Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010529.1 Corchorus capsularis cultivar CVL-1 contig10550, 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: 1706
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30


Found at i:452 original size:18 final size:18

Alignment explanation


    Indices: 424--496  Score: 119
    Period size: 18  Copynumber: 4.1  Consensus size: 18

        414 TAGTGAGGAA

                *          *  
        424 AATGGAGAACCTGACGGT
          1 AATGAAGAACCTGACAGT

            *                 
        442 GATGAAGAACCTGACAGT
          1 AATGAAGAACCTGACAGT

                              
        460 AATGAAGAACCTGACAGT
          1 AATGAAGAACCTGACAGT

                              
        478 AATGAAGAACCTGACAGT
          1 AATGAAGAACCTGACAGT

             
        496 A
          1 A

        497 GTAGTGATGA


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  18   51  1.00

ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16


Consensus pattern (18 bp):   
AATGAAGAACCTGACAGT

Found at i:1656 original size:25 final size:25

Alignment explanation


    Indices: 1621--1700  Score: 97
    Period size: 27  Copynumber: 3.1  Consensus size: 25

       1611 TGCGTCCCTA

                             *        
       1621 GGGAGACCTCCCCTGGCTCGCTGCTG
          1 GGGAG-CCTCCCCTGGCGCGCTGCTG

                       *             * 
       1647 GGGAGCCTCCCTTGGCGCGCGCTGCCG
          1 GGGAGCCTCCCCT-G-GCGCGCTGCTG

                 *                   
       1674 GGGAGTCTCCCCTGGCGCGCTGCTG
          1 GGGAGCCTCCCCTGGCGCGCTGCTG

              
       1699 GG
          1 GG

       1701 CCTCCT


Statistics
Matches: 46,  Mismatches: 6, Indels: 5
        0.81            0.11        0.09

Matches are distributed among these distances:
  25   19  0.41
  26    7  0.15
  27   20  0.43

ACGTcount: A:0.05, C:0.38, G:0.40, T:0.17


Consensus pattern (25 bp):   
GGGAGCCTCCCCTGGCGCGCTGCTG

Done.