Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013535.1 Kokia drynarioides strain JFW-HI SEQ_128561, 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: 5512
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2193 original size:11 final size:11

Alignment explanation


    Indices: 2179--2218  Score: 55
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       2169 GGAAGAAAGT

                       
       2179 AGAGAGAATCG
          1 AGAGAGAATCG

                    ** 
       2190 AGAGAGAAAAG
          1 AGAGAGAATCG

                       
       2201 AGAGA-AATCG
          1 AGAGAGAATCG

                    
       2211 AGAGAGAA
          1 AGAGAGAA

       2219 AGTGAGTACT


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  10    8  0.33
  11   16  0.67

ACGTcount: A:0.55, C:0.05, G:0.35, T:0.05


Consensus pattern (11 bp):   
AGAGAGAATCG

Found at i:2200 original size:23 final size:22

Alignment explanation


    Indices: 2148--2219  Score: 78
    Period size: 21  Copynumber: 3.2  Consensus size: 22

       2138 AAATCGAACC

                              *     
       2148 AGAAAAGTAGAAGAAAATGGAG-G
          1 AGAAAAGTAG-AG-AAATCGAGAG

                                    
       2171 A-AGAAAGTAGAGAGAATCGAGAG
          1 AGA-AAAGTAGAGA-AATCGAGAG

                                  
       2194 AGAAAAG-AGAGAAATCGAGAG
          1 AGAAAAGTAGAGAAATCGAGAG

                 
       2215 AGAAA
          1 AGAAA

       2220 GTGAGTACTA


Statistics
Matches: 44,  Mismatches: 1, Indels: 10
        0.80            0.02        0.18

Matches are distributed among these distances:
  21   15  0.34
  22   14  0.32
  23   14  0.32
  24    1  0.02

ACGTcount: A:0.57, C:0.03, G:0.33, T:0.07


Consensus pattern (22 bp):   
AGAAAAGTAGAGAAATCGAGAG

Found at i:5200 original size:158 final size:158

Alignment explanation


    Indices: 4964--5271  Score: 402
    Period size: 158  Copynumber: 1.9  Consensus size: 158

       4954 TAATCATATA

                     *                   *            **                     
       4964 TGCTCACACGAGCTGTGGGTCGAGATGTGGGGCTACACGATGTTGCTCACACAAGCTGTGGAGAA
          1 TGCTCACACAAGCTGTGGGTCGAGATGTGAGGCTACACGATGCCGCTCACACAAGCTGTGGAGAA

                   *      *                   **            **   *        *  
       5029 TCCGTAATAAATGCTGGACCTCAGCCATC-AGTATTACATCTAAGACCNGCACCCATATAACCTA
         66 TCCGTAACAAATGCAGGACCTCAGCCATCGA-TAGGACATCTAAGACCAACACACATATAACATA

                                         
       5093 CAATGCTCACACGAGCTGTGAAATGGGCC
        130 CAATGCTCACACGAGCTGTGAAATGGGCC

                                        *                *      *            
       5122 TGCTCACACAAGCTGTGGGTCGAGATGTTAGGCTACACGATGCCGTTCACACGAGCTGTGGAGAA
          1 TGCTCACACAAGCTGTGGGTCGAGATGTGAGGCTACACGATGCCGCTCACACAAGCTGTGGAGAA

              *     *            *  *                                      **
       5187 TCTGTAACCAATGCAGGACCTTAGTCATCGATAGGACATCTAAGACCAACACACATATAACATGT
         66 TCCGTAACAAATGCAGGACCTCAGCCATCGATAGGACATCTAAGACCAACACACATATAACATAC

                          *     
       5252 AATGCTCACACGAGTTGTGA
        131 AATGCTCACACGAGCTGTGA

       5272 GTCGAGATGT


Statistics
Matches: 127,  Mismatches: 22, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
 158  126  0.99
 159    1  0.01

ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22


Consensus pattern (158 bp):   
TGCTCACACAAGCTGTGGGTCGAGATGTGAGGCTACACGATGCCGCTCACACAAGCTGTGGAGAA
TCCGTAACAAATGCAGGACCTCAGCCATCGATAGGACATCTAAGACCAACACACATATAACATAC
AATGCTCACACGAGCTGTGAAATGGGCC

Found at i:5360 original size:132 final size:132

Alignment explanation


    Indices: 5122--5366  Score: 355
    Period size: 132  Copynumber: 1.9  Consensus size: 132

       5112 GAAATGGGCC

                             *                           *                   
       5122 TGCTCACACAAGCTGTGGGTCGAGATGTTAGGCTACACGATGCCGTTCACACGAGCTGTGGAGAA
          1 TGCTCACACAAGCTGTGAGTCGAGATGTTAGGCTACACGATGCCGCTCACACGAGCTGTGGAGAA

              ***          *     *  *                                        
       5187 TCTGTAACCAATGCAGGACCTTAGTCATCGATAGGACATCTAAGACCAACACACATATAACATGT
         66 TCCACAACCAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAACACACATATAACATGT

              
       5252 AA
        131 AA

                     *  *                       *      *                     
       5254 TGCTCACACGAGTTGTGAGTCGAGATGTTAGGCTACGCGATGCTGCTCACACGAGCTGTGGAGAA
          1 TGCTCACACAAGCTGTGAGTCGAGATGTTAGGCTACACGATGCCGCTCACACGAGCTGTGGAGAA

                            *             *     *           
       5319 TCCACAACCAATGCAATACCTCAGCCATCGGTAGGATATCTAAGACCA
         66 TCCACAACCAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCA

       5367 GCACCCGAAT


Statistics
Matches: 98,  Mismatches: 15, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 132   98  1.00

ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22


Consensus pattern (132 bp):   
TGCTCACACAAGCTGTGAGTCGAGATGTTAGGCTACACGATGCCGCTCACACGAGCTGTGGAGAA
TCCACAACCAATGCAAGACCTCAGCCATCGATAGGACATCTAAGACCAACACACATATAACATGT
AA
Done.