Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03603.M4

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: 7102
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30


Found at i:4089 original size:168 final size:162

Alignment explanation


    Indices: 3546--4060  Score: 877
    Period size: 162  Copynumber: 3.1  Consensus size: 162

       3536 TGCGCCCAAT

                                   *                       *                 
       3546 TTGCAAACTCTGAAGATAGAGAGATGCTTTGGAATGGAAGAAATAATTCAAGACTCACAAGTATC
          1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC

                                   *    *                                    
       3611 AACCATAAGCTTCCAATGCCTAAGGGAATTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
         66 AACCATAAGCTTCCAATGCCTAATGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT

                                            
       3676 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
        131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

                                      *                                      
       3708 TTGCAAACTCTGAAGATAGAGAGGTGTTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
          1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC

              *  *      *                         *                          
       3773 AATCACAAGCTTTCAATGCCTAATGGAAGTACAAGTCAAAGAATGCAATAAATTGAAATTTCTCT
         66 AACCATAAGCTTCCAATGCCTAATGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT

                *                           
       3838 TCCCCATGTGTGTTGCTAATAGTCTTGGGAAA
        131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

                                                                             
       3870 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATT
          1 TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAG---T

                                                                     *       
       3935 ATCAACCATAAGCTTCCAATTATGCCTAATGGAAGTACAAGTCACAGAATGCAATAATTTGAAAT
         63 ATCAACCATAAGCTTCC-A--ATGCCTAATGGAAGTACAAGTCACAGAATGCAATAAATTGAAAT

                                                  
       4000 TTCTCTTCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
        125 TTCTCTTCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

                                   
       4038 TTGCAAACTCTGAAGATAGAGAG
          1 TTGCAAACTCTGAAGATAGAGAG

       4061 CTGTTCCCAA


Statistics
Matches: 330,  Mismatches: 17, Indels: 6
        0.93            0.05        0.02

Matches are distributed among these distances:
 162  212  0.64
 165   15  0.05
 166    1  0.00
 168  102  0.31

ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28


Consensus pattern (162 bp):   
TTGCAAACTCTGAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
AACCATAAGCTTCCAATGCCTAATGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

Found at i:5339 original size:162 final size:162

Alignment explanation


    Indices: 5067--5883  Score: 1305
    Period size: 162  Copynumber: 5.0  Consensus size: 162

       5057 TCGTTTGTAA

                                                     *                       
       5067 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAATATCAACCATAAGCTTTCAATGC
          1 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC

                     *                                                       
       5132 CTAAGGGAATTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA
         66 CTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA

                                       *    
       5197 TAGTCTTGGGAAATTGCAAACTCTGAAAATAG
        131 TAGTCTTGGGAAATTGCAAACTCTGAAGATAG

                *               *                                            
       5229 AGAGATGCTTTGGAATGGAAAAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC
          1 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC

                *              *         *                                   
       5294 CTAATGGAAGTACAAGTCAAAGAATGCAACAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA
         66 CTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA

                                            
       5359 TAGTCTTGGGAAATTGCAAACTCTGAAGATAG
        131 TAGTCTTGGGAAATTGCAAACTCTGAAGATAG

                       *                         *             *             
       5391 AGAGGTGCTTTAGAATGGAAGAAATAATCCAAGACTCGCAAGTATCAACCACAAGCTTTCAATGC
          1 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC

                                      *   * *                                
       5456 CTAAGGGAAGTACAAGTCACAGAATGTAATGATTTGAAATTTCTCTTCCCAATGTGTGTTGCTAA
         66 CTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA

                                 *  *       
       5521 TAGTCTTGGGAAATTGCAAACCCTAAAGATAG
        131 TAGTCTTGGGAAATTGCAAACTCTGAAGATAG

                                                                             
       5553 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC
          1 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC

                                      *   * *                 *              
       5618 CTAAGGGAAGTACAAGTCACAGAATGTAATGATTTGAAATTTCTCTTCCCGATGTGTGTTGCTAA
         66 CTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA

                                 *          
       5683 TAGTCTTGGGAAATTGCAAACCCTGAAGATAG
        131 TAGTCTTGGGAAATTGCAAACTCTGAAGATAG

                                        *                                    
       5715 AGAGGTGCTTTGGAATGGAAGAAATAATTCAAGACTCACAAGTATTGTCAACCATAAG-TTTCCA
          1 AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTA---TCAACCATAAGCTTT-CA

               *    *              *    *          *        *                
       5779 ATGTCTAATGGAAGTACAAGTCAGAGAAAGCAATAAATTAAAATTTCTTTTCCCAATGTGTGTTG
         62 ATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTG

                          *      *               
       5844 CTAATAGTCTTGGGCAATTGCGAA-TCCTGAAGATAG
        127 CTAATAGTCTTGGGAAATTGCAAACT-CTGAAGATAG

                
       5880 AGAG
          1 AGAG

       5884 ATGTTCCAAA


Statistics
Matches: 610,  Mismatches: 40, Indels: 7
        0.93            0.06        0.01

Matches are distributed among these distances:
 162  503  0.82
 164    3  0.00
 165  104  0.17

ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27


Consensus pattern (162 bp):   
AGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATCAACCATAAGCTTTCAATGC
CTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCTTCCCAATGTGTGTTGCTAA
TAGTCTTGGGAAATTGCAAACTCTGAAGATAG

Found at i:6988 original size:21 final size:21

Alignment explanation


    Indices: 6962--7006  Score: 90
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       6952 AAAGGAATAT

                                 
       6962 GATAGTGATTTTTCAATTGAA
          1 GATAGTGATTTTTCAATTGAA

                                 
       6983 GATAGTGATTTTTCAATTGAA
          1 GATAGTGATTTTTCAATTGAA

               
       7004 GAT
          1 GAT

       7007 TAATCATTGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.33, C:0.04, G:0.20, T:0.42


Consensus pattern (21 bp):   
GATAGTGATTTTTCAATTGAA
Done.