Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006683.1 Kokia drynarioides strain JFW-HI SEQ_121277, 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: 7984
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--30  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

                                                   
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

         31 TTCTTTGATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:5522 original size:11 final size:11

Alignment explanation


    Indices: 5506--5549  Score: 52
    Period size: 12  Copynumber: 3.8  Consensus size: 11

       5496 CAGATTAATG

                    *  
       5506 AAGAAAAATAA
          1 AAGAAAAAAAA

                        
       5517 AAGAAAGAAAAA
          1 AAGAAA-AAAAA

                     *  
       5529 AAGAAGAAACAA
          1 AAGAA-AAAAAA

                     
       5541 AAGAAAAAA
          1 AAGAAAAAA

       5550 GGAAAAAAGG


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  11    9  0.32
  12   18  0.64
  13    1  0.04

ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02


Consensus pattern (11 bp):   
AAGAAAAAAAA

Found at i:5526 original size:15 final size:15

Alignment explanation


    Indices: 5506--5569  Score: 55
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       5496 CAGATTAATG

                            
       5506 AAGAAAAATAA-AAGA
          1 AAGAAAAA-AAGAAGA

                           
       5521 AAGAAAAAAAGAAGA
          1 AAGAAAAAAAGAAGA

              *    *       
       5536 AACAAAAGAA-AA-A
          1 AAGAAAAAAAGAAGA

             *       *     
       5549 AGGAAAAAAGGAA-A
          1 AAGAAAAAAAGAAGA

                   
       5563 AAGAAAA
          1 AAGAAAA

       5570 GGAGAGGTCG


Statistics
Matches: 40,  Mismatches: 7, Indels: 5
        0.77            0.13        0.10

Matches are distributed among these distances:
  13    7  0.17
  14   13  0.32
  15   20  0.50

ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02


Consensus pattern (15 bp):   
AAGAAAAAAAGAAGA

Found at i:5532 original size:12 final size:12

Alignment explanation


    Indices: 5506--5546  Score: 50
    Period size: 11  Copynumber: 3.5  Consensus size: 12

       5496 CAGATTAATG

                     *  
       5506 AAGAAA-AATAA
          1 AAGAAAGAAAAA

                        
       5517 AAGAAAGAAAAA
          1 AAGAAAGAAAAA

                         
       5529 AAG-AAGAAACAA
          1 AAGAAAGAAA-AA

                  
       5541 AAGAAA
          1 AAGAAA

       5547 AAAGGAAAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  11   12  0.46
  12   12  0.46
  13    2  0.08

ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02


Consensus pattern (12 bp):   
AAGAAAGAAAAA

Found at i:7184 original size:3 final size:3

Alignment explanation


    Indices: 7178--7223  Score: 51
    Period size: 3  Copynumber: 15.3  Consensus size: 3

       7168 TATGTTTTCA

                         *                                               
       7178 AAT AAT -AT ATT AATT AAT AAT AAT AAT AAT -AT AAT AAAT AAT AAT
          1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT

             
       7223 A
          1 A

       7224 TTTTATTATT


Statistics
Matches: 37,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
   2    4  0.11
   3   27  0.73
   4    6  0.16

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (3 bp):   
AAT

Found at i:7208 original size:24 final size:24

Alignment explanation


    Indices: 7178--7223  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       7168 TATGTTTTCA

                     *   *          
       7178 AATAATATATTAATTAATAATAAT
          1 AATAATATAATAAATAATAATAAT

                                  
       7202 AATAATATAATAAATAATAATA
          1 AATAATATAATAAATAATAATA

       7224 TTTTATTATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (24 bp):   
AATAATATAATAAATAATAATAAT

Done.