Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_634 ID=scaffold_634-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: 6253
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.26

Warning! 1160 characters in sequence are not A, C, G, or T


Found at i:618 original size:23 final size:23

Alignment explanation


    Indices: 588--632  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        578 GAGTTAAAGG

                      *            
        588 AAACTAGAAGCAGGTTCAGCCTA
          1 AAACTAGAAGAAGGTTCAGCCTA

                             *    
        611 AAACTAGAAGAAGGTTCGGCCT
          1 AAACTAGAAGAAGGTTCAGCCT

        633 TGCCAGCATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18


Consensus pattern (23 bp):   
AAACTAGAAGAAGGTTCAGCCTA

Found at i:1424 original size:16 final size:16

Alignment explanation


    Indices: 1403--1436  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1393 ATTTTTTTCT

                            
       1403 TACATTAATTACAATA
          1 TACATTAATTACAATA

                            
       1419 TACATTAATTACAATA
          1 TACATTAATTACAATA

              
       1435 TA
          1 TA

       1437 TTCAATAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38


Consensus pattern (16 bp):   
TACATTAATTACAATA

Found at i:1445 original size:18 final size:16

Alignment explanation


    Indices: 1403--1446  Score: 52
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1393 ATTTTTTTCT

                *           
       1403 TACATTAATTACAATA
          1 TACAATAATTACAATA

                *           
       1419 TACATTAATTACAATA
          1 TACAATAATTACAATA

                        
       1435 TATTCAATAATT
          1 TA--CAATAATT

       1447 TAAATTTTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  16   18  0.72
  18    7  0.28

ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41


Consensus pattern (16 bp):   
TACAATAATTACAATA

Found at i:2514 original size:16 final size:16

Alignment explanation


    Indices: 2490--2529  Score: 62
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       2480 GCCTAAGAGA

                            
       2490 AAATTGGGCTGGATTT
          1 AAATTGGGCTGGATTT

              *         *   
       2506 AAGTTGGGCTGGGTTT
          1 AAATTGGGCTGGATTT

                    
       2522 AAATTGGG
          1 AAATTGGG

       2530 GGAGGGTGTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.23, C:0.05, G:0.38, T:0.35


Consensus pattern (16 bp):   
AAATTGGGCTGGATTT
Done.