Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008530.1 Kokia drynarioides strain JFW-HI SEQ_123207, 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: 2572
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31


Found at i:926 original size:21 final size:21

Alignment explanation


    Indices: 901--958  Score: 98
    Period size: 21  Copynumber: 2.8  Consensus size: 21

        891 CTGTGCAAAT

                        **       
        901 TTCTACCGATACTTGTGCTAG
          1 TTCTACCGATACAAGTGCTAG

                                 
        922 TTCTACCGATACAAGTGCTAG
          1 TTCTACCGATACAAGTGCTAG

                            
        943 TTCTACCGATACAAGT
          1 TTCTACCGATACAAGT

        959 ATGATTTCTA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   35  1.00

ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33


Consensus pattern (21 bp):   
TTCTACCGATACAAGTGCTAG

Found at i:967 original size:21 final size:22

Alignment explanation


    Indices: 922--996  Score: 77
    Period size: 21  Copynumber: 3.5  Consensus size: 22

        912 CTTGTGCTAG

                                  *
        922 TTCTACCGATACAAGTGC-T-AG
          1 TTCTACCGATACAAGT-CATGAT

                                  
        943 TTCTACCGATACAAGT-ATGAT
          1 TTCTACCGATACAAGTCATGAT

                    *             
        964 TTCTACCGCTACAAGTCATG-T
          1 TTCTACCGATACAAGTCATGAT

            **          
        985 AACTACCGATAC
          1 TTCTACCGATAC

        997 CAAAAACTCC


Statistics
Matches: 46,  Mismatches: 5, Indels: 6
        0.81            0.09        0.11

Matches are distributed among these distances:
  20    1  0.02
  21   42  0.91
  22    3  0.07

ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29


Consensus pattern (22 bp):   
TTCTACCGATACAAGTCATGAT

Found at i:1403 original size:251 final size:251

Alignment explanation


    Indices: 960--1459  Score: 883
    Period size: 251  Copynumber: 2.0  Consensus size: 251

        950 GATACAAGTA

                               *    *                       *    *           
        960 TGATTTCTACCGCTACAAGTCATGTAACTACCGATACCAAAAACTCCATAGAGCAAAAATTCATA
          1 TGATTTCTACCGCTACAAGCCATGCAACTACCGATACCAAAAACTCCAGAGAGAAAAAATTCATA

                *                  *            *                      *     
       1025 CCCTGCAACTTCTATCGATACAAGCTTACCTACTACCGATACATCAGTACTATGAACTATCGATA
         66 CCCTACAACTTCTATCGATACAAACTTACCTACTACAGATACATCAGTACTATGAACTACCGATA

                            *                                                
       1090 CCTGCAATTAAACTACTGATACAATACAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTTCTA
        131 CCTGCAATTAAACTACCGATACAATACAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTTCTA

                                                                    
       1155 CCGATACATGCAATAATTCTACCGAAACTAGTATGCAAAATTTCATTAAAGACATC
        196 CCGATACATGCAATAATTCTACCGAAACTAGTATGCAAAATTTCATTAAAGACATC

                                                                             
       1211 TGATTTCTACCGCTACAAGCCATGCAACTACCGATACCAAAAACTCCAGAGAGAAAAAATTCATA
          1 TGATTTCTACCGCTACAAGCCATGCAACTACCGATACCAAAAACTCCAGAGAGAAAAAATTCATA

                                                        *                    
       1276 CCCTACAACTTCTATCGATACAAACTTACCTACTACAGATACATTAGTACTATGAACTACCGATA
         66 CCCTACAACTTCTATCGATACAAACTTACCTACTACAGATACATCAGTACTATGAACTACCGATA

                      *                                                      
       1341 CCTGCAATTAGACTACCGATACAATACAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTTCTA
        131 CCTGCAATTAAACTACCGATACAATACAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTTCTA

             *          *                                         
       1406 CTGATACATGCAGTAATTCTACCGAAACTAGTATGCAAAATTTCATTAAAGACA
        196 CCGATACATGCAATAATTCTACCGAAACTAGTATGCAAAATTTCATTAAAGACA

       1460 CCAAGACACA


Statistics
Matches: 236,  Mismatches: 13, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 251  236  1.00

ACGTcount: A:0.37, C:0.27, G:0.11, T:0.26


Consensus pattern (251 bp):   
TGATTTCTACCGCTACAAGCCATGCAACTACCGATACCAAAAACTCCAGAGAGAAAAAATTCATA
CCCTACAACTTCTATCGATACAAACTTACCTACTACAGATACATCAGTACTATGAACTACCGATA
CCTGCAATTAAACTACCGATACAATACAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTTCTA
CCGATACATGCAATAATTCTACCGAAACTAGTATGCAAAATTTCATTAAAGACATC
Done.