Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_989 ID=scaffold_989-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: 1676
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32


Found at i:1191 original size:3 final size:3

Alignment explanation


    Indices: 1183--1245  Score: 126
    Period size: 3  Copynumber: 21.0  Consensus size: 3

       1173 AAAACATTTA

                                                                           
       1183 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                               
       1231 AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT

       1246 GGACATGTAA


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   60  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:1415 original size:13 final size:13

Alignment explanation


    Indices: 1399--1424  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1389 AAATAATAAA

                         
       1399 AAAATATACATAT
          1 AAAATATACATAT

                         
       1412 AAAATATACATAT
          1 AAAATATACATAT

       1425 TTTAAAATGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31


Consensus pattern (13 bp):   
AAAATATACATAT

Found at i:1601 original size:3 final size:3

Alignment explanation


    Indices: 1593--1642  Score: 100
    Period size: 3  Copynumber: 16.7  Consensus size: 3

       1583 ATGAGCAACC

                                                                           
       1593 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

              
       1641 AA
          1 AA

       1643 AATCTAATTT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   47  1.00

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


Consensus pattern (3 bp):   
AAT

Done.