Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012498.1 Kokia drynarioides strain JFW-HI SEQ_127502, 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, 853

Length: 1422
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40


Found at i:55 original size:2 final size:2

Alignment explanation


    Indices: 37--81  Score: 63
    Period size: 2  Copynumber: 22.5  Consensus size: 2

         27 GATAAACCTT

                     *        *                  *                        
         37 TA TA TA AA TA TA CA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
         79 TA T
          1 TA T

         82 TGACATCATC


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:516 original size:251 final size:251

Alignment explanation


    Indices: 63--532  Score: 692
    Period size: 251  Copynumber: 1.9  Consensus size: 251

         53 TATATATATG

                                                                           * 
         63 TATATATATATATATATATTGACATCATCTTAGCAATTTATATATTGACATTTGTCATTACTCGA
          1 TATATATATATATATATATTGACATCATCTTAGCAATTTATATATTGACATTTGTCATTACTCAA

             *  *        *                    *    *         *  *          * 
        128 TGTCGAAATGAACTTGTATATATTCTCTCCTCCCTCTCAGATAAACTTAGTTTTTCTCCCATTCA
         66 TCTCAAAATGAACCTGTATATATTCTCTCCTCCCACTCAAATAAACTTAATTCTTCTCCCATTAA

             *       *       *  *                              *             
        193 ATCTTATTTCTTCTCTTCTCTCATTTCTTCATCTTTTTCTCTTTGTTAGTTTATATAAAGATGAT
        131 AACTTATTTATTCTCTTATCCCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATATAAAGATGAT

            *          *                                            
        258 TAAAGGAAAAGGAAAAGTGAGTAATGAGGTTGCTTCCAAACCTTCAGTTAAACCTT
        196 GAAAGGAAAAGAAAAAGTGAGTAATGAGGTTGCTTCCAAACCTTCAGTTAAACCTT

                     *             *                              *  *       
        314 TATATATATGTATATATATTGACGTCATCTTAG-AATTATATATATTGACATTTTTCTTTACTCA
          1 TATATATATATATATATATTGACATCATCTTAGCAATT-TATATATTGACATTTGTCATTACTCA

                                              *                              
        378 ATACT-AAAATGAACCTGTATATATTCTCTCCTCTCACTCAAATAAACTTAATTCTTCTCCCATT
         65 AT-CTCAAAATGAACCTGTATATATTCTCTCCTCCCACTCAAATAAACTTAATTCTTCTCCCATT

                            *                                         *  *   
        442 AAAACTTATTTATTCTTTTATCCCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATATTAATATG
        129 AAAACTTATTTATTCTCTTATCCCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATATAAAGATG

                                      
        507 ATGAAAGGAAAAGAAAAAGTGAGTAA
        194 ATGAAAGGAAAAGAAAAAGTGAGTAA

        533 AAAGCCTGTT


Statistics
Matches: 193,  Mismatches: 24, Indels: 4
        0.87            0.11        0.02

Matches are distributed among these distances:
 250    4  0.02
 251  188  0.97
 252    1  0.01

ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43


Consensus pattern (251 bp):   
TATATATATATATATATATTGACATCATCTTAGCAATTTATATATTGACATTTGTCATTACTCAA
TCTCAAAATGAACCTGTATATATTCTCTCCTCCCACTCAAATAAACTTAATTCTTCTCCCATTAA
AACTTATTTATTCTCTTATCCCATTTCTTCATCTTTTTCTCTTTGTTAGTTGATATAAAGATGAT
GAAAGGAAAAGAAAAAGTGAGTAATGAGGTTGCTTCCAAACCTTCAGTTAAACCTT

Found at i:1135 original size:125 final size:124

Alignment explanation


    Indices: 987--1235  Score: 471
    Period size: 125  Copynumber: 2.0  Consensus size: 124

        977 GTACAATAAT

                                    *                                        
        987 ATAATTTAAAAAAATTAATCCTATTCAATTTAAATAAAATGATGATCCGTAAAAGAATTTATGTA
          1 ATAATTTAAAAAAATTAATCCTATCCAATTTAAATAAAATGATGATCCGTAAAAGAATTTATGTA

                                          *                            
       1052 ACTTATTACGTGTTGGTTTATCATTTAAAGTACATTAAAGTAGTATTTATATTTCATAC
         66 ACTTATTACGTGTTGGTTTATCATTTAAAGCACATTAAAGTAGTATTTATATTTCATAC

                                                                             
       1111 ATAATTTTAAAAAAATTAATCCTATCCAATTTAAATAAAATGATGATCCGTAAAAGAATTTATGT
          1 ATAA-TTTAAAAAAATTAATCCTATCCAATTTAAATAAAATGATGATCCGTAAAAGAATTTATGT

                                                                        
       1176 AACTTATTACGTGTTGGTTTATCATTTAAAGCACATTAAAGTAGTATTTATATTTCATAC
         65 AACTTATTACGTGTTGGTTTATCATTTAAAGCACATTAAAGTAGTATTTATATTTCATAC

       1236 CGAACATTCA


Statistics
Matches: 122,  Mismatches: 2, Indels: 1
        0.98            0.02        0.01

Matches are distributed among these distances:
 124    4  0.03
 125  118  0.97

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40


Consensus pattern (124 bp):   
ATAATTTAAAAAAATTAATCCTATCCAATTTAAATAAAATGATGATCCGTAAAAGAATTTATGTA
ACTTATTACGTGTTGGTTTATCATTTAAAGCACATTAAAGTAGTATTTATATTTCATAC

Done.