Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003355.1 Kokia drynarioides strain JFW-HI SEQ_116074, 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: 10008
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35


Found at i:152 original size:34 final size:34

Alignment explanation


    Indices: 100--182  Score: 148
    Period size: 34  Copynumber: 2.4  Consensus size: 34

         90 AAACAGATGC

                *                              
        100 ACAGGTAAGCTTACAAAGCTTAGTAGGTTCGTAGA
          1 ACAGTTAA-CTTACAAAGCTTAGTAGGTTCGTAGA

                                              
        135 ACAGTTAACTTACAAAGCTTAGTAGGTTCGTAGA
          1 ACAGTTAACTTACAAAGCTTAGTAGGTTCGTAGA

                          
        169 ACAGTTAACTTACA
          1 ACAGTTAACTTACA

        183 GAATGTTATA


Statistics
Matches: 47,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  34   40  0.85
  35    7  0.15

ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28


Consensus pattern (34 bp):   
ACAGTTAACTTACAAAGCTTAGTAGGTTCGTAGA

Found at i:4321 original size:21 final size:22

Alignment explanation


    Indices: 4262--4321  Score: 54
    Period size: 21  Copynumber: 2.9  Consensus size: 22

       4252 TCAACAAAAA

                    *        *    
       4262 TTATAAAATAATTCAAATTAAT
          1 TTATAAAAAAATTCAAAATAAT

                 *       **       
       4284 TT-T-CAAAAATTTTAAAT-AT
          1 TTATAAAAAAATTCAAAATAAT

                               
       4303 TTATAAAAAAATTCAAAAT
          1 TTATAAAAAAATTCAAAAT

       4322 TGATATTTTA


Statistics
Matches: 28,  Mismatches: 8, Indels: 5
        0.68            0.20        0.12

Matches are distributed among these distances:
  19    4  0.14
  20   10  0.36
  21   12  0.43
  22    2  0.07

ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40


Consensus pattern (22 bp):   
TTATAAAAAAATTCAAAATAAT

Found at i:4964 original size:15 final size:15

Alignment explanation


    Indices: 4946--4975  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4936 TTTTCTTGTC

                           
       4946 AAGTATTTATTTCAG
          1 AAGTATTTATTTCAG

                           
       4961 AAGTATTTATTTCAG
          1 AAGTATTTATTTCAG

       4976 GTTTTTTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47


Consensus pattern (15 bp):   
AAGTATTTATTTCAG

Found at i:7875 original size:45 final size:45

Alignment explanation


    Indices: 7802--8000  Score: 206
    Period size: 45  Copynumber: 4.5  Consensus size: 45

       7792 CCTGTATTAG

                  *           * *      *      * *        
       7802 GGAAACATCTTGTTTCCTCTGTCCATATCCTGTTGCTAGCATCAA
          1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA

                              *    *   *        *    *   
       7847 GGAAACTTCTTGTTTCCTATATCTATATCCTGTTT-GA-CACCAA
          1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA

                *  *                     *               *
       7890 GGAAGCTCCTTGTTTCCTGTATCCATAGCATGTTTCCAGC-TCCAT
          1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCAT-CAA

                                                 *  *   *
       7935 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCGGCTTCAG
          1 GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA

                                 
       7980 GGAAACTTCTTGTTTCCTGTA
          1 GGAAACTTCTTGTTTCCTGTA

       8001 CATGTAGTTT


Statistics
Matches: 129,  Mismatches: 21, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
  43   34  0.26
  44    2  0.02
  45   92  0.71
  46    1  0.01

ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38


Consensus pattern (45 bp):   
GGAAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCAGCATCAA

Done.