Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g02231.N1

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: 8636
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35


Found at i:520 original size:15 final size:15

Alignment explanation


    Indices: 500--530  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        490 GTAAGGATTA

                           
        500 AATTGAAATTTTACC
          1 AATTGAAATTTTACC

                           
        515 AATTGAAATTTTACC
          1 AATTGAAATTTTACC

             
        530 A
          1 A

        531 TATCTTTTGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39


Consensus pattern (15 bp):   
AATTGAAATTTTACC

Found at i:4868 original size:22 final size:23

Alignment explanation


    Indices: 4836--4885  Score: 66
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       4826 TTTAAAGCCA

                         **        
       4836 TTATTTATGAGTTTTATTTAAAT
          1 TTATTTATGAGTTAGATTTAAAT

                                   
       4859 TTATTT-TGAGTTAGATTTAAAT
          1 TTATTTATGAGTTAGATTTAAAT

            *    
       4881 ATATT
          1 TTATT

       4886 CTAATTTTCA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  22   18  0.75
  23    6  0.25

ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58


Consensus pattern (23 bp):   
TTATTTATGAGTTAGATTTAAAT

Found at i:5368 original size:69 final size:69

Alignment explanation


    Indices: 5110--5355  Score: 350
    Period size: 69  Copynumber: 3.6  Consensus size: 69

       5100 AAAGTTATCT

                    *        *               **    *             *           
       5110 CTCTCTTCCAATCAGTTTTCTGGAAATATATCTATCCTTGAGAGCCTAACATTACTTGAATCTTT
          1 CTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTTCAGAGCCTAACATTGCTTGAATCTTT

                
       5175 GGAC
         66 GGAC

                   *                        *                          *     
       5179 CTCTCTTTTAATCTA-TTCTCTGGAAATATATTTGCCCTTCAGAGCCTAACATTGCTTGCATCTT
          1 CTCTCTTCTAATC-AGTTCTCTGGAAATATATCTGCCCTTCAGAGCCTAACATTGCTTGAATCTT

                 
       5243 TGGAC
         65 TGGAC

                   *      *  *            *                                  
       5248 CTCTCTTTTAATCAATTTTCTGGAAATATACCTGCCCTTCAGAGCCTAACATTGCTTGAATCTTT
          1 CTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTTCAGAGCCTAACATTGCTTGAATCTTT

            *   
       5313 AGAC
         66 GGAC

                                                   
       5317 CTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTT
          1 CTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTT

       5356 GAAAGTCTAA


Statistics
Matches: 157,  Mismatches: 18, Indels: 4
        0.88            0.10        0.02

Matches are distributed among these distances:
  68    1  0.01
  69  155  0.99
  70    1  0.01

ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39


Consensus pattern (69 bp):   
CTCTCTTCTAATCAGTTCTCTGGAAATATATCTGCCCTTCAGAGCCTAACATTGCTTGAATCTTT
GGAC

Found at i:5384 original size:138 final size:138

Alignment explanation


    Indices: 5110--5384  Score: 356
    Period size: 138  Copynumber: 2.0  Consensus size: 138

       5100 AAAGTTATCT

                          *               *   *    *                         
       5110 CTCTCTTCCAATCAGTTTTCTGGAAATATATCTATCCTTGAGAGCCTAACATTACTTGAATCTTT
          1 CTCTCTTCCAATCAATTTTCTGGAAATATACCTACCCTTCAGAGCCTAACATTACTTGAATCTTT

            *          *                       *         *           * * *   
       5175 GGACCTCTCTTTTAATCTATTCTCTGGAAATATATTTGCCCTTCAGAGCCTAACATTGCTTGCAT
         66 AGACCTCTCTTCTAATCTATTCTCTGGAAATATATCTGCCCTTCAAAGCCTAACATTCCCTCCAT

             *      
       5240 CTTTGGAC
        131 CGTTGGAC

                   **                        *                   *           
       5248 CTCTCTTTTAATCAATTTTCTGGAAATATACCTGCCCTTCAGAGCCTAACATTGCTTGAATCTTT
          1 CTCTCTTCCAATCAATTTTCTGGAAATATACCTACCCTTCAGAGCCTAACATTACTTGAATCTTT

                                                        *    *               
       5313 AGACCTCTCTTCTAATC-AGTTCTCTGGAAATATATCTGCCCTTGAAAGTCTAACA-TCCCTCCA
         66 AGACCTCTCTTCTAATCTA-TTCTCTGGAAATATATCTGCCCTTCAAAGCCTAACATTCCCTCC-

                     
       5376 ATCGTTGGA
        129 ATCGTTGGA

       5385 TGTTTCAAAC


Statistics
Matches: 117,  Mismatches: 18, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
 137    5  0.04
 138  112  0.96

ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37


Consensus pattern (138 bp):   
CTCTCTTCCAATCAATTTTCTGGAAATATACCTACCCTTCAGAGCCTAACATTACTTGAATCTTT
AGACCTCTCTTCTAATCTATTCTCTGGAAATATATCTGCCCTTCAAAGCCTAACATTCCCTCCAT
CGTTGGAC

Done.