Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00797.C2

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: 4540
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35


Found at i:985 original size:37 final size:37

Alignment explanation


    Indices: 944--1018  Score: 132
    Period size: 37  Copynumber: 2.0  Consensus size: 37

        934 TGATTATCAA

                                      *          
        944 GTTAGTTTGACTTATTTGTTAACTTTGCTACATTAGG
          1 GTTAGTTTGACTTATTTGTTAACTTTACTACATTAGG

                     *                           
        981 GTTAGTTTGGCTTATTTGTTAACTTTACTACATTAGG
          1 GTTAGTTTGACTTATTTGTTAACTTTACTACATTAGG

             
       1018 G
          1 G

       1019 ATCAAATTGA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  37   36  1.00

ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48


Consensus pattern (37 bp):   
GTTAGTTTGACTTATTTGTTAACTTTACTACATTAGG

Found at i:3653 original size:27 final size:27

Alignment explanation


    Indices: 3630--3780  Score: 178
    Period size: 27  Copynumber: 5.6  Consensus size: 27

       3620 TTTTACCTTT

                 *                     
       3630 ATAGGATAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTC

                                       
       3657 ATAGGGTAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTC

                          *             
       3684 ATAGGGTAAAATGATCGAAATA-CCTCC
          1 ATAGGGTAAAATGACCGAAATACCCT-C

               *           *           *
       3711 ATAAGGTAAAATGACTGAAAATACCCTT
          1 ATAGGGTAAAATGACCG-AAATACCCTC

            *              * *        *
       3739 GTAGGGTAAAATGACTGTAATACCCTT
          1 ATAGGGTAAAATGACCGAAATACCCTC

            *  *           
       3766 GTAAGGTAAAATGAC
          1 ATAGGGTAAAATGAC

       3781 AGATTTGTTC


Statistics
Matches: 111,  Mismatches: 10, Indels: 6
        0.87            0.08        0.05

Matches are distributed among these distances:
  26    3  0.03
  27   85  0.77
  28   20  0.18
  29    3  0.03

ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23


Consensus pattern (27 bp):   
ATAGGGTAAAATGACCGAAATACCCTC

Found at i:3751 original size:55 final size:54

Alignment explanation


    Indices: 3630--3780  Score: 187
    Period size: 55  Copynumber: 2.8  Consensus size: 54

       3620 TTTTACCTTT

                 *                        *                       
       3630 ATAGGATAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAATGACCGAAATACCCTC

                          *                            *           *
       3684 ATAGGGTAAAATGATCGAAATA-CCTCCATAAGGTAAAATGACTGAAAATACCCTT
          1 ATAGGGTAAAATGACCGAAATACCCT-CATAAGGTAAAATGACCG-AAATACCCTC

            *              * *        **              
       3739 GTAGGGTAAAATGACTGTAATACCCTTGTAAGGTAAAATGAC
          1 ATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAATGAC

       3781 AGATTTGTTC


Statistics
Matches: 83,  Mismatches: 11, Indels: 5
        0.84            0.11        0.05

Matches are distributed among these distances:
  53    3  0.04
  54   36  0.43
  55   41  0.49
  56    3  0.04

ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23


Consensus pattern (54 bp):   
ATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAATGACCGAAATACCCTC

Found at i:4127 original size:18 final size:18

Alignment explanation


    Indices: 4100--4191  Score: 132
    Period size: 18  Copynumber: 5.1  Consensus size: 18

       4090 TCTGCTTGCA

                              
       4100 TACTGCACTGATTACTGT
          1 TACTGCACTGATTACTGT

                 *            
       4118 TACTGTACTGATTACTGT
          1 TACTGCACTGATTACTGT

                   *    *      
       4136 TACTGCATTGATCA-TGGT
          1 TACTGCACTGATTACT-GT

                              
       4154 TACTGCACTGATTACTGT
          1 TACTGCACTGATTACTGT

                          *   
       4172 TACTGCACTGATTAATGT
          1 TACTGCACTGATTACTGT

              
       4190 TA
          1 TA

       4192 TTGAAATGGG


Statistics
Matches: 65,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  17    1  0.02
  18   63  0.97
  19    1  0.02

ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40


Consensus pattern (18 bp):   
TACTGCACTGATTACTGT
Done.