Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000883.1 Kokia drynarioides strain JFW-HI SEQ_112003, 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: 42613
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:7951 original size:55 final size:55

Alignment explanation


    Indices: 7888--7995  Score: 182
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       7878 CACTCATCCC

                     *                         *                    
       7888 CATATTTTTCATGATTATTGAT-CTAGTGCATCAATAAAATTAAAAAAAAAAAACT
          1 CATATTTTTAATGATTATTGATAC-AGTGCATCAACAAAATTAAAAAAAAAAAACT

                                                                 
       7943 CATATTTTTAATGATTATTGATACAGTGCATCAACAAAATTAAAAAAAAAAAA
          1 CATATTTTTAATGATTATTGATACAGTGCATCAACAAAATTAAAAAAAAAAAA

       7996 AAAGGCTCAA


Statistics
Matches: 50,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  55   49  0.98
  56    1  0.02

ACGTcount: A:0.50, C:0.10, G:0.07, T:0.32


Consensus pattern (55 bp):   
CATATTTTTAATGATTATTGATACAGTGCATCAACAAAATTAAAAAAAAAAAACT

Found at i:25410 original size:29 final size:31

Alignment explanation


    Indices: 25339--25411  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      25329 GCCCTTTAAG

                            *            *  
      25339 CTTGTCC-AAAAATATTTAGTTGGTACTTGAA
          1 CTTGTCCAAAAAATATCTAGTTGGTAC-TAAA

               *                           
      25370 CTTATCCAAAAAATA-CTAGTTGGTAC-AAA
          1 CTTGTCCAAAAAATATCTAGTTGGTACTAAA

                         
      25399 CTTGTCCAAAAAA
          1 CTTGTCCAAAAAA

      25412 ATTACTTTTT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  29   14  0.38
  31   16  0.43
  32    7  0.19

ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32


Consensus pattern (31 bp):   
CTTGTCCAAAAAATATCTAGTTGGTACTAAA

Found at i:32518 original size:66 final size:66

Alignment explanation


    Indices: 32444--32573  Score: 260
    Period size: 66  Copynumber: 2.0  Consensus size: 66

      32434 ATGTTTACTT

                                                                             
      32444 GCTATTTTCTTTTAGCTTAATCAAAGTTTTTATAAATTCATAACGAAAGTTATAAAAAATAAAGT
          1 GCTATTTTCTTTTAGCTTAATCAAAGTTTTTATAAATTCATAACGAAAGTTATAAAAAATAAAGT

             
      32509 C
         66 C

                                                                            
      32510 GCTATTTTCTTTTAGCTTAATCAAAGTTTTTATAAATTCATAACGAAAGTTATAAAAAATAAAG
          1 GCTATTTTCTTTTAGCTTAATCAAAGTTTTTATAAATTCATAACGAAAGTTATAAAAAATAAAG

      32574 ATTCACATTT


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  66   64  1.00

ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39


Consensus pattern (66 bp):   
GCTATTTTCTTTTAGCTTAATCAAAGTTTTTATAAATTCATAACGAAAGTTATAAAAAATAAAGT
C
Done.