Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009694.1 Kokia drynarioides strain JFW-HI SEQ_124413, 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, 766

Length: 1278
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28


Found at i:393 original size:216 final size:211

Alignment explanation


    Indices: 1--1278  Score: 1215
    Period size: 216  Copynumber: 5.9  Consensus size: 211

                 *    *                   *       *           *           ** 
          1 TAGACCAAATAATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTAT
          1 TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGT

             *               *        *                                      
         66 CTTGAATACTTTAAGAAATCGAAGTTATAGAAGAACTCGTAAAAGTATGTCAAGTTTGGAAGTTC
         66 CATGAATACTTTAAGAACT-GAAGTTTTAGAAGAACTCGTAAAAGT-TGTCAAGTTTGGAAGTTC

               *     *                             *           *             
        131 GTCTAAGAGCCAAGAGAGAAA-AACCTCTCACGTAAATAGGTTTTTAATTCGAAGACCAAAAGTT
        129 GTCCAAGA-ACAAGAGAGAAACAA-CTCTCACGTAAATAAGTTTTTAATT-AAAGACCAAAAGTT

                 *           *    
        195 GTTTAGAAATTGACAAATTATT
        191 GTTTACAAA-TGACAAACTATT

                  *               * *  *         *                *          
        217 TAGACATAATGATGCGATTTCCTGTGCTTGGAATGTTTGAAAAATTACTCGAAGAAATGGATCGT
          1 TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGT

                                         *            * *           *        
        282 CATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTAAGACTTCGTCAAGTTCGGAAGTTC
         66 CATGAATACTTTAA-GAACTGAAGTTTTAGAAGAACTCGTAAAAGTT-GTCAAGTTTGGAAGTTC

                                          *        *           *           * 
        347 GTCCAAGAACAAGGAGAGAAACAACTCTCATGTAAATAACTTTTTAATTTATAGACCAAAAGTCG
        129 GTCCAAGAACAA-GAGAGAAACAACTCTCACGTAAATAAGTTTTTAA-TTAAAGACCAAAAGTTG

                                 
        412 TTTACAAAATGACAAACTATT
        192 TTTAC-AAATGACAAACTATT

                 *    *    *                       *                      *  
        433 TAGACTAAATTATGCAATTTCCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGAATGGATTGT
          1 TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGT

                              *  *            *    *            **    *      
        498 CATGAATACTTTAATGGAGC-AAAGTTATT-GAACAACTGGTAAAAGTTTGTGGAGTTAGGAAGT
         66 CATGAATACTTTAA--GAACTGAAGTT-TTAGAAGAACTCGTAAAAG-TTGTCAAGTTTGGAAGT

             *     *   *       *  *    *               *                     
        561 TTGTCCATGATCCAAGAGATAGTA-AATTCTCACGTAAATAAGCTTTTAATTAAATGACCAAAAG
        127 TCGTCCAAGA-ACAAGAGAGA-AACAACTCTCACGTAAATAAGTTTTTAATTAAA-GACCAAAAG

                *                 **
        625 TTGTATACCAAATGACAAACTAAG
        189 TTGTTTA-CAAATGACAAACTATT

            *             *        *                       *              *  
        649 CAGACAAAATGATGTGATTTCCCAAGCATGGAATGTTC-AGAAAATTGCTCGAAGGAATGGAACG
          1 TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTACTCGAAGGAATGGATCG

                                *      *             *                *      
        713 TCATGAATACTTTATAGAACCGAAGTTGTAGAAGAACTCGTCAAAGTTTGTCAAGTTTAGAAGTT
         65 TCATGAATACTTTA-AGAACTGAAGTTTTAGAAGAACTCGTAAAAG-TTGTCAAGTTTGGAAGTT

             *     * *               *     *              *         *        
        778 CATCCAATATCTAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTCATTCAAAGAGCAAAAGTT
        128 CGTCCAAGAAC-AAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATT-AAAGACCAAAAGTT

                                   
        843 GTTTACCAAATGACAAA-TAGTT
        191 GTTTA-CAAATGACAAACTA-TT

                  *                  *      *               *                
        865 TAGAAAAAAAATGATGCGATTTCCCAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATC
          1 TAG--ACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATC

             *              *       *   *  *                 *        **     
        930 GCCATGAATACTTTATGGAACTGATGTTATAAAAGAACTCGTAAAAGTTTTCCAAGTTCAGAAGT
         64 GTCATGAATACTTTA-AGAACTGAAGTTTTAGAAGAACTCGTAAAAGTTGT-CAAGTTTGGAAGT

