Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6784.1

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: 9784
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:2921 original size:18 final size:18

Alignment explanation


    Indices: 2900--2934  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2890 TTTTTCTTTT

                               
       2900 TCAATTT-TTTTCTCAATC
          1 TCAATTTCTTTT-TCAATC

                             
       2918 TCAATTTCTTTTTCAAT
          1 TCAATTTCTTTTTCAAT

       2935 TTTCTTTTCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   12  0.75
  19    4  0.25

ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57


Consensus pattern (18 bp):   
TCAATTTCTTTTTCAATC

Found at i:3889 original size:12 final size:12

Alignment explanation


    Indices: 3873--3910  Score: 58
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       3863 TTTTTGCTCG

                        
       3873 ATTTTTTTTTCA
          1 ATTTTTTTTTCA

            *         * 
       3885 CTTTTTTTTTGA
          1 ATTTTTTTTTCA

                        
       3897 ATTTTTTTTTCA
          1 ATTTTTTTTTCA

              
       3909 AT
          1 AT

       3911 CAAATTTTTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74


Consensus pattern (12 bp):   
ATTTTTTTTTCA

Found at i:3889 original size:24 final size:24

Alignment explanation


    Indices: 3862--3908  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3852 CTTTTCTTTT

                                     
       3862 TTTTTTGCTCG-ATTTTTTTTTCAC
          1 TTTTTT-CTCGAATTTTTTTTTCAC

                  * *              
       3886 TTTTTTTTTGAATTTTTTTTTCA
          1 TTTTTTCTCGAATTTTTTTTTCA

       3909 ATCAAATTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    2  0.10
  24   18  0.90

ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72


Consensus pattern (24 bp):   
TTTTTTCTCGAATTTTTTTTTCAC

Found at i:3893 original size:31 final size:31

Alignment explanation


    Indices: 3829--3894  Score: 82
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       3819 TAACACTTGA

                                    *      
       3829 TTTTTTTTGCTCACCTTTTTTTTCTTTTCTT
          1 TTTTTTTTGCTCACCTTTTTTTTCCTTTCTT

                           *                 
       3860 TTTTTTTTGCTCGA-TTTTTTTTTCACTTT-TT
          1 TTTTTTTTGCTC-ACCTTTTTTTTC-CTTTCTT

                
       3891 TTTT
          1 TTTT

       3895 GAATTTTTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  31   27  0.87
  32    4  0.13

ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76


Consensus pattern (31 bp):   
TTTTTTTTGCTCACCTTTTTTTTCCTTTCTT

Found at i:3921 original size:18 final size:17

Alignment explanation


    Indices: 3896--3940  Score: 90
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       3886 TTTTTTTTTG

                             
       3896 AATTTTTTTTTCAATCA
          1 AATTTTTTTTTCAATCA

                             
       3913 AATTTTTTTTTCAATCA
          1 AATTTTTTTTTCAATCA

                       
       3930 AATTTTTTTTT
          1 AATTTTTTTTT

       3941 GATTTTTTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   28  1.00

ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64


Consensus pattern (17 bp):   
AATTTTTTTTTCAATCA

Found at i:5671 original size:10 final size:10

Alignment explanation


    Indices: 5658--5695  Score: 51
    Period size: 10  Copynumber: 3.8  Consensus size: 10

       5648 AAGAAGCTAA

                      
       5658 ATTGAGCTCG
          1 ATTGAGCTCG

                      
       5668 ATTGAGCT-G
          1 ATTGAGCTCG

                       
       5677 ACTTGAGCTCG
          1 A-TTGAGCTCG

             *      
       5688 AGTGAGCT
          1 ATTGAGCT

       5696 GGAAACGAGC


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
   9    2  0.08
  10   21  0.84
  11    2  0.08

ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29


Consensus pattern (10 bp):   
ATTGAGCTCG

Found at i:5682 original size:20 final size:20

Alignment explanation


    Indices: 5659--5696  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5649 AGAAGCTAAA

                      *         
       5659 TTGAGCTCGATTGAGCTGAC
          1 TTGAGCTCGAGTGAGCTGAC

                              
       5679 TTGAGCTCGAGTGAGCTG
          1 TTGAGCTCGAGTGAGCTG

       5697 GAAACGAGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29


Consensus pattern (20 bp):   
TTGAGCTCGAGTGAGCTGAC

Found at i:7325 original size:20 final size:20

Alignment explanation


    Indices: 7302--7348  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       7292 GGGTTAAGAT

                            *   
       7302 TGAGCTGAATTGAGCTTGAA
          1 TGAGCTGAATTGAGCTCGAA

                *   *          *
       7322 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGAATTGAGCTCGAA

                   
       7342 TGAGCTG
          1 TGAGCTG

       7349 GAAACGAGCT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCGAA
Done.