Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010227.1 Corchorus capsularis cultivar CVL-1 contig10248, 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: 22852
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:882 original size:45 final size:45

Alignment explanation


    Indices: 810--898  Score: 142
    Period size: 45  Copynumber: 2.0  Consensus size: 45

        800 ATTACTTCTA

                                  *                      
        810 TAGCTCATCATTAATCCAGGGTGGGGATCTTTTAGTAATTCCACC
          1 TAGCTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCACC

                 *         * *                          
        855 TAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
          1 TAGCTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCAC

        899 TGCTTTATTA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   40  1.00

ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36


Consensus pattern (45 bp):   
TAGCTCATCATTAATCCAGGGTAGGGATCTTTTAGTAATTCCACC

Found at i:1639 original size:7 final size:7

Alignment explanation


    Indices: 1629--1661  Score: 57
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       1619 TGTACTTGCA

                   
       1629 ACTTAGT
          1 ACTTAGT

                   
       1636 ACTTAGT
          1 ACTTAGT

                   
       1643 ACTTAGT
          1 ACTTAGT

                *  
       1650 ACTTGGT
          1 ACTTAGT

                 
       1657 ACTTA
          1 ACTTA

       1662 CCATACATAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42


Consensus pattern (7 bp):   
ACTTAGT

Found at i:22716 original size:14 final size:14

Alignment explanation


    Indices: 22697--22732  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

      22687 TACATTTTGA

                        * 
      22697 TTAAAAAAATATTT
          1 TTAAAAAAATATAT

                          
      22711 TTAAAAAAATATAT
          1 TTAAAAAAATATAT

            *       
      22725 ATAAAAAA
          1 TTAAAAAA

      22733 TGGATGAGGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (14 bp):   
TTAAAAAAATATAT
Done.