Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008011.1 Corchorus capsularis cultivar CVL-1 contig08032, 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: 9457
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:43 original size:2 final size:2

Alignment explanation


    Indices: 36--104  Score: 77
    Period size: 2  Copynumber: 34.0  Consensus size: 2

         26 GAGATTCGTT

                         *        *        *                               
         36 TA TA TA TA TC TA TA TC TA TA TC TA TA CTA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA

                         *                         
         79 TA TA TA TA TT TA TA TA T- TA TA CTA TA
          1 TA TA TA TA TA TA TA TA TA TA TA -TA TA

        105 CTCTCTCCGT


Statistics
Matches: 56,  Mismatches: 8, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
   1    1  0.02
   2   51  0.91
   3    4  0.07

ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:272 original size:25 final size:25

Alignment explanation


    Indices: 239--286  Score: 71
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        229 AACTTTTTAG

                *                     
        239 TACATATTTTTTTTA-AATTAAATTT
          1 TACAAATTTTTTTTATAA-TAAATTT

                                   
        264 TACAAATTTTTTTTATAATAAAT
          1 TACAAATTTTTTTTATAATAAAT

        287 GGTCAAAGTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   19  0.90
  26    2  0.10

ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56


Consensus pattern (25 bp):   
TACAAATTTTTTTTATAATAAATTT

Found at i:293 original size:24 final size:25

Alignment explanation


    Indices: 238--293  Score: 62
    Period size: 25  Copynumber: 2.3  Consensus size: 25

        228 AAACTTTTTA

                 *                  *
        238 GTACATATTTTTTTTAAATTAAATT
          1 GTACAAATTTTTTTTAAATTAAATG

            *                         
        263 TTACAAATTTTTTTTATAA-TAAATG
          1 GTACAAATTTTTTTTA-AATTAAATG

                   
        288 GT-CAAA
          1 GTACAAA

        294 GTTTAGTGTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  24    4  0.15
  25   20  0.77
  26    2  0.08

ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50


Consensus pattern (25 bp):   
GTACAAATTTTTTTTAAATTAAATG
Done.