Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011512.1 Kokia drynarioides strain JFW-HI SEQ_126497, 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: 48033
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:361 original size:23 final size:25

Alignment explanation


    Indices: 335--380  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        325 CCAATTAGGG

                                     
        335 AATTAT-TGTTTAG-ATTTAATTCA
          1 AATTATCTGTTTAGAATTTAATTCA

                    *              
        358 AATTATCTTTTTAGAATTTAATT
          1 AATTATCTGTTTAGAATTTAATT

        381 TGAATCCAAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    6  0.30
  24    6  0.30
  25    8  0.40

ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54


Consensus pattern (25 bp):   
AATTATCTGTTTAGAATTTAATTCA

Found at i:5506 original size:14 final size:14

Alignment explanation


    Indices: 5484--5515  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

       5474 CATCACTTTC

                *         
       5484 CTTCCACAATTTTT
          1 CTTCAACAATTTTT

                          
       5498 CTTCAACAATTTTT
          1 CTTCAACAATTTTT

                
       5512 CTTC
          1 CTTC

       5516 CCATTTCTTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50


Consensus pattern (14 bp):   
CTTCAACAATTTTT

Found at i:16342 original size:9 final size:9

Alignment explanation


    Indices: 16328--16354  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

      16318 CTTTCTCTGA

                     
      16328 GCTACTGCT
          1 GCTACTGCT

                     
      16337 GCTACTGCT
          1 GCTACTGCT

                     
      16346 GCTACTGCT
          1 GCTACTGCT

      16355 ACTTGGTGAT


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

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.11, C:0.33, G:0.22, T:0.33


Consensus pattern (9 bp):   
GCTACTGCT

Found at i:24325 original size:20 final size:20

Alignment explanation


    Indices: 24302--24347  Score: 65
    Period size: 20  Copynumber: 2.3  Consensus size: 20

      24292 ACTTTCTCAA

                   *            
      24302 TTTTTTATATTCCCTCGTAT
          1 TTTTTTACATTCCCTCGTAT

                 *      *       
      24322 TTTTTGACATTCTCTCGTAT
          1 TTTTTTACATTCCCTCGTAT

                  
      24342 TTTTTT
          1 TTTTTT

      24348 GGTACTTCTT


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

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (20 bp):   
TTTTTTACATTCCCTCGTAT

Found at i:24356 original size:22 final size:21

Alignment explanation


    Indices: 24283--24370  Score: 55
    Period size: 22  Copynumber: 4.3  Consensus size: 21

      24273 TTTTTTTAGG

                                *
      24283 TTTTTTGGTACTT-TCTC-AA
          1 TTTTTTGGTACTTCTCTCGAT

                   *      *      
      24302 TTTTTT-ATA-TTCCCTCG-T
          1 TTTTTTGGTACTTCTCTCGAT

                                    
      24320 ATTTTTT-G-ACATTCTCTCGTAT
          1 -TTTTTTGGTAC-TTCTCTCG-AT

                           *      
      24342 TTTTTTGGTACTTCTTTCGAGT
          1 TTTTTTGGTACTTCTCTCGA-T

                   
      24364 TTTTTTG
          1 TTTTTTG

      24371 TATTCCATTC


Statistics
Matches: 53,  Mismatches: 6, Indels: 17
        0.70            0.08        0.22

Matches are distributed among these distances:
  17    2  0.04
  18    6  0.11
  19   12  0.23
  20    7  0.13
  21    7  0.13
  22   17  0.32
  23    2  0.04

ACGTcount: A:0.12, C:0.16, G:0.11, T:0.60


Consensus pattern (21 bp):   
TTTTTTGGTACTTCTCTCGAT
Done.