Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003194.1 Kokia drynarioides strain JFW-HI SEQ_115807, 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: 2314
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25


Found at i:739 original size:208 final size:208

Alignment explanation


    Indices: 187--912  Score: 882
    Period size: 208  Copynumber: 3.5  Consensus size: 208

        177 TCAGATAGAA

                        *   *           *          *   **                  * 
        187 GAGTGAAACTTTTGAATCCCAACTTCCTAATGAGATACTGAGATCCAGGTCGAAGCAATAAAATG
          1 GAGTGAAAC-TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACG

                              **         *        *                *         
        252 GTCATCTTCCTGACGAGACGCAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAG
         65 GTCATCTTCCTGACGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATA-AGAGAAG

                         * * *                         *                *    
        317 TGGATTAAAACAAATAAAGCGGTCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCGATGA
        129 TGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGA

                           
        382 AGCAAAGCTCAATGT
        194 AGCAAAGCTCAATGT

                                                        *    *           *** 
        397 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGAAGGTTGAAGCAATAAATTTG
          1 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG

                              *             *               *          *    *
        462 TCATCTTCCTGACGAGATGCAG-GAAGT-GAATCAAATCCGTCTTCCTAATGAGATACAAAGAAC
         66 TCATCTTCCTGACGAGATACAGAGAAGTAG-ACCAAATCCGTCTTCCTGATGAGATA-AGAGAAG

                                *           *         *                      
        525 TGGATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGA-AAGTAGACCAAATCAATGA
        129 TGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGA

                           
        589 AGCAAAGCTCAATGT
        194 AGCAAAGCTCAATGT

                          **    *                 *                         *
        604 GAGTGAAACTTCGAGTCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGA
          1 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG

               *        *       *                  *                         
        669 TCACCTTCCTGATGAGATACTGAGAAGTAGACCAAATCCATCTTCCTGATGAGATAAGGAGAAGT
         66 TCATCTTCCTGACGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATAA-GAGAAGT

                                                                 * *         
        734 GGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACTAGATCAAATGA
        130 GGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATC-AATGA

              *    *       
        799 AGAAAAGTTCAATGT
        194 AGCAAAGCTCAATGT

                   *   **        *              * *      *    *           *  
        814 GAGTGAAGCTTTAAACCCCTATCTTCCTGATGAGATGCAAAGAAGTAGGTTGAAGCAATAAAGCG
          1 GAGTGAAACTTCGAACCCC-AACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACG

                        **                    
        879 GTCATCTTCCTGGTGAGATACAGAGAAGTAGACC
         65 GTCATCTTCCTGACGAGATACAGAGAAGTAGACC

        913 GAGCGATGAA


Statistics
Matches: 442,  Mismatches: 67, Indels: 13
        0.85            0.13        0.02

Matches are distributed among these distances:
 207  108  0.24
 208  145  0.33
 209   80  0.18
 210   41  0.09
 211   68  0.15

ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23


Consensus pattern (208 bp):   
GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG
TCATCTTCCTGACGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATAAGAGAAGTG
GATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGAAG
CAAAGCTCAATGT
Done.