Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2324

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: 16070
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30


Found at i:1503 original size:40 final size:40

Alignment explanation


    Indices: 1459--1608  Score: 248
    Period size: 40  Copynumber: 3.8  Consensus size: 40

       1449 AACTTCGCAC

                                                    
       1459 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT

                                                    
       1499 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT

                                            *       *
       1539 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTT

               *             *            
       1579 GCATAAATGCCTTCGGGACTTAGCCCGGAT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT

       1609 GTATTCAAAT


Statistics
Matches: 105,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  40  101  0.96
  41    4  0.04

ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25


Consensus pattern (40 bp):   
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT

Found at i:9969 original size:40 final size:40

Alignment explanation


    Indices: 9917--10146  Score: 336
    Period size: 40  Copynumber: 5.8  Consensus size: 40

       9907 ATAACCACAA

                  *               *     *    *      
       9917 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC

                *                               *   
       9957 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC

                                                   *
       9997 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC

                                                   *
      10037 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC

                                            *       *
      10077 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC

               *             *            
      10117 GCATAAATGCCTTCGGGACTTAGCCCGGAT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT

      10147 GTATTCAAAT


Statistics
Matches: 176,  Mismatches: 13, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
  40  172  0.98
  41    4  0.02

ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26


Consensus pattern (40 bp):   
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC

Found at i:12423 original size:71 final size:67

Alignment explanation


    Indices: 12346--12486  Score: 183
    Period size: 67  Copynumber: 2.0  Consensus size: 67

      12336 CACCAGATAT

                      * * *                                                  
      12346 AGATATTATGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGAG
          1 AGATATTATGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGAG

                  
      12411 GCTGCC
         62 GCTGCC

                   *        *                        *               *       
      12417 AGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGTGAGGCTG
          1 AGATATTATGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCTG

              
      12482 CC
         66 CC

               
      12484 AGA
          1 AGA

      12487 ATGCTTCCTC


Statistics
Matches: 63,  Mismatches: 7, Indels: 4
        0.85            0.09        0.05

Matches are distributed among these distances:
  67   40  0.63
  71   23  0.37

ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19


Consensus pattern (67 bp):   
AGATATTATGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCTG
CC

Found at i:12464 original size:27 final size:26

Alignment explanation


    Indices: 12416--12467  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      12406 GCGAGGCTGC

                             *        
      12416 CAGATATTGTGACGAAGTCACCAGAA
          1 CAGATATTGTGACGAAGCCACCAGAA

                        *   *         
      12442 CAGATATATGTGGCGAGGCCACCAGA
          1 CAGATAT-TGTGACGAAGCCACCAGA

      12468 TTGCAGTGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17


Consensus pattern (26 bp):   
CAGATATTGTGACGAAGCCACCAGAA

Found at i:13126 original size:27 final size:27

Alignment explanation


    Indices: 13096--13151  Score: 67
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      13086 TAGTCATTTC

                 *   *            *    
      13096 ACCCTCCAGGGGTAAATCAGTAGTTCT
          1 ACCCTACAGAGGTAAATCAGTAATTCT

                          **           
      13123 ACCCTACAGAGGTATTTCAGTAATTCT
          1 ACCCTACAGAGGTAAATCAGTAATTCT

              
      13150 AC
          1 AC

      13152 AACTTATCCA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29


Consensus pattern (27 bp):   
ACCCTACAGAGGTAAATCAGTAATTCT
Done.