Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1125

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: 25229
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1047 original size:4 final size:4

Alignment explanation


    Indices: 1038--1067  Score: 51
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       1028 TTTGTTTCTC

                             *                   
       1038 ATCT ATCT ATCT ATTT ATCT ATCT ATCT AT
          1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT

       1068 ATATTGTGAC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53


Consensus pattern (4 bp):   
ATCT

Found at i:4900 original size:6 final size:6

Alignment explanation


    Indices: 4891--4918  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       4881 TGTGCGTGTG

                                            
       4891 AGGGGA AGGGGA AGGGGA AGGGGA AGGG
          1 AGGGGA AGGGGA AGGGGA AGGGGA AGGG

       4919 ACAAAGAACC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00


Consensus pattern (6 bp):   
AGGGGA

Found at i:19715 original size:9 final size:8

Alignment explanation


    Indices: 19690--19714  Score: 50
    Period size: 8  Copynumber: 3.1  Consensus size: 8

      19680 TCAATTAAAA

                    
      19690 TATTTTTT
          1 TATTTTTT

                    
      19698 TATTTTTT
          1 TATTTTTT

                    
      19706 TATTTTTT
          1 TATTTTTT

             
      19714 T
          1 T

      19715 TGAATAGTAA


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:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (8 bp):   
TATTTTTT

Found at i:22317 original size:12 final size:13

Alignment explanation


    Indices: 22299--22328  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      22289 GTTTGTGATT

                         
      22299 TAATATAAATATA
          1 TAATATAAATATA

                         
      22312 -AATATAAATATA
          1 TAATATAAATATA

                 
      22324 TAATA
          1 TAATA

      22329 ATTATTTAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (13 bp):   
TAATATAAATATA

Found at i:23208 original size:31 final size:32

Alignment explanation


    Indices: 23173--23263  Score: 103
    Period size: 32  Copynumber: 2.9  Consensus size: 32

      23163 TAATAAACAT

                   *       *     *          
      23173 CAACTTTTATTTT-TGAAACGGTAACAAATTA
          1 CAACTTTAATTTTGTAAAACGATAACAAATTA

                  *            *           *
      23204 CAACTTCAATTTTGTAAAATGATAACAAATTT
          1 CAACTTTAATTTTGTAAAACGATAACAAATTA

                           *   *        
      23236 CAACTTTAATTTTGTTAAATGATAACAA
          1 CAACTTTAATTTTGTAAAACGATAACAA

      23264 TATTCCTTTA


Statistics
Matches: 51,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  31   11  0.22
  32   40  0.78

ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38


Consensus pattern (32 bp):   
CAACTTTAATTTTGTAAAACGATAACAAATTA

Found at i:23240 original size:32 final size:32

Alignment explanation


    Indices: 23194--23263  Score: 113
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      23184 TTTGAAACGG

                                            
      23194 TAACAAATTACAACTTCAATTTTGTAAAATGA
          1 TAACAAATTACAACTTCAATTTTGTAAAATGA

                     *      *        *      
      23226 TAACAAATTTCAACTTTAATTTTGTTAAATGA
          1 TAACAAATTACAACTTCAATTTTGTAAAATGA

                  
      23258 TAACAA
          1 TAACAA

      23264 TATTCCTTTA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37


Consensus pattern (32 bp):   
TAACAAATTACAACTTCAATTTTGTAAAATGA
Done.