Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012149.1 Kokia drynarioides strain JFW-HI SEQ_127148, 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: 3530
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:1469 original size:17 final size:18

Alignment explanation


    Indices: 1435--1470  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1425 TTTGGTTTTT

                              
       1435 TATTAAATAATCTAAAAA
          1 TATTAAATAATCTAAAAA

                  *           
       1453 TATTAATTAAT-TAAAAA
          1 TATTAAATAATCTAAAAA

             
       1470 T
          1 T

       1471 TATATTGATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    7  0.41
  18   10  0.59

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (18 bp):   
TATTAAATAATCTAAAAA

Found at i:2738 original size:59 final size:59

Alignment explanation


    Indices: 2655--2940  Score: 373
    Period size: 59  Copynumber: 4.9  Consensus size: 59

       2645 ACGTCCGGAA

                    *     *            *                                 
       2655 TCAAAAATAGGA-TCTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTC-GAGG
          1 TCAAAAATGGGATTTTTGGG-AGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCAG-GG

                                                          *    *       
       2714 TCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGG
          1 TCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCAGGG

            *                                              *            
       2772 GCTAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAGATTCAGGG
          1 TC-AAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCAGGG

                    *          *    *           *              *       
       2832 TCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAATAGTAA-TTTTAGAAGGTTCAGGG
          1 TCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCAGGG

                     *         *    **                         
       2890 TCAAAAATGAGATTTTTGGAAGTTTTGGGGTAAAATGGTAATTTTTAGAAG
          1 TCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTAGAAG

       2941 GTTTGAGGAC


Statistics
Matches: 205,  Mismatches: 18, Indels: 8
        0.89            0.08        0.03

Matches are distributed among these distances:
  58   55  0.27
  59  140  0.68
  60   10  0.05

ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33


Consensus pattern (59 bp):   
TCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTAGAAGATTCAGGG

Found at i:2945 original size:29 final size:29

Alignment explanation


    Indices: 2672--2943  Score: 204
    Period size: 30  Copynumber: 9.3  Consensus size: 29

       2662 TAGGATCTTG

                                          
       2672 GGAA-GTTCGAGGGTAAAATGGTAATTTTT
          1 GGAAGGTTCG-GGGTAAAATGGTAATTTTT

            *    *    *             *      
       2701 AGAAGATTCGAGGTCAAAAATGG-GATTTTT
          1 GGAAGGTTCGGGGT--AAAATGGTAATTTTT

              *                           
       2731 GGGA-GTTCGGGGGTAAAATGGTAATTTTT
          1 GGAAGGTTC-GGGGTAAAATGGTAATTTTT

                                    *      
       2760 GGAAGGTTCGGGGCTAAAAATGG-GATTTTT
          1 GGAAGGTTCGGGG-T-AAAATGGTAATTTTT

              *                           
       2790 GGGA-GTTCGGGGGTAAAATGGTAATTTTT
          1 GGAAGGTTC-GGGGTAAAATGGTAATTTTT

                 *   *                      
       2819 GGAAGATTCAGGGTCAAAAATAGG--ATTTTT
          1 GGAAGGTTCGGGGT--AAAAT-GGTAATTTTT

                 *  *          *         
       2849 GGAAGTTTGGGGGTAAAATAGTAA-TTTT
          1 GGAAGGTTCGGGGTAAAATGGTAATTTTT

            *        *                      
       2877 AGAAGGTTCAGGGTCAAAAAT-G-AGATTTTT
          1 GGAAGGTTCGGGGT--AAAATGGTA-ATTTTT

                 *  *                    
       2907 GGAAGTTTTGGGGTAAAATGGTAATTTTT
          1 GGAAGGTTCGGGGTAAAATGGTAATTTTT

            *       
       2936 AGAAGGTT
          1 GGAAGGTT

       2944 TGAGGACCTC


Statistics
Matches: 191,  Mismatches: 30, Indels: 44
        0.72            0.11        0.17

Matches are distributed among these distances:
  27    1  0.01
  28   39  0.20
  29   56  0.29
  30   74  0.39
  31   19  0.10
  32    2  0.01

ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33


Consensus pattern (29 bp):   
GGAAGGTTCGGGGTAAAATGGTAATTTTT
Done.