Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005048.1 Corchorus capsularis cultivar CVL-1 contig05066, 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: 15325
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:364 original size:178 final size:178

Alignment explanation


    Indices: 47--473  Score: 462
    Period size: 178  Copynumber: 2.4  Consensus size: 178

         37 CCGATCAAGG

                                  *  *           *           *               
         47 TGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATCTGCAACTTTCATGGAAGACTCGAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGCAAGACTCGAAAACTA

                             *              *  *     *       *      *      * 
        112 AATTTAATGTTTCAAGTTTAAAAAAAGCTTCCGAATAATTAGTTATTTCTGTTAACTAGAAAGGA
         66 AATTTAATGTTTCAAGTATAAAAAAAGCTTCCAAAAAATTAATTATTTCGGTTAACAAGAAAGAA

                          *     *         *        **       
        177 CGATCCACTTAATATAACATTACTTTTGCTGCAGATGTCTTATTGAGC
        131 CGATCCACTTAATAAAACATAACTTTTGCTCCAGATGTCCGATTGAGC

                                         **                  *  *      *  *  
        225 TGATTCAAGTGTCTCA-TAAAAGATTATTTTATGATCTACAACTTTCATTCATGACTCGCAAGCT
          1 TGATTCAAGTGTCT-ATTAAAAGATTATTCCATGATCTACAACTTTCATGCAAGACTCGAAAACT

             *                        *                  *         *      *  
        289 AGATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAAAATTAATTTTTTCGGTTAGCAAGAATGA
         65 AAATTTAATGTTTCAAGTATAAAAAAAGCTTCCAAAAAATTAATTATTTCGGTTAACAAGAAAGA

                                    *                        *
        354 ACTG-TCCACTTAATAAAACATAATTTTTGCTCCAGATGTCCGATTGAGG
        130 AC-GATCCACTTAATAAAACATAACTTTTGCTCCAGATGTCCGATTGAGC

                          *      * * *  * *      *           * *    *        
        403 TGATTCAAGTGTCTGTTAAAATACTGTTTCGTGATCTTCAACTTTCATGTAGGACTTGAAAAGCT
          1 TGATTCAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGCAAGACTCGAAAA-CT

                  
        468 AAATTT
         65 AAATTT

        474 GATTTCTCAA


Statistics
Matches: 202,  Mismatches: 43, Indels: 7
        0.80            0.17        0.03

Matches are distributed among these distances:
 178  193  0.96
 179    9  0.04

ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36


Consensus pattern (178 bp):   
TGATTCAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGCAAGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAAAGCTTCCAAAAAATTAATTATTTCGGTTAACAAGAAAGAA
CGATCCACTTAATAAAACATAACTTTTGCTCCAGATGTCCGATTGAGC

Found at i:5129 original size:3 final size:3

Alignment explanation


    Indices: 5121--5158  Score: 60
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       5111 GGTAGAAAAG

                                                               
       5121 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA

       5159 CACTTGGATA


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   2    2  0.06
   3   28  0.85
   4    3  0.09

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (3 bp):   
TAA

Found at i:8296 original size:20 final size:20

Alignment explanation


    Indices: 8271--8315  Score: 58
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       8261 TAAGAGTTAC

                                  
       8271 AATTATCAAG-CAAA-AAAATT
          1 AATTAT-AAGTCAAATAAAA-T

                                
       8291 AATTATAAGTCAAATAAAAT
          1 AATTATAAGTCAAATAAAAT

                 
       8311 AATTA
          1 AATTA

       8316 CACGTTAGGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    3  0.13
  20   16  0.70
  21    4  0.17

ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29


Consensus pattern (20 bp):   
AATTATAAGTCAAATAAAAT
Done.