Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005028.1 Corchorus capsularis cultivar CVL-1 contig05046, 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, 916

Length: 1528
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Found at i:539 original size:28 final size:29

Alignment explanation


    Indices: 492--557  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        482 CGTTTAGACG

                     *                    
        492 TTTTGCCCCCTGAACTTCAATCTT-GGACA
          1 TTTTG-CCCATGAACTTCAATCTTGGGACA

                                *       *
        521 TTTTGCCCATGAACTTCAATTTTGGGACG
          1 TTTTGCCCATGAACTTCAATCTTGGGACA

                    
        550 TTTTGCCC
          1 TTTTGCCC

        558 CCTCAACCTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  28   16  0.48
  29   17  0.52

ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38


Consensus pattern (29 bp):   
TTTTGCCCATGAACTTCAATCTTGGGACA

Found at i:613 original size:30 final size:30

Alignment explanation


    Indices: 579--657  Score: 88
    Period size: 29  Copynumber: 2.7  Consensus size: 30

        569 CGGCTCCGTT

                 *                       *
        579 AAGTTGAGGGGGCAAAACGTTCCAAAATTG
          1 AAGTTCAGGGGGCAAAACGTTCCAAAATTA

                     *       *       *    
        609 AAGTTCAGGAGGCAAAATG-TCCAAGATTA
          1 AAGTTCAGGGGGCAAAACGTTCCAAAATTA

                 *     *        
        638 AAGTTTAGGGGACAAAACGT
          1 AAGTTCAGGGGGCAAAACGT

        658 CTAAACGATA


Statistics
Matches: 39,  Mismatches: 9, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
  29   23  0.59
  30   16  0.41

ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20


Consensus pattern (30 bp):   
AAGTTCAGGGGGCAAAACGTTCCAAAATTA

Done.