Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005749.1 Corchorus capsularis cultivar CVL-1 contig05767, 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: 8737
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32


Found at i:524 original size:15 final size:16

Alignment explanation


    Indices: 504--541  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        494 TGCTCAAATG

                            
        504 TCGGGTC-ATTTGGGT
          1 TCGGGTCAATTTGGGT

                             
        519 TCGGGTCAATTCTGGGT
          1 TCGGGTCAATT-TGGGT

                   
        536 T-GGGTC
          1 TCGGGTC

        542 GTTTTCGGTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    7  0.33
  16    8  0.38
  17    6  0.29

ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37


Consensus pattern (16 bp):   
TCGGGTCAATTTGGGT

Found at i:902 original size:97 final size:97

Alignment explanation


    Indices: 736--925  Score: 353
    Period size: 97  Copynumber: 2.0  Consensus size: 97

        726 TAATTTGGGA

                                                 *                           
        736 TTAATAAAAATTCTTTTCCATTTGTAGTTATAACATATTTTGATAAAATAGTTATAAGAAATTTT
          1 TTAATAAAAATTCTTTTCCATTTGTAGTTATAACATACTTTGATAAAATAGTTATAAGAAATTTT

                            *               
        801 ATTAATATAACTGATATTTTAAATCTCATATT
         66 ATTAATATAACTGATAATTTAAATCTCATATT

                                                                             
        833 TTAATAAAAATTCTTTTCCATTTGTAGTTATAACATACTTTGATAAAATAGTTATAAGAAATTTT
          1 TTAATAAAAATTCTTTTCCATTTGTAGTTATAACATACTTTGATAAAATAGTTATAAGAAATTTT

                                *       
        898 ATTAATATAACTGATAATTTCAATCTCA
         66 ATTAATATAACTGATAATTTAAATCTCA

        926 AAGATTTAAA


Statistics
Matches: 90,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  97   90  1.00

ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45


Consensus pattern (97 bp):   
TTAATAAAAATTCTTTTCCATTTGTAGTTATAACATACTTTGATAAAATAGTTATAAGAAATTTT
ATTAATATAACTGATAATTTAAATCTCATATT

Found at i:1016 original size:2 final size:2

Alignment explanation


    Indices: 1003--1036  Score: 50
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        993 TTTATACTAA

                                *                             
       1003 AT AT ACT AT AT AT AC AT AT AT AT AT AT AT AT AT A
          1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1037 ATAGACTTTC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2   27  0.93
   3    2  0.07

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Found at i:2051 original size:32 final size:33

Alignment explanation


    Indices: 1994--2057  Score: 87
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       1984 GGTTGATCAG

                                *            
       1994 GTTCGGGTCCTTTTGGGTTTTGGTC-ATTTCGA
          1 GTTCGGGTCCTTTTGGGTTTGGGTCAATTTCGA

                      *                      
       2026 GTTCGGGTCATTTTTGGG-TTGGGTCAATTTCG
          1 GTTCGGGTC-CTTTTGGGTTTGGGTCAATTTCG

       2058 GTTTCAGGTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  32   15  0.54
  33   13  0.46

ACGTcount: A:0.08, C:0.14, G:0.33, T:0.45


Consensus pattern (33 bp):   
GTTCGGGTCCTTTTGGGTTTGGGTCAATTTCGA

Found at i:8459 original size:22 final size:22

Alignment explanation


    Indices: 8434--8605  Score: 100
    Period size: 22  Copynumber: 7.9  Consensus size: 22

       8424 TATGATCCCA

                *                 
       8434 TTATAAAATTTTGATAACCTTC
          1 TTATGAAATTTTGATAACCTTC

                        *   **** *
       8456 TTATGAAATTTTAATAGTGATA
          1 TTATGAAATTTTGATAACCTTC

                 *        *      *
       8478 TTATGGAATTTTGAGAACCTTT
          1 TTATGAAATTTTGATAACCTTC

                   *    **        
       8500 TTAT-AATTTTTTTTAACCTTC
          1 TTATGAAATTTTGATAACCTTC

                         *      * 
       8521 TTATGAAATTTTGTTAACCTCC
          1 TTATGAAATTTTGATAACCTTC

            *  * *                 
       8543 CTAAGGAATTTTGA-AGACC-TC
          1 TTATGAAATTTTGATA-ACCTTC

             *                      
       8564 AATATGAAATTTTGATAA-CTTCC
          1 -TTATGAAATTTTGATAACCTT-C

            **                 
       8587 CAATGAAATTTTGATAACC
          1 TTATGAAATTTTGATAACC

       8606 AACACTATAT


Statistics
Matches: 109,  Mismatches: 34, Indels: 13
        0.70            0.22        0.08

Matches are distributed among these distances:
  21   18  0.17
  22   88  0.81
  23    3  0.03

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43


Consensus pattern (22 bp):   
TTATGAAATTTTGATAACCTTC

Done.