Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008840.1 Corchorus olitorius cultivar O-4 contig08867, 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, 744
Length: 1240
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Found at i:409 original size:154 final size:151
Alignment explanation
Indices: 1--1240 Score: 1780
Period size: 154 Copynumber: 8.1 Consensus size: 151
*
1 AAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
**
66 GATTCAAAACGGAACTAATGGTTCCCGAAAGG-CCACAAATAACAA--GTTCCAAATGAGCTAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCA-AAATAACAAGTGTTCCAAATGAGCTAAA
*
128 AACTTTACAGTGGACTAATCTCACC
127 AACTTCACAGTGGACTAATCTCACC
* *
153 AAAATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGCAGCGAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
* *
218 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCACAAAATAACAAGTGTTCCAAATTAGCTAAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
283 ACTTCACAGTGGACTAATCTCACT
128 ACTTCACAGTGGACTAATCTCACC
**
307 AAAATGATTATAGTTAGGCCATAAACAAT-G-GAAAA-ATC-A-TTTTGCCAAATCGAAGACGAT
1 AAAATGATTATAGTTAGGCCATAAACAATGGAGAAAACATCGAGGGTTGCCAAATCGAAGACGAT
** * * *
367 TCAAAACGTCACTAATGGGCCCTGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACT
66 TCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
*
432 TTACAGTGGACTAATCTCACC
131 TCACAGTGGACTAATCTCACC
*
453 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCTAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
** * *
518 GATTCAAAACGGAACTAATGGTTCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAACTAAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
583 ACTTCACAGTGGACTAATCTCACA
128 ACTTCACAGTGGACTAATCTCACC
* * *
607 AAAATGATTATAGTTAGGCTATAAACAATGGATAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
** * * *
672 GATTCAAAACGTCACTAATGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
737 ACTTTACAGTGGACTAATCTCACC
128 ACTTCACAGTGGACTAATCTCACC
*
761 AAAATGATTACAGTTAGGCCATAAACAATGGTAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
* * *
826 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGATACAAATGAGCTAAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* *
891 ACTTCACAATGGACTAATCTCACG
128 ACTTCACAGTGGACTAATCTCACC
* * *
915 AAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATGGAATAC
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAAGAC
* *
980 GATTCAAAACGGAACTAATGGGCCCCGAACGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAA
63 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
1045 ACTTCACAGTGGACTAATCTCACC
128 ACTTCACAGTGGACTAATCTCACC
*
1069 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCAAGGGTTGCCAAATC-AATGA
1 AAAATGATTATAGTTAGGCCATAAACAATGG--AGAAAA-CATCGAGGGTTGCCAAATCGAA-GA
*
1133 CGATTCAAAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
62 CGATTCAAAACGGA-ACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-A
1197 AAAACTTCACAGTGGACTAATCTCACC
125 AAAACTTCACAGTGGACTAATCTCACC
1224 AAAATGATTATAGTTAG
1 AAAATGATTATAGTTAG
Statistics
Matches: 991, Mismatches: 83, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
146 125 0.13
147 2 0.00
148 2 0.00
150 10 0.01
152 104 0.10
153 8 0.01
154 695 0.70
155 45 0.05
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (151 bp):
AAAATGATTATAGTTAGGCCATAAACAATGGAGAAAACATCGAGGGTTGCCAAATCGAAGACGAT
TCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
TCACAGTGGACTAATCTCACC
Found at i:1045 original size:462 final size:453
Alignment explanation
Indices: 1--1240 Score: 1966
Period size: 462 Copynumber: 2.7 Consensus size: 453
*
1 AAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
66 GATTCAAAACGGAACTAATGGTTCCCGAAAGGCCACAAATAACAA--GTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGTTCCCGAAAGGCCA-AAATAACAAGTGTTCCAAATGAGCTAAAA
* *
129 ACTTTACAGTGGACTAATCTCACCAAAATGAATATAGTTAGGCCATAAACAATGGAAAGAAAAGC
130 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * *
194 AGCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGAAAGGCACAAAAT
195 ATCGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGCCCAAAAT
* *
258 AACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTA
259 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
** **
323 GGCCATAAACAATGGAAAAATCATTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
324 GGCCATAAACAATGGAAAAATCAGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
* * * * * *
388 CTGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACC
389 CCGAAAGGCCCAAAATAACAAATGATACAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
*
453 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCTAGGGTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
*
518 GATTCAAAACGGAACTAATGGTTCCCGAAAGGCACAAAATAACAAGTGTTCCAAATGAACTAAAA
66 GATTCAAAACGGAACTAATGGTTCCCGAAAGGC-CAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * *
583 ACTTCACAGTGGACTAATCTCACAAAAATGATTATAGTTAGGCTATAAACAATGGATAGAAAAGC
130 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * * *
648 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCTGATAGGCCCAAAATA
195 ATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA
* *
713 ACAAGTGTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTACAGTTAG
260 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
778 GCCATAAACAATGGTAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
325 GCCATAAACAAT-G---GAAAA--ATC-A-GGTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* *
843 ATGGGCCCCGAAAGGCCTAAAATAACAAGTGATACAAATGAGCTAAAAACTTCACAATGGACTAA
382 ATGGGCCCCGAAAGGCCCAAAATAACAAATGATACAAATGAGCTAAAAACTTCACAATGGACTAA
*
908 TCTCACG
447 TCTCACC
* * *
915 AAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATGGAATAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
** *
980 GATTCAAAACGGAACTAATGGGCCCCGAACGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGTTCCCGAAAGGCC-AAAATAACAAGTGTTCCAAATGAGCTAAAA
1045 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
130 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
1110 ATCAAGGGTTGCCAAATC-AATGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAAT
195 ATCGAGGGTTGCCAAATCGAA-GACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAAT
1174 AACAAGTGTTCCAAATGAGCTAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
259 AACAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1239 AG
323 AG
Statistics
Matches: 721, Mismatches: 52, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
452 105 0.15
453 3 0.00
454 205 0.28
455 1 0.00
458 5 0.01
460 3 0.00
461 4 0.01
462 352 0.49
463 43 0.06
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (453 bp):
AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGAC
GATTCAAAACGGAACTAATGGTTCCCGAAAGGCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
TCGAGGGTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAAATCAGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
GAAAGGCCCAAAATAACAAATGATACAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
Done.