Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000938.1 Kokia drynarioides strain JFW-HI SEQ_112096, 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: 1826
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36

Warning! 14 characters in sequence are not A, C, G, or T


Found at i:523 original size:15 final size:15

Alignment explanation


    Indices: 511--581  Score: 97
    Period size: 15  Copynumber: 4.7  Consensus size: 15

        501 TTTTGGGTAG

                           
        511 TTTGTAATTGGGTCA
          1 TTTGTAATTGGGTCA

                           
        526 TTTGTAATTGGGTCA
          1 TTTGTAATTGGGTCA

             *          *  
        541 TCTGTAATTGGGCCA
          1 TTTGTAATTGGGTCA

                 *      *  
        556 TTTGTTATTGGGCCA
          1 TTTGTAATTGGGTCA

            *          
        571 CTTGTAATTGG
          1 TTTGTAATTGG

        582 ACTTTGTTTT


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   50  1.00

ACGTcount: A:0.18, C:0.11, G:0.27, T:0.44


Consensus pattern (15 bp):   
TTTGTAATTGGGTCA

Found at i:697 original size:16 final size:17

Alignment explanation


    Indices: 613--698  Score: 106
    Period size: 17  Copynumber: 5.2  Consensus size: 17

        603 TTGGTCTTTC

                         *    
        613 TAAATTT-AATTTTATAA
          1 TAAATTTAAATTTCA-AA

                             
        630 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTCAAA

                             
        647 TAAATTTAAATTTCAAA
          1 TAAATTTAAATTTCAAA

                *            
        664 TAAACTTAAATTT-AAA
          1 TAAATTTAAATTTCAAA

                   *      *  
        680 TAAA-TTCAATTTCCAA
          1 TAAATTTAAATTTCAAA

               
        696 TAA
          1 TAA

        699 GTCCAGACAA


Statistics
Matches: 63,  Mismatches: 4, Indels: 5
        0.88            0.06        0.07

Matches are distributed among these distances:
  15    7  0.11
  16   12  0.19
  17   38  0.60
  18    6  0.10

ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAAATTTAAATTTCAAA

Found at i:1667 original size:139 final size:139

Alignment explanation


    Indices: 1246--1667  Score: 731
    Period size: 139  Copynumber: 3.0  Consensus size: 139

       1236 NNNNNNNNNT

                                                                             
       1246 GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATC
          1 GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATC

                                                                           * 
       1311 CCATCACTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAAT
         66 CCATCACTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGT

                     
       1376 ATCCCAT-A
        131 ATCCCATCA

                                          *                                  
       1384 TGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGAT
          1 -GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGAT

                                                *                         *  
       1449 CCCATCACTGTTTCAATCCGCTTCTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTCTTAG
         65 CCCATCACTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAG

                     *
       1514 TATCCCATCT
        130 TATCCCATCA

                                                                            *
       1524 GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATT
          1 GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATC

                            *  *                                             
       1589 CCATCACTGTTTCAATTCGTTTCTCTGTATCTCATCAAGG-AGACGAATTTGGTTCACTTCTCAG
         66 CCATCACTGTTTCAATCCGCTTCTCTGTATCTCATC-AGGAAGACGAATTTGGTTCACTTCTCAG

                *     
       1653 TATCTCATCA
        130 TATCCCATCA

                 
       1663 GGAAG
          1 GGAAG

       1668 CTAACCGTTT


Statistics
Matches: 268,  Mismatches: 13, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
 139  265  0.99
 140    3  0.01

ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36


Consensus pattern (139 bp):   
GGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATC
CCATCACTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGT
ATCCCATCA
Done.