Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009356.1 Kokia drynarioides strain JFW-HI SEQ_124063, 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: 73973
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:2603 original size:13 final size:13

Alignment explanation


    Indices: 2585--2609  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2575 AAATTTTATC

                         
       2585 ATTTTTTATATTT
          1 ATTTTTTATATTT

                        
       2598 ATTTTTTATATT
          1 ATTTTTTATATT

       2610 GTTCTTATTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (13 bp):   
ATTTTTTATATTT

Found at i:33139 original size:73 final size:73

Alignment explanation


    Indices: 33020--33166  Score: 285
    Period size: 73  Copynumber: 2.0  Consensus size: 73

      33010 TACTCCCAAA

                                                                             
      33020 TCACATAAAGCTTTACCTAAATAAGGATTCCCAATGGAGCATGAAATTGTAAAGGTGCCAGGGTC
          1 TCACATAAAGCTTTACCTAAATAAGGATTCCCAATGGAGCATGAAATTGTAAAGGTGCCAGGGTC

                    
      33085 TTTCATTT
         66 TTTCATTT

                                    *                                        
      33093 TCACATAAAGCTTTACCTAAATAATGATTCCCAATGGAGCATGAAATTGTAAAGGTGCCAGGGTC
          1 TCACATAAAGCTTTACCTAAATAAGGATTCCCAATGGAGCATGAAATTGTAAAGGTGCCAGGGTC

                    
      33158 TTTCATTT
         66 TTTCATTT

             
      33166 T
          1 T

      33167 TGGTCGCAAC


Statistics
Matches: 73,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  73   73  1.00

ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Consensus pattern (73 bp):   
TCACATAAAGCTTTACCTAAATAAGGATTCCCAATGGAGCATGAAATTGTAAAGGTGCCAGGGTC
TTTCATTT

Found at i:34043 original size:80 final size:80

Alignment explanation


    Indices: 33910--34069  Score: 293
    Period size: 80  Copynumber: 2.0  Consensus size: 80

      33900 TGTACTTGCG

                          *                                                  
      33910 AATTCTTATTATAATTTTACTATTGGCTGTTATTATAACTCCCTTGCCTATAACTCCCTTGATTT
          1 AATTCTTATTATAACTTTACTATTGGCTGTTATTATAACTCCCTTGCCTATAACTCCCTTGATTT

                           
      33975 GAGGAATTGCCATAT
         66 GAGGAATTGCCATAT

                                      *                   *                  
      33990 AATTCTTATTATAACTTTACTATTGGTTGTTATTATAACTCCCTTGTCTATAACTCCCTTGATTT
          1 AATTCTTATTATAACTTTACTATTGGCTGTTATTATAACTCCCTTGCCTATAACTCCCTTGATTT

                           
      34055 GAGGAATTGCCATAT
         66 GAGGAATTGCCATAT

      34070 CTATATGTGG


Statistics
Matches: 77,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  80   77  1.00

ACGTcount: A:0.26, C:0.18, G:0.11, T:0.44


Consensus pattern (80 bp):   
AATTCTTATTATAACTTTACTATTGGCTGTTATTATAACTCCCTTGCCTATAACTCCCTTGATTT
GAGGAATTGCCATAT

Found at i:50712 original size:29 final size:29

Alignment explanation


    Indices: 50656--50712  Score: 71
    Period size: 28  Copynumber: 2.0  Consensus size: 29

      50646 CTAATTGAAT

                             *   *       
      50656 TTTAAATTTTTAAGTTTCATTCTTTGTTG
          1 TTTAAATTTTTAAGTTTAATTATTTGTTG

                         *               
      50685 TTTAAA-TTTTAATTTTAATTATTATGTT
          1 TTTAAATTTTTAAGTTTAATTATT-TGTT

      50713 AATAAAGGGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  28   14  0.58
  29   10  0.42

ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63


Consensus pattern (29 bp):   
TTTAAATTTTTAAGTTTAATTATTTGTTG

Found at i:60390 original size:15 final size:15

Alignment explanation


    Indices: 60359--60401  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

      60349 TTCTTCCTTC

                    *      
      60359 TCTTCTTCCTTTCCT
          1 TCTTCTTCTTTTCCT

                        *  
      60374 TCTTCTTCTTTTTCT
          1 TCTTCTTCTTTTCCT

                *        
      60389 TCATCCTTCTTTT
          1 TC-TTCTTCTTTT

      60402 AAGCAGCTCT


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

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65


Consensus pattern (15 bp):   
TCTTCTTCTTTTCCT

Found at i:73144 original size:22 final size:23

Alignment explanation


    Indices: 73118--73175  Score: 64
    Period size: 24  Copynumber: 2.5  Consensus size: 23

      73108 TAAAACTTTA

                          *        
      73118 TTTATAAATATATATATAT-AAT
          1 TTTATAAATATATAAATATAAAT

                               *     
      73140 TTTATAATAATATATAAATCTAAAT
          1 TTTAT-A-AATATATAAATATAAAT

              *        
      73165 TTCATAAATAT
          1 TTTATAAATAT

      73176 TCTAATTGAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  22    5  0.17
  23    6  0.20
  24   12  0.40
  25    7  0.23

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (23 bp):   
TTTATAAATATATAAATATAAAT
Done.