Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003316.1 Kokia drynarioides strain JFW-HI SEQ_116008, 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: 4708
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30


Found at i:59 original size:29 final size:29

Alignment explanation


    Indices: 16--264  Score: 169
    Period size: 29  Copynumber: 8.5  Consensus size: 29

          6 AAAACATTCT

                                           
         16 AAAAATTACCA-TTTT-ACCCCCGAACTTCC
          1 AAAAA-TACCATTTTTGA-CCCCGAACTTCC

                  *             *        *
         45 AAAAATCCCATTTTTGA-CCTGAACCTTCT
          1 AAAAATACCATTTTTGACCCCGAA-CTTCC

                                   *     **
         74 AAAAATTACCA-TTTT-ACCCCTAAACTTTT
          1 AAAAA-TACCATTTTTGACCCC-GAACTTCC

                  *                      *
        103 AAAAATCCCATTTTTGACCCCGAACCTT-T
          1 AAAAATACCATTTTTGACCCCGAA-CTTCC

                        *                  
        132 AAAAATTACCA-GTTT-ACCCTCGAACTTCC
          1 AAAAA-TACCATTTTTGACCC-CGAACTTCC

                   *                     *
        161 AAAAATATCATTTTTGA-CCCGAACCTTCT
          1 AAAAATACCATTTTTGACCCCGAA-CTTCC

                 *                         
        190 AATAATTACCA-TTTT-ACCCTCGAACTTCC
          1 AA-AAATACCATTTTTGACCC-CGAACTTCC

                  *            *      *   
        219 AAAAATCCCATTTTTTGACTCCGAACCTCC
          1 AAAAATACCA-TTTTTGACCCCGAACTTCC

                            
        249 AAAAACTACCATTTTT
          1 AAAAA-TACCATTTTT

        265 CCCTCGTGTA


Statistics
Matches: 175,  Mismatches: 23, Indels: 43
        0.73            0.10        0.18

Matches are distributed among these distances:
  28   36  0.21
  29   80  0.46
  30   52  0.30
  31    7  0.04

ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33


Consensus pattern (29 bp):   
AAAAATACCATTTTTGACCCCGAACTTCC

Found at i:107 original size:58 final size:58

Alignment explanation


    Indices: 12--270  Score: 353
    Period size: 58  Copynumber: 4.4  Consensus size: 58

          2 ACCAAAAACA

                                   *                            *     
         12 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTGAACC
          1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCGAACC

                                      *     **                          
         70 TTCTAAAAATTACCATTTTACCC-CTAAACTTTTAAAAATCCCATTTTTGACCCCGAACC
          1 TTCTAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGA-CCCGAACC

                           *                       **                 
        129 TT-TAAAAATTACCAGTTTACCCTCGAACTTCCAAAAATATCATTTTTGACCCGAACC
          1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCGAACC

                  *                                                     
        186 TTCTAATAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACTCCGAACC
          1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGAC-CCGAACC

               *     *         *      
        246 -TCCAAAAACTACCATTTTTCCCTCG
          1 TTCTAAAAATTACCATTTTACCCTCG

        271 TGTATCCAAA


Statistics
Matches: 177,  Mismatches: 18, Indels: 11
        0.86            0.09        0.05

Matches are distributed among these distances:
  57   11  0.06
  58  120  0.68
  59   39  0.22
  60    7  0.04

ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33


Consensus pattern (58 bp):   
TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCGAACC

Done.