Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3157

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: 22758
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:3657 original size:40 final size:38

Alignment explanation


    Indices: 3566--3788  Score: 182
    Period size: 40  Copynumber: 5.6  Consensus size: 38

       3556 TCCTCGTTCA

                          *  *     *    *      *   
       3566 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC

             *                                     
       3605 AGTGCCTTCGGGACTTAACCCGGATTTAATGACTCGCAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC

                                                    
       3644 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGGATTTAATA-CTCGCAC

               *         *                            
       3684 AAAGGCCTTCGGGGCTTAACCCGGAACTTGT-AT-CTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGG-A-TT-TAATACTCGCAC

                               **      *  *      *    
       3724 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
          1 -AATGCCTTCGGGA-CTTAACCCGGATTTAAT-AC-TCGCAC

              *              *      
       3765 AAAGCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       3789 CAGCATTCAA


Statistics
Matches: 153,  Mismatches: 20, Indels: 21
        0.79            0.10        0.11

Matches are distributed among these distances:
  37    1  0.01
  38    2  0.01
  39   36  0.24
  40  100  0.65
  41    9  0.06
  42    4  0.03
  43    1  0.01

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26


Consensus pattern (38 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCAC

Found at i:3797 original size:41 final size:41

Alignment explanation


    Indices: 3720--3797  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

       3710 CTTGTATCTC

                                   *     * *         
       3720 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
       3761 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

       3798 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

Found at i:8444 original size:15 final size:15

Alignment explanation


    Indices: 8424--8457  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       8414 TATCAAGTTG

                           
       8424 AAAAAAATTCGTGAA
          1 AAAAAAATTCGTGAA

                           
       8439 AAAAAAATTCGTGAA
          1 AAAAAAATTCGTGAA

                
       8454 AAAA
          1 AAAA

       8458 GAAGAAGAAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18


Consensus pattern (15 bp):   
AAAAAAATTCGTGAA

Found at i:11776 original size:22 final size:22

Alignment explanation


    Indices: 11725--11790  Score: 80
    Period size: 21  Copynumber: 3.0  Consensus size: 22

      11715 GGTATTTGGG

                   *      *       
      11725 AATTGGTTCGAAATAGTATGG-
          1 AATTGGTACGAAATGGTATGGT

                                  
      11746 AATTGGTACGAAATGGTATGGT
          1 AATTGGTACGAAATGGTATGGT

             *          *          
      11768 ATTTGGTACGAATTGGTAATGGT
          1 AATTGGTACGAAATGGT-ATGGT

      11791 TGAAAAGGAC


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   19  0.49
  22   15  0.38
  23    5  0.13

ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35


Consensus pattern (22 bp):   
AATTGGTACGAAATGGTATGGT

Found at i:14561 original size:17 final size:17

Alignment explanation


    Indices: 14539--14573  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      14529 TACTGGAATA

                              
      14539 AATTAATT-ATTTAAGTT
          1 AATTAATTAATTT-AGTT

                             
      14556 AATTAATTAATTTAGTT
          1 AATTAATTAATTTAGTT

             
      14573 A
          1 A

      14574 CAGCTCTTAA


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

Matches are distributed among these distances:
  17   13  0.76
  18    4  0.24

ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51


Consensus pattern (17 bp):   
AATTAATTAATTTAGTT

Found at i:15946 original size:11 final size:10

Alignment explanation


    Indices: 15930--15959  Score: 51
    Period size: 10  Copynumber: 2.9  Consensus size: 10

      15920 TTCGTAACGT

                       
      15930 AAAAAAAAGTC
          1 AAAAAAAA-TC

                      
      15941 AAAAAAAATC
          1 AAAAAAAATC

                     
      15951 AAAAAAAAT
          1 AAAAAAAAT

      15960 TGAGTTGGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   11  0.58
  11    8  0.42

ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10


Consensus pattern (10 bp):   
AAAAAAAATC
Done.