Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3777

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: 13551
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30


Found at i:1550 original size:23 final size:23

Alignment explanation


    Indices: 1520--1565  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1510 AACTAACATT

                                   
       1520 GATACGCCTCACCTCGAGATCGA
          1 GATACGCCTCACCTCGAGATCGA

                                   
       1543 GATACGCCTCACCTCGAGATCGA
          1 GATACGCCTCACCTCGAGATCGA

       1566 ATTGAGTCGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17


Consensus pattern (23 bp):   
GATACGCCTCACCTCGAGATCGA

Found at i:5946 original size:15 final size:15

Alignment explanation


    Indices: 5926--5980  Score: 69
    Period size: 15  Copynumber: 3.8  Consensus size: 15

       5916 ACTCTCCTCA

                     *     
       5926 TTCTTTTCTTTCTTT
          1 TTCTTTTCTCTCTTT

                    *      
       5941 TTCTTTTCACTCTTT
          1 TTCTTTTCTCTCTTT

              *            
       5956 TTGTTTT-TCTCTTT
          1 TTCTTTTCTCTCTTT

                        
       5970 TTCTTTT-TCTC
          1 TTCTTTTCTCTC

       5981 GATCAATAGA


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  14   16  0.46
  15   19  0.54

ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75


Consensus pattern (15 bp):   
TTCTTTTCTCTCTTT

Found at i:11412 original size:19 final size:18

Alignment explanation


    Indices: 11376--11415  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      11366 TTTCCACTCG

                         *    
      11376 TTTCTTTTTCAACTTCTC
          1 TTTCTTTTTCAACATCTC

                      *        
      11394 TTTCTTTTTCCACAATCTC
          1 TTTCTTTTTCAAC-ATCTC

               
      11413 TTT
          1 TTT

      11416 GTTTGTTGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   12  0.63
  19    7  0.37

ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60


Consensus pattern (18 bp):   
TTTCTTTTTCAACATCTC

Found at i:12487 original size:13 final size:13

Alignment explanation


    Indices: 12469--12507  Score: 78
    Period size: 13  Copynumber: 3.0  Consensus size: 13

      12459 ACTAGCTCTC

                         
      12469 TTTTTTTTCACAA
          1 TTTTTTTTCACAA

                         
      12482 TTTTTTTTCACAA
          1 TTTTTTTTCACAA

                         
      12495 TTTTTTTTCACAA
          1 TTTTTTTTCACAA

      12508 CTTGATATCC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   26  1.00

ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62


Consensus pattern (13 bp):   
TTTTTTTTCACAA
Done.