Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021786.1 Corchorus olitorius cultivar O-4 contig21819, 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: 1776
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32


Found at i:530 original size:45 final size:43

Alignment explanation


    Indices: 474--557  Score: 105
    Period size: 45  Copynumber: 1.9  Consensus size: 43

        464 AATTCCTATG

                           *             *             
        474 TAATATATATAATAATTAAAATACGTACATTAATTAAATATAA
          1 TAATATATATAATAACTAAAATACGTACAATAATTAAATATAA

                            *  *      *              
        517 TAATAATACTATAATAGCTGAAATACTTACAATAATTAAAT
          1 TAAT-ATA-TATAATAACTAAAATACGTACAATAATTAAAT

        558 TCTCAGGTAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  43    4  0.12
  44    3  0.09
  45   27  0.79

ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36


Consensus pattern (43 bp):   
TAATATATATAATAACTAAAATACGTACAATAATTAAATATAA

Found at i:1170 original size:51 final size:51

Alignment explanation


    Indices: 1099--1205  Score: 137
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       1089 TATTTCTGAA

                         *         **                           
       1099 AGAAAAACACGAATACAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACAAG
          1 AGAAAAACACGAAAACAGTGTTTGAATGTCCGGAGACAAGATCT-AAACAAG

                      *    *               *                   
       1150 AGAAAAACACTAAAAGAGTGTTTGAATGTCCTGAGACAAGATCTAAACAAG
          1 AGAAAAACACGAAAACAGTGTTTGAATGTCCGGAGACAAGATCTAAACAAG

                  
       1201 A-AAAA
          1 AGAAAA

       1206 TATGAAGAAC


Statistics
Matches: 49,  Mismatches: 6, Indels: 3
        0.84            0.10        0.05

Matches are distributed among these distances:
  50    4  0.08
  51   44  0.90
  52    1  0.02

ACGTcount: A:0.48, C:0.13, G:0.20, T:0.20


Consensus pattern (51 bp):   
AGAAAAACACGAAAACAGTGTTTGAATGTCCGGAGACAAGATCTAAACAAG
Done.