Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003225.1 Kokia drynarioides strain JFW-HI SEQ_115865, 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, 616

Length: 1027
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40


Found at i:375 original size:216 final size:216

Alignment explanation


    Indices: 1--1027  Score: 1346
    Period size: 216  Copynumber: 4.8  Consensus size: 216

                                                    *            *           
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAATATTCCATGCCTGTGAAATCGCATC
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCTGGGAAATCGCATC

                               *                      *                      
         66 ATTTGGTCTAAATAGTTTACCATTTTGCAAACAAGTTTTGGTTTTTGAATTAAAAACTTATTTAC
         66 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC

                                                                             
        131 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTCT
        131 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTCT

                             *   
        196 TCTATAACATCGGATACTTAA
        196 TCTATAACATCGGATACATAA

                                                    *            **          
        217 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAATATTCCATGCCTGTAAAATCGCATC
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCTGGGAAATCGCATC

                                                                             
        282 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC
         66 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC

            *            *                                                   
        347 ATGAGAATTGTTTGTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTCT
        131 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTCT

              * *                
        412 TCAAAAACATCGGATACATAA
        196 TCTATAACATCGGATACATAA

                   *                                          *              
        433 AGTATTCCAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTTGGGAAATCGCATC
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCTGGGAAATCGCATC

                     **  *                     *           *       *         
        498 ATTTGGTCTGTATTGTTTATCATTTTGCAAACAAGCTTTGGTCTTTGTATTAAAACCTTATTTAC
         66 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC

                                    *           *               *   *  *  * *
        563 GTGAGAATTGTTTCTCTCTTTGTTTTCTGGACGAACATTCAAACTTGTCAAAATTTTACGAGCTA
        131 GTGAGAATTGTTTCTCTCTTTGTTCT-TGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTC

              * *       *  *    *   
        628 TTTTTTAA-ATTTGGCT-CTGTAA
        195 TTCTATAACA-TCGGATAC-ATAA

                     * *    *    *  *  *   *   *                         **  
        650 AGTATTCAACAAGATCCATTCCTTAGAGCAAATTTCCGAACATTCCATG-CTCGGGAAATCAAAT
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCT-GGGAAATCGCAT

                               *        *      *                          *  
        714 CATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATATA
         65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA

            *                    *      *         * **      *       *     *  
        779 TGTGAGAATTG-TT-TCTCTTCGTTCTTAGACGAACTTCCGTACTTGTGAAACTTTTACTAGGTC
        130 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTC

              *      * *    *     
        842 TTTTATAACTTTGGATCCATAA
        195 TTCTATAACATCGGATACATAA

                            *    *     * *                        **         
        864 AGTATTCAAGACGATCCATTCCTTCGAGCTATTTTTCGAACATTCCATG-CTCGATAAATCGCAT
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCT-GGGAAATCGCAT

                               *  *                                * *       
        928 CATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAATATTTATTTA
         65 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTA

                                               
        993 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAA
        130 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAA


Statistics
Matches: 710,  Mismatches: 93, Indels: 16
        0.87            0.11        0.02

Matches are distributed among these distances:
 214  166  0.23
 215   13  0.02
 216  373  0.53
 217  158  0.22

ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40


Consensus pattern (216 bp):   
AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCCTGGGAAATCGCATC
ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTAC
GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTCT
TCTATAACATCGGATACATAA

Found at i:997 original size:431 final size:430

Alignment explanation


    Indices: 1--1027  Score: 1355
    Period size: 431  Copynumber: 2.4  Consensus size: 430

                                                    *                        
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAATATTCCATGC-CTGTGAAATCGCAT
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTC-GT-AAATCGCAT

                                *                      *                     
         65 CATTTGGTCTAAATAGTTTACCATTTTGCAAACAAGTTTTGGTTTTTGAATTAAAAACTTATTTA
         64 CATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATT-AAAACTTATTTA

                                                *               *      *  * *
        130 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCAAACTTGTCAAACTTTAACTAGTTC
        128 CGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACATTCAAACTTGTCAAAATTTAACGAGCTA

                                           * *    *    *  *      *   *    *  
        195 TTCTATAACATCGGATACTTAAAGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAATAT
        193 TTCTATAACATCGGATACTTAAAGTATTCAACAAGATCCATTCCTTAGAACAAATTTCCGAACAT

