Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006250.1 Kokia drynarioides strain JFW-HI SEQ_120821, 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: 3609
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28


Found at i:1779 original size:39 final size:39

Alignment explanation


    Indices: 1723--1802  Score: 142
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       1713 CCAAGAGTAA

                        *                          
       1723 TAGGAATCCTTTTATAAAGGGCACATGACCACAATCTTT
          1 TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT

                                            *      
       1762 TAGGAATCCTTTCATAAAGGGCACATGACCACTATCTTT
          1 TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT

              
       1801 TA
          1 TA

       1803 TTTCAATAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31


Consensus pattern (39 bp):   
TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT

Found at i:3225 original size:7 final size:7

Alignment explanation


    Indices: 3197--3264  Score: 64
    Period size: 7  Copynumber: 9.1  Consensus size: 7

       3187 GAAGAAGAAG

                 * 
       3197 AAGAAGA
          1 AAGAAAA

                    
       3204 AAGAAAGA
          1 AAGAAA-A

                    
       3212 AATGAAAA
          1 AA-GAAAA

                   
       3220 AAGAAAA
          1 AAGAAAA

               *   
       3227 AAGGAAA
          1 AAGAAAA

                   
       3234 AAGAAAA
          1 AAGAAAA

              *     
       3241 TAGGAAAA
          1 -AAGAAAA

                *   
       3249 AAGGGAAA
          1 AA-GAAAA

                   
       3257 AAGAAAA
          1 AAGAAAA

             
       3264 A
          1 A

       3265 GAGAGGTCGA


Statistics
Matches: 50,  Mismatches: 7, Indels: 8
        0.77            0.11        0.12

Matches are distributed among these distances:
   7   28  0.56
   8   18  0.36
   9    4  0.08

ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03


Consensus pattern (7 bp):   
AAGAAAA

Found at i:3265 original size:14 final size:15

Alignment explanation


    Indices: 3197--3264  Score: 52
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       3187 GAAGAAGAAG

                 *          
       3197 AAGAAGAAAGAAAGA-
          1 AAGAAAAAAGAAA-AT

                            
       3212 AATGAAAAAAGAAAA-
          1 AA-GAAAAAAGAAAAT

               *           
       3227 AAGGAAAAAGAAAAT
          1 AAGAAAAAAGAAAAT

             *         *    
       3242 AGGAAAAAAGGGAAA-
          1 AAGAAAAAA-GAAAAT

                    
       3257 AAGAAAAA
          1 AAGAAAAA

       3265 GAGAGGTCGA


Statistics
Matches: 44,  Mismatches: 6, Indels: 6
        0.79            0.11        0.11

Matches are distributed among these distances:
  14   11  0.25
  15   19  0.43
  16   14  0.32

ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03


Consensus pattern (15 bp):   
AAGAAAAAAGAAAAT
Done.