Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015849.1 Corchorus capsularis cultivar CVL-1 contig15870, 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: 5895
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Found at i:729 original size:5 final size:5

Alignment explanation


    Indices: 719--748  Score: 60
    Period size: 5  Copynumber: 6.0  Consensus size: 5

        709 GTCTCGGTCA

                                               
        719 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG
          1 TGGAG TGGAG TGGAG TGGAG TGGAG TGGAG

        749 CGGCTGCTGC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   25  1.00

ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20


Consensus pattern (5 bp):   
TGGAG

Found at i:3921 original size:24 final size:24

Alignment explanation


    Indices: 3876--3921  Score: 56
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       3866 AAGGAAAATC

                      *   *         
       3876 AGTAAAACCAGGATCATAAATCAT
          1 AGTAAAACCAAGATAATAAATCAT

                   *         *    
       3900 AGTAAAATCAAGATAATCAATC
          1 AGTAAAACCAAGATAATAAATC

       3922 CAAAACCAAG


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   18  1.00

ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22


Consensus pattern (24 bp):   
AGTAAAACCAAGATAATAAATCAT

Found at i:5623 original size:82 final size:82

Alignment explanation


    Indices: 5476--5639  Score: 242
    Period size: 82  Copynumber: 2.0  Consensus size: 82

       5466 GGCGCACTTC

                    *     *                                        *         
       5476 TCCCGCCATTAGTATGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGGGTAAGTAGA
          1 TCCCGCCAATAGTACGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA

                  *          
       5541 GACATTTTTTGAAACGT
         66 GACATTCTTTGAAACGT

                                            *     *                          
       5558 TCCCGCCAATAGTACGTCTCAGATTAT-GTTTGTAAGTGGAGACAGTTGTTGAGACGAGTAA-TA
          1 TCCCGCCAATAGTACGTCTCAGATT-TGGTTTCT-AGTAGAGACAGTTGTTGAGACGAGTAAGTA

                               
       5621 GAGACATTCTTTGAAACGT
         64 GAGACATTCTTTGAAACGT

       5640 ACTATTTTAA


Statistics
Matches: 74,  Mismatches: 6, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  82   48  0.65
  83   26  0.35

ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32


Consensus pattern (82 bp):   
TCCCGCCAATAGTACGTCTCAGATTTGGTTTCTAGTAGAGACAGTTGTTGAGACGAGTAAGTAGA
GACATTCTTTGAAACGT
Done.