Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002593.1 Kokia drynarioides strain JFW-HI SEQ_114801, 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: 17493
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34


Found at i:6729 original size:16 final size:18

Alignment explanation


    Indices: 6698--6734  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       6688 TCATAATCCG

                  *           
       6698 TTTCATCTCAATTCT-AT
          1 TTTCATATCAATTCTAAT

                              
       6715 TTTCATATC-ATTCTAAT
          1 TTTCATATCAATTCTAAT

               
       6732 TTT
          1 TTT

       6735 TAGTTTCATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  16    5  0.28
  17   13  0.72

ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57


Consensus pattern (18 bp):   
TTTCATATCAATTCTAAT

Found at i:7798 original size:18 final size:18

Alignment explanation


    Indices: 7775--7809  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       7765 TAAATTAATA

                        *     
       7775 AATATTATTATTTATTAT
          1 AATATTATTATTAATTAT

                             
       7793 AATATTATTATTAATTA
          1 AATATTATTATTAATTA

       7810 ATATATCATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (18 bp):   
AATATTATTATTAATTAT

Found at i:7815 original size:18 final size:18

Alignment explanation


    Indices: 7768--7815  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       7758 ATAATACTAA

                              
       7768 ATTAA-TAA-ATATTATT
          1 ATTAATTAATATATTATT

               *               
       7784 ATTTATT-ATAATATTATT
          1 ATTAATTAAT-ATATTATT

                          
       7802 ATTAATTAATATAT
          1 ATTAATTAATATAT

       7816 CATTTGAAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 6
        0.76            0.06        0.18

Matches are distributed among these distances:
  16    5  0.19
  17    1  0.04
  18   18  0.69
  19    2  0.08

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (18 bp):   
ATTAATTAATATATTATT

Found at i:15531 original size:3 final size:3

Alignment explanation


    Indices: 15523--15568  Score: 56
    Period size: 3  Copynumber: 15.3  Consensus size: 3

      15513 GTTTGAGTAG

                            *   *         *                 *            
      15523 TGT TGT TGT TGT GGT AGT TGT TGC TGT TGT TGT TGT GGT TGT TGT T
          1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T

      15569 ATTGCTCATC


Statistics
Matches: 36,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.02, C:0.02, G:0.37, T:0.59


Consensus pattern (3 bp):   
TGT

Found at i:15544 original size:12 final size:12

Alignment explanation


    Indices: 15524--15568  Score: 65
    Period size: 12  Copynumber: 3.8  Consensus size: 12

      15514 TTTGAGTAGT

                        
      15524 GTTGTTGTTGTG
          1 GTTGTTGTTGTG

              *          
      15536 GTAGTTGTTGCT-
          1 GTTGTTGTTG-TG

                        
      15548 GTTGTTGTTGTG
          1 GTTGTTGTTGTG

                     
      15560 GTTGTTGTT
          1 GTTGTTGTT

      15569 ATTGCTCATC


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  11    1  0.03
  12   27  0.93
  13    1  0.03

ACGTcount: A:0.02, C:0.02, G:0.38, T:0.58


Consensus pattern (12 bp):   
GTTGTTGTTGTG
Done.