Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005185.1 Kokia drynarioides strain JFW-HI SEQ_119042, 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, 678

Length: 1130
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41


Found at i:392 original size:216 final size:215

Alignment explanation


    Indices: 4--1130  Score: 1539
    Period size: 216  Copynumber: 5.2  Consensus size: 215

          1 TTA

                                             *            **                 
          4 AATTAAAAACTTATTTACGTGAGAATTGTTTCTTTCTTTG-TCTTTATACGAACTTTCGAACTTG
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC-TTGGACGAACTTTCGAACTTG

                        *    *    *             *    *       *       *       
         68 TCAAACTTTTACAAGTTCTTTTATAACTTTGGATCCATAAATTATTCAAGAAGATCCGTTCCTTT
         65 TCAAACTTTTACTAGTTATTTTTTAAC-TTGGATCCCTAAAGTATTCAACAAGATCCATT-CTTT

                         *  * *           *      *         *                 
        133 -GAGCAATTTTTCAAATAGTCCATGCTCGGCAAATCGAATCATTTGGCCTAAATAGTTTGTCATT
        128 CGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT

                             *     
        197 TTGCAAACAAGTTTTGGACTTTG
        193 TTGCAAACAAGTTTTGGTCTTTG

                       *                                        *        * * 
        220 AATTAAAAACTAATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAAGTTTCGAACCTAT
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT

                            *    *             *            * *    *         
        285 CAAACTTTTACTAGTTCTTTTATAACATTGGATCCTTAAAGTATTCAAGACGATCTATTCTTTCG
         66 CAAACTTTTACTAGTTATTTTTTAAC-TTGGATCCCTAAAGTATTCAACAAGATCCATTCTTTCG

                                                         * *      *         *
        350 AGCAA-TTTTCTGAACATTCCATGCTCGGGAAATCGCATCATTTGATTTAAATAATTTGTCATTC
        130 AGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT

                                 *
        414 TGCAAACAAGTTTTGGTCTTTA
        194 TGCAAACAAGTTTTGGTCTTTG

                                                                             
        436 AATTAAAAACTTA-TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT

             *         *                 * *     *             *       *   * 
        500 CGAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTTAAGTATTCAACAAAATCCATTTTTTAG
         66 CAAACTTTTACTAGTTATTTTTTAACTT-GGATCCCTAAAGTATTCAACAAGATCCATTCTTTCG

                                  *  *          *   *           *            
        565 AGCAATTTTTCGAACATTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATGGTTTGTCATTTT
        130 AGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTT

                          *      
        630 GCAAACAAGTTTTGTTCTTTG
        195 GCAAACAAGTTTTGGTCTTTG

                                       *           *                    *    
        651 AATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTTATTCTTGGACGAACTTTCGAAATTGT
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT

            *                                                             *  
        716 AAAACTTTTA-TGAGTTATTTTTTAACTTCAGG-TCCCTAAAGTATTCAACAAGATCCATTCCTT
         66 CAAACTTTTACT-AGTTATTTTTTAACTT--GGATCCCTAAAGTATTCAACAAGATCCATTCTTT

                                         *                                   
        779 CGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT
        128 CGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATT

                            *      
        844 TTGCAAACAAGTTTTGTTCTTTG
        193 TTGCAAACAAGTTTTGGTCTTTG

                                                   *                    *    
        867 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTATTCTTGGACGAACTTTCGAAATTGT
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT

            *            *               **             *                *   
        932 AAAACTTTTA-TGGGTTATTTTTTAACTTCAAGTCCCTAAAGTAATCAACAAGATCCATTCCTTC
         66 CAAACTTTTACT-AGTTATTTTTTAACTTGGA-TCCCTAAAGTATTCAACAAGATCCATTCTTTC

                                        *                     *              
        996 GAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAGATAGTTTGTCATTT
        129 GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT

                                  
       1061 TGCAAACAAGTTTTGGTCTTTG
        194 TGCAAACAAGTTTTGGTCTTTG

                                                            
       1083 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGA
          1 AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGA


Statistics
Matches: 819,  Mismatches: 82, Indels: 20
        0.89            0.09        0.02

Matches are distributed among these distances:
 214    2  0.00
 215  187  0.23
 216  627  0.77
 217    3  0.00

ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40


Consensus pattern (215 bp):   
AATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACTTGT
CAAACTTTTACTAGTTATTTTTTAACTTGGATCCCTAAAGTATTCAACAAGATCCATTCTTTCGA
GCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTG
CAAACAAGTTTTGGTCTTTG

Found at i:821 original size:431 final size:430

Alignment explanation


    Indices: 1--1130  Score: 1579
    Period size: 431  Copynumber: 2.6  Consensus size: 430

