Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02147.F1

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: 6021
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26


Found at i:455 original size:42 final size:43

Alignment explanation


    Indices: 408--500  Score: 102
    Period size: 42  Copynumber: 2.2  Consensus size: 43

        398 CGACGCGTTT

                                *      *       *     *  
        408 AAGAGATCGGAAGA-AG-GATCGAGATCGAGAAAGGGAAAGGGA
          1 AAGAGATCGG-AGATAGAGAGCGAGATAGAGAAAGAGAAAGAGA

                  *                    *               
        450 AAGAGAAC-GAGATAGAGAGCGAGATATAGAAAGAGAAAGAGA
          1 AAGAGATCGGAGATAGAGAGCGAGATAGAGAAAGAGAAAGAGA

                     
        492 AAGAGATCG
          1 AAGAGATCG

        501 CTTTAGTAGA


Statistics
Matches: 41,  Mismatches: 7, Indels: 5
        0.77            0.13        0.09

Matches are distributed among these distances:
  40    3  0.07
  41    3  0.07
  42   35  0.85

ACGTcount: A:0.49, C:0.06, G:0.37, T:0.08


Consensus pattern (43 bp):   
AAGAGATCGGAGATAGAGAGCGAGATAGAGAAAGAGAAAGAGA

Found at i:467 original size:6 final size:6

Alignment explanation


    Indices: 434--497  Score: 56
    Period size: 6  Copynumber: 10.7  Consensus size: 6

        424 GATCGAGATC

                    *      *          *     *      **     *  *     
        434 GAGAAA GGGAAA GGGAAA GAGAAC GAGATA GAGAGC GAGATA TAGAAA
          1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA

                              
        482 GAGAAA GAGAAA GAGA
          1 GAGAAA GAGAAA GAGA

        498 TCGCTTTAGT


Statistics
Matches: 46,  Mismatches: 12, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
   6   46  1.00

ACGTcount: A:0.55, C:0.03, G:0.38, T:0.05


Consensus pattern (6 bp):   
GAGAAA

Found at i:5802 original size:34 final size:34

Alignment explanation


    Indices: 5759--5839  Score: 162
    Period size: 34  Copynumber: 2.4  Consensus size: 34

       5749 GTATATAAAC

                                              
       5759 AAGTAGGGTTTAACAACCATGAACAAAAAGGAAA
          1 AAGTAGGGTTTAACAACCATGAACAAAAAGGAAA

                                              
       5793 AAGTAGGGTTTAACAACCATGAACAAAAAGGAAA
          1 AAGTAGGGTTTAACAACCATGAACAAAAAGGAAA

                         
       5827 AAGTAGGGTTTAA
          1 AAGTAGGGTTTAA

       5840 ACTTGCGGGC


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   47  1.00

ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17


Consensus pattern (34 bp):   
AAGTAGGGTTTAACAACCATGAACAAAAAGGAAA
Done.