Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_825 ID=scaffold_825-JGI_221_v2.0

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: 5209
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.24

Warning! 1825 characters in sequence are not A, C, G, or T


Found at i:261 original size:30 final size:28

Alignment explanation


    Indices: 208--279  Score: 119
    Period size: 30  Copynumber: 2.5  Consensus size: 28

        198 TTTTTTTAAG

                                        
        208 TATATTATTAT-TTTATTGTAATTATAT
          1 TATATTATTATATTTATTGTAATTATAT

                                          
        235 TATATTATTATATTATATTGTAAATTATAT
          1 TATATTATTATATT-TATTGT-AATTATAT

                           
        265 TATATTATTATATTT
          1 TATATTATTATATTT

        280 TAAATAAACA


Statistics
Matches: 42,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
  27   11  0.26
  28    2  0.05
  29    7  0.17
  30   22  0.52

ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61


Consensus pattern (28 bp):   
TATATTATTATATTTATTGTAATTATAT

Found at i:278 original size:5 final size:5

Alignment explanation


    Indices: 208--272  Score: 53
    Period size: 5  Copynumber: 12.6  Consensus size: 5

        198 TTTTTTTAAG

                          *     *                                   
        208 TATAT TATTAT TTTAT TGTAAT TATAT TATA- T-TAT TATAT TATATT
          1 TATAT TA-TAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATA-T

               *                  
        254 GTAAAT TATAT TATAT TAT
          1 -TATAT TATAT TATAT TAT

        273 TATATTTTAA


Statistics
Matches: 49,  Mismatches: 5, Indels: 12
        0.74            0.08        0.18

Matches are distributed among these distances:
   3    2  0.04
   4    2  0.04
   5   32  0.65
   6   10  0.20
   7    3  0.06

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60


Consensus pattern (5 bp):   
TATAT

Found at i:2964 original size:13 final size:13

Alignment explanation


    Indices: 2946--2973  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       2936 CGATCTCTTC

                         
       2946 TGGGTATTCTATA
          1 TGGGTATTCTATA

                         
       2959 TGGGTATTCTATA
          1 TGGGTATTCTATA

              
       2972 TG
          1 TG

       2974 TTCTTTTATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46


Consensus pattern (13 bp):   
TGGGTATTCTATA
Done.