Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_449 ID=scaffold_449-JGI_221_v2.0

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: 6868
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27


Found at i:27 original size:17 final size:17

Alignment explanation


    Indices: 1--36  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

                 *           
          1 TTTTGGCTGCATGACAT
          1 TTTTGACTGCATGACAT

                         *   
         18 TTTTGACTGCATGGCAT
          1 TTTTGACTGCATGACAT

              
         35 TT
          1 TT

         37 CATCATATAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44


Consensus pattern (17 bp):   
TTTTGACTGCATGACAT

Found at i:4769 original size:87 final size:87

Alignment explanation


    Indices: 4661--4868  Score: 301
    Period size: 87  Copynumber: 2.4  Consensus size: 87

       4651 CAGTGAAATT

                 *                                                      * *  
       4661 ATAAATCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCTTGCCTTCTTGCA
          1 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCTTGCCTTCCTACA

              *                   
       4726 TCGACAACGAAGCAGATCGAAA
         66 TCAACAACGAAGCAGATCGAAA

                                                                             
       4748 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCTTGCCTTCCTACA
          1 ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCTTGCCTTCCTACA

             *    *          *   *
       4813 TTAACAGCGAAGCAGATTGAAG
         66 TCAACAACGAAGCAGATCGAAA

                *      *                       
       4835 ATACCAGCCTTACCTCCCTC-GATTGCAGTGGAGC
          1 ATA-AAGCCTTGCCTCCCTCAG-TTGCAGTGGAGC

       4869 TGGTTGATGG


Statistics
Matches: 109,  Mismatches: 10, Indels: 3
        0.89            0.08        0.02

Matches are distributed among these distances:
  87   83  0.76
  88   26  0.24

ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24


Consensus pattern (87 bp):   
ATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGCAAATCTTGCCTTCCTACA
TCAACAACGAAGCAGATCGAAA

Found at i:4805 original size:44 final size:44

Alignment explanation


    Indices: 4663--4805  Score: 125
    Period size: 44  Copynumber: 3.2  Consensus size: 44

       4653 GTGAAATTAT

                                                         
       4663 AAATCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGC
          1 AAAT-CTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGC

                       * *      *    ** *         *         
       4708 AAATCTTGCCTTCTTGCA-TCGACAACGAAGC-AGATCGAAA-ATA--
          1 AAATCTTGCCTCCCT-CAGTTG-CAGTGGAGCAAG-T-TAAAGATAGC

              **                                        
       4751 AAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGC
          1 AAATCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGC

                       
       4795 AAATCTTGCCT
          1 AAATCTTGCCT

       4806 TCCTACATTA


Statistics
Matches: 71,  Mismatches: 18, Indels: 19
        0.66            0.17        0.18

Matches are distributed among these distances:
  41    3  0.04
  42   12  0.17
  43   15  0.21
  44   22  0.31
  45   16  0.23
  46    3  0.04

ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24


Consensus pattern (44 bp):   
AAATCTTGCCTCCCTCAGTTGCAGTGGAGCAAGTTAAAGATAGC

Found at i:5142 original size:107 final size:107

Alignment explanation


    Indices: 4956--5171  Score: 405
    Period size: 107  Copynumber: 2.0  Consensus size: 107

       4946 AGTGGAATAG

                                                                             
       4956 ATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTAC
          1 ATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTAC

                                                  *   
       5021 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
         66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCT

                  *                                          *               
       5063 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGGCGGATTTTAC
          1 ATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTAC

                                                      
       5128 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCT
         66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCT

              
       5170 AT
          1 AT

       5172 CTCCCTGGGC


Statistics
Matches: 106,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 107  106  1.00

ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28


Consensus pattern (107 bp):   
ATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCT

Found at i:5332 original size:46 final size:45

Alignment explanation


    Indices: 5250--5339  Score: 110
    Period size: 46  Copynumber: 2.0  Consensus size: 45

       5240 AAGTTGCAAT

                                *          *             
       5250 GGGGCAGACTAAGGAAGCAAGTCTTATCCTCTTGAAGTTACAGTA
          1 GGGGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTA

                           **                        *    
       5295 GGGGCAGACTGAAGGTTGCAAATCTTAT-CTCCCTGAAGTTGCAGT
          1 GGGGCAGACT-AAGGAAGCAAATCTTATCCT-CCTGAAGTTACAGT

       5340 GGAGCGGATT


Statistics
Matches: 38,  Mismatches: 5, Indels: 3
        0.83            0.11        0.07

Matches are distributed among these distances:
  45   12  0.32
  46   26  0.68

ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26


Consensus pattern (45 bp):   
GGGGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTA
Done.