Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2025

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, 994

Length: 1658
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35


Found at i:745 original size:2 final size:2

Alignment explanation


    Indices: 738--786  Score: 62
    Period size: 2  Copynumber: 24.5  Consensus size: 2

        728 AACAAATCTA

                                  * *                              *     *
        738 AT AT AT AT AT AT AT AG CT AT AT AT AT AT AT AT AT AT AG AT AG
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                      
        780 AT AT AT A
          1 AT AT AT A

        787 ATAAATTAAA


Statistics
Matches: 39,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43


Consensus pattern (2 bp):   
AT

Found at i:960 original size:12 final size:11

Alignment explanation


    Indices: 943--986  Score: 52
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        933 ATTTCAGAAA

                       
        943 AAAAAAATTGT
          1 AAAAAAATTGT

                       * 
        954 GAAAAAAAATTCT
          1 --AAAAAAATTGT

                       
        967 AAAAAAATTGT
          1 AAAAAAATTGT

                     
        978 AAAGAAAAT
          1 AAA-AAAAT

        987 AGGAAATTAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  11   13  0.46
  12    5  0.18
  13   10  0.36

ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23


Consensus pattern (11 bp):   
AAAAAAATTGT

Found at i:960 original size:13 final size:12

Alignment explanation


    Indices: 942--986  Score: 56
    Period size: 13  Copynumber: 3.8  Consensus size: 12

        932 AATTTCAGAA

                        
        942 AAAAAAAATTGT
          1 AAAAAAAATTGT

                       * 
        954 GAAAAAAAATTCT
          1 -AAAAAAAATTGT

                        
        967 -AAAAAAATTGT
          1 AAAAAAAATTGT

               *     
        978 AAAGAAAAT
          1 AAAAAAAAT

        987 AGGAAATTAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  11   10  0.36
  12    7  0.25
  13   11  0.39

ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22


Consensus pattern (12 bp):   
AAAAAAAATTGT

Found at i:1150 original size:23 final size:24

Alignment explanation


    Indices: 1124--1174  Score: 61
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1114 TTAATAATTA

                                     
       1124 TTTTGAT-ATTAAAATTATAA-AAT
          1 TTTTGATAATTAAAATTA-AATAAT

                *         *         
       1147 TTTTTATAATTAAATTTAAATAAT
          1 TTTTGATAATTAAAATTAAATAAT

                
       1171 TTTT
          1 TTTT

       1175 TTATTATTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  23    8  0.33
  24   16  0.67

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55


Consensus pattern (24 bp):   
TTTTGATAATTAAAATTAAATAAT

Found at i:1183 original size:25 final size:25

Alignment explanation


    Indices: 1112--1191  Score: 78
    Period size: 25  Copynumber: 3.2  Consensus size: 25

       1102 AATGATAAAT

                             *        
       1112 ATTT-AATAATTATTTTGA-TATTAA
          1 ATTTAAATAATT-TTTTTATTATTAA

             *                  *     
       1136 AATTATAA-AA-TTTTTTATAATTAA
          1 ATTTA-AATAATTTTTTTATTATTAA

                                     
       1160 ATTTAAATAATTTTTTTATTATTAA
          1 ATTTAAATAATTTTTTTATTATTAA

                   
       1185 ATATTAA
          1 AT-TTAA

       1192 TTCAAGTAAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 10
        0.75            0.08        0.17

Matches are distributed among these distances:
  23    7  0.16
  24   15  0.33
  25   17  0.38
  26    6  0.13

ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54


Consensus pattern (25 bp):   
ATTTAAATAATTTTTTTATTATTAA
Done.