Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold727

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: 8391
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36


Found at i:60 original size:42 final size:42

Alignment explanation


    Indices: 1--305  Score: 280
    Period size: 42  Copynumber: 7.1  Consensus size: 42

                                           *         *
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCA
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG

                 *                      * *           
         43 CTAAATAACATGATCTTTAGCGGCGTTTGTCTCTAAGCGCCG
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG

                                              *   *   * 
         85 CTAAAGAACATGATCTTTAGCGGCGTTTTTGGTTGTAAACGCTG
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTT--TTCTAAGCGCCG

                     **           *        *      *   *    **
        129 C-AAACGTTTGCGA-GATTTTCGTTAGCGGCCTTTTTTGC--GGCGCTT
          1 CTAAA-G--AAC-ATGA---TCTTTAGCGGCGTTTTTTTCTAAGCGCCG

                                                      
        174 CT--AGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG

               *                            *         
        214 CTATAGAACATGATCTTTAGCGGCGTTTTTTTATAAGCGCCG
          1 CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG

                                     *        *         
        256 CTAAAGAACATGATCTTTAGCGGCCTTTTTTTATGTAAGCGCCG
          1 CTAAAGAACATGATCTTTAGCGG-CGTTTTTT-TCTAAGCGCCG

             *    
        300 CAAAAG
          1 CTAAAG

        306 TTAGCGACGT


Statistics
Matches: 213,  Mismatches: 33, Indels: 32
        0.77            0.12        0.12

Matches are distributed among these distances:
  38   17  0.08
  40    7  0.03
  41    3  0.01
  42  124  0.58
  43   11  0.05
  44   26  0.12
  45    5  0.02
  46    3  0.01
  47    2  0.01
  49   15  0.07

ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33


Consensus pattern (42 bp):   
CTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCG

Found at i:336 original size:171 final size:171

Alignment explanation


    Indices: 5--347  Score: 501
    Period size: 171  Copynumber: 2.0  Consensus size: 171

          1 CTAA

                                                       *                     
          5 AGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCACTAAATAACATGATCTTTAGCGGCGTT
          1 AGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTT

                 *                                 *                 *     * 
         70 TGTCTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGGTTGTAAACGCTGCAAACG
         66 TGTCTATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCCTTTTTGGTTGTAAACGCCGCAAAAG

              *        *    *      *                 
        135 TTTGCGAGATTTTCGTTAGCGGCCTTTTTTGCGGCGCTTCT
        131 TTAGCGAGATTGTCGTCAGCGGCATTTTTTGCGGCGCTTCT

                                       *         *   *                       
        176 AGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTATAGAACATGATCTTTAGCGGCGTT
          1 AGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTT

             * *                                          *       *          
        241 TTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCCTTTTT-TTATGTAAGCGCCGCAAAA
         66 TGTCTATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCCTTTTTGGT-TGTAAACGCCGCAAAA

                                             *         
        305 GTTAGCGACG-TTGTCGTCAGCGGCATTTTTTGTGGCGCTTCT
        130 GTTAGCGA-GATTGTCGTCAGCGGCATTTTTTGCGGCGCTTCT

             
        347 A
          1 A

        348 CAAGCGCCGG


Statistics
Matches: 153,  Mismatches: 17, Indels: 4
        0.88            0.10        0.02

Matches are distributed among these distances:
 170    1  0.01
 171  151  0.99
 172    1  0.01

ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34


Consensus pattern (171 bp):   
AGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTT
TGTCTATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCCTTTTTGGTTGTAAACGCCGCAAAAG
TTAGCGAGATTGTCGTCAGCGGCATTTTTTGCGGCGCTTCT

Found at i:5263 original size:21 final size:21

Alignment explanation


    Indices: 5237--5287  Score: 93
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       5227 TATAGTTTAG

                                 
       5237 GGTTTAGGGGATAAGGGTTGT
          1 GGTTTAGGGGATAAGGGTTGT

                    *            
       5258 GGTTTAGGCGATAAGGGTTGT
          1 GGTTTAGGGGATAAGGGTTGT

                     
       5279 GGTTTAGGG
          1 GGTTTAGGG

       5288 TCTAGGTTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33


Consensus pattern (21 bp):   
GGTTTAGGGGATAAGGGTTGT

Found at i:6442 original size:47 final size:48

Alignment explanation


    Indices: 6372--6464  Score: 179
    Period size: 47  Copynumber: 2.0  Consensus size: 48

       6362 CACGAATCGA

                                                            
       6372 TTTTATTTCCCTCTTTTTTTTCGTGTTTAGGGTTCAATATCGTTAAGG
          1 TTTTATTTCCCTCTTTTTTTTCGTGTTTAGGGTTCAATATCGTTAAGG

                                                          
       6420 TTTTA-TTCCCTCTTTTTTTTCGTGTTTAGGGTTCAATATCGTTAA
          1 TTTTATTTCCCTCTTTTTTTTCGTGTTTAGGGTTCAATATCGTTAA

       6465 CAATCCATTT


Statistics
Matches: 45,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  47   40  0.89
  48    5  0.11

ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55


Consensus pattern (48 bp):   
TTTTATTTCCCTCTTTTTTTTCGTGTTTAGGGTTCAATATCGTTAAGG

Found at i:7171 original size:22 final size:22

Alignment explanation


    Indices: 7144--7190  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       7134 GTCTTTCTAC

                                  
       7144 TTAGGTTTAATCAGTATAAAAT
          1 TTAGGTTTAATCAGTATAAAAT

                             *    
       7166 TTAGGTTTAATCAGTATTAAAT
          1 TTAGGTTTAATCAGTATAAAAT

               
       7188 TTA
          1 TTA

       7191 AGAAAATTTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45


Consensus pattern (22 bp):   
TTAGGTTTAATCAGTATAAAAT
Done.