Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold480

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: 28741
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32


Found at i:8302 original size:40 final size:40

Alignment explanation


    Indices: 8225--8440  Score: 332
    Period size: 39  Copynumber: 5.5  Consensus size: 40

       8215 AAACCAAGTA

                     *                        *      
       8225 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
          1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG

                               *                    
       8264 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                      *                             
       8304 CCTTC-GGACCTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                                    
       8343 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                              *       *   *         
       8383 CCTTCGGGACTTAGCCCGAAT-TAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                               
       8422 CCTTCGGGACTTAGCCCGG
          1 CCTTCGGGACTTAGCCCGG

       8441 TTATCATCCG


Statistics
Matches: 164,  Mismatches: 10, Indels: 6
        0.91            0.06        0.03

Matches are distributed among these distances:
  39   85  0.52
  40   79  0.48

ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:8356 original size:79 final size:79

Alignment explanation


    Indices: 8225--8444  Score: 329
    Period size: 79  Copynumber: 2.8  Consensus size: 79

       8215 AAACCAAGTA

                     **                      *                               
       8225 CCTTCGGGATTTAG-CCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAG
          1 CCTTCGGGACCTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG

                           
       8289 TAACTCGCACAAATG
         65 TAACTCGCACAAATG

                                                                       *     
       8304 CCTTC-GGACCTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
          1 CCTTCGGGACCTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG

                           
       8368 TAACTCGCACAAATG
         65 TAACTCGCACAAATG

                      *       *           *                                
       8383 CCTTCGGGACTTAGCCCGAAT-TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 CCTTCGGGACCTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

       8445 CATCCGGATA


Statistics
Matches: 129,  Mismatches: 9, Indels: 6
        0.90            0.06        0.04

Matches are distributed among these distances:
  78    7  0.05
  79  109  0.84
  80   13  0.10

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (79 bp):   
CCTTCGGGACCTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGT
AACTCGCACAAATG

Found at i:10706 original size:14 final size:14

Alignment explanation


    Indices: 10687--10713  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      10677 ATATTTAACT

                          
      10687 TGTTCTTAATTATG
          1 TGTTCTTAATTATG

                         
      10701 TGTTCTTAATTAT
          1 TGTTCTTAATTAT

      10714 TGCTTTGATA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59


Consensus pattern (14 bp):   
TGTTCTTAATTATG

Found at i:20911 original size:19 final size:20

Alignment explanation


    Indices: 20887--20924  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      20877 GGTACCACCA

                                 
      20887 AAACAT-ATATCA-CATCTTT
          1 AAACATCAT-TCATCATCTTT

                               
      20906 AAACATCATTCATCATCTT
          1 AAACATCATTCATCATCTT

      20925 ACCACCTTAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37


Consensus pattern (20 bp):   
AAACATCATTCATCATCTTT

Found at i:21587 original size:30 final size:30

Alignment explanation


    Indices: 21553--21610  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      21543 ATTTAATAGG

                                          
      21553 AACTTTAAAAAAATTACACTTTTGCCCCAA
          1 AACTTTAAAAAAATTACACTTTTGCCCCAA

                  *** *                 
      21583 AACTTTTGCATAATTACACTTTTGCCCC
          1 AACTTTAAAAAAATTACACTTTTGCCCC

      21611 TAGGCTCGGG


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34


Consensus pattern (30 bp):   
AACTTTAAAAAAATTACACTTTTGCCCCAA
Done.