isoform.fa.s87206.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01481.F17

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: 4427
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34


Found at i:1355 original size:7 final size:7

Alignment explanation


    Indices: 1345--1373  Score: 58
    Period size: 7  Copynumber: 4.1  Consensus size: 7

       1335 CTATGTTACA

                   
       1345 TGTCAAG
          1 TGTCAAG

                   
       1352 TGTCAAG
          1 TGTCAAG

                   
       1359 TGTCAAG
          1 TGTCAAG

                   
       1366 TGTCAAG
          1 TGTCAAG

             
       1373 T
          1 T

       1374 TTGTGGTGTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   22  1.00

ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31


Consensus pattern (7 bp):   
TGTCAAG

Found at i:2179 original size:220 final size:221

Alignment explanation


    Indices: 1822--2234  Score: 774
    Period size: 220  Copynumber: 1.9  Consensus size: 221

       1812 AAGTTCCCTT

                                                                             
       1822 AACCATGAAGCTTTATAAACTAAGTGTAATGGTGAAATGGGCTCCTAAAGGCTTGCAAATTATCA
          1 AACCATGAAGCTTTATAAACTAAGTGTAATGGTGAAATGGGCTCCTAAAGGCTTGCAAATTATCA

                                                          * *                
       1887 ATACAGAGTTCTATTTTGCATGAAAGCTTCTTAGTGAGCTCTGTGATAGAAGATCTTACGGTTGT
         66 ATACAGAGTTCTATTTTGCATGAAAGCTTCTTAGTGAGCTCTGTGACAAAAGATCTTACGGTTGT

            *                                                                
       1952 GGCC-TTTTTTAAAATTGATATTTCTAACGCCTCATGCGAAAATCCTACTGCAATTTGTAAACAT
        131 AGCCTTTTTTTAAAATTGATATTTCTAACGCCTCATGCGAAAATCCTACTGCAATTTGTAAACAT

                                      
       2016 CATGAGCCCTGATGTTTGAGATGTGA
        196 CATGAGCCCTGATGTTTGAGATGTGA

                             *                                               
       2042 AACCATGAAGCTTTATATACTAAGTGTAATGGTGAAATGGGCTCCTAAAGGCTTGCAAATTATCA
          1 AACCATGAAGCTTTATAAACTAAGTGTAATGGTGAAATGGGCTCCTAAAGGCTTGCAAATTATCA

                                                                             
       2107 ATACAGAGTTCTATTTTGCATGAAAGCTTCTTAGTGAGCTCTGTGACAAAAGATCTTACGGTTGT
         66 ATACAGAGTTCTATTTTGCATGAAAGCTTCTTAGTGAGCTCTGTGACAAAAGATCTTACGGTTGT

                                        *                                  
       2172 AGCCTTTTTTTAAAATTGATATTTCTAAGGCCTCATGCGAAAATCCTACTGCAATTTGTAAAC
        131 AGCCTTTTTTTAAAATTGATATTTCTAACGCCTCATGCGAAAATCCTACTGCAATTTGTAAAC

       2235 TTCTAATAAG


Statistics
Matches: 187,  Mismatches: 5, Indels: 1
        0.97            0.03        0.01

Matches are distributed among these distances:
 220  130  0.70
 221   57  0.30

ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Consensus pattern (221 bp):   
AACCATGAAGCTTTATAAACTAAGTGTAATGGTGAAATGGGCTCCTAAAGGCTTGCAAATTATCA
ATACAGAGTTCTATTTTGCATGAAAGCTTCTTAGTGAGCTCTGTGACAAAAGATCTTACGGTTGT
AGCCTTTTTTTAAAATTGATATTTCTAACGCCTCATGCGAAAATCCTACTGCAATTTGTAAACAT
CATGAGCCCTGATGTTTGAGATGTGA
Done.