Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3953

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, 372

Length: 620
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52


Found at i:93 original size:3 final size:3

Alignment explanation


    Indices: 61--129  Score: 53
    Period size: 3  Copynumber: 24.3  Consensus size: 3

         51 TTATACTCAT

                                                                          
         61 TTA TTCA TTA TTA -TA TT- TCTA -TA TTA -TA TTA TTA TT- TT- TGTA
          1 TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA

                                     *           
        103 TTA TTA TTA -TA TTA TTA TCA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T

        130 AGTTGCTCTT


Statistics
Matches: 55,  Mismatches: 2, Indels: 18
        0.73            0.03        0.24

Matches are distributed among these distances:
   2   12  0.22
   3   39  0.71
   4    4  0.07

ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64


Consensus pattern (3 bp):   
TTA

Found at i:104 original size:11 final size:11

Alignment explanation


    Indices: 62--129  Score: 50
    Period size: 11  Copynumber: 5.8  Consensus size: 11

         52 TATACTCATT

                        
         62 TATTCATTATTA
          1 TATT-ATTATTA

                 *       
         74 TATTTCTATATTA
          1 TA-TTAT-TATTA

                       
         87 TATTATTATT-
          1 TATTATTATTA

             *          
         97 TTTGTATTATTA
          1 TAT-TATTATTA

                        
        109 T-TATATTATTA
          1 TAT-TATTATTA

                      
        120 TCATTATTAT
          1 T-ATTATTAT

        130 AGTTGCTCTT


Statistics
Matches: 46,  Mismatches: 4, Indels: 12
        0.74            0.06        0.19

Matches are distributed among these distances:
  10    2  0.04
  11   21  0.46
  12   13  0.28
  13   10  0.22

ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63


Consensus pattern (11 bp):   
TATTATTATTA

Found at i:125 original size:17 final size:16

Alignment explanation


    Indices: 82--130  Score: 55
    Period size: 17  Copynumber: 2.9  Consensus size: 16

         72 TATATTTCTA

                            
         82 TATTATATTATTAT-T
          1 TATTATATTATTATAT

             *                
         97 TTTGTATTATTATTATAT
          1 TAT-TA-TATTATTATAT

                            
        115 TATTATCATTATTATA
          1 TATTAT-ATTATTATA

        131 GTTGCTCTTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
  15    2  0.07
  16    3  0.11
  17   20  0.71
  18    3  0.11

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63


Consensus pattern (16 bp):   
TATTATATTATTATAT

Found at i:160 original size:21 final size:21

Alignment explanation


    Indices: 136--178  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        126 TTATAGTTGC

                          *      
        136 TCTTACATATATACGTATATT
          1 TCTTACATATATACATATATT

                **               
        157 TCTTTTATATATACATATATT
          1 TCTTACATATATACATATATT

             
        178 T
          1 T

        179 TTCTAGATAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53


Consensus pattern (21 bp):   
TCTTACATATATACATATATT
Done.