Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3105

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: 29102
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:737 original size:6 final size:7

Alignment explanation


    Indices: 718--748  Score: 62
    Period size: 7  Copynumber: 4.4  Consensus size: 7

        708 AAATGAGACA

                   
        718 AATTTTT
          1 AATTTTT

                   
        725 AATTTTT
          1 AATTTTT

                   
        732 AATTTTT
          1 AATTTTT

                   
        739 AATTTTT
          1 AATTTTT

               
        746 AAT
          1 AAT

        749 AGAAAGCTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   24  1.00

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


Consensus pattern (7 bp):   
AATTTTT

Found at i:4367 original size:78 final size:77

Alignment explanation


    Indices: 4210--4360  Score: 187
    Period size: 78  Copynumber: 1.9  Consensus size: 77

       4200 TGAATATTTC

                                        *                       *            
       4210 AAATCCTAAGATTACATTATTATGCCCCGCAAGAATGACAGTCATGAAAGCAGCAATCTTGAATT
          1 AAATCCTAAGATTACATTATTATGCCCCACAAGAATGACAGTCATGAAAGCAACAATCTTGAATT

                *       
       4275 GATGGTGACAAA
         66 GATGATGACAAA

                           *           *       *   **        *             * 
       4287 AAATCCTAAGATTACGTTATTATGCTCTCACAAGATTGATGGTCA-GTAGAGCAACAATCTTGGA
          1 AAATCCTAAGATTACATTATTATGC-CCCACAAGAATGACAGTCATG-AAAGCAACAATCTTGAA

                      
       4351 TTGATGATGA
         64 TTGATGATGA

       4361 TGAAAAAAGC


Statistics
Matches: 62,  Mismatches: 10, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  77   25  0.40
  78   37  0.60

ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28


Consensus pattern (77 bp):   
AAATCCTAAGATTACATTATTATGCCCCACAAGAATGACAGTCATGAAAGCAACAATCTTGAATT
GATGATGACAAA

Found at i:18502 original size:20 final size:21

Alignment explanation


    Indices: 18477--18523  Score: 64
    Period size: 19  Copynumber: 2.4  Consensus size: 21

      18467 GGTAATAACT

                                 
      18477 TTAGTAAATCTTTAAAAAT-A
          1 TTAGTAAATCTTTAAAAATGA

                     *           
      18497 TTAGT-AATTTTTAAAAATGA
          1 TTAGTAAATCTTTAAAAATGA

                    
      18517 TT-GTAAA
          1 TTAGTAAA

      18524 AATGTTGAGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  19   14  0.58
  20   10  0.42

ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43


Consensus pattern (21 bp):   
TTAGTAAATCTTTAAAAATGA

Found at i:21263 original size:97 final size:98

Alignment explanation


    Indices: 21122--21317  Score: 385
    Period size: 97  Copynumber: 2.0  Consensus size: 98

      21112 TTGGAACATT

                                                                             
      21122 ACTCTTCTGAGCAATAAGTTGAAAGATTATCCTTTCCTTTCTTAGCAACAGGTTGAGGTGGAACA
          1 ACTCTTCTGAGCAATAAGTTGAAAGATTATCCTTTCCTTTCTTAGCAACAGGTTGAGGTGGAACA

                                             
      21187 CCAGAAGCTGTTAGACCACTTGGAGTTACTGGC
         66 CCAGAAGCTGTTAGACCACTTGGAGTTACTGGC

                                                                             
      21220 ACTCTTCTGAGCAATAAGTTG-AAGATTATCCTTTCCTTTCTTAGCAACAGGTTGAGGTGGAACA
          1 ACTCTTCTGAGCAATAAGTTGAAAGATTATCCTTTCCTTTCTTAGCAACAGGTTGAGGTGGAACA

                                             
      21284 CCAGAAGCTGTTAGACCACTTGGAGTTACTGGC
         66 CCAGAAGCTGTTAGACCACTTGGAGTTACTGGC

             
      21317 A
          1 A

      21318 TGCCACTGCC


Statistics
Matches: 98,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  97   77  0.79
  98   21  0.21

ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30


Consensus pattern (98 bp):   
ACTCTTCTGAGCAATAAGTTGAAAGATTATCCTTTCCTTTCTTAGCAACAGGTTGAGGTGGAACA
CCAGAAGCTGTTAGACCACTTGGAGTTACTGGC

Found at i:25525 original size:18 final size:19

Alignment explanation


    Indices: 25504--25555  Score: 72
    Period size: 19  Copynumber: 2.8  Consensus size: 19

      25494 TTTTTAAAAA

                               
      25504 TATAAAT-TTTTGAATTTT
          1 TATAAATATTTTGAATTTT

                               
      25522 TATAAATATTTTGAA-TTT
          1 TATAAATATTTTGAATTTT

              *             
      25540 TAAAAATTATTTTGAA
          1 TATAAA-TATTTTGAA

      25556 ACGTTGAATT


Statistics
Matches: 31,  Mismatches: 1, Indels: 3
        0.89            0.03        0.09

Matches are distributed among these distances:
  18   15  0.48
  19   16  0.52

ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54


Consensus pattern (19 bp):   
TATAAATATTTTGAATTTT

Found at i:25809 original size:17 final size:20

Alignment explanation


    Indices: 25787--25842  Score: 57
    Period size: 19  Copynumber: 3.0  Consensus size: 20

      25777 TTGTATTTAT

                                
      25787 TATTTAA-AA-TTT-TGATG
          1 TATTTAATAAGTTTATGATG

                             *  
      25804 TATTTAATAAGTTTATGCTG
          1 TATTTAATAAGTTTATGATG

                     **         
      25824 TATTT-ATATTTTTATGATG
          1 TATTTAATAAGTTTATGATG

      25843 GTTTAAACAC


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  17    7  0.22
  18    2  0.06
  19   14  0.44
  20    9  0.28

ACGTcount: A:0.30, C:0.02, G:0.12, T:0.55


Consensus pattern (20 bp):   
TATTTAATAAGTTTATGATG
Done.