Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013817.1 Kokia drynarioides strain JFW-HI SEQ_128845, 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: 333904
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33

Warning! 141 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:303506 original size:26 final size:26

Alignment explanation


    Indices: 303403--303512  Score: 75
    Period size: 26  Copynumber: 4.2  Consensus size: 26

     303393 TTATAGTAAA

                        *              
     303403 AAAATATAATTTAATTATTT-T-AA-T
          1 AAAATATAATTTTATT-TTTATAAATT

               *    *             *     
     303427 AAATTATATTTTTATAATTTTAAAAATT
          1 AAAATATAATTTTAT--TTTTATAAATT

               *            *    *     
     303455 AAATTA-AATTTTTATATTTAGAAATT
          1 AAAATATAA-TTTTATTTTTATAAATT

                                    *  
     303481 AAAATATAATTTTATTTTTATTAATTT
          1 AAAATATAATTTTATTTTTA-TAAATT

                 
     303508 AAAAT
          1 AAAAT

     303513 TTTAAAAATT


Statistics
Matches: 67,  Mismatches: 11, Indels: 13
        0.74            0.12        0.14

Matches are distributed among these distances:
  24   12  0.18
  25    3  0.04
  26   25  0.37
  27   14  0.21
  28   13  0.19

ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52


Consensus pattern (26 bp):   
AAAATATAATTTTATTTTTATAAATT

Found at i:309385 original size:143 final size:143

Alignment explanation


    Indices: 309127--309412  Score: 554
    Period size: 143  Copynumber: 2.0  Consensus size: 143

     309117 TAACAGGATT

                                                                             
     309127 ATCCTACAAACACAACTAATATTAATACTATCCTAGCCACCACTTAAGCACAATACTTAACTAGA
          1 ATCCTACAAACACAACTAATATTAATACTATCCTAGCCACCACTTAAGCACAATACTTAACTAGA

                                                         *                   
     309192 ATAACTTATGTGTAGCTTTCGGAACCAGTGCAGGAGTAGGTTGCATGGGGAAGGTGGAGGTAAAT
         66 ATAACTTATGTGTAGCTTTCGGAACCAGTGCAGGAGTAGGTTGCACGGGGAAGGTGGAGGTAAAT

                         
     309257 CGTCAGCCTCGAA
        131 CGTCAGCCTCGAA

                           *                                                 
     309270 ATCCTACAAACACAATTAATATTAATACTATCCTAGCCACCACTTAAGCACAATACTTAACTAGA
          1 ATCCTACAAACACAACTAATATTAATACTATCCTAGCCACCACTTAAGCACAATACTTAACTAGA

                                                                             
     309335 ATAACTTATGTGTAGCTTTCGGAACCAGTGCAGGAGTAGGTTGCACGGGGAAGGTGGAGGTAAAT
         66 ATAACTTATGTGTAGCTTTCGGAACCAGTGCAGGAGTAGGTTGCACGGGGAAGGTGGAGGTAAAT

                         
     309400 CGTCAGCCTCGAA
        131 CGTCAGCCTCGAA

     309413 GTCGTGATCA


Statistics
Matches: 141,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 143  141  1.00

ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24


Consensus pattern (143 bp):   
ATCCTACAAACACAACTAATATTAATACTATCCTAGCCACCACTTAAGCACAATACTTAACTAGA
ATAACTTATGTGTAGCTTTCGGAACCAGTGCAGGAGTAGGTTGCACGGGGAAGGTGGAGGTAAAT
CGTCAGCCTCGAA

Found at i:310279 original size:2 final size:2

Alignment explanation


    Indices: 310266--310297  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

     310256 CAACACCTTT

                      *                                    
     310266 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC

     310298 TATAATTTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03


Consensus pattern (2 bp):   
AC

Found at i:315239 original size:2 final size:2

Alignment explanation


    Indices: 315232--315262  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

     315222 ACATACATTC

                                                 *        
     315232 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

     315263 AAAATAGTCT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:316583 original size:21 final size:21

Alignment explanation


    Indices: 316537--316583  Score: 51
    Period size: 20  Copynumber: 2.3  Consensus size: 21

     316527 GGGTTATTTG

                      *     * *  
     316537 GGTTAAAAGGTTTGGGTTTAA
          1 GGTTAAAAGGGTTGGGGTAAA

             *                   
     316558 -TTTAAAAGGGTTGGGGTAAA
          1 GGTTAAAAGGGTTGGGGTAAA

                  
     316578 GGTTAA
          1 GGTTAA

     316584 TAAAGGTTTC


Statistics
Matches: 20,  Mismatches: 5, Indels: 2
        0.74            0.19        0.07

Matches are distributed among these distances:
  20   16  0.80
  21    4  0.20

ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34


Consensus pattern (21 bp):   
GGTTAAAAGGGTTGGGGTAAA

Found at i:331380 original size:23 final size:24

Alignment explanation


    Indices: 331320--331386  Score: 75
    Period size: 23  Copynumber: 2.8  Consensus size: 24

     331310 AAAAAATAAA

                          *          
     331320 CGGTCAATAGTCAACGGGTC-AGGT
          1 CGGTCAA-AGTCAATGGGTCGAGGT

              *                     
     331344 CGATCAAAGTCAATGGGTCGA-GT
          1 CGGTCAAAGTCAATGGGTCGAGGT

            *             *     
     331367 TGGTCAAAGTCAATAGGTCG
          1 CGGTCAAAGTCAATGGGTCG

     331387 TGTTCGATTT


Statistics
Matches: 37,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  23   30  0.81
  24    7  0.19

ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22


Consensus pattern (24 bp):   
CGGTCAAAGTCAATGGGTCGAGGT

Done.