Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004820.1 Corchorus capsularis cultivar CVL-1 contig04838, 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: 7261
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31


Found at i:2459 original size:167 final size:165

Alignment explanation


    Indices: 2082--2533  Score: 602
    Period size: 166  Copynumber: 2.7  Consensus size: 165

       2072 TGAGTCATTT

                                                                       *     
       2082 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
          1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT

                                               *         * *    ** *   *     
       2147 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGGTTAGTTCTCCAGCTCATCATCAATCCTTG
         65 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAACTCAAAAGCAAGCCTTG

              *                    *         *  
       2212 ATGGGGATCTTTTATCAATTCCACGACTCTATTCAA
        130 ATAGGGATCTTTTATCAATTCCAAGACTCTATTAAA

               *          *             *                 *         *        
       2248 GTCCATTGAGAAATTACCAAAAAGATTACTTATTTAATCCCCTCAATAATCAAAAGCTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT

                                               *  *                          
       2313 TTAAGTAATCTGCCAAGTAGG-AAAGGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCT
         65 TTAAGTAATCTGCCAAGTAGGTAAA-GACGAAAAAGATTAGTTCTCTAACT-CAAAAGCAAGCCT

              *                        *           
       2377 TGGTAGGGATCTTTTAGT-AATTCCAATACTCTATTAAA
        128 TGATAGGGATCTTTTA-TCAATTCCAAGACTCTATTAAA

                            *                                                
       2415 GTCAATTGAGAAATGAACAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAAGTTAGGACA
          1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATC-AAAAGTTAGGACA

             *         *                                     *    
       2480 TATATAGTAATATGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTATCTCA
         64 TTTA-AGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAACTCA

       2534 TCATTTATAT


Statistics
Matches: 247,  Mismatches: 32, Indels: 12
        0.85            0.11        0.04

Matches are distributed among these distances:
 165    3  0.01
 166  100  0.40
 167   84  0.34
 168   18  0.07
 169   39  0.16
 170    3  0.01

ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28


Consensus pattern (165 bp):   
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAACTCAAAAGCAAGCCTTGA
TAGGGATCTTTTATCAATTCCAAGACTCTATTAAA

Found at i:3462 original size:27 final size:27

Alignment explanation


    Indices: 3408--3462  Score: 83
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       3398 TAAATGGGTA

                              * *  *   
       3408 TGGATATGTTAATATTAGTAGGAGAAC
          1 TGGATATGTTAATATTAGCAAGAAAAC

                                       
       3435 TGGATATGTTAATATTAGCAAGAAAAC
          1 TGGATATGTTAATATTAGCAAGAAAAC

             
       3462 T
          1 T

       3463 TTAATATTTA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33


Consensus pattern (27 bp):   
TGGATATGTTAATATTAGCAAGAAAAC
Done.