Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000459.1 Corchorus capsularis cultivar CVL-1 contig00459, 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: 1776
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35


Found at i:193 original size:52 final size:54

Alignment explanation


    Indices: 131--235  Score: 160
    Period size: 55  Copynumber: 2.0  Consensus size: 54

        121 CGAAATTATA

                          *                 **                    
        131 TTATTTTTATG-TTGT-ATTACAAATTAATATGTGATTTATTATATTTATTTTT
          1 TTATTTTTATGATTATAATTACAAATTAATATACGATTTATTATATTTATTTTT

                                                                 
        183 TTATTTTTATGATTTATAATTACAAATTAATATACGATTTATTATATTTATTT
          1 TTATTTTTATGA-TTATAATTACAAATTAATATACGATTTATTATATTTATTT

        236 ATTTGTACGT


Statistics
Matches: 47,  Mismatches: 3, Indels: 3
        0.89            0.06        0.06

Matches are distributed among these distances:
  52   11  0.23
  54    3  0.06
  55   33  0.70

ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59


Consensus pattern (54 bp):   
TTATTTTTATGATTATAATTACAAATTAATATACGATTTATTATATTTATTTTT

Found at i:259 original size:55 final size:54

Alignment explanation


    Indices: 146--259  Score: 133
    Period size: 55  Copynumber: 2.1  Consensus size: 54

        136 TTTATGTTGT

                           **                       ** *           
        146 ATTACAAATTAATATGTGATTTATTATATTTATTTTTTTATTTTTATGATTTATA
          1 ATTACAAATTAATATACGATTTATTATATTTATTTTTTTACGTGTAT-ATTTATA

                                                                     
        201 ATTACAAATTAATATACGATTTATTATATTTATTTATTTGTACGTGT-T-TTTATGA
          1 ATTACAAATTAATATACGATTTATTATATTTATTT-TTT-TACGTGTATATTTAT-A

                
        256 ATTA
          1 ATTA

        260 TTAACACACG


Statistics
Matches: 51,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  54    5  0.10
  55   38  0.75
  56    4  0.08
  57    4  0.08

ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56


Consensus pattern (54 bp):   
ATTACAAATTAATATACGATTTATTATATTTATTTTTTTACGTGTATATTTATA
Done.