Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014685.1 Kokia drynarioides strain JFW-HI SEQ_129724, 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: 21706
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.33

Warning! 229 characters in sequence are not A, C, G, or T


Found at i:50 original size:25 final size:26

Alignment explanation


    Indices: 17--72  Score: 80
    Period size: 25  Copynumber: 2.2  Consensus size: 26

          7 AGGAAACTCT

                         *            
         17 TTATTTTATTTAATATTAATA-AA-A
          1 TTATTTTATTTAACATTAATATAATA

                                       
         41 TTATATTTATTTAACATTAATATAATA
          1 TTAT-TTTATTTAACATTAATATAATA

                 
         68 TTATT
          1 TTATT

         73 ATAAAATTTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  24    4  0.14
  25   16  0.57
  26    3  0.11
  27    5  0.18

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (26 bp):   
TTATTTTATTTAACATTAATATAATA

Found at i:4264 original size:44 final size:44

Alignment explanation


    Indices: 4201--4290  Score: 153
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       4191 AAAACGAGAA

                       *                                
       4201 AAGGATGAGTTTCATCGTTTCCACTCCTTCCATCAACAATATTC
          1 AAGGATGAGTTCCATCGTTTCCACTCCTTCCATCAACAATATTC

                                   *         *          
       4245 AAGGATGAGTTCCATCGTTTCCATTCCTTCCATTAACAATATTC
          1 AAGGATGAGTTCCATCGTTTCCACTCCTTCCATCAACAATATTC

              
       4289 AA
          1 AA

       4291 TACTCCTTGT


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  44   43  1.00

ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34


Consensus pattern (44 bp):   
AAGGATGAGTTCCATCGTTTCCACTCCTTCCATCAACAATATTC

Found at i:4348 original size:18 final size:18

Alignment explanation


    Indices: 4327--4402  Score: 98
    Period size: 18  Copynumber: 4.2  Consensus size: 18

       4317 TTACAAGTCG

                              
       4327 GTATGCTCTAATGAGCCA
          1 GTATGCTCTAATGAGCCA

                    *  **     
       4345 GTATGCTCGAACAAGCCA
          1 GTATGCTCTAATGAGCCA

            *          *      
       4363 ATATGCTCTAAAGAGCCA
          1 GTATGCTCTAATGAGCCA

                    *         
       4381 GTATGCTCAAATGAGCCA
          1 GTATGCTCTAATGAGCCA

                
       4399 GTAT
          1 GTAT

       4403 ACTATTTCTT


Statistics
Matches: 48,  Mismatches: 10, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   48  1.00

ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24


Consensus pattern (18 bp):   
GTATGCTCTAATGAGCCA

Found at i:11880 original size:44 final size:45

Alignment explanation


    Indices: 11809--11907  Score: 112
    Period size: 44  Copynumber: 2.2  Consensus size: 45

      11799 AATTACTAAT

                *           *                    *        
      11809 TAATCCTTAAATTTTCTTAACCTTTCTTA-TTTAGACTACACATTC
          1 TAATTCTTAAATTTTCCTAACCTTTCTTATTTTA-ACCACACATTC

                      *         *                   *    
      11854 TAATTCTTAATTTTTCCTAATC-TTCTTATTTTAACCACATATTC
          1 TAATTCTTAAATTTTCCTAACCTTTCTTATTTTAACCACACATTC

               *      
      11898 TAACTCTTAA
          1 TAATTCTTAA

      11908 CTCAACACTA


Statistics
Matches: 46,  Mismatches: 7, Indels: 3
        0.82            0.12        0.05

Matches are distributed among these distances:
  44   24  0.52
  45   22  0.48

ACGTcount: A:0.29, C:0.21, G:0.01, T:0.48


Consensus pattern (45 bp):   
TAATTCTTAAATTTTCCTAACCTTTCTTATTTTAACCACACATTC
Done.