Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005704.1 Kokia drynarioides strain JFW-HI SEQ_119918, 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, 924

Length: 1541
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30


Found at i:147 original size:19 final size:19

Alignment explanation


    Indices: 103--151  Score: 55
    Period size: 19  Copynumber: 2.5  Consensus size: 19

         93 AAAATAATAA

                             *  
        103 AAAAATCAAATCAAATGTAT
          1 AAAAAT-AAATCAAATGAAT

                                 
        123 ACAAAATAAAT-AAATGAATT
          1 A-AAAATAAATCAAATGAA-T

                     
        143 AAAAATAAA
          1 AAAAATAAA

        152 ATATCCTCAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19   14  0.54
  20    7  0.27
  21    5  0.19

ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22


Consensus pattern (19 bp):   
AAAAATAAATCAAATGAAT

Found at i:399 original size:7 final size:7

Alignment explanation


    Indices: 387--411  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

        377 AATTGAGTCC

                   
        387 AAATTTT
          1 AAATTTT

                   
        394 AAATTTT
          1 AAATTTT

                   
        401 AAATTTT
          1 AAATTTT

                
        408 AAAT
          1 AAAT

        412 AAGTTTGAAT


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

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (7 bp):   
AAATTTT

Found at i:451 original size:34 final size:34

Alignment explanation


    Indices: 413--479  Score: 98
    Period size: 34  Copynumber: 2.0  Consensus size: 34

        403 ATTTTAAATA

                        *                     
        413 AGTTTGAATCTATTTTAAATTCAAATTCATTTTG
          1 AGTTTGAATCTACTTTAAATTCAAATTCATTTTG

                     *           *     *     
        447 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
          1 AGTTTGAATCTACTTTAAATTCAAATTCATTTT

        480 AAATTAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   29  1.00

ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54


Consensus pattern (34 bp):   
AGTTTGAATCTACTTTAAATTCAAATTCATTTTG

Found at i:473 original size:17 final size:17

Alignment explanation


    Indices: 453--489  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

        443 TTTGAGTTTG

                           * 
        453 AATTTACTTTAAATTTA
          1 AATTTACTTTAAATTAA

                  *          
        470 AATTTATTTTAAATTAA
          1 AATTTACTTTAAATTAA

               
        487 AAT
          1 AAT

        490 AAAATTAAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51


Consensus pattern (17 bp):   
AATTTACTTTAAATTAA

Found at i:1207 original size:19 final size:20

Alignment explanation


    Indices: 1185--1222  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1175 TTAACATTAA

                                
       1185 TAATAATAATAAAT-TTTTT
          1 TAATAATAATAAATATTTTT

                               
       1204 TAATAATAATAAATATTTT
          1 TAATAATAATAAATATTTT

       1223 GGTAATATTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (20 bp):   
TAATAATAATAAATATTTTT

Done.