AAAATGATTATAGTTAGGCCATAA
* * *
765 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGTGCA
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* *
830 CCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
*
895 AAAATGATTATAATTAGGCCATAA
131 AAAATGATTATAGTTAGGCCATAA
* * **
919 ACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCCAAGACGATTCAAAACGTCACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
*
984 CCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
1049 AAAATGATTATAGTTAGGCCATAA
131 AAAATGATTATAGTTAGGCCATAA
* *
1073 ACAATGGAAA-AAAAACATTGAGCGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* *
1137 CCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCT
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1198 GATGCGCCAA
Statistics
Matches: 956, Mismatches: 81, Indels: 15
0.91 0.08 0.01
Matches are distributed among these distances:
150 17 0.02
151 52 0.05
152 196 0.21
153 216 0.23
154 475 0.50
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (154 bp):
ACAATGGAAAGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAAATGATTATAGTTAGGCCATAA
Found at i:893 original size:458 final size:460
Alignment explanation
Indices: 1--1197 Score: 1936
Period size: 458 Copynumber: 2.6 Consensus size: 460
* *
1 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACGTCACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
* **
66 CCGATA-GCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATTGTGGACTAATCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
* * *
130 AAATGATTATAGTTAGGCCATAAACGATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAAACG
131 AAATGATTATAGTTAGGCCATAAACAATGG-AAAAAAAGCATTGAGAGTTGCCAAATCGAAGACG
* *
195 ATTCAAAACGGAACTAATGAGCCACGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
195 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* *
260 CTTCAAAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
260 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* ** *
325 TTGAGATTTGCCAAATCCAAGACGATTCAAAACGTCACTAAAGGGCCCCGATAGACCCAAAATAA
325 TTGAGAGTTGCCAAATCCAAGACGATTCAAAACGGAACTAAAGGGCACCGATAGACCCAAAATAA
* *
390 CAAGTGTTCCAAATGAGCTAAAAACAACACACTGGACTAATCTCACCAAAATGATTATAGTTAGG
390 CAAGTGTTCCAAATGAGCTAAAAACAACACAATGGACTAATCTCACCAAAATGATTATAATTAGG
455 -CATAA
455 CCATAA
* * * **
460 ACAATAGAAAAAAAAACATTGAGGATTGCC-AATCGAAGACGATTCAAAACGGAACTAATGGGCC
1 ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
* *
524 CCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAACCTCACC
66 CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
* *
588 AAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGATTTGCCAAATCGAAGACG
131 AAATGATTATAGTTAGGCCATAAACAATGGAA-AAAAAGCATTGAGAGTTGCCAAATCGAAGACG
**
653 ATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
195 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
718 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
260 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * * * *
783 TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGTGCACCTATAGGCCCAAAATAA
325 TTGAGAGTTGCCAAATCCAAGACGATTCAAAACGGAACTAAAGGGCACCGATAGACCCAAAATAA
**
848 CAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAATTAGG
390 CAAGTGTTCCAAATGAGCTAAAAACAACACAATGGACTAATCTCACCAAAATGATTATAATTAGG
913 CCATAA
455 CCATAA
*
919 ACAATGGAAAGAAAAGCATTGA-GATTTGCCAAATCCAAGACGATTCAAAACGTCACTAATGGGC
1 ACAATGGAAAGAAAAGCATTGAGGA-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
*
983 CCCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
65 CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAC
* *
1048 CAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAACATTGAGCGTTGCCAAATCGAAGAC
130 C-AAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAGCATTGAGAGTTGCCAAATCGAAGAC
*
1113 GATTCAAAACGGAACTAATGGGCCCCTATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
194 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
1178 ACTTCACAGTGGACAAATCT
259 ACTTCACAGTGGACTAATCT
1198 GATGCGCCAA
Statistics
Matches: 677, Mismatches: 54, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
457 2 0.00
458 359 0.53
459 84 0.12
460 66 0.10
461 134 0.20
462 32 0.05
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (460 bp):
ACAATGGAAAGAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAGCATTGAGAGTTGCCAAATCGAAGACGA
TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGAGAGTTGCCAAATCCAAGACGATTCAAAACGGAACTAAAGGGCACCGATAGACCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACAACACAATGGACTAATCTCACCAAAATGATTATAATTAGGC
CATAA
Done.