Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01384.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: 3254
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33


Found at i:279 original size:6 final size:6

Alignment explanation


    Indices: 268--301  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

        258 GCTCGCAGAT

                                                   
        268 CCACCG CCACCG CCACCG CCACCG CCACCG CCAC
          1 CCACCG CCACCG CCACCG CCACCG CCACCG CCAC

        302 TACAACCAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.18, C:0.68, G:0.15, T:0.00


Consensus pattern (6 bp):   
CCACCG

Found at i:1420 original size:158 final size:158

Alignment explanation


    Indices: 1132--1439  Score: 521
    Period size: 158  Copynumber: 1.9  Consensus size: 158

       1122 AGCCTTGTCC

                          *                                                  
       1132 ATGGTTGGATTTATTGGTGTTCTCAAGTTCTTCACCTAGGCACACCTATGCTATGCGCCTTAGCG
          1 ATGGTTGGATTTATCGGTGTTCTCAAGTTCTTCACCTAGGCACACCTATGCTATGCGCCTTAGCG

                                                                   *         
       1197 CTAGGCAACAAAAGCACCTCAACCCTTTCAGGCGAGGCACATTTGATCAGGCACATTTCTGGTGC
         66 CTAGGCAACAAAAGCACCTCAACCCTTTCAGGCGAGGCACATTTGATCAGGCACACTTCTGGTGC

                         *              
       1262 TCTTAACTGCATTCTTTTTTGTAACACT
        131 TCTTAACTGCATTATTTTTTGTAACACT

                                                       **                    
       1290 ATGGTTGGATTTATCGGTGTTCTCAAGTT-TTGCACCTAGGCATGCCTATGCCT-TGCGCCTTAG
          1 ATGGTTGGATTTATCGGTGTTCTCAAGTTCTT-CACCTAGGCACACCTATG-CTATGCGCCTTAG

                                                    *                        
       1353 CGCTAGGCAACAAAAGCACCTCAACCCTTTCAGGCGAGGCGCATTTGATCAGGCACACTTCTGGT
         64 CGCTAGGCAACAAAAGCACCTCAACCCTTTCAGGCGAGGCACATTTGATCAGGCACACTTCTGGT

                        *         
       1418 GCTCTTAACTGCGTTATTTTTT
        129 GCTCTTAACTGCATTATTTTTT

       1440 ATAAGGTGAT


Statistics
Matches: 141,  Mismatches: 7, Indels: 4
        0.93            0.05        0.03

Matches are distributed among these distances:
 157    2  0.01
 158  137  0.97
 159    2  0.01

ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32


Consensus pattern (158 bp):   
ATGGTTGGATTTATCGGTGTTCTCAAGTTCTTCACCTAGGCACACCTATGCTATGCGCCTTAGCG
CTAGGCAACAAAAGCACCTCAACCCTTTCAGGCGAGGCACATTTGATCAGGCACACTTCTGGTGC
TCTTAACTGCATTATTTTTTGTAACACT

Found at i:3078 original size:32 final size:32

Alignment explanation


    Indices: 3042--3112  Score: 124
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       3032 GTGGTTGGTT

                  *                         
       3042 GTGTTTTGGTGGGAGCAGCAGCAAACCCGGTC
          1 GTGTTTAGGTGGGAGCAGCAGCAAACCCGGTC

                                           *
       3074 GTGTTTAGGTGGGAGCAGCAGCAAACCCGGTG
          1 GTGTTTAGGTGGGAGCAGCAGCAAACCCGGTC

                   
       3106 GTGTTTA
          1 GTGTTTA

       3113 AGTGTCATTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24


Consensus pattern (32 bp):   
GTGTTTAGGTGGGAGCAGCAGCAAACCCGGTC
Done.