Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023746.1 Corchorus olitorius cultivar O-4 contig23779, 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: 6536
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:5560 original size:30 final size:31

Alignment explanation


    Indices: 5499--5560  Score: 76
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       5489 AAAATAAGAG

                                      *    
       5499 ATTTTTTTTCTTTTCTAAAAACGCAGGAACA
          1 ATTTTTTTTCTTTTCTAAAAACGCAGAAACA

                                             
       5530 ATTTTTTTT-TTTT-TAAGAAAACGCA-AAACA
          1 ATTTTTTTTCTTTTCT-A-AAAACGCAGAAACA

             
       5560 A
          1 A

       5561 AAAAAAAAAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  29    1  0.04
  30   10  0.36
  31   17  0.61

ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42


Consensus pattern (31 bp):   
ATTTTTTTTCTTTTCTAAAAACGCAGAAACA

Found at i:6084 original size:15 final size:16

Alignment explanation


    Indices: 6060--6099  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       6050 AGAGGTTGAA

                 *          
       6060 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       6075 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       6091 AGAAAACAA
          1 AGAAAACAA

       6100 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.