Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007835.1 Corchorus olitorius cultivar O-4 contig07862, 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: 1973
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32


Found at i:955 original size:13 final size:12

Alignment explanation


    Indices: 937--981  Score: 54
    Period size: 14  Copynumber: 3.5  Consensus size: 12

        927 ATTTTATTAC

                         
        937 TGTTTTATTAAAT
          1 TGTTTTA-TAAAT

                        
        950 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
        962 GGTTTTAAATAAAT
          1 TGTTTT--ATAAAT

                  
        976 TGTTTT
          1 TGTTTT

        982 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    7  0.25
  14   11  0.39

ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:1960 original size:153 final size:154

Alignment explanation


    Indices: 1617--1969  Score: 539
    Period size: 154  Copynumber: 2.3  Consensus size: 154

       1607 GGTCGAGTCG

                 *                                           * **            
       1617 GTGGATTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGTGAAGCATTGAGGG
          1 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG

                                      *            *       *             *   
       1682 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCTCCGATAGGCCAAAAATAACAAGTGT
         66 TTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGACCAAAAATAACAACTGT

                                   *
       1747 TCCAAATGAGCTAAAAACTTCACT
        131 TCCAAATGAGCTAAAAACTTCACA

                                 *                                           
       1771 GTGGACTAATCTCACCAAAATAATTATATGTT-GGCCATAAACAATGGAAAGAAAAGCATTGAGG
          1 GTGGACTAATCTCACCAAAATGATTATA-GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG

                           *            **             *        *            
       1835 GTTGCCAAATCGAAGGCGATTCAAAACATCACTAATGGGCCCCTATAGACC-CAAATAACAACTG
         65 GTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGACCAAAAATAACAACTG

                       *             
       1899 TTCCAAATGAGTTAAAAACTTCACA
        130 TTCCAAATGAGCTAAAAACTTCACA

                                                          
       1924 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
          1 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

       1970 TAAA


Statistics
Matches: 180,  Mismatches: 17, Indels: 5
        0.89            0.08        0.02

Matches are distributed among these distances:
 152    3  0.02
 153   75  0.42
 154   99  0.55
 155    3  0.02

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23


Consensus pattern (154 bp):   
GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG
TTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGACCAAAAATAACAACTGT
TCCAAATGAGCTAAAAACTTCACA
Done.