Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010249.1 Kokia drynarioides strain JFW-HI SEQ_125084, 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: 15267
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36


Found at i:39 original size:4 final size:4

Alignment explanation


    Indices: 19--85  Score: 73
    Period size: 4  Copynumber: 16.5  Consensus size: 4

          9 AACACATTAC

                       *                     *   *      *               
         19 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT

                                   
         67 CTTT CCTTT CTTT CTTT CT
          1 CTTT -CTTT CTTT CTTT CT

         86 CGTTTATTTG


Statistics
Matches: 53,  Mismatches: 7, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   43  0.81
   5    7  0.13

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (4 bp):   
CTTT

Found at i:65 original size:29 final size:27

Alignment explanation


    Indices: 25--82  Score: 80
    Period size: 29  Copynumber: 2.1  Consensus size: 27

         15 TTACCTTTCT

                                       
         25 TTCCTTCTTCTTTCTTTCCTCTCCTTC
          1 TTCCTTCTTCTTTCTTTCCTCTCCTTC

                                  *  *   
         52 TTCCTTTCTTTCTTTCTTTCCTTTCTTTC
          1 TTCC-TTC-TTCTTTCTTTCCTCTCCTTC

              
         81 TT
          1 TT

         83 TCTCGTTTAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  27    4  0.15
  28    3  0.11
  29   20  0.74

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (27 bp):   
TTCCTTCTTCTTTCTTTCCTCTCCTTC

Found at i:85 original size:17 final size:15

Alignment explanation


    Indices: 19--84  Score: 70
    Period size: 13  Copynumber: 4.6  Consensus size: 15

          9 AACACATTAC

                           
         19 CTTTCTTTCCTTCTT
          1 CTTTCTTTCCTTCTT

                           
         34 CTTTCTTTCC-TC-T
          1 CTTTCTTTCCTTCTT

             *               
         47 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCC-TTC-TT

                           
         63 CTTTCTTTCC-T-TT
          1 CTTTCTTTCCTTCTT

                     
         76 CTTTCTTTC
          1 CTTTCTTTC

         85 TCGTTTATTT


Statistics
Matches: 44,  Mismatches: 2, Indels: 12
        0.76            0.03        0.21

Matches are distributed among these distances:
  12    4  0.09
  13   16  0.36
  14    4  0.09
  15   11  0.25
  16    5  0.11
  17    4  0.09

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (15 bp):   
CTTTCTTTCCTTCTT

Found at i:3310 original size:65 final size:65

Alignment explanation


    Indices: 3194--3338  Score: 182
    Period size: 65  Copynumber: 2.2  Consensus size: 65

       3184 TGATTTATAC

                 *                                    *   *     *          * 
       3194 ATATTAAATCTCATTATATGAACCAAATTGATTAAGATTTAGTTTATTTTTTGTCTCACATTATA
          1 ATATTTAATCTCATTATATGAACCAAATTGATTAAGATTTAGCTTACTTTTTATCTCACATTACA

            *          *                 *    * *                      *     
       3259 GTATTTAATCTGATTATATGAACCAAATTTATTAGGGTTTAGCTTACTTTTTATCTCACGTTACA
          1 ATATTTAATCTCATTATATGAACCAAATTGATTAAGATTTAGCTTACTTTTTATCTCACATTACA

                     *     
       3324 ATATTTAATTTCATT
          1 ATATTTAATCTCATT

       3339 GTCATCGTTA


Statistics
Matches: 66,  Mismatches: 14, Indels: 0
        0.82            0.17        0.00

Matches are distributed among these distances:
  65   66  1.00

ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47


Consensus pattern (65 bp):   
ATATTTAATCTCATTATATGAACCAAATTGATTAAGATTTAGCTTACTTTTTATCTCACATTACA

Found at i:12580 original size:29 final size:28

Alignment explanation


    Indices: 12493--12574  Score: 110
    Period size: 29  Copynumber: 2.9  Consensus size: 28

      12483 AATTGGGGTT

                           *            
      12493 TTGGATCCCTTAAAAGTTGAAAAAAAAA
          1 TTGGATCCCTTAAAAATTGAAAAAAAAA

              ** *                       
      12521 TTTAAGCCCTTAAAAATTGAAAAAAAAAA
          1 TTGGATCCCTTAAAAATTG-AAAAAAAAA

                            *        
      12550 TTGGATCCCTTAAAAACTGAAAAAA
          1 TTGGATCCCTTAAAAATTGAAAAAA

      12575 TTAATTTTCG


Statistics
Matches: 45,  Mismatches: 8, Indels: 2
        0.82            0.15        0.04

Matches are distributed among these distances:
  28   21  0.47
  29   24  0.53

ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24


Consensus pattern (28 bp):   
TTGGATCCCTTAAAAATTGAAAAAAAAA

Found at i:14869 original size:31 final size:34

Alignment explanation


    Indices: 14807--14870  Score: 89
    Period size: 33  Copynumber: 2.0  Consensus size: 34

      14797 TTTTTATTAT

                               *              
      14807 TTTAAAAATAAATTAAAAATATAAAATTATTTTA
          1 TTTAAAAATAAATTAAAAACATAAAATTATTTTA

                 *                           
      14841 TTTAATAA-AAATTAAAAACA-AAAA-TATTTT
          1 TTTAAAAATAAATTAAAAACATAAAATTATTTT

      14871 TAGCCCAAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  31    6  0.21
  32    4  0.14
  33   11  0.39
  34    7  0.25

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (34 bp):   
TTTAAAAATAAATTAAAAACATAAAATTATTTTA
Done.