Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_470 ID=scaffold_470-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: 7871
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.26

Warning! 1206 characters in sequence are not A, C, G, or T


Found at i:1673 original size:28 final size:28

Alignment explanation


    Indices: 1633--1690  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       1623 TCAAAAGGAG

                                        
       1633 AAAGATCAGAAACATTGAAAGTAGCACT
          1 AAAGATCAGAAACATTGAAAGTAGCACT

                                        
       1661 AAAGATCAGAAACATTGAAAGTAGCACT
          1 AAAGATCAGAAACATTGAAAGTAGCACT

              
       1689 AA
          1 AA

       1691 CACTATACTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17


Consensus pattern (28 bp):   
AAAGATCAGAAACATTGAAAGTAGCACT

Found at i:5301 original size:12 final size:12

Alignment explanation


    Indices: 5284--5309  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       5274 AAGAAGATGG

                        
       5284 AGCTCGATTAGT
          1 AGCTCGATTAGT

                        
       5296 AGCTCGATTAGT
          1 AGCTCGATTAGT

              
       5308 AG
          1 AG

       5310 AAGTAGAACC


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:0.27, C:0.15, G:0.27, T:0.31


Consensus pattern (12 bp):   
AGCTCGATTAGT

Found at i:7532 original size:31 final size:32

Alignment explanation


    Indices: 7494--7556  Score: 119
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       7484 AGGCAAATTA

                                            
       7494 CAAGAGTAATTG-AATCCTAATAAAACTCTTT
          1 CAAGAGTAATTGAAATCCTAATAAAACTCTTT

                                            
       7525 CAAGAGTAATTGAAATCCTAATAAAACTCTTT
          1 CAAGAGTAATTGAAATCCTAATAAAACTCTTT

       7557 AAAATTATCT


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  31   12  0.39
  32   19  0.61

ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32


Consensus pattern (32 bp):   
CAAGAGTAATTGAAATCCTAATAAAACTCTTT

Done.