Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002942.1 Kokia drynarioides strain JFW-HI SEQ_115389, 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: 20842
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35


Found at i:6180 original size:71 final size:71

Alignment explanation


    Indices: 6062--6205  Score: 243
    Period size: 71  Copynumber: 2.0  Consensus size: 71

       6052 CAATAATCAA

                                                *     *                      
       6062 CACAAACTTAACCCAAAAACATTTTCCAAACTGTCTTTGATCTGGTTGATATATCCCTATATTAA
          1 CACAAACTTAACCCAAAAACATTTTCCAAACTGTCTCTGATCAGGTTGATATATCCCTATATTAA

                  
       6127 GTAATT
         66 GTAATT

                               *      *                                      
       6133 CACAAACTTAACCCAAAAATATTTTCTAAACTGTCTCTGATCAGGTTGATATATCCCTATATTAA
          1 CACAAACTTAACCCAAAAACATTTTCCAAACTGTCTCTGATCAGGTTGATATATCCCTATATTAA

               *  
       6198 GTAGTT
         66 GTAATT

              
       6204 CA
          1 CA

       6206 GAATTCGAAT


Statistics
Matches: 68,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  71   68  1.00

ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35


Consensus pattern (71 bp):   
CACAAACTTAACCCAAAAACATTTTCCAAACTGTCTCTGATCAGGTTGATATATCCCTATATTAA
GTAATT

Found at i:6323 original size:36 final size:36

Alignment explanation


    Indices: 6276--6349  Score: 139
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       6266 TCAGAATCTA

                                     *          
       6276 AAAATAAATTCAAATACATGTATTTTGACTAGCTAG
          1 AAAATAAATTCAAATACATGTATTTCGACTAGCTAG

                                                
       6312 AAAATAAATTCAAATACATGTATTTCGACTAGCTAG
          1 AAAATAAATTCAAATACATGTATTTCGACTAGCTAG

              
       6348 AA
          1 AA

       6350 CGATGAAAAT


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   37  1.00

ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31


Consensus pattern (36 bp):   
AAAATAAATTCAAATACATGTATTTCGACTAGCTAG

Found at i:7014 original size:18 final size:17

Alignment explanation


    Indices: 6955--7035  Score: 51
    Period size: 17  Copynumber: 4.6  Consensus size: 17

       6945 TCGTTCTCTC

                           *  
       6955 TTTCTTTTTCTTTCTCTT
          1 TTTC-TTTTCTTTCTATT

                      *          
       6973 TTTCTTTTCTCTCTTGATAAT
          1 TTTCTTTTCTTTC-T-AT--T

                              
       6994 TTTCTCTTTCTTTCTA--
          1 TTTCT-TTTCTTTCTATT

                     *    *  
       7010 TTT-TTTTCCTTCTCTT
          1 TTTCTTTTCTTTCTATT

                      
       7026 TTTCTTTTCT
          1 TTTCTTTTCT

       7036 CTCTTGCTCA


Statistics
Matches: 49,  Mismatches: 6, Indels: 17
        0.68            0.08        0.24

Matches are distributed among these distances:
  14    8  0.16
  15    1  0.02
  16    6  0.12
  17   13  0.27
  18    5  0.10
  19    1  0.02
  20    1  0.02
  21    7  0.14
  22    7  0.14

ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72


Consensus pattern (17 bp):   
TTTCTTTTCTTTCTATT

Found at i:10289 original size:50 final size:51

Alignment explanation


    Indices: 10142--10290  Score: 142
    Period size: 50  Copynumber: 3.0  Consensus size: 51

      10132 GTCCCCTTTC

                    *         *         *     *     *       *   
      10142 TTTGAAACTATCCATGCTGATGTATTTGAATGAGGAAAATGTAT-TCAAGCA
          1 TTTGAAACCATCCATGCTCATGTATTTGGATGAGAAAAATATATCT-ATGCA

                   *                   *   *   *   *  *        
      10193 TTTGAAATCATCCATGCTC-TGTATTTAGATAAGATAAACATCTCTATGCA
          1 TTTGAAACCATCCATGCTCATGTATTTGGATGAGAAAAATATATCTATGCA

                           **                                
      10243 -TTGAAACCATCCATAATCATGTATTTGGATGAGAAAAATATATCTATG
          1 TTTGAAACCATCCATGCTCATGTATTTGGATGAGAAAAATATATCTATG

      10291 AAAATGAAAT


Statistics
Matches: 76,  Mismatches: 20, Indels: 5
        0.75            0.20        0.05

Matches are distributed among these distances:
  49   15  0.20
  50   44  0.58
  51   17  0.22

ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34


Consensus pattern (51 bp):   
TTTGAAACCATCCATGCTCATGTATTTGGATGAGAAAAATATATCTATGCA

Found at i:11233 original size:20 final size:20

Alignment explanation


    Indices: 11196--11233  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      11186 ATCATATGTG

                   *            
      11196 AAATTTTGATATAGAATTGA
          1 AAATTTTAATATAGAATTGA

                               
      11216 AAATTTTAACTATA-AATT
          1 AAATTTTAA-TATAGAATT

      11234 TCATGTAAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  20   12  0.75
  21    4  0.25

ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42


Consensus pattern (20 bp):   
AAATTTTAATATAGAATTGA

Found at i:20211 original size:6 final size:6

Alignment explanation


    Indices: 20200--20234  Score: 52
    Period size: 6  Copynumber: 5.7  Consensus size: 6

      20190 TTTTATTTCA

                                   *                
      20200 TAATTT TAATTT TAATTT TAGTTT TAAATTT TAAT
          1 TAATTT TAATTT TAATTT TAATTT T-AATTT TAAT

      20235 CCCCAATTTC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
   6   21  0.81
   7    5  0.19

ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63


Consensus pattern (6 bp):   
TAATTT

Done.