Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g00658.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: 1805
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20


Found at i:1298 original size:36 final size:36

Alignment explanation


    Indices: 1253--1324  Score: 108
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       1243 GTTAAAGAAT

                                  *             
       1253 TAGACGCAGAGCCAGAGAAAGAGCAAAAGGCAGAGA
          1 TAGACGCAGAGCCAGAGAAAGACCAAAAGGCAGAGA

                *            **                 
       1289 TAGAGGCAGAGCCAGAGGCAGACCAAAAGGCAGAGA
          1 TAGACGCAGAGCCAGAGAAAGACCAAAAGGCAGAGA

       1325 CGGAGGCACA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.44, C:0.18, G:0.35, T:0.03


Consensus pattern (36 bp):   
TAGACGCAGAGCCAGAGAAAGACCAAAAGGCAGAGA

Found at i:1319 original size:24 final size:24

Alignment explanation


    Indices: 1295--1436  Score: 167
    Period size: 24  Copynumber: 5.9  Consensus size: 24

       1285 GAGATAGAGG

                 *          *      *
       1295 CAGAGCCAGAGGCAGACCAAAAGG
          1 CAGAGACAGAGGCAGAGCAAAAGA

                   *      *         
       1319 CAGAGACGGAGGCACAGCAAAAGA
          1 CAGAGACAGAGGCAGAGCAAAAGA

                    *   *   *       
       1343 CAGAGACACAGGTAGAACAAAAGA
          1 CAGAGACAGAGGCAGAGCAAAAGA

                *                   
       1367 CAGATACAGAGGCAGAGCAAAAGA
          1 CAGAGACAGAGGCAGAGCAAAAGA

                             *      
       1391 CAGAGACAGAGGCAGAGAAAAAGA
          1 CAGAGACAGAGGCAGAGCAAAAGA

                 *  *             
       1415 CAGAGCCAAAGGCAGAGGCAAA
          1 CAGAGACAGAGGCAGA-GCAAA

       1437 GCAAAAGGCG


Statistics
Matches: 98,  Mismatches: 19, Indels: 1
        0.83            0.16        0.01

Matches are distributed among these distances:
  24   94  0.96
  25    4  0.04

ACGTcount: A:0.49, C:0.19, G:0.31, T:0.01


Consensus pattern (24 bp):   
CAGAGACAGAGGCAGAGCAAAAGA

Found at i:1331 original size:36 final size:36

Alignment explanation


    Indices: 1258--1332  Score: 105
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       1248 AGAATTAGAC

                             *             *    
       1258 GCAGAGCCAGAGAAAGAGCAAAAGGCAGAGATAGAG
          1 GCAGAGCCAGAGAAAGACCAAAAGGCAGAGACAGAG

                        **                  *   
       1294 GCAGAGCCAGAGGCAGACCAAAAGGCAGAGACGGAG
          1 GCAGAGCCAGAGAAAGACCAAAAGGCAGAGACAGAG

               
       1330 GCA
          1 GCA

       1333 CAGCAAAAGA


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.43, C:0.19, G:0.37, T:0.01


Consensus pattern (36 bp):   
GCAGAGCCAGAGAAAGACCAAAAGGCAGAGACAGAG

Found at i:1429 original size:48 final size:47

Alignment explanation


    Indices: 1278--1436  Score: 149
    Period size: 48  Copynumber: 3.3  Consensus size: 47

       1268 AGAAAGAGCA

                          *  *     *           *     *       
       1278 AAAGGCAGAG-ATAGAGGCAGAGCCAGAGGCAGACCAAAAGGCAGAGAC
          1 AAAGGCAGAGCA-AAAGACAGAGACAGAGGCAGA-AAAAAGACAGAGAC

            **     *                 *   *               *  
       1326 GGAGGCACAGCAAAAGACAGAGACACAGGTAGAACAAAAGACAGATAC
          1 AAAGGCAGAGCAAAAGACAGAGACAGAGGCAGAA-AAAAGACAGAGAC

             *                                            * 
       1374 AGAGGCAGAGCAAAAGACAGAGACAGAGGCAGAGAAAAAGACAGAGCC
          1 AAAGGCAGAGCAAAAGACAGAGACAGAGGCAGA-AAAAAGACAGAGAC

                           
       1422 AAAGGCAGAGGCAAA
          1 AAAGGCAGA-GCAAA

       1437 GCAAAAGGCG


Statistics
Matches: 89,  Mismatches: 18