Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03674.F7

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: 4073
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:940 original size:21 final size:21

Alignment explanation


    Indices: 914--959  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        904 GAAGTCTAGC

                  *       *      
        914 TAAAAAGCTGAATTTGGTTGA
          1 TAAAAAACTGAATTCGGTTGA

                            *    
        935 TAAAAAACTGAATTCGTTTGA
          1 TAAAAAACTGAATTCGGTTGA

                
        956 TAAA
          1 TAAA

        960 GTTGTGATGA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33


Consensus pattern (21 bp):   
TAAAAAACTGAATTCGGTTGA

Found at i:3829 original size:165 final size:162

Alignment explanation


    Indices: 3525--3847  Score: 477
    Period size: 165  Copynumber: 2.0  Consensus size: 162

       3515 TGTGCCCAAT

                    **             *                              **         
       3525 TTGCAAACTTTGAAGATAAAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
          1 TTGCAAACCCTGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAGACAAACAAGTATC

                        *      *     *          *        *   * *             
       3590 AACCATAAGCTTTCAATACTTAAGGGAAGTACAAGTTACAGAATGTAATGATTTGAAATTTCTCT
         66 AACCATAAGCTTCCAATACCTAAGGAAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT

                                            
       3655 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
        131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

                              **                                             
       3687 TTGCAAACCCTGAAGATAGTGAGATGCTTTGGAATGGAAGAAATAATCCAAGACAAACAAGTATC
          1 TTGCAAACCCTGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAGACAAACAAG--T-

                                                                             
       3752 ATCAACCATAAGCTTCCAA-AGCCTAAGGAAAGTACAAGTCACAGAATGCAATAAATTGAAATTT
         63 ATCAACCATAAGCTTCCAATA-CCTAAGGAAAGTACAAGTCACAGAATGCAATAAATTGAAATTT

                                            
       3816 CTCTTCCCAATGTGTGTTGCTAATAGTCTTGG
        127 CTCTTCCCAATGTGTGTTGCTAATAGTCTTGG

       3848 CACTACAGGA


Statistics
Matches: 143,  Mismatches: 14, Indels: 5
        0.88            0.09        0.03

Matches are distributed among these distances:
 162   54  0.38
 164    2  0.01
 165   87  0.61

ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28


Consensus pattern (162 bp):   
TTGCAAACCCTGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAGACAAACAAGTATC
AACCATAAGCTTCCAATACCTAAGGAAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA

Found at i:3979 original size:40 final size:41

Alignment explanation


    Indices: 3935--4038  Score: 129
    Period size: 41  Copynumber: 2.6  Consensus size: 41

       3925 CATTTTACCA

                              *                   *  
       3935 AAAACGCTGCTAAAA-ACTGAGCAATAGCGGCGCTTTTGGT
          1 AAAACGCTGCTAAAAGACAGAGCAATAGCGGCGCTTTTAGT

                 **              * **                
       3975 AAAACAATGCTAAAAGACAGATCTTTAGCGGCGCTTTTAGT
          1 AAAACGCTGCTAAAAGACAGAGCAATAGCGGCGCTTTTAGT

                   *               
       4016 AAAACGCCGCTAAAAGACAGAGC
          1 AAAACGCTGCTAAAAGACAGAGC

       4039 TTTAGCCAAA


Statistics
Matches: 52,  Mismatches: 11, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  40   13  0.25
  41   39  0.75

ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20


Consensus pattern (41 bp):   
AAAACGCTGCTAAAAGACAGAGCAATAGCGGCGCTTTTAGT

Done.