Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01555.M1

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: 5060
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37


Found at i:2170 original size:26 final size:26

Alignment explanation


    Indices: 2134--2193  Score: 111
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       2124 GCTAAGGTGG

                          *           
       2134 TGCATATTAGTCAGTCCATGGATCAA
          1 TGCATATTAGTCAGCCCATGGATCAA

                                      
       2160 TGCATATTAGTCAGCCCATGGATCAA
          1 TGCATATTAGTCAGCCCATGGATCAA

                    
       2186 TGCATATT
          1 TGCATATT

       2194 CGGTTTTCTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   33  1.00

ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Consensus pattern (26 bp):   
TGCATATTAGTCAGCCCATGGATCAA

Found at i:3902 original size:41 final size:42

Alignment explanation


    Indices: 3843--3971  Score: 145
    Period size: 49  Copynumber: 3.0  Consensus size: 42

       3833 CCCCGTCAAT

                        *                             
       3843 AAAAAAAAA-AAGAAGAAAAAGTACTGGGTTAATTGCCTT-G
          1 AAAAAAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTTAG

              *                            *               
       3883 AAGAAAAAAGAAAAAGAAAAAGTACTGGGTTTATTGCCTTCAAAAAG
          1 AAAAAAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTT-----AG

                        *                             
       3930 AAAAAGGAAAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTT
          1 AAAAA--AAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTT

       3972 CAAATAAGAA


Statistics
Matches: 74,  Mismatches: 6, Indels: 9
        0.83            0.07        0.10

Matches are distributed among these distances:
  40    8  0.11
  41   28  0.38
  47    5  0.07
  49   33  0.45

ACGTcount: A:0.52, C:0.08, G:0.21, T:0.19


Consensus pattern (42 bp):   
AAAAAAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTTAG

Found at i:3955 original size:49 final size:50

Alignment explanation


    Indices: 3888--3985  Score: 171
    Period size: 49  Copynumber: 2.0  Consensus size: 50

       3878 CCTTGAAGAA

                                      *                       
       3888 AAAAGAAAAAGAAAAAGTACTGGGTTTATTGCCTTCAAA-AAGAAAAAGG
          1 AAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAATAAGAAAAAGG

                 *                                           
       3937 AAAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAATAAGAAAAAG
          1 AAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAATAAGAAAAAG

       3986 TACAGGGTAA


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  49   37  0.80
  50    9  0.20

ACGTcount: A:0.53, C:0.08, G:0.20, T:0.18


Consensus pattern (50 bp):   
AAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAATAAGAAAAAGG

Found at i:4194 original size:15 final size:16

Alignment explanation


    Indices: 4174--4210  Score: 67
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       4164 CTGTGGTGCT

                            
       4174 TATCCCATTCGAGGG-
          1 TATCCCATTCGAGGGA

                            
       4189 TATCCCATTCGAGGGA
          1 TATCCCATTCGAGGGA

                  
       4205 TATCCC
          1 TATCCC

       4211 GGTTTTGGTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   15  0.71
  16    6  0.29

ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27


Consensus pattern (16 bp):   
TATCCCATTCGAGGGA

Done.