Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010585.1 Kokia drynarioides strain JFW-HI SEQ_125512, 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, 976

Length: 1627
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.30

Warning! 220 characters in sequence are not A, C, G, or T


Found at i:159 original size:16 final size:16

Alignment explanation


    Indices: 115--164  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

        105 TAAACTTGGC

                     *      
        115 TAATTAATTTTCAAAA
          1 TAATTAATTATCAAAA

                             
        131 T-A-TAA-TATACAAAA
          1 TAATTAATTAT-CAAAA

                            
        145 TAATTAATTATCAAAA
          1 TAATTAATTATCAAAA

                
        161 TAAT
          1 TAAT

        165 ACCCCCATCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  13    2  0.07
  14    9  0.31
  15    2  0.07
  16   13  0.45
  17    3  0.10

ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38


Consensus pattern (16 bp):   
TAATTAATTATCAAAA

Found at i:189 original size:59 final size:59

Alignment explanation


    Indices: 126--249  Score: 221
    Period size: 59  Copynumber: 2.1  Consensus size: 59

        116 AATTAATTTT

                          *                                            
        126 CAAAATATAATATACAAAATAATTAATTATCAAAATAATACCCCCATCATATTATTGAC
          1 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATACCCCCATCATATTATTGAC

                                                    *               *  
        185 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTTAC
          1 CAAAATATAATATAAAAAATAATTAATTATCAAAATAATACCCCCATCATATTATTGAC

                  
        244 CAAAAT
          1 CAAAAT

        250 GGTACAAAAT


Statistics
Matches: 62,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  59   62  1.00

ACGTcount: A:0.52, C:0.15, G:0.01, T:0.31


Consensus pattern (59 bp):   
CAAAATATAATATAAAAAATAATTAATTATCAAAATAATACCCCCATCATATTATTGAC

Found at i:220 original size:30 final size:30

Alignment explanation


    Indices: 115--221  Score: 96
    Period size: 30  Copynumber: 3.6  Consensus size: 30

        105 TAAACTTGGC

                     *                    
        115 TAATTAATTTTCAAAATATAATATACAAAA
          1 TAATTAATTATCAAAATATAATATACAAAA

                                    * *** 
        145 TAATTAATTATC-AAA-ATAATA-CCCCCA
          1 TAATTAATTATCAAAATATAATATACAAAA

                         *              *    
        172 TCATATT-ATTGACCAAAATATAATATAAAAAA
          1 T-A-ATTAATT-ATCAAAATATAATATACAAAA

                              
        204 TAATTAATTATCAAAATA
          1 TAATTAATTATCAAAATA

        222 ATATCCCCAT


Statistics
Matches: 58,  Mismatches: 12, Indels: 14
        0.69            0.14        0.17

Matches are distributed among these distances:
  27    3  0.05
  28   10  0.17
  29    8  0.14
  30   25  0.43
  31   10  0.17
  32    2  0.03

ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34


Consensus pattern (30 bp):   
TAATTAATTATCAAAATATAATATACAAAA

Found at i:247 original size:29 final size:29

Alignment explanation


    Indices: 147--249  Score: 77
    Period size: 29  Copynumber: 3.5  Consensus size: 29

        137 ATACAAAATA

                    *          *         
        147 ATTAATTATCAAAATAATACCCCCATCAT
          1 ATTAATTACCAAAATAATATCCCCATCAT

                                     ** **  
        176 ATT-ATTGACCAAAATATAATAT--AAAAAAT
          1 ATTAATT-ACC-AAA-ATAATATCCCCATCAT

                     *                    
        205 AATTAATTATCAAAATAATATCCCCATCAT
          1 -ATTAATTACCAAAATAATATCCCCATCAT

                *          
        235 ATTATTTACCAAAAT
          1 ATTAATTACCAAAAT

        250 GGTACAAAAT


Statistics
Matches: 54,  Mismatches: 13, Indels: 14
        0.67            0.16        0.17

Matches are distributed among these distances:
  28   10  0.19
  29   24  0.44
  30   11  0.20
  31    9  0.17

ACGTcount: A:0.50, C:0.17, G:0.01, T:0.33


Consensus pattern (29 bp):   
ATTAATTACCAAAATAATATCCCCATCAT
Done.