Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003664.1 Kokia drynarioides strain JFW-HI SEQ_116577, 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, 610

Length: 1018
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32


Found at i:166 original size:46 final size:46

Alignment explanation


    Indices: 115--333  Score: 239
    Period size: 46  Copynumber: 4.7  Consensus size: 46

        105 ACGGAACAAA

                                              *         *     
        115 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAATGTTGGGC-AA-
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAA-G-T--ACTAAT

                   *     *   *    *  *    *               
        161 CAGAGAGCACACATAGTGCTAAACAAAGAGTACACAAAGTACTAAT
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT

                                          *               
        207 CAGAGAGTACACAAAGTACTAATCAGAGAGTACACAAAGTACTAAT
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT

                                                    *     
        253 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAT
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT

                   *     *   *                 
        299 CAGAGAGAACACACAGTGCTAATAACAGAGAGCAC
          1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC

        334 GAGACGTGCT


Statistics
Matches: 150,  Mismatches: 17, Indels: 10
        0.85            0.10        0.06

Matches are distributed among these distances:
  44    1  0.01
  45    2  0.01
  46  115  0.77
  47   10  0.07
  48   22  0.15

ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15


Consensus pattern (46 bp):   
CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT

Found at i:185 original size:23 final size:23

Alignment explanation


    Indices: 161--333  Score: 220
    Period size: 23  Copynumber: 7.4  Consensus size: 23

        151 TGTTGGGCAA

                         *   *    *
        161 CAGAGAGCACACATAGTGCTAAA
          1 CAGAGAGCACACAAAGTACTAAT

              *    *               
        184 CAAAGAGTACACAAAGTACTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                   *               
        207 CAGAGAGTACACAAAGTACTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                   *               
        230 CAGAGAGTACACAAAGTACTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                   *               
        253 CAGAGAGTACACAAAGTACTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                             *     
        276 CAGAGAGCACACAAAGTGCTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                   *     *   *     
        299 CAGAGAGAACACACAGTGCTAAT
          1 CAGAGAGCACACAAAGTACTAAT

                        
        322 AACAGAGAGCAC
          1 --CAGAGAGCAC

        334 GAGACGTGCT


Statistics
Matches: 137,  Mismatches: 11, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
  23  128  0.93
  25    9  0.07

ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14


Consensus pattern (23 bp):   
CAGAGAGCACACAAAGTACTAAT

Found at i:321 original size:69 final size:69

Alignment explanation


    Indices: 115--330  Score: 260
    Period size: 69  Copynumber: 3.1  Consensus size: 69

        105 ACGGAACAAA

                                              *                      *     * 
        115 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAATGTTGGGC-AA-CAGAGAGCACACATA
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAA-G-T--GCTAATCAGAGAGAACACAAA

                   *
        176 GTGCTAAA
         62 GTGCTAAT

              *                           *         *            *         * 
        184 CAAAGAGTACACAAAGTACTAATCAGAGAGTACACAAAGTACTAATCAGAGAGTACACAAAGTAC
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGAACACAAAGTGC

                
        249 TAAT
         66 TAAT

                                                                       *     
        253 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGAACACACAGTGC
          1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGAACACAAAGTGC

                
        318 TAAT
         66 TAAT

                     
        322 AACAGAGAG
          1 --CAGAGAG

        331 CACGAGACGT


Statistics
Matches: 127,  Mismatches: 14, Indels: 10
        0.84            0.09        0.07

Matches are distributed among these distances:
  67    1  0.01
  68    2  0.02
  69   92  0.72
  70   12  0.09
  71   20  0.16

ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15


Consensus pattern (69 bp):   
CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGAACACAAAGTGC
TAAT

Found at i:348 original size:23 final size:23

Alignment explanation


    Indices: 159--354  Score: 160
    Period size: 23  Copynumber: 8.4  Consensus size: 23

        149 AATGTTGGGC

                           *       
        159 AACAGAGAGCACACATAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                *    *     *   *   
        182 AACAAAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *       *     *   *   
        205 ATCAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *       *     *   *   
        228 ATCAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *       *     *   *   
        251 ATCAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *             *       
        274 ATCAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *       *              
        297 ATCAGAGAGAACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
        321 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                      
        345 AACAGAGAGC
          1 AACAGAGAGC

        355 GCGCTACTGT


Statistics
Matches: 157,  Mismatches: 13, Indels: 6
        0.89            0.07        0.03

Matches are distributed among these distances:
  23  137  0.87
  24    2  0.01
  25   15  0.10
  26    3  0.02

ACGTcount: A:0.46, C:0.19, G:0.20, T:0.14


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA
Done.