Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016314.1 Corchorus capsularis cultivar CVL-1 contig16335, 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: 3965
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29


Found at i:321 original size:19 final size:18

Alignment explanation


    Indices: 288--323  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        278 TTGAAATAAT

                              
        288 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
        306 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

        324 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:1887 original size:33 final size:32

Alignment explanation


    Indices: 1851--1988  Score: 152
    Period size: 33  Copynumber: 4.2  Consensus size: 32

       1841 AAAGGATCAT

                                            *
       1851 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCGT
          1 GTGGCCGGTTGTGGCCGGGCATGGCC-AGTCGC

                  *     *                    
       1884 GTGGCCAGTTGTTGCCGGGCATGGCCTAGTCGC
          1 GTGGCCGGTTGTGGCCGGGCATGGCC-AGTCGC

              *            *       *         
       1917 GTTGCCGGTTGTGGCTGGGCATGTCCATGTCGC
          1 GTGGCCGGTTGTGGCCGGGCATGGCCA-GTCGC

                                   **         
       1950 GTGGCCGG-TGATGGCCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTTG-TGGCCGGGCATGGCC-AGTCGC

                  
       1983 GTGGCC
          1 GTGGCC

       1989 AGTCACTTGT


Statistics
Matches: 90,  Mismatches: 12, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  32    3  0.03
  33   86  0.96
  34    1  0.01

ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23


Consensus pattern (32 bp):   
GTGGCCGGTTGTGGCCGGGCATGGCCAGTCGC

Done.