                      *      **                                     *        
        260 TCCATGCCTGTAAAATCGCATCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTC
        258 TCCATGCCTGGAAAATCAAATCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAATTTTGGTC

                              *                       *      *         *     
        325 TTTGAATTAAAAACTTATTTACATGAGAATTGTTTGTCTCTTTGTTCTTGGACGAACTTTCAAAC
        323 TTTGAATTAAAAACTTATATACATGAGAATTGTTTGTCTCTTCGTTCTTAGACGAACTTCCAAAC

                              *                        
        390 TTGTCAAACTTTAACTAGTTCTTCAAAAACATCGGATACATAA
        388 TTGTCAAACTTTAACTAGGTCTTCAAAAACATCGGATACATAA

                   *                                            * *          
        433 AGTATTCCAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTTGGGAAATCGCATC
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGC-TCGTAAATCGCATC

                     **  *                     *           *                 
        498 ATTTGGTCTGTATTGTTTATCATTTTGCAAACAAGCTTTGGTCTTTGTATTAAAACCTTATTTAC
         65 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAA-CTTATTTAC

                                    *                               *        
        563 GTGAGAATTGTTTCTCTCTTTGTTTTCTGGACGAACATTCAAACTTGTCAAAATTTTACGAGCTA
        129 GTGAGAATTGTTTCTCTCTTTGTTCT-TGGACGAACATTCAAACTTGTCAAAATTTAACGAGCTA

              * *       *  *                                   *             
        628 TTTTTTAA-ATTTGGCT-CTGTAAAGTATTCAACAAGATCCATTCCTTAGAGCAAATTTCCGAAC
        193 TTCTATAACA-TCGGATACT-TAAAGTATTCAACAAGATCCATTCCTTAGAACAAATTTCCGAAC

                          *                            *        *            
        691 ATTCCATG-CTCGGGAAATCAAATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAATTTTG
        256 ATTCCATGCCT-GGAAAATCAAATCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAATTTTG

                                    **                                      *
        755 GTCTTTGAATTAAAAACTTATATATGTGAGAATTG-TT-TCTCTTCGTTCTTAGACGAACTTCCG
        320 GTCTTTGAATTAAAAACTTATATACATGAGAATTGTTTGTCTCTTCGTTCTTAGACGAACTTCCA

            *      *       *          ** *   * *    *     
        818 TACTTGTGAAACTTTTACTAGGTCTTTTATAACTTTGGATCCATAA
        385 AACTTGTCAAACTTTAACTAGGTCTTCAAAAACATCGGATACATAA

                            *    *     * *                                   
        864 AGTATTCAAGACGATCCATTCCTTCGAGCTATTTTTCGAACATTCCATGCTCGATAAATCGCATC
          1 AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTCG-TAAATCGCATC

                              *  *                                  *        
        929 ATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTTGGTCTTTGAATTAAATATTTATTTAC
         65 ATTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAA-ACTTATTTAC

                                              
        994 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAA
        129 GTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAA


Statistics
Matches: 515,  Mismatches: 71, Indels: 20
        0.85            0.12        0.03

Matches are distributed among these distances:
 430   10  0.02
 431  197  0.38
 432  144  0.28
 433  164  0.32

ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40


Consensus pattern (430 bp):   
AGTATTCAAGACGATCTATTCTTTCGAACAATTTTTCGAACATTCCATGCTCGTAAATCGCATCA
TTTGGTCTAAATAGTTTATCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAACTTATTTACGT
GAGAATTGTTTCTCTCTTTGTTCTTGGACGAACATTCAAACTTGTCAAAATTTAACGAGCTATTC
TATAACATCGGATACTTAAAGTATTCAACAAGATCCATTCCTTAGAACAAATTTCCGAACATTCC
ATGCCTGGAAAATCAAATCATTTGGTCTAAATAGTTTATCATTTTGCAAACAAATTTTGGTCTTT
GAATTAAAAACTTATATACATGAGAATTGTTTGTCTCTTCGTTCTTAGACGAACTTCCAAACTTG
TCAAACTTTAACTAGGTCTTCAAAAACATCGGATACATAA
Done.