Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007362.1 Kokia drynarioides strain JFW-HI SEQ_121978, 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: 18033
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36


Found at i:3144 original size:33 final size:33

Alignment explanation


    Indices: 3102--3168  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       3092 TCTATCGATG

                                             
       3102 TCATCTATTCATAGGAAGAGAAGGTAGAACCCT
          1 TCATCTATTCATAGGAAGAGAAGGTAGAACCCT

                                             
       3135 TCATCTATTCATAGGAAGAGAAGGTAGAACCCT
          1 TCATCTATTCATAGGAAGAGAAGGTAGAACCCT

             
       3168 T
          1 T

       3169 GCTGAGTTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25


Consensus pattern (33 bp):   
TCATCTATTCATAGGAAGAGAAGGTAGAACCCT

Found at i:5347 original size:21 final size:21

Alignment explanation


    Indices: 5300--5349  Score: 55
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       5290 ATTTTGTGTT

                   *   *         
       5300 TTTATATGAAAGTTTAATAAA
          1 TTTATATTAAAATTTAATAAA

             *             *   * 
       5321 TATATATTAAAATTTTATATA
          1 TTTATATTAAAATTTAATAAA

                    
       5342 TTTATATT
          1 TTTATATT

       5350 TTATTTTAAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52


Consensus pattern (21 bp):   
TTTATATTAAAATTTAATAAA

Found at i:10872 original size:8 final size:8

Alignment explanation


    Indices: 10859--10884  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

      10849 TCAGAAGTTC

                    
      10859 TCACCTTA
          1 TCACCTTA

                    
      10867 TCACCTTA
          1 TCACCTTA

                    
      10875 TCACCTTA
          1 TCACCTTA

              
      10883 TC
          1 TC

      10885 TTTTTGTGCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38


Consensus pattern (8 bp):   
TCACCTTA

Found at i:15319 original size:26 final size:26

Alignment explanation


    Indices: 15268--15321  Score: 65
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      15258 AATTATTTCC

                                 *    
      15268 TTATTTCAAATTTTCATTTACTAAGT
          1 TTATTTCAAATTTTCATTTACAAAGT

                  *        *           
      15294 TTATTTTAATATTTTTATTTA-AAAGT
          1 TTATTTCAA-ATTTTCATTTACAAAGT

              
      15320 TT
          1 TT

      15322 CAAAGTTATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26   14  0.58
  27   10  0.42

ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59


Consensus pattern (26 bp):   
TTATTTCAAATTTTCATTTACAAAGT
Done.