Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1399

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: 25152
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32


Found at i:3554 original size:12 final size:12

Alignment explanation


    Indices: 3537--3574  Score: 51
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       3527 GAAAGGAAAT

                  *     
       3537 AAAAAATAAAGA
          1 AAAAAAGAAAGA

                     *  
       3549 AAAAAAGAATG-
          1 AAAAAAGAAAGA

                        
       3560 AAAAAAGAAAGA
          1 AAAAAAGAAAGA

               
       3572 AAA
          1 AAA

       3575 GAACATAGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  11   10  0.45
  12   12  0.55

ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05


Consensus pattern (12 bp):   
AAAAAAGAAAGA

Found at i:11213 original size:68 final size:65

Alignment explanation


    Indices: 11138--11308  Score: 168
    Period size: 66  Copynumber: 2.6  Consensus size: 65

      11128 CATCATGTGT

                                                      *             * *      
      11138 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
          1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATAC-AGTGAAGGACACCA

                 
      11201 TGTAG
         61 TGTAG

                          **                          * *                    
      11206 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCAGGTGAAGGACACCATGTA
          1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACA-GTGAAGGACACCATGTA

             
      11271 G
         65 G

                           *   *    *        *    
      11272 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
          1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG

      11309 GTTGGTACTG


Statistics
Matches: 89,  Mismatches: 11, Indels: 9
        0.82            0.10        0.08

Matches are distributed among these distances:
  63    1  0.01
  64   23  0.26
  65   18  0.20
  66   34  0.38
  68   13  0.15

ACGTcount: A:0.32, C:0.16, G:0.29, T:0.22


Consensus pattern (65 bp):   
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACAGTGAAGGACACCATGTAG

Found at i:11243 original size:64 final size:64

Alignment explanation


    Indices: 11162--11344  Score: 194
    Period size: 66  Copynumber: 2.8  Consensus size: 64

      11152 AGACATTATG

                                  *                                   *    *
      11162 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
          1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA

                              *     *        * *                             
      11226 ATGTAGCTAGGTCGCATGCGTGGTTC-AGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
          1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT

              
      11290 AA
         63 AA

                *        *     *              *                     
      11292 AT-TGGCTAGGTCACATGGTTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
          1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC

      11345 GAACTATATG


Statistics
Matches: 98,  Mismatches: 15, Indels: 13
        0.78            0.12        0.10

Matches are distributed among these distances:
  62    1  0.01
  63   20  0.20
  64   24  0.24
  65   20  0.20
  66   32  0.33
  67    1  0.01

ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24


Consensus pattern (64 bp):   
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA

Found at i:15409 original size:39 final size:40

Alignment explanation


    Indices: 15348--15458  Score: 197
    Period size: 39  Copynumber: 2.8  Consensus size: 40

      15338 AAAAAAATAT

                                                    
      15348 CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAAC
          1 CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAAC

                                                    
      15388 CGGGTTAAGT-CCGAAGGCATTCGTGCGGGTTATTATAAC
          1 CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAAC

                                  *    *    
      15427 CGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
          1 CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT

      15459 GTTACATCCG


Statistics
Matches: 68,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  39   39  0.57
  40   29  0.43

ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29


Consensus pattern (40 bp):   
CGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAAC

Found at i:23679 original size:40 final size:40

Alignment explanation


    Indices: 23624--23741  Score: 218
    Period size: 40  Copynumber: 3.0  Consensus size: 40

      23614 TGGAAAAAAA

                                                    
      23624 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
          1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT

                                                    
      23664 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
          1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT

                                        *    *    
      23704 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
          1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT

      23742 GTTACATCCG


Statistics
Matches: 76,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  40   76  1.00

ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29


Consensus pattern (40 bp):   
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Done.