Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002439.1 Kokia drynarioides strain JFW-HI SEQ_114551, 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: 3024
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:198 original size:30 final size:30

Alignment explanation


    Indices: 138--311  Score: 206
    Period size: 30  Copynumber: 5.8  Consensus size: 30

        128 GTCCCTAAAT

                 *               ** *     
        138 TTTTCTAAAATTACATTTT-AAACACAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                                          
        167 TTTTCCAAAATTACATTTTGACCCCCAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                           *   *     *    
        197 TTTTCCAAAATTACAATTTAACCCCTAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                      ** *         * *    
        227 TTTTCCAAAAGCATATTTTGACCTCTAAAC
          1 TTTTCCAAAATTACATTTTGACCCCCAAAC

                                           
        257 TTTTCCAAAATTACATTTTGACCCCTCAAAC
          1 TTTTCCAAAATTACATTTTGACCCC-CAAAC

                       * *          
        288 TTTTCCAAAATCATATTTTGACCC
          1 TTTTCCAAAATTACATTTTGACCC

        312 TTGAACTTCT


Statistics
Matches: 123,  Mismatches: 20, Indels: 2
        0.85            0.14        0.01

Matches are distributed among these distances:
  29   18  0.15
  30   79  0.64
  31   26  0.21

ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36


Consensus pattern (30 bp):   
TTTTCCAAAATTACATTTTGACCCCCAAAC

Found at i:245 original size:60 final size:60

Alignment explanation


    Indices: 138--311  Score: 242
    Period size: 60  Copynumber: 2.9  Consensus size: 60

        128 GTCCCTAAAT

                 *               * *                 * *                
        138 TTTTCTAAAATTACATTTTAAACAC-AAACTTTTCCAAAATTACATTTTGACCCCCAAAC
          1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

                           *                        *            * *    
        197 TTTTCCAAAATTACAATTTAACCCCTAAACTTTTCCAAAAGCATATTTTGACCTCTAAAC
          1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

                               *                                   
        257 TTTTCCAAAATTACATTTTGACCCCTCAAACTTTTCCAAAATCATATTTTGACCC
          1 TTTTCCAAAATTACATTTTAACCCCT-AAACTTTTCCAAAATCATATTTTGACCC

        312 TTGAACTTCT


Statistics
Matches: 100,  Mismatches: 13, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  59   21  0.21
  60   53  0.53
  61   26  0.26

ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36


Consensus pattern (60 bp):   
TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCCCAAAC

Found at i:291 original size:31 final size:31

Alignment explanation


    Indices: 162--311  Score: 207
    Period size: 30  Copynumber: 4.9  Consensus size: 31

        152 ATTTTAAACA

                                           
        162 CAAACTTTTCCAAAATTACATTTTGACCCC-
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                                *   *      
        192 CAAACTTTTCCAAAATTACAATTTAACCCCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                           ** *         *  
        223 -AAACTTTTCCAAAAGCATATTTTGACCTCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                                           
        253 -AAACTTTTCCAAAATTACATTTTGACCCCT
          1 CAAACTTTTCCAAAATTACATTTTGACCCCT

                            * *          
        283 CAAACTTTTCCAAAATCATATTTTGACCC
          1 CAAACTTTTCCAAAATTACATTTTGACCC

        312 TTGAACTTCT


Statistics
Matches: 104,  Mismatches: 14, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
  30   78  0.75
  31   26  0.25

ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35


Consensus pattern (31 bp):   
CAAACTTTTCCAAAATTACATTTTGACCCCT

Found at i:1432 original size:88 final size:88

Alignment explanation


    Indices: 1239--1425  Score: 320
    Period size: 88  Copynumber: 2.1  Consensus size: 88

       1229 CAATAACTTT

                              *                                           *  
       1239 AAAAATAATTTGGGTGGTGTCAATATTTTTAACGTCTCACGTATAATATTCGTACCAAATATTTG
          1 AAAAATAATTTGGGTGGTATCAATATTTTTAACGTCTCACGTATAATATTCGTACCAAATATCTG

             *                     
       1304 TGTTACCCATATTTTGTAACAAG
         66 TATTACCCATATTTTGTAACAAG

                                          *                         *        
       1327 AAAAATAATTTGGGTGGTATCAATATTTTTGACGTCTCACGTATAATATTCGTACCCAATATCTG
          1 AAAAATAATTTGGGTGGTATCAATATTTTTAACGTCTCACGTATAATATTCGTACCAAATATCTG

                                 * 
       1392 TATTACCCATATTTTGTAACAGG
         66 TATTACCCATATTTTGTAACAAG

                       
       1415 AAAAATAATTT
          1 AAAAATAATTT

       1426 AAGTGGTGCC


Statistics
Matches: 93,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  88   93  1.00

ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38


Consensus pattern (88 bp):   
AAAAATAATTTGGGTGGTATCAATATTTTTAACGTCTCACGTATAATATTCGTACCAAATATCTG
TATTACCCATATTTTGTAACAAG
Done.