Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013691.1 Kokia drynarioides strain JFW-HI SEQ_128719, 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: 2180
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39


Found at i:442 original size:20 final size:20

Alignment explanation


    Indices: 417--463  Score: 76
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        407 TGTTTTTTGC

                                
        417 TGTTTTTAATGTTTTGGTGT
          1 TGTTTTTAATGTTTTGGTGT

                    *         * 
        437 TGTTTTTATTGTTTTGGTTT
          1 TGTTTTTAATGTTTTGGTGT

                   
        457 TGTTTTT
          1 TGTTTTT

        464 GCTGTTATTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  20   25  1.00

ACGTcount: A:0.06, C:0.00, G:0.21, T:0.72


Consensus pattern (20 bp):   
TGTTTTTAATGTTTTGGTGT

Found at i:469 original size:20 final size:20

Alignment explanation


    Indices: 403--469  Score: 73
    Period size: 20  Copynumber: 3.4  Consensus size: 20

        393 ACTGATTTAA

                       *  *     
        403 TTACTGTTTT-TTGCTGTTT
          1 TTACTGTTTTGGTGTTGTTT

               *                
        422 TTAATGTTTTGGTGTTGTTT
          1 TTACTGTTTTGGTGTTGTTT

               *         *      
        442 TTATTGTTTTGGTTTTGTTT
          1 TTACTGTTTTGGTGTTGTTT

              *     
        462 TTGCTGTT
          1 TTACTGTT

        470 ATTTTTGCTG


Statistics
Matches: 40,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  19    9  0.22
  20   31  0.77

ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69


Consensus pattern (20 bp):   
TTACTGTTTTGGTGTTGTTT

Found at i:483 original size:24 final size:24

Alignment explanation


    Indices: 456--505  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 24

        446 TGTTTTGGTT

                   *    *           
        456 TTGTTTTTGCTGTTATTTTTGCTG
          1 TTGTTTTGGCTGCTATTTTTGCTG

                     *           *  
        480 TTGTTTTGGTTGCTATTTTTGTTG
          1 TTGTTTTGGCTGCTATTTTTGCTG

              
        504 TT
          1 TT

        506 TGGATGTTAT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.04, C:0.06, G:0.22, T:0.68


Consensus pattern (24 bp):   
TTGTTTTGGCTGCTATTTTTGCTG

Found at i:516 original size:20 final size:21

Alignment explanation


    Indices: 478--528  Score: 59
    Period size: 20  Copynumber: 2.4  Consensus size: 21

        468 TTATTTTTGC

                       *         
        478 TGTTGTTTTGGTTGCTATTTT
          1 TGTTGTTTTGGATGCTATTTT

                          *      
        499 TGTTG-TTTGGATGTTATTTT
          1 TGTTGTTTTGGATGCTATTTT

             *        
        519 TATGTGTTTT
          1 TGT-TGTTTT

        529 TACTATTGTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  20   15  0.60
  21    7  0.28
  22    3  0.12

ACGTcount: A:0.08, C:0.02, G:0.24, T:0.67


Consensus pattern (21 bp):   
TGTTGTTTTGGATGCTATTTT

Found at i:678 original size:13 final size:13

Alignment explanation


    Indices: 654--686  Score: 50
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        644 TATTTTAATT

                          
        654 TGTTTCTTTTTTAA
          1 TGTTT-TTTTTTAA

                         
        668 TGTTTTTTTTTAA
          1 TGTTTTTTTTTAA

                   
        681 T-TTTTT
          1 TGTTTTT

        687 AAGTGTATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    5  0.26
  13    9  0.47
  14    5  0.26

ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79


Consensus pattern (13 bp):   
TGTTTTTTTTTAA
Done.