Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014207.1 Kokia drynarioides strain JFW-HI SEQ_129240, 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: 16072
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:9995 original size:3 final size:3

Alignment explanation


    Indices: 9987--10012  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       9977 ATTAACTTCG

                                              
       9987 TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TA

      10013 ATTTTATTTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:10433 original size:17 final size:17

Alignment explanation


    Indices: 10409--10482  Score: 98
    Period size: 17  Copynumber: 4.4  Consensus size: 17

      10399 TTGGAAATTG

                              
      10409 AATTTATTT-AAATTTTA
          1 AATTTATTTGAAA-TTTA

             *               
      10426 AGTTTATTTGAAATTTA
          1 AATTTATTTGAAATTTA

                             
      10443 AATTTATTTGAAATTTA
          1 AATTTATTTGAAATTTA

                          *   
      10460 AATTTATTAT-AAAATTA
          1 AATTTATT-TGAAATTTA

                  
      10477 AATTTA
          1 AATTTA

      10483 GAAAGTCCAA


Statistics
Matches: 52,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
  17   48  0.92
  18    4  0.08

ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53


Consensus pattern (17 bp):   
AATTTATTTGAAATTTA

Found at i:11245 original size:11 final size:11

Alignment explanation


    Indices: 11225--11283  Score: 50
    Period size: 11  Copynumber: 5.3  Consensus size: 11

      11215 TAAATGTTAA

                        
      11225 TATATATTTACT
          1 TATATATTTA-T

                       
      11237 TAT-TATTTAT
          1 TATATATTTAT

                      *
      11247 TATATA-TTAA
          1 TATATATTTAT

                      *  
      11257 TATGATCATTAAT
          1 TAT-AT-ATTTAT

               *       
      11270 TATCTATTTAT
          1 TATATATTTAT

               
      11281 TAT
          1 TAT

      11284 TTAGTTCGAA


Statistics
Matches: 38,  Mismatches: 5, Indels: 9
        0.73            0.10        0.17

Matches are distributed among these distances:
  10   10  0.26
  11   18  0.47
  12    5  0.13
  13    5  0.13

ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58


Consensus pattern (11 bp):   
TATATATTTAT

Found at i:12436 original size:30 final size:29

Alignment explanation


    Indices: 12372--12600  Score: 189
    Period size: 30  Copynumber: 7.8  Consensus size: 29

      12362 CCCTAAATTG

                     *              **   
      12372 TTCAAAAATTCCATTTTT-ACCCCCGAAC
          1 TTCAAAAATCCCATTTTTAACCCCAAAAC

                                          
      12400 TTCAAAAAATCCCA-TTTTAACCCCAAAAC
          1 TTC-AAAAATCCCATTTTTAACCCCAAAAC

                      *              **   
      12429 ATTCAAAAATTCCA-TTTT-ACCCCCGAAC
          1 -TTCAAAAATCCCATTTTTAACCCCAAAAC

                       *         *   *    
      12457 TTCCAAAAATCTCATTTTTAAGCCCGAAAC
          1 TT-CAAAAATCCCATTTTTAACCCCAAAAC

                      * *             *   
      12487 TTTCAAAAATTCTATTTTTAACCCC-GAAC
          1 -TTCAAAAATCCCATTTTTAACCCCAAAAC

                                   *      
      12516 TTCCAAAAATCCCATTTTTAACCTCAAAAC
          1 TT-CAAAAATCCCATTTTTAACCCCAAAAC

                      * *      *     *    
      12546 TTTCAAAAATTCTATTTTTTACCCCTAAAC
          1 -TTCAAAAATCCCATTTTTAACCCCAAAAC

               *               *     
      12576 TTTTAAAAATCCCATTTTTGACCCC
          1 -TTCAAAAATCCCATTTTTAACCCC

      12601 GAATTTTCCC


Statistics
Matches: 162,  Mismatches: 29, Indels: 18
        0.78            0.14        0.09

Matches are distributed among these distances:
  27    2  0.01
  28   26  0.16
  29   56  0.35
  30   74  0.46
  31    4  0.02

ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33


Consensus pattern (29 bp):   
TTCAAAAATCCCATTTTTAACCCCAAAAC

Found at i:12464 original size:58 final size:59

Alignment explanation


    Indices: 12372--12600  Score: 309
    Period size: 59  Copynumber: 3.9  Consensus size: 59

      12362 CCCTAAATTG

                                           *                          *
      12372 TTCAAAAATTCCATTTTTACCCCCGAACTTCAAAAAATCCCA-TTTTAACCCCAAAACA
          1 TTCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT

                                                   *         *   *     
      12430 TTCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCTCATTTTTAAGCCCGAAACT
          1 TTCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT

                       *       *                               *       
      12488 TTCAAAAATTCTATTTTTAACCCCGAACTTCCAAAAATCCCATTTTTAACCTCAAAACT
          1 TTCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT

                       *            **     **               *     
      12547 TTCAAAAATTCTATTTTTTACCCCTAAACTTTTAAAAATCCCATTTTTGACCCC
          1 TTCAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC

      12601 GAATTTTCCC


Statistics
Matches: 150,  Mismatches: 18, Indels: 4
        0.87            0.10        0.02

Matches are distributed among these distances:
  57   26  0.17
  58   38  0.25
  59   53  0.35
  60   33  0.22

ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33


Consensus pattern (59 bp):   
TTCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT

Done.