Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009619.1 Kokia drynarioides strain JFW-HI SEQ_124335, 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: 2719
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30


Found at i:627 original size:72 final size:72

Alignment explanation


    Indices: 489--858  Score: 469
    Period size: 72  Copynumber: 5.1  Consensus size: 72

        479 TTTCAAATTG

                                           *                  *          * * 
        489 ATTAGATGTTGAATCCCCTCCGGAAGCGATGTTAAATTGGGCAAA--AACCAGAGAACAAGATAT
          1 ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAACGAGAG-A-AAGCTCT

                     
        552 TGCAGATTT
         64 TGCAGATTT

                                      *                      **          *   
        561 ATTAGATGTTGAATCCCCTCCGGAAGTGATGCTAAATTGGG-AAGATTATTGAGAGAAAGCCCTT
          1 ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAA-ATTAACGAGAGAAAGCTCTT

                    
        625 GCAGATTT
         65 GCAGATTT

                           **              *   *                       *     
        633 ATTAGATGTTGAATCGTCTCCGGAAGCGATGTTAACTTGGGCAAATTAACGAGAGAAAGATCTTG
          1 ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAACGAGAGAAAGCTCTTG

                   
        698 CAGATTT
         66 CAGATTT

                                 *                         **                
        705 ATTAGATGTTGAATCCCCTCCTGAAGCGATGCTAAATTGGGCAAATTCGCGAGAGAAAGC-CTTT
          1 ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAACGAGAGAAAGCTC-TT

                    
        769 GCAGATTT
         65 GCAGATTT

                            *                        *     ***             * 
        777 ATTAGATGTTGAATCCTCTCCGGAAGCGATGCTAAATTGGGAAAATTCTTGAGAGAAAGCTCTCG
          1 ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAACGAGAGAAAGCTCTTG

                   
        842 CAGATTT
         66 CAGATTT

               *      
        849 ATTGGATGTT
          1 ATTAGATGTT

        859 CCCATTGCAT


Statistics
Matches: 260,  Mismatches: 32, Indels: 12
        0.86            0.11        0.04

Matches are distributed among these distances:
  71    3  0.01
  72  248  0.95
  73    4  0.02
  74    5  0.02

ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Consensus pattern (72 bp):   
ATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAACGAGAGAAAGCTCTTG
CAGATTT

Found at i:715 original size:144 final size:144

Alignment explanation


    Indices: 489--858  Score: 521
    Period size: 144  Copynumber: 2.6  Consensus size: 144

        479 TTTCAAATTG

                            *                                 *            * 
        489 ATTAGATGTTGAATCCCCTCCGGAAGCGATGTTAAATTGGGCAAA--AACCAGAGAACAAGATAT
          1 ATTAGATGTTGAATCCTCTCCGGAAGCGATGTTAAATTGGGCAAATTAACGAGAG-A-AAGATCT

                                               *                      **     
        552 TGCAGATTTATTAGATGTTGAATCCCCTCCGGAAGTGATGCTAAATTGGG-AAGATTATTGAGAG
         64 TGCAGATTTATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAA-ATTAGCGAGAG

                             
        616 AAAGCCCTTGCAGATTT
        128 AAAGCCCTTGCAGATTT

                           *                   *                             
        633 ATTAGATGTTGAATCGTCTCCGGAAGCGATGTTAACTTGGGCAAATTAACGAGAGAAAGATCTTG
          1 ATTAGATGTTGAATCCTCTCCGGAAGCGATGTTAAATTGGGCAAATTAACGAGAGAAAGATCTTG

                                        *                         *          
        698 CAGATTTATTAGATGTTGAATCCCCTCCTGAAGCGATGCTAAATTGGGCAAATTCGCGAGAGAAA
         66 CAGATTTATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAGCGAGAGAAA

               *          
        763 GCCTTTGCAGATTT
        131 GCCCTTGCAGATTT

                                           *         *     ***         *   * 
        777 ATTAGATGTTGAATCCTCTCCGGAAGCGATGCTAAATTGGGAAAATTCTTGAGAGAAAGCTCTCG
          1 ATTAGATGTTGAATCCTCTCCGGAAGCGATGTTAAATTGGGCAAATTAACGAGAGAAAGATCTTG

                      *      
        842 CAGATTTATTGGATGTT
         66 CAGATTTATTAGATGTT

        859 CCCATTGCAT


Statistics
Matches: 202,  Mismatches: 21, Indels: 6
        0.88            0.09        0.03

Matches are distributed among these distances:
 144  192  0.95
 145    3  0.01
 146    7  0.03

ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29


Consensus pattern (144 bp):   
ATTAGATGTTGAATCCTCTCCGGAAGCGATGTTAAATTGGGCAAATTAACGAGAGAAAGATCTTG
CAGATTTATTAGATGTTGAATCCCCTCCGGAAGCGATGCTAAATTGGGCAAATTAGCGAGAGAAA
GCCCTTGCAGATTT
Done.