Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2149

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: 14393
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:91 original size:43 final size:43

Alignment explanation


    Indices: 12--100  Score: 117
    Period size: 43  Copynumber: 2.1  Consensus size: 43

          2 AATTTTACTA

                              * *        * *           
         12 TTTTGTTATATCTAATATTTTATTTAATTTTTTATCTATATAT
          1 TTTTGTTATATCTAATATCTGATTTAATTATATATCTATATAT

                                     *                  
         55 TTTTGTTATATCT-ATATCTGATTTCATCTATATATCTATATAT
          1 TTTTGTTATATCTAATATCTGATTTAAT-TATATATCTATATAT

               
         98 TTT
          1 TTT

        101 ATTATATATT


Statistics
Matches: 40,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  42   11  0.28
  43   29  0.73

ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62


Consensus pattern (43 bp):   
TTTTGTTATATCTAATATCTGATTTAATTATATATCTATATAT

Found at i:2933 original size:20 final size:19

Alignment explanation


    Indices: 2885--2935  Score: 68
    Period size: 18  Copynumber: 2.6  Consensus size: 19

       2875 CAAGAGAAAG

                                
       2885 TATCGATACCTTAATTAAAA
          1 TATC-ATACCTTAATTAAAA

                        *      
       2905 TAT-ATACCTTAGTTAAAA
          1 TATCATACCTTAATTAAAA

                         
       2923 TATCAATACCTTA
          1 TATC-ATACCTTA

       2936 TCCTTCAATG


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  18   17  0.61
  20   11  0.39

ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37


Consensus pattern (19 bp):   
TATCATACCTTAATTAAAA

Found at i:4114 original size:22 final size:21

Alignment explanation


    Indices: 4084--4128  Score: 63
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       4074 CTTTTTTTAA

                *                 
       4084 TAATTAAAAATACAAAATAAAT
          1 TAATAAAAAATACAAAA-AAAT

                        *        
       4106 TAATAAAAAATAGAAAAAAAT
          1 TAATAAAAAATACAAAAAAAT

              
       4127 TA
          1 TA

       4129 TTTTATAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    6  0.29
  22   15  0.71

ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24


Consensus pattern (21 bp):   
TAATAAAAAATACAAAAAAAT

Found at i:8497 original size:66 final size:68

Alignment explanation


    Indices: 8391--8522  Score: 205
    Period size: 66  Copynumber: 2.0  Consensus size: 68

       8381 AATCTTGGAA

                                               *                             
       8391 TTGCTGCACCATTACATCTGCATGACAAAACCAATGGGAATGAGAGTAGCTAAGCATAGT-CCTA
          1 TTGCTGCACCATTACATCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTA

               
       8455 GTG
         66 GTG

                     *              *                        * *             
       8458 TTGCTGCACTATTAC-TCTGCATGGCAAAACCAATAGGAATGAGAGTAGTTGAGCATAGTACCTA
          1 TTGCTGCACCATTACATCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTA

             
       8522 G
         66 G

       8523 AGCTGTCCCC


Statistics
Matches: 59,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  66   40  0.68
  67   19  0.32

ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25


Consensus pattern (68 bp):   
TTGCTGCACCATTACATCTGCATGACAAAACCAATAGGAATGAGAGTAGCTAAGCATAGTACCTA
GTG

Found at i:13048 original size:20 final size:21

Alignment explanation


    Indices: 13009--13051  Score: 70
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      12999 TAATATTCTT

                         *       
      13009 GAAAAGAAATTAAGTGAATTA
          1 GAAAAGAAATTAAATGAATTA

                                 
      13030 GAAAAGAAA-TAAATGAATTA
          1 GAAAAGAAATTAAATGAATTA

              
      13050 GA
          1 GA

      13052 GGAAAAAAGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20   12  0.57
  21    9  0.43

ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21


Consensus pattern (21 bp):   
GAAAAGAAATTAAATGAATTA

Found at i:13066 original size:21 final size:20

Alignment explanation


    Indices: 13009--13066  Score: 55
    Period size: 21  Copynumber: 2.8  Consensus size: 20

      12999 TAATATTCTT

                      *  *       
      13009 GAAAAGAAATTAAGTGAATTA
          1 GAAAAGAAA-GAAATGAATTA

                     *          
      13030 GAAAAGAAATAAATGAATTA
          1 GAAAAGAAAGAAATGAATTA

                              
      13050 GAGGAAA-AAAGAAATGA
          1 GA--AAAGAAAGAAATGA

      13067 GTTGCAAGTG


Statistics
Matches: 33,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   12  0.36
  21   18  0.55
  22    3  0.09

ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17


Consensus pattern (20 bp):   
GAAAAGAAAGAAATGAATTA
Done.