Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012504.1 Kokia drynarioides strain JFW-HI SEQ_127508, 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, 969

Length: 1616
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28


Found at i:855 original size:438 final size:431

Alignment explanation


    Indices: 5--1616  Score: 1489
    Period size: 438  Copynumber: 3.7  Consensus size: 431

          1 TTCT

                           * *      *  *   *         ***       *           * 
          5 CGAGCATGGAATGTTTGGAATATTTCTTGAAAGAATGGATCACCTTGAATACTTTAAGGAAC-CA
          1 CGAGCATGGAATGTTCGAAATATTGCTCGAAGGAATGGATCGTATTGAATAGTTTAAGGAACTGA

                *            *            *                *                 
         69 ATGTCATAA-AAGAACTTGTAAAAGCTTGAAAAGTTCAGAAGTTCATTTAAGAACCAAGAGAGAA
         66 A-GTTATAAGAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAGAGAA

                       *                        *                            
        133 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAATGACAAAATAT
        130 ACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAATAT

                               *   *                 *              *  *     
        198 TTAGACC-AAGTGATGCGAATTCTCGAGCATGGAATGTTCGCAAAATTGCTCGAAGAAACGGATC
        195 TTAGACCGAA-TGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATC

            *           * **      *               * *          **        *   
        262 ATCTTGAATACTTTGTGGAACCGAAGTTA-AAACAGAAATAGTAAAAGTTTTCCTAGTTCAAAAG
        259 GTCTTGAATACTCTAAGGAACCAAAGTTATAAA-AG-ACTCGTAAAAGTTTGACTAGTTCAGAAG

                                               *             *   * **        
        326 TTCGTCCAAGAACCAAGAGAGAAACAATT-TACACATAAATAAGTATTTAATTCAGTGACCAAAA
        322 TTCGTCCAAGAACCAAGAGAGAAACAATTCT-CACGTAAATAAGT-TTTTATTTAAAGACCAAAA

                *    *     * *          *    *               
        390 GTTTTTTTTAAGAAACGGCAAACTATTTTGACCGAATGATGCGATTTCC
        385 G-TTGTTTTCA-AAATGACAAACTATTTAGACCAAATGATGCGATTTCC

                         *                    *      *                       
        439 CGAGCATGGAATGGTCGAAATATTGCTCGAAGGATTGGATCATATTGAATAGTTTAAGGAACTGA
          1 CGAGCATGGAATGTTCGAAATATTGCTCGAAGGAATGGATCGTATTGAATAGTTTAAGGAACTGA

                            * *                          **        **  *     
        504 AGTTATTACAGAAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAATGAAAAGAGA
         66 AGTTA-TA-AGAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAGAGA

              *           *                   *    *           *            *
        569 AATAATTCTCACATTAATATA-TTTTTAATTCAAGGACTAAAAAGTTGTTTGCAAAATGACAAAC
        129 AACAATTCTCACATAAATA-AGTTTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGACAAAA

              *                *            *             *    * *           
        633 TAGTTAGACCGAATGATGCTATTTCCCGAGCACGGAATGTTCGGAATATTGATTGAAGGAATGGA
        192 TATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGA

             *                                                *              
        698 TTGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGGACTCGTAAAAAGCTTGACTAGTTCAGA
        257 TCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAA-GACTCGT-AAAAGTTTGACTAGTTCAGA

                 *  *                                   *           *        
        763 AGTTCATCTAAGAACCAA-AGGAGAAACAATTCTCACGTAAATATGTTTTTAGTTTGAAGACCAA
        320 AGTTCGTCCAAGAACCAAGA-GAGAAACAATTCTCACGTAAATAAGTTTTTA-TTTAAAGACCAA

              *                                  *     *     *
        827 AACTTAGTTTTCAAAATGACAAACTATTTAGACCAAAAGATGCAATTTCT
        383 AAGTT-GTTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCC

