Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008625.1 Kokia drynarioides strain JFW-HI SEQ_123304, 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, 847

Length: 1412
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41


Found at i:381 original size:216 final size:216

Alignment explanation


    Indices: 1--1412  Score: 1363
    Period size: 216  Copynumber: 6.6  Consensus size: 216

                     *     *                          *                 * *  
          1 AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTAGTCG
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

                  **                 **     *          *             *       
         66 AACTTCCAAACTTGTCAAACTTTTATTAGTT-ATTT-TAACTTTGGTTCCTTAAAGTGTTCAAGA
         66 AACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA

                          *         * *              *       *       *     * 
        129 CGATCCATTCCTTCTAGCAATTTTTTGAACATTCCATGCTCAAGAAATCACATCATTAGGTCCGA
        131 CGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAA

                *         *      
        194 ATAGCTTGTCATTTCGTAAAC
        196 ATAGTTTGTCATTTTGTAAAC

                                  *         *    *      *      *      *      
        215 AACTTTTGGTCTTTGAATTAAAGACTTATTTACGTGAAAATTGTCTCTCTCCTGGTTCATGGCCG
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

               *       *              *                *                     
        280 AACATCTGAACATGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
         66 AACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA

             *                        * **                    *       ***    
        345 CAATCCATTCCTTCGAGCAATTTTCTGAGTATTCCATGCTCGAGAAATCGTATCATTTCCACCAA
        131 CGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAA

            *      * *           
        410 GTAGTTTTTTATTTTGTAAAC
        196 ATAGTTTGTCATTTTGTAAAC

                *  **                               **               *    ** 
        431 AACTATTACTCTTTGAATT--AAACTTATTTATGTGAGAACGGTTTCTCTCTTGGTTGTTGGTTG
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

                   *        *         *        *     *    **       *         
        494 AACTTC-CAAGCCTT-CCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCCTTACAGTATTCAA
         66 AACTTCTGAA--CTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA

            *                                  *                             
        557 AACGATCCATTCCTTC--G----------AACATTTCATGCTC-AGGAAATCGCATCATTTGGTC
        129 GACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGA-GAAATCGCATCATTTGGTC

                                    
        609 CAAATAGTTTGTCATTTTGTAAAC
        193 CAAATAGTTTGTCATTTTGTAAAC

                                             *  * *   *       *          ** *
        633 AACTTTTGGT-TTTAGAATTAAAAACTTATTTACGTAATAATGGTTTCTCCCTTGGTTCTTTACT
          1 AACTTTTGGTCTTT-GAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC

            *               *                *     *   *  *                  
        697 AAACTT-TCGAACTTGCCAAACTTTTACGAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAA
         65 GAACTTCT-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA

               *  *     *              *                *           *    **  
        761 GACAATTCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAAGT-GCATAATTTTTTC
        129 GACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAGAAA-TCGCATCATTTGGTC

                  *   *  *      *  *
        825 CAAATATTTTATCCTTTTGTTAAT
        193 CAAATAGTTTGTCATTTTGTAAAC

                      *                                          *        *  
        849 AACTTTTGGTGTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTAGTTCTTGGTCG
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

                                    * *                                 * *  
        914 AACTTCTGAACTTGTCAAACTTTTTCAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTTAGGA
         66 AACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA

                 *                   *       *   *          *                
        979 CGATCGATTCCTTCGAGCAATTTTCCAAACATTTCATTCTCGAGAAATTGCATCATTTGGTCCAA
        131 CGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAA

                  *     *        *
       1044 ATAGTTAGTTC-CTTTGTAAAA
        196 ATAGTTTG-TCATTTTGTAAAC

                                            *         *       *  *     *    *
       1065 AACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCTCTTTTAGTTCTAGGCCA
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

                    *     *                 *            *        *          
       1130 AACTT-TCAAACTTTTCAAACATTTT-CGAGTCCTTTTATAACTTTGGTTCCTTTAAGTATTCAA
         66 AACTTCT-GAACTTGTCAAAC-TTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAA

            *                  *             *   * * *                     * 
       1193 TACGATCCATTTCC-TCGAACAATTTT-TCAAATATTTCGTTCTCGAGAAATCGCATCATTTGAT
        129 GACGATCCA-TTCCTTCGAGCAATTTTCT-AAACATTCCATGCTCGAGAAATCGCATCATTTGGT

                 * * *               
       1256 CCAAAGAATCTGTCATTTTGTAAAC
        192 CCAAATAGTTTGTCATTTTGTAAAC

                           *        *        *                               
       1281 AACTTTTGGTCTTTGGATTAAAAATTTATTTATATGAGAATTGTTT-TCTCTTGGTTCTTGGCCG
          1 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG

                                                         *                   
       1345 AACTTCTGAACTTGTCAAA-TTTCT-CGAGTTCTTTTATAACTTCAGTTCCTTAAAGTATTCAAG
         66 AACTTCTGAACTTGTCAAACTTT-TACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG

                 
       1408 ACGAT
        130 ACGAT


Statistics
Matches: 970,  Mismatches: 192, Indels: 72
        0.79            0.16        0.06

Matches are distributed among these distances:
 201    4  0.00
 202   59  0.06
 203    3  0.00
 204   92  0.09
 205    2  0.00
 206    1  0.00
 212    1  0.00
 213    5  0.01
 214  211  0.22
 215   38  0.04
 216  539  0.56
 217   15  0.02

ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41


Consensus pattern (216 bp):   
AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG
AACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAA
ATAGTTTGTCATTTTGTAAAC

Done.