Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00797.F1

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: 1841
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32


Found at i:954 original size:27 final size:27

Alignment explanation


    Indices: 931--1081  Score: 178
    Period size: 27  Copynumber: 5.6  Consensus size: 27

        921 TTTTACCTTT

                 *                     
        931 ATAGGATAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTC

                                       
        958 ATAGGGTAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTC

                          *             
        985 ATAGGGTAAAATGATCGAAATA-CCTCC
          1 ATAGGGTAAAATGACCGAAATACCCT-C

               *           *           *
       1012 ATAAGGTAAAATGACTGAAAATACCCTT
          1 ATAGGGTAAAATGACCG-AAATACCCTC

            *              * *        *
       1040 GTAGGGTAAAATGACTGTAATACCCTT
          1 ATAGGGTAAAATGACCGAAATACCCTC

            *  *           
       1067 GTAAGGTAAAATGAC
          1 ATAGGGTAAAATGAC

       1082 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:1052 original size:55 final size:54

Alignment explanation


    Indices: 931--1081  Score: 187
    Period size: 55  Copynumber: 2.8  Consensus size: 54

        921 TTTTACCTTT

                 *                        *                       
        931 ATAGGATAAAATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTC
          1 ATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAATGACCGAAATACCCTC

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

            *              * *        **              
       1040 GTAGGGTAAAATGACTGTAATACCCTTGTAAGGTAAAATGAC
          1 ATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAATGAC

       1082 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:1428 original size:18 final size:18

Alignment explanation


    Indices: 1401--1492  Score: 132
    Period size: 18  Copynumber: 5.1  Consensus size: 18

       1391 TCTGCTTGCA

                              
       1401 TACTGCACTGATTACTGT
          1 TACTGCACTGATTACTGT

                 *            
       1419 TACTGTACTGATTACTGT
          1 TACTGCACTGATTACTGT

                   *    *      
       1437 TACTGCATTGATCA-TGGT
          1 TACTGCACTGATTACT-GT

                              
       1455 TACTGCACTGATTACTGT
          1 TACTGCACTGATTACTGT

                          *   
       1473 TACTGCACTGATTAATGT
          1 TACTGCACTGATTACTGT

              
       1491 TA
          1 TA

       1493 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.