Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008180.1 Kokia drynarioides strain JFW-HI SEQ_122839, 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: 2273
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40


Found at i:647 original size:76 final size:75

Alignment explanation


    Indices: 509--663  Score: 202
    Period size: 76  Copynumber: 2.1  Consensus size: 75

        499 CTCGGATCCT

                                        *                     **           * 
        509 TAAAGTATTCAAGACGATCTATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCAGCAAATCTC
          1 TAAAGTATTCAAGACGATCTATTCCTTCAAGCAATTTTCCAAACATTCCACACTCAGCAAATCGC

                       
        574 ATCATTTGGTC
         66 A-CATTTGGTC

                      *             *             ***              * *       
        585 TAAAGTATTCCAGACGATCTATTCTTTCAAGCAATTTTTTGAACATTCCACACTCGGGAAATCGC
          1 TAAAGTATTCAAGACGATCTATTCCTTCAAGCAATTTTCCAAACATTCCACACTCAGCAAATCGC

                      
        650 ACATTTGGTC
         66 ACATTTGGTC

                
        660 TAAA
          1 TAAA

        664 TAGTTTGTCA


Statistics
Matches: 68,  Mismatches: 11, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  75   13  0.19
  76   55  0.81

ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33


Consensus pattern (75 bp):   
TAAAGTATTCAAGACGATCTATTCCTTCAAGCAATTTTCCAAACATTCCACACTCAGCAAATCGC
ACATTTGGTC

Found at i:958 original size:216 final size:215

Alignment explanation


    Indices: 585--2273  Score: 1938
    Period size: 216  Copynumber: 7.8  Consensus size: 215

        575 TCATTTGGTC

                      * *      *        *         *           **           * 
        585 TAAAGTATTCCAGACGATCTATTCTTTCAAGCAATTTTTTGAACATTCCACACTCGGGAAATCGC
          1 TAAAGTATTCAACACGATCCATTCTTTCGAGCAATTTTCTGAACATTCCATGCTC-GGAAATCAC

                                                      *                      
        650 A-CATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTTGTCTTTGAATTAAAAACTTATT
         65 ATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT

            *          *                 *                                   
        714 CACGTGAGAATAGTTTCTCTCTTTGTTCTCGGACGAACTTCCGAACTTGTCAAACTTTTACTAGT
        130 TACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGT

                                *
        779 TCTTTTATAACTTCGGATCCA
        195 TCTTTTATAACTTCGGATCCT

                      * *      *                              *              
        800 TAAAGTATTCCAGACGATCTATTCTTTCGAGCAATTTTCTGAACATTCCACGCTCGAGAAATCAC
          1 TAAAGTATTCAACACGATCCATTCTTTCGAGCAATTTTCTGAACATTCCATGCTCG-GAAATCAC

                   *                 *                                       
        865 ATCATTTAGTCTAAATAGTTTGTCACTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
         65 ATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT

            *                *                              *    *     *   **
        930 GACGTGAGAATTGTTTCCCTCTTTGTTCTTGGACGAACTTCCGAACTTATCAAGCTTTTTCTAAA
        130 TACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGT

                      *  * *     
        995 TCTTTTATAAATTTGAATCCT
        195 TCTTTTATAACTTCGGATCCT

                  *                 *   *                    *     *         
       1016 TAAAGTCTTCAACACGATCCATTCCTTCAAGCAATTTTTCT-AACATTCTATGCTTGGCAAATCA
          1 TAAAGTATTCAACACGATCCATTCTTTCGAGCAA-TTTTCTGAACATTCCATGCTCGG-AAATCA

                    *                                                        
       1080 CATCATTTAGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT
         64 CATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT

              *                  *            *        *   *       *     *  *
       1145 TTTCGTGAGAATTGTTTCTCTTTTTGTTCTTGGATGAACTTCCCAACATGTCAAAATTTTATTAA
        129 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAG

            *      *         *     
       1210 ATCTTTTGT-ACATTCGAATCCT
        194 TTCTTTTATAAC-TTCGGATCCT

            *             *         *   *                                  * 
       1232 GAAAGTATTCAACATGATCCATTCCTTCAAGCAATTTTCCT-AACATTCCATGCTCGGCAAATTA
          1 TAAAGTATTCAACACGATCCATTCTTTCGAGCAATTTT-CTGAACATTCCATGCTCGG-AAATCA

                            *                  *                             
       1296 CATCATTTGGTCTAAAAAGTTTGTCATTTTGCAAAAAAGTTTTGGTCTTTGAATTAAAAACTTAT
         64 CATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT

                         *    *         *     *    *                         
       1361 TTACGTGAGAATTATTTCACTCTTTGTTGTTGGATGAACATCCGAACTTGTCAAACTTTTACT-G
        129 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAG

             *          *           
       1425 AATCTTTTATAAATTC-GATTCCT
        194 -TTCTTTTATAACTTCGGA-TCCT

                *       *                       *   *                        
       1448 TAAAATATTCAATA-GATCCATTCCTTT-GAGCAATATTCCGAACATTCCA-GACTCGGCAAATC
          1 TAAAGTATTCAACACGATCCATT-CTTTCGAGCAATTTTCTGAACATTCCATG-CTCGG-AAATC

                *                     *                **        *           
       1510 ACATAATTTGGTCTAAATAGTTTGTCTTTTTGCAAACAAGTTTCAGTCTTTGAGTTAAAAACTTA
         63 ACATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTA

                 *                        *           *       *            * 
       1575 -TTACTTGAGAATTGTTTCTCTCTTTGTTCATGGACGAACTTTCGAACTTATCAAACTTTTACAA
        128 TTTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTA

               *              *     
       1639 GTTATTTT-TAACTTCGGTTCCCT
        193 GTTCTTTTATAACTTCGGAT-CCT

                          *             *                       *   *       *
       1662 T-AAGTATTCAACAAGATCCAATT-TTTAGAGCAATTTTCTGAACATTCCATCCTTAGGAAATCG
          1 TAAAGTATTCAACACGATCC-ATTCTTTCGAGCAATTTTCTGAACATTCCATGC-TCGGAAATCA

                    *                      *      *                * *       
       1725 CATCATTTTGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTCAGAACTTAT
         64 CATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT

                        *  *         *     *  *    *   *                    *
       1790 TTACGTGAGAATGGTATCTCTCTTTCTTCTTAGATGAACGT-CTAAGCTTGTCAAACTTTTACTT
        129 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAA-CTTGTCAAACTTTTACTA

               *        *          
       1854 GTTATTTTATAATTTCGGATCCT
        193 GTTCTTTTATAACTTCGGATCCT

                        *           *                *          *           *
       1877 TAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT-TCAAACATTCCATTCTCGGGAAATCG
          1 TAAAGTATTCAACACGATCCATTCTTTCGAGCAATTTTCT-GAACATTCCATGCTC-GGAAATCA

               *                            *                 *              
       1941 CATTATTTGGTCTAAATAGTTTGTCATTTTGCTAACAAGTTTTGGTCTTTAAATTAAAAACTTAT
         64 CATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT

             *      *                **      *                 *           * 
       2006 TCACGTGAAAATTGTTTCTCTCTTTAATCTTGGGCGAAC-TCTCGAACTTGCCAAACTTTTACGA
        129 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTC-CGAACTTGTCAAACTTTTACTA

               *    *              *
       2070 GTTATTTTTTAACTTC-GATTCCC
        193 GTTCTTTTATAACTTCGGA-TCCT

                        * *             *     *    *                         
       2093 TAAAGTATTCAATAAGATCCATT-TCTTAGAGCATTTTTTTGAACATTCCATGCTCGAGAAATCA
          1 TAAAGTATTCAACACGATCCATTCT-TTCGAGCAATTTTCTGAACATTCCATGCTCG-GAAATCA

              *                *           **          *                     
       2157 CAGCATTTGGTCTAAATAGCTTGTCATTTTGTGAACAAGTTTTAGTCTTTGAATTAAAAACTTAT
         64 CATCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTAT

                                                                
       2222 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTC
        129 TTACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTC


Statistics
Matches: 1260,  Mismatches: 180, Indels: 67
        0.84            0.12        0.04

Matches are distributed among these distances:
 213   20  0.02
 214  154  0.12
 215  236  0.19
 216  837  0.66
 217   13  0.01

ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40


Consensus pattern (215 bp):   
TAAAGTATTCAACACGATCCATTCTTTCGAGCAATTTTCTGAACATTCCATGCTCGGAAATCACA
TCATTTGGTCTAAATAGTTTGTCATTTTGCAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTT
ACGTGAGAATTGTTTCTCTCTTTGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACTAGTT
CTTTTATAACTTCGGATCCT

Found at i:1322 original size:21 final size:20

Alignment explanation


    Indices: 1298--1337  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1288 GCAAATTACA

                      *          
       1298 TCATTTGGTCTAAAAAGTTTG
          1 TCATTTGG-CAAAAAAGTTTG

                  *            
       1319 TCATTTTGCAAAAAAGTTT
          1 TCATTTGGCAAAAAAGTTT

       1338 TGGTCTTTGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20   10  0.59
  21    7  0.41

ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42


Consensus pattern (20 bp):   
TCATTTGGCAAAAAAGTTTG

Done.