Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008655.1 Kokia drynarioides strain JFW-HI SEQ_123336, 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: 14096
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:5975 original size:39 final size:39

Alignment explanation


    Indices: 5932--6010  Score: 140
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       5922 GTTTTCCATG

                                                   
       5932 TAAAATCTCCGTGTTTTATTATTCCTTTTTCTTATTGCT
          1 TAAAATCTCCGTGTTTTATTATTCCTTTTTCTTATTGCT

                     *              *              
       5971 TAAAATCTCTGTGTTTTATTATTCTTTTTTCTTATTGCT
          1 TAAAATCTCCGTGTTTTATTATTCCTTTTTCTTATTGCT

             
       6010 T
          1 T

       6011 TGTGATTCTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.18, C:0.15, G:0.08, T:0.59


Consensus pattern (39 bp):   
TAAAATCTCCGTGTTTTATTATTCCTTTTTCTTATTGCT

Found at i:9893 original size:30 final size:30

Alignment explanation


    Indices: 9843--9903  Score: 81
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       9833 TCCCAAGAAG

                                 *         
       9843 GATTTAACTGTAGAAAATGAATTGATTGTGT
          1 GATTTAACTGTAGAAAATGAAATGATT-TGT

                                           
       9874 GATTTAA-TGT-GAGAAATGAAATGATTTGT
          1 GATTTAACTGTAGA-AAATGAAATGATTTGT

             
       9903 G
          1 G

       9904 GATGTAGACT


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  29    6  0.21
  30   15  0.54
  31    7  0.25

ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38


Consensus pattern (30 bp):   
GATTTAACTGTAGAAAATGAAATGATTTGT

Found at i:10190 original size:51 final size:51

Alignment explanation


    Indices: 10134--10320  Score: 207
    Period size: 51  Copynumber: 3.6  Consensus size: 51

      10124 CTATAAACGA

                    *                                    *     
      10134 AAAGGTCATATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
          1 AAAGGTCAGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                   *            *                  * * *       
      10185 AAAGGTCCGATGACTAAGTGCCATCGTGAGTAAATGAATTCATGATGGATT
          1 AAAGGTCAGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                            *                *          *      **
      10236 AAAGGTCCA-ATGACTCAGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
          1 AAAGGT-CAGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATT

                    *                         
      10288 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
          1 AA-AGGTCAGATGACTA-AGTGTCATCGTGAGTA

      10321 TTAAATGAAA


Statistics
Matches: 112,  Mismatches: 19, Indels: 8
        0.81            0.14        0.06

Matches are distributed among these distances:
  51   76  0.68
  52   11  0.10
  53   24  0.21
  54    1  0.01

ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29


Consensus pattern (51 bp):   
AAAGGTCAGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

Found at i:10259 original size:102 final size:104

Alignment explanation


    Indices: 10134--10320  Score: 265
    Period size: 102  Copynumber: 1.8  Consensus size: 104

      10124 CTATAAACGA

                                                       *      **             
      10134 AAAGGTCATATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCGATG
          1 AAAGGTCATATGACTAAGTGTCATCGTGAGTAAATGAATTCCTATACGGAACAAGAGGTCCGATG

                                                    
      10197 ACTA-AGTGCCATCGTGAGTAAATGAATTCATGATGGATT
         66 ACTATA-TGCCATCGTGAGTAAATGAATTCATGATGGATT

                            *                *             *                 
      10236 AAAGGTCCA-ATGACTCAGTGTCATCGTGAGTATATGAATTCCTATATGGAACAAGAGGTCCGAT
          1 AAAGGT-CATATGACTAAGTGTCATCGTGAGTAAATGAATTCCTATACGGAACAAGAGGTCCGAT

                     *           
      10300 GACTATATGTCATCGTGAGTA
         65 GACTATATGCCATCGTGAGTA

      10321 TTAAATGAAA


Statistics
Matches: 74,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
 102   33  0.45
 103   13  0.18
 104   27  0.36
 105    1  0.01

ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29


Consensus pattern (104 bp):   
AAAGGTCATATGACTAAGTGTCATCGTGAGTAAATGAATTCCTATACGGAACAAGAGGTCCGATG
ACTATATGCCATCGTGAGTAAATGAATTCATGATGGATT
Done.