Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00233.F9

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: 4614
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29


Found at i:1607 original size:42 final size:42

Alignment explanation


    Indices: 1561--1719  Score: 153
    Period size: 42  Copynumber: 3.8  Consensus size: 42

       1551 TCATGCAAGG

                            *      **                 
       1561 TCAAGATCCAAATCAAAATCACCCCTTAGTTATCGGAGAAGA
          1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

                           *                     *     
       1603 TCAAGAT-CAAAGTCTAGATCACCAATTAGTTATCGGCGAAGA
          1 TCAAGATCCAAA-TCAAGATCACCAATTAGTTATCGGAGAAGA

                 *     *              * *    *  *     
       1645 TCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGAA-A
          1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

                  *                     *      
       1686 GTCAAGGT-CAAAGTCAAGATCACCAATCAGTTAT
          1 -TCAAGATCCAAA-TCAAGATCACCAATTAGTTAT

       1720 AGGCGAAGGA


Statistics
Matches: 100,  Mismatches: 13, Indels: 8
        0.83            0.11        0.07

Matches are distributed among these distances:
  41    8  0.08
  42   89  0.89
  43    3  0.03

ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23


Consensus pattern (42 bp):   
TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA

Found at i:1720 original size:42 final size:43

Alignment explanation


    Indices: 1599--1726  Score: 188
    Period size: 42  Copynumber: 3.0  Consensus size: 43

       1589 GTTATCGGAG

                     *        *           *      *     
       1599 AAGATCAAGATCAAAGTCTAGATCACCAATTAGTTATCGGCG-
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

                        *                   *          
       1641 AAGATCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGA
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

                                                       
       1684 AAG-TCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
          1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

             
       1726 A
          1 A

       1727 GGAGGAGATC


Statistics
Matches: 77,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  42   74  0.96
  43    3  0.04

ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21


Consensus pattern (43 bp):   
AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA

Found at i:2528 original size:45 final size:45

Alignment explanation


    Indices: 2455--2551  Score: 140
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       2445 TAAGAAATCT

                            * *   **                     
       2455 AAGCATCGGGATAGAAGGCGGTTGAGGTCAAGATCTGCTGATGGC
          1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC

                                                **       
       2500 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTTTTGATGGC
          1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC

                   
       2545 AAGCATC
          1 AAGCATC

       2552 ACAGAGGAAG


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  45   46  1.00

ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21


Consensus pattern (45 bp):   
AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC

Found at i:4322 original size:16 final size:16

Alignment explanation


    Indices: 4277--4322  Score: 56
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       4267 ATCTTCGGTC

                            
       4277 TTCCTCTTTCTTTCTT
          1 TTCCTCTTTCTTTCTT

               * *   *      
       4293 TTCTTTTTTTTTTCTT
          1 TTCCTCTTTCTTTCTT

                *         
       4309 TTCCCCTTTCTTTC
          1 TTCCTCTTTCTTTC

       4323 CAGATTTTTT


Statistics
Matches: 23,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72


Consensus pattern (16 bp):   
TTCCTCTTTCTTTCTT
Done.