Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2465

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: 36804
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:5919 original size:10 final size:9

Alignment explanation


    Indices: 5898--5931  Score: 50
    Period size: 9  Copynumber: 3.7  Consensus size: 9

       5888 GAATTTCGTC

                     
       5898 TTTTTTGAT
          1 TTTTTTGAT

                    *
       5907 TTTTTTGAC
          1 TTTTTTGAT

                     
       5916 TTTTTTGAT
          1 TTTTTTGAT

                   
       5925 TATTTTT
          1 T-TTTTT

       5932 TTGTGGGATT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
   9   17  0.77
  10    5  0.23

ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76


Consensus pattern (9 bp):   
TTTTTTGAT

Found at i:13160 original size:24 final size:25

Alignment explanation


    Indices: 13107--13160  Score: 60
    Period size: 24  Copynumber: 2.2  Consensus size: 25

      13097 AACAAATTCT

                        *         *  
      13107 TTTTTTCATTTTCATCACTCGTTTC
          1 TTTTTTCATTTTAATCACTCGTCTC

                                      
      13132 -TTTTTC-TTTTGAATCACTC-TCTC
          1 TTTTTTCATTTT-AATCACTCGTCTC

                  
      13155 TTTTTT
          1 TTTTTT

      13161 TATCACTCAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 5
        0.78            0.06        0.16

Matches are distributed among these distances:
  23    7  0.28
  24   18  0.72

ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63


Consensus pattern (25 bp):   
TTTTTTCATTTTAATCACTCGTCTC

Found at i:22326 original size:20 final size:20

Alignment explanation


    Indices: 22303--22349  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      22293 GGGTTAAGAT

                            *   
      22303 TGAGCTGAATTGAGCTTGAG
          1 TGAGCTGAATTGAGCTCGAG

                *   *           
      22323 TGAGTTGACTTGAGCTCGAG
          1 TGAGCTGAATTGAGCTCGAG

                   
      22343 TGAGCTG
          1 TGAGCTG

      22350 GAAACGAGCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30


Consensus pattern (20 bp):   
TGAGCTGAATTGAGCTCGAG

Found at i:27193 original size:12 final size:12

Alignment explanation


    Indices: 27176--27201  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      27166 CCGTAGTTCC

                        
      27176 TATTTTGCTAAA
          1 TATTTTGCTAAA

                        
      27188 TATTTTGCTAAA
          1 TATTTTGCTAAA

              
      27200 TA
          1 TA

      27202 GAGGGTCTCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50


Consensus pattern (12 bp):   
TATTTTGCTAAA

Found at i:30397 original size:19 final size:18

Alignment explanation


    Indices: 30361--30400  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      30351 TTTCCACTCG

                         *    
      30361 TTTCTTTTTCAACTTCTC
          1 TTTCTTTTTCAACATCTC

                      *        
      30379 TTTCTTTTTCCACAATCTC
          1 TTTCTTTTTCAAC-ATCTC

               
      30398 TTT
          1 TTT

      30401 GTTTGTTGAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   12  0.63
  19    7  0.37

ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60


Consensus pattern (18 bp):   
TTTCTTTTTCAACATCTC

Found at i:30532 original size:18 final size:17

Alignment explanation


    Indices: 30473--30533  Score: 59
    Period size: 18  Copynumber: 3.4  Consensus size: 17

      30463 GCACTCTTTC

                      *        
      30473 TTTTCTTTCTCCAATCTTT
          1 TTTTCTTT-TTCAAT-TTT

              *              
      30492 TTCTCTTTTTCAATTTT
          1 TTTTCTTTTTCAATTTT

                         *     
      30509 TGTTTCTTTTTCAGTTTCT
          1 T-TTTCTTTTTCAATTT-T

                  
      30528 TTTTCT
          1 TTTTCT

      30534 CTCGTCACTC


Statistics
Matches: 36,  Mismatches: 4, Indels: 5
        0.80            0.09        0.11

Matches are distributed among these distances:
  17    4  0.11
  18   23  0.64
  19    9  0.25

ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69


Consensus pattern (17 bp):   
TTTTCTTTTTCAATTTT
Done.