Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01664.N4

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: 2063
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:356 original size:3 final size:3

Alignment explanation


    Indices: 348--374  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

        338 AACCCGATAA

                                               
        348 AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG

        375 TTAGAATGAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:1413 original size:23 final size:23

Alignment explanation


    Indices: 1387--1444  Score: 107
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       1377 TAAGTGCTGC

                                   
       1387 AAATTGAAGTGTTTAAATGTTGT
          1 AAATTGAAGTGTTTAAATGTTGT

                       *           
       1410 AAATTGAAGTGCTTAAATGTTGT
          1 AAATTGAAGTGTTTAAATGTTGT

                        
       1433 AAATTGAAGTGT
          1 AAATTGAAGTGT

       1445 CTGGAAATTG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  23   33  1.00

ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40


Consensus pattern (23 bp):   
AAATTGAAGTGTTTAAATGTTGT

Found at i:1440 original size:46 final size:45

Alignment explanation


    Indices: 1376--1576  Score: 154
    Period size: 46  Copynumber: 4.6  Consensus size: 45

       1366 CTACTGTTTT

                *     *                                   
       1376 TTAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGA-AGTG
          1 TTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TG

                    *                   *                 
       1421 CTTAAATGTTGTAAATTGAAGTG--T--CTG--G-AAATTGAGATG
          1 -TTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGATG

              **                     *          *          
       1460 TTTTATCGCTGT-AATTG-AGTTGTATAAATGTTGTTAATTGAGATG
          1 TTAAAT-GCTGTAAATTGAAG-TGTTTAAATGTTGTAAATTGAGATG

                       *                   *               
       1505 TTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGA-AGTG
          1 TTAAA-TGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TG

                    *        *        
       1551 CTTAAATGTTGTAAATTAAAGTGTTT
          1 -TTAAATGCTGTAAATTGAAGTGTTT

       1577 TAAGTACTAC


Statistics
Matches: 122,  Mismatches: 18, Indels: 30
        0.72            0.11        0.18

Matches are distributed among these distances:
  37    2  0.02
  38   11  0.09
  39   13  0.11
  40    3  0.02
  42    4  0.03
  44    2  0.02
  45   18  0.15
  46   62  0.51
  47    7  0.06

ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40


Consensus pattern (45 bp):   
TTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGATG

Found at i:1521 original size:23 final size:23

Alignment explanation


    Indices: 1505--1647  Score: 128
    Period size: 23  Copynumber: 6.1  Consensus size: 23

       1495 AATTGAGATG

                                    
       1505 TTAAAGTGCTGCAAATTGAAGTGT
          1 TTAAA-TGCTGCAAATTGAAGTGT

                      *           *
       1529 TTAAATGCTGTAAATTGAAGTGC
          1 TTAAATGCTGCAAATTGAAGTGT

                   *  *     *       
       1552 TTAAATGTTGTAAATTAAAGTGTT
          1 TTAAATGCTGCAAATTGAAGTG-T

                * *  *             
       1576 TTAAGTACTACAAATTGAAGTGT
          1 TTAAATGCTGCAAATTGAAGTGT

               **     *             
       1599 TTAGTTGCTGGAAATTG-AGATGT
          1 TTAAATGCTGCAAATTGAAG-TGT

               *                    
       1622 TT-TATCGCTGCAAATTGAAGTGT
          1 TTAAAT-GCTGCAAATTGAAGTGT

               
       1645 TTA
          1 TTA

       1648 GTTGCTGGAA


Statistics
Matches: 95,  Mismatches: 19, Indels: 10
        0.77            0.15        0.08

Matches are distributed among these distances:
  22    3  0.03
  23   69  0.73
  24   23  0.24

ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38


Consensus pattern (23 bp):   
TTAAATGCTGCAAATTGAAGTGT

Found at i:2043 original size:18 final size:18

Alignment explanation


    Indices: 2020--2063  Score: 79
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2010 GCTGTATTTC

                             *
       2020 GACTTGCTGTTAGTAAAG
          1 GACTTGCTGTTAGTAAAA

                              
       2038 GACTTGCTGTTAGTAAAA
          1 GACTTGCTGTTAGTAAAA

                    
       2056 GACTTGCT
          1 GACTTGCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34


Consensus pattern (18 bp):   
GACTTGCTGTTAGTAAAA
Done.