Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002776.1 Kokia drynarioides strain JFW-HI SEQ_115103, 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: 7606
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Found at i:3037 original size:54 final size:54

Alignment explanation


    Indices: 2966--3074  Score: 191
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       2956 CTCTTTACTA

                   *    *                                  *      
       2966 TATTTGCGAGCAGTCTTTTCAAGTTTAGAGTCGTGAAGAAGTGGTCCTGACGGG
          1 TATTTGCAAGCAATCTTTTCAAGTTTAGAGTCGTGAAGAAGTGGTCCCGACGGG

                                                                  
       3020 TATTTGCAAGCAATCTTTTCAAGTTTAGAGTCGTGAAGAAGTGGTCCCGACGGG
          1 TATTTGCAAGCAATCTTTTCAAGTTTAGAGTCGTGAAGAAGTGGTCCCGACGGG

             
       3074 T
          1 T

       3075 TTCCTCTAGT


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  54   52  1.00

ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31


Consensus pattern (54 bp):   
TATTTGCAAGCAATCTTTTCAAGTTTAGAGTCGTGAAGAAGTGGTCCCGACGGG

Found at i:3145 original size:20 final size:20

Alignment explanation


    Indices: 3112--3172  Score: 65
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       3102 TGCCAGAAGC

                    **          
       3112 AAATAAAAGGGAAAAAATTA
          1 AAATAAAAATGAAAAAATTA

              *                  
       3132 AATTAAAAATGAAAATAA-TA
          1 AAATAAAAATGAAAA-AATTA

                                
       3152 AAATAAAAAT-AAAAAA-TA
          1 AAATAAAAATGAAAAAATTA

               
       3170 AAA
          1 AAA

       3173 AATGGCTAAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  18    7  0.19
  19    4  0.11
  20   23  0.64
  21    2  0.06

ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18


Consensus pattern (20 bp):   
AAATAAAAATGAAAAAATTA

Found at i:3154 original size:14 final size:12

Alignment explanation


    Indices: 3123--3172  Score: 55
    Period size: 14  Copynumber: 3.9  Consensus size: 12

       3113 AATAAAAGGG

                   *    
       3123 AAAAAATTAAAT
          1 AAAAAATAAAAT

            *            
       3135 TAAAAATGAAAAT
          1 AAAAAAT-AAAAT

                          
       3148 AATAAAATAAAAAT
          1 AA-AAAAT-AAAAT

                       
       3162 AAAAAATAAAA
          1 AAAAAATAAAA

       3173 AATGGCTAAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  12   10  0.31
  13   10  0.31
  14   12  0.38

ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20


Consensus pattern (12 bp):   
AAAAAATAAAAT

Found at i:3173 original size:13 final size:13

Alignment explanation


    Indices: 3131--3173  Score: 59
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       3121 GGAAAAAATT

                *      * 
       3131 AAATTAAAAATGA
          1 AAATAAAAAATAA

                          
       3144 AAATAATAAAATAA
          1 AAATAA-AAAATAA

                         
       3158 AAATAAAAAATAA
          1 AAATAAAAAATAA

               
       3171 AAA
          1 AAA

       3174 ATGGCTAAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  13   15  0.56
  14   12  0.44

ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19


Consensus pattern (13 bp):   
AAATAAAAAATAA

Found at i:3175 original size:14 final size:14

Alignment explanation


    Indices: 3137--3173  Score: 58
    Period size: 14  Copynumber: 2.7  Consensus size: 14

       3127 AATTAAATTA

                 *        
       3137 AAAATGAAAATAAT
          1 AAAATAAAAATAAT

                          
       3151 AAAATAAAAATAA-
          1 AAAATAAAAATAAT

                      
       3164 AAAATAAAAA
          1 AAAATAAAAA

       3174 ATGGCTAAAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  13   10  0.45
  14   12  0.55

ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16


Consensus pattern (14 bp):   
AAAATAAAAATAAT

Found at i:3829 original size:15 final size:15

Alignment explanation


    Indices: 3809--3847  Score: 53
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       3799 GCACATCAAA

                        *  
       3809 CAAGAATTAATATAT
          1 CAAGAATTAATAAAT

                     *     
       3824 CAAGAA-TACTAAAT
          1 CAAGAATTAATAAAT

                      
       3838 CAAGAATTAA
          1 CAAGAATTAA

       3848 GCACACATAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 2
        0.80            0.12        0.08

Matches are distributed among these distances:
  14   12  0.60
  15    8  0.40

ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26


Consensus pattern (15 bp):   
CAAGAATTAATAAAT
Done.