Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011375.1 Kokia drynarioides strain JFW-HI SEQ_126356, 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: 16856
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Found at i:307 original size:30 final size:26

Alignment explanation


    Indices: 271--339  Score: 75
    Period size: 30  Copynumber: 2.5  Consensus size: 26

        261 AATTTGACAG

                                          
        271 GTGGTGCCTTTGAGGTAGGCAGGACCAATA
          1 GTGGTGCCTTTG-GGTAGGC-GG--CAATA

                      *             *  
        301 GTGGTGCCTACTGGGTAGGCGGCACTA
          1 GTGGTGCCT-TTGGGTAGGCGGCAATA

                        
        328 GTGGTGCCTTTG
          1 GTGGTGCCTTTG

        340 TCAAAACTAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  26    2  0.06
  27   13  0.37
  29    2  0.06
  30   16  0.46
  31    2  0.06

ACGTcount: A:0.16, C:0.19, G:0.39, T:0.26


Consensus pattern (26 bp):   
GTGGTGCCTTTGGGTAGGCGGCAATA

Found at i:7366 original size:54 final size:54

Alignment explanation


    Indices: 7308--7476  Score: 205
    Period size: 54  Copynumber: 3.1  Consensus size: 54

       7298 TTGTTATGAA

                     *                                         *  
       7308 ATTTTAATAAAATTATTATTAAATATAATTTAATAATAATAATAATTTAATTAT
          1 ATTTTAATATAATTATTATTAAATATAATTTAATAATAATAATAATTTAATAAT

                   *                      *                          
       7362 ATTTTAACATAATTATTATTAAATATAATTAAATAAAATAATATATAATTTAATAAT
          1 ATTTTAATATAATTATTATTAAATATAATTTAAT--AATAATA-ATAATTTAATAAT

                                          *   *   *   *     *       
       7419 ATTTTTAATATAATTATTATTAAAATATAAATTAGTAAAAATTATAATAT-ATAAT
          1 A-TTTTAATATAATTATTATT-AAATATAATTTAATAATAATAATAATTTAATAAT

               
       7474 ATT
          1 ATT

       7477 AGAAAAATAA


Statistics
Matches: 99,  Mismatches: 11, Indels: 10
        0.82            0.09        0.08

Matches are distributed among these distances:
  54   33  0.33
  55    6  0.06
  56   13  0.13
  57   18  0.18
  58   18  0.18
  59   11  0.11

ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46


Consensus pattern (54 bp):   
ATTTTAATATAATTATTATTAAATATAATTTAATAATAATAATAATTTAATAAT

Found at i:7482 original size:24 final size:25

Alignment explanation


    Indices: 7434--7484  Score: 70
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       7424 TAATATAATT

                                     
       7434 ATTATTAAAATATAAATTAGTAAAA
          1 ATTATTAAAATATAAATTAGTAAAA

                    *                 
       7459 ATTA-TAATATATAATATTAG-AAAA
          1 ATTATTAAAATATAA-ATTAGTAAAA

              
       7483 AT
          1 AT

       7485 AATACATAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  24   15  0.62
  25    9  0.38

ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37


Consensus pattern (25 bp):   
ATTATTAAAATATAAATTAGTAAAA

Found at i:13801 original size:17 final size:17

Alignment explanation


    Indices: 13779--13812  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      13769 AAAAAAATCC

                             
      13779 ATTTAAATGTTATTTAA
          1 ATTTAAATGTTATTTAA

                             
      13796 ATTTAAATGTTATTTAA
          1 ATTTAAATGTTATTTAA

      13813 TCATGTAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53


Consensus pattern (17 bp):   
ATTTAAATGTTATTTAA
Done.