Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001774.1 Kokia drynarioides strain JFW-HI SEQ_113498, 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: 7223
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:3520 original size:29 final size:29

Alignment explanation


    Indices: 3487--3549  Score: 72
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       3477 TGCATGATCA

                        *                
       3487 ACATGACTACTGTTACTGATAAACTGAGT
          1 ACATGACTACTGCTACTGATAAACTGAGT

                 **           *   *    * 
       3516 ACATGTTTACTGCTACTGTTAATCTGATT
          1 ACATGACTACTGCTACTGATAAACTGAGT

                 
       3545 ACATG
          1 ACATG

       3550 CTAAATATGT


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Consensus pattern (29 bp):   
ACATGACTACTGCTACTGATAAACTGAGT

Found at i:3816 original size:91 final size:90

Alignment explanation


    Indices: 3690--3858  Score: 196
    Period size: 91  Copynumber: 1.9  Consensus size: 90

       3680 CTTACTCACC

                                    **              * **     *         *    *
       3690 GCTTTTATATGCAAACCCATTGTGTCTTCACAACTACTGGTAGTGTATTGACCTGCAAATACTAG
          1 GCTTTTATATGCAAACCCATTGTGAATTCACAACTACTGGCAACGTATTAACCTGC-AACACTAA

                                      
       3755 TGGTTCATCCACAATTTTTACTGGCA
         65 TGGTTCATCCACAATTTTTACTGGCA

                    *        *             *     *               *           
       3781 GCTTTTATCTGCAAA-CTAGTTGTGAATTCATAACTATTGGCAACGTATTAACTTGCAACACTAA
          1 GCTTTTATATGCAAACCCA-TTGTGAATTCACAACTACTGGCAACGTATTAACCTGCAACACTAA

                          
       3845 TGGTTCATCCACAA
         65 TGGTTCATCCACAA

       3859 ACTAGAGTGT


Statistics
Matches: 64,  Mismatches: 13, Indels: 3
        0.80            0.16        0.04

Matches are distributed among these distances:
  90   22  0.34
  91   42  0.66

ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34


Consensus pattern (90 bp):   
GCTTTTATATGCAAACCCATTGTGAATTCACAACTACTGGCAACGTATTAACCTGCAACACTAAT
GGTTCATCCACAATTTTTACTGGCA

Found at i:6105 original size:10 final size:9

Alignment explanation


    Indices: 6092--6202  Score: 50
    Period size: 9  Copynumber: 12.2  Consensus size: 9

       6082 TATTCCAATA

                      
       6092 TTTTATATAT
          1 TTTTATAT-T

                     
       6102 TTTTATATT
          1 TTTTATATT

                *    
       6111 TTTTGTATT
          1 TTTTATATT

             *    *    
       6120 TATTAGAATAT
          1 TTTTA-TAT-T

              *  * * 
       6131 TTGTAGAGT
          1 TTTTATATT

                     *
       6140 TTTTATATGG
          1 TTTTATAT-T

                    * 
       6150 TTTTATGAAT
          1 TTTTAT-ATT

                     
       6160 TTTTATA-T
          1 TTTTATATT

             *       
       6168 TGTTATA-T
          1 TTTTATATT

                     
       6176 TTTTA-A-T
          1 TTTTATATT

                 *   
       6183 TTTTAGATT
          1 TTTTATATT

                *    
       6192 TTTTGTATT
          1 TTTTATATT

              
       6201 TT
          1 TT

       6203 AATAAGTTTT


Statistics
Matches: 77,  Mismatches: 18, Indels: 13
        0.71            0.17        0.12

Matches are distributed among these distances:
   7    7  0.09
   8   13  0.17
   9   29  0.38
  10   23  0.30
  11    5  0.06

ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66


Consensus pattern (9 bp):   
TTTTATATT

Found at i:6108 original size:8 final size:8

Alignment explanation


    Indices: 6089--6194  Score: 61
    Period size: 8  Copynumber: 12.0  Consensus size: 8

       6079 ATATATTCCA

                     
       6089 ATATTTTAT
          1 ATATTTT-T

                    
       6098 ATATTTTT
          1 ATATTTTT

                     
       6106 ATATTTTTT
          1 ATA-TTTTT

            *        
       6115 GTATTTATT
          1 ATATTT-TT

                     * 
       6124 AGAATATTTGT
          1 ---ATATTTTT

             *       
       6135 AGAGTTTTT
          1 ATA-TTTTT

                      
       6144 ATATGGTTTT
          1 ATAT--TTTT

                      
       6154 ATGAATTTTT
          1 AT--ATTTTT

                 *  
       6164 ATATTGTT
          1 ATATTTTT

                    
       6172 ATATTTTT
          1 ATATTTTT

                    
       6180 A-ATTTTT
          1 ATATTTTT

             *      
       6187 AGATTTTT
          1 ATATTTTT

       6195 TGTATTTTAA


Statistics
Matches: 78,  Mismatches: 8, Indels: 23
        0.72            0.07        0.21

Matches are distributed among these distances:
   7    7  0.09
   8   29  0.37
   9   22  0.28
  10   12  0.15
  11    1  0.01
  12    7  0.09

ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64


Consensus pattern (8 bp):   
ATATTTTT

Found at i:6225 original size:30 final size:31

Alignment explanation


    Indices: 6182--6246  Score: 78
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       6172 ATATTTTTAA

                  * *                      
       6182 TTTTTAGATTTTTTGTAT-TTTAATAAGTTT
          1 TTTTTACAATTTTTGTATATTTAATAAGTTT

                          *        *        
       6212 TTTTTACAATTTTTTTATAGTTTTATAAGTTT
          1 TTTTTACAATTTTTGTATA-TTTAATAAGTTT

               
       6244 TTT
          1 TTT

       6247 AACATTTTCA


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  30   15  0.52
  32   14  0.48

ACGTcount: A:0.23, C:0.02, G:0.08, T:0.68


Consensus pattern (31 bp):   
TTTTTACAATTTTTGTATATTTAATAAGTTT
Done.