Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2052

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: 17444
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33


Found at i:3070 original size:50 final size:50

Alignment explanation


    Indices: 3016--3371  Score: 572
    Period size: 50  Copynumber: 7.1  Consensus size: 50

       3006 GTTGTCATTA

                               *                              
       3016 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                                                 *  *         
       3066 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGTCCGTAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                                                              
       3116 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                                                               
       3166 TTGA-TGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
          1 TTGACT-ATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                                                 *  **        
       3216 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGGTCGTAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                                                              
       3266 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

                               *     *   *    * *       *      
       3316 TTGACTATTCTTCACCAACATTTGATAATAGAGAAATGT-AGCCATAATTG
          1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGA-CCGTAATTG

                  
       3366 TTGACT
          1 TTGACT

       3372 CTAAGCAACT


Statistics
Matches: 286,  Mismatches: 17, Indels: 6
        0.93            0.06        0.02

Matches are distributed among these distances:
  49    2  0.01
  50  283  0.99
  51    1  0.00

ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Consensus pattern (50 bp):   
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG

Found at i:11047 original size:19 final size:19

Alignment explanation


    Indices: 11023--11060  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      11013 GGACTTTGGC

                               
      11023 ATGTTCATATCTTTTATTG
          1 ATGTTCATATCTTTTATTG

                               
      11042 ATGTTCATATCTTTTATTG
          1 ATGTTCATATCTTTTATTG

      11061 TTATTTATTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58


Consensus pattern (19 bp):   
ATGTTCATATCTTTTATTG

Found at i:11728 original size:1 final size:1

Alignment explanation


    Indices: 11718--11808  Score: 74
    Period size: 1  Copynumber: 91.0  Consensus size: 1

      11708 TGGCAATTGG

                 *       *    *        **     *          *    *        **    
      11718 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAGGAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

             *             *          
      11783 AGAAAAAAAAAAAAACAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      11809 GTGAAGATTT


Statistics
Matches: 70,  Mismatches: 20, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
   1   70  1.00

ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00


Consensus pattern (1 bp):   
A

Found at i:11765 original size:32 final size:31

Alignment explanation


    Indices: 11716--11806  Score: 152
    Period size: 32  Copynumber: 3.0  Consensus size: 31

      11706 CATGGCAATT

                                           
      11716 GGAAAAAG--AAAAAAACAAAACAAAAAAAA
          1 GGAAAAAGAAAAAAAAACAAAACAAAAAAAA

                                            
      11745 GGAAAAAGAAAAAAAAAACAAAACAAAAAAAA
          1 GGAAAAAG-AAAAAAAAACAAAACAAAAAAAA

                                           
      11777 GGAAAAAGAAAAAAAAA-AAAACAAAAAAAA
          1 GGAAAAAGAAAAAAAAACAAAACAAAAAAAA

      11807 AAGTGAAGAT


Statistics
Matches: 59,  Mismatches: 0, Indels: 5
        0.92            0.00        0.08

Matches are distributed among these distances:
  29    8  0.14
  30   13  0.22
  31    9  0.15
  32   29  0.49

ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00


Consensus pattern (31 bp):   
GGAAAAAGAAAAAAAAACAAAACAAAAAAAA

Done.