Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004612.1 Kokia drynarioides strain JFW-HI SEQ_118121, 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: 11874
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37


Found at i:1184 original size:3 final size:3

Alignment explanation


    Indices: 1176--1229  Score: 108
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1166 TTAAGAACTA

                                                                           
       1176 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                   
       1224 AAT AAT
          1 AAT AAT

       1230 TAACCACTAC


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   51  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:1425 original size:24 final size:24

Alignment explanation


    Indices: 1401--1451  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       1391 ATGTCAAATA

                      *              
       1401 TTATATAAATGTTTAATATATATAT
          1 TTAT-TAAATATTTAATATATATAT

                          * *       
       1426 TTATTAAATATTTATTTTATATAT
          1 TTATTAAATATTTAATATATATAT

              
       1450 TT
          1 TT

       1452 TAATCTTGTC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   19  0.83
  25    4  0.17

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


Consensus pattern (24 bp):   
TTATTAAATATTTAATATATATAT

Found at i:3892 original size:422 final size:419

Alignment explanation


    Indices: 3103--3956  Score: 1239
    Period size: 422  Copynumber: 2.0  Consensus size: 419

       3093 TTAAGATTTT

                                 **                                          
       3103 TTATAATAGTCAATCGAAAAAGGGAAAGTTTCATATCAAGTCTCTGAACGTTTTAATCTGTCACA
          1 TTATAATAGTCAATCGAAAAAAAGAAAGTTTCATATCAAGTCTCTGAACGTTTTAATCTGTCACA

                                                         *                 * 
       3168 CTTCAGTCCGATGCTATCACTGTGTCAGACAATATCAATAAAAAATTATTTTTTTAAAAAAAGTC
         66 CTTCAGTCCGATGCTATCACTGTGTCAGACAATATCAATAAAAAACTA---TTTTAAAAAAAGAC

                           *       *                                         
       3233 ATACGATTACATGATGATTGTGGGAAAATAGGGTTTATCTCTCGAAAACAAGAGAAGAAAATTCT
        128 ATACGATTACATGATAATTGTGGAAAAATAGGGTTTATCTCTCGAAAACAAGAGAAGAAAATTCT

                                     *                        *              
       3298 GTGAAGGATAAGGAAGAAAAAGTAATGAAGACAGAAACAAAAACAGAAACGTTACCATTTATTCC
        193 GTGAAGGATAAGGAAGAAAAAGTAACGAAGACAG-----AAAACAGAAACATTACCATTTATTCC

                                                                  *    *     
       3363 TAGAAGGCGACATGTCTATCTCTAGAAAACAACTGGTGAAGAAAATTTTGTTAGGATAAGGAAGA
        253 TAGAAGGCGACATGTCTATCTCTAGAAAACAACTGGTGAAGAAAATTTTGTTAGAATAAAGAAGA

                          *                               *    *             
       3428 AAAATTAATGAAGATAGCGAAACAGAAACATTAACATTTATTCTAAGACATGAATTTCTGGTTAG
        318 AAAATTAATGAAGACAGCGAAACAGAAACATTAACATTTATTCTAAAACATAAATTTCTGGTTAG

                **                               
       3493 GAGTCTAATACAATTTATTTTAGAATTTTTGAATATA
        383 GAGTAGAATACAATTTATTTTAGAATTTTTGAATATA

                          *           *                           ** *       
       3530 TTATAATAGTCAATTGAAAAAAAGAATGTTTCATATCAAGTCTCTGAACGTTTTGGTTTGTCACA
          1 TTATAATAGTCAATCGAAAAAAAGAAAGTTTCATATCAAGTCTCTGAACGTTTTAATCTGTCACA

                 *          *             * *                                
       3595 CTTCATTCCGATG-TCGTCACTGTGTCAGATAGTATCAATAAAAAACTA-TTTAAAAAAA-ACAT
         66 CTTCAGTCCGATGCT-ATCACTGTGTCAGACAATATCAATAAAAAACTATTTTAAAAAAAGACAT

              *   * *                                                        
       3657 ACTATTTCTTGATAATTGTGGAAAAATAGGGTTTATCTCTCGAAAACAAGAGAAGAAAATTCTGT
        130 ACGATTACATGATAATTGTGGAAAAATAGGGTTTATCTCTCGAAAACAAGAGAAGAAAATTCTGT

                               *                *                            
       3722 GAAGGATAAGGAAGAAAAATTAACGAAGACAG-AAATAGAAACATTACCATTTATTCCTAGAAGG
        195 GAAGGATAAGGAAGAAAAAGTAACGAAGACAGAAAACAGAAACATTACCATTTATTCCTAGAAGG

                              *   *  *                                       
       3786 CGACATGTCTATCTCTAGGAAATAAGTGGTGAAGAAAATTTTGTTAGAATAAAGAAGAAAAATTA
        260 CGACATGTCTATCTCTAGAAAACAACTGGTGAAGAAAATTTTGTTAGAATAAAGAAGAAAAATTA

                 *                                          *                
       3851 ATGAATACAGCGAAACAGAAACAGAAACATTAACATTTATTCTAAAACCTAAATTTCTGGTTAGG
        325 ATGAAGACA--G---C-GAAACAGAAACATTAACATTTATTCTAAAACATAAATTTCTGGTTAGG

                                                
       3916 AGTAGAATACAATTTATTTTAGAATTTTTGAATATA
        384 AGTAGAATACAATTTATTTTAGAATTTTTGAATATA

                 
       3952 TTATA
          1 TTATA

       3957 TATATTTAAG


Statistics
Matches: 386,  Mismatches: 34, Indels: 19
        0.88            0.08        0.04

Matches are distributed among these distances:
 416   97  0.25
 418    1  0.00
 421    1  0.00
 422  177  0.46
 423   10  0.03
 426    1  0.00
 427   99  0.26

ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30


Consensus pattern (419 bp):   
TTATAATAGTCAATCGAAAAAAAGAAAGTTTCATATCAAGTCTCTGAACGTTTTAATCTGTCACA
CTTCAGTCCGATGCTATCACTGTGTCAGACAATATCAATAAAAAACTATTTTAAAAAAAGACATA
CGATTACATGATAATTGTGGAAAAATAGGGTTTATCTCTCGAAAACAAGAGAAGAAAATTCTGTG
AAGGATAAGGAAGAAAAAGTAACGAAGACAGAAAACAGAAACATTACCATTTATTCCTAGAAGGC
GACATGTCTATCTCTAGAAAACAACTGGTGAAGAAAATTTTGTTAGAATAAAGAAGAAAAATTAA
TGAAGACAGCGAAACAGAAACATTAACATTTATTCTAAAACATAAATTTCTGGTTAGGAGTAGAA
TACAATTTATTTTAGAATTTTTGAATATA
Done.