Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold670

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: 15559
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:4094 original size:23 final size:23

Alignment explanation


    Indices: 4063--4111  Score: 73
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       4053 TTTAAAAAAA

                                    
       4063 TAAAAAATAATAATAATCA-TAAT
          1 TAAAAAATAATAATAAT-ATTAAT

                *                  
       4086 TAAATAATAATAATAATATTAAT
          1 TAAAAAATAATAATAATATTAAT

               
       4109 TAA
          1 TAA

       4112 TTAAAAAAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  22    1  0.04
  23   23  0.96

ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35


Consensus pattern (23 bp):   
TAAAAAATAATAATAATATTAAT

Found at i:4519 original size:30 final size:29

Alignment explanation


    Indices: 4448--4548  Score: 105
    Period size: 31  Copynumber: 3.3  Consensus size: 29

       4438 CAGCTATAGC

                             *      *  *  *
       4448 AAAAGAAGAATAAAAGAAAAACAAAAACAAC
          1 AAAAGAA-AA-AAAAGACAAACAACAAGAAA

                                            
       4479 AAAAGAAAAAAAATGA-AAACAACAATAGAAA
          1 AAAAGAAAAAAAA-GACAAACAAC-A-AGAAA

                                          
       4510 AAAAGAAAAAAAAGACGAAACAACAAGAAA
          1 AAAAGAAAAAAAAGAC-AAACAACAAGAAA

                     
       4540 AAAAGAAAA
          1 AAAAGAAAA

       4549 GTTACTTTGC


Statistics
Matches: 62,  Mismatches: 3, Indels: 11
        0.82            0.04        0.14

Matches are distributed among these distances:
  29   10  0.16
  30   21  0.34
  31   24  0.39
  32    7  0.11

ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03


Consensus pattern (29 bp):   
AAAAGAAAAAAAAGACAAACAACAAGAAA

Found at i:4520 original size:23 final size:23

Alignment explanation


    Indices: 4464--4513  Score: 73
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       4454 AGAATAAAAG

                 *                 
       4464 AAAAACAAAAACAACAAAAGAAA
          1 AAAAATAAAAACAACAAAAGAAA

                  *          *     
       4487 AAAAATGAAAACAACAATAGAAA
          1 AAAAATAAAAACAACAAAAGAAA

                
       4510 AAAA
          1 AAAA

       4514 GAAAAAAAAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.80, C:0.10, G:0.06, T:0.04


Consensus pattern (23 bp):   
AAAAATAAAAACAACAAAAGAAA

Found at i:4660 original size:3 final size:3

Alignment explanation


    Indices: 4617--4643  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       4607 AACACAGCAG

                                               
       4617 CAA CAA CAA CAA CAA CAA CAA CAA CAA
          1 CAA CAA CAA CAA CAA CAA CAA CAA CAA

       4644 GCAAGTAGCA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00


Consensus pattern (3 bp):   
CAA

Found at i:13749 original size:22 final size:21

Alignment explanation


    Indices: 13722--13773  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 21

      13712 TTGCAAGTTG

                                   
      13722 AAATAAAAAATTTAGCTAATG-A
          1 AAATAAAAAA-TTAGCTAA-GAA

                    *             
      13744 AAATAAATGAATTAGCTAAGAA
          1 AAATAAA-AAATTAGCTAAGAA

                    
      13766 AAATAAAA
          1 AAATAAAA

      13774 CTTGCATGAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  21    1  0.04
  22   23  0.88
  23    2  0.08

ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23


Consensus pattern (21 bp):   
AAATAAAAAATTAGCTAAGAA
Done.