Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00211.N1

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, 964

Length: 1607
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33


Found at i:153 original size:12 final size:11

Alignment explanation


    Indices: 132--176  Score: 56
    Period size: 12  Copynumber: 4.0  Consensus size: 11

        122 ATAAAAACAC

                       
        132 TATAATATATA
          1 TATAATATATA

                        
        143 TATACATATATA
          1 TATA-ATATATA

                 *     
        155 -ATAAAATATA
          1 TATAATATATA

                        
        165 TACTAATATATA
          1 TA-TAATATATA

        177 AAAAAAAATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 5
        0.81            0.06        0.14

Matches are distributed among these distances:
  10    6  0.21
  11    8  0.28
  12   15  0.52

ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40


Consensus pattern (11 bp):   
TATAATATATA

Found at i:163 original size:22 final size:22

Alignment explanation


    Indices: 133--182  Score: 66
    Period size: 22  Copynumber: 2.3  Consensus size: 22

        123 TAAAAACACT

                *                  
        133 ATAATATATATA-TACATATATA
          1 ATAAAATATATACTA-ATATATA

                                  
        155 ATAAAATATATACTAATATATA
          1 ATAAAATATATACTAATATATA

             *    
        177 AAAAAA
          1 ATAAAA

        183 AATAATAATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22   23  0.92
  23    2  0.08

ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34


Consensus pattern (22 bp):   
ATAAAATATATACTAATATATA

Found at i:165 original size:20 final size:20

Alignment explanation


    Indices: 140--181  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        130 ACTATAATAT

                                 
        140 ATATATAC-ATATATAATAAA
          1 ATATATACAATATATAA-AAA

                                 
        160 ATATATACTAATATATAAAAA
          1 ATATATAC-AATATATAAAAA

             
        181 A
          1 A

        182 AAATAATAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  20    8  0.40
  21    4  0.20
  22    8  0.40

ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33


Consensus pattern (20 bp):   
ATATATACAATATATAAAAA

Found at i:224 original size:18 final size:17

Alignment explanation


    Indices: 179--228  Score: 64
    Period size: 18  Copynumber: 2.8  Consensus size: 17

        169 AATATATAAA

                             
        179 AAAAAATAATAATATTG
          1 AAAAAATAATAATATTG

                 **            
        196 ATAAACTTAATAATATTAG
          1 A-AAAAATAATAATATT-G

                          
        215 AAAAAATAATAATA
          1 AAAAAATAATAATA

        229 ATATTTAATA


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  17    1  0.04
  18   24  0.89
  19    2  0.07

ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30


Consensus pattern (17 bp):   
AAAAAATAATAATATTG

Found at i:227 original size:21 final size:21

Alignment explanation


    Indices: 157--233  Score: 74
    Period size: 19  Copynumber: 3.8  Consensus size: 21

        147 CATATATAAT

                      *            
        157 AAAATATATACTAATATATA-AA
          1 AAAATA-ATAATAATAT-TAGAA

                                *
        179 AAAA-AATAATAATATT-GAT
          1 AAAATAATAATAATATTAGAA

               *                 
        198 AAACT--TAATAATATTAGAA
          1 AAAATAATAATAATATTAGAA

                             
        217 AAAATAATAATAATATT
          1 AAAATAATAATAATATT

        234 TAATAAAGAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 11
        0.74            0.08        0.18

Matches are distributed among these distances:
  18   10  0.22
  19   11  0.24
  20    9  0.20
  21   11  0.24
  22    4  0.09

ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32


Consensus pattern (21 bp):   
AAAATAATAATAATATTAGAA

Found at i:1259 original size:25 final size:25

Alignment explanation


    Indices: 1231--1289  Score: 91
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       1221 GTTTTTGATT

                                     
       1231 TTGGGTTTTAGTGTTTGGGCTACTA
          1 TTGGGTTTTAGTGTTTGGGCTACTA

                     *              *
       1256 TTGGGTTTTGGTGTTTGGGCTACTG
          1 TTGGGTTTTAGTGTTTGGGCTACTA

              *      
       1281 TTAGGTTTT
          1 TTGGGTTTT

       1290 GATGTAAATG


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   31  1.00

ACGTcount: A:0.08, C:0.07, G:0.34, T:0.51


Consensus pattern (25 bp):   
TTGGGTTTTAGTGTTTGGGCTACTA

Done.