Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009807.1 Kokia drynarioides strain JFW-HI SEQ_124528, 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: 2203
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38


Found at i:242 original size:31 final size:31

Alignment explanation


    Indices: 207--395  Score: 124
    Period size: 31  Copynumber: 6.2  Consensus size: 31

        197 GATTAGGTAT

                                    *      
        207 CAAATTAGAAAAAAGAGTCAAGTTCAAGTAC
          1 CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC

                      ***          *        
        238 CAAATTAGACTCCAA-A---AAGCTTAAGTAC
          1 CAAATTAGA-AAAAAGAGTCAAGTTTAAGTAC

                *           *               
        266 CAACCTTA-AAAAAAGTGTCAAGTTTAAGTAC
          1 CAA-ATTAGAAAAAAGAGTCAAGTTTAAGTAC

                    *    * *         *     
        297 CAAATTAGGAAAATGGGTCAAGTTTGAGTAC
          1 CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC

            *                 **            
        328 TAAATTAGACAAAAA-A-AAAAGTTTAAGTAC
          1 CAAATTAGA-AAAAAGAGTCAAGTTTAAGTAC

                    *      *                  
        358 CAAATTAAAAAAAAAAATGTCAAGTTT-AGATAC
          1 CAAATT-AGAAAAAAGA-GTCAAGTTTAAG-TAC

                 
        391 CAAAT
          1 CAAAT

        396 GTTATATTAA


Statistics
Matches: 118,  Mismatches: 27, Indels: 24
        0.70            0.16        0.14

Matches are distributed among these distances:
  27    2  0.02
  28   14  0.12
  29    3  0.03
  30   24  0.20
  31   53  0.45
  32    8  0.07
  33   14  0.12

ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23


Consensus pattern (31 bp):   
CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC

Found at i:255 original size:59 final size:59

Alignment explanation


    Indices: 192--304  Score: 156
    Period size: 59  Copynumber: 1.9  Consensus size: 59

        182 TTAATATTAA

                      *   *                                             
        192 AAAAAGATTAGGTATCAA-ATTAGAAAAAAGAGTCAAGTTCAAGTACCAAATTAGACTCC
          1 AAAAAGATTAAGTACCAACATTA-AAAAAAGAGTCAAGTTCAAGTACCAAATTAGACTCC

                  *            *          *        *              
        251 AAAAAGCTTAAGTACCAACCTTAAAAAAAGTGTCAAGTTTAAGTACCAAATTAG
          1 AAAAAGATTAAGTACCAACATTAAAAAAAGAGTCAAGTTCAAGTACCAAATTAG

        305 GAAAATGGGT


Statistics
Matches: 47,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  59   44  0.94
  60    3  0.06

ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23


Consensus pattern (59 bp):   
AAAAAGATTAAGTACCAACATTAAAAAAAGAGTCAAGTTCAAGTACCAAATTAGACTCC

Found at i:357 original size:30 final size:28

Alignment explanation


    Indices: 316--374  Score: 82
    Period size: 30  Copynumber: 2.0  Consensus size: 28

        306 AAAATGGGTC

                  *     *                 
        316 AAGTTTGAGTACTAAATTAGACAAAAAAAA
          1 AAGTTTAAGTACCAAATTA-A-AAAAAAAA

                                        
        346 AAGTTTAAGTACCAAATTAAAAAAAAAA
          1 AAGTTTAAGTACCAAATTAAAAAAAAAA

             
        374 A
          1 A

        375 TGTCAAGTTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  28    9  0.33
  29    1  0.04
  30   17  0.63

ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22


Consensus pattern (28 bp):   
AAGTTTAAGTACCAAATTAAAAAAAAAA

Found at i:382 original size:27 final size:30

Alignment explanation


    Indices: 323--382  Score: 72
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        313 GTCAAGTTTG

                 *                      * 
        323 AGTACTAAATTAGACAAAAAAAAAAGTTTA
          1 AGTACCAAATTAGACAAAAAAAAAAGTTCA

                                    *     
        353 AGTACCAAATTA-A-AAAAAAAAATG-TCA
          1 AGTACCAAATTAGACAAAAAAAAAAGTTCA

               
        380 AGT
          1 AGT

        383 TTAGATACCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  27    5  0.19
  28   10  0.37
  29    1  0.04
  30   11  0.41

ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22


Consensus pattern (30 bp):   
AGTACCAAATTAGACAAAAAAAAAAGTTCA

Found at i:919 original size:18 final size:18

Alignment explanation


    Indices: 896--942  Score: 51
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        886 AAATATTTAC

                              
        896 TTTAATATTTTTAATGAA
          1 TTTAATATTTTTAATGAA

                  * *       * 
        914 TTTAATGTATTTAATGTA
          1 TTTAATATTTTTAATGAA

                        
        932 -TTATATATTTT
          1 TTTA-ATATTTT

        943 AATTTTTTAT


Statistics
Matches: 23,  Mismatches: 5, Indels: 2
        0.77            0.17        0.07

Matches are distributed among these distances:
  17    3  0.13
  18   20  0.87

ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60


Consensus pattern (18 bp):   
TTTAATATTTTTAATGAA

Found at i:1273 original size:19 final size:19

Alignment explanation


    Indices: 1249--1295  Score: 58
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       1239 AAAAAAAAGG

                   *          *
       1249 TTAATTTTATGAGGTGGAC
          1 TTAATTTAATGAGGTGGAA

                  *     *      
       1268 TTAATTAAATGATGTGGAA
          1 TTAATTTAATGAGGTGGAA

                     
       1287 TTAATTTAA
          1 TTAATTTAA

       1296 GATATGACGT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43


Consensus pattern (19 bp):   
TTAATTTAATGAGGTGGAA
Done.