Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000320.1 Kokia drynarioides strain JFW-HI SEQ_111084, 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: 2318
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37


Found at i:578 original size:17 final size:17

Alignment explanation


    Indices: 558--640  Score: 96
    Period size: 17  Copynumber: 4.9  Consensus size: 17

        548 AAATAAATTT

                             
        558 TAAATTTAAATTTATAA
          1 TAAATTTAAATTTATAA

                            **
        575 TAAATTTAAATTTCA-GC
          1 TAAATTTAAATTT-ATAA

                             
        592 TAAATTTAAATTTATAA
          1 TAAATTTAAATTTATAA

                *    *    *  
        609 TAAACTTAATTTTAAAA
          1 TAAATTTAAATTTATAA

                     *     
        626 TAAATTTAAGTTTAT
          1 TAAATTTAAATTTAT

        641 TAGGCCCAGA


Statistics
Matches: 54,  Mismatches: 10, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  16    1  0.02
  17   52  0.96
  18    1  0.02

ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46


Consensus pattern (17 bp):   
TAAATTTAAATTTATAA

Found at i:598 original size:34 final size:34

Alignment explanation


    Indices: 558--640  Score: 112
    Period size: 34  Copynumber: 2.4  Consensus size: 34

        548 AAATAAATTT

                                 *        * **
        558 TAAATTTAAATTTATAATAAATTTAAATTTCAGC
          1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA

                                      *       
        592 TAAATTTAAATTTATAATAAACTTAATTTTAAAA
          1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA

                     *     
        626 TAAATTTAAGTTTAT
          1 TAAATTTAAATTTAT

        641 TAGGCCCAGA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   43  1.00

ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46


Consensus pattern (34 bp):   
TAAATTTAAATTTATAATAAACTTAAATTTAAAA

Found at i:1352 original size:205 final size:205

Alignment explanation


    Indices: 1017--1816  Score: 1199
    Period size: 205  Copynumber: 3.9  Consensus size: 205

       1007 TCTTTGTGTT

                *       * *       * *      *      *      *         *     * * 
       1017 TCATTAGGAAGAAGGATTTGGTTCGCTTCTTTGTATCTCATCAGGGAGCTAACCACTTTATTGTT
          1 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACC-TTTTATAGCT

                         *     *          *    *      *      *  **    *      
       1082 TCGACCTGCTTCTCAGTGTTTCATCAGGAAACTGGAGTTCGAAGATTTGCTCACATCGGGCGTGA
         65 TCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGA

                                 *          *          *    *        *      *
       1147 GTTTGATTTGGTCTTCTTCTCGGTATCTCATCGGGAAGATGACTGCGTAGTTTGTTTCAATTCGT
        130 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATTCGC

                       
       1212 TTCTCTGTATC
        195 TTCTCTGTATC

                      *            *      *                                  
       1223 TCATCAGGAAAACGAATTTGGTCTACTTCTCCGTATCTTATCAGGAAGCTAACCTTTTATAGCTT
          1 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACCTTTTATAGCTT

                                                                             
       1288 CGACCTGC-TCTTCAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGA
         66 CGACCTGCTTCTT-AGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGA

                           *                          *   *                  
       1352 GTTTGATTTGGTCTTGTTCTCAGTATCTCATCAGGAAGATGATCGCATCGTTTGTTTTAATTCGC
        130 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATTCGC

                       
       1417 TTCTCTGTATC
        195 TTCTCTGTATC

                                                                 *           
       1428 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACATTTTAT-GACT
          1 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACCTTTTATAG-CT

                                           *                   *   *         
       1492 TCGACCTGCTTCTTAGTGTCTCATCAGGAAGTTGGGGTTCGAGGATTTGTTTGTAACGAGCGTGA
         65 TCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGA

                                                                         *   
       1557 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCCGC
        130 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATTCGC

                       
       1622 TTCTCTGTATC
        195 TTCTCTGTATC

                                                                         *   
       1633 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACCTTTTATAACTT
          1 TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACCTTTTATAGCTT

                                     *                                       
       1698 CGACCTGCTTCTTAGTGTCTCATCAAGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGAG
         66 CGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGAG

                                          *                       
       1763 TTTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCGCGTCGTTTGT
        131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT

       1817 GGATAATCAC


Statistics
Matches: 540,  Mismatches: 50, Indels: 9
        0.90            0.08        0.02

Matches are distributed among these distances:
 204    4  0.01
 205  489  0.91
 206   47  0.09

ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37


Consensus pattern (205 bp):   
TCATCAGGAAGACGAATTTGGTCCACTTCTTCGTATCTTATCAGGAAGCTAACCTTTTATAGCTT
CGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAGGATTTGTTCGTATCGAGCGTGAG
TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATTCGCT
TCTCTGTATC
Done.