Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009527.1 Kokia drynarioides strain JFW-HI SEQ_124239, 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: 12527
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.34

Warning! 191 characters in sequence are not A, C, G, or T


Found at i:2353 original size:42 final size:41

Alignment explanation


    Indices: 2301--2395  Score: 131
    Period size: 40  Copynumber: 2.3  Consensus size: 41

       2291 TTGGTTTAAG

                 *                                     
       2301 GGTAAAAGATTGGACAATGG-TTTCAATCTGCCCCATGATCAA
          1 GGTAAGAGATTGG--AATGGTTTTCAATCTGCCCCATGATCAA

                                                   **
       2343 GGTAAGAGATT-GAATGGTTTTCAATCTGCCCCATGATCTG
          1 GGTAAGAGATTGGAATGGTTTTCAATCTGCCCCATGATCAA

                         
       2383 GGTAAGAGATTGG
          1 GGTAAGAGATTGG

       2396 TGATGTAACT


Statistics
Matches: 48,  Mismatches: 3, Indels: 5
        0.86            0.05        0.09

Matches are distributed among these distances:
  39    5  0.10
  40   31  0.65
  41    2  0.04
  42   10  0.21

ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28


Consensus pattern (41 bp):   
GGTAAGAGATTGGAATGGTTTTCAATCTGCCCCATGATCAA

Found at i:3134 original size:23 final size:22

Alignment explanation


    Indices: 3102--3213  Score: 84
    Period size: 23  Copynumber: 5.0  Consensus size: 22

       3092 GCTGGGGAAA

                 *         *      
       3102 CAGTAAGCACACACATTGCAAT
          1 CAGTAGGCACACACAGTGCAAT

                                   
       3124 CCAGTAGGCACACACAGTGCAAT
          1 -CAGTAGGCACACACAGTGCAAT

                    *    *  **     
       3147 CAGTAGGCGCACATAGCACAAAT
          1 CAGTAGGCACACACAGTGC-AAT

                 *                 *
       3170 CAGTAAGCACACGA-AGTGCAAAA
          1 CAGTAGGCACAC-ACAGTGC-AAT

                 *                
       3193 CAGTAAGCACACGA-AGTGCAA
          1 CAGTAGGCACAC-ACAGTGCAA

       3214 AAGAGTAAGC


Statistics
Matches: 76,  Mismatches: 11, Indels: 5
        0.83            0.12        0.05

Matches are distributed among these distances:
  22   17  0.22
  23   58  0.76
  24    1  0.01

ACGTcount: A:0.41, C:0.26, G:0.21, T:0.12


Consensus pattern (22 bp):   
CAGTAGGCACACACAGTGCAAT

Found at i:3214 original size:23 final size:23

Alignment explanation


    Indices: 3165--3246  Score: 128
    Period size: 23  Copynumber: 3.6  Consensus size: 23

       3155 GCACATAGCA

                *                  
       3165 CAAATCAGTAAGCACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

                                   
       3188 CAAAACAGTAAGCACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

                 *           *     
       3211 CAAAAGAGTAAGCACACAAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

             *           
       3234 CGAAACAGTAAGC
          1 CAAAACAGTAAGC

       3247 GCGCTAGCAT


Statistics
Matches: 54,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   54  1.00

ACGTcount: A:0.48, C:0.21, G:0.22, T:0.10


Consensus pattern (23 bp):   
CAAAACAGTAAGCACACGAAGTG

Found at i:10362 original size:22 final size:22

Alignment explanation


    Indices: 10331--10387  Score: 78
    Period size: 22  Copynumber: 2.6  Consensus size: 22

      10321 GCTGGGGAAA

                 *                
      10331 CAGTAAGCACACACAGTACAAT
          1 CAGTAGGCACACACAGTACAAT

                        *    *    
      10353 CAGTAGGCACACTCAGTGCAAT
          1 CAGTAGGCACACACAGTACAAT

                    *    
      10375 CAGTAGGCGCACA
          1 CAGTAGGCACACA

      10388 TAACTCAAAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.37, C:0.28, G:0.21, T:0.14


Consensus pattern (22 bp):   
CAGTAGGCACACACAGTACAAT

Found at i:10424 original size:23 final size:23

Alignment explanation


    Indices: 10393--10496  Score: 172
    Period size: 23  Copynumber: 4.5  Consensus size: 23

      10383 GCACATAACT

                *                  
      10393 CAAATCAGTAAGCACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

             *         *           
      10416 CGAAACAGTAAACACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

                                   
      10439 CAAAACAGTAAGCACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

                                   
      10462 CAAAACAGTAAGCACACGAAGTG
          1 CAAAACAGTAAGCACACGAAGTG

             *          
      10485 CGAAACAGTAAG
          1 CAAAACAGTAAG

      10497 AGTGCTAGCG


Statistics
Matches: 75,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  23   75  1.00

ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10


Consensus pattern (23 bp):   
CAAAACAGTAAGCACACGAAGTG

Done.