Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008280.1 Corchorus capsularis cultivar CVL-1 contig08301, 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: 2032
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32


Found at i:95 original size:15 final size:14

Alignment explanation


    Indices: 44--136  Score: 58
    Period size: 11  Copynumber: 7.1  Consensus size: 14

         34 TTATGATTAG

                        * 
         44 TTTTAATTAGTTAA
          1 TTTTAATTAGTTTA

              **      *   
         58 TTAAAATTA-CTTA
          1 TTTTAATTAGTTTA

            *             
         71 GTTT-ATTAGTTTA
          1 TTTTAATTAGTTTA

                           
         84 TGTTTAATTAG--TA
          1 T-TTTAATTAGTTTA

              *           
         97 -TCTAATTAGTTTA
          1 TTTTAATTAGTTTA

                           
        110 TTATTAATTAG--TA
          1 TT-TTAATTAGTTTA

                          
        123 -TTTAATTAGTTTA
          1 TTTTAATTAGTTTA

             
        136 T
          1 T

        137 GATTAAAATG


Statistics
Matches: 58,  Mismatches: 11, Indels: 20
        0.65            0.12        0.22

Matches are distributed among these distances:
  11   16  0.28
  12    5  0.09
  13   14  0.24
  14   11  0.19
  15   12  0.21

ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56


Consensus pattern (14 bp):   
TTTTAATTAGTTTA

Found at i:104 original size:26 final size:26

Alignment explanation


    Indices: 75--142  Score: 102
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         65 TACTTAGTTT

                                      
         75 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGTTTAATTAGTATCTA

                                    *  
        101 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAGTATCTA

                       *    
        127 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

        143 AATGAAGGAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   37  0.97

ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAGTATCTA

Found at i:1346 original size:52 final size:52

Alignment explanation


    Indices: 1268--1374  Score: 205
    Period size: 52  Copynumber: 2.1  Consensus size: 52

       1258 TAGAGCTGTC

                                                                
       1268 AAATCTAAGCCGAACCCGATAACTCGTCCAATCCGACATAATCCGATTTGAT
          1 AAATCTAAGCCGAACCCGATAACTCGTCCAATCCGACATAATCCGATTTGAT

                            *                                   
       1320 AAATCTAAGCCGAACCTGATAACTCGTCCAATCCGACATAATCCGATTTGAT
          1 AAATCTAAGCCGAACCCGATAACTCGTCCAATCCGACATAATCCGATTTGAT

               
       1372 AAA
          1 AAA

       1375 AAAAGTAAAC


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   54  1.00

ACGTcount: A:0.36, C:0.27, G:0.13, T:0.23


Consensus pattern (52 bp):   
AAATCTAAGCCGAACCCGATAACTCGTCCAATCCGACATAATCCGATTTGAT
Done.