Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016024.1 Corchorus olitorius cultivar O-4 contig16057, 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, 964
Length: 1608
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Found at i:433 original size:154 final size:154
Alignment explanation
Indices: 1--1603 Score: 2411
Period size: 154 Copynumber: 10.5 Consensus size: 154
* * * * * *
1 TAACATGTGTTCCAAATGAGCTGAAATCTTTACAGTGGACTAATCTTACCAAAATGATTATAATT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
66 AGTCCA-CAACAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGAGGATTCAATATGTCA
66 AGTCCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCA
*
130 CAAATGGGCCCCGATAGGCCCAAAA
130 CTAATGGGCCCCGATAGGCCCAAAA
* **
155 TAACAAGTGTTCCAAACGAGCTAAAAACTTCATGGTGGACTAATCTCACC-AAATG-----A-TT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
213 AGTCCCTAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAGTCGAAGACGATTCAAAACGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
* *
278 TAATGGGCCTCGATAGGCCCCAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
302 TAATAAGTGTTCCAAATGAGCGAAAAACTTCACAGTGGACTAGTCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
367 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
432 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
456 TAACAAGTGTTCCAAACGAGTTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
521 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTTAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
586 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
*
610 TAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
675 AGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAGGATTCAAAATGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
*
740 TAATGGGCCTCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
*
764 TAAC-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATGTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
828 AGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACTATTCAAAACGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
*
893 TAATGGGACCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* *
917 TAACAAGTGTTGCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
982 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
*
1047 TAATGGGCCTCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * * *
1071 TAACATGTGTTCCAAACGAGCTAAAAACTTCACGGTGGACTAATCTTACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* **
1136 AGTGCC-T-AACTAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
66 AGT-CCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTC
* *
1199 ACTAATGGGGCCCGAAAGGCCCAAAA
129 ACTAATGGGCCCCGATAGGCCCAAAA
* * *
1225 TAACTAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCGAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
1290 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGGCGATTCAAAACAG-AA
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-TGTCA
1354 CTAATGGGCCCCGATAGGCCCAAAA
130 CTAATGGGCCCCGATAGGCCCAAAA
* * *
1379 TAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTACAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
1444 AGTCCACAAACAATGGAATGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCGAAACGTCAC
66 AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
** * *
1509 TAATGGGCCATGATAGGCCCCAAG
131 TAATGGGCCCCGATAGGCCCAAAA
* * * *
1533 TAATAAGTGTTCCAAATGAACTAAAAACTTTATAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1598 AGTCCA
66 AGTCCA
1604 CAAGA
Statistics
Matches: 1317, Mismatches: 117, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
147 120 0.09
148 9 0.01
153 159 0.12
154 1023 0.78
155 6 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (154 bp):
TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAC
TAATGGGCCCCGATAGGCCCAAAA
Found at i:1171 original size:615 final size:615
Alignment explanation
Indices: 7--1603 Score: 2556
Period size: 615 Copynumber: 2.6 Consensus size: 615
1 TAACAT
* * * * *
7 GTGTTCCAAATGAGCTGAAATCTTTACAGTGGACTAATCTTACCAAAATGATTATAATTAGTCCA
1 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
* * * *
72 -CAACAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGAGGATTCAATATGTCACAAATG
66 TAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAAAATGTCACTAATG
**
136 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCATGGTGGACTAATCT
130 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
201 CACC-AAATG----A-TTAGTCCCTAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAGTCGAA
195 CACCAAAATGATTAAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
* *
260 GACGATTCAAAACGTCACTAATGGGCCTCGATAGGCCCCAAATAATAAGTGTTCCAAATGAGCGA
260 GACGATTCAAAACGTCACTAATGGGCCACGATAGGCCCCAAATAATAAGTGTTCCAAATGAGCTA
*
325 AAAACTTCACAGTGGACTAGTCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAA
325 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAA
390 AGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAA
390 AGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAA
*
455 ATAACAAGTGTTCCAAACGAGTTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGT
455 ATAACAAGTGTTCCAAACGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGT
* * **
520 TAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTTA
520 TAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
*
585 CTAATGGGCCCCGATAGGCCCAAAATAA-TAA
585 CTAATGGGCCCCGAAAGGCCCAAAATAACT-A
616 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
1 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
*
681 TAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAGGATTCAAAATGTCACTAATGG
66 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAAAATGTCACTAATGG
* * *
746 GCCTCGATAGGCCCAAAATAAC-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATGTC
131 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTC
*
810 ACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAA
196 ACCAAAATGATTA-AGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAA
* * * *
875 GACTATTCAAAACGTCACTAATGGGACC-CGATAGGCCCAAAATAACAAGTGTTGCAAATGAGCT
260 GACGATTCAAAACGTCACTAATGGG-CCACGATAGGCCCCAAATAATAAGTGTTCCAAATGAGCT
*
939 AAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
324 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAA
*
1004 AAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCTCGATAGGCCCAA
389 AAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAA
* *
1069 AATAACATGTGTTCCAAACGAGCTAAAAACTTCACGGTGGACTAATCTTACCAAAATGATTATAG
454 AATAACAAGTGTTCCAAACGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAG
1134 TTAGTGCC-T-AACTAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
519 TTAGT-CCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
*
1197 GAACTAATGGGGCCCGAAAGGCCCAAAATAACTA
582 GAACTAATGGGCCCCGAAAGGCCCAAAATAACTA
* * *
1231 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCATCGAAATGATTATAGTTAGGCCA
1 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
* *
1296 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG-GCGATTCAAAACAG-AACTAAT
66 TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAG-GATTCAAAA-TGTCACTAAT
*
1359 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGTACTAATC
129 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATC
* *
1424 TCACCAAAATGATTACAGTTAGTCCACAAACAATGGAATGAAAAGCATTGAGGTTTGCCAAATCG
194 TCACCAAAATGATTA-AGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * *
1489 AAGACGATTCGAAACGTCACTAATGGGCCATGATAGGCCCCAAGTAATAAGTGTTCCAAATGAAC
258 AAGACGATTCAAAACGTCACTAATGGGCCACGATAGGCCCCAAATAATAAGTGTTCCAAATGAGC
* *
1554 TAAAAACTTTATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
323 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
1604 CAAGA
Statistics
Matches: 912, Mismatches: 60, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
608 41 0.04
609 142 0.16
610 3 0.00
614 5 0.01
615 516 0.57
616 205 0.22
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (615 bp):
GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCA
TAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAAAATGTCACTAATGG
GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTAAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGTCACTAATGGGCCACGATAGGCCCCAAATAATAAGTGTTCCAAATGAGCTAA
AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAA
GCATTGAGGTTTGCCAAATCGAAGAGGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAA
TAACAAGTGTTCCAAACGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTT
AGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAAC
TAATGGGCCCCGAAAGGCCCAAAATAACTA
Done.