Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005863.1 Kokia drynarioides strain JFW-HI SEQ_120184, 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: 5005
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34


Found at i:561 original size:199 final size:199

Alignment explanation


    Indices: 177--923  Score: 1235
    Period size: 199  Copynumber: 3.7  Consensus size: 199

        167 CTGTGTAGTT

                     *    *   *           *     *      *                     
        177 TGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGATGAATTTTGGTTCACTTCTCAGTACCTCA
          1 TGTTTCAATCCGCTCCTCCGTATCTCATCAGGAAGACGAA-TTCGGTTCACTTCTCAGTACCTCA

                                 *    *          *                           
        242 TCTGGAAGCTAACCATTTATTGCTTCTACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGTTTTG
         65 TCTGGAAGCTAACCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTG

                                                                             
        307 AAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCC
        130 AAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCC

                 
        372 ATCAC
        195 ATCAC

                              *   *      *                                 * 
        377 TGTTTCAATCCGCTCCTCTGTACCTCATCGGGAAGACGAATTCGGTTCACTTCTCAGTACCTCCT
          1 TGTTTCAATCCGCTCCTCCGTATCTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTACCTCAT

                                   *    *                   *                
        442 CTGGAAGCTAACCATTTATTTCTCCCACATGCTTCTCAGTGTCTCATCCGGAA-CTTGGGTTTTG
         66 CTGGAAGCTAACCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGC-TGGGTTTTG

                                                   *                         
        506 AAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTTAGTGCCTCATCAGGAAGATGATCCC
        130 AAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCC

                 
        571 ATCAC
        195 ATCAC

                                     *            *    *                     
        576 TGTTTCAATCCGCTCCTCCGTATCTTATCAGGAAGACGGATTCAGTTCACTTCTCAGTACCTCAT
          1 TGTTTCAATCCGCTCCTCCGTATCTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTACCTCAT

                      *                                    *                 
        641 CTGGAAGCTATCCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATTAGGAAGCTGGGTTTTGA
         66 CTGGAAGCTAACCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGA

                                                                             
        706 AGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCCA
        131 AGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCCA

                
        771 TCAC
        196 TCAC

                                     *                                       
        775 TGTTTCAATCCGCTCCTCCGTATCTTATCAGGAAGACGAATTCGGTTCACTTCTCAGTACCTCAT
          1 TGTTTCAATCCGCTCCTCCGTATCTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTACCTCAT

                      *                                           *          
        840 CTGGAAGCTATCCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGTTTTGA
         66 CTGGAAGCTAACCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGA

                          *    
        905 AGATTTGCTCGTTTTGAGC
        131 AGATTTGCTCGTTTCGAGC

        924 GTGGGCTTGG


Statistics
Matches: 512,  Mismatches: 33, Indels: 5
        0.93            0.06        0.01

Matches are distributed among these distances:
 198    1  0.00
 199  476  0.93
 200   35  0.07

ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36


Consensus pattern (199 bp):   
TGTTTCAATCCGCTCCTCCGTATCTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTACCTCAT
CTGGAAGCTAACCATTTATTTCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTTGA
AGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGCCTCATCAGGAAGATGATCCCA
TCAC

Found at i:1827 original size:42 final size:42

Alignment explanation


    Indices: 1746--1827  Score: 103
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1736 GTTCCAGGAT

                                  *      *    *       
       1746 GCCCTTTGCGAGTTTTCATCCTGAACCCCTTTTTTTTTTAAC
          1 GCCCTTTGCGAGTTTTCATCCTCAACCCCATTTTGTTTTAAC

                      *     *                        
       1788 GCCCTTTGCGGGTTTTTAT-CTCAACTCCCATTTTGTTTTA
          1 GCCCTTTGCGAGTTTTCATCCTCAAC-CCCATTTTGTTTTA

       1828 GGTGAAGTAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  41    5  0.15
  42   29  0.85

ACGTcount: A:0.13, C:0.27, G:0.13, T:0.46


Consensus pattern (42 bp):   
GCCCTTTGCGAGTTTTCATCCTCAACCCCATTTTGTTTTAAC
Done.