Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00008.P22

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: 7973
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:1360 original size:78 final size:78

Alignment explanation


    Indices: 1231--1386  Score: 231
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       1221 CTCATATTCT

                       *                      *                         *    
       1231 ACCATTAAACCGTGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATC
          1 ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC

                    *    
       1296 ACCATGGAGTTTG
         66 ACCATGGACTTTG

                            **          *             *                *     
       1309 ACCATTAAACCCTGATTGCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
          1 ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC

                         
       1374 ACCATGGACTTTG
         66 ACCATGGACTTTG

       1387 TGTACCAGAA


Statistics
Matches: 69,  Mismatches: 9, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  78   69  1.00

ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29


Consensus pattern (78 bp):   
ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGGACTTTG

Found at i:5637 original size:20 final size:22

Alignment explanation


    Indices: 5597--5641  Score: 67
    Period size: 20  Copynumber: 2.1  Consensus size: 22

       5587 AGGGATATTT

                                  
       5597 AGGTTTGGGGCCTAAGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

                          *       
       5619 AGGTTTGGGG-CT-TGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

               
       5639 AGG
          1 AGG

       5642 CTTAAGGTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20   10  0.45
  21    2  0.09
  22   10  0.45

ACGTcount: A:0.11, C:0.07, G:0.49, T:0.33


Consensus pattern (22 bp):   
AGGTTTGGGGCCTAAGGGTTTG

Found at i:5791 original size:105 final size:105

Alignment explanation


    Indices: 5609--5819  Score: 332
    Period size: 105  Copynumber: 2.0  Consensus size: 105

       5599 GTTTGGGGCC

                       * *                                      *    *      *
       5609 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                  *            *                    
       5674 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

                                          *        *                         
       5714 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                                         *          
       5779 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

             
       5819 T
          1 T

       5820 TGGTTACTGG


Statistics
Matches: 96,  Mismatches: 10, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 105   96  1.00

ACGTcount: A:0.11, C:0.08, G:0.36, T:0.45


Consensus pattern (105 bp):   
TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

Found at i:7395 original size:66 final size:66

Alignment explanation


    Indices: 7313--7447  Score: 225
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       7303 AAGTATTGAT

                                                                       *  *  
       7313 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTAC
          1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC

             
       7378 C
         66 C

                                     *    *              *                   
       7379 AGGCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAAC
          1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC

             
       7444 C
         66 C

               
       7445 AGG
          1 AGG

       7448 GTATGTATGA


Statistics
Matches: 64,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  66   64  1.00

ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21


Consensus pattern (66 bp):   
AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
C
Done.