Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009684.1 Kokia drynarioides strain JFW-HI SEQ_124402, 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: 3600
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37


Found at i:177 original size:29 final size:29

Alignment explanation


    Indices: 134--400  Score: 279
    Period size: 29  Copynumber: 9.1  Consensus size: 29

        124 GAAGGTCCCT

                                          
        134 AAACTATCCAAAAATTCCATTTTTACCCCG
          1 AAACT-TCCAAAAATTCCATTTTTACCCCG

                                         **
        164 AAACTTCCAAAAA-TCACATTTTTTACCCTA
          1 AAACTTCCAAAAATTC-CA-TTTTTACCCCG

               *   *    *               *
        194 AAATTTCTAAAATTTCCATTTTTACCCCT
          1 AAACTTCCAAAAATTCCATTTTTACCCCG

                          *       *     *
        223 AAACTTCCAAAAATCCCATTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTACCCCG

                                         *
        252 AAACTTCCAAAAATTCCA-TTTTACCCCCC
          1 AAACTTCCAAAAATTCCATTTTTA-CCCCG

                    *     *       *     *
        281 AAACTTCCTAAAATCCCATTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTACCCCG

               *                        * 
        310 AAAGTTCCAAAAATTCCATTTTTACCCTTG
          1 AAACTTCCAAAAATTCCATTTTTACCC-CG

                          *            ** 
        340 -AACTTCCAAAAATCCCATTTTTGACCTTG
          1 AAACTTCCAAAAATTCCATTTTT-ACCCCG

                                          
        369 AAACTTCCAAAAATTCCATTTTTAACCCCG
          1 AAACTTCCAAAAATTCCATTTTT-ACCCCG

              
        399 AA
          1 AA

        401 TTTTTCCAAA


Statistics
Matches: 196,  Mismatches: 33, Indels: 16
        0.80            0.13        0.07

Matches are distributed among these distances:
  28    6  0.03
  29  128  0.65
  30   60  0.31
  31    2  0.01

ACGTcount: A:0.36, C:0.30, G:0.03, T:0.32


Consensus pattern (29 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCG

Found at i:296 original size:58 final size:59

Alignment explanation


    Indices: 134--397  Score: 345
    Period size: 58  Copynumber: 4.5  Consensus size: 59

        124 GAAGGTCCCT

                                         *               *       *    * 
        134 AAACTATCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCACATTTTTTACCCTA
          1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA

               *   *    *                                              
        194 AAATTTCTAAAATTTCCATTTTTACCCCTAAACTTCCAAAAATCCCA-TTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA

                                         *        *                     
        252 AAACTTCCAAAAATTCCA-TTTTACCCCCCAAACTTCCTAAAATCCCA-TTTTGACCCCA
          1 AAACTTCCAAAAATTCCATTTTTA-CCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA

               *                       * *                          ***
        310 AAAGTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTTG
          1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA

                                         
        369 AAACTTCCAAAAATTCCATTTTTAACCCC
          1 AAACTTCCAAAAATTCCATTTTT-ACCCC

        398 GAATTTTTCC


Statistics
Matches: 178,  Mismatches: 22, Indels: 8
        0.86            0.11        0.04

Matches are distributed among these distances:
  57    5  0.03
  58   92  0.52
  59   73  0.41
  60    8  0.04

ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32


Consensus pattern (59 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA

Found at i:467 original size:28 final size:28

Alignment explanation


    Indices: 405--458  Score: 81
    Period size: 28  Copynumber: 1.9  Consensus size: 28

        395 CCCGAATTTT

                                **      
        405 TCCAAAATTACCATTTCACCTTCGAGAA
          1 TCCAAAATTACCATTTCACCCCCGAGAA

                            *         
        433 TCCAAAATTACCATTTTACCCCCGAG
          1 TCCAAAATTACCATTTCACCCCCGAG

        459 TATTTAAAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  28   23  1.00

ACGTcount: A:0.33, C:0.31, G:0.07, T:0.28


Consensus pattern (28 bp):   
TCCAAAATTACCATTTCACCCCCGAGAA

Found at i:1441 original size:31 final size:31

Alignment explanation


    Indices: 1383--1441  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1373 TGTGAAATCA

                       *         **        
       1383 TATACATGAAATTTTAATTATGGTTCAAATG
          1 TATACATGAAACTTTAATTATAATTCAAATG

                 *             *        
       1414 TATACGTGAAACTTTAATTTTAATTCAA
          1 TATACATGAAACTTTAATTATAATTCAA

       1442 TTACACATGT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   23  1.00

ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42


Consensus pattern (31 bp):   
TATACATGAAACTTTAATTATAATTCAAATG
Done.