Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005815.1 Kokia drynarioides strain JFW-HI SEQ_120099, 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: 1762
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34


Found at i:1677 original size:33 final size:33

Alignment explanation


    Indices: 1547--1751  Score: 148
    Period size: 33  Copynumber: 6.2  Consensus size: 33

       1537 TACCCCTCTT

                         *     *   *          
       1547 ACATCACCCTCCCTACA-AGCTTTTACCCC-TCA
          1 ACATCACCCTCCCCA-ATAACTTCTACCCCTTCA

             * *            *   * *  *       
       1579 ATAGCACCCTCCCCAACAACGTGTAACCCTTCA
          1 ACATCACCCTCCCCAATAACTTCTACCCCTTCA

               *    *  *               **     
       1612 ACAACACCTTCACC-ATCAACTTCTACATCTTCA
          1 ACATCACCCTCCCCAAT-AACTTCTACCCCTTCA

                 *            *      *       
       1645 ACATCGCCCTCCCCAATAGCTTCTATCCCTTCA
          1 ACATCACCCTCCCCAATAACTTCTACCCCTTCA

               *    * **                      
       1678 ACAACACCTTTACC-ATCAACTTCTACCCCTTCA
          1 ACATCACCCTCCCCAAT-AACTTCTACCCCTTCA

                            *                
       1711 ACATCACCCTCCCCAACAACTTCTACCCCTTCA
          1 ACATCACCCTCCCCAATAACTTCTACCCCTTCA

               *    
       1744 ACAACACC
          1 ACATCACC

       1752 TTCACCATAA


Statistics
Matches: 129,  Mismatches: 38, Indels: 11
        0.72            0.21        0.06

Matches are distributed among these distances:
  31    1  0.01
  32   23  0.18
  33  102  0.79
  34    3  0.02

ACGTcount: A:0.29, C:0.45, G:0.03, T:0.23


Consensus pattern (33 bp):   
ACATCACCCTCCCCAATAACTTCTACCCCTTCA

Found at i:1677 original size:66 final size:66

Alignment explanation


    Indices: 1583--1759  Score: 264
    Period size: 66  Copynumber: 2.7  Consensus size: 66

       1573 CCCTCAATAG

                            * *  *                                  *        
       1583 CACCCTCCCCAACAACGTGTAACCCTTCAACAACACCTTCACCATCAACTTCTACATCTTCAACA
          1 CACCCTCCCCAACAACTTCTACCCCTTCAACAACACCTTCACCATCAACTTCTACACCTTCAACA

             
       1648 T
         66 T

             *          * *      *                 *               *         
       1649 CGCCCTCCCCAATAGCTTCTATCCCTTCAACAACACCTTTACCATCAACTTCTACCCCTTCAACA
          1 CACCCTCCCCAACAACTTCTACCCCTTCAACAACACCTTCACCATCAACTTCTACACCTTCAACA

             
       1714 T
         66 T

                                                         
       1715 CACCCTCCCCAACAACTTCTACCCCTTCAACAACACCTTCACCAT
          1 CACCCTCCCCAACAACTTCTACCCCTTCAACAACACCTTCACCAT

       1760 AAA


Statistics
Matches: 97,  Mismatches: 14, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  66   97  1.00

ACGTcount: A:0.29, C:0.45, G:0.02, T:0.24


Consensus pattern (66 bp):   
CACCCTCCCCAACAACTTCTACCCCTTCAACAACACCTTCACCATCAACTTCTACACCTTCAACA
T

Found at i:1745 original size:18 final size:18

Alignment explanation


    Indices: 1694--1748  Score: 55
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       1684 CCTTTACCAT

                              
       1694 CAACTTCTACCCCTTCAA
          1 CAACTTCTACCCCTTCAA

                          **   
       1712 C-A--TC-ACCCTCCCCAA
          1 CAACTTCTACCC-CTTCAA

                              
       1727 CAACTTCTACCCCTTCAA
          1 CAACTTCTACCCCTTCAA

                
       1745 CAAC
          1 CAAC

       1749 ACCTTCACCA


Statistics
Matches: 28,  Mismatches: 4, Indels: 10
        0.67            0.10        0.24

Matches are distributed among these distances:
  14    4  0.14
  15    7  0.25
  16    1  0.04
  17    1  0.04
  18   11  0.39
  19    4  0.14

ACGTcount: A:0.29, C:0.49, G:0.00, T:0.22


Consensus pattern (18 bp):   
CAACTTCTACCCCTTCAA
Done.