Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009959.1 Corchorus olitorius cultivar O-4 contig09991, 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: 3203
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34


Found at i:1076 original size:76 final size:76

Alignment explanation


    Indices: 928--1079  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

        918 TACCGAGCCA

                        *      *                                        *    
        928 TGACACAGCCCATCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGTACCC
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC

                       
        993 AGCTGGAGTCG
         66 AGCTGGAGTCG

                  *             *                            *              *
       1004 TGACACTGCCCACCTGGGTCCTCAAGC-AAACCACATGGGTGC-TCAAGGC-AACCATGTGGGCG
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAA-CACATGGGT-CTTC-AGACAAACCATGTGGGCA

              *  *        
       1066 CCTAGGTGGAGTCG
         63 CCCAGCTGGAGTCG

       1080 GGGCCCTTGT


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    3  0.05
  76   57  0.89
  77    4  0.06

ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTGGGCACCC
AGCTGGAGTCG

Found at i:1911 original size:19 final size:19

Alignment explanation


    Indices: 1855--1904  Score: 82
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       1845 GTCAAGCTAA

                *    *         
       1855 TGTTGGTCCAAGTGACAAT
          1 TGTTAGTCCTAGTGACAAT

                               
       1874 TGTTAGTCCTAGTGACAAT
          1 TGTTAGTCCTAGTGACAAT

                        
       1893 TGTTAGTCCTAG
          1 TGTTAGTCCTAG

       1905 GTTCAATGGG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   29  1.00

ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36


Consensus pattern (19 bp):   
TGTTAGTCCTAGTGACAAT
Done.