Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011827.1 Kokia drynarioides strain JFW-HI SEQ_126823, 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: 5155
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35


Found at i:1182 original size:23 final size:23

Alignment explanation


    Indices: 1139--1182  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1129 AAAATTAAAT

                        * *        
       1139 TATAATTTTTAAGATAGTAAAAA
          1 TATAATTTTTAAAAGAGTAAAAA

                            *    
       1162 TATAATTTTTAAAAGATTAAA
          1 TATAATTTTTAAAAGAGTAAA

       1183 TCAAAATTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41


Consensus pattern (23 bp):   
TATAATTTTTAAAAGAGTAAAAA

Found at i:2001 original size:17 final size:17

Alignment explanation


    Indices: 1948--2025  Score: 70
    Period size: 17  Copynumber: 4.6  Consensus size: 17

       1938 GGATTAACAG

                          *  
       1948 AATTTAAATTTATTTTA
          1 AATTTAAATTTATTATA

             *                
       1965 AGTTTAAATTTACTTA-A
          1 AATTTAAATTTA-TTATA

                      *      
       1982 AATTTAAATTGATTATA
          1 AATTTAAATTTATTATA

                 * *   *      
       1999 AATTTGAGTTAAATT-TA
          1 AATTTAAATT-TATTATA

                      
       2016 AATTTAAATT
          1 AATTTAAATT

       2026 AATGTCCAAA


Statistics
Matches: 49,  Mismatches: 9, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
  16    3  0.06
  17   41  0.84
  18    5  0.10

ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50


Consensus pattern (17 bp):   
AATTTAAATTTATTATA

Found at i:3185 original size:29 final size:27

Alignment explanation


    Indices: 3143--3227  Score: 98
    Period size: 28  Copynumber: 2.9  Consensus size: 27

       3133 TAAAATAAAA

                                         
       3143 AAAAATCTCATTTTGACCTCGAAACTTCC
          1 AAAAAT-TCATTTT-ACCTCGAAACTTCC

                             * *        
       3172 AAAAATTACATTTTACCCCCAAACTTCC
          1 AAAAATT-CATTTTACCTCGAAACTTCC

                                        
       3200 AAAAATTCCATTTTTAACCTCGAAACTT
          1 AAAAATT-CA-TTTT-ACCTCGAAACTT

       3228 AAATTACCAT


Statistics
Matches: 48,  Mismatches: 5, Indels: 5
        0.83            0.09        0.09

Matches are distributed among these distances:
  28   22  0.46
  29   16  0.33
  30   10  0.21

ACGTcount: A:0.38, C:0.27, G:0.04, T:0.32


Consensus pattern (27 bp):   
AAAAATTCATTTTACCTCGAAACTTCC

Found at i:3318 original size:29 final size:28

Alignment explanation


    Indices: 3286--3379  Score: 91
    Period size: 29  Copynumber: 3.2  Consensus size: 28

       3276 TAAAACTTTC

                      *                  
       3286 AAAAATTACCCTTTTACCCCTGAATATCT
          1 AAAAATTACCATTTTACCCC-GAATATCT

                     *       *     * *    
       3315 AAAAATT-CTATTTTGATCCCGATTTTCCT
          1 AAAAATTACCATTTT-ACCCCGAATAT-CT

                                     *   
       3344 AAAAATTACCATTTTACCCCCGAATGTCT
          1 AAAAATTACCATTTTA-CCCCGAATATCT

                   
       3373 AAAAATT
          1 AAAAATT

       3380 CTGTTTTGTG


Statistics
Matches: 52,  Mismatches: 9, Indels: 8
        0.75            0.13        0.12

Matches are distributed among these distances:
  28    9  0.17
  29   30  0.58
  30   13  0.25

ACGTcount: A:0.35, C:0.23, G:0.05, T:0.36


Consensus pattern (28 bp):   
AAAAATTACCATTTTACCCCGAATATCT

Found at i:3359 original size:58 final size:59

Alignment explanation


    Indices: 3282--3438  Score: 185
    Period size: 58  Copynumber: 2.7  Consensus size: 59

       3272 ACCCTAAAAC

                           *         *                                 
       3282 TTTC-AAAAATTACCCTTTTACCCCTGAATATCTAAAAATTCT-ATTT-TGATCCCGAT
          1 TTTCTAAAAATTACCATTTTACCCCCGAATATCTAAAAATTCTGATTTGTGATCCCGAT

                                           *             *         *    
       3338 TTTCCTAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCTGTTTTGTGATCTCGAT
          1 TTT-CTAAAAATTACCATTTTACCCCCGAATATCTAAAAATTCTGATTTGTGATCCCGAT

               * * * *     *            *            
       3398 TTTTTTATAGTTACCGTTTTACCCCCGAGTATCTAAAAATT
          1 TTTCTAAAAATTACCATTTTACCCCCGAATATCTAAAAATT

       3439 TCATTTTTAG


Statistics
Matches: 85,  Mismatches: 12, Indels: 5
        0.83            0.12        0.05

Matches are distributed among these distances:
  56    3  0.04
  57    1  0.01
  58   35  0.41
  59   34  0.40
  60   12  0.14

ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41


Consensus pattern (59 bp):   
TTTCTAAAAATTACCATTTTACCCCCGAATATCTAAAAATTCTGATTTGTGATCCCGAT

Done.