Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001116.1 Corchorus capsularis cultivar CVL-1 contig01116, 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: 11225
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:420 original size:14 final size:14

Alignment explanation


    Indices: 403--448  Score: 56
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        393 GAACATATAT

                          
        403 AAAATTAACTGAAA
          1 AAAATTAACTGAAA

                *           
        417 AAAAGTAACGTCGAAA
          1 AAAATTAAC-T-GAAA

                    *     
        433 AAAATTAATTGAAA
          1 AAAATTAACTGAAA

              
        447 AA
          1 AA

        449 GTTGACAAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  14   14  0.52
  15    2  0.07
  16   11  0.41

ACGTcount: A:0.63, C:0.07, G:0.11, T:0.20


Consensus pattern (14 bp):   
AAAATTAACTGAAA

Found at i:9403 original size:27 final size:27

Alignment explanation


    Indices: 9355--9427  Score: 76
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       9345 TGTCATATAA

                   *      *             
       9355 AAATATCTATA-AAGATATTATTAATTG
          1 AAATATCAATATAATATA-TATTAATTG

                                  **   
       9382 AAATATCAATATAATATATATTTTTTG
          1 AAATATCAATATAATATATATTAATTG

              * *              
       9409 AATTCTCAATATAATATAT
          1 AAATATCAATATAATATAT

       9428 TCTAAACACC


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  27   34  0.87
  28    5  0.13

ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44


Consensus pattern (27 bp):   
AAATATCAATATAATATATATTAATTG

Found at i:10168 original size:9 final size:9

Alignment explanation


    Indices: 10154--10212  Score: 57
    Period size: 9  Copynumber: 6.7  Consensus size: 9

      10144 ATAATAATTT

                     
      10154 TTATATATA
          1 TTATATATA

                     
      10163 TTATATATA
          1 TTATATATA

             * * *   
      10172 TCAGAAATA
          1 TTATATATA

              *      
      10181 TTTTATATA
          1 TTATATATA

                   * 
      10190 TTATATAAA
          1 TTATATATA

             *       
      10199 TAATATA-A
          1 TTATATATA

                  
      10207 TTATAT
          1 TTATAT

      10213 TTAGGTTAAT


Statistics
Matches: 39,  Mismatches: 11, Indels: 1
        0.76            0.22        0.02

Matches are distributed among these distances:
   8    6  0.15
   9   33  0.85

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (9 bp):   
TTATATATA
Done.