Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004428.1 Kokia drynarioides strain JFW-HI SEQ_117816, 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: 5462
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35


Found at i:284 original size:30 final size:29

Alignment explanation


    Indices: 244--350  Score: 115
    Period size: 29  Copynumber: 3.7  Consensus size: 29

        234 AATATGAATG

                 *                *       
        244 AGGGTAAAAATGTAATTTTCAAAAAAAATT
          1 AGGGTTAAAATGTAATTTT-AAGAAAAATT

                               **    **  
        274 AGGGTTAAAATGTAATTTTTGGAAAGTTT
          1 AGGGTTAAAATGTAATTTTAAGAAAAATT

            *                  *        *
        303 GGGGTTAAAATGTAATTTTGAGAAAAATC
          1 AGGGTTAAAATGTAATTTTAAGAAAAATT

             *                 
        332 AAGGTTAAAATGTAATTTT
          1 AGGGTTAAAATGTAATTTT

        351 TGGAAAGTTT


Statistics
Matches: 63,  Mismatches: 14, Indels: 1
        0.81            0.18        0.01

Matches are distributed among these distances:
  29   45  0.71
  30   18  0.29

ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36


Consensus pattern (29 bp):   
AGGGTTAAAATGTAATTTTAAGAAAAATT

Found at i:316 original size:29 final size:29

Alignment explanation


    Indices: 272--423  Score: 171
    Period size: 29  Copynumber: 5.2  Consensus size: 29

        262 TCAAAAAAAA

                                         
        272 TTAGGGTTAAAATGTAATTTTTGGAAAGT
          1 TTAGGGTTAAAATGTAATTTTTGGAAAGT

              *                         **
        301 TTGGGGTTAAAATGTAA-TTTTGAGAAAAA
          1 TTAGGGTTAAAATGTAATTTTTG-GAAAGT

             * *                         
        330 TCAAGGTTAAAATGTAATTTTTGGAAAGT
          1 TTAGGGTTAAAATGTAATTTTTGGAAAGT

              **   *     *               
        359 TTTTGGTCAAAATTTAATTTTTGGAAAGT
          1 TTAGGGTTAAAATGTAATTTTTGGAAAGT

                     *             *  *   
        388 TTAAGGGTTGAAATGTAATTTTTAGACAGT
          1 TT-AGGGTTAAAATGTAATTTTTGGAAAGT

                  
        418 TTAGGG
          1 TTAGGG

        424 ACCTCCTGGG


Statistics
Matches: 100,  Mismatches: 20, Indels: 6
        0.79            0.16        0.05

Matches are distributed among these distances:
  28    5  0.05
  29   68  0.68
  30   27  0.27

ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40


Consensus pattern (29 bp):   
TTAGGGTTAAAATGTAATTTTTGGAAAGT

Found at i:345 original size:58 final size:58

Alignment explanation


    Indices: 245--419  Score: 190
    Period size: 58  Copynumber: 3.0  Consensus size: 58

        235 ATATGAATGA

                               * *        *                            
        245 GGGTAAAAATGTAATTTTCAAAAAAAATTAGGGTTAAAATGTAATTTTTGGAAAGTTTG
          1 GGGTAAAAATGTAATTTT-GAGAAAAATTAAGGTTAAAATGTAATTTTTGGAAAGTTTG

                *                      *                             *
        304 GGGTTAAAATGTAATTTTGAGAAAAATCAAGGTTAAAATGTAATTTTTGGAAAGTTTT
          1 GGGTAAAAATGTAATTTTGAGAAAAATTAAGGTTAAAATGTAATTTTTGGAAAGTTTG

            *   *     *              **         *             *  *     
        362 TGGTCAAAATTTAATTTTTG-GAAAGTTTAAGGGTTGAAATGTAATTTTTAGACAGTTT
          1 GGGTAAAAATGTAA-TTTTGAGAAAAATTAA-GGTTAAAATGTAATTTTTGGAAAGTTT

        420 AGGGACCTCC


Statistics
Matches: 99,  Mismatches: 15, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
  58   53  0.54
  59   46  0.46

ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39


Consensus pattern (58 bp):   
GGGTAAAAATGTAATTTTGAGAAAAATTAAGGTTAAAATGTAATTTTTGGAAAGTTTG

Found at i:1215 original size:17 final size:16

Alignment explanation


    Indices: 1191--1222  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

       1181 TTTTTTGGGT

                            
       1191 TTTAATATATTTTTTA
          1 TTTAATATATTTTTTA

                            
       1207 TTTATATATATTTTTT
          1 TTTA-ATATATTTTTT

       1223 TACACATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (16 bp):   
TTTAATATATTTTTTA

Found at i:1760 original size:20 final size:20

Alignment explanation


    Indices: 1735--1774  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1725 TTTGAGCTTT

                                 
       1735 TTTTGTAA-TTGGACAATTAA
          1 TTTTGTAATTTGGAC-ATTAA

                                
       1755 TTTTGTAATTTGGACATTAA
          1 TTTTGTAATTTGGACATTAA

       1775 AACAAAAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20   13  0.68
  21    6  0.32

ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47


Consensus pattern (20 bp):   
TTTTGTAATTTGGACATTAA

Found at i:2169 original size:24 final size:24

Alignment explanation


    Indices: 2141--2203  Score: 90
    Period size: 24  Copynumber: 2.6  Consensus size: 24

       2131 AGAAATAATC

                                    
       2141 TTTCAGTTAAACTCTGTTTAATTG
          1 TTTCAGTTAAACTCTGTTTAATTG

                 *              *   
       2165 TTTCAATTAAACTCTGTTTATTTG
          1 TTTCAGTTAAACTCTGTTTAATTG

               *   *       
       2189 TTTGAGTCAAACTCT
          1 TTTCAGTTAAACTCT

       2204 TATTAGTTTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   34  1.00

ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49


Consensus pattern (24 bp):   
TTTCAGTTAAACTCTGTTTAATTG
Done.