                                                *            **              
          1 TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTTTCTTTG-TCTTTATACGAACTTTCGAAC
          1 TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC-TTGGACGAACTTTCGAAC

                           *    *    *      **     *    *       *       *    
         65 TTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGATCCATAAATTATTCAAGAAGATCCGTTCC
         65 TTGTCAAACTTTTACGAGTTATTTTTTAACTTCAG-TCCCTAAAGTATTCAACAAGATCCATT-C

                           *  * *           *      *         *               
        130 TTTGAGCAATTTTTCAAATAGTCCATGCTCGGCAAATCGAATCATTTGGCCTAAATAGTTTGTCA
        128 TTTGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCA

                               *                *                            
        195 TTTTGCAAACAAGTTTTGGACTTTGAATTAAAAACTAATTTACGTGAGAATTGTTTCTCTCTTTG
        193 TTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTG

                        *       *    *               *                  *    
        260 TTCTTGGACGAAGTTTCGAACCTATCAAACTTTTACTAGTTCTTTTATAACATTGGATCCTTAAA
        258 TTCTTGGACGAACTTTCGAAACTATAAAACTTTTACTAGTTATTTTATAACATTGGATCCCTAAA

                    * *    *    *                               *            
        325 GTATTCAAGACGATCTATTCTTTCGAGCAATTTTCTGAACATTCCATGCTCGGGAAATCGCATCA
        323 GTATTCAACAAGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCA

                  *                                    
        390 TTTGATTTAAATAATTTGTCATTCTGCAAACAAGTTTTGGTCT
        388 TTTGATCTAAATAATTTGTCATTCTGCAAACAAGTTTTGGTCT

                                                                             
        433 TTAAATTAAAAACTTA-TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACT
          1 TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACT

                *                                   *             *       *  
        497 TGTCGAACTTTTACGAGTTATTTTTTAACTTCAGTTCCCTTAAGTATTCAACAAAATCCATTTTT
         66 TGTCAAACTTTTACGAGTTATTTTTTAACTTCAG-TCCCTAAAGTATTCAACAAGATCCATTCTT

                                     *  *          *   *           *         
        562 TAGAGCAATTTTTCGAACATTCCATCCTTGGGAAATCGCGTCACTTGGTCTAAATGGTTTGTCAT
        130 T-GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT

                             *                                 *           * 
        627 TTTGCAAACAAGTTTTGTTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTCTTTAT
        194 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT

                                * *                       *                  
        692 TCTTGGACGAACTTTCGAAATTGTAAAACTTTTA-TGAGTTATTTTTTAAC-TTCAGG-TCCCTA
        259 TCTTGGACGAACTTTCGAAACTATAAAACTTTTACT-AGTTATTTTATAACATT--GGATCCCTA

                                                                             
        754 AAGTATTCAACAAGATCCATTCCTTCGAGCAATTTT-TCGAACATTCCATGCTCGAGAAATCGCA
        321 AAGTATTCAACAAGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGAGAAATCGCA

                   *        *         *               *   
        818 TCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGTTCT
        385 TCATTTGATCTAAATAATTTGTCATTCTGCAAACAAGTTTTGGTCT

              *                                       *                    * 
        864 TTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTATTCTTGGACGAACTTTCGAAAT
          1 TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACT

               *         * *                              *                  
        929 TGTAAAACTTTTATGGGTTATTTTTTAACTTCAAGTCCCTAAAGTAATCAACAAGATCCATTCCT
         66 TGTCAAACTTTTACGAGTTATTTTTTAACTTC-AGTCCCTAAAGTATTCAACAAGATCCATT-CT

             *                            *                     *            
        994 TCGAGCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAGATAGTTTGTCAT
        129 TTGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCAT

                                                                             
       1059 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT
        194 TTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGT

                   
       1124 TCTTGGA
        259 TCTTGGA


Statistics
Matches: 616,  Mismatches: 73, Indels: 18
        0.87            0.10        0.03

Matches are distributed among these distances:
 430    7  0.01
 431  362  0.59
 432  243  0.39
 433    4  0.01

ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41


Consensus pattern (430 bp):   
TTAAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTTCGAACT
TGTCAAACTTTTACGAGTTATTTTTTAACTTCAGTCCCTAAAGTATTCAACAAGATCCATTCTTT
GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTT
TGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTTGTTC
TTGGACGAACTTTCGAAACTATAAAACTTTTACTAGTTATTTTATAACATTGGATCCCTAAAGTA
TTCAACAAGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAATCGCATCATTT
GATCTAAATAATTTGTCATTCTGCAAACAAGTTTTGGTCT
Done.