Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold10163.1

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: 3917
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32


Found at i:2387 original size:11 final size:11

Alignment explanation


    Indices: 2371--2420  Score: 68
    Period size: 11  Copynumber: 4.6  Consensus size: 11

       2361 ATAAATCACT

                       
       2371 TTTTTTTCGAA
          1 TTTTTTTCGAA

                       
       2382 TTTTTTT--AA
          1 TTTTTTTCGAA

                       
       2391 TTTTTTTCGAA
          1 TTTTTTTCGAA

                    *   
       2402 TTTTTTTTTGAA
          1 -TTTTTTTCGAA

                   
       2414 TTTTTTT
          1 TTTTTTT

       2421 TAACTTGTGT


Statistics
Matches: 35,  Mismatches: 1, Indels: 6
        0.83            0.02        0.14

Matches are distributed among these distances:
   9    9  0.26
  11   16  0.46
  12   10  0.29

ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74


Consensus pattern (11 bp):   
TTTTTTTCGAA

Found at i:2387 original size:12 final size:12

Alignment explanation


    Indices: 2370--2421  Score: 67
    Period size: 12  Copynumber: 4.7  Consensus size: 12

       2360 CATAAATCAC

                        
       2370 TTTTTTTTCGAA
          1 TTTTTTTTCGAA

                        
       2382 -TTTTTTT--AA
          1 TTTTTTTTCGAA

                        
       2391 -TTTTTTTCGAA
          1 TTTTTTTTCGAA

                    *   
       2402 TTTTTTTTTGAA
          1 TTTTTTTTCGAA

                    
       2414 TTTTTTTT
          1 TTTTTTTT

       2422 AACTTGTGTA


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
   9    9  0.25
  11    9  0.25
  12   18  0.50

ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75


Consensus pattern (12 bp):   
TTTTTTTTCGAA

Found at i:2396 original size:20 final size:20

Alignment explanation


    Indices: 2371--2408  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2361 ATAAATCACT

                                
       2371 TTTTTTTCGAATTTTTTTAA
          1 TTTTTTTCGAATTTTTTTAA

                              
       2391 TTTTTTTCGAATTTTTTT
          1 TTTTTTTCGAATTTTTTT

       2409 TTGAATTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74


Consensus pattern (20 bp):   
TTTTTTTCGAATTTTTTTAA

Found at i:2438 original size:32 final size:32

Alignment explanation


    Indices: 2368--2440  Score: 78
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       2358 TGCATAAATC

                                   *  * *    
       2368 ACTTTTTTTTCGAATTTTTTTAATTTTTTTCGA
          1 ACTTTTTTTTCGAATTTTTTTAACTTGTGTC-A

                      *                      
       2401 A-TTTTTTTTTGAATTTTTTTTAACTTGTGT-A
          1 ACTTTTTTTTCGAA-TTTTTTTAACTTGTGTCA

                     
       2432 ACTTTTTTT
          1 ACTTTTTTT

       2441 GTTGTACTAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 5
        0.79            0.09        0.12

Matches are distributed among these distances:
  31    2  0.06
  32   18  0.53
  33   14  0.41

ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68


Consensus pattern (32 bp):   
ACTTTTTTTTCGAATTTTTTTAACTTGTGTCA

Found at i:2796 original size:14 final size:14

Alignment explanation


    Indices: 2779--2818  Score: 53
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       2769 CGAATGGAAT

                     *    
       2779 GGTAGGAACGAAAG
          1 GGTAGGAACAAAAG

                          
       2793 GGTAGGAACAAAAG
          1 GGTAGGAACAAAAG

             *  *       
       2807 GATATGAACAAA
          1 GGTAGGAACAAA

       2819 TTGGTCGGTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10


Consensus pattern (14 bp):   
GGTAGGAACAAAAG
Done.