Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01386.P1

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: 8575
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:150 original size:69 final size:69

Alignment explanation


    Indices: 35--173  Score: 215
    Period size: 69  Copynumber: 2.0  Consensus size: 69

         25 TCAGATCTGC

                               *   *                 *                 *     
         35 AACCTTCAAAGTGAAGAAGTCTCTGCAAAGATCGATGAAGCCTATCACAGTGAAGGAAAGAGGTG
          1 AACCTTCAAAGTGAAGAAGGCTCGGCAAAGATCGATGAAGCATATCACAGTGAAGGAAAAAGGTG

                
        100 GATT
         66 GATT

                          *                 *              *                 
        104 AACCTTCAAAGTGATGAAGGCTCGGCAAAGATTGATGAAGCATATCAGAGTGAAGGAAAAAGGTG
          1 AACCTTCAAAGTGAAGAAGGCTCGGCAAAGATCGATGAAGCATATCACAGTGAAGGAAAAAGGTG

                
        169 GATT
         66 GATT

             
        173 A
          1 A

        174 CCAGGAGCCG


Statistics
Matches: 63,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  69   63  1.00

ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20


Consensus pattern (69 bp):   
AACCTTCAAAGTGAAGAAGGCTCGGCAAAGATCGATGAAGCATATCACAGTGAAGGAAAAAGGTG
GATT

Found at i:3863 original size:31 final size:31

Alignment explanation


    Indices: 3828--3891  Score: 128
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       3818 GAATCCTAAG

                                           
       3828 TATGTACTACATAAACAACAGGATAAGTTGC
          1 TATGTACTACATAAACAACAGGATAAGTTGC

                                           
       3859 TATGTACTACATAAACAACAGGATAAGTTGC
          1 TATGTACTACATAAACAACAGGATAAGTTGC

              
       3890 TA
          1 TA

       3892 GCATCTTGGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27


Consensus pattern (31 bp):   
TATGTACTACATAAACAACAGGATAAGTTGC

Found at i:5248 original size:21 final size:20

Alignment explanation


    Indices: 5223--5280  Score: 64
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       5213 TAAATTTATG

                                
       5223 TTAATTAAGCTTATTATTAA
          1 TTAATTAAGCTTATTATTAA

                       *   *      
       5243 TTTAATTAAGGTTTAGT-TTAA
          1 -TTAATTAA-GCTTATTATTAA

                             
       5264 TTAATTAAGACTTATTA
          1 TTAATTAAG-CTTATTA

       5281 ATTTTAACTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 6
        0.75            0.10        0.15

Matches are distributed among these distances:
  19    1  0.03
  20   12  0.40
  21   12  0.40
  22    5  0.17

ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50


Consensus pattern (20 bp):   
TTAATTAAGCTTATTATTAA

Found at i:6040 original size:31 final size:31

Alignment explanation


    Indices: 6002--6063  Score: 106
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       5992 TTTTCGTTCG

                                           
       6002 AGAGAATGTACCAGCTGGCAAATTAGTCATT
          1 AGAGAATGTACCAGCTGGCAAATTAGTCATT

                              *     *      
       6033 AGAGAATGTACCAGCTGGTAAATTGGTCATT
          1 AGAGAATGTACCAGCTGGCAAATTAGTCATT

       6064 GGCCATGTCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27


Consensus pattern (31 bp):   
AGAGAATGTACCAGCTGGCAAATTAGTCATT

Found at i:7838 original size:45 final size:45

Alignment explanation


    Indices: 7774--7879  Score: 126
    Period size: 45  Copynumber: 2.4  Consensus size: 45

       7764 TACTATTTTT

                  * *                                *     
       7774 AGCTCATTGGAGCTTACTGTTTCAGCTCG-TATGAGCTTACTGTT-C
          1 AGCTCAATAGAGCTTACTGTTT-AGCTCGATA-GAGCTTACCGTTCC

                     *                *                  
       7819 AGCTCAATATAGCTTACTGTTTAGCTTGATAGAGCTTACCGTTCC
          1 AGCTCAATAGAGCTTACTGTTTAGCTCGATAGAGCTTACCGTTCC

                  *         
       7864 AGCTCATTAGAGCTTA
          1 AGCTCAATAGAGCTTA

       7880 TTATTAATCA


Statistics
Matches: 52,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  44   16  0.31
  45   36  0.69

ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36


Consensus pattern (45 bp):   
AGCTCAATAGAGCTTACTGTTTAGCTCGATAGAGCTTACCGTTCC

Found at i:7874 original size:23 final size:22

Alignment explanation


    Indices: 7774--7879  Score: 99
    Period size: 22  Copynumber: 4.7  Consensus size: 22

       7764 TACTATTTTT

                    *              
       7774 AGCTCATTGGAGCTTACTGTTTC
          1 AGCTCATTAGAGCTTACTG-TTC

                  *                
       7797 AGCTC-GTATGAGCTTACTGTTC
          1 AGCTCATTA-GAGCTTACTGTTC

                  *  *           *
       7819 AGCTCAATATAGCTTACTGTTT
          1 AGCTCATTAGAGCTTACTGTTC

                 *            *     
       7841 AGCTTGA-TAGAGCTTACCGTTCC
          1 AGC-TCATTAGAGCTTACTGTT-C

                            
       7864 AGCTCATTAGAGCTTA
          1 AGCTCATTAGAGCTTA

       7880 TTATTAATCA


Statistics
Matches: 68,  Mismatches: 10, Indels: 10
        0.77            0.11        0.11

Matches are distributed among these distances:
  22   37  0.54
  23   31  0.46

ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36


Consensus pattern (22 bp):   
AGCTCATTAGAGCTTACTGTTC
Done.