Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2042

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: 25696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:745 original size:8 final size:8

Alignment explanation


    Indices: 732--756  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

        722 ACGGACACAA

                    
        732 TCGACTAC
          1 TCGACTAC

                    
        740 TCGACTAC
          1 TCGACTAC

                    
        748 TCGACTAC
          1 TCGACTAC

             
        756 T
          1 T

        757 TTTGACTTCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   17  1.00

ACGTcount: A:0.24, C:0.36, G:0.12, T:0.28


Consensus pattern (8 bp):   
TCGACTAC

Found at i:7454 original size:20 final size:20

Alignment explanation


    Indices: 7431--7469  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7421 ATTTGTATGT

                           *     
       7431 AATTAATAAA-AAATCAATTA
          1 AATT-ATAAATAAATAAATTA

                               
       7451 AATTATAAATAAATAAATT
          1 AATTATAAATAAATAAATT

       7470 TAAACACATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    5  0.29
  20   12  0.71

ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33


Consensus pattern (20 bp):   
AATTATAAATAAATAAATTA

Found at i:11543 original size:20 final size:20

Alignment explanation


    Indices: 11509--11550  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      11499 TAACAATTAA

                     **      *  
      11509 ATAATATTATTTGAATAGTT
          1 ATAATATTAAATGAATAATT

                                
      11529 ATAATATTAAATGAATAATT
          1 ATAATATTAAATGAATAATT

              
      11549 AT
          1 AT

      11551 GTGTTTATTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45


Consensus pattern (20 bp):   
ATAATATTAAATGAATAATT

Found at i:19878 original size:21 final size:21

Alignment explanation


    Indices: 19854--19956  Score: 84
    Period size: 21  Copynumber: 5.0  Consensus size: 21

      19844 ATATAAGAGC

                                 
      19854 TGAACGAAAACCCATAAGGGT
          1 TGAACGAAAACCCATAAGGGT

                  *  * * *    * *
      19875 TGAACGGAAGCTCGTAAGAGC
          1 TGAACGAAAACCCATAAGGGT

                                 
      19896 TG-ACGAAAACCCATAAGGGT
          1 TGAACGAAAACCCATAAGGGT

                  *  * * *    *  
      19916 TGAACGGAAGCTCGTAAGAGT
          1 TGAACGAAAACCCATAAGGGT

                 *               
      19937 TGAA-AAAAACCCATAAGGGT
          1 TGAACGAAAACCCATAAGGGT

      19957 GAAACTAAAG


Statistics
Matches: 58,  Mismatches: 23, Indels: 3
        0.69            0.27        0.04

Matches are distributed among these distances:
  20   24  0.41
  21   34  0.59

ACGTcount: A:0.40, C:0.17, G:0.27, T:0.16


Consensus pattern (21 bp):   
TGAACGAAAACCCATAAGGGT

Found at i:19907 original size:41 final size:41

Alignment explanation


    Indices: 19847--19956  Score: 184
    Period size: 41  Copynumber: 2.7  Consensus size: 41

      19837 TGAACGAATA

                                                      
      19847 TAAGAGCTGAACGAAAACCCATAAGGGTTGAACGGAAGCTCG
          1 TAAGAGCTG-ACGAAAACCCATAAGGGTTGAACGGAAGCTCG

                                                     
      19889 TAAGAGCTGACGAAAACCCATAAGGGTTGAACGGAAGCTCG
          1 TAAGAGCTGACGAAAACCCATAAGGGTTGAACGGAAGCTCG

                  *   **               
      19930 TAAGAGTTGAAAAAAACCCATAAGGGT
          1 TAAGAGCTGACGAAAACCCATAAGGGT

      19957 GAAACTAAAG


Statistics
Matches: 65,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  41   56  0.86
  42    9  0.14

ACGTcount: A:0.40, C:0.17, G:0.27, T:0.15


Consensus pattern (41 bp):   
TAAGAGCTGACGAAAACCCATAAGGGTTGAACGGAAGCTCG

Found at i:20143 original size:23 final size:24

Alignment explanation


    Indices: 20103--20149  Score: 69
    Period size: 23  Copynumber: 2.0  Consensus size: 24

      20093 TACTTGGGTA

                               *    
      20103 ATTTGCCATCAATTCATCCTTTGC
          1 ATTTGCCATCAATTCATCCATTGC

                   *                
      20127 ATTTGCCGTC-ATTCATCCATTGC
          1 ATTTGCCATCAATTCATCCATTGC

      20150 CACAGAACGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  23   12  0.57
  24    9  0.43

ACGTcount: A:0.19, C:0.30, G:0.11, T:0.40


Consensus pattern (24 bp):   
ATTTGCCATCAATTCATCCATTGC
Done.