Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011802.1 Corchorus olitorius cultivar O-4 contig11835, 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, 909
Length: 1516
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1516 Score: 2309
Period size: 154 Copynumber: 9.9 Consensus size: 154
* * *
1 AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTACA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * *
66 CTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCACATCGAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
131 AACTAATGGGCCCCGATAGGCCCA
131 AACTAATGGGCCCCGATAGGCCCA
*
155 AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
220 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
285 AACTAATGGGCCCCGATAGGCCCA
131 AACTAATGGGCCCCGATAGGCCCA
309 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTAT
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTAT
* * *
373 AGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACG
65 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
*
438 GTACTAATGGGCCCCG-TAAGGCCCA
130 GAACTAATGGGCCCCGAT-AGGCCCA
* * * * *
463 AAATTACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAC--ATGTCTCTAAAATTTGATTA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA--TGATTA
*
526 TAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
64 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
** *
591 GTCACTAATGGGCCCGGATAGGCCCA
129 GGAACTAATGGGCCCCGATAGGCCCA
* *
617 AAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * *
682 GTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAACG
66 GTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
** *
746 TCACTAATGGGCCCAGATAGGCCC-
130 GAACTAATGGGCCCCGATAGGCCCA
770 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACCA--GGACTAATCTCACCAAAATGATTAT
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA-CAGTGGACTAATCTCACCAAAATGATTAT
* *
833 AGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTTGGCAAATCGAAGACGATTCAAAAC
65 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAAC
898 GGAACTAATGGGCCCCGATAGGCCCA
129 GGAACTAATGGGCCCCGATAGGCCCA
* * * * *
924 AAATAAGAAGTGTTACCAAATGAGACT-AAAACTTCACAATGCACTAATCTCATC-AAATGATTG
1 AAATAACAAGTGTT-CCAAATGAG-CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * * *
987 TAGTTAGTCCATAAACAATGGAAAG-AAAGCATTGAGGTTTGCCAAATCGAAGACGAATCAATAT
64 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
** *
1051 GTCACAAATGGGCCCCGATAGGCCCA
129 GGAACTAATGGGCCCCGATAGGCCCA
* * *
1077 AAATAACAAGTGTTCCAAACGAGCT-AAAACTTCACAGTTGACTAATCTCACCAAAATGATTACA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* *
1141 GTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
1206 AACTAATGGGCCCCGATAGGCCCA
131 AACTAATGGGCCCCGATAGGCCCA
* * *
1230 AAATAACAAGTGTTTCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTCTA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
** *
1295 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGGTAAATCGAAAACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
1360 AACTAATGGGCCCCGATAGGCCCA
131 AACTAATGGGCCCCGATAGGCCCA
* * * * *
1384 AAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAATGCACTAATCTCATCAAAATGATTGTA
1 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * *
1449 GTTAGTCCATAAACAATGGACAGAAAAGCATTGAGGTTTGCCAAATCTAAGACGATTCAAAACGG
66 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
1514 AAC
131 AAC
Statistics
Matches: 1254, Mismatches: 89, Indels: 38
0.91 0.06 0.03
Matches are distributed among these distances:
151 26 0.02
152 104 0.08
153 225 0.18
154 824 0.66
155 53 0.04
156 22 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
AACTAATGGGCCCCGATAGGCCCA
Found at i:1477 original size:767 final size:767
Alignment explanation
Indices: 1--1512 Score: 2376
Period size: 767 Copynumber: 2.0 Consensus size: 767
1 AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTACA
1 AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAG-TGACTAATCTCACCAAAATGATTACA
* *
66 CTTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCACATCGAAGACGATTCAAAACGG
65 CTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
* *
131 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGG
130 AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAATGC
196 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
195 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
261 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
260 CAAATCGAAGACGAATCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
326 AATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
325 AACGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTACAGTTAGGCCATAAACAAT
* * * *
391 GGATAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGTACTAATGGGCCCCGTA
390 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGTA
* * * * * *
456 AGGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGACATGTCTCTAAAATTT
455 AGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACATCTCACCAAAA-TT
* *
521 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTC
519 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTC
** * *
586 AAAACGTCACTAATGGGCCCGGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTC
584 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* * * *
651 ACAGTGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACTTAAAGAAAAGCTTTGA
649 ACAATGCACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACTGAAAGAAAAGCATTGA
716 GGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCC
714 GGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCC
* *
770 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACCAG-GACTAATCTCACCAAAATGATTATA
1 AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCA-CAGTGACTAATCTCACCAAAATGATTACA
* *
834 GTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTTGGCAAATCGAAGACGATTCAAAACG
65 CTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACG
* *
899 GAACTAATGGGCCCCGATAGGCCCAAAATAAGAAGTGTTACCAAATGAGACT-AAAACTTCACAA
129 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT-CCAAACGAG-CTAAAAACTTCACAA
* * *
963 TGCACTAATCTCATC-AAATGATTGTAGTTAGTCCATAAACAATGGAAAG-AAAGCATTGAGGTT
192 TGCACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
* * **
1026 TGCCAAATCGAAGACGAATCAATATGTCACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
257 TGCCAAATCGAAGACGAATCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* *
1091 CCAAACGAGCT-AAAACTTCACAGTTGAC-TAATCTCACCAAAATGATTACAGTTAGTCCATAAA
322 CCAAACGAGCTAAAAACTTCACAGTGGACAT-ATCTCACCAAAATGATTACAGTTAGGCCATAAA
*
1154 TAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
386 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
*
1219 CG-ATAGGCCCAAAATAACAAGTGTTTCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACC
451 CGTA-AGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGAC--ATCTCACC
* **
1283 AAAA-TGATTCTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGGTAAATCGAAAA
513 AAAATTGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAA
*
1347 CGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAA
578 CGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * *
1412 AACTTCACAATGCACTAATCTCATCAAAATGATTGTAGTTAGTCCATAAACAA-TGGACAGAAAA
643 AACTTCACAATGCACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-GAAAGAAAA
* *
1476 GCATTGAGGTTTGCCAAATCTAAGACGATTCAAAACG
707 GCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACG
1513 GAAC
Statistics
Matches: 680, Mismatches: 54, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
766 3 0.00
767 360 0.53
768 141 0.21
769 139 0.20
770 35 0.05
771 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (767 bp):
AAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGACTAATCTCACCAAAATGATTACAC
TTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAATGCA
CTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
AAATCGAAGACGAATCAAAACGGAACAAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ACGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTACAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGTAA
GGCCCAAAATAACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACATCTCACCAAAATTGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAA
AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AATGCACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACTGAAAGAAAAGCATTGAGG
TTTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCCC
Done.