Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1561

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: 12465
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35


Found at i:522 original size:14 final size:14

Alignment explanation


    Indices: 498--540  Score: 52
    Period size: 15  Copynumber: 3.0  Consensus size: 14

        488 TATATTTTTC

                           
        498 AAAAATATAATAACT
          1 AAAAAT-TAATAACT

                         * 
        513 AAAAATTAATAAAAT
          1 AAAAATTAAT-AACT

                          
        528 AAAAATT-ATAACT
          1 AAAAATTAATAACT

        541 TTATAATAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  13    3  0.12
  14    6  0.24
  15   16  0.64

ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28


Consensus pattern (14 bp):   
AAAAATTAATAACT

Found at i:808 original size:15 final size:16

Alignment explanation


    Indices: 790--822  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        780 ATTACTTAAA

                            
        790 TATTTATT-ATATAAT
          1 TATTTATTAATATAAT

                            
        805 TATTTATTAATATAAT
          1 TATTTATTAATATAAT

              
        821 TA
          1 TA

        823 ATTAAAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.47
  16    9  0.53

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (16 bp):   
TATTTATTAATATAAT

Found at i:7747 original size:150 final size:146

Alignment explanation


    Indices: 7491--7771  Score: 370
    Period size: 150  Copynumber: 1.9  Consensus size: 146

       7481 ATTTTAATAT

                    *                                   *                    
       7491 TAAATATAGTTAATAATTAATAAAAATATGCATTTGACTCAATATTCTTATTTTAATATAAAATT
          1 TAAATATAATTAATAATTAATAAAAATATGCATTTGACTCAATAGTCTTATTTTAATATAAAATT

             *                 *                                             
       7556 ACAATATTAAAATTCAAATTTAATCAACTATAAACAATTTTTTATAAAAAAATAAAATATATATA
         66 AAAATATTAAAATTCAAATCTAATCAACTATAAA-AATTTTTT-T--AAAAATAAAATATATATA

                                
       7621 AAATCAATTTGAATATTAAA
        127 AAATCAATTTGAATATTAAA

                                         *          *                        
       7641 TAAATATAATTAATAATTAATAAAAATATTC-TATTGACTTAATAGT-TTATTTTTAATATAAAA
          1 TAAATATAATTAATAATTAATAAAAATATGCAT-TTGACTCAATAGTCTTA-TTTTAATATAAAA

                                    *     *    * **           *              
       7704 TTAAAATATTAAAAATTC-AATCTCATCAATTATAGATTTTTTTTTAAAATTAAAATATATATAA
         64 TTAAAATATT-AAAATTCAAATCTAATCAACTATAAAAATTTTTTTAAAAATAAAATATATATAA

                
       7768 AATC
        128 AATC

       7772 TTTTTTTACT


Statistics
Matches: 116,  Mismatches: 12, Indels: 10
        0.84            0.09        0.07

Matches are distributed among these distances:
 146   22  0.19
 148    1  0.01
 149   10  0.09
 150   76  0.66
 151    7  0.06

ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41


Consensus pattern (146 bp):   
TAAATATAATTAATAATTAATAAAAATATGCATTTGACTCAATAGTCTTATTTTAATATAAAATT
AAAATATTAAAATTCAAATCTAATCAACTATAAAAATTTTTTTAAAAATAAAATATATATAAAAT
CAATTTGAATATTAAA

Found at i:9283 original size:20 final size:19

Alignment explanation


    Indices: 9254--9303  Score: 64
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       9244 CAGTTTCATG

                            *   
       9254 TATCGATACAATTGAGTATA
          1 TATCGATACAA-TGAGCATA

               *              *
       9274 TATTGATACAATGAGCATG
          1 TATCGATACAATGAGCATA

                       
       9293 TATCGATACAA
          1 TATCGATACAA

       9304 AGCATAATGT


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  19   16  0.62
  20   10  0.38

ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32


Consensus pattern (19 bp):   
TATCGATACAATGAGCATA
Done.