Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009844.1 Kokia drynarioides strain JFW-HI SEQ_124571, 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: 3439
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26


Found at i:158 original size:17 final size:17

Alignment explanation


    Indices: 136--202  Score: 98
    Period size: 17  Copynumber: 3.9  Consensus size: 17

        126 GAAAATTGAA

                       *     
        136 TTTAAATTTAAGTTTAT
          1 TTTAAATTTAAATTTAT

                             
        153 TTTAAATTTAAATTTAT
          1 TTTAAATTTAAATTTAT

              *              
        170 TTGAAATTTAAATTTAT
          1 TTTAAATTTAAATTTAT

             *    *         
        187 TATAAAATTAAATTTA
          1 TTTAAATTTAAATTTA

        203 GAAAGTCCAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   45  1.00

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54


Consensus pattern (17 bp):   
TTTAAATTTAAATTTAT

Found at i:178 original size:7 final size:6

Alignment explanation


    Indices: 134--202  Score: 58
    Period size: 6  Copynumber: 12.0  Consensus size: 6

        124 ATGAAAATTG

                           *      *                                 
        134 AATTTA AATTTA AGTTT- ATTTTA AATTTA AATTT- -ATTTGA AATTTA
          1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA

                             *          
        180 AATTT- -ATTATA AAATTA AATTTA
          1 AATTTA AATT-TA AATTTA AATTTA

        203 GAAAGTCCAT


Statistics
Matches: 51,  Mismatches: 5, Indels: 14
        0.73            0.07        0.20

Matches are distributed among these distances:
   4    7  0.14
   5    5  0.10
   6   33  0.65
   7    6  0.12

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52


Consensus pattern (6 bp):   
AATTTA

Found at i:255 original size:15 final size:15

Alignment explanation


    Indices: 235--289  Score: 83
    Period size: 15  Copynumber: 3.7  Consensus size: 15

        225 AAACAAAGTT

                        *  
        235 CAATTACAAATGACC
          1 CAATTACAAATGGCC

                    *      
        250 CAATTACAGATGGCC
          1 CAATTACAAATGGCC

               *           
        265 CAAATACAAATGGCC
          1 CAATTACAAATGGCC

                      
        280 CAATTACAAA
          1 CAATTACAAA

        290 CTACCCAAAA


Statistics
Matches: 35,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   35  1.00

ACGTcount: A:0.45, C:0.25, G:0.11, T:0.18


Consensus pattern (15 bp):   
CAATTACAAATGGCC

Found at i:297 original size:30 final size:30

Alignment explanation


    Indices: 239--298  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        229 AAAGTTCAAT

                               *   *      
        239 TACAAATGACCCAATTACAGATGGCCCAAA
          1 TACAAATGACCCAATTACAAATGACCCAAA

                    *                      
        269 TACAAATGGCCCAATTACAAACT-ACCCAAA
          1 TACAAATGACCCAATTACAAA-TGACCCAAA

        299 AGCCCAAACT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  30   25  0.96
  31    1  0.04

ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17


Consensus pattern (30 bp):   
TACAAATGACCCAATTACAAATGACCCAAA

Found at i:433 original size:10 final size:10

Alignment explanation


    Indices: 418--446  Score: 58
    Period size: 10  Copynumber: 2.9  Consensus size: 10

        408 CCAACTTGCA

                      
        418 CTGCCACCGG
          1 CTGCCACCGG

                      
        428 CTGCCACCGG
          1 CTGCCACCGG

                     
        438 CTGCCACCG
          1 CTGCCACCG

        447 CCACTGTCGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.10, C:0.52, G:0.28, T:0.10


Consensus pattern (10 bp):   
CTGCCACCGG
Done.