Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6684.1

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: 10391
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:3439 original size:22 final size:22

Alignment explanation


    Indices: 3409--3452  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3399 TTTGGTATTT

                                  
       3409 GGGAATTGGTACGAAATGGTAA
          1 GGGAATTGGTACGAAATGGTAA

                *                 
       3431 GGGATTTGGTACGAAATGGTAA
          1 GGGAATTGGTACGAAATGGTAA

       3453 TGGTTCAAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25


Consensus pattern (22 bp):   
GGGAATTGGTACGAAATGGTAA

Found at i:3589 original size:22 final size:22

Alignment explanation


    Indices: 3559--3602  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3549 TGTGGTATTT

                                  
       3559 GGGAATTGGTACGAAATGGTAA
          1 GGGAATTGGTACGAAATGGTAA

                *                 
       3581 GGGATTTGGTACGAAATGGTAA
          1 GGGAATTGGTACGAAATGGTAA

       3603 TGGTTCAAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25


Consensus pattern (22 bp):   
GGGAATTGGTACGAAATGGTAA

Found at i:3632 original size:150 final size:150

Alignment explanation


    Indices: 3401--3700  Score: 591
    Period size: 150  Copynumber: 2.0  Consensus size: 150

       3391 TGGTACGTTT

                                                                             
       3401 TGGTATTTGGGAATTGGTACGAAATGGTAAGGGATTTGGTACGAAATGGTAATGGTTCAAAAAGG
          1 TGGTATTTGGGAATTGGTACGAAATGGTAAGGGATTTGGTACGAAATGGTAATGGTTCAAAAAGG

                                               *                             
       3466 TCAAGAGTGAACCAACACTAAAGAAAAGTGTCGACCCGAAACTTATAGGACCAAATTGAGTTGGA
         66 TCAAGAGTGAACCAACACTAAAGAAAAGTGTCGACACGAAACTTATAGGACCAAATTGAGTTGGA

                                
       3531 AATGGTTGATAAGGACCTTG
        131 AATGGTTGATAAGGACCTTG

                                                                             
       3551 TGGTATTTGGGAATTGGTACGAAATGGTAAGGGATTTGGTACGAAATGGTAATGGTTCAAAAAGG
          1 TGGTATTTGGGAATTGGTACGAAATGGTAAGGGATTTGGTACGAAATGGTAATGGTTCAAAAAGG

                                                                             
       3616 TCAAGAGTGAACCAACACTAAAGAAAAGTGTCGACACGAAACTTATAGGACCAAATTGAGTTGGA
         66 TCAAGAGTGAACCAACACTAAAGAAAAGTGTCGACACGAAACTTATAGGACCAAATTGAGTTGGA

                                
       3681 AATGGTTGATAAGGACCTTG
        131 AATGGTTGATAAGGACCTTG

       3701 ACCCGATACT


Statistics
Matches: 149,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 150  149  1.00

ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25


Consensus pattern (150 bp):   
TGGTATTTGGGAATTGGTACGAAATGGTAAGGGATTTGGTACGAAATGGTAATGGTTCAAAAAGG
TCAAGAGTGAACCAACACTAAAGAAAAGTGTCGACACGAAACTTATAGGACCAAATTGAGTTGGA
AATGGTTGATAAGGACCTTG

Found at i:8963 original size:76 final size:76

Alignment explanation


    Indices: 8837--9007  Score: 342
    Period size: 76  Copynumber: 2.2  Consensus size: 76

       8827 CGAAACGTGA

                                                                             
       8837 AAAAAAATCAAAAAAAATTTGAGTTGTAATTTAATTTTTTTCCCTTGTATTTAGCTTACTATTGT
          1 AAAAAAATCAAAAAAAATTTGAGTTGTAATTTAATTTTTTTCCCTTGTATTTAGCTTACTATTGT

                       
       8902 ATTGGAGTAAC
         66 ATTGGAGTAAC

                                                                             
       8913 AAAAAAATCAAAAAAAATTTGAGTTGTAATTTAATTTTTTTCCCTTGTATTTAGCTTACTATTGT
          1 AAAAAAATCAAAAAAAATTTGAGTTGTAATTTAATTTTTTTCCCTTGTATTTAGCTTACTATTGT

                       
       8978 ATTGGAGTAAC
         66 ATTGGAGTAAC

                               
       8989 AAAAAAATCAAAAAAAATT
          1 AAAAAAATCAAAAAAAATT

       9008 CGAAAAAAAA


Statistics
Matches: 95,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  76   95  1.00

ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39


Consensus pattern (76 bp):   
AAAAAAATCAAAAAAAATTTGAGTTGTAATTTAATTTTTTTCCCTTGTATTTAGCTTACTATTGT
ATTGGAGTAAC

Found at i:10029 original size:18 final size:17

Alignment explanation


    Indices: 9994--10046  Score: 61
    Period size: 18  Copynumber: 3.0  Consensus size: 17

       9984 AGAAAAGAAA

                         *    
       9994 ATTGAAAAAGAGAGTGAG
          1 ATTGAAAAAGA-AATGAG

                              
      10012 ATTGAAGAAAGAAATGAG
          1 ATTGAA-AAAGAAATGAG

             *  *            
      10030 AGTGTAAAAGAAATGAG
          1 ATTGAAAAAGAAATGAG

      10047 TGTCATGGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  17   11  0.35
  18   15  0.48
  19    5  0.16

ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17


Consensus pattern (17 bp):   
ATTGAAAAAGAAATGAG

Found at i:10085 original size:12 final size:12

Alignment explanation


    Indices: 10068--10092  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      10058 AAGAGAGAGG

                        
      10068 GTTTGAAAAAGA
          1 GTTTGAAAAAGA

                        
      10080 GTTTGAAAAAGA
          1 GTTTGAAAAAGA

             
      10092 G
          1 G

      10093 AAGAGTGAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24


Consensus pattern (12 bp):   
GTTTGAAAAAGA
Done.