Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008931.1 Kokia drynarioides strain JFW-HI SEQ_123622, 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: 15270
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:212 original size:51 final size:50

Alignment explanation


    Indices: 123--222  Score: 128
    Period size: 51  Copynumber: 2.0  Consensus size: 50

        113 AAACTAAACG

                                       *  *                   
        123 AAAAAAAATAAATTTAATAAAGTTGGTGCCTACCATCAGTGTCCCAAAAT
          1 AAAAAAAATAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCAAAAT

                       *                 *  * *         *     
        173 AAAAAAAATTATATTTAATAAAGTTGGTATCGGCTATCAGTGTCTCAAAA
          1 AAAAAAAA-TAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCAAAA

        223 CACCAAAAAA


Statistics
Matches: 42,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  50    8  0.19
  51   34  0.81

ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29


Consensus pattern (50 bp):   
AAAAAAAATAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCAAAAT

Found at i:231 original size:51 final size:51

Alignment explanation


    Indices: 118--239  Score: 127
    Period size: 51  Copynumber: 2.4  Consensus size: 51

        108 CGCAAAAACT

                *                           *  *               
        118 AAACGAAAAAAAATAAATTTAATAAAGTTGGTGCCTACCATCAGTGTCCCA
          1 AAACAAAAAAAAATAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCA

               *        *  *                 *  * *         *  
        169 AAATAAAAAAAATTATATTTAATAAAGTTGGTATCGGCTATCAGTGTCTCA
          1 AAACAAAAAAAAATAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCA

                 **      *      
        220 AAACACCAAAAAACAAATTT
          1 AAACAAAAAAAAATAAATTT

        240 CTCGGGTCCC


Statistics
Matches: 55,  Mismatches: 16, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  51   55  1.00

ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26


Consensus pattern (51 bp):   
AAACAAAAAAAAATAAATTTAATAAAGTTGGTACCGACCATCAGTGTCCCA

Found at i:747 original size:18 final size:18

Alignment explanation


    Indices: 706--748  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        696 AAATTTTAAA

                              
        706 ATTTTTTAAATATTTATG
          1 ATTTTTTAAATATTTATG

             *      *      * *
        724 AGTTTTTATATATTTTTT
          1 ATTTTTTAAATATTTATG

                   
        742 ATTTTTT
          1 ATTTTTT

        749 TAGAGTTAAG


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70


Consensus pattern (18 bp):   
ATTTTTTAAATATTTATG

Found at i:6290 original size:10 final size:10

Alignment explanation


    Indices: 6268--6305  Score: 51
    Period size: 9  Copynumber: 3.8  Consensus size: 10

       6258 ACACTTTTAC

                      
       6268 TTTATTTTG-
          1 TTTATTTTGT

                      
       6277 TTTATTTTGT
          1 TTTATTTTGT

                     * 
       6287 TTTATTTTATT
          1 TTTATTTT-GT

                    
       6298 TTTATTTT
          1 TTTATTTT

       6306 CTTTAATAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   9    9  0.35
  10    8  0.31
  11    9  0.35

ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82


Consensus pattern (10 bp):   
TTTATTTTGT
Done.