Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013629.1 Kokia drynarioides strain JFW-HI SEQ_128657, 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: 8590
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1148 original size:23 final size:23

Alignment explanation


    Indices: 1122--1208  Score: 142
    Period size: 23  Copynumber: 3.8  Consensus size: 23

       1112 TTTGCACAAT

                                   
       1122 AATCACATTAACTTTTAAGCATA
          1 AATCACATTAACTTTTAAGCATA

                                    
       1145 AATCACA-TATACTTTTAAGCATA
          1 AATCACATTA-ACTTTTAAGCATA

                                   
       1168 AATCACATTAACTTTTAAGCATA
          1 AATCACATTAACTTTTAAGCATA

                               
       1191 AATCACATGT-ACTTTTAA
          1 AATCACAT-TAACTTTTAA

       1209 CACATTTAAT


Statistics
Matches: 61,  Mismatches: 0, Indels: 6
        0.91            0.00        0.09

Matches are distributed among these distances:
  22    2  0.03
  23   56  0.92
  24    3  0.05

ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36


Consensus pattern (23 bp):   
AATCACATTAACTTTTAAGCATA

Found at i:1623 original size:23 final size:23

Alignment explanation


    Indices: 1596--1705  Score: 163
    Period size: 23  Copynumber: 4.8  Consensus size: 23

       1586 TTTGCACAAT

                                   
       1596 AATCACATTAACTTTTAAGCATA
          1 AATCACATTAACTTTTAAGCATA

                                    
       1619 AATCACA-TATACTTTTAAGCATA
          1 AATCACATTA-ACTTTTAAGCATA

                                    
       1642 AATCACA-TATACTTTTAAGCATA
          1 AATCACATTA-ACTTTTAAGCATA

             *                     
       1665 AGTCACATTAACTTTTAAGCATA
          1 AATCACATTAACTTTTAAGCATA

                               
       1688 AATCACATGT-ACTTTTAA
          1 AATCACAT-TAACTTTTAA

       1706 CACATTTAAT


Statistics
Matches: 82,  Mismatches: 2, Indels: 6
        0.91            0.02        0.07

Matches are distributed among these distances:
  22    2  0.02
  23   77  0.94
  24    3  0.04

ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35


Consensus pattern (23 bp):   
AATCACATTAACTTTTAAGCATA

Found at i:4604 original size:39 final size:39

Alignment explanation


    Indices: 4478--4711  Score: 157
    Period size: 39  Copynumber: 6.0  Consensus size: 39

       4468 TTTATAACTT

                      * *         *  **     *    *  
       4478 GCAATGACACAGCAAACACTACGATAATATTACTGAACTG
          1 GCAATGACACTGTAAACACTACAATGTTA-TAATGAAATG

               *     *           *    * *  *        
       4518 GCAGTGACAATGTAAACACTAAAATGCTGTAGTG-AATCG
          1 GCAATGACACTGTAAACACTACAATGTTATAATGAAAT-G

             * *              *             *      
       4557 GTAGTGACACTGTAAACATTACAATGTTATAAGGAAATG
          1 GCAATGACACTGTAAACACTACAATGTTATAATGAAATG

                                           *    *  
       4596 GCAATGACACTGTAAACACTACAATGTTATACTGAACTG
          1 GCAATGACACTGTAAACACTACAATGTTATAATGAAATG

              *  *      *        *          *    *  
       4635 GCGATCACACTGGAAACA-TCGCAATGTTATATTGAAGTG
          1 GCAATGACACTGTAAACACT-ACAATGTTATAATGAAATG

             *            *       * *        *    
       4674 GTAATGACACTGTAGACACTACCAGGTTATAATCAAAT
          1 GCAATGACACTGTAAACACTACAATGTTATAATGAAAT

       4712 TATTACATAA


Statistics
Matches: 148,  Mismatches: 42, Indels: 9
        0.74            0.21        0.05

Matches are distributed among these distances:
  38    3  0.02
  39  121  0.82
  40   24  0.16

ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25


Consensus pattern (39 bp):   
GCAATGACACTGTAAACACTACAATGTTATAATGAAATG
Done.