Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008096.1 Corchorus olitorius cultivar O-4 contig08123, 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: 2125
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33


Found at i:1842 original size:30 final size:29

Alignment explanation


    Indices: 1765--1960  Score: 200
    Period size: 30  Copynumber: 6.7  Consensus size: 29

       1755 CACACTCAGA

                                       * 
       1765 GGCATTTTGGTCA-TTTTGCATATCCATG
          1 GGCATTTTGGTCATTTTTGCATATCCAGG

                                    *     
       1793 GGCATTTTGGTCA-TTTTGCATATTC-GAG
          1 GGCATTTTGGTCATTTTTGCATATCCAG-G

                                   *  *    
       1821 GGCATTTTGGTCATTTTTTGCACAATTCAGG
          1 GGCATTTTGGTCA-TTTTTGCA-TATCCAGG

                        * *      *   *  *
       1852 GGCATTTTGGTCGTGTTTGCACATCTAGA
          1 GGCATTTTGGTCATTTTTGCATATCCAGG

              *                   *       
       1881 GGTATTTTGGTCATTTTTTGCACATCCAGG
          1 GGCATTTTGGTCA-TTTTTGCATATCCAGG

              *     *                    
       1911 GGTATTTTTGTCATTTTTGCATATCCAGG
          1 GGCATTTTGGTCATTTTTGCATATCCAGG

                  *              
       1940 GGCATTATGGTCAGTTTTTGC
          1 GGCATTTTGGTCA-TTTTTGC

       1961 GCTTTTAATT


Statistics
Matches: 142,  Mismatches: 19, Indels: 12
        0.82            0.11        0.07

Matches are distributed among these distances:
  28   38  0.27
  29   40  0.28
  30   46  0.32
  31   17  0.12
  32    1  0.01

ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43


Consensus pattern (29 bp):   
GGCATTTTGGTCATTTTTGCATATCCAGG

Found at i:1911 original size:59 final size:58

Alignment explanation


    Indices: 1754--1960  Score: 215
    Period size: 59  Copynumber: 3.6  Consensus size: 58

       1744 CCGACCATTC

                                              *     *                  
       1754 GCACA-CTCAGAGGCATTTTGGTCA--TTTTGCATATCCATGGGCATTTTGGTCATTTT
          1 GCACATCT-AGAGGCATTTTGGTCATTTTTTGCACATCCAGGGGCATTTTGGTCATTTT

               *    *                             *                *     
       1810 GCATAT-TCGAGGGCATTTTGGTCATTTTTTGCACAATTCAGGGGCATTTTGGTCGTGTTT
          1 GCACATCTAGA-GGCATTTTGGTCATTTTTTGCAC-ATCCAGGGGCATTTTGGTCAT-TTT

                         *                             *     *         
       1870 GCACATCTAGAGGTATTTTGGTCATTTTTTGCACATCCAGGGGTATTTTTGTCATTTTT
          1 GCACATCTAGAGGCATTTTGGTCATTTTTTGCACATCCAGGGGCATTTTGGTCA-TTTT

               *   *  *      *      *       
       1929 GCATATCCAGGGGCATTATGGTCAGTTTTTGC
          1 GCACATCTAGAGGCATTTTGGTCATTTTTTGC

       1961 GCTTTTAATT


Statistics
Matches: 124,  Mismatches: 19, Indels: 13
        0.79            0.12        0.08

Matches are distributed among these distances:
  55    2  0.02
  56   18  0.15
  58    7  0.06
  59   63  0.51
  60   31  0.25
  61    3  0.02

ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41


Consensus pattern (58 bp):   
GCACATCTAGAGGCATTTTGGTCATTTTTTGCACATCCAGGGGCATTTTGGTCATTTT
Done.