Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00098.N3

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: 8535
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:575 original size:110 final size:113

Alignment explanation


    Indices: 271--604  Score: 545
    Period size: 110  Copynumber: 3.0  Consensus size: 113

        261 AAATGTGAAT

                                        *        *                           
        271 TTTTAAGTCTTTTTCCCCCTTCTTTTTCTCAAAATCGATCCCCCCTTTCTTTTTCCCAAACCATT
          1 TTTTAAGTCTTTTTCCCCCTTCTTTTTCCCAAAATCGGTCCCCCCTTTCTTTTTCCCAAACCATT

                                                      *     
        336 TCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCCAATCG
         66 TCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCAAATCG

                                                *         *                * 
        384 TTTTAAGGT-TTTTT-CCCCTTCTTTTTCCCAAAATGGGT-CCCCCGTTCTTTTTCCCAAACCGT
          1 TTTTAA-GTCTTTTTCCCCCTTCTTTTTCCCAAAATCGGTCCCCCCTTTCTTTTTCCCAAACCAT

                                               *             
        446 TTCTCCCTACCCCGATTCCC-TT-TTTTT-CCCCAGTTTCCCCAAATCG
         65 TTCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCAAATCG

                                                                             
        492 TTTTAAGTCTTTTTCCCCCTTCTTTTTCCCAAAATCGGTCCCCCCTTTCTTTTTCCCAAACCATT
          1 TTTTAAGTCTTTTTCCCCCTTCTTTTTCCCAAAATCGGTCCCCCCTTTCTTTTTCCCAAACCATT

                                                *           
        557 TCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATCTCCCCAAATCG
         66 TCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCAAATCG

        605 GCAGCCCTCT


Statistics
Matches: 202,  Mismatches: 12, Indels: 14
        0.89            0.05        0.06

Matches are distributed among these distances:
 107    2  0.01
 108   28  0.14
 109   28  0.14
 110   44  0.22
 111   44  0.22
 112   26  0.13
 113   28  0.14
 114    2  0.01

ACGTcount: A:0.15, C:0.38, G:0.06, T:0.41


Consensus pattern (113 bp):   
TTTTAAGTCTTTTTCCCCCTTCTTTTTCCCAAAATCGGTCCCCCCTTTCTTTTTCCCAAACCATT
TCTCCCTACCCCGATTCCCTTTATTTTTCCCCCAATTTCCCCAAATCG

Found at i:647 original size:25 final size:25

Alignment explanation


    Indices: 602--672  Score: 94
    Period size: 25  Copynumber: 3.0  Consensus size: 25

        592 TCTCCCCAAA

                                     
        602 TCGGCAG-CC-CT-CTGCATCTCCG
          1 TCGGCAGCCCACTGCTGCATCTCCG

             *                       
        624 TTGGCAGCCCACTGCTGCATCTCCG
          1 TCGGCAGCCCACTGCTGCATCTCCG

                      *       *     
        649 TCGGCAGCCCTCTGCTGCTTCTCC
          1 TCGGCAGCCCACTGCTGCATCTCC

        673 TTGTAAGCTG


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  22    6  0.14
  23    2  0.05
  24    2  0.05
  25   32  0.76

ACGTcount: A:0.08, C:0.44, G:0.23, T:0.25


Consensus pattern (25 bp):   
TCGGCAGCCCACTGCTGCATCTCCG

Found at i:1669 original size:2 final size:2

Alignment explanation


    Indices: 1662--1695  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1652 ACATTTAAAA

                                                              
       1662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1696 GACAAATACA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Done.