Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000442.1 Kokia drynarioides strain JFW-HI SEQ_111289, 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: 10721
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36


Found at i:2396 original size:27 final size:26

Alignment explanation


    Indices: 2374--2437  Score: 96
    Period size: 26  Copynumber: 2.5  Consensus size: 26

       2364 GTTTTTCCAG

                                       
       2374 ATTTTACAATTT-CCCTATATTTT-AA
          1 ATTTTACAATTTGCCCT-TATTTTCAA

                                       
       2399 ATTTTACAAATTTGCCCTTATTTTCAA
          1 ATTTTAC-AATTTGCCCTTATTTTCAA

                        
       2426 ATTTTACAATTT
          1 ATTTTACAATTT

       2438 TGCCTCTATT


Statistics
Matches: 36,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  25    7  0.19
  26   16  0.44
  27   13  0.36

ACGTcount: A:0.31, C:0.16, G:0.02, T:0.52


Consensus pattern (26 bp):   
ATTTTACAATTTGCCCTTATTTTCAA

Found at i:2439 original size:27 final size:27

Alignment explanation


    Indices: 2374--2584  Score: 117
    Period size: 27  Copynumber: 7.6  Consensus size: 27

       2364 GTTTTTCCAG

                                        
       2374 ATTTTACAA-TTT-CCCTATATTTT-AA
          1 ATTTTACAATTTTGCCCT-TATTTTCAA

                     *                 
       2399 ATTTTACAAATTTGCCCTTATTTTCAA
          1 ATTTTACAATTTTGCCCTTATTTTCAA

                                  *    ***
       2426 ATTTTACAATTTTGCCTCTATTTTTTTGGG
          1 ATTTTACAATTTTGCC-C--TTATTTTCAA

             *    * *                   *
       2456 ACTTTATAGTTTTGCACC-TAGTTTTCAG
          1 ATTTTACAATTTTGC-CCTTA-TTTTCAA

                  *      *              
       2484 ATTTTATAATTTTACCAC-TATTTTCAA
          1 ATTTTACAATTTTGCC-CTTATTTTCAA

             *    * *    *   *          
       2511 AGTTTATAGTTTTTCCCCTATTTTCGAA
          1 ATTTTACAATTTTGCCCTTATTTTC-AA

                              *      *   
       2539 ATTTTACAATTTTGCCTCCTACTTTACAA
          1 ATTTTACAATTTTGCC-CTTA-TTTTCAA

             *      *        
       2568 AATTTACAGTTTTGCCC
          1 ATTTTACAATTTTGCCC

       2585 ATAATTTTAT


Statistics
Matches: 148,  Mismatches: 25, Indels: 23
        0.76            0.13        0.12

Matches are distributed among these distances:
  25    9  0.06
  26   10  0.07
  27   49  0.33
  28   36  0.24
  29   20  0.14
  30   23  0.16
  31    1  0.01

ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49


Consensus pattern (27 bp):   
ATTTTACAATTTTGCCCTTATTTTCAA

Found at i:5737 original size:14 final size:15

Alignment explanation


    Indices: 5709--5737  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       5699 AAAAATTATC

                           
       5709 AAATTCAATACCTAA
          1 AAATTCAATACCTAA

                           
       5724 AAATTCAA-ACCTAA
          1 AAATTCAATACCTAA

       5738 TATAAAAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24


Consensus pattern (15 bp):   
AAATTCAATACCTAA
Done.