Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00699.P2

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: 7585
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:4535 original size:19 final size:19

Alignment explanation


    Indices: 4511--4550  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4501 TTCTTTGTGG

                               
       4511 CTGGAAAACTATTATGTTT
          1 CTGGAAAACTATTATGTTT

                               
       4530 CTGGAAAACTATTATGTTT
          1 CTGGAAAACTATTATGTTT

              
       4549 CT
          1 CT

       4551 TTGTGGCTGG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42


Consensus pattern (19 bp):   
CTGGAAAACTATTATGTTT

Found at i:4554 original size:46 final size:49

Alignment explanation


    Indices: 4498--4622  Score: 175
    Period size: 54  Copynumber: 2.5  Consensus size: 49

       4488 CAAGGAAGTT

                                                             
       4498 TGTTTCTTTGTGGCTGGAAAACTATTATG-TT-T-CTGGAAAACTATTA
          1 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA

                                                            *     
       4544 TGTTTCTTTGTGGCTGGAAAACTATTATGTTTCTTTGTGGCTGGAAAATTATTA
          1 TGTTTCTTTGTGGCTGGAAAACTATTATG----TTTGT-GCTGGAAAACTATTA

                                     
       4598 TGTTTCTTTGTGGCTGGAAAACTAT
          1 TGTTTCTTTGTGGCTGGAAAACTAT

       4623 GTTTCTTTTG


Statistics
Matches: 70,  Mismatches: 1, Indels: 8
        0.89            0.01        0.10

Matches are distributed among these distances:
  46   29  0.41
  51    2  0.03
  52    1  0.01
  54   38  0.54

ACGTcount: A:0.23, C:0.10, G:0.22, T:0.45


Consensus pattern (49 bp):   
TGTTTCTTTGTGGCTGGAAAACTATTATGTTTGTGCTGGAAAACTATTA

Found at i:4568 original size:27 final size:27

Alignment explanation


    Indices: 4530--4622  Score: 177
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       4520 TATTATGTTT

                                       
       4530 CTGGAAAACTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                                       
       4557 CTGGAAAACTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                    *                  
       4584 CTGGAAAATTATTATGTTTCTTTGTGG
          1 CTGGAAAACTATTATGTTTCTTTGTGG

                        
       4611 CTGGAAAACTAT
          1 CTGGAAAACTAT

       4623 GTTTCTTTTG


Statistics
Matches: 64,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   64  1.00

ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43


Consensus pattern (27 bp):   
CTGGAAAACTATTATGTTTCTTTGTGG

Found at i:5639 original size:126 final size:126

Alignment explanation


    Indices: 5414--5663  Score: 396
    Period size: 126  Copynumber: 2.0  Consensus size: 126

       5404 GGGCCCGAAG

                       *                                                     
       5414 AATCACCAATCGAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
          1 AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT

                                  *                                      
       5479 TATTTGTTGAAGACCCCGTAGCGTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
         66 TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA

                                                              *    *  *      
       5540 AATCACCAATCAAGTATGAGAAAG-ATCTCTAAGTTTGTTTTGAATTAAGTTTTTTAGTAAATGT
          1 AATCACCAATCAAGTATGAG--AGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGT

                             *                          *    *           
       5604 A-TATTTGTTGAAGACCTCGTAGCCTTGTGTGGCTTAATTTGTAGTTTTGCAGTCATATAG
         64 ATTATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAG

       5664 GAAACTTCTG


Statistics
Matches: 114,  Mismatches: 8, Indels: 4
        0.90            0.06        0.03

Matches are distributed among these distances:
 126   74  0.65
 127   38  0.33
 128    2  0.02

ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39


Consensus pattern (126 bp):   
AATCACCAATCAAGTATGAGAGTATCTCTAAGTTTGTTTTGAATTAAGCTTTTAAGAAAATGTAT
TATTTGTTGAAGACCCCGTAGCCTTGTGTGGCTTAATTTGTACTTTTACAGTCATATAGAA
Done.