Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003041.1 Kokia drynarioides strain JFW-HI SEQ_115567, 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: 2399
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38


Found at i:329 original size:15 final size:15

Alignment explanation


    Indices: 309--347  Score: 69
    Period size: 15  Copynumber: 2.6  Consensus size: 15

        299 TTTGGTCATC

                           
        309 TGTAATTGGGCCATT
          1 TGTAATTGGGCCATT

                      *    
        324 TGTAATTGGGTCATT
          1 TGTAATTGGGCCATT

                     
        339 TGTAATTGG
          1 TGTAATTGG

        348 ACTTTGTTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.21, C:0.08, G:0.28, T:0.44


Consensus pattern (15 bp):   
TGTAATTGGGCCATT

Found at i:463 original size:16 final size:17

Alignment explanation


    Indices: 379--464  Score: 106
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        369 TTGGACTTTC

                         *    
        379 TAAATTT-AATTTTATAA
          1 TAAATTTAAATTTCA-AA

                             
        396 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTCAAA

                             
        413 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTCAAA

                *            
        430 TAAACTTAAATTT-AAA
          1 TAAATTTAAATTTCAAA

                   *      *  
        446 TAAA-TTCAATTTCCAA
          1 TAAATTTAAATTTCAAA

               
        462 TAA
          1 TAA

        465 GTCCAGACAA


Statistics
Matches: 63,  Mismatches: 4, Indels: 5
        0.88            0.06        0.07

Matches are distributed among these distances:
  15    7  0.11
  16   12  0.19
  17   38  0.60
  18    6  0.10

ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAAATTTAAATTTCAAA

Found at i:2185 original size:31 final size:31

Alignment explanation


    Indices: 2116--2196  Score: 117
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       2106 AACTATAAAA

                   *   *      *            
       2116 ATTTCTAATTTAGTCACTAACATTTTAGATC
          1 ATTTCTATTTTGGTCACTCACATTTTAGATC

                                 *         
       2147 ATTTCTATTTTGGTCACTCACGTTTTAGATC
          1 ATTTCTATTTTGGTCACTCACATTTTAGATC

                     *         
       2178 ATTTCTATTATGGTCACTC
          1 ATTTCTATTTTGGTCACTC

       2197 TCCATTAAAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   45  1.00

ACGTcount: A:0.25, C:0.19, G:0.10, T:0.47


Consensus pattern (31 bp):   
ATTTCTATTTTGGTCACTCACATTTTAGATC
Done.