Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006330.1 Corchorus olitorius cultivar O-4 contig06355, 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: 2354
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:641 original size:31 final size:29

Alignment explanation


    Indices: 538--642  Score: 97
    Period size: 31  Copynumber: 3.5  Consensus size: 29

        528 AATAAGGCTG

                           *               *
        538 AAATCTCAAAT-AGGTCCCCGAACTTTGCCAT
          1 AAATCTCAAATAAGGGCCCC-AACTTT--CAA

                  *            *         
        569 AAATCTTAAATAAGGGCCCAAACTTT-AA
          1 AAATCTCAAATAAGGGCCCCAACTTTCAA

                 *                          
        597 CAAATGTCAAATAAGGGCCCCAACTATTCGAA
          1 -AAATCTCAAATAAGGGCCCCAACT-TTC-AA

                          
        629 AAATCTCAAATAAG
          1 AAATCTCAAATAAG

        643 TCCATCCACT


Statistics
Matches: 61,  Mismatches: 8, Indels: 10
        0.77            0.10        0.13

Matches are distributed among these distances:
  28    1  0.02
  29   21  0.34
  30    2  0.03
  31   29  0.48
  32    8  0.13

ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23


Consensus pattern (29 bp):   
AAATCTCAAATAAGGGCCCCAACTTTCAA

Found at i:745 original size:16 final size:14

Alignment explanation


    Indices: 716--774  Score: 50
    Period size: 15  Copynumber: 4.0  Consensus size: 14

        706 TAAGTCCTTT

                            
        716 TTTCCATTTTATTTAA
          1 TTTCC-TTTTATTT-A

                           
        732 TTTCCTTTTAATTTA
          1 TTTCCTTTT-ATTTA

                           
        747 TTT--TTTGTATTTA
          1 TTTCCTTT-TATTTA

                *          
        760 TTTCTTTTTCATTTA
          1 TTTCCTTTT-ATTTA

        775 ATTTAAATGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 11
        0.78            0.00        0.22

Matches are distributed among these distances:
  13   11  0.29
  14    2  0.05
  15   16  0.42
  16    9  0.24

ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69


Consensus pattern (14 bp):   
TTTCCTTTTATTTA
Done.