Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014482.1 Kokia drynarioides strain JFW-HI SEQ_129521, 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: 11882
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32


Found at i:1135 original size:29 final size:28

Alignment explanation


    Indices: 1103--1190  Score: 72
    Period size: 29  Copynumber: 3.0  Consensus size: 28

       1093 TGGAAGATTC

                                          
       1103 GGGGTCAAAAAT-AGAATTTTTAGACATCT
          1 GGGGT-AAAAATGA-AATTTTTAGACATCT

                         *       *  *   * 
       1132 GGGGT-AAAATGGTAATTTTTGGAGAGTTT
          1 GGGGTAAAAAT-GAAATTTTTAGACA-TCT

                            *            
       1161 GGGGTTAAAAATGAAAATTTTAGACATCT
          1 GGGG-TAAAAATGAAATTTTTAGACATCT

             
       1190 G
          1 G

       1191 AGATAAAATG


Statistics
Matches: 45,  Mismatches: 9, Indels: 10
        0.70            0.14        0.16

Matches are distributed among these distances:
  27    5  0.11
  28   10  0.22
  29   14  0.31
  30   11  0.24
  31    5  0.11

ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33


Consensus pattern (28 bp):   
GGGGTAAAAATGAAATTTTTAGACATCT

Found at i:1264 original size:59 final size:57

Alignment explanation


    Indices: 1080--1325  Score: 273
    Period size: 58  Copynumber: 4.2  Consensus size: 57

       1070 ATTCAGGAGG

                                     *          *                     
       1080 AAAATGGTAA-TTTTGGAAGATTCGGGGTCAAAAATAGAATTTTTAGACATCTGGGGT
          1 AAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATGGAA-TTTTAGACATCTGGGGT

                                    * *   *        *               * * 
       1137 AAAATGGTAATTTTTGG-AGAGTTTGGGGTTAAAAATGAAAATTTTAGACATCTGAGAT
          1 AAAATGGTAATTTTTGGAAGA-TTCGAGGTCAAAAATG-GAATTTTAGACATCTGGGGT

                                 *     *                         *     
       1195 AAAATGGTAATTTTTGGAAGACTCGAGATCAAAAAATGGAATTTTAGACATCCGGGGGT
          1 AAAATGGTAATTTTTGGAAGATTCGAGGTC-AAAAATGGAATTTTAGACAT-CTGGGGT

                                          *             *  *   *       
       1254 AAAATGGTAATTTTTGGAAGATTCGAGGTCGAAAATGGAATTTTGGAAAGTTTAGGGGT
          1 AAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATGGAATTTTAGACA-TCT-GGGGT

                          
       1313 AAAAT-GTAATTTT
          1 AAAATGGTAATTTT

       1326 CAAACAATTA


Statistics
Matches: 159,  Mismatches: 22, Indels: 15
        0.81            0.11        0.08

Matches are distributed among these distances:
  57   13  0.08
  58   91  0.57
  59   55  0.35

ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32


Consensus pattern (57 bp):   
AAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATGGAATTTTAGACATCTGGGGT

Found at i:2515 original size:19 final size:18

Alignment explanation


    Indices: 2490--2541  Score: 59
    Period size: 19  Copynumber: 2.8  Consensus size: 18

       2480 TTTATTTCTT

                          *   
       2490 TATTATTATTATTATTAA
          1 TATTATTATTATTAATAA

                    *          
       2508 TCATTATTTTTATTAATAA
          1 T-ATTATTATTATTAATAA

              *  *         
       2527 TAATAATATTATTAA
          1 TATTATTATTATTAA

       2542 ACATTAATGT


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  18   12  0.43
  19   16  0.57

ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56


Consensus pattern (18 bp):   
TATTATTATTATTAATAA

Found at i:3259 original size:17 final size:16

Alignment explanation


    Indices: 3228--3263  Score: 54
    Period size: 17  Copynumber: 2.2  Consensus size: 16

       3218 AACCATTTTC

                    *       
       3228 AAATTTAATTAAATTT
          1 AAATTTAAATAAATTT

                             
       3244 AAATTTAAAATAAATTT
          1 AAATTT-AAATAAATTT

               
       3261 AAA
          1 AAA

       3264 ACCATTTTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    6  0.33
  17   12  0.67

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (16 bp):   
AAATTTAAATAAATTT

Found at i:3287 original size:45 final size:46

Alignment explanation


    Indices: 3195--3288  Score: 129
    Period size: 45  Copynumber: 2.1  Consensus size: 46

       3185 ATTTTGGACT

                         *   *                  *     *   
       3195 TTTAAATTTAATATTAAGTTTAAAACCATTTTCAAATTTAATTAAA
          1 TTTAAATTTAATAATAAATTTAAAACCATTTTCAAACTTAATAAAA

                                                           
       3241 TTTAAATTTAA-AATAAATTTAAAACCATTTT-AAACTTAATCAAAA
          1 TTTAAATTTAATAATAAATTTAAAACCATTTTCAAACTTAAT-AAAA

               
       3286 TTT
          1 TTT

       3289 GATCCAAAGC


Statistics
Matches: 43,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  44    8  0.19
  45   24  0.56
  46   11  0.26

ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44


Consensus pattern (46 bp):   
TTTAAATTTAATAATAAATTTAAAACCATTTTCAAACTTAATAAAA

Found at i:4378 original size:26 final size:27

Alignment explanation


    Indices: 4325--4378  Score: 67
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       4315 TCTAATTCTA

                         *         *   
       4325 TACCAAATTGAACTAAAAAAATTTAAG
          1 TACCAAATTGAACGAAAAAAATTCAAG

                                        
       4352 TACCAAATT-AA-GAAAAAAATATCAAG
          1 TACCAAATTGAACGAAAAAAAT-TCAAG

             
       4378 T
          1 T

       4379 TAAATTCTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  25    8  0.33
  26    7  0.29
  27    9  0.38

ACGTcount: A:0.57, C:0.11, G:0.07, T:0.24


Consensus pattern (27 bp):   
TACCAAATTGAACGAAAAAAATTCAAG
Done.