Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010001.1 Kokia drynarioides strain JFW-HI SEQ_124759, 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: 1993
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.26

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:649 original size:349 final size:347

Alignment explanation


    Indices: 1--952  Score: 1356
    Period size: 349  Copynumber: 2.7  Consensus size: 347

                                                     *       *              *
          1 ATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTACAAACTTGCGATAAATAAAATAG
          1 ATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTGCAAACTTACGATAAATAAAATAA

                               *      * *        *             *             
         66 TACAAAAAGAAAAAAAAACTAAAAGAGGGGTGCAACATGAGGACTTCCCAGAAGGTCACCCATCC
         66 TACAAAAAGAAAAAAAAACAAAAAGAAGAGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCC

                     *      *      *    *                                    
        131 TAGTACTACCCTCGCCAAAGCACGCTTAGCTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCT
        131 TAGTACTACTCTCGCCCAAGCACACTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCT

            *        *    * *      *         *          *       *            
        196 AGTATGATCGCACCCACTATGTTTTGCGCAATCAATTTACATAAGGGCTACCATTCATCCCATTC
        196 GGTATGATCACACCTATTATG-TCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTC

                                                                             
        261 GTGCCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGAAAGACGTATTTTCGCGGATAAA
        260 GTGCCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGAAAGACGTATTTTCGCGGATAAA

                                   
        326 AATAAAATAAAAACACGCTAATA
        325 AATAAAATAAAAACACGCTAATA

                     *                                 *                     
        349 ATGTCCATTTTATCCCATGAAGCTTTACTATTTCGCAAAATTGTAAACTTACGATAAATAAAATA
          1 ATGTCCA-TGTATCCCATGAAGCTTTACTATTTCGCAAAATTGCAAACTTACGATAAATAAAATA

                                               *   *                         
        414 ATACAAAAAGAAAAAAAAACAAAAAGAAGAGTGCAGCACAAGGACTT-CCACGGAGGTCACCCAT
         65 ATACAAAAAGAAAAAAAAACAAAAAGAAGAGTGCAACACGAGGACTTCCCA-GGAGGTCACCCAT

                          *                                       *          
        478 CCTAGTACTACTCTTGCCCAAGCACACTTAACTGCGGAGTTCTGATGGGATCCGATGCATTAGTG
        129 CCTAGTACTACTCTCGCCCAAGCACACTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTG

                *      *                                          *          
        543 CTGGAATGATCTCACCTATTATGTCCAT-CGCAATCTATTTACATAAAGGCTACTTTTCATCCCA
        194 CTGGTATGATCACACCTATTATGT-C-TGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCA

                             *                           *              *    
        607 TTCGTGCCTCGAATTTGGATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGAT
        257 TTCGTGCCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGAAAGACGTATTTTCGCGGAT

                               **     
        672 AAAAATAAAATAAAAACACTTTAATA
        322 AAAAATAAAATAAAAACACGCTAATA

                          *  *    *  *                                       
        698 ATGTCCATGTATCCTATCAAGCATTGCTATTTCGCAAAATTGCAAACTTACGATAAATAAAATAA
          1 ATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTGCAAACTTACGATAAATAAAATAA

             *                *                               *              
        763 TGCAAAAAG-AAAAAAAATAAAAAGAAGAGTGCAACACGAGGACTTCCCAAGAGGTCACCCATCC
         66 TACAAAAAGAAAAAAAAACAAAAAGAAGAGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCC

               *                               *        * *                  
        827 TAGAACTACTCTCGCCCAAGCACGA-TTAACTGCGTAGTTCTGAAGAGATCCGGTGCATTAGTGC
        131 TAGTACTACTCTCGCCCAAGCAC-ACTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGC

                  *                             *    *               *     
        891 TGGTATTATCACA-CTCATTATGTGCTGCGCAATCTTTTTAAATAAAGGCTACCTTTGATCCC
        195 TGGTATGATCACACCT-ATTATGT-CTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCC

        953 GTTCNNNNNN


Statistics
Matches: 538,  Mismatches: 58, Indels: 17
        0.88            0.09        0.03

Matches are distributed among these distances:
 346    3  0.01
 347  152  0.28
 348   75  0.14
 349  307  0.57
 350    1  0.00

ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26


Consensus pattern (347 bp):   
ATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTGCAAACTTACGATAAATAAAATAA
TACAAAAAGAAAAAAAAACAAAAAGAAGAGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCC
TAGTACTACTCTCGCCCAAGCACACTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCT
GGTATGATCACACCTATTATGTCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTCG
TGCCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGAAAGACGTATTTTCGCGGATAAAA
ATAAAATAAAAACACGCTAATA

Found at i:1716 original size:349 final size:348

Alignment explanation


    Indices: 1007--1993  Score: 1424
    Period size: 349  Copynumber: 2.8  Consensus size: 348

        997 NNNNNNNNNN

                          *          *                                       
       1007 AAAAAGAAAAAAAATA-AAAAGAAGAGTGCAACACGAGGACTTCCCA-AGAGGTCACCCATCCTA
          1 AAAAAGAAAAAAAAAACAAAAGAAGGGTGCAACACGAGGACTTCCCAGA-AGGTCACCCATCCTA

                                  *    *    *        *       *               
       1070 GTACTACTCTCGCCCAAGCACGATTAATTGCGTAGTTCTGAAGGGATCCAGTGCATTAGTGCTGG
         65 GTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGG

               *                *           *    *               *  *  *     
       1135 TATTATCACACCCATTATGTGCTGCGCAATCTTTTTAAATAAAGGCTACCTTTGATTCCGTTCGT
        130 TATGATCACACCCATTATGTCCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTCGT

                                               *         *         *         
       1200 GCCTCGAATTTGAATGTAAATATGCCCAAATAATGTTCGGGAAGATGTATTTTCGCGGATAAAAA
        195 GCCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGAT-AAAA

             *                                                               
       1265 ACAAAATAAAAACACACTAATAATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTAC
        259 ATAAAATAAAAACACACTAATAATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTAC

                  *              *   
       1330 AAACTTGCGATAAATAAAATAGTAC
        324 AAACTTACGATAAATAAAATAATAC

                           *       *          *                              
       1355 AAAAAGAAAAAAAAACCAAAAGAGGGGTGCAACATGAGGACTTCCCAGAAGGTCACCCATCCTAG
          1 AAAAAGAAAAAAAAAACAAAAGAAGGGTGCAACACGAGGACTTCCCAGAAGGTCACCCATCCTAG

                  *   *  *           *                                       
       1420 TACTACCCTCACCAAAGCACGCTTAGCTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGT
         66 TACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGT

                  *      *     **  *      *          *       *               
       1485 ATGATCGCACCCACTATGTTTTGTGCAATCAATTTACATAAGGGCTACCATTCATCCCATTCGTG
        131 ATGATCACACCCATTATGTCCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTG

                                                   *                         
       1550 CCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGAAAGACGTATTTTCGTGGATAAAAAT
        196 CCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGATAAAAAT

                         *                                        *      **  
       1615 AAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTATTTCGTAAAATTGTAA
        261 AAAATAAAAACACACTAATAATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTACAA

                                   
       1680 ACTTACGATAAATAAAATAATAC
        326 ACTTACGATAAATAAAATAATAC

                                          * *   *             *              
       1703 AAAAAGAAAAAAAAAACAAAAAGAAGGGTGTAGCACAAGGACTT-CCAGGGAGGTCACCCATCCT
          1 AAAAAGAAAAAAAAAAC-AAAAGAAGGGTGCAACACGAGGACTTCCCA-GAAGGTCACCCATCCT

                       *          *                                          
       1767 AGTACTACTCTTGCCCAAGCACACTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTG
         64 AGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTG

             *      *    *         *                          *              
       1832 GAATGATCTCACCTATTATGTCCAGCGCAATCTATTTACATAAAGGCTACTTTTCATCCCATTCG
        129 GTATGATCACACCCATTATGTCCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTCG

                                                                             
       1897 TGCCTCGAATTT-AGATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGATAAA
        194 TGCCTCGAATTTGA-ATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGATAAA

                            **               
       1961 AATAAAATAAAAACACTTTAATAATGTCCATGT
        258 AATAAAATAAAAACACACTAATAATGTCCATGT


Statistics
Matches: 567,  Mismatches: 67, Indels: 9
        0.88            0.10        0.01

Matches are distributed among these distances:
 348  121  0.21
 349  445  0.78
 350    1  0.00

ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26


Consensus pattern (348 bp):   
AAAAAGAAAAAAAAAACAAAAGAAGGGTGCAACACGAGGACTTCCCAGAAGGTCACCCATCCTAG
TACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGT
ATGATCACACCCATTATGTCCTGCGCAATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTG
CCTCGAATTTGAATGTAAATATGCCCAAATAATGCTCGGGAAGACGTATTTTCGTGGATAAAAAT
AAAATAAAAACACACTAATAATGTCCATGTATCCCATGAAGCTTTACTATTTCGCAAAATTACAA
ACTTACGATAAATAAAATAATAC
Done.