Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009208.1 Kokia drynarioides strain JFW-HI SEQ_123913, 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: 4667
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:1110 original size:56 final size:56

Alignment explanation


    Indices: 1019--1234  Score: 265
    Period size: 56  Copynumber: 3.9  Consensus size: 56

       1009 TTGCATAGCC

                                                                      
       1019 TTACGCTCTAACCGAGACGTAAGCAAAA-CATAGCTCTAC-CTGAGCTATACATGGCA
          1 TTACGCTCTAACCGAGACGTAAG-AAAATCATAGCTCTACTC-GAGCTATACATGGCA

              * *      *                           * *    *     **  
       1075 TTGCACTCTAATCGAGACGTAAGAAAATCATAGCTCTACCCAAGCTGTACATAACA
          1 TTACGCTCTAACCGAGACGTAAGAAAATCATAGCTCTACTCGAGCTATACATGGCA

                   *   *           *                      *   *     
       1131 TTACGCTTTAAGCGAGACGTAAGCAAATCATAGCTCTACTCGAGCTGTACCTGGCA
          1 TTACGCTCTAACCGAGACGTAAGAAAATCATAGCTCTACTCGAGCTATACATGGCA

                                   *        *               
       1187 TTACGCTCTAACCGAGACGTAAGCAAATCATAACTCTACTCGAGCTAT
          1 TTACGCTCTAACCGAGACGTAAGAAAATCATAGCTCTACTCGAGCTAT

       1235 CCTTTAATGA


Statistics
Matches: 137,  Mismatches: 21, Indels: 4
        0.85            0.13        0.02

Matches are distributed among these distances:
  55    4  0.03
  56  132  0.96
  57    1  0.01

ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24


Consensus pattern (56 bp):   
TTACGCTCTAACCGAGACGTAAGAAAATCATAGCTCTACTCGAGCTATACATGGCA

Found at i:1216 original size:112 final size:112

Alignment explanation


    Indices: 1019--1225  Score: 308
    Period size: 112  Copynumber: 1.8  Consensus size: 112

       1009 TTGCATAGCC

                                                                      *      
       1019 TTACGCTCTAACCGAGACGTAAGCAAAACATAGCTCTACCTGAGCTATACATGGCATTGCACTCT
          1 TTACGCTCTAACCGAGACGTAAGCAAAACATAGCTCTACCTGAGCTATACATGGCATTACACTCT

              *                    *                       
       1084 AATCGAGACGTAAGAAAATCATAGCTCTACCCAAGCTGTACATAACA
         66 AACCGAGACGTAAGAAAATCATAACTCTACCCAAGCTGTACATAACA

                   *   *               *                   *   *         *   
       1131 TTACGCTTTAAGCGAGACGTAAGCAAATCATAGCTCTA-CTCGAGCTGTACCTGGCATTACGCTC
          1 TTACGCTCTAACCGAGACGTAAGCAAAACATAGCTCTACCT-GAGCTATACATGGCATTACACTC

                           *               
       1195 TAACCGAGACGTAAGCAAATCATAACTCTAC
         65 TAACCGAGACGTAAGAAAATCATAACTCTAC

       1226 TCGAGCTATC


Statistics
Matches: 84,  Mismatches: 10, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
 111    2  0.02
 112   82  0.98

ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23


Consensus pattern (112 bp):   
TTACGCTCTAACCGAGACGTAAGCAAAACATAGCTCTACCTGAGCTATACATGGCATTACACTCT
AACCGAGACGTAAGAAAATCATAACTCTACCCAAGCTGTACATAACA

Found at i:3215 original size:12 final size:12

Alignment explanation


    Indices: 3200--3233  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       3190 ATCTTCCTCT

                      * 
       3200 TCTTCTTCAGGA
          1 TCTTCTTCAGAA

                        
       3212 TCTTCTTCAGAA
          1 TCTTCTTCAGAA

             *        
       3224 TTTTCTTCAG
          1 TCTTCTTCAG

       3234 CTTGCTATTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47


Consensus pattern (12 bp):   
TCTTCTTCAGAA
Done.