Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00834.F3

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: 4027
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34


Found at i:1169 original size:19 final size:21

Alignment explanation


    Indices: 1141--1188  Score: 64
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       1131 TTATTATTTA

                                 
       1141 TTTTAGTTTTGATTCTAA-AT
          1 TTTTAGTTTTGATTCTAATAT

                      *   *      
       1161 TTTTA-TTTTTATTTTAATAT
          1 TTTTAGTTTTGATTCTAATAT

                    
       1181 TTTTAGTT
          1 TTTTAGTT

       1189 AAAATTTTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  19   10  0.42
  20   12  0.50
  21    2  0.08

ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69


Consensus pattern (21 bp):   
TTTTAGTTTTGATTCTAATAT

Found at i:1275 original size:29 final size:29

Alignment explanation


    Indices: 1241--1304  Score: 78
    Period size: 28  Copynumber: 2.2  Consensus size: 29

       1231 ATTCTTCTCA

                                     *    
       1241 ATATTTTGATAATGAATTTTA-AATTTTTT
          1 ATATTTTG-TAATGAATTTTATAATATTTT

                     *                   
       1270 ATA-TTTGTCATGAATTTTATAATATTTT
          1 ATATTTTGTAATGAATTTTATAATATTTT

              *    
       1298 ATTTTTT
          1 ATATTTT

       1305 TAAAATTTCA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  27   11  0.37
  28   13  0.43
  29    6  0.20

ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61


Consensus pattern (29 bp):   
ATATTTTGTAATGAATTTTATAATATTTT

Found at i:2322 original size:33 final size:33

Alignment explanation


    Indices: 2199--2341  Score: 121
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       2189 TGTTGACTAC

                           *                 * 
       2199 TGGGGAGGGTGATGTTGAAG-GGTTAGAAGT-TCA
          1 TGGGGAGGGTGATGTAGAAGAGG-TAGAA-TCTGA

                                 *            
       2232 TGGGGAGGGTGATG-ATGAAGGGGTAGAATCTGA
          1 TGGGGAGGGTGATGTA-GAAGAGGTAGAATCTGA

               *  * *    *     *            *
       2265 TGGTGAAGATGATCTAGAAAAGGTAGAATCTGG
          1 TGGGGAGGGTGATGTAGAAGAGGTAGAATCTGA

                             *       *  *    
       2298 TGGGGAGGGTGATGTAGGAGAGGTACAAGCTGA
          1 TGGGGAGGGTGATGTAGAAGAGGTAGAATCTGA

               *       
       2331 TGGAGAGGGTG
          1 TGGGGAGGGTG

       2342 TTTCTGCTAC


Statistics
Matches: 87,  Mismatches: 19, Indels: 8
        0.76            0.17        0.07

Matches are distributed among these distances:
  32    1  0.01
  33   83  0.95
  34    3  0.03

ACGTcount: A:0.28, C:0.04, G:0.45, T:0.22


Consensus pattern (33 bp):   
TGGGGAGGGTGATGTAGAAGAGGTAGAATCTGA

Found at i:2517 original size:51 final size:51

Alignment explanation


    Indices: 2445--2601  Score: 208
    Period size: 51  Copynumber: 3.1  Consensus size: 51

       2435 GTGAAGTTGC

                *                     * *              *       
       2445 TGCTAATGAATAT-CTGGTGATTTTGTACCATCAGATGGAGTGAATAATGT
          1 TGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGT

                          *                 *      *           
       2495 TGCTGATGAATATGTTGGTGATTTTGCAACATTAGATGGTGTGGATAATGT
          1 TGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGT

                             *               *   *  *          
       2546 TGCTGATGAATATGCTGATGATTTTGCAACATCTGATAGACTGGATAATGT
          1 TGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGT

                 
       2597 TGCTG
          1 TGCTG

       2602 CTGCACGTAC


Statistics
Matches: 92,  Mismatches: 14, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  50   12  0.13
  51   80  0.87

ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37


Consensus pattern (51 bp):   
TGCTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAGTGGATAATGT
Done.