Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008411.1 Corchorus olitorius cultivar O-4 contig08438, 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, 699

Length: 1165
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27


Found at i:539 original size:50 final size:47

Alignment explanation


    Indices: 477--622  Score: 159
    Period size: 50  Copynumber: 3.0  Consensus size: 47

        467 TTACAATAAG

                               *                              
        477 ATTGCATTCCATTTGTGAGCCCAAGATCCAAATTCGCTTTACAAAGTAAA
          1 ATTGCATTCCATTTGTGAGACCAAGATCCAAATTCGCTTT-CAAAG--AA

                 *             **       *                    *
        527 ATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCGAAACGAG
          1 ATTGCATTCCATTTGTGAGACCAAGATCCAAATTCGC-TTTC-AAA-GAA

                                                           
        577 ATTGCATTCCATTTGTGAGACCAAGA-CCAAAGTTCGCTGTTCAAAG
          1 ATTGCATTCCATTTGTGAGACCAAGATCCAAA-TTCGCT-TTCAAAG

        623 GGCATTTTAG


Statistics
Matches: 82,  Mismatches: 9, Indels: 12
        0.80            0.09        0.12

Matches are distributed among these distances:
  48    1  0.01
  49    8  0.10
  50   66  0.80
  51    6  0.07
  52    1  0.01

ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32


Consensus pattern (47 bp):   
ATTGCATTCCATTTGTGAGACCAAGATCCAAATTCGCTTTCAAAGAA

Found at i:1155 original size:50 final size:51

Alignment explanation


    Indices: 1028--1165  Score: 242
    Period size: 51  Copynumber: 2.7  Consensus size: 51

       1018 AATGCTTTGA

                    *   *                                      
       1028 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGT
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGT

            *                                                  
       1079 TTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGG-
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGT

                                                 
       1129 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA
          1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA


Statistics
Matches: 83,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  50   36  0.43
  51   47  0.57

ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29


Consensus pattern (51 bp):   
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACAGGT
Done.