Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003003.1 Corchorus capsularis cultivar CVL-1 contig03011, 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, 666

Length: 1110
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41


Found at i:29 original size:2 final size:2

Alignment explanation


    Indices: 22--48  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

         12 ATTTATTATT

                                                    
         22 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

         49 TTCTTTCTTC


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:159 original size:8 final size:9

Alignment explanation


    Indices: 138--162  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

        128 TCTTCGTTTT

                     
        138 TTTTTTCTA
          1 TTTTTTCTA

                     
        147 TTTTTTCTA
          1 TTTTTTCTA

                   
        156 TTTTTTC
          1 TTTTTTC

        163 CGTTGACTTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80


Consensus pattern (9 bp):   
TTTTTTCTA

Found at i:626 original size:87 final size:87

Alignment explanation


    Indices: 535--834  Score: 469
    Period size: 87  Copynumber: 3.5  Consensus size: 87

        525 TAAAGAGAAT

                                        *                                  * 
        535 TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATATTTTAAGAAAATAAATAAATTATGA
          1 TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATATTTTAAGAAAATAAATAAATTATAA

                                  
        600 AGATTTAATAATAATGATAATA
         66 AGATTTAATAATAATGATAATA

                              *                                   *          
        622 TTTTCTAAATCTTGCCAAGTTGTGGGAGCTTTAGAAGATATTTTAAGAAAATAAGTAAATTATAA
          1 TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATATTTTAAGAAAATAAATAAATTATAA

                *       *         
        687 AGATATAATAATGATGATAATA
         66 AGATTTAATAATAATGATAATA

                          *   *      *  *     *                *             
        709 TTTTCTAAATCTTGTCAAGTTGTGGAAGGTTTAGGAG-TATTTTAAG-AAACAAATAAATTATAA
          1 TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATATTTTAAGAAAATAAATAAATTATAA

                             *    
        772 AGATTTAATAATAATGAAAATA
         66 AGATTTAATAATAATGATAATA

                                                     
        794 TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATAT
          1 TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATAT

        835 AAAAAAGGAA


Statistics
Matches: 192,  Mismatches: 20, Indels: 3
        0.89            0.09        0.01

Matches are distributed among these distances:
  85   66  0.34
  86   12  0.06
  87  114  0.59

ACGTcount: A:0.42, C:0.06, G:0.16, T:0.37


Consensus pattern (87 bp):   
TTTTCTAAATCTTGCCAAATTGTGGGAGCTTTAGAAGATATTTTAAGAAAATAAATAAATTATAA
AGATTTAATAATAATGATAATA

Done.