Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004343.1 Kokia drynarioides strain JFW-HI SEQ_117678, 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, 610

Length: 1017
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32


Found at i:730 original size:59 final size:59

Alignment explanation


    Indices: 634--1017  Score: 509
    Period size: 59  Copynumber: 6.5  Consensus size: 59

        624 CCCCGGAGGT

                *                           *                          
        634 CCCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
          1 CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

                *                                    *                 
        693 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTT-A
          1 CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

                *                       *    **                       * 
        751 GCCCCGAACCTTCCAAAAATTACCATTTCACCCTTGAACTTCCAAAAATCCCATTTTTAA
          1 -CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

                                 *     *    *                       *  
        811 CCCTGAACCTTCCAAAAATTAACATTTCACCCTCGAACTTCCAAAAATCCCATTTTCGA
          1 CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

               *   *                              *   *     * *        
        870 CCCCGAATCTTCCAAAAATTACCATTTTACCCCCGAACATCCTAAAATTCGATTTTTGA
          1 CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

               *   *       *                 **                        *
        929 CCCCGAATCTTCCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGT
          1 CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-GA

                *                        
        989 CCCTAAACCTTCCAAAAATTACCATTTTA
          1 CCCTGAACCTTCCAAAAATTACCATTTTA


Statistics
Matches: 287,  Mismatches: 35, Indels: 5
        0.88            0.11        0.02

Matches are distributed among these distances:
  58    1  0.00
  59  259  0.90
  60   27  0.09

ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30


Consensus pattern (59 bp):   
CCCTGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA

Found at i:935 original size:177 final size:178

Alignment explanation


    Indices: 634--1015  Score: 570
    Period size: 177  Copynumber: 2.2  Consensus size: 178

        624 CCCCGGAGGT

                                       *                            *     *  
        634 CCCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAA
          1 CCCTAAACCTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCAA

                                            *                                
        699 ACCTTCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTTAGCCCCGAACCTTC
         66 ACCTTCCAAAAATTACCATTTTACCCCCGAACATCAAAAAATCCCATTTTTAGCCCCGAACCTTC

                                * *                         
        764 CAAAAATTACCATTTCACCCTTGAACTTCCAAAAATCCCATTTTT-AA
        131 CAAAAATTACCATTTCACCCCTAAACTTCCAAAAATCCCATTTTTGAA

                *                *                                         * 
        811 CCCTGAACCTTCCAAAAATTAACATTTCACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCGA
          1 CCCTAAACCTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCAA

             *                                 **     * *                *   
        876 ATCTTCCAAAAATTACCATTTTACCCCCGAACATCCTAAAATTCGATTTTT-GACCCCGAATCTT
         66 ACCTTCCAAAAATTACCATTTTACCCCCGAACATCAAAAAATCCCATTTTTAG-CCCCGAACCTT

                *           *                              **
        940 CCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGT
        130 CCAAAAATTACCATTTCACCCCTAAACTTCCAAAAATCCCATTTTTGAA

                                       
        989 CCCTAAACCTTCCAAAAATTACCATTT
          1 CCCTAAACCTTCCAAAAATTACCATTT

       1016 TA


Statistics
Matches: 182,  Mismatches: 21, Indels: 3
        0.88            0.10        0.01

Matches are distributed among these distances:
 176    1  0.01
 177  156  0.86
 178   25  0.14

ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30


Consensus pattern (178 bp):   
CCCTAAACCTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCAA
ACCTTCCAAAAATTACCATTTTACCCCCGAACATCAAAAAATCCCATTTTTAGCCCCGAACCTTC
CAAAAATTACCATTTCACCCCTAAACTTCCAAAAATCCCATTTTTGAA
Done.