Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01351.P4

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: 41143
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:11076 original size:40 final size:39

Alignment explanation


    Indices: 11014--11311  Score: 438
    Period size: 40  Copynumber: 7.5  Consensus size: 39

      11004 AAACCAAGTA

                     *    *                   *      
      11014 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
          1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG

                                       **           
      11053 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG

                                                    
      11093 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG

                                                    
      11133 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACAAATG

                                                    
      11173 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG

                                                    
      11213 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG

                                      *   *     *   
      11253 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAGATG
          1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG

                               
      11293 CCTTCGGGACTTAGCCCGG
          1 CCTTCGGGACTTAGCCCGG

      11312 TTATCATCCG


Statistics
Matches: 245,  Mismatches: 10, Indels: 7
        0.94            0.04        0.03

Matches are distributed among these distances:
  39   15  0.06
  40  229  0.93
  41    1  0.00

ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23


Consensus pattern (39 bp):   
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG

Found at i:29306 original size:14 final size:14

Alignment explanation


    Indices: 29283--29316  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

      29273 ATAAAATTTT

                 *        
      29283 AAATTGAGTTAATC
          1 AAATTAAGTTAATC

                       *  
      29297 AAATTAAGTTATTC
          1 AAATTAAGTTAATC

                  
      29311 AAATTA
          1 AAATTA

      29317 TTTGAGTTAA


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

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38


Consensus pattern (14 bp):   
AAATTAAGTTAATC

Found at i:29509 original size:19 final size:19

Alignment explanation


    Indices: 29487--29527  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      29477 TAAAAAATAA

                               
      29487 AAAATAATTTCCAAAATTC
          1 AAAATAATTTCCAAAATTC

                      **       
      29506 AAAATAATTTTTAAAATTC
          1 AAAATAATTTCCAAAATTC

               
      29525 AAA
          1 AAA

      29528 TTATTAATAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34


Consensus pattern (19 bp):   
AAAATAATTTCCAAAATTC

Found at i:31811 original size:2 final size:2

Alignment explanation


    Indices: 31804--31847  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      31794 CTCTTAATTT

                                                                          
      31804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
      31846 TA
          1 TA

      31848 CTTTCTTTTA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:34136 original size:7 final size:7

Alignment explanation


    Indices: 34119--34153  Score: 52
    Period size: 7  Copynumber: 4.7  Consensus size: 7

      34109 CAAAAATAAC

                    
      34119 CTTTCTTT
          1 CTTT-TTT

                   
      34127 CTTTTTT
          1 CTTTTTT

                   
      34134 CTTTTTT
          1 CTTTTTT

                    
      34141 CTTTTTCT
          1 CTTTTT-T

                 
      34149 CTTTT
          1 CTTTT

      34154 CTCTCTAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   7   16  0.62
   8   10  0.38

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (7 bp):   
CTTTTTT

Found at i:38073 original size:17 final size:17

Alignment explanation


    Indices: 38051--38087  Score: 74
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      38041 CCCATCGGTC

                             
      38051 ATAGAATCTCATACTTG
          1 ATAGAATCTCATACTTG

                             
      38068 ATAGAATCTCATACTTG
          1 ATAGAATCTCATACTTG

               
      38085 ATA
          1 ATA

      38088 ATTTTTCTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35


Consensus pattern (17 bp):   
ATAGAATCTCATACTTG
Done.