Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3763

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: 11215
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:2671 original size:3 final size:3

Alignment explanation


    Indices: 2652--2691  Score: 62
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       2642 GTATATGCAT

                     *                                          
       2652 ATA ATA AAA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA

       2692 TGAAAATACA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   3   31  0.91
   4    3  0.09

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:3184 original size:24 final size:24

Alignment explanation


    Indices: 3157--3202  Score: 67
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       3147 GAGAGAAAAA

                *                    
       3157 AAAGGAGAGAAGGGG-AGAGGGAAG
          1 AAAGAAGAG-AGGGGAAGAGGGAAG

                                  
       3181 AAAGAAGAGAGGGGAAGAGGGA
          1 AAAGAAGAGAGGGGAAGAGGGA

       3203 GCTCGGCCAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    5  0.25
  24   15  0.75

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (24 bp):   
AAAGAAGAGAGGGGAAGAGGGAAG

Found at i:3330 original size:16 final size:16

Alignment explanation


    Indices: 3297--3343  Score: 51
    Period size: 16  Copynumber: 3.0  Consensus size: 16

       3287 GAAAAGGTCA

                    *  * *  
       3297 ATTTTTTTTTTTTTTT
          1 ATTTTTTTATTATATT

                            
       3313 ATTTTTTTATTATATT
          1 ATTTTTTTATTATATT

               *            
       3329 ATTATTTTA-TATATT
          1 ATTTTTTTATTATATT

       3344 TTAGTATATA


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  15    6  0.22
  16   21  0.78

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (16 bp):   
ATTTTTTTATTATATT

Found at i:4883 original size:127 final size:127

Alignment explanation


    Indices: 4627--5019  Score: 645
    Period size: 127  Copynumber: 3.1  Consensus size: 127

       4617 TTAACTCATT

                                                                             
       4627 TCTCGCAATATGAGTTGAATT-TTGA-AAACAGAAATTGAAATTACCTCATCGTATCCTGAGG-T
          1 TCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT

                    *                                                      
       4689 CAACTCACTTCTAGCAATATGAGTTGATTTTG-AAAAGTAGGAATTAAAAGGTTCAACCCACC
         65 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC

                                       *                                     
       4751 TCTCGCAATATGAGTTGATTCTTGACAGACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
          1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC

                                                                          
       4816 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC
         66 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC

                     *                                                       
       4878 TCTCGCAATGTGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
          1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC

                                                 * **   *             *    
       4943 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA-CAAAAATGAAAAGGCTT-AACTCACC
         66 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGG-TTCAACCCACC

                            
       5004 TCTCGCAATAATGAGT
          1 TCTCGCAAT-ATGAGT

       5020 CAATTTAAAA


Statistics
Matches: 253,  Mismatches: 10, Indels: 9
        0.93            0.04        0.03

Matches are distributed among these distances:
 123    3  0.01
 124   21  0.08
 125   35  0.14
 126   58  0.23
 127  136  0.54

ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29


Consensus pattern (127 bp):   
TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC
Done.