isoform.fa.s11384.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00404.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: 4213
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25


Found at i:978 original size:201 final size:201

Alignment explanation


    Indices: 689--1111  Score: 720
    Period size: 201  Copynumber: 2.1  Consensus size: 201

        679 ATACCCTTGA

                               *                             *               
        689 AAGAAGCTGCTAGTACAGAAGAAACAAAAGCAGAAGCTTGCCTAGTTCCTGCAGGTGGAGATGAA
          1 AAGAAGCTGCTAGTACAGATGAAACAAAAGCAGAAGCTTGCCTAGTTCCGGCAGGTGGAGATGAA

                * *                                                        * 
        754 AGTACTTGTGGAACCAAGACAGGCCAGGTTTCCGGTGATCGTGGTGGAAAGGAATATCCAAGTGT
         66 AGTAATCGTGGAACCAAGACAGGCCAGGTTTCCGGTGATCGTGGTGGAAAGGAATATCCAAGTAT

                                                                             
        819 TGACAAGCAGAAACCTGATGAGAAAGAAGAAGATATTACTGTAAATGATGAAACTGAGGAACAAT
        131 TGACAAGCAGAAACCTGATGAGAAAGAAGAAGATATTACTGTAAATGATGAAACTGAGGAACAAT

                  
        884 CCTCAC
        196 CCTCAC

                        *               *                                    
        890 AAGAAGCTGCTAATACAGATGAAACAAATGCAGAAGCTTGCCTAGTTCCGGCAGGTGGAGATGAA
          1 AAGAAGCTGCTAGTACAGATGAAACAAAAGCAGAAGCTTGCCTAGTTCCGGCAGGTGGAGATGAA

                          **                *                *               
        955 AGTAATCGTGGAACTGAGACAGGCCAGGTTTCTGGTGATCGTGGTGGAATGGAATATCCAAGTAT
         66 AGTAATCGTGGAACCAAGACAGGCCAGGTTTCCGGTGATCGTGGTGGAAAGGAATATCCAAGTAT

                       **                                                    
       1020 TGACAAGCAGACCCCTGATGAGAAAGAAGAAGATATTACTGTAAATGATGAAACTGAGGAACAAT
        131 TGACAAGCAGAAACCTGATGAGAAAGAAGAAGATATTACTGTAAATGATGAAACTGAGGAACAAT

                  
       1085 CCTCAC
        196 CCTCAC

                         *       
       1091 AAGAAGCTGCTAGCACAGATG
          1 AAGAAGCTGCTAGTACAGATG

       1112 TATTAGAGAG


Statistics
Matches: 207,  Mismatches: 15, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 201  207  1.00

ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20


Consensus pattern (201 bp):   
AAGAAGCTGCTAGTACAGATGAAACAAAAGCAGAAGCTTGCCTAGTTCCGGCAGGTGGAGATGAA
AGTAATCGTGGAACCAAGACAGGCCAGGTTTCCGGTGATCGTGGTGGAAAGGAATATCCAAGTAT
TGACAAGCAGAAACCTGATGAGAAAGAAGAAGATATTACTGTAAATGATGAAACTGAGGAACAAT
CCTCAC

Found at i:3968 original size:3 final size:3

Alignment explanation


    Indices: 3960--4000  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       3950 TGGGTTGGTT

                                                                  
       3960 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       4001 TAATTGAAGC


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Done.