Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006622.1 Kokia drynarioides strain JFW-HI SEQ_121212, 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: 4375
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:2538 original size:579 final size:577

Alignment explanation


    Indices: 1428--2571  Score: 1467
    Period size: 579  Copynumber: 2.0  Consensus size: 577

       1418 GCCCCTAAAT

                        **                    *                  *    *      
       1428 GTACTCCCGTTCGGTGTAGATTTAAGCTTTCTGCTAGTATACGAGACAAGTTGTAAATGTAGTGT
          1 GTACTCCCGTTCAATGTAGATTTAAGCTTTCTGCAAGTATACGAGACAAGTTGAAAATATAGTGT

                     *      *                                        *       
       1493 GTTACAACGGAACATTTAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCGATAGTAA
         66 GTTACAACGAAACATTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCAATAGTAA

                                                                             
       1558 ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA
        131 ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA

                        *                        *               *           
       1623 AAGTGTTTTGAGTGCATAAAAATAAAAAGATAAAATAGAATAGAAAATAAAAGCAAAAGATTGAG
        196 AAGTGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAG

            **                **          **             *         * *    *  
       1688 TTGTAGAAATCTTATAAATGGCTTTGGGGATTTTAGGTCGTTTCCGTATGAGTTATTTAATTTTT
        261 AAGTAGAAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTGAATTGTT

            *                                                *               
       1753 TGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATCTCTTGATCTTCTGCC
        326 GGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATCTTCTGCC

                 *   *                   *                                  *
       1818 AGCATGGCATGCCGATAGAGATTACTTATTGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAG
        391 AGCATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAA

            *       *                              *    *               *  * 
       1883 GGTGTTCATGGATGGACAATACCAATTTTGGGTTCATTCTCACCTAGATGACTTTCTAAGTTTGT
        456 CGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTTCTAAGGTTAT

                              * *           *                        
       1948 CAAACCTAGTGTTTGTTCGATGCTCTTCCTTTTCCAAATAGCTGACTGCCCCCGAAC
        521 CAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGACTGCCCCCGAAC

                                   **                   * ** *               
       2005 GTACTCCCGTTCAATGTAGATTTTGGCTTT-TCGCAAGTATACGGGTTAGGTTGAAAATATAGTG
          1 GTACTCCCGTTCAATGTAGATTTAAGCTTTCT-GCAAGTATACGAGACAAGTTGAAAATATAGTG

                                      *   *                                  
       2069 TGTTACAACGAAACACTTGA-TAGTATTCCGAGGATCGTACCCAAAGGAGGCTT-AAGACAATAG
         65 TGTTACAACGAAACA-TTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAG-CAATAG

                 **   *                          *  *                 *  *   
       2132 TAAATTGAATCCCTGCAAAGAGTAAAATTAATTAGTACTTGTTTTAGGGTTTATAGTATGAGAAA
        128 TAAATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAA

                                *     *                      *               
       2197 TAAAAGAGTTGTTTTGAGAGTATAAATAT-AAAAGAT-AAATAAAATAGGAAATAAAAGAAAAAG
        193 T-AAA-AG-TGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAG

            *                                            *           **  *   
       2260 TTTGAGAAGTAGAAAATCTTATAAACAGCTTTGGGGAAATTAGGTTGTTTCCATATGCTTTCCTG
        255 ATTGAGAAGTAG-AAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTG

            *        *     *       *  *                                   *  
       2325 GATTGTTGGGTTTTGGGGATTTTCCTTCAATCAACTAGTCACTACCCTAGTTGGATATCTTGGTC
        319 AATTGTTGGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATC

                  *             *                                            
       2390 TT-TCGTC-GACATAGCAAGTCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAA-TCGGT
        384 TTCT-GCCAG-CATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACT-GGT

                                     **                 *                    
       2452 TTGGGGAAAACGTGTTCAAGGATGGGTAATACCAATTTTGGGTTGATTCCCACCGAGATGACTTT
        446 TTGGGGAAAACGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTT

               *        ***                 *                      
       2517 CTAGGGTTATCAGGTCTAGTGTTTGTTCAACGTTCTTCCTTTCCCAAATAGCTGA
        511 CTAAGGTTATCAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGA

       2572 TTCGAAACGT


Statistics
Matches: 482,  Mismatches: 75, Indels: 18
        0.84            0.13        0.03

Matches are distributed among these distances:
 576    4  0.01
 577  160  0.33
 578   42  0.09
 579  259  0.54
 580   17  0.04

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33


Consensus pattern (577 bp):   
GTACTCCCGTTCAATGTAGATTTAAGCTTTCTGCAAGTATACGAGACAAGTTGAAAATATAGTGT
GTTACAACGAAACATTGAGTAGTACTCCAAGGATCGTACCCAAAGGAGGCTTAAAGCAATAGTAA
ATCAAATACCTGCAAAGAGTAAAATTAATTAGTAATTATTTTAGGGTTTATAGTACGAAAAATAA
AAGTGTTTTGAGAGCATAAAAATAAAAAGATAAAATAAAATAGAAAATAAAAGAAAAAGATTGAG
AAGTAGAAATCTTATAAACAGCTTTGGGGAAATTAGGTCGTTTCCATATGAGTTACTGAATTGTT
GGATTTTGAGGATTTTACTCCAATCAACTAGTCACTACCCTAGTTGGATATCTTGATCTTCTGCC
AGCATAGCAAGCCGATAGAGATTACTTATCGCTAGATGTCACAATCTAAACTGGTTTGGGGAAAA
CGTGTTCAAGGATGGACAATACCAATTTTGGGTTCATTCCCACCGAGATGACTTTCTAAGGTTAT
CAAACCTAGTGTTTGTTCAACGCTCTTCCTTTCCCAAATAGCTGACTGCCCCCGAAC
Done.