Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014365.1 Corchorus capsularis cultivar CVL-1 contig14386, 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: 8304
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37


Found at i:252 original size:120 final size:120

Alignment explanation


    Indices: 56--288  Score: 364
    Period size: 120  Copynumber: 1.9  Consensus size: 120

         46 CAATAAATTG

                                                              *      *       
         56 GTTGATTAATAAGGCCTTAACGGATTGTTCGAAAAAAATGAAGCCTTAATTGACCGAGCCTTAAT
          1 GTTGATTAATAAGGCCTTAACGGATTGTTCGAAAAAAA-GAAGCCTTAATGGACCGAACCTTAAT

                  *        *                                        
        121 TAACAAGCTTTGGCCGATTTGCTCCAAAATTATCAATAAATTTGTCAATTTTATTA
         65 TAACAAACTTTGGCCAATTTGCTCCAAAATTATCAATAAATTTGTCAATTTTATTA

                                                                             
        177 GTTGATTAATAATGG-CTTAACGGATTGTTC--AAAAAAGAAAGGCCTTAATGGACCGAACCTTA
          1 GTTGATTAATAA-GGCCTTAACGGATTGTTCGAAAAAAAG-AA-GCCTTAATGGACCGAACCTTA

            *                                                 
        239 GTTAACAAACTTTGGCCAATTTGCTCCAAAATTATCAATAAATTTGTCAA
         63 ATTAACAAACTTTGGCCAATTTGCTCCAAAATTATCAATAAATTTGTCAA

        289 CTTCTATCTC


Statistics
Matches: 104,  Mismatches: 5, Indels: 7
        0.90            0.04        0.06

Matches are distributed among these distances:
 118    1  0.01
 119    8  0.08
 120   66  0.63
 121   27  0.26
 122    2  0.02

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (120 bp):   
GTTGATTAATAAGGCCTTAACGGATTGTTCGAAAAAAAGAAGCCTTAATGGACCGAACCTTAATT
AACAAACTTTGGCCAATTTGCTCCAAAATTATCAATAAATTTGTCAATTTTATTA

Found at i:6245 original size:3 final size:3

Alignment explanation


    Indices: 6237--6279  Score: 86
    Period size: 3  Copynumber: 14.3  Consensus size: 3

       6227 ATATAGTAAT

                                                                     
       6237 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

       6280 ATATGAAATA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:7002 original size:28 final size:28

Alignment explanation


    Indices: 6971--7043  Score: 110
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       6961 GGGTCATCCA

                                        
       6971 GGGGTATTTTGGTCATTTTCACATCTAG
          1 GGGGTATTTTGGTCATTTTCACATCTAG

                *              **   *   
       6999 GGGGCATTTTGGTCATTTTTGCATTTAG
          1 GGGGTATTTTGGTCATTTTCACATCTAG

                             
       7027 GGGGTATTTTGGTCATT
          1 GGGGTATTTTGGTCATT

       7044 CTTAATCTAC


Statistics
Matches: 40,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  28   40  1.00

ACGTcount: A:0.15, C:0.11, G:0.29, T:0.45


Consensus pattern (28 bp):   
GGGGTATTTTGGTCATTTTCACATCTAG
Done.