Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008343.1 Kokia drynarioides strain JFW-HI SEQ_123009, 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: 5726
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Found at i:3131 original size:21 final size:19

Alignment explanation


    Indices: 3107--3162  Score: 58
    Period size: 20  Copynumber: 2.7  Consensus size: 19

       3097 TTTTACCCAA

                                 
       3107 AAAAAATAGAGAAAAGAAAAT
          1 AAAAAA-AGA-AAAAGAAAAT

                            *    
       3128 AAAAGAAAAGAAAAAGGAAAT
          1 -AAA-AAAAGAAAAAGAAAAT

                          
       3149 AGAAAAAAGAAAAA
          1 A-AAAAAAGAAAAA

       3163 AGGAGAGGTC


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  20   11  0.35
  21   11  0.35
  22    6  0.19
  23    3  0.10

ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05


Consensus pattern (19 bp):   
AAAAAAAGAAAAAGAAAAT

Found at i:3163 original size:21 final size:21

Alignment explanation


    Indices: 3106--3166  Score: 70
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       3096 CTTTTACCCA

                       *     *    
       3106 AAAAAAATAGAGAAAAGAAAAT
          1 AAAAAAA-AGAAAAAAGGAAAT

                                  
       3128 AAAAGAAAAG-AAAAAGGAAAT
          1 AAAA-AAAAGAAAAAAGGAAAT

             *                
       3149 AGAAAAAAGAAAAAAGGA
          1 AAAAAAAAGAAAAAAGGA

       3167 GAGGTCAAGA


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  20    5  0.15
  21   20  0.59
  22    6  0.18
  23    3  0.09

ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05


Consensus pattern (21 bp):   
AAAAAAAAGAAAAAAGGAAAT

Found at i:4305 original size:96 final size:95

Alignment explanation


    Indices: 4141--4368  Score: 287
    Period size: 96  Copynumber: 2.4  Consensus size: 95

       4131 TGAAGCGGTT

                 *     *       *       * *     *      *                      
       4141 ATCTTTCTGATAAGATACAAAGAAGTGGACCAAAACAATGAAGTAGAGCTCAACATCCTTAAGGT
          1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCTTAAGGT

                                           
       4206 TACAGTGGAATAGAGCGAAACTTCAAAACCC
         66 TACAGTGGAATAGAGCGAAACTTC-AAACCC

                  *                                              **      *   
       4237 ATCTTCTTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAATGT-CTATGAGG
          1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCT-TAAGG

                      *        *           
       4301 TTACAGTGGAGTAGAGCGATACTTCAAACCC
         65 TTACAGTGGAATAGAGCGAAACTTCAAACCC

                     *              *   *        
       4332 ATCTTCCTGGTGAGATACAGAGAAATGTGTCAAAATA
          1 ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATA

       4369 GGTAGCAGAT


Statistics
Matches: 114,  Mismatches: 17, Indels: 3
        0.85            0.13        0.02

Matches are distributed among these distances:
  95   41  0.36
  96   73  0.64

ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24


Consensus pattern (95 bp):   
ATCTTCCTGATGAGATACAGAGAAGTGTATCAAAATAATGAAATAGAGCTCAACATCCTTAAGGT
TACAGTGGAATAGAGCGAAACTTCAAACCC

Found at i:4643 original size:46 final size:45

Alignment explanation


    Indices: 4519--4644  Score: 153
    Period size: 45  Copynumber: 2.8  Consensus size: 45

       4509 TACATCATCG

                   *                                   * 
       4519 TCTAATCGTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACTA
          1 TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA

              *            *  *        *       *    *   *
       4564 TCCAATCTTTTACCCTTACTCAAGAGGAGCAGATTTAAGCTACCG
          1 TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA

             *                                  
       4609 TTTAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
          1 TCTAATCTTTTACCCCTAA-TCAAGAGGGGCAGATT

       4645 AAAGTTGTAA


Statistics
Matches: 66,  Mismatches: 14, Indels: 1
        0.81            0.17        0.01

Matches are distributed among these distances:
  45   51  0.77
  46   15  0.23

ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29


Consensus pattern (45 bp):   
TCTAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCA
Done.