Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006439.1 Kokia drynarioides strain JFW-HI SEQ_121021, 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: 4814
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33


Found at i:3088 original size:33 final size:33

Alignment explanation


    Indices: 3020--3184  Score: 138
    Period size: 33  Copynumber: 5.0  Consensus size: 33

       3010 GAGGAGAGTA

                      **  *   *               
       3020 ATGTTGAAGGACTAGAAGTTGATGGTG-AGGGTG
          1 ATGTTGAAGGGGTACAAGCTGATGG-GAAGGGTG

                              *     *     *  
       3053 ATGTTGAAGGGGTACAAGTTGATGAGAAGGATG
          1 ATGTTGAAGGGGTACAAGCTGATGGGAAGGGTG

                **  *                 *      
       3086 ATGTAAAAAGGGTACAAGCTGATGGGGAGGGTG
          1 ATGTTGAAGGGGTACAAGCTGATGGGAAGGGTG

                **                            
       3119 ATGTAAAAGGGGTACAAGCTGATGGGGAA-GGTG
          1 ATGTTGAAGGGGTACAAGCTGAT-GGGAAGGGTG

                    *    **                   
       3152 ATGTTGAAAGGGTGGAAGCTGATAGGG-AGGGTG
          1 ATGTTGAAGGGGTACAAGCTGAT-GGGAAGGGTG

       3185 TGACTGCTAC


Statistics
Matches: 109,  Mismatches: 20, Indels: 6
        0.81            0.15        0.04

Matches are distributed among these distances:
  32    2  0.02
  33  103  0.94
  34    4  0.04

ACGTcount: A:0.31, C:0.04, G:0.43, T:0.22


Consensus pattern (33 bp):   
ATGTTGAAGGGGTACAAGCTGATGGGAAGGGTG

Found at i:3116 original size:66 final size:66

Alignment explanation


    Indices: 3039--3184  Score: 186
    Period size: 66  Copynumber: 2.2  Consensus size: 66

       3029 GACTAGAAGT

                  *           **            *                                
       3039 TGATGGTGAGGGTGATGTTGAAGGGGTACAAGTTGAT-GAGAAGGATGATGTAAAAAGGGTACAA
          1 TGATGGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGG-TGATGTAAAAAGGGTACAA

              
       3103 GC
         65 GC

                                                   *           **       **   
       3105 TGATGGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGGGAAGGTGATGTTGAAAGGGTGGAAG
          1 TGATGGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGGTGATGTAAAAAGGGTACAAG

             
       3170 C
         66 C

                *         
       3171 TGATAGGGAGGGTG
          1 TGATGGGGAGGGTG

       3185 TGACTGCTAC


Statistics
Matches: 69,  Mismatches: 10, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  66   63  0.91
  67    6  0.09

ACGTcount: A:0.30, C:0.04, G:0.45, T:0.21


Consensus pattern (66 bp):   
TGATGGGGAGGGTGATGTAAAAGGGGTACAAGCTGATGGAGAAGGTGATGTAAAAAGGGTACAAG
C

Found at i:3235 original size:12 final size:12

Alignment explanation


    Indices: 3218--3249  Score: 64
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       3208 GATGAGTATG

                        
       3218 GTGGTGGGGAAA
          1 GTGGTGGGGAAA

                        
       3230 GTGGTGGGGAAA
          1 GTGGTGGGGAAA

                    
       3242 GTGGTGGG
          1 GTGGTGGG

       3250 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.