Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008190.1 Kokia drynarioides strain JFW-HI SEQ_122849, 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: 5106
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31


Found at i:112 original size:16 final size:14

Alignment explanation


    Indices: 91--134  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 14

         81 ATTTTTATGG

                           
         91 ATTAAAGAATAATTA
          1 ATTAAA-AATAATTA

                        *  
        106 TATTAAAAATAAATA
          1 -ATTAAAAATAATTA

                          
        121 ATATAAAAATAATT
          1 AT-TAAAAATAATT

        135 CAATATGTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    2  0.08
  15   17  0.68
  16    6  0.24

ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34


Consensus pattern (14 bp):   
ATTAAAAATAATTA

Found at i:1321 original size:16 final size:16

Alignment explanation


    Indices: 1300--1331  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1290 ATAATTTGAA

                            
       1300 AATAAAGATAAAATGT
          1 AATAAAGATAAAATGT

                   *        
       1316 AATAAAGGTAAAATGT
          1 AATAAAGATAAAATGT

       1332 GATCCACAAC


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

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25


Consensus pattern (16 bp):   
AATAAAGATAAAATGT

Found at i:2172 original size:26 final size:26

Alignment explanation


    Indices: 2129--2182  Score: 72
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       2119 ATTTTAGGCG

                                   *  
       2129 CAATTCTGGACACATTCATGCAGTGA
          1 CAATTCTGGACACATTCATGCAGCGA

                    *   **            
       2155 CAATTCTGTACATGTTCATGCAGCGA
          1 CAATTCTGGACACATTCATGCAGCGA

              
       2181 CA
          1 CA

       2183 TTCCTAGGTG


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28


Consensus pattern (26 bp):   
CAATTCTGGACACATTCATGCAGCGA

Found at i:2214 original size:37 final size:38

Alignment explanation


    Indices: 2172--2260  Score: 101
    Period size: 38  Copynumber: 2.4  Consensus size: 38

       2162 GTACATGTTC

                               *                   
       2172 ATGCAGCGACA-TTCCTAGGTGCAA-TTGAAGAATACTT
          1 ATGCAGCGACAGTT-CTAGATGCAATTTGAAGAATACTT

                  *  *                         *  
       2209 ATGCAGTGATAGTTCTAGATGCAATTTGAAGAATATTT
          1 ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT

                 *   *    
       2247 ATGCAACGATAGTT
          1 ATGCAGCGACAGTT

       2261 TTGGGTGCAT


Statistics
Matches: 44,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  37   18  0.41
  38   26  0.59

ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31


Consensus pattern (38 bp):   
ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT

Found at i:2249 original size:38 final size:37

Alignment explanation


    Indices: 2186--2260  Score: 105
    Period size: 38  Copynumber: 2.0  Consensus size: 37

       2176 AGCGACATTC

                *                       **       
       2186 CTAGGTGCAATTGAAGAATACTTATGCAGTGATAGTT
          1 CTAGATGCAATTGAAGAATACTTATGCAACGATAGTT

                                 *                
       2223 CTAGATGCAATTTGAAGAATATTTATGCAACGATAGTT
          1 CTAGATGCAA-TTGAAGAATACTTATGCAACGATAGTT

       2261 TTGGGTGCAT


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  37    9  0.27
  38   24  0.73

ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33


Consensus pattern (37 bp):   
CTAGATGCAATTGAAGAATACTTATGCAACGATAGTT

Found at i:2373 original size:36 final size:36

Alignment explanation


    Indices: 2285--2373  Score: 108
    Period size: 36  Copynumber: 2.5  Consensus size: 36

       2275 AAAATATTCC

                       *     *       *          
       2285 TGCAGCGACATTTTTGGTGCAATCTGGAAGTGCTCA
          1 TGCAGCGACATGTTTGGCGCAATCTAGAAGTGCTCA

               * *                  *            
       2321 TGCGGTGACA-GTTTTGGCGCAATTTAGAAGTGCTCA
          1 TGCAGCGACATG-TTTGGCGCAATCTAGAAGTGCTCA

                             
       2357 TGCAGCGACATGTTTGG
          1 TGCAGCGACATGTTTGG

       2374 GGGTAATTCT


Statistics
Matches: 43,  Mismatches: 8, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
  36   42  0.98
  37    1  0.02

ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30


Consensus pattern (36 bp):   
TGCAGCGACATGTTTGGCGCAATCTAGAAGTGCTCA

Found at i:2933 original size:2 final size:2

Alignment explanation


    Indices: 2926--2959  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       2916 TAATATACAC

                                                              
       2926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2960 TTTTTTTTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.