Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005926.1 Kokia drynarioides strain JFW-HI SEQ_120303, 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: 9845
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37


Found at i:216 original size:19 final size:20

Alignment explanation


    Indices: 173--218  Score: 53
    Period size: 19  Copynumber: 2.5  Consensus size: 20

        163 ATTACAAAAA

                                
        173 ATAAAAA-TAAAAATAGTTT
          1 ATAAAAATTAAAAATAGTTT

              *      *          
        192 -TTAAAATTCAAAATA-TTT
          1 ATAAAAATTAAAAATAGTTT

                     
        210 ATAAAAATT
          1 ATAAAAATT

        219 TCTAAATTTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 4
        0.76            0.10        0.14

Matches are distributed among these distances:
  18    8  0.36
  19   14  0.64

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


Consensus pattern (20 bp):   
ATAAAAATTAAAAATAGTTT

Found at i:265 original size:34 final size:34

Alignment explanation


    Indices: 201--265  Score: 85
    Period size: 34  Copynumber: 1.9  Consensus size: 34

        191 TTTAAAATTC

                *           *       **        
        201 AAAATATTTATAAAAATTTCTAAATTTATATTTT
          1 AAAAAATTTATAAAAAATTCTAAAAATATATTTT

                     *                     
        235 AAAAAATTTGTAAAAAATTCTAAAAATATAT
          1 AAAAAATTTATAAAAAATTCTAAAAATATAT

        266 ATAAAAAGTT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  34   26  1.00

ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42


Consensus pattern (34 bp):   
AAAAAATTTATAAAAAATTCTAAAAATATATTTT

Found at i:1121 original size:22 final size:22

Alignment explanation


    Indices: 1093--1145  Score: 97
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       1083 AGGAAAGTGT

                                  
       1093 ATTGCGATATCCAAACTTTGGA
          1 ATTGCGATATCCAAACTTTGGA

                                  
       1115 ATTGCGATATCCAAACTTTGGA
          1 ATTGCGATATCCAAACTTTGGA

              *      
       1137 ATAGCGATA
          1 ATTGCGATA

       1146 CCTCTAACAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Consensus pattern (22 bp):   
ATTGCGATATCCAAACTTTGGA

Found at i:4012 original size:26 final size:23

Alignment explanation


    Indices: 3951--4028  Score: 102
    Period size: 23  Copynumber: 3.3  Consensus size: 23

       3941 TAATCTAATA

                                   
       3951 TGAAATGTATTTATTTATTTTCT
          1 TGAAATGTATTTATTTATTTTCT

                                      
       3974 TGAAATGTATTTATTTATTTAAATCT
          1 TGAAATGTATTTATTTATTT---TCT

                   **              
       4000 TGAAATGCCTTTATTTATTTTCT
          1 TGAAATGTATTTATTTATTTTCT

             *    
       4023 TTAAAT
          1 TGAAAT

       4029 ATATATAATT


Statistics
Matches: 49,  Mismatches: 3, Indels: 6
        0.84            0.05        0.10

Matches are distributed among these distances:
  23   28  0.57
  26   21  0.43

ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56


Consensus pattern (23 bp):   
TGAAATGTATTTATTTATTTTCT

Found at i:5242 original size:6 final size:6

Alignment explanation


    Indices: 5221--5260  Score: 53
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       5211 ATCTTGCATC

                    *          *                   *      
       5221 GGCAGT GACAGT GGCAGG GGCAGT GGCAGT GGCAAT GGCA
          1 GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCA

       5261 ATCATGAGAC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.23, C:0.17, G:0.47, T:0.12


Consensus pattern (6 bp):   
GGCAGT

Found at i:9810 original size:30 final size:30

Alignment explanation


    Indices: 9769--9840  Score: 101
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       9759 AAAAGGGTAA

                  *                        
       9769 TTTTGGGAGTTTCGAGAGT-AAAAATGAAAT
          1 TTTTGGAAGTTTCG-GAGTAAAAAATGAAAT

                        *  *              
       9799 TTTTGGAAGTTTTGGGGTAAAAAATGAAAT
          1 TTTTGGAAGTTTCGGAGTAAAAAATGAAAT

                        
       9829 TTTTGGAAGTTT
          1 TTTTGGAAGTTT

       9841 TGGGG


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  29    3  0.08
  30   35  0.92

ACGTcount: A:0.33, C:0.01, G:0.26, T:0.39


Consensus pattern (30 bp):   
TTTTGGAAGTTTCGGAGTAAAAAATGAAAT

Found at i:9841 original size:30 final size:30

Alignment explanation


    Indices: 9788--9845  Score: 116
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       9778 TTTCGAGAGT

                                          
       9788 AAAAATGAAATTTTTGGAAGTTTTGGGGTA
          1 AAAAATGAAATTTTTGGAAGTTTTGGGGTA

                                        
       9818 AAAAATGAAATTTTTGGAAGTTTTGGGG
          1 AAAAATGAAATTTTTGGAAGTTTTGGGG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36


Consensus pattern (30 bp):   
AAAAATGAAATTTTTGGAAGTTTTGGGGTA
Done.