Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006035.1 Kokia drynarioides strain JFW-HI SEQ_120497, 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: 18384
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34


Found at i:299 original size:4 final size:4

Alignment explanation


    Indices: 290--356  Score: 82
    Period size: 4  Copynumber: 16.5  Consensus size: 4

        280 AAACACATTA

                        *                     *           *             
        290 TCTT TCTT TCAT TC-T TCTT TCTT TCCTC TCTT TCTT CCTT TCTT TCTT
          1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT

                                   
        338 TCTTT TCTT TCTT TCTT TC
          1 TC-TT TCTT TCTT TCTT TC

        357 CTGTTTATTT


Statistics
Matches: 55,  Mismatches: 5, Indels: 6
        0.83            0.08        0.09

Matches are distributed among these distances:
   3    3  0.05
   4   45  0.82
   5    7  0.13

ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69


Consensus pattern (4 bp):   
TCTT

Found at i:338 original size:25 final size:25

Alignment explanation


    Indices: 304--356  Score: 79
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        294 TCTTTCATTC

                                     
        304 TTCTTTCTTTCCTCTCTTTCTTCCT
          1 TTCTTTCTTTCCTCTCTTTCTTCCT

                       * *        *  
        329 TTCTTTCTTTCTTTTCTTTCTTTCT
          1 TTCTTTCTTTCCTCTCTTTCTTCCT

               
        354 TTC
          1 TTC

        357 CTGTTTATTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70


Consensus pattern (25 bp):   
TTCTTTCTTTCCTCTCTTTCTTCCT

Found at i:10140 original size:21 final size:21

Alignment explanation


    Indices: 10114--10165  Score: 70
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      10104 TGAGACAATA

                                  
      10114 CTACCGATACAAGT-ATGACTT
          1 CTACCGATACAAGTCATG-CTT

                   *   *         
      10135 CTACCGAAACATGTCATGCTT
          1 CTACCGATACAAGTCATGCTT

                      
      10156 CTACCGATAC
          1 CTACCGATAC

      10166 TAAAAACTCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  21   24  0.89
  22    3  0.11

ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27


Consensus pattern (21 bp):   
CTACCGATACAAGTCATGCTT

Found at i:11031 original size:52 final size:52

Alignment explanation


    Indices: 10953--11242  Score: 454
    Period size: 52  Copynumber: 5.6  Consensus size: 52

      10943 AATTTAATAT

                                 *     *       * *     *        
      10953 TCACGATGACACATAGTCATCAGACCTCTTAATCCGTGAAGGAATCATATAC
          1 TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

                             *                 *                
      11005 TCACGATGACACATAGTAATCGGACCTTTTAATCCGTAAAGGATTCATATAC
          1 TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

                    *      *                                    
      11057 TCACGATGGCACATAATCATCGGACCTTTTAATCCATAAAGGATTCATATAC
          1 TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

               *    *                                           
      11109 TCAGGATGTCACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC
          1 TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

                *   *                                           
      11161 TCACAATGCCACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC
          1 TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

             *                            
      11213 TTACGATGACACATAGTCATCGGACCTTTT
          1 TCACGATGACACATAGTCATCGGACCTTTT

      11243 CTTTATTTAC


Statistics
Matches: 220,  Mismatches: 18, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  52  220  1.00

ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29


Consensus pattern (52 bp):   
TCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCATATAC

Done.