Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_384 ID=scaffold_384-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: 7654
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31


Found at i:126 original size:27 final size:28

Alignment explanation


    Indices: 92--162  Score: 76
    Period size: 27  Copynumber: 2.6  Consensus size: 28

         82 TGTAATTAAA

                            *            
         92 ATAA-ACATATTTAATTTAT-GACTTAAT
          1 ATAAGACATATTTAATATATGGAC-TAAT

                        *  *            
        119 A-AAGACATATTAAAGATATGGACTAAT
          1 ATAAGACATATTTAATATATGGACTAAT

                    *        
        146 ATAAGACACATTTAATA
          1 ATAAGACATATTTAATA

        163 AGCTAAATTA


Statistics
Matches: 35,  Mismatches: 6, Indels: 5
        0.76            0.13        0.11

Matches are distributed among these distances:
  26    2  0.06
  27   18  0.51
  28   15  0.43

ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34


Consensus pattern (28 bp):   
ATAAGACATATTTAATATATGGACTAAT

Found at i:3282 original size:20 final size:21

Alignment explanation


    Indices: 3259--3314  Score: 60
    Period size: 22  Copynumber: 2.6  Consensus size: 21

       3249 TCTGGCAAAA

                                 
       3259 ACACTTGTTTTTTCATTT-TC
          1 ACACTTGTTTTTTCATTTGTC

                   *        *      
       3279 ACACTCTTTCTTTTTCTTTTGTC
          1 ACACT-TGT-TTTTTCATTTGTC

              *          
       3302 ACTCTTGTTTTTT
          1 ACACTTGTTTTTT

       3315 TATCACTCTC


Statistics
Matches: 29,  Mismatches: 4, Indels: 5
        0.76            0.11        0.13

Matches are distributed among these distances:
  20    5  0.17
  21    7  0.24
  22   11  0.38
  23    6  0.21

ACGTcount: A:0.11, C:0.21, G:0.05, T:0.62


Consensus pattern (21 bp):   
ACACTTGTTTTTTCATTTGTC

Found at i:3313 original size:21 final size:22

Alignment explanation


    Indices: 3262--3314  Score: 65
    Period size: 21  Copynumber: 2.5  Consensus size: 22

       3252 GGCAAAAACA

                                  
       3262 CTTGTTTTTTCATTTTCACACT
          1 CTTGTTTTTTCATTTTCACACT

                             **    
       3284 CTT-TCTTTTTC-TTTTGTCACT
          1 CTTGT-TTTTTCATTTTCACACT

                      
       3305 CTTGTTTTTT
          1 CTTGTTTTTT

       3315 TATCACTCTC


Statistics
Matches: 27,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  21   17  0.63
  22   10  0.37

ACGTcount: A:0.08, C:0.21, G:0.06, T:0.66


Consensus pattern (22 bp):   
CTTGTTTTTTCATTTTCACACT

Found at i:3349 original size:15 final size:15

Alignment explanation


    Indices: 3329--3382  Score: 58
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       3319 ACTCTCATCA

                           
       3329 TTCTTTTCTTTCTTT
          1 TTCTTTTCTTTCTTT

                    **     
       3344 TTCTTTTCACTCTTT
          1 TTCTTTTCTTTCTTT

              *            
       3359 TTGTTTTC--TCTTT
          1 TTCTTTTCTTTCTTT

                       
       3372 TTCTCTTTCTT
          1 TTCT-TTTCTT

       3383 GCTCAATAGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 5
        0.78            0.10        0.12

Matches are distributed among these distances:
  13    8  0.25
  14    4  0.12
  15   20  0.62

ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74


Consensus pattern (15 bp):   
TTCTTTTCTTTCTTT

Found at i:5510 original size:12 final size:13

Alignment explanation


    Indices: 5480--5512  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       5470 ACACAAAATA

                         
       5480 ATTTTTTTTTCAG
          1 ATTTTTTTTTCAG

             *           
       5493 AATTTTTTTTC-G
          1 ATTTTTTTTTCAG

                    
       5505 ATTTTTTT
          1 ATTTTTTT

       5513 ACAAACTCGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  12    8  0.44
  13   10  0.56

ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73


Consensus pattern (13 bp):   
ATTTTTTTTTCAG
Done.