Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007250.1 Corchorus capsularis cultivar CVL-1 contig07271, 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: 13202
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31


Found at i:12451 original size:31 final size:29

Alignment explanation


    Indices: 12410--12516  Score: 126
    Period size: 31  Copynumber: 3.6  Consensus size: 29

      12400 TGGGGCTAAA

                                        *  
      12410 TGCTCAATTTGGTCCTAAACCCTTCACGGTC
          1 TGCTCAATTTGGTCCTAAA-CCTTCA-GATC

                 *                     * 
      12441 TGCTCGATTTGGTCCTAAACCTTCAGACC
          1 TGCTCAATTTGGTCCTAAACCTTCAGATC

                 *                          
      12470 TGCTCGATTTGGTCCTAAACCTTCCA-ATTTC
          1 TGCTCAATTTGGTCCTAAACCTT-CAGA--TC

                            
      12501 TGCTCAATTTGGTCCT
          1 TGCTCAATTTGGTCCT

      12517 TTTTCAGACA


Statistics
Matches: 68,  Mismatches: 5, Indels: 6
        0.86            0.06        0.08

Matches are distributed among these distances:
  29   26  0.38
  30    8  0.12
  31   34  0.50

ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36


Consensus pattern (29 bp):   
TGCTCAATTTGGTCCTAAACCTTCAGATC

Found at i:12482 original size:29 final size:30

Alignment explanation


    Indices: 12410--12493  Score: 125
    Period size: 29  Copynumber: 2.8  Consensus size: 30

      12400 TGGGGCTAAA

                 *                      ** 
      12410 TGCTCAATTTGGTCCTAAACCCTTCACGGTC
          1 TGCTCGATTTGGTCCTAAA-CCTTCACGACC

                                          
      12441 TGCTCGATTTGGTCCTAAACCTTCA-GACC
          1 TGCTCGATTTGGTCCTAAACCTTCACGACC

                                    
      12470 TGCTCGATTTGGTCCTAAACCTTC
          1 TGCTCGATTTGGTCCTAAACCTTC

      12494 CAATTTCTGC


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  29   26  0.52
  30    6  0.12
  31   18  0.36

ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33


Consensus pattern (30 bp):   
TGCTCGATTTGGTCCTAAACCTTCACGACC

Found at i:12711 original size:3 final size:3

Alignment explanation


    Indices: 12703--12741  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

      12693 TCCAAATCTT

                                                               
      12703 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

      12742 ATTCTTCCAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

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


Consensus pattern (3 bp):   
TTA

Done.