Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006573.1 Kokia drynarioides strain JFW-HI SEQ_121159, 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: 17723
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Found at i:3340 original size:164 final size:164

Alignment explanation


    Indices: 3069--3388  Score: 489
    Period size: 164  Copynumber: 2.0  Consensus size: 164

       3059 ATTTTCAATC

                                          *              *                   
       3069 ATCCATTAACTAAATTTTTAGTGAGTAACATGTGAAATTAACAAGGTGATACAACATTACACACA
          1 ATCCATTAACTAAATTTTTAGTGAGTAACACGTGAAATTAACAAGCTGATACAACATTACACACA

                          *                    *                 **    *    *
       3134 CGATAATAGATTTAGTCCATACTCTCCAATTGAATCATCCTAAATCCCTAAGCCTTTTGCATTTT
         66 CGATAATAGATTTACTCCATACTCTCCAATTGAATAATCCTAAATCCCTAAGCAATTTGAATTTC

                                              
       3199 AAAATTTCAATCTTCATGCAAATGACGATCGTTA
        131 AAAATTTCAATCTTCATGCAAATGACGATCGTTA

                        *          *                                        *
       3233 ATCCATTAACTAGATTTTTAGTGTGTAACACGTGAAATTAACAAGCTGAT-CTAACATTACACAT
          1 ATCCATTAACTAAATTTTTAGTGAGTAACACGTGAAATTAACAAGCTGATAC-AACATTACACAC

                     *            *                            *             
       3297 ACGATAATATATTTACTCCATATTCTCCAATTGAATAATCCTAAATCCCTATGCAATTTGAATTT
         65 ACGATAATAGATTTACTCCATACTCTCCAATTGAATAATCCTAAATCCCTAAGCAATTTGAATTT

                *                      
       3362 CAAACTTTCAATCTTCATGCAAATGAC
        130 CAAAATTTCAATCTTCATGCAAATGAC

       3389 CGTGAAACTG


Statistics
Matches: 140,  Mismatches: 15, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 163    1  0.01
 164  139  0.99

ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34


Consensus pattern (164 bp):   
ATCCATTAACTAAATTTTTAGTGAGTAACACGTGAAATTAACAAGCTGATACAACATTACACACA
CGATAATAGATTTACTCCATACTCTCCAATTGAATAATCCTAAATCCCTAAGCAATTTGAATTTC
AAAATTTCAATCTTCATGCAAATGACGATCGTTA

Found at i:10353 original size:20 final size:21

Alignment explanation


    Indices: 10325--10365  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      10315 TGCCATGGAA

                *      *         
      10325 ATTTGCTTAATTGAT-ATTAT
          1 ATTTCCTTAATGGATCATTAT

                                 
      10345 ATTTCCTTAATGGATCATTAT
          1 ATTTCCTTAATGGATCATTAT

      10366 TTAGATGGTC


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20   13  0.72
  21    5  0.28

ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51


Consensus pattern (21 bp):   
ATTTCCTTAATGGATCATTAT

Found at i:17012 original size:30 final size:32

Alignment explanation


    Indices: 16973--17043  Score: 96
    Period size: 31  Copynumber: 2.3  Consensus size: 32

      16963 CATTTAACAC

                                             
      16973 AACAGTCACTTAAC-TT-T-GAAAATGTGACAA
          1 AACAGTCACTTAACGTTATCGAAAA-GTGACAA

                *                           
      17003 AACAATCAC-TAACGTTATCGAAAAGTGACAA
          1 AACAGTCACTTAACGTTATCGAAAAGTGACAA

                      
      17034 AACAGTCACT
          1 AACAGTCACT

      17044 GATTAATAGT


Statistics
Matches: 35,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  29    4  0.11
  30   10  0.29
  31   16  0.46
  32    5  0.14

ACGTcount: A:0.45, C:0.20, G:0.13, T:0.23


Consensus pattern (32 bp):   
AACAGTCACTTAACGTTATCGAAAAGTGACAA

Found at i:17120 original size:14 final size:14

Alignment explanation


    Indices: 17101--17129  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      17091 AAAATAACCC

                          
      17101 TAAACCAAAATATG
          1 TAAACCAAAATATG

                          
      17115 TAAACCAAAATATG
          1 TAAACCAAAATATG

             
      17129 T
          1 T

      17130 GAATAACAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24


Consensus pattern (14 bp):   
TAAACCAAAATATG

Found at i:17584 original size:29 final size:29

Alignment explanation


    Indices: 17542--17601  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      17532 GATATGCATT

                                         
      17542 TAGTTACATAAAACAAAACAGAATGATTG
          1 TAGTTACATAAAACAAAACAGAATGATTG

                                         
      17571 TAGTTACATAAAACAAAACAGAATGATTG
          1 TAGTTACATAAAACAAAACAGAATGATTG

              
      17600 TA
          1 TA

      17602 AAACAGACTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25


Consensus pattern (29 bp):   
TAGTTACATAAAACAAAACAGAATGATTG
Done.