Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01273.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: 5703
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31


Found at i:458 original size:18 final size:18

Alignment explanation


    Indices: 415--452  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        405 ACGTCCAGTA

                              
        415 TAACTTTTGTTTTTTCTT
          1 TAACTTTTGTTTTTTCTT

                              
        433 TAACTTTTGTTTTTTCTT
          1 TAACTTTTGTTTTTTCTT

              
        451 TA
          1 TA

        453 TTTTTTCAAA


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

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.13, C:0.11, G:0.05, T:0.71


Consensus pattern (18 bp):   
TAACTTTTGTTTTTTCTT

Found at i:1096 original size:27 final size:26

Alignment explanation


    Indices: 1061--1188  Score: 69
    Period size: 27  Copynumber: 4.7  Consensus size: 26

       1051 GTATTGTTGC

                *                      
       1061 AGTGCGTTCAACACCCAGTGGTGTTTT
          1 AGTGAGTTCAACA-CCAGTGGTGTTTT

                                 *  *   
       1088 AGTGAGTTCAA-ATGCCAGTGATGCTTT
          1 AGTGAGTTCAACA--CCAGTGGTGTTTT

              **                    ** 
       1115 AGCCAGTTCGAACACCAGTGGTGTCGT
          1 AGTGAGTTC-AACACCAGTGGTGTTTT

              *      *    *      **    
       1142 AGCGAGTTTGAACAACAGTGGAATTTT
          1 AGTGAG-TTCAACACCAGTGGTGTTTT

              *         *       
       1169 AGGGAGTTCAAAAACCAGTG
          1 AGTGAGTTC-AACACCAGTG

       1189 TTATCAATGC


Statistics
Matches: 75,  Mismatches: 21, Indels: 10
        0.71            0.20        0.09

Matches are distributed among these distances:
  26    3  0.04
  27   67  0.89
  28    4  0.05
  29    1  0.01

ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27


Consensus pattern (26 bp):   
AGTGAGTTCAACACCAGTGGTGTTTT

Found at i:1347 original size:81 final size:81

Alignment explanation


    Indices: 1196--1393  Score: 209
    Period size: 81  Copynumber: 2.4  Consensus size: 81

       1186 GTGTTATCAA

                       * *                   *  **    *           *    ***   
       1196 TGCTGATAGTGTTACAGCTAGTTTAAATGCTGGAAGTTTTGCTTCAAGTTCTAATGCTTTGGGTG
          1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG

            *               
       1261 TTGCAATGAGTTCTAC
         66 CTGCAATGAGTTCTAC

                 *             *    *                                        
       1277 TGCTGGTAGTGCTGCAGCTTGTTTTAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG
          1 TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG

                            
       1342 CTGCAATGAGTTCTAC
         66 CTGCAATGAGTTCTAC

             *   *          * *      *           
       1358 TTCTGTTAGT-CTTGCGGGTAGTTTGAATGCTGGTAG
          1 TGCTGATAGTGC-TGCAGCTAGTTTAAATGCTGGTAG

       1394 TGTTGCTGAA


Statistics
Matches: 96,  Mismatches: 20, Indels: 2
        0.81            0.17        0.02

Matches are distributed among these distances:
  80    1  0.01
  81   95  0.99

ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38


Consensus pattern (81 bp):   
TGCTGATAGTGCTGCAGCTAGTTTAAATGCTGGTAGCATTGCCTCAAGTTCTAAAGCTTCCAGTG
CTGCAATGAGTTCTAC

Found at i:2898 original size:93 final size:93

Alignment explanation


    Indices: 2739--3018  Score: 434
    Period size: 93  Copynumber: 3.0  Consensus size: 93

       2729 ATTACATGGT

                  *       *                                 *      *     *   
       2739 GGTGTTGCAACTCACGCAGAACATTTTATGCAAGCTAAAGAAACTGAGGCCAGTGTTGAGGCCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                                       *
       2804 GGTTGCTTCTAAAATGATTTCTTCTGCG
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

                        *    *                                               
       2832 GGTGTTACAACTAATGCTGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       2897 GGTTGCTTCTCAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             *               *  *                                           *
       2925 GATGTTACAACTCATGCCGAGCATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCT
          1 GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA

                      *                 
       2990 GGTTGCTTCTGAAATGATTTCTTCTGCA
         66 GGTTGCTTCTAAAATGATTTCTTCTGCA

             
       3018 G
          1 G

       3019 ACCATGATGT


Statistics
Matches: 172,  Mismatches: 15, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  93  172  1.00

ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29


Consensus pattern (93 bp):   
GGTGTTACAACTCATGCAGAACATTTTATGCAAGCTAAAGAAACTGAGCCCAGTGGTGAGGGCCA
GGTTGCTTCTAAAATGATTTCTTCTGCA

Done.