Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008293.1 Kokia drynarioides strain JFW-HI SEQ_122958, 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: 10240
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:3140 original size:21 final size:21

Alignment explanation


    Indices: 3109--3159  Score: 59
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3099 TATAACATAC

                *                 
       3109 AATATAATAATAACA-AAAATA
          1 AATAAAATAATAACATAAAA-A

               *       *         
       3130 AATGAAATAATCACATAAAAA
          1 AATAAAATAATAACATAAAAA

                     
       3151 AATAAAATA
          1 AATAAAATA

       3160 CATTATGACA


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  21   21  0.84
  22    4  0.16

ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22


Consensus pattern (21 bp):   
AATAAAATAATAACATAAAAA

Found at i:5148 original size:51 final size:49

Alignment explanation


    Indices: 5030--5161  Score: 131
    Period size: 51  Copynumber: 2.7  Consensus size: 49

       5020 GCAGTAGCAG

                         * *                  *             *
       5030 TATATCTGCAAATCAATGGTGGCTTGTCCACATATTAAATTAGTGACAG
          1 TATATCTGCAAATTAGTGGTGGCTTGTCCACATAGTAAATTAGTGACAA

              *  *    *                            *       *   
       5079 TAAATTTGCACATTAGTGGTGGCTTGTCCACATCAGTATTATTAGTGGCAA
          1 TATATCTGCAAATTAGTGGTGGCTTGTCCACAT-AGTA-AATTAGTGACAA

             *                      *        
       5130 TTTATCTGCAAATTAGTGG-GGACGTGTCCACA
          1 TATATCTGCAAATTAGTGGTGG-CTTGTCCACA

       5162 AATGGTGTTT


Statistics
Matches: 66,  Mismatches: 14, Indels: 4
        0.79            0.17        0.05

Matches are distributed among these distances:
  49   28  0.42
  50    5  0.08
  51   33  0.50

ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Consensus pattern (49 bp):   
TATATCTGCAAATTAGTGGTGGCTTGTCCACATAGTAAATTAGTGACAA

Found at i:7280 original size:20 final size:19

Alignment explanation


    Indices: 7241--7316  Score: 82
    Period size: 20  Copynumber: 3.9  Consensus size: 19

       7231 TCTCTCTCAA

                      *     *  
       7241 CAAAAA-TTACAAAAAATT
          1 CAAAAATTTATAAAAATTT

                                
       7259 CAAAATATTTATAAAAATTT
          1 CAAAA-ATTTATAAAAATTT

                                
       7279 CAAAAATTTATAAAAAATTT
          1 CAAAAATTTAT-AAAAATTT

            *          *      
       7299 AAAAAATTCTAAAAAAAT
          1 CAAAAATT-TATAAAAAT

       7317 ATATAATTTT


Statistics
Matches: 50,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
  18    5  0.10
  19    7  0.14
  20   36  0.72
  21    2  0.04

ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30


Consensus pattern (19 bp):   
CAAAAATTTATAAAAATTT

Found at i:7313 original size:11 final size:10

Alignment explanation


    Indices: 7242--7316  Score: 59
    Period size: 9  Copynumber: 7.6  Consensus size: 10

       7232 CTCTCTCAAC

                       
       7242 AAAAA-TTACA
          1 AAAAATTTA-A

                    * 
       7252 AAAAA-TTCA
          1 AAAAATTTAA

               *     *
       7261 AAATATTTAT
          1 AAAAATTTAA

                     *
       7271 AAAAATTT-C
          1 AAAAATTTAA

                       
       7280 AAAAATTTATA
          1 AAAAATTTA-A

                      
       7291 AAAAATTT-A
          1 AAAAATTTAA

                       
       7300 AAAAATTCTAA
          1 AAAAATT-TAA

                  
       7311 AAAAAT
          1 AAAAAT

       7317 ATATAATTTT


Statistics
Matches: 53,  Mismatches: 7, Indels: 9
        0.77            0.10        0.13

Matches are distributed among these distances:
   9   21  0.40
  10   17  0.32
  11   15  0.28

ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31


Consensus pattern (10 bp):   
AAAAATTTAA
Done.