                            *             *  *  *    *  *       *          * 
        877 CGAGCATGGAATGTTTGGAAA-ATTGCTCGTAGAAACGGATGGTCTTGAATACTTTAAGGAACCG
          1 CGAGCATGGAATG-TTCGAAATATTGCTCGAAGGAATGGATCGTATTGAATAGTTTAAGGAACTG

                        *            *  *        * *    *   *               *
        941 AAGTTATAA-AATAACTCGTAAAAGTTTTACAAGTTCGGTAGTTAATCCAAGAACCAAGAGAGAG
         65 AAGTTATAAGAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAGAGAA

                  *                    *      *                          *   
       1005 ACAATTTTCACATAAATAAGTTTTTAACTCAAAGGCCAAAAGTTGTTTACAAAATGACAAACTAT
        130 ACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAATAT

               *   *  *   *             *                          *         
       1070 TTAAACCAAAAGATTCGATTT-CCGCAGAATGGAATGTTC-GAAAATTGCTCG-ATGAAGTGGAT
        195 TTAGACCGAATGATGCGATTTCCCG-AGCATGGAATGTTCGGAAAATTGCTCGAAGGAA-TGGAT

               * *    *     *            *     *   *     *             *   * 
       1132 CATTTATATATAATACACTTCAAGGAACCGAAGTTTTAACA-ACTTGTAAAAGTTTGACAAGTCC
        258 C--GTCT-T-GAATACTC-T-AAGGAACCAAAGTTATAAAAGACTCGTAAAAGTTTGACTAGTTC

            *                               *  *     *               *       
       1196 GGAAGTTCGTCCAAGAACCAAGAGAGAAACAAATCGCACGTCAATAAGTTTTTAATTCAAAGACC
        317 AGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT-ATTTAAAGACC

                      **                         *              * 
       1261 AAAAGTTGTTCACAAAATGACAAACTATTTAGATCAAAAAATGATGCGATTTTC
        381 AAAAGTTGTTTTCAAAATGACAAACTATTTAGA-C--CAAATGATGCGATTTCC

                      *             *     *              *  *                
       1315 CGA--ATGTTAAATGTTCGAAAATTTTG-TAGAAGGAATGGATCGCATAGAAT-GCTTTAAGGAA
          1 CGAGCATG--GAATGTTCG-AAATATTGCTCGAAGGAATGGATCGTATTGAATAG-TTTAAGGAA

                     *       *           *           *                *      
       1376 CCT-AAGTTGT-AGAAGGACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCTAAGAAACAAGAG
         62 -CTGAAGTTATAAGAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAG

                           *                                                 
       1439 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAA
        126 AGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAA

                                      * *             *    *   *  *   *     *
       1504 ATATTTAGACCGAATGATGCGATTTCTCAAGCATGGAATGTTTGGAATATTTCTTGAAAGAATGA
        191 ATATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGG

                *          *           *  *                 
       1569 ATCGCCTTGAATACTTTAAGGAACCAATGTCATAAAAGATCTCGTAAA
        256 ATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGA-CTCGTAAA


Statistics
Matches: 941,  Mismatches: 196, Indels: 81
        0.77            0.16        0.07

Matches are distributed among these distances:
 432    4  0.00
 433   32  0.03
 434  112  0.12
 435  111  0.12
 436   80  0.09
 437   96  0.10
 438  385  0.41
 439  116  0.12
 440    5  0.01

ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28


Consensus pattern (431 bp):   
CGAGCATGGAATGTTCGAAATATTGCTCGAAGGAATGGATCGTATTGAATAGTTTAAGGAACTGA
AGTTATAAGAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAGAGAAA
CAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAATATT
TAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGT
CTTGAATACTCTAAGGAACCAAAGTTATAAAAGACTCGTAAAAGTTTGACTAGTTCAGAAGTTCG
TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTATTTAAAGACCAAAAGTTGTT
TTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCC
Done.