Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008107.1 Kokia drynarioides strain JFW-HI SEQ_122765, 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: 11061
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33


Found at i:1447 original size:30 final size:29

Alignment explanation


    Indices: 1173--1434  Score: 357
    Period size: 30  Copynumber: 8.8  Consensus size: 29

       1163 TTTGACCACC

                     *                    
       1173 AAACTTCTCAAAAATTACATTTTAACCCCT
          1 AAACTTCTCTAAAATTACATTTTAA-CCCT

                                          
       1203 AAACTTCTCTAAAATTACATTTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTAACCC-T

                                    *      
       1233 AAACTTC-CTCAAAATTACATTTTGACCCTT
          1 AAACTTCTCT-AAAATTACATTTTAACCC-T

                               *      *   
       1263 AAACTTCTCTAAAATTACTTTTTTAAACCT
          1 AAACTTCTCTAAAATTAC-ATTTTAACCCT

                         *         * *    
       1293 CAAACTTCTCTAAGATTACATTTGACCCCT
          1 -AAACTTCTCTAAAATTACATTTTAACCCT

                                          
       1323 AAACTTCTCTAAAATTACA-TTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTAACCC-T

                                          
       1352 AAACTTCTCTAAAATTACATTTTAACCTCT
          1 AAACTTCTCTAAAATTACATTTTAACC-CT

                             *            
       1382 AAACTTCTCTAAAATTATATTTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTAACCC-T

                                   
       1412 AAACTTCTCTAAAATTACATTTT
          1 AAACTTCTCTAAAATTACATTTT

       1435 GATCTCTAAA


Statistics
Matches: 208,  Mismatches: 15, Indels: 18
        0.86            0.06        0.07

Matches are distributed among these distances:
  28    6  0.03
  29   44  0.21
  30  131  0.63
  31   27  0.13

ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39


Consensus pattern (29 bp):   
AAACTTCTCTAAAATTACATTTTAACCCT

Found at i:1464 original size:60 final size:60

Alignment explanation


    Indices: 1173--1447  Score: 403
    Period size: 60  Copynumber: 4.6  Consensus size: 60

       1163 TTTGACCACC

                     *             *                                    
       1173 AAACTTCTCAAAAATTACATTTTAACCCCTAAACTTCTCTAAAATTACATTTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCTT

                                         *                    *      *   *
       1233 AAACTTC-CTCAAAATTACATTTTGACCCTTAAACTTCTCTAAAATTACTTTTTTAAACCTC
          1 AAACTTCTCT-AAAATTACATTTTGACCCCTAAACTTCTCTAAAATTAC-ATTTTAACCCTT

                        *                                               
       1294 AAACTTCTCTAAGATTACA-TTTGACCCCTAAACTTCTCTAAAATTACA-TTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCTT

                                   *   *                   *            
       1352 AAACTTCTCTAAAATTACATTTTAACCTCTAAACTTCTCTAAAATTATATTTTAACCCTT
          1 AAACTTCTCTAAAATTACATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCTT

                                     * *        
       1412 AAACTTCTCTAAAATTACATTTTGATCTCTAAACTT
          1 AAACTTCTCTAAAATTACATTTTGACCCCTAAACTT

       1448 TCCAAAGATT


Statistics
Matches: 193,  Mismatches: 17, Indels: 10
        0.88            0.08        0.05

Matches are distributed among these distances:
  58   26  0.13
  59   27  0.14
  60  114  0.59
  61   24  0.12
  62    2  0.01

ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39


Consensus pattern (60 bp):   
AAACTTCTCTAAAATTACATTTTGACCCCTAAACTTCTCTAAAATTACATTTTAACCCTT

Found at i:5066 original size:26 final size:26

Alignment explanation


    Indices: 5026--5082  Score: 80
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       5016 TGGGCGTAAT

                                      
       5026 TCTGGACATGCTCATACAGTGACAAC
          1 TCTGGACATGCTCATACAGTGACAAC

                            *         *
       5052 TCTGGACAT-CATCATGCAGTGACAAT
          1 TCTGGACATGC-TCATACAGTGACAAC

                 
       5078 TCTGG
          1 TCTGG

       5083 GTGCAATTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  25    1  0.04
  26   27  0.96

ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26


Consensus pattern (26 bp):   
TCTGGACATGCTCATACAGTGACAAC
Done.