Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3971

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, 369

Length: 615
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45


Found at i:115 original size:17 final size:17

Alignment explanation


    Indices: 93--144  Score: 59
    Period size: 19  Copynumber: 2.9  Consensus size: 17

         83 ATGGAAACAT

                  *  *       
         93 AATCTTCAAGGATATGC
          1 AATCTTAAAAGATATGC

                       *       
        110 AATCTTAGATATGATATGC
          1 AATCTTA-A-AAGATATGC

                            
        129 AATCTTAAAAGATATG
          1 AATCTTAAAAGATATG

        145 ATATGCAATA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  17   13  0.43
  18    2  0.07
  19   15  0.50

ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33


Consensus pattern (17 bp):   
AATCTTAAAAGATATGC

Found at i:144 original size:22 final size:21

Alignment explanation


    Indices: 103--168  Score: 91
    Period size: 22  Copynumber: 3.1  Consensus size: 21

         93 AATCTTCAAG

                                 
        103 GATATGCAATCTT--AGATAT
          1 GATATGCAATCTTAAAGATAT

                                  
        122 GATATGCAATCTTAAAAGATAT
          1 GATATGCAATCTT-AAAGATAT

                      *           
        144 GATATGCAATATTAGAAGATAT
          1 GATATGCAATCTTA-AAGATAT

               
        166 GAT
          1 GAT

        169 TTTGTAATCT


Statistics
Matches: 42,  Mismatches: 1, Indels: 5
        0.88            0.02        0.10

Matches are distributed among these distances:
  19   13  0.31
  21    1  0.02
  22   28  0.67

ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33


Consensus pattern (21 bp):   
GATATGCAATCTTAAAGATAT

Found at i:185 original size:22 final size:21

Alignment explanation


    Indices: 103--185  Score: 89
    Period size: 22  Copynumber: 3.9  Consensus size: 21

         93 AATCTTCAAG

                                 
        103 GATATGCAATCTT--AGATAT
          1 GATATGCAATCTTAGAGATAT

                           *      
        122 GATATGCAATCTTAAAAGATAT
          1 GATATGCAATCTT-AGAGATAT

                      *           
        144 GATATGCAATATTAGAAGATAT
          1 GATATGCAATCTTAG-AGATAT

                *  *            
        166 GATTTTGTAATCTTAGAGAT
          1 GA-TATGCAATCTTAGAGAT

        186 TTAATTTGTA


Statistics
Matches: 54,  Mismatches: 5, Indels: 7
        0.82            0.08        0.11

Matches are distributed among these distances:
  19   13  0.24
  21    1  0.02
  22   30  0.56
  23   10  0.19

ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36


Consensus pattern (21 bp):   
GATATGCAATCTTAGAGATAT

Found at i:428 original size:23 final size:23

Alignment explanation


    Indices: 384--428  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        374 TCTTATTTTG

                     *       *     
        384 TTGATTTGTGTATAATTTATTTA
          1 TTGATTTGTATATAATTGATTTA

                         **       
        407 TTGATTTGTATATCGTTGATTT
          1 TTGATTTGTATATAATTGATTT

        429 CAAATCTTTT


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60


Consensus pattern (23 bp):   
TTGATTTGTATATAATTGATTTA
Done.