Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold631

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: 26555
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:1536 original size:13 final size:12

Alignment explanation


    Indices: 1503--1533  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       1493 TAGTTTCTTC

                        
       1503 AAAAAAATTCAA
          1 AAAAAAATTCAA

                        
       1515 AAAAAAATTCAA
          1 AAAAAAATTCAA

                   
       1527 AAAAAAA
          1 AAAAAAA

       1534 ATTGGTTTCC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13


Consensus pattern (12 bp):   
AAAAAAATTCAA

Found at i:11518 original size:19 final size:20

Alignment explanation


    Indices: 11494--11538  Score: 65
    Period size: 19  Copynumber: 2.3  Consensus size: 20

      11484 CTTTTCATTC

                     *          
      11494 TCTTTTTTTGAATTTTC-TT
          1 TCTTTTTTTCAATTTTCTTT

                       *        
      11513 TCTTTTTTTCATTTTTCTTT
          1 TCTTTTTTTCAATTTTCTTT

                  
      11533 TCTTTT
          1 TCTTTT

      11539 GTATTTTCGC


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   15  0.65
  20    8  0.35

ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78


Consensus pattern (20 bp):   
TCTTTTTTTCAATTTTCTTT

Found at i:15294 original size:17 final size:16

Alignment explanation


    Indices: 15250--15292  Score: 77
    Period size: 16  Copynumber: 2.7  Consensus size: 16

      15240 AGACCGTATG

                        *   
      15250 CAATTTTTTTTCTTTT
          1 CAATTTTTTTTCCTTT

                            
      15266 CAATTTTTTTTCCTTT
          1 CAATTTTTTTTCCTTT

                       
      15282 CAATTTTTTTT
          1 CAATTTTTTTT

      15293 TCGATTTTGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72


Consensus pattern (16 bp):   
CAATTTTTTTTCCTTT

Found at i:15678 original size:22 final size:22

Alignment explanation


    Indices: 15627--15692  Score: 80
    Period size: 21  Copynumber: 3.0  Consensus size: 22

      15617 GGTATTTGGG

                   *      *       
      15627 AATTGGTTCGAAATAGTATGG-
          1 AATTGGTACGAAATGGTATGGT

                                  
      15648 AATTGGTACGAAATGGTATGGT
          1 AATTGGTACGAAATGGTATGGT

             *          *          
      15670 ATTTGGTACGAATTGGTAATGGT
          1 AATTGGTACGAAATGGT-ATGGT

      15693 TTAAAGAGGT


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   19  0.49
  22   15  0.38
  23    5  0.13

ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35


Consensus pattern (22 bp):   
AATTGGTACGAAATGGTATGGT
Done.