Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013762.1 Kokia drynarioides strain JFW-HI SEQ_128790, 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, 722

Length: 1204
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35


Found at i:170 original size:23 final size:23

Alignment explanation


    Indices: 106--327  Score: 190
    Period size: 23  Copynumber: 9.8  Consensus size: 23

         96 GAGAGTATCG

                *                 *
        106 AAGTACTAAACAGAGAGCACA-T
          1 AAGTGCTAAACAGAGAGCACACA

                      *    *          
        128 AAGTGCTGGGCAACAAAGAGCACACA
          1 AAGTGCT---AAACAGAGAGCACACA

                             *     
        154 AAGTGCTAAACAGAGAGTACACA
          1 AAGTGCTAAACAGAGAGCACACA

                         *         
        177 AA--G-T--AC--TGAGCACACA
          1 AAGTGCTAAACAGAGAGCACACA

                     *             
        193 AAGTGCTAATCAGAGAGCACACA
          1 AAGTGCTAAACAGAGAGCACACA

                     *             
        216 AAGTGCTAATCAGAGAGCACACA
          1 AAGTGCTAAACAGAGAGCACACA

            *                  *     
        239 TAGTGCTAATAACAGAGAGTACACA
          1 AAGTGCT-A-AACAGAGAGCACACA

            *   *    *             
        264 GAGTACTAATCAGAGAGCACACA
          1 AAGTGCTAAACAGAGAGCACACA

            *        *             
        287 CAGTGCTAATCAGAGAGCACACA
          1 AAGTGCTAAACAGAGAGCACACA

            *        *        
        310 CAGTGCTAATCAGAGAGC
          1 AAGTGCTAAACAGAGAGC

        328 GCTAGTGTTC


Statistics
Matches: 167,  Mismatches: 20, Indels: 25
        0.79            0.09        0.12

Matches are distributed among these distances:
  16   10  0.06
  18    3  0.02
  19    1  0.01
  20    1  0.01
  21    2  0.01
  22    6  0.04
  23  105  0.63
  24    2  0.01
  25   30  0.18
  26    7  0.04

ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14


Consensus pattern (23 bp):   
AAGTGCTAAACAGAGAGCACACA

Found at i:199 original size:39 final size:39

Alignment explanation


    Indices: 145--219  Score: 132
    Period size: 39  Copynumber: 1.9  Consensus size: 39

        135 GGGCAACAAA

                                      *            
        145 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

                              *                 
        184 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT

        220 GCTAATCAGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  39   34  1.00

ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12


Consensus pattern (39 bp):   
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

Found at i:236 original size:46 final size:46

Alignment explanation


    Indices: 184--327  Score: 216
    Period size: 46  Copynumber: 3.1  Consensus size: 46

        174 ACAAAGTACT

                                                          
        184 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA
          1 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA

                     *                  *     *   *         
        230 GAGCACACATAGTGCTAATAACAGAGAGTACACAGAGTACTAATCAGA
          1 GAGCACACAAAGTGCTAAT--CAGAGAGCACACAAAGTGCTAATCAGA

                     *                      *             
        278 GAGCACACACAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA
          1 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA

                
        324 GAGC
          1 GAGC

        328 GCTAGTGTTC


Statistics
Matches: 88,  Mismatches: 8, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  46   46  0.52
  48   42  0.48

ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14


Consensus pattern (46 bp):   
GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA

Found at i:281 original size:71 final size:69

Alignment explanation


    Indices: 188--326  Score: 224
    Period size: 71  Copynumber: 2.0  Consensus size: 69

        178 AGTACTGAGC

                     *                                         *             
        188 ACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACATAGTGCTAATAACA
          1 ACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAT--CA

                  
        253 GAGAGT
         64 GAGAGT

                 *                      *                                    
        259 ACACAGAGTACTAATCAGAGAGCACACACAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA
          1 ACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA

               
        324 GAG
         66 GAG

        327 CGCTAGTGTT


Statistics
Matches: 64,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  69    7  0.11
  71   57  0.89

ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14


Consensus pattern (69 bp):   
ACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA
GAGT
Done.