Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007079.1 Kokia drynarioides strain JFW-HI SEQ_121688, 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: 12399
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33


Found at i:2041 original size:56 final size:56

Alignment explanation


    Indices: 1928--2033  Score: 140
    Period size: 56  Copynumber: 1.9  Consensus size: 56

       1918 CACACGCTCG

                  *         *               *     *   *    *        
       1928 TGTGCCGAGCCCGTGTCTCACTAAATAGTATGTACACATGATTAGATGCACACCCA
          1 TGTGCCCAGCCCGTGTATCACTAAATAGTATGCACACACGATCAGATACACACCCA

                       *                                 *    
       1984 TGTGCCCAGCCTGTGTATCACTAAATAGTATGCACACACGATCAGGTACA
          1 TGTGCCCAGCCCGTGTATCACTAAATAGTATGCACACACGATCAGATACA

       2034 TGGCCATGGT


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  56   42  1.00

ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25


Consensus pattern (56 bp):   
TGTGCCCAGCCCGTGTATCACTAAATAGTATGCACACACGATCAGATACACACCCA

Found at i:4654 original size:52 final size:52

Alignment explanation


    Indices: 4573--4755  Score: 217
    Period size: 52  Copynumber: 3.5  Consensus size: 52

       4563 AACGAAAAGG

                       *            *          *                
       4573 TCCGATGACTAAGTGTCATCGTGAATATATGAATCATTTACGGATTATGAG-
          1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGA

            *            *      *                                
       4624 GCTCGATGACTATTTGTCATTGTGAGTATATGAATCCTTTACGGATTATGAGA
          1 TC-CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGA

                          *           *     *           **      
       4677 TCCGATGACTATGTATCATCGTGAGTGTATGATTCCTTTACGGAACA-GAGA
          1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGA

               *        *       *       
       4728 TCCAATGACTATTTGTCATCATGAGTAT
          1 TCCGATGACTATGTGTCATCGTGAGTAT

       4756 TAAATGAAAC


Statistics
Matches: 111,  Mismatches: 19, Indels: 4
        0.83            0.14        0.03

Matches are distributed among these distances:
  51   28  0.25
  52   82  0.74
  53    1  0.01

ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35


Consensus pattern (52 bp):   
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGA

Found at i:11100 original size:28 final size:23

Alignment explanation


    Indices: 11044--11088  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      11034 GATATTCTAA

                *                  
      11044 ATATACATGTGAAATAAAAATTT
          1 ATATTCATGTGAAATAAAAATTT

                                  
      11067 ATATTCATGTGAAATAAAAATT
          1 ATATTCATGTGAAATAAAAATT

      11089 GCTCCTATAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36


Consensus pattern (23 bp):   
ATATTCATGTGAAATAAAAATTT
Done.