               *             *                              *          *     
        995 TCGGCCAAGAACCAAGATAGAAACAACTCTCACGTAAGA-AAGTTTTTCATTGAAAGACGAAAAG
        127 TCGTCCAAGAA-CAAGAGAGAAACAACTCTCACGTAA-ATAAGTTTTTAATT-AAAGACCAAAAG

             *      *          *    
       1059 TAGTTTAGAAAATGACAAAGTATT
        189 TTGTTTA-CAAATGACAAACTATT

                 *                    *   *       *       *   *         * *  
       1083 TAGACCAAATGATGCGATTTCCCGAGTATGTAATGTTCAAAAAATTGCTCTAA-GAATGGGTTGT
          1 TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGT

             *               *                              *                
       1147 CTTGAATACTTTAAGAAATCGAAGTTATT-GAAGAACTCGTAAAAGCTCGTCAAGTTTGGAAGTT
         66 CATGAATACTTTAAGAACT-GAAGTT-TTAGAAGAACTCGTAAAAG-TTGTCAAGTTTGGAAGTT

             *  *             *              *     *                         
       1211 CATCTAAGAACCAAGAGAAAAACAACTCTCACGGAAATAGGTTTTTAATTCAAAGACCAAAAGTT
        128 CGTCCAAGAA-CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATT-AAAGACCAAAAGTT

               
       1276 GTT
        191 GTT


Statistics
Matches: 873,  Mismatches: 157, Indels: 65
        0.80            0.14        0.06

Matches are distributed among these distances:
 214    5  0.01
 215  123  0.14
 216  532  0.61
 217   31  0.04
 218  177  0.20
 219    5  0.01

ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28


Consensus pattern (211 bp):   
TAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGT
CATGAATACTTTAAGAACTGAAGTTTTAGAAGAACTCGTAAAAGTTGTCAAGTTTGGAAGTTCGT
CCAAGAACAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTAAAGACCAAAAGTTGTTTA
CAAATGACAAACTATT

Found at i:841 original size:432 final size:428

Alignment explanation


    Indices: 1--1274  Score: 1366
    Period size: 432  Copynumber: 2.9  Consensus size: 428

                 *                                *           *            * 
          1 TAGACCAAATAATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTACTCTAAGGAATGGATTAT
          1 TAGACAAAATAATGCGATTTCCCGAGCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATTGT

             *              *                              *         *       
         66 CTTGAATACTTTAA-GAAATCGAAGTTATAGAAGAACTCGTAAAAGTATGTCAAGTTTGGAAGTT
         66 CATGAATACTTTAATGGAA-CGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTAGGAAGTT

                *    *        *                     *           *            
        130 CGTCTAAGAGCCAAGAGAGA-AAAACCTCTCACGTAAATAGGTTTTTAATTCGAAGACCAAAAGT
        130 CGTCCAAGAACCAAGAGATAGAAAA-CTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGT

                      *       *          *               * *  *          *   
        194 TGTTTAGAAATTGACAAATTATTTAGACATAATGATGCGATTTCCTGTGCTTGGAATGTT-TGAA
        194 TGTTTA-AAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCAG-A

                 *       *                             *      *  *           
        258 AAATTACTCGAAGAAATGGATCGTCATGAATACTTTAAGGAACTGAAGTTTTAAAAGAACTCGTA
        257 AAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAA-GAACCGAAGTTATAGAAGAACTCGTA

               *           *        *                                      * 
        323 AGACTTCGTCAAGTTCGGAAGTTCGTCCAAGAACAAGGAGAGAAACAACTCTCATGTAAATAACT
        321 A-AGTTCGTCAAGTTTGGAAGTTCATCCAAGAACAA-GAGAGAAACAACTCTCATGTAAATAAGT

                    * *                                   
        388 TTTTAATTTATAGACCAAAAGTCGTTTACAAAATGACAAACTA-TT
        384 TTTTAATTCAAAGACCAAAAGTCGTTTACAAAATGACAAA-TAGTT

                 *    *    *              *        *                         
        433 TAGACTAAATTATGCAATTTCCCGAGCATGGAATGTTCGGAAAATTACTCGAAGGAATGGATTGT
          1 TAGACAAAATAATGCGATTTCCCGAGCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATTGT

                              * *       *   *    *            **            *
        498 CATGAATACTTTAATGGAGCAAAGTTATTGAACAACTGGTAAAAGTTTGTGGAGTTAGGAAGTTT
         66 CATGAATACTTTAATGGAACGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTAGGAAGTTC

                 *  *           *   *               *                        
        563 GTCCATGATCCAAGAGATAGTAAATTCTCACGTAAATAAGCTTTTAATT-AAATGACCAAAAGTT
        131 GTCCAAGAACCAAGAGATAGAAAACTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAAAGTT

              *   *             ***             *        *                   
        627 GTATACCAAATGACAAACTAAGCAGACAAAATGATGTGATTTCCCAAGCATGGAATGTTCAGAAA
        195 GTTTA-AAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAA

                              *                             *                
        692 ATTGCTCGAAGGAATGGAACGTCATGAATACTTTATAGAACCGAAGTTGTAGAAGAACTCGTCAA
        259 ATTGCTCGAAGGAATGGATCGTCATGAATACTTTA-AGAACCGAAGTTATAGAAGAACTCGT-AA

                *         *             * *               *                  
        757 AGTTTGTCAAGTTTAGAAGTTCATCCAATATCTAAGAGAGAAACAATTCTCATGTAAATAAGTTT
        322 AGTTCGTCAAGTTTGGAAGTTCATCCAAGAAC-AAGAGAGAAACAACTCTCATGTAAATAAGTTT

              *         *       *      *               
        822 TTCATTCAAAGAGCAAAAGTTGTTTACCAAATGACAAATAGTT
        386 TTAATTCAAAGACCAAAAGTCGTTTACAAAATGACAAATAGTT

                  *     *            *                      *               *
        865 TAGAAAAAAAATGATGCGATTTCCCAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATC
          1 TAG--ACAAAATAATGCGATTTCCCGAGCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATT

             *                       *      *                                
        930 GCCATGAATACTTT-ATGGAACTGATGTTATAAAAGAACTCGTAAAAGTTT-TCCAAGTTCA-GA
         64 GTCATGAATACTTTAATGGAAC-GAAGTTATAGAAGAACTCGTAAAAGTTTGT-CAAGTT-AGGA

                  *                                              *   *      *
        992 AGTTCGGCCAAGAACC-A-AGATAGAAACAACTCTCACGTAAGA-AAGTTTTTCATTGAAAGACG
        126 AGTTCGTCCAAGAACCAAGAGATAG-AA-AACTCTCACGTAA-ATAAGTTTTTAATTCAAAGACC

                  *                 *         *                    *   *     
       1054 AAAAGTAGTTTAGAAAATGACAAAGTATTTAGACCAAATGATGCGATTTCCCGAGTATGTAATGT
        188 AAAAGTTGTTTA-AAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGT

               *          *         * *   *                *         *       
       1119 TCAAAAAATTGCTCTAA-GAATGGGTTGTCTTGAATACTTTAAGAAATCGAAGTTATTGAAGAAC
        252 TCAGAAAATTGCTCGAAGGAATGGATCGTCATGAATACTTTAAG-AACCGAAGTTATAGAAGAAC

                     *                      *             *            * *   
       1183 TCGTAAAAGCTCGTCAAGTTTGGAAGTTCATCTAAGAACCAAGAGAAAAACAACTCTCACGGAAA
        316 TCGT-AAAGTTCGTCAAGTTTGGAAGTTCATCCAAGAA-CAAGAGAGAAACAACTCTCATGTAAA

              *                        
       1248 TAGGTTTTTAATTCAAAGACCAAAAGT
        379 TAAGTTTTTAATTCAAAGACCAAAAGT

       1275 TGTT


Statistics
Matches: 694,  Mismatches: 129, Indels: 37
        0.81            0.15        0.04

Matches are distributed among these distances:
 431    4  0.01
 432  355  0.51
 433  133  0.19
 434  197  0.28
 435    5  0.01

ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28


Consensus pattern (428 bp):   
TAGACAAAATAATGCGATTTCCCGAGCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATTGT
CATGAATACTTTAATGGAACGAAGTTATAGAAGAACTCGTAAAAGTTTGTCAAGTTAGGAAGTTC
GTCCAAGAACCAAGAGATAGAAAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTG
TTTAAAAATGACAAACTATTTAGACAAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAAT
TGCTCGAAGGAATGGATCGTCATGAATACTTTAAGAACCGAAGTTATAGAAGAACTCGTAAAGTT
CGTCAAGTTTGGAAGTTCATCCAAGAACAAGAGAGAAACAACTCTCATGTAAATAAGTTTTTAAT
TCAAAGACCAAAAGTCGTTTACAAAATGACAAATAGTT
Done.