Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010700.1 Kokia drynarioides strain JFW-HI SEQ_125647, 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: 9514
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37


Found at i:274 original size:9 final size:9

Alignment explanation


    Indices: 249--340  Score: 51
    Period size: 9  Copynumber: 9.7  Consensus size: 9

        239 CCTTTTTTAT

                  *  
        249 TTATTACTA
          1 TTATTAATA

               *     
        258 TTAATAATA
          1 TTATTAATA

                      
        267 TTATTAATAA
          1 TTATTAAT-A

                      
        277 TTATTAATGA
          1 TTATTAAT-A

             **         
        287 GACAGTT-ATCA
          1 -TTA-TTAAT-A

                   *  
        298 CTTATTATTA
          1 -TTATTAATA

                  *  
        308 TTATTATTA
          1 TTATTAATA

                  *  
        317 TTATTATTA
          1 TTATTAATA

                  *  
        326 TTATTATTA
          1 TTATTAATA

                  
        335 TTATTA
          1 TTATTA

        341 TACTTATGAG


Statistics
Matches: 68,  Mismatches: 11, Indels: 8
        0.78            0.13        0.09

Matches are distributed among these distances:
   9   47  0.69
  10   13  0.19
  11    6  0.09
  12    2  0.03

ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54


Consensus pattern (9 bp):   
TTATTAATA

Found at i:307 original size:3 final size:3

Alignment explanation


    Indices: 299--341  Score: 86
    Period size: 3  Copynumber: 14.3  Consensus size: 3

        289 CAGTTATCAC

                                                                     
        299 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

        342 ACTTATGAGC


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:995 original size:17 final size:17

Alignment explanation


    Indices: 975--1038  Score: 83
    Period size: 17  Copynumber: 3.8  Consensus size: 17

        965 AAATGAATTT

                     *    *  
        975 TAAATTTAAGTTTATAA
          1 TAAATTTAAATTTAAAA

                          *  
        992 TAAATTTAAATTTAGAA
          1 TAAATTTAAATTTAAAA

                *    *       
       1009 TAAACTTAATTTTAAAA
          1 TAAATTTAAATTTAAAA

                         
       1026 TAAATTTAAATTT
          1 TAAATTTAAATTT

       1039 GTTAGGCCAA


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  17   40  1.00

ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:8856 original size:16 final size:15

Alignment explanation


    Indices: 8835--8864  Score: 51
    Period size: 16  Copynumber: 1.9  Consensus size: 15

       8825 ATTTAAAATA

                            
       8835 ATTTTAATACTTTTTT
          1 ATTTTAATA-TTTTTT

                          
       8851 ATTTTAATATTTTT
          1 ATTTTAATATTTTT

       8865 AAAAATTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70


Consensus pattern (15 bp):   
ATTTTAATATTTTTT

Found at i:9208 original size:24 final size:25

Alignment explanation


    Indices: 9176--9228  Score: 81
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       9166 TAAATGGATG

                     *               
       9176 TTTAACCTTTCATCTCCCTTAA-TT
          1 TTTAACCTTCCATCTCCCTTAACTT

                           *         
       9200 TTTAACCTTCCATCTTCCTTAACTT
          1 TTTAACCTTCCATCTCCCTTAACTT

                
       9225 TTTA
          1 TTTA

       9229 TATTCTTATA


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

Matches are distributed among these distances:
  24   20  0.77
  25    6  0.23

ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51


Consensus pattern (25 bp):   
TTTAACCTTCCATCTCCCTTAACTT
Done.