Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006438.1 Kokia drynarioides strain JFW-HI SEQ_121020, 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: 4809
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33


Found at i:3056 original size:33 final size:31

Alignment explanation


    Indices: 3004--3183  Score: 144
    Period size: 33  Copynumber: 5.5  Consensus size: 31

       2994 TTACTGTTGA

                       *  *           *  *   
       3004 CTGATGAGGAGAGTAATGTTGAAGGACTAAAAG
          1 CTGATG-GGAGGGTGATGTTGAAGG-GTACAAG

                                             
       3037 CTGATGGTGAGGGTGATGTTGAAGGGGTACAAG
          1 CTGATGG-GAGGGTGATGTTGAA-GGGTACAAG

            *       *   *      **            
       3070 TTGATGAGAAGGATGATGTAAAATGGGTACAAG
          1 CTGATG-GGAGGGTGATGTTGAA-GGGTACAAG

                               **            
       3103 CTGATGGGGAGGGTGATGTAAAAGGGGTACAAG
          1 CTGAT-GGGAGGGTGATGTTGAA-GGGTACAAG

                      *                  *   
       3136 CTGATGGGGAAGGTGATGTTGAAAGGGTAGAAG
          1 CTGAT-GGGAGGGTGATGTTG-AAGGGTACAAG

                           
       3169 CTGATAGGGAGGGTG
          1 CTGAT-GGGAGGGTG

       3184 TGATTGCTAC


Statistics
Matches: 122,  Mismatches: 20, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
  32    1  0.01
  33  115  0.94
  34    6  0.05

ACGTcount: A:0.32, C:0.05, G:0.42, T:0.22


Consensus pattern (31 bp):   
CTGATGGGAGGGTGATGTTGAAGGGTACAAG

Found at i:3109 original size:66 final size:65

Alignment explanation


    Indices: 3034--3183  Score: 187
    Period size: 66  Copynumber: 2.3  Consensus size: 65

       3024 GAAGGACTAA

                                  **            *                            
       3034 AAGCTGATGGTGAGGGTGATGTTGAAGGGGTACAAGTTGAT-GAGAAGGATGATG-TAAAATGGG
          1 AAGCTGATGG-GAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGG-TGATGTTAAAA-GGG

               
       3097 TAC
         63 TAC

                                                       *            *        
       3100 AAGCTGATGGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGGGAAGGTGATGTTGAAAGGGTA
          1 AAGCTGAT-GGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGGTGATGTTAAAAGGGTA

            *
       3165 G
         65 C

                              
       3166 AAGCTGATAGGGAGGGTG
          1 AAGCTGAT-GGGAGGGTG

       3184 TGATTGCTAC


Statistics
Matches: 74,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  66   62  0.84
  67   12  0.16

ACGTcount: A:0.31, C:0.05, G:0.43, T:0.21


Consensus pattern (65 bp):   
AAGCTGATGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGGTGATGTTAAAAGGGTAC

Found at i:3234 original size:12 final size:12

Alignment explanation


    Indices: 3217--3248  Score: 64
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       3207 AATGAGTATG

                        
       3217 GTGGTGGGGAAA
          1 GTGGTGGGGAAA

                        
       3229 GTGGTGGGGAAA
          1 GTGGTGGGGAAA

                    
       3241 GTGGTGGG
          1 GTGGTGGG

       3249 CAAATAAGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.19, C:0.00, G:0.62, T:0.19


Consensus pattern (12 bp):   
GTGGTGGGGAAA
Done.