Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00491.F2

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: 2161
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28


Found at i:638 original size:3 final size:3

Alignment explanation


    Indices: 630--667  Score: 51
    Period size: 3  Copynumber: 12.7  Consensus size: 3

        620 CAAAGGTGGA

                              *                                
        630 AAC AAC AAC AAC AAG AAC AAC AACC AA- AAC AAC AAC AA
          1 AAC AAC AAC AAC AAC AAC AAC AA-C AAC AAC AAC AAC AA

        668 GGGTGGTCAG


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   2    2  0.06
   3   26  0.84
   4    3  0.10

ACGTcount: A:0.68, C:0.29, G:0.03, T:0.00


Consensus pattern (3 bp):   
AAC

Found at i:901 original size:3 final size:3

Alignment explanation


    Indices: 893--970  Score: 59
    Period size: 3  Copynumber: 25.0  Consensus size: 3

        883 AAGATTTCAG

                         *                                           **    
        893 TGA TGA TGA TTA TGA TGA TGA TGA CTTGGA TGA TGA TTG- TGA TCT TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA --T-GA TGA TGA -TGA TGA TGA TGA

                             **           *        
        941 TGA TGA TGA TGA TTT TGA TGA TGG TGA TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA

        971 GTTGGATGAT


Statistics
Matches: 58,  Mismatches: 12, Indels: 10
        0.73            0.15        0.12

Matches are distributed among these distances:
   2    2  0.03
   3   50  0.86
   4    3  0.05
   5    1  0.02
   6    2  0.03

ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40


Consensus pattern (3 bp):   
TGA

Found at i:916 original size:18 final size:17

Alignment explanation


    Indices: 893--980  Score: 83
    Period size: 18  Copynumber: 5.1  Consensus size: 17

        883 AAGATTTCAG

                             
        893 TGATGATGA-TT-ATGA
          1 TGATGATGATTTGATGA

                        *     
        908 TGATGATGACTTGGATGA
          1 TGATGATGA-TTTGATGA

                               
        926 TGATTG-TGATCTTGATGA
          1 TGA-TGATGAT-TTGATGA

                              
        944 TGATGATGATTTTGATGA
          1 TGATGATGA-TTTGATGA

              *         *     
        962 TGGTGATGAGTTGGATGA
          1 TGATGATGA-TTTGATGA

             
        980 T
          1 T

        981 CATCGTCATC


Statistics
Matches: 61,  Mismatches: 5, Indels: 11
        0.79            0.06        0.14

Matches are distributed among these distances:
  15    9  0.15
  17    4  0.07
  18   45  0.74
  19    3  0.05

ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40


Consensus pattern (17 bp):   
TGATGATGATTTGATGA

Found at i:1315 original size:15 final size:15

Alignment explanation


    Indices: 1280--1316  Score: 53
    Period size: 12  Copynumber: 2.7  Consensus size: 15

       1270 CATATCAAGG

                           
       1280 TGGCGGTGGTAAAAA
          1 TGGCGGTGGTAAAAA

                           
       1295 ---CGGTGGTAAAAA
          1 TGGCGGTGGTAAAAA

                      
       1307 TGGCGGTGGT
          1 TGGCGGTGGT

       1317 TTACCTCAGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 6
        0.76            0.00        0.24

Matches are distributed among these distances:
  12   12  0.63
  15    7  0.37

ACGTcount: A:0.27, C:0.08, G:0.43, T:0.22


Consensus pattern (15 bp):   
TGGCGGTGGTAAAAA

Found at i:1772 original size:18 final size:18

Alignment explanation


    Indices: 1749--1786  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1739 TTACATGCCA

                              
       1749 CCATACCCATATCAATAT
          1 CCATACCCATATCAATAT

                    *    *    
       1767 CCATACCCGTATCCATAT
          1 CCATACCCATATCAATAT

              
       1785 CC
          1 CC

       1787 CCAACCTCAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26


Consensus pattern (18 bp):   
CCATACCCATATCAATAT
Done.