Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013911.1 Corchorus olitorius cultivar O-4 contig13944, 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: 2781
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41


Found at i:639 original size:25 final size:25

Alignment explanation


    Indices: 588--642  Score: 74
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        578 ATCATTACTT

                             * *     
        588 AACTATTGTAGTTTTTTTTTCTCAA
          1 AACTATTGTAGTTTTTTCTACTCAA

                                   *  
        613 AACTATTGTAGTTTTATTCTACTAAA
          1 AACTATTGTAGTTTT-TTCTACTCAA

                
        639 AACT
          1 AACT

        643 CTATTTTTAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  25   15  0.58
  26   11  0.42

ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49


Consensus pattern (25 bp):   
AACTATTGTAGTTTTTTCTACTCAA

Found at i:2464 original size:25 final size:25

Alignment explanation


    Indices: 2421--2477  Score: 80
    Period size: 25  Copynumber: 2.3  Consensus size: 25

       2411 ATTTTTTTCA

                                     
       2421 AATATATTTCTAAATTGTCATTATT
          1 AATATATTTCTAAATTGTCATTATT

                         *            
       2446 AATATATTT-TAATTATGTCATTATT
          1 AATATATTTCTAAAT-TGTCATTATT

              *    
       2471 AAAATAT
          1 AATATAT

       2478 AATTTTTGTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24    4  0.14
  25   25  0.86

ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51


Consensus pattern (25 bp):   
AATATATTTCTAAATTGTCATTATT

Found at i:2476 original size:27 final size:25

Alignment explanation


    Indices: 2420--2483  Score: 76
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       2410 TATTTTTTTC

                                      
       2420 AAATATATTTCTAAATTGTCATTATT
          1 AAATATATTT-TAAATTGTCATTATT

                         *            
       2446 -AATATATTTTAATTATGTCATTATT
          1 AAATATATTTTAAAT-TGTCATTATT

                         
       2471 AAAATATAATTTT
          1 -AAATAT-ATTTT

       2484 TGTGTATTTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  24    4  0.12
  25   19  0.58
  27    5  0.15
  28    5  0.15

ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52


Consensus pattern (25 bp):   
AAATATATTTTAAATTGTCATTATT
Done.