Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02301.P4

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: 6911
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:2151 original size:34 final size:34

Alignment explanation


    Indices: 2108--2175  Score: 136
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       2098 TGATGAGGAA

                                              
       2108 GGTAAGAGTATGATCAGTACTTTACATACAAAAT
          1 GGTAAGAGTATGATCAGTACTTTACATACAAAAT

                                              
       2142 GGTAAGAGTATGATCAGTACTTTACATACAAAAT
          1 GGTAAGAGTATGATCAGTACTTTACATACAAAAT

       2176 ACTTCATCAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29


Consensus pattern (34 bp):   
GGTAAGAGTATGATCAGTACTTTACATACAAAAT

Found at i:2383 original size:19 final size:18

Alignment explanation


    Indices: 2361--2454  Score: 77
    Period size: 19  Copynumber: 5.2  Consensus size: 18

       2351 TGAATAAAAC

                  *            
       2361 TTATCTTCCTAAATAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       2380 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

                   **  *        
       2398 TTA---AAATATATACATAT
          1 TTATCTACCTAAATA-A-AT

                  *      *     
       2415 TTATCTTCCTAAAGAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       2434 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

               
       2452 TTA
          1 TTA

       2455 AAATATATAC


Statistics
Matches: 58,  Mismatches: 12, Indels: 11
        0.72            0.15        0.14

Matches are distributed among these distances:
  15    6  0.10
  16    1  0.02
  17    5  0.09
  18   10  0.17
  19   32  0.55
  20    4  0.07

ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40


Consensus pattern (18 bp):   
TTATCTACCTAAATAAAT

Found at i:2424 original size:54 final size:54

Alignment explanation


    Indices: 2361--2470  Score: 211
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       2351 TGAATAAAAC

                         *                                        
       2361 TTATCTTCCTAAATAAGATTTATCTACCTAAATAAATTTAAAATATATACATAT
          1 TTATCTTCCTAAAGAAGATTTATCTACCTAAATAAATTTAAAATATATACATAT

                                                                  
       2415 TTATCTTCCTAAAGAAGATTTATCTACCTAAATAAATTTAAAATATATACATAT
          1 TTATCTTCCTAAAGAAGATTTATCTACCTAAATAAATTTAAAATATATACATAT

              
       2469 TT
          1 TT

       2471 CAACACCCTC


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.44, C:0.13, G:0.03, T:0.41


Consensus pattern (54 bp):   
TTATCTTCCTAAAGAAGATTTATCTACCTAAATAAATTTAAAATATATACATAT

Found at i:4825 original size:42 final size:42

Alignment explanation


    Indices: 4778--4858  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       4768 CCTAAATGGA

                      *                               
       4778 AAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAGGG
          1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGGG

                                              *    
       4820 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAA
          1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA

       4859 AAAAAAAAAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31


Consensus pattern (42 bp):   
AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAGGG

Found at i:4911 original size:19 final size:18

Alignment explanation


    Indices: 4887--4930  Score: 70
    Period size: 19  Copynumber: 2.4  Consensus size: 18

       4877 AATATGAATA

                      *       
       4887 AAATTTATCTTCCTAAAT
          1 AAATTTATCTACCTAAAT

                               
       4905 AAGATTTATCTACCTAAAT
          1 AA-ATTTATCTACCTAAAT

                   
       4924 AAATTTA
          1 AAATTTA

       4931 AAATATGTAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  18    7  0.29
  19   17  0.71

ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41


Consensus pattern (18 bp):   
AAATTTATCTACCTAAAT
Done.