Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006036.1 Kokia drynarioides strain JFW-HI SEQ_120498, 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: 2477
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32


Found at i:29 original size:10 final size:9

Alignment explanation


    Indices: 4--66  Score: 54
    Period size: 10  Copynumber: 6.6  Consensus size: 9

          1 AAA

                     *
          4 ATAAAAATGA
          1 ATAAAAAT-T

                  *  
         14 ATAAAAGTT
          1 ATAAAAATT

                     
         23 ATAAAAATT
          1 ATAAAAATT

                  **  
         32 ATTAAATTTT
          1 A-TAAAAATT

                      
         42 ATTAAAAATT
          1 A-TAAAAATT

                      
         52 ATAAAAAATT
          1 AT-AAAAATT

                 
         62 ATAAA
          1 ATAAA

         67 CAAACATTTG


Statistics
Matches: 44,  Mismatches: 7, Indels: 5
        0.79            0.12        0.09

Matches are distributed among these distances:
   9   13  0.30
  10   31  0.70

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35


Consensus pattern (9 bp):   
ATAAAAATT

Found at i:37 original size:19 final size:19

Alignment explanation


    Indices: 4--66  Score: 63
    Period size: 19  Copynumber: 3.3  Consensus size: 19

          1 AAA

                    * *     *  
          4 ATAAAAATGAATAAAAGTT
          1 ATAAAAATTATTAAAAATT

                           **  
         23 ATAAAAATTATTAAATTTT
          1 ATAAAAATTATTAAAAATT

                        *       
         42 ATTAAAAATTATAAAAAATT
          1 A-TAAAAATTATTAAAAATT

                 
         62 ATAAA
          1 ATAAA

         67 CAAACATTTG


Statistics
Matches: 36,  Mismatches: 7, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  19   20  0.56
  20   16  0.44

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35


Consensus pattern (19 bp):   
ATAAAAATTATTAAAAATT

Found at i:160 original size:19 final size:20

Alignment explanation


    Indices: 122--172  Score: 59
    Period size: 19  Copynumber: 2.6  Consensus size: 20

        112 AAAATATTAT

                *    *          
        122 AAAATTTTATAAAATCGTAA
          1 AAAAATTTAAAAAATCGTAA

            *                   
        142 GAAAATTTAAAAAAT-GTAA
          1 AAAAATTTAAAAAATCGTAA

                  *     
        161 AAAAATATAAAA
          1 AAAAATTTAAAA

        173 TTTATAGAAT


Statistics
Matches: 26,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  19   14  0.54
  20   12  0.46

ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27


Consensus pattern (20 bp):   
AAAAATTTAAAAAATCGTAA
Done.