Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011919.1 Kokia drynarioides strain JFW-HI SEQ_126917, 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: 11204
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26


Found at i:557 original size:13 final size:13

Alignment explanation


    Indices: 539--565  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        529 AATGATGGAG

                         
        539 TTAGAGGAGTCAC
          1 TTAGAGGAGTCAC

                         
        552 TTAGAGGAGTCAC
          1 TTAGAGGAGTCAC

             
        565 T
          1 T

        566 GCGTAGACAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26


Consensus pattern (13 bp):   
TTAGAGGAGTCAC

Found at i:9769 original size:208 final size:208

Alignment explanation


    Indices: 9217--9942  Score: 882
    Period size: 208  Copynumber: 3.5  Consensus size: 208

       9207 TCAGATAGAA

                        *   *           *          *   **                  * 
       9217 GAGTGAAACTTTTGAATCCCAACTTCCTAATGAGATACTGAGATCCAGGTCGAAGCAATAAAATG
          1 GAGTGAAAC-TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACG

                              **         *        *                *         
       9282 GTCATCTTCCTGACGAGACGCAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAG
         65 GTCATCTTCCTGACGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATA-AGAGAAG

                         * * *                         *                *    
       9347 TGGATTAAAACAAATAAAGCGGTCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCGATGA
        129 TGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGA

                           
       9412 AGCAAAGCTCAATGT
        194 AGCAAAGCTCAATGT

                                                        *    *           *** 
       9427 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGAAGGTTGAAGCAATAAATTTG
          1 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG

                              *             *               *          *    *
       9492 TCATCTTCCTGACGAGATGCAG-GAAGT-GAATCAAATCCGTCTTCCTAATGAGATACAAAGAAC
         66 TCATCTTCCTGACGAGATACAGAGAAGTAG-ACCAAATCCGTCTTCCTGATGAGATA-AGAGAAG

                                *           *         *                      
       9555 TGGATTAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGA-AAGTAGACCAAATCAATGA
        129 TGGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGA

                           
       9619 AGCAAAGCTCAATGT
        194 AGCAAAGCTCAATGT

                          **    *                 *                         *
       9634 GAGTGAAACTTCGAGTCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGA
          1 GAGTGAAACTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG

               *        *       *                  *                         
       9699 TCACCTTCCTGATGAGATACTGAGAAGTAGACCAAATCCATCTTCCTGATGAGATAAGGAGAAGT
         66 TCATCTTCCTGACGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATAA-GAGAAGT

                                                                 * *         
       9764 GGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACTAGATCAAATGA
        130 GGATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATC-AATGA

              *    *       
       9829 AGAAAAGTTCAATGT
        194 AGCAAAGCTCAATGT

                   *   **        *              * *      *    *           *  
       9844 GAGTGAAGCTTTAAACCCCTATCTTCCTGATGAGATGCAAAGAAGTAGGTTGAAGCAATAAAGCG
          1 GAGTGAAACTTCGAACCCC-AACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAACG

                        **                    
       9909 GTCATCTTCCTGGTGAGATACAGAGAAGTAGACC
         65 GTCATCTTCCTGACGAGATACAGAGAAGTAGACC

       9943 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.