Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008219.1 Kokia drynarioides strain JFW-HI SEQ_122883, 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: 1681
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41


Found at i:384 original size:216 final size:216

Alignment explanation


    Indices: 6--1681  Score: 1779
    Period size: 216  Copynumber: 7.8  Consensus size: 216

          1 TTGTA

                         *                          *  *      *  *        *  
          6 TTTGAATTAAAAAGTTATTTACA-TGAGAATTGTTTCTCTATTAGTTCTTTGCAGAACTTTCGAA
          1 TTTGAATTAAAAACTTATTTA-AGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAA

                           *             **     *       *          *         
         70 CTTGTCAAACTTTTACGAGTTCTTTTATATTTTTGGGTCCTTAAGGTATTCAAGATGATCCATTC
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

                   *      *                       *             **  *        
        135 CTTCGAGTAATTTTACGAACATTCCATGCTCGGGAAATTGCATCATTTGGTCTGAAGAGTTTGTC
        130 CTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTC

                      *       *   
        200 ATTTTGTAAAGAACTTTTTGTC
        195 ATTTTGTAAACAACTTTTGGTC

               *                    *                          *  *  *   **  
        222 TTTAAATTAAAAACTTATTTAAGTAAGAATTGTTTCTCT-TGTGGTTCTTGCCCAAATTTTTGAA
          1 TTTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCT-TGGTTCTTGGCCGAACTTTCAAA

                                          *   *            *                 
        286 CTTGTCAAACTTTTATGAGTTCTTTTATAAATTTTGTTCCTTAAAGTTTTCAAGACGATCCATTC
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

                                               *    *        ** *            
        351 CGTT-GAGCAATTTTTCGAACATTCCATGCTCGGGGAATCACATCATTTATTGCAAATAGTTTGT
        130 C-TTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGT

                                   
        415 CATTTTGTAAACAACTTTTGGTC
        194 CATTTTGTAAACAACTTTTGGTC

            *        *           *         *         *                    *  
        438 ATTGAATTACAAACTTATTTACGTGAGAATTATTTCTCTCTGGGTTCTTGGCCGAAC-TTCTGAA
          1 TTTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-AAA

                                         *   *                  *  *      *  
        502 CTTGTCAAACTTTTATGAGTTCTTTTATATCTTAGGTTCCTTAAAGTATTCAGGATGATCCAATC
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

                *    *     *   *       *   *           *  *  *      *        
        567 CTTCAAGCACTTTTTAGAAAATTCCATACTCTGGAAATCGCATTATCTGATCCAAAAAGGTTT-T
        130 CTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATA-GTTTGT

            *              *        
        631 TATTTTGTAAACAAAATTTT-GTC
        194 CATTTTGTAAAC-AACTTTTGGTC

                              *  *                      **             *     
        654 TTTGAATTAAAAACTTATCTACGTGAGAATTGTTTCTCTCTTGGGACTTGGCCGAACTTCCAAAC
          1 TTTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAAC

             *       *  *                      *                    *   *    
        719 TAGTCAAACATTGACT-AGTT-TTGTTATAACTTTTGTTCCTTAAAGTATTCAAGATGATACATT
         66 TTGTCAAACTTTTA-TGAGTTCTT-TTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATT

                                                         *                   
        782 CCTGT-GAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATAATTTGGTCCAAATAGTTTG
        129 CCT-TCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTG

                             *    *  *
        846 TCAATTTTGTAAGA-AATTTTTTGTA
        193 TC-ATTTTGTAA-ACAACTTTTGGTC

                                            *    *  *   *        *        *  
        871 TTTGAATTAAAAACTTATTTAAGTGAGAATTCTTTTCACTGTTGATTCTTGGCTGAACTTTCGAA
          1 TTTGAATTAAAAACTTATTTAAGTGAGAATT-GTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAA

                            *             *    *                     *  *   *
        936 CTTGTCAAACTTTTATTAGTTCTTTTATAATTTTGTTTCCTTAAAGTATTCAAGACGGTCTATTG
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

               *      *      *        *    *        *               *        
       1001 CTTGGAG-AAATTTTCAAAACATTCCGTGCTTGGGAAATCACATCATTTGGTCCAATTAGTTT-T
        130 CTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGT

               *                    
       1064 CCACTTTGTAAACAACTTTTGGTC
        194 -CATTTTGTAAACAACTTTTGGTC

                      *                          *             ***           
       1088 TTTGAATTAAGAACTTATTTACA-TGAGAATTGTTTCACTCTT-GTTCTTGATTGAACTTTCAAA
          1 TTTGAATTAAAAACTTATTTA-AGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAA

               *                                    *              *         
       1151 CTTTTCAAA-TTTTATGAGTTCTTTTATAACTTTGGTTCCATAAAGTATTCAAGATGATCCATTC
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

             *              *            *          *  *     *               
       1215 TATTC-AGCAATTTTTTGAACATTCCATGGTCGGGAAATCACACCATTTAGTCCAAATAGTTTGT
        130 -CTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGT

                                   
       1279 CATTTTGTAAACAACTTTTGGTC
        194 CATTTTGTAAACAACTTTTGGTC

                      *      *   *                      *       **           
       1302 TTTGAATTAATAACTTCTTTTCAG-GAGAATTGTTTCTCTCTT-TTTCTTGGTTGAACTTTCAAA
          1 TTTGAATTAAAAACTT-ATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAA

               *     *     * *    *    *     *                               
       1365 CTTTTCAAAATTTTACGGGTTCCTTTACAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTC
         65 CTTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

             *  *           *           *                       *            
       1430 CATCCAGCAATTTTTCAAACATTCCATGGTCGGGAAATCGCATCATTTGGTCGAAATAGTTTGTC
        130 CTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTC

            *        *           *
       1495 CTTTTGTAAGCAACTTTTGGTA
        195 ATTTTGTAAACAACTTTTGGTC

                            *   ** *               *      *  *         *     
       1517 TTTGAATTAAAAACTTCTTTCGGGGAGAATTGTTTCTCTGTTGGTTTTTTGCCGAACTTCCAAAC
          1 TTTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAAC

              *       *    *                                 *               
       1582 TTAT-AGAACCTTTACGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATCCAAGACGATCCATTC
         66 TTGTCA-AACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTC

                               *   *            
       1646 CTTCGAGCAATTTTTCGAAAATTTCATGCTCGGGAA
        130 CTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAA


Statistics
Matches: 1220,  Mismatches: 206, Indels: 68
        0.82            0.14        0.05

Matches are distributed among these distances:
 214  178  0.15
 215  203  0.17
 216  605  0.50
 217  111  0.09
 218  121  0.10
 219    2  0.00

ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41


Consensus pattern (216 bp):   
TTTGAATTAAAAACTTATTTAAGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCAAAC
TTGTCAAACTTTTATGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCC
TTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCA
TTTTGTAAACAACTTTTGGTC

Done.