Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011954.1 Corchorus capsularis cultivar CVL-1 contig11975, 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: 3526
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:320 original size:28 final size:28

Alignment explanation


    Indices: 289--369  Score: 110
    Period size: 27  Copynumber: 2.9  Consensus size: 28

        279 GCATTAGGGT

                  *   *                 
        289 CACCCAAGGGTATTTTGGTCATTTTTTG
          1 CACCCAGGGGCATTTTGGTCATTTTTTG

                                        
        317 CACCCAGGGGCATTTTGGTCA-TTTTTG
          1 CACCCAGGGGCATTTTGGTCATTTTTTG

            *  *            *         
        344 TACTCAGGGGCATTTTAGTCATTTTT
          1 CACCCAGGGGCATTTTGGTCATTTTT

        370 AGGTTCACCT


Statistics
Matches: 47,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  27   24  0.51
  28   23  0.49

ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42


Consensus pattern (28 bp):   
CACCCAGGGGCATTTTGGTCATTTTTTG

Found at i:2937 original size:52 final size:51

Alignment explanation


    Indices: 2880--3241  Score: 448
    Period size: 51  Copynumber: 7.1  Consensus size: 51

       2870 AAGGTATAAC

                           *                                    
       2880 CTTTGGGTAAAAGATGGAATTTTTAAGAGTAATTAGTAAATAAAAATGTCAT
          1 CTTTGGGTAAAAGATTGAATTTTT-AGAGTAATTAGTAAATAAAAATGTCAT

                           *                                    
       2932 CTTTGGGTAAAAGATGGAATTTTTAAGAGTAATTAGTAAATAAAAATGTCAT
          1 CTTTGGGTAAAAGATTGAATTTTT-AGAGTAATTAGTAAATAAAAATGTCAT

             *                         *            *          
       2984 CCTTGGGTAAAAGATTGAATTTTTAGAATAATTAGTAAATGAAAATGTCAT
          1 CTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATGTCAT

                                *    *            *    *  * * *
       3035 CTTTGGGTAAAAGATTGAATCTTTAAAGTAATTAGTAAGTAAAGATTTAAC
          1 CTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATGTCAT

                 **           *                                   
       3086 CTTTGAATAAAAGATTTGGATTTTT-GAGTAATT-GCTAAATAAAAATGTCGA-
          1 CTTTGGGTAAAAGA-TTGAATTTTTAGAGTAATTAG-TAAATAAAAATGTC-AT

                                *                      *  * *  
       3137 CTTTGGGTAAAAGATTGAATCTTTAGAGTAATTAGTAAATAAAGATCTAAT
          1 CTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATGTCAT

                 **                                            
       3188 CTTTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAAT-AAAATGTCAT
          1 CTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATGTCAT

                  
       3237 -TTTGG
          1 CTTTGG

       3242 AATTAGAAGT


Statistics
Matches: 267,  Mismatches: 37, Indels: 16
        0.83            0.12        0.05

Matches are distributed among these distances:
  48    4  0.01
  49    7  0.03
  50   24  0.09
  51  148  0.55
  52   84  0.31

ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36


Consensus pattern (51 bp):   
CTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAAATGTCAT

Done.