Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007862.1 Kokia drynarioides strain JFW-HI SEQ_122501, 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: 9196
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Found at i:5288 original size:36 final size:36

Alignment explanation


    Indices: 5234--5468  Score: 208
    Period size: 36  Copynumber: 6.6  Consensus size: 36

       5224 TCGATGGAAA

                                                
       5234 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

              *   *     *          *             
       5270 GCATACTTCTCGGTTAGAGCGTATTGCTATGT-AATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAA-T

            *                   *        * *  * 
       5306 TCTTACGTCTCGATTAGAGCATAATGCTAAGAGATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

                                      *  *    * 
       5342 GCTTAC-TCTCGATTAGAGCGTAATGATACGTGATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

              *   *             *  *             
       5377 GCATACATCTCGATTAGAGCTTATTGCTATGT-AATT
          1 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAA-T

            *           *      *               * 
       5413 ACTTACGTCTCGGTTAGAGGGTAATGCTAAT-TGACT
          1 GCTTACGTCTCGATTAGAGCGTAATGCT-ATGTGAAT

            *    *      *       
       5449 ACTTATGTCTCGGTTAGAGC
          1 GCTTACGTCTCGATTAGAGC

       5469 ATAAGCCCAT


Statistics
Matches: 159,  Mismatches: 34, Indels: 12
        0.78            0.17        0.06

Matches are distributed among these distances:
  35   33  0.21
  36  122  0.77
  37    4  0.03

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (36 bp):   
GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAAT

Found at i:5393 original size:71 final size:72

Alignment explanation


    Indices: 5241--5438  Score: 211
    Period size: 71  Copynumber: 2.8  Consensus size: 72

       5231 AAAGCTTACG

                         *          *  *   *   *                *  *  *      
       5241 TCTCGATTAGAGCGTAATGCTATGTGAATGCATACTTCTCGGTTAGAGCGTATTGCTATGTAATT
          1 TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT

            * *   *
       5306 TCTTACG
         66 GCATACA

                                  *                  *                   *   
       5313 TCTCGATTAGAGCATAATGCTAAGAGATTGCTTAC-TCTCGATTAGAGCGTAATGATACGTGATT
          1 TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT

                   
       5377 GCATACA
         66 GCATACA

                         *  *             *                  *      
       5384 TCTCGATTAGAGCTTATTGCTATGTA-ATTACTTACGTCTCGGTTAGAGGGTAATG
          1 TCTCGATTAGAGCATAATGCTATG-AGATTGCTTACGTCTCGGTTAGAGCGTAATG

       5439 CTAATTGACT


Statistics
Matches: 105,  Mismatches: 19, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
  71   57  0.54
  72   48  0.46

ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35


Consensus pattern (72 bp):   
TCTCGATTAGAGCATAATGCTATGAGATTGCTTACGTCTCGGTTAGAGCGTAATGATACGTAATT
GCATACA

Found at i:5430 original size:107 final size:108

Alignment explanation


    Indices: 5234--5442  Score: 321
    Period size: 107  Copynumber: 1.9  Consensus size: 108

       5224 TCGATGGAAA

                                      *  *            *     *                
       5234 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAATGCATACTTCTCGGTTAGAGCGTATTGCTA
          1 GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA

                   *                                   
       5299 TGTAATTTCTTACGTCTCGATTAGAGCATAATGCTAAGAGATT
         66 TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAAGAGATT

                                              *                     *        
       5342 GCTTAC-TCTCGATTAGAGCGTAATGATACGTGATTGCATACATCTCGATTAGAGCTTATTGCTA
          1 GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA

                               *      **         
       5406 TGTAATTACTTACGTCTCGGTTAGAGGGTAATGCTAA
         66 TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAA

       5443 TTGACTACTT


Statistics
Matches: 91,  Mismatches: 10, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
 107   85  0.93
 108    6  0.07

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (108 bp):   
GCTTACGTCTCGATTAGAGCGTAATGATACGTGAATGCATACATCTCGATTAGAGCGTATTGCTA
TGTAATTACTTACGTCTCGATTAGAGCATAATGCTAAGAGATT

Found at i:7462 original size:20 final size:20

Alignment explanation


    Indices: 7434--7478  Score: 81
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       7424 GCTAATACCA

                *               
       7434 AGGAAATGAGAAGTCATTAG
          1 AGGACATGAGAAGTCATTAG

                                
       7454 AGGACATGAGAAGTCATTAG
          1 AGGACATGAGAAGTCATTAG

                 
       7474 AGGAC
          1 AGGAC

       7479 GAAACACATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   24  1.00

ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18


Consensus pattern (20 bp):   
AGGACATGAGAAGTCATTAG

Found at i:9039 original size:53 final size:53

Alignment explanation


    Indices: 8941--9047  Score: 153
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       8931 GAAATAACGA

                             *                    *              
       8941 GTTATACAAAATAAAAAGTCAAACCGATAGAAAAATAATTCAAATAACAAAGT
          1 GTTATACAAAATAAAAAATCAAACCGATAGAAAAATAAATCAAATAACAAAGT

                                    *   *                  *      
       8994 GTTATACAAAATAAAAAATCAAACTGATTGAAAAATAACAT-AAATATCAAAGT
          1 GTTATACAAAATAAAAAATCAAACCGATAGAAAAATAA-ATCAAATAACAAAGT

             
       9047 G
          1 G

       9048 ATAATTTAAT


Statistics
Matches: 48,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  53   47  0.98
  54    1  0.02

ACGTcount: A:0.58, C:0.10, G:0.09, T:0.22


Consensus pattern (53 bp):   
GTTATACAAAATAAAAAATCAAACCGATAGAAAAATAAATCAAATAACAAAGT
Done.