Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1027

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: 9609
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35


Found at i:2747 original size:16 final size:15

Alignment explanation


    Indices: 2724--2758  Score: 52
    Period size: 17  Copynumber: 2.2  Consensus size: 15

       2714 TAATTAATTT

                             
       2724 TTTAAAAAATTTATATA
          1 TTTAAAAAA-TTATA-A

                           
       2741 TTTAAAAAATTATAA
          1 TTTAAAAAATTATAA

               
       2756 TTT
          1 TTT

       2759 TATAATTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    4  0.22
  16    5  0.28
  17    9  0.50

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (15 bp):   
TTTAAAAAATTATAA

Found at i:4041 original size:31 final size:31

Alignment explanation


    Indices: 3995--4071  Score: 86
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       3985 AAAAAAATTT

                      *            *  *      
       3995 AAATTTAATTATAAAT-ATAAATTTATTTTTTA
          1 AAATTT-ATTTTAAATAATAAA-ATAATTTTTA

                                           
       4027 AAATTTATTTTAAATAATAAAATAATTTTTA
          1 AAATTTATTTTAAATAATAAAATAATTTTTA

                   *       
       4058 AAA-TTAATTTAAAT
          1 AAATTTATTTTAAAT

       4072 GTTTTAAAAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  30   10  0.25
  31   19  0.47
  32   11  0.28

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (31 bp):   
AAATTTATTTTAAATAATAAAATAATTTTTA

Found at i:5438 original size:3 final size:3

Alignment explanation


    Indices: 5430--5485  Score: 94
    Period size: 3  Copynumber: 18.3  Consensus size: 3

       5420 GTTACGGGTA

                                              *                             
       5430 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TCTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC

                     
       5479 TTC TTC T
          1 TTC TTC T

       5486 GCTGGGGAAT


Statistics
Matches: 50,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
   3   47  0.94
   4    3  0.06

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


Consensus pattern (3 bp):   
TTC

Found at i:6340 original size:3 final size:3

Alignment explanation


    Indices: 6332--6371  Score: 53
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       6322 ATTTATTTAC

                         *                   *                  
       6332 TAT TAT TAT TGT TAT TAT TAT TAAT AAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT

       6372 GTTACTGTTA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   3   30  0.94
   4    2  0.06

ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62


Consensus pattern (3 bp):   
TAT

Found at i:6350 original size:22 final size:22

Alignment explanation


    Indices: 6324--6383  Score: 59
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       6314 ATGCTTTTAT

                              *   
       6324 TTATTTACTATTATTATTGTTA
          1 TTATTTACTATTATTATTATTA

                   *    *          
       6346 TTA-TTATTAATAATTATTATTA
          1 TTATTTACT-ATTATTATTATTA

                      *     
       6368 TTATGTTACTGTTATT
          1 TTAT-TTACTATTATT

       6384 CAGGTATTTG


Statistics
Matches: 29,  Mismatches: 6, Indels: 5
        0.73            0.15        0.12

Matches are distributed among these distances:
  21    4  0.14
  22   17  0.59
  23    4  0.14
  24    4  0.14

ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62


Consensus pattern (22 bp):   
TTATTTACTATTATTATTATTA

Found at i:9118 original size:78 final size:78

Alignment explanation


    Indices: 8989--9144  Score: 312
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       8979 AAACAAGGCC

                                                                             
       8989 CGAACCAGCAAAGACGTTAATATTTCCAGGTTAGGTTACTTTCATTTCGTTATTCACCAAACAAA
          1 CGAACCAGCAAAGACGTTAATATTTCCAGGTTAGGTTACTTTCATTTCGTTATTCACCAAACAAA

                         
       9054 CGAACATGTTCCG
         66 CGAACATGTTCCG

                                                                             
       9067 CGAACCAGCAAAGACGTTAATATTTCCAGGTTAGGTTACTTTCATTTCGTTATTCACCAAACAAA
          1 CGAACCAGCAAAGACGTTAATATTTCCAGGTTAGGTTACTTTCATTTCGTTATTCACCAAACAAA

                         
       9132 CGAACATGTTCCG
         66 CGAACATGTTCCG

       9145 TTCACTTCAA


Statistics
Matches: 78,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  78   78  1.00

ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29


Consensus pattern (78 bp):   
CGAACCAGCAAAGACGTTAATATTTCCAGGTTAGGTTACTTTCATTTCGTTATTCACCAAACAAA
CGAACATGTTCCG
Done.