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, 1000

Length: 14487
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:5434 original size:89 final size:89

Alignment explanation


    Indices: 5283--5460  Score: 320
    Period size: 89  Copynumber: 2.0  Consensus size: 89

       5273 TTAATTAGGG

                         *                                                   
       5283 GCAGCCACCATCCGTTTTATCCACTAGAAAAGAGCCATGTAAATTGTGCTTTTATTGAGAAATGG
          1 GCAGCCACCATCCATTTTATCCACTAGAAAAGAGCCATGTAAATTGTGCTTTTATTGAGAAATGG

                            *       
       5348 TAACCATAAAGTTTCTGTCAATTT
         66 TAACCATAAAGTTTCTATCAATTT

                     *                                               *       
       5372 GCAGCCACCGTCCATTTTATCCACTAGAAAAGAGCCATGTAAATTGTGCTTTTATTGTGAAATGG
          1 GCAGCCACCATCCATTTTATCCACTAGAAAAGAGCCATGTAAATTGTGCTTTTATTGAGAAATGG

                                    
       5437 TAACCATAAAGTTTCTATCAATTT
         66 TAACCATAAAGTTTCTATCAATTT

       5461 TTTAATAAAG


Statistics
Matches: 85,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  89   85  1.00

ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33


Consensus pattern (89 bp):   
GCAGCCACCATCCATTTTATCCACTAGAAAAGAGCCATGTAAATTGTGCTTTTATTGAGAAATGG
TAACCATAAAGTTTCTATCAATTT

Found at i:5524 original size:24 final size:22

Alignment explanation


    Indices: 5471--5532  Score: 54
    Period size: 24  Copynumber: 2.7  Consensus size: 22

       5461 TTTAATAAAG

                          *        
       5471 TAAATTGTTAAAAATTTTCTTAA
          1 TAAATT-TTAAAAAATTTCTTAA

            *                       *
       5494 AACAATTATTAAAAAATTTCTTTAT
          1 TA-AATT-TTAAAAAATTTC-TTAA

                           
       5519 TAAA-TTTAAAAAAT
          1 TAAATTTTAAAAAAT

       5533 ATATATAAAT


Statistics
Matches: 32,  Mismatches: 5, Indels: 5
        0.76            0.12        0.12

Matches are distributed among these distances:
  22    9  0.28
  23    2  0.06
  24   17  0.53
  25    4  0.12

ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44


Consensus pattern (22 bp):   
TAAATTTTAAAAAATTTCTTAA

Found at i:9142 original size:16 final size:16

Alignment explanation


    Indices: 9109--9142  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9099 CAAAACTGTT

                       * *  
       9109 AACATTAATGGGAGAC
          1 AACATTAATGGCAAAC

                            
       9125 AACATTAATGGCAAAC
          1 AACATTAATGGCAAAC

              
       9141 AA
          1 AA

       9143 TACAAAGTGG


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18


Consensus pattern (16 bp):   
AACATTAATGGCAAAC

Found at i:11964 original size:21 final size:21

Alignment explanation


    Indices: 11938--11978  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11928 AGACGAGCAA

                   * *           
      11938 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
      11959 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

      11979 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG

Found at i:13916 original size:16 final size:16

Alignment explanation


    Indices: 13883--13916  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      13873 GGAGATTGTT

                       * *  
      13883 AACATTAATGGGAGAC
          1 AACATTAATGGCAAAC

                            
      13899 AACATTAATGGCAAAC
          1 AACATTAATGGCAAAC

              
      13915 AA
          1 AA

      13917 TACAAAGTGG


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18


Consensus pattern (16 bp):   
AACATTAATGGCAAAC
Done.