Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019908.1 Corchorus olitorius cultivar O-4 contig19941, 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: 6039
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28


Found at i:838 original size:72 final size:72

Alignment explanation


    Indices: 501--822  Score: 470
    Period size: 72  Copynumber: 4.5  Consensus size: 72

        491 AGTAGCAAGA

                                                        **                   
        501 ATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGGCTACAATTG-AA-ATGAAGAAGATAAT
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATG--GAAGATAAT

                     
        563 CACATAAGG
         64 CACATAAGG

                     *                                          *       *    
        572 ATTGTGCGATGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATACGGAAGATTATCA
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATAATCA

            **     
        637 TGTAAGG
         66 CATAAGG

                                 *  *   *                                    
        644 ATTGTGCGAAGGACTGCCAAACGTTGGAGCTGCCTCGGCTACAACCGCAATATGGAAGATAATCA
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATAATCA

                   
        709 CATAAGG
         66 CATAAGG

                       *          *                                  *  *    
        716 ATTGTGCGAAGTACTGCCAAATATGGGAACTGCCTCGGCTACAACCGCAATATGGAAAATTATCA
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATAATCA

             *     
        781 CGTAAGG
         66 CATAAGG

                                               
        788 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCT
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCT

        823 TGCCTTCAAT


Statistics
Matches: 223,  Mismatches: 25, Indels: 5
        0.88            0.10        0.02

Matches are distributed among these distances:
  71   17  0.08
  72  202  0.91
  73    2  0.01
  74    2  0.01

ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21


Consensus pattern (72 bp):   
ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATATGGAAGATAATCA
CATAAGG

Found at i:846 original size:144 final size:144

Alignment explanation


    Indices: 501--846  Score: 525
    Period size: 144  Copynumber: 2.4  Consensus size: 144

        491 AGTAGCAAGA

                                                         * *                 
        501 ATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGGCTACAATTGAAATGAAGAAGATAATCA
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATAATCA

                            *            *                                  *
        565 CATAAGGATTGTGCGATGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATACGGAAG
         66 CATAAGGATTGTGCGAAGGACTGCCAAATATGGGAACTGCCTCGGCTACAACCGCAATACGGAAA

                   *      
        630 ATTATCATGTAAGG
        131 ATTATCACGTAAGG

                                 *  *   *               *         *          
        644 ATTGTGCGAAGGACTGCCAAACGTTGGAGCTGCCTCGGCTACAACCGCAAT-ATGGAAGATAATC
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-AGAAGATAATC

                               *                                        *    
        708 ACATAAGGATTGTGCGAAGTACTGCCAAATATGGGAACTGCCTCGGCTACAACCGCAATATGGAA
         65 ACATAAGGATTGTGCGAAGGACTGCCAAATATGGGAACTGCCTCGGCTACAACCGCAATACGGAA

                           
        773 AATTATCACGTAAGG
        130 AATTATCACGTAAGG

                                               * *  *                  
        788 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTTGCCTTCAATCGCAATGAAGAAGA
          1 ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGA

        847 GGACCATGTG


Statistics
Matches: 179,  Mismatches: 21, Indels: 5
        0.87            0.10        0.02

Matches are distributed among these distances:
 143   19  0.11
 144  159  0.89
 145    1  0.01

ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21


Consensus pattern (144 bp):   
ATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATAATCA
CATAAGGATTGTGCGAAGGACTGCCAAATATGGGAACTGCCTCGGCTACAACCGCAATACGGAAA
ATTATCACGTAAGG
Done.