Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005312.1 Kokia drynarioides strain JFW-HI SEQ_119246, 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, 656

Length: 1094
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41


Found at i:436 original size:30 final size:30

Alignment explanation


    Indices: 394--682  Score: 194
    Period size: 29  Copynumber: 9.8  Consensus size: 30

        384 CGAACTTTTC

                                  **     *
        394 AAAATT-CCATTTTTAACCTCAGTTTTCCT
          1 AAAATTACCATTTTTAACCTCAAATTTCCA

                               *           *
        423 AAAATTACCA-TTTT-ACCCCTAAACTTT-CT
          1 AAAATTACCATTTTTAACCTC-AAA-TTTCCA

                           *    *  *       
        452 AAAA-TACCATTTTTGACCTTAATTTCTCCA
          1 AAAATTACCATTTTTAACCTCAAATT-TCCA

                            *  *           
        482 AAAATTA-CATTTTTACCCCCAAAATTTCC-
          1 AAAATTACCATTTTTAACCTC-AAATTTCCA

                  *        *      *         
        511 AAAA-TCCCATTTTTTACCTC-GATTTCTCTA
          1 AAAATTACCATTTTTAACCTCAAATTTC-C-A

                            *    *  *     
        541 AAAATTACCATTTTTACCCTCGAACTTCCA
          1 AAAATTACCATTTTTAACCTCAAATTTCCA

                                  *         
        571 AAAATT-CCATTTTTAACC-CATATTTCTCAA
          1 AAAATTACCATTTTTAACCTCAAATTTC-C-A

                  *         *    *  *     
        601 AAAATTGCCA-TTTTACCCTCGAACTTCCA
          1 AAAATTACCATTTTTAACCTCAAATTTCCA

                                           
        630 AAAATT-CCATTTTTAACCTCAAATTTTCC-
          1 AAAATTACCATTTTTAACCTCAAA-TTTCCA

                            *        
        659 AAAATTACCA-TTTTACCCTCAAAT
          1 AAAATTACCATTTTTAACCTCAAAT

        683 AACTAAAAAT


Statistics
Matches: 204,  Mismatches: 34, Indels: 45
        0.72            0.12        0.16

Matches are distributed among these distances:
  27    5  0.02
  28   22  0.11
  29   86  0.42
  30   59  0.29
  31   28  0.14
  32    4  0.02

ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38


Consensus pattern (30 bp):   
AAAATTACCATTTTTAACCTCAAATTTCCA

Found at i:515 original size:59 final size:59

Alignment explanation


    Indices: 367--681  Score: 304
    Period size: 59  Copynumber: 5.4  Consensus size: 59

        357 AAGTTTTTAG

                               *  *   *                      *       * 
        367 AAATTA-CATTTTACCCCCGAACTTTTCAAAATTCCATTTTTAACCTCAGTTT-TCCTA
          1 AAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCTCAATTTCTCCAA

                              *   *    *     *        *    *           
        424 AAATTACCATTTTACCCCTAAACTTTCTAAAATACCATTTTTGACCTTAATTTCTCCAA
          1 AAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCTCAATTTCTCCAA

                                              *        *     *       *  
        483 AAATTA-CATTTTTACCCCCAAAATTTCCAAAATCCCATTTTTTACCTCGATTTCTCTAA
          1 AAATTACCA-TTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCTCAATTTCTCCAA

                              *  *  *                                  *  
        542 AAATTACCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTAACC-CATATTTCTCAAA
          1 AAATTACCA-TTTTACCCCCAAAATTTCC-AAAATTCCATTTTTAACCTCA-ATTTCTCCAA

                 *           *  *  *                                     
        602 AAATTGCCATTTTACCCTC-GAACTTCCAAAAATTCCATTTTTAACCTCAAATTT-TCC-A
          1 AAATTACCATTTTACCCCCAAAATTTCC-AAAATTCCATTTTTAACCTC-AATTTCTCCAA

                             *    
        660 AAATTACCATTTTACCCTCAAA
          1 AAATTACCATTTTACCCCCAAA

        682 TAACTAAAAA


Statistics
Matches: 221,  Mismatches: 28, Indels: 16
        0.83            0.11        0.06

Matches are distributed among these distances:
  57    6  0.03
  58   59  0.27
  59  105  0.48
  60   50  0.23
  61    1  0.00

ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38


Consensus pattern (59 bp):   
AAATTACCATTTTACCCCCAAAATTTCCAAAATTCCATTTTTAACCTCAATTTCTCCAA

Done.