Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013798.1 Kokia drynarioides strain JFW-HI SEQ_128826, 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: 20788
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33


Found at i:2119 original size:40 final size:40

Alignment explanation


    Indices: 2064--2159  Score: 147
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       2054 ATAAGTTCAT

                    *                      *        
       2064 AAGTCTTCTTTTTAATCAATCTTATGCTCTATCGAGTCAC
          1 AAGTCTTCCTTTTAATCAATCTTATGCTCTAACGAGTCAC

                                                  **
       2104 AAGTCTTCCTTTTAATCAATCTTATGCTCTAACGAGTCGT
          1 AAGTCTTCCTTTTAATCAATCTTATGCTCTAACGAGTCAC

                            
       2144 AAGTCTTCCCTTTTAA
          1 AAGTCTT-CCTTTTAA

       2160 AAACAAACAT


Statistics
Matches: 51,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  40   43  0.84
  41    8  0.16

ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42


Consensus pattern (40 bp):   
AAGTCTTCCTTTTAATCAATCTTATGCTCTAACGAGTCAC

Found at i:2226 original size:41 final size:42

Alignment explanation


    Indices: 2181--2459  Score: 316
    Period size: 41  Copynumber: 6.6  Consensus size: 42

       2171 ACACTCATTT

                                                      
       2181 CGAGACATGAGTCTTCCTTTAATATAA-TCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATTCTCATTCTCATCC

                            *                         
       2222 CGAGACATGAGTCTTCTTTTAATATAA-TCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATTCTCATTCTCATCC

                   *          *                       
       2263 CGAGACAAGAGTCTTCCTCTAATATAA-TCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATTCTCATTCTCATCC

                *                    *    *    *        
       2304 CGAGTCATGAGTCTTCCTTTAATTAAAATTTTCATGCTCAAT-C
          1 CGAGACATGAGTCTTCCTTTAA-TATAATTCTCATTCTC-ATCC

             *      *                          *  * * *
       2347 CAAGACATTAGTCTTCCTTTAATATAAATTCTCATGCTTAACT
          1 CGAGACATGAGTCTTCCTTTAATAT-AATTCTCATTCTCATCC

                       *                             *  
       2390 CGAGACATGAGACTTCCTTTAATATAAATTCTC-TTACTCAACC
          1 CGAGACATGAGTCTTCCTTTAATAT-AATTCTCATT-CTCATCC

                    *                  
       2433 CGAGACATAAGTCTTCCATTTATATAT
          1 CGAGACATGAGTCTTCC-TTTA-ATAT

       2460 CGAGTTTCTC


Statistics
Matches: 204,  Mismatches: 26, Indels: 12
        0.84            0.11        0.05

Matches are distributed among these distances:
  41   97  0.48
  42    8  0.04
  43   89  0.44
  44    6  0.03
  45    4  0.02

ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37


Consensus pattern (42 bp):   
CGAGACATGAGTCTTCCTTTAATATAATTCTCATTCTCATCC

Found at i:13779 original size:13 final size:13

Alignment explanation


    Indices: 13757--13787  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

      13747 AAGTCAACGA

                 *       
      13757 TCAACGGTCAAAG
          1 TCAACAGTCAAAG

                         
      13770 TCAACAGTCAAAG
          1 TCAACAGTCAAAG

                 
      13783 TCAAC
          1 TCAAC

      13788 GAGTTGAGTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16


Consensus pattern (13 bp):   
TCAACAGTCAAAG

Found at i:18063 original size:43 final size:41

Alignment explanation


    Indices: 17838--18073  Score: 276
    Period size: 41  Copynumber: 5.6  Consensus size: 41

      17828 ACACTCATTT

                            *          *             
      17838 CGAGACATGAGTCTTCTTTTAATATAACCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCC

                 * *                                 
      17879 CGAGATAGGAGTCTTCCTTTAATATAATCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCC

                           *                         
      17920 CGAGACATGAGTCTTTCTTTAATATAATCTCATTCTCATCC
          1 CGAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCC

                *           *               *  *    *  
      17961 CGAGTCATGAGTCTTCTTTTAATATAAATTCTTATGCTCAACC
          1 CGAGACATGAGTCTTCCTTTAATAT-AA-TCTCATTCTCATCC

             *                                       *  
      18004 CAAGACATGAGTCTTCCTTTAATATAAATTCTC-TTGCTCAACC
          1 CGAGACATGAGTCTTCCTTTAATAT-AA-TCTCATT-CTCATCC

            *    *                     
      18047 TGAGATATGAGTCTTCCATTTATATAT
          1 CGAGACATGAGTCTTCC-TTTA-ATAT

      18074 CAAGTTTCTC


Statistics
Matches: 169,  Mismatches: 21, Indels: 6
        0.86            0.11        0.03

Matches are distributed among these distances:
  41   97  0.57
  42    3  0.02
  43   61  0.36
  44    4  0.02
  45    4  0.02

ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38


Consensus pattern (41 bp):   
CGAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCC
Done.