Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014940.1 Kokia drynarioides strain JFW-HI SEQ_129983, 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: 11007
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:337 original size:29 final size:28

Alignment explanation


    Indices: 305--405  Score: 94
    Period size: 29  Copynumber: 3.5  Consensus size: 28

        295 TTCGAGGTCG

                                         
        305 AAAATGAAATTTTTAGAAGTTCAGGGGTA
          1 AAAATGAAATTTTTAGAAGTTC-GGGGTA

                 *         *        *     
        334 AAAATAAAATTTTTAAAAGTTTCGAGGTCA
          1 AAAATGAAATTTTTAGAAG-TTCGGGGT-A

                  **      *    *         
        364 AAAATGGGATTTTTTGAAGCTCGAGGGTA
          1 AAAATGAAATTTTTAGAAGTTCG-GGGTA

                  *      
        393 AAAATGTAATTTT
          1 AAAATGAAATTTT

        406 CAAACAGTTT


Statistics
Matches: 57,  Mismatches: 12, Indels: 6
        0.76            0.16        0.08

Matches are distributed among these distances:
  29   36  0.63
  30   21  0.37

ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34


Consensus pattern (28 bp):   
AAAATGAAATTTTTAGAAGTTCGGGGTA

Found at i:345 original size:58 final size:58

Alignment explanation


    Indices: 247--415  Score: 153
    Period size: 59  Copynumber: 2.9  Consensus size: 58

        237 ATTCGGGGTT

                                             ****       * *            *
        247 AAAATGGAATTTTTAGACA-TTCGGGGGTAAAAGGCTAA-TTTCGAGAGTTTCGAGGTCG
          1 AAAATGGAATTTTTAGA-AGTTC-GGGGTAAAAATAAAATTTTCAAAAGTTTCGAGGTCA

                  *                                   *                
        305 AAAATGAAATTTTTAGAAGTTCAGGGGTAAAAATAAAATTTTTAAAAGTTTCGAGGTCA
          1 AAAATGGAATTTTTAGAAGTTC-GGGGTAAAAATAAAATTTTCAAAAGTTTCGAGGTCA

                   *      *    *              **                
        364 AAAATGGGATTTTTTGAAGCTCGAGGGTAAAAATGTAATTTTCAAACAGTTT
          1 AAAATGGAATTTTTAGAAGTTCG-GGGTAAAAATAAAATTTTCAAA-AGTTT

        416 AAGGACCTCT


Statistics
Matches: 90,  Mismatches: 17, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  57    1  0.01
  58   31  0.34
  59   53  0.59
  60    5  0.06

ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32


Consensus pattern (58 bp):   
AAAATGGAATTTTTAGAAGTTCGGGGTAAAAATAAAATTTTCAAAAGTTTCGAGGTCA

Found at i:377 original size:30 final size:30

Alignment explanation


    Indices: 292--369  Score: 97
    Period size: 29  Copynumber: 2.6  Consensus size: 30

        282 TAATTTCGAG

                        *               * 
        292 AGTTTCGAGGTCGAAAATGAAATTTTTAGA
          1 AGTTTCGAGGTCAAAAATGAAATTTTTAAA

                    *          *           
        322 AG-TTCAGGGGT-AAAAATAAAATTTTTAAA
          1 AGTTTC-GAGGTCAAAAATGAAATTTTTAAA

                               
        351 AGTTTCGAGGTCAAAAATG
          1 AGTTTCGAGGTCAAAAATG

        370 GGATTTTTTG


Statistics
Matches: 39,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  29   24  0.62
  30   15  0.38

ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31


Consensus pattern (30 bp):   
AGTTTCGAGGTCAAAAATGAAATTTTTAAA

Found at i:1449 original size:12 final size:12

Alignment explanation


    Indices: 1434--1464  Score: 53
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       1424 ATTATTACTG

                        
       1434 TTATTAATAATA
          1 TTATTAATAATA

                        
       1446 TTATTAATAATA
          1 TTATTAATAATA

                   
       1458 TTCATTA
          1 TT-ATTA

       1465 GGTTGTAACT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   14  0.78
  13    4  0.22

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


Consensus pattern (12 bp):   
TTATTAATAATA

Found at i:2177 original size:17 final size:17

Alignment explanation


    Indices: 2148--2221  Score: 76
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       2138 ATTAATTTTT

                *          * 
       2148 AATTGAAAATAAATTTA
          1 AATTTAAAATAAATTCA

                    *        
       2165 AATTTAAAGTAAATTCA
          1 AATTTAAAATAAATTCA

              * *     *    * 
       2182 AACTCAAAATGAATTTA
          1 AATTTAAAATAAATTCA

              *              
       2199 AAATTAAAATAAATTCA
          1 AATTTAAAATAAATTCA

                  
       2216 AATTTA
          1 AATTTA

       2222 TTTAAAATTA


Statistics
Matches: 44,  Mismatches: 13, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  17   44  1.00

ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34


Consensus pattern (17 bp):   
AATTTAAAATAAATTCA

Found at i:2191 original size:34 final size:34

Alignment explanation


    Indices: 2153--2217  Score: 103
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       2143 TTTTTAATTG

                          *     *             
       2153 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
          1 AAAATAAATTTAAAATTAAAATAAATTCAAACTC

                 *                         
       2187 AAAATGAATTTAAAATTAAAATAAATTCAAA
          1 AAAATAAATTTAAAATTAAAATAAATTCAAA

       2218 TTTATTTAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  34   28  1.00

ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31


Consensus pattern (34 bp):   
AAAATAAATTTAAAATTAAAATAAATTCAAACTC
Done.