Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004089.1 Kokia drynarioides strain JFW-HI SEQ_117259, 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: 2723
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2050 original size:14 final size:14

Alignment explanation


    Indices: 2033--2085  Score: 63
    Period size: 14  Copynumber: 3.8  Consensus size: 14

       2023 AGTGTTTACG

                  *       
       2033 GTTTAGAGTTTCAA
          1 GTTTAGGGTTTCAA

                  *      *
       2047 GTTTAGTGTTT-AT
          1 GTTTAGGGTTTCAA

                           
       2060 GATTTAGGGTTTCAA
          1 G-TTTAGGGTTTCAA

                       
       2075 GTTTAGGGTTT
          1 GTTTAGGGTTT

       2086 ATAATTTAGG


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  13    2  0.06
  14   29  0.88
  15    2  0.06

ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49


Consensus pattern (14 bp):   
GTTTAGGGTTTCAA

Found at i:2055 original size:28 final size:28

Alignment explanation


    Indices: 2022--2112  Score: 94
    Period size: 28  Copynumber: 3.2  Consensus size: 28

       2012 TTAATCAATC

                       *                
       2022 TAGTGTTTACGGTTTAGAGTTTCAAGTT
          1 TAGTGTTTACGATTTAGAGTTTCAAGTT

                     *       *          
       2050 TAGTGTTTATGATTTAGGGTTTCAAGTT
          1 TAGTGTTTACGATTTAGAGTTTCAAGTT

               *     **           *      
       2078 TAGGGTTTATAATTTAG-GTTTTAGAGTT
          1 TAGTGTTTACGATTTAGAGTTTCA-AGTT

              *    
       2106 TAATGTT
          1 TAGTGTT

       2113 ATGAGATTTA


Statistics
Matches: 54,  Mismatches: 8, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  27    5  0.09
  28   49  0.91

ACGTcount: A:0.23, C:0.03, G:0.24, T:0.49


Consensus pattern (28 bp):   
TAGTGTTTACGATTTAGAGTTTCAAGTT

Found at i:2107 original size:14 final size:14

Alignment explanation


    Indices: 2033--2107  Score: 57
    Period size: 14  Copynumber: 5.4  Consensus size: 14

       2023 AGTGTTTACG

                  *        
       2033 GTTTAGAGTTTCA-A
          1 GTTTAGGGTTT-AGA

                  *        
       2047 GTTTAGTGTTTATGA
          1 GTTTAGGGTTTA-GA

                           
       2062 -TTTAGGGTTTCA-A
          1 GTTTAGGGTTT-AGA

                        * 
       2075 GTTTAGGGTTTATA
          1 GTTTAGGGTTTAGA

            *      *      
       2089 ATTTAGGTTTTAGA
          1 GTTTAGGGTTTAGA

                 
       2103 GTTTA
          1 GTTTA

       2108 ATGTTATGAG


Statistics
Matches: 50,  Mismatches: 6, Indels: 10
        0.76            0.09        0.15

Matches are distributed among these distances:
  13    3  0.06
  14   45  0.90
  15    2  0.04

ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49


Consensus pattern (14 bp):   
GTTTAGGGTTTAGA

Found at i:2429 original size:45 final size:45

Alignment explanation


    Indices: 2365--2479  Score: 151
    Period size: 45  Copynumber: 2.6  Consensus size: 45

       2355 GAAAAGAATA

                  *  *                *                   
       2365 GAGTATCGCTGTAGCTCGTCAAACT-CAGCCTGATATCCTTCCCTT
          1 GAGTATTGCGGTAGCTCGTCAAACTGAAG-CTGATATCCTTCCCTT

                                   *                **   
       2410 GAGTATTGCGGTAGCTCGTCAAATTGAAGCTGATATCCTTGGCTT
          1 GAGTATTGCGGTAGCTCGTCAAACTGAAGCTGATATCCTTCCCTT

                        *            
       2455 GAGTATTGCGGTGGCTCGTCAAACT
          1 GAGTATTGCGGTAGCTCGTCAAACT

       2480 AAATATTTAT


Statistics
Matches: 61,  Mismatches: 8, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  45   59  0.97
  46    2  0.03

ACGTcount: A:0.21, C:0.23, G:0.24, T:0.31


Consensus pattern (45 bp):   
GAGTATTGCGGTAGCTCGTCAAACTGAAGCTGATATCCTTCCCTT
Done.