Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold372

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: 395264
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.32

Warning! 23199 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:380510 original size:6 final size:6

Alignment explanation


    Indices: 380499--380525  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

     380489 AAATGGCTCA

                                           
     380499 TTTCTT TTTCTT TTTCTT TTTCTT TTT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTT

     380526 GGAAATAGAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (6 bp):   
TTTCTT

Found at i:382263 original size:19 final size:18

Alignment explanation


    Indices: 382220--382263  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 18

     382210 TGAACTTATT

                             *
     382220 AATT-TTTTTAATTTTTG
          1 AATTATTTTTAATTTTTA

               *               
     382237 AATAATTTTATAATTTTTA
          1 AATTATTTT-TAATTTTTA

                    
     382256 AATTATTT
          1 AATTATTT

     382264 GTTGACATGA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  17    3  0.14
  18    4  0.18
  19   15  0.68

ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64


Consensus pattern (18 bp):   
AATTATTTTTAATTTTTA

Found at i:384212 original size:24 final size:24

Alignment explanation


    Indices: 384177--384222  Score: 67
    Period size: 25  Copynumber: 1.9  Consensus size: 24

     384167 TCCCCTTAGC

                      *              
     384177 AAAT-AAACCCAATTTTATAAATAA
          1 AAATAAAACCAAATTTTA-AAATAA

                                  
     384201 AAATAAAACCAAATTTTAAAAT
          1 AAATAAAACCAAATTTTAAAAT

     384223 GTCCACAGTC


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  24    8  0.40
  25   12  0.60

ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28


Consensus pattern (24 bp):   
AAATAAAACCAAATTTTAAAATAA

Found at i:385393 original size:9 final size:9

Alignment explanation


    Indices: 385376--385413  Score: 58
    Period size: 9  Copynumber: 4.2  Consensus size: 9

     385366 TTAATTATAA

                     
     385376 TACTATTAT
          1 TACTATTAT

              *      
     385385 TATTATTAT
          1 TACTATTAT

                     
     385394 TACTATTAT
          1 TACTATTAT

                 *   
     385403 TACTACTAT
          1 TACTATTAT

              
     385412 TA
          1 TA

     385414 TTATAGATGT


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   9   26  1.00

ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55


Consensus pattern (9 bp):   
TACTATTAT

Found at i:385400 original size:12 final size:12

Alignment explanation


    Indices: 385379--385417  Score: 60
    Period size: 12  Copynumber: 3.2  Consensus size: 12

     385369 ATTATAATAC

                 *      
     385379 TATTATTATTAT
          1 TATTACTATTAT

                        
     385391 TATTACTATTAT
          1 TATTACTATTAT

              *         
     385403 TACTACTATTAT
          1 TATTACTATTAT

               
     385415 TAT
          1 TAT

     385418 AGATGTTATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59


Consensus pattern (12 bp):   
TATTACTATTAT

Found at i:385429 original size:3 final size:3

Alignment explanation


    Indices: 385379--385417  Score: 51
    Period size: 3  Copynumber: 13.0  Consensus size: 3

     385369 ATTATAATAC

                                  *           *   *            
     385379 TAT TAT TAT TAT TAT TAC TAT TAT TAC TAC TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

     385418 AGATGTTATT


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59


Consensus pattern (3 bp):   
TAT

Done.