Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022614.1 Corchorus olitorius cultivar O-4 contig22647, 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: 3124
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31


Found at i:1185 original size:50 final size:51

Alignment explanation


    Indices: 1110--1206  Score: 160
    Period size: 50  Copynumber: 1.9  Consensus size: 51

       1100 TTACAATAAA

                 *                                             
       1110 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCG-CTTTTCAAAGTAGG
          1 ATTGCATTCCATTTGTAAGTCCAAGATCAAAATTCGTCTTTTCAAAGTAGG

                            *                    *         
       1160 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGTTTTTTCAAAG
          1 ATTGCATTCCATTTGTAAGTCCAAGATCAAAATTCGTCTTTTCAAAG

       1207 GGCATTTAAG


Statistics
Matches: 43,  Mismatches: 3, Indels: 1
        0.91            0.06        0.02

Matches are distributed among these distances:
  50   34  0.79
  51    9  0.21

ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37


Consensus pattern (51 bp):   
ATTGCATTCCATTTGTAAGTCCAAGATCAAAATTCGTCTTTTCAAAGTAGG

Found at i:1939 original size:50 final size:50

Alignment explanation


    Indices: 1864--2439  Score: 1026
    Period size: 50  Copynumber: 11.5  Consensus size: 50

       1854 CCGAATGCTT

                                                              
       1864 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                                              
       1914 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                                *           * 
       1964 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAATTATCAATA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

            *                                             *    
       2014 CAGGCTTTTCCACAAGCCCAAACTCGTTTCCATACGAGTCAATTATGAACA
          1 TAGGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACA

                            *                                 
       2065 TAGGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                      *                       
       2115 TAGGCTTTTCCACAAGCCAAACTCGTCTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                      *                       
       2165 TAGGCTTTTCCACAAGCCAAACTCGTCTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                         *                                    
       2215 TAGGCTTTTCCACGAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                                              
       2265 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

                                         *                    
       2315 TAGGCTTTTCCACAAGCCAAACTCGTTTCTATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

             *              *   *                             
       2365 TGGGCTTTTCCACAAGTCAAGCTCGTTTCCATACGAGTCAATTATCAACA
          1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

               *                     
       2415 TAGACTTTTCCACAAGCCAAACTCG
          1 TAGGCTTTTCCACAAGCCAAACTCG

       2440 AGGATCTCTC


Statistics
Matches: 502,  Mismatches: 23, Indels: 2
        0.95            0.04        0.00

Matches are distributed among these distances:
  50  456  0.91
  51   46  0.09

ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28


Consensus pattern (50 bp):   
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA

Found at i:2985 original size:25 final size:25

Alignment explanation


    Indices: 2956--3003  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       2946 GTATTTTGCG

                                     
       2956 TTCATGTAGCTCAAAGCTAATTTCA
          1 TTCATGTAGCTCAAAGCTAATTTCA

                           *       
       2981 TTCATGTAGCTCAAATCTAATTT
          1 TTCATGTAGCTCAAAGCTAATTT

       3004 GACATTGCAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40


Consensus pattern (25 bp):   
TTCATGTAGCTCAAAGCTAATTTCA
Done.