Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01664.N3

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: 2066
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


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:1416 original size:23 final size:23

Alignment explanation


    Indices: 1390--1447  Score: 107
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       1380 TAAGTGCTGC

                                   
       1390 AAATTGAAGTGTTTAAATGTTGT
          1 AAATTGAAGTGTTTAAATGTTGT

                       *           
       1413 AAATTGAAGTGCTTAAATGTTGT
          1 AAATTGAAGTGTTTAAATGTTGT

                        
       1436 AAATTGAAGTGT
          1 AAATTGAAGTGT

       1448 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:1443 original size:46 final size:45

Alignment explanation


    Indices: 1379--1579  Score: 154
    Period size: 46  Copynumber: 4.6  Consensus size: 45

       1369 CTACTGTTTT

                *     *                                   
       1379 TTAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGA-AGTG
          1 TTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TG

                    *                   *                 
       1424 CTTAAATGTTGTAAATTGAAGTG--T--CTG--G-AAATTGAGATG
          1 -TTAAATGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGATG

              **                     *          *          
       1463 TTTTATCGCTGT-AATTG-AGTTGTATAAATGTTGTTAATTGAGATG
          1 TTAAAT-GCTGTAAATTGAAG-TGTTTAAATGTTGTAAATTGAGATG

                       *                   *               
       1508 TTAAAGTGCTGCAAATTGAAGTGTTTAAATGCTGTAAATTGA-AGTG
          1 TTAAA-TGCTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TG

                    *        *        
       1554 CTTAAATGTTGTAAATTAAAGTGTTT
          1 -TTAAATGCTGTAAATTGAAGTGTTT

       1580 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:1524 original size:23 final size:23

Alignment explanation


    Indices: 1508--1650  Score: 128
    Period size: 23  Copynumber: 6.1  Consensus size: 23

       1498 AATTGAGATG

                                    
       1508 TTAAAGTGCTGCAAATTGAAGTGT
          1 TTAAA-TGCTGCAAATTGAAGTGT

                      *           *
       1532 TTAAATGCTGTAAATTGAAGTGC
          1 TTAAATGCTGCAAATTGAAGTGT

                   *  *     *       
       1555 TTAAATGTTGTAAATTAAAGTGTT
          1 TTAAATGCTGCAAATTGAAGTG-T

                * *  *             
       1579 TTAAGTACTACAAATTGAAGTGT
          1 TTAAATGCTGCAAATTGAAGTGT

               **     *             
       1602 TTAGTTGCTGGAAATTG-AGATGT
          1 TTAAATGCTGCAAATTGAAG-TGT

               *                    
       1625 TT-TATCGCTGCAAATTGAAGTGT
          1 TTAAAT-GCTGCAAATTGAAGTGT

               
       1648 TTA
          1 TTA

       1651 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:2046 original size:18 final size:18

Alignment explanation


    Indices: 2023--2066  Score: 79
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2013 GCTGTATTTC

                             *
       2023 GACTTGCTGTTAGTAAAG
          1 GACTTGCTGTTAGTAAAA

                              
       2041 GACTTGCTGTTAGTAAAA
          1 GACTTGCTGTTAGTAAAA

                    
       2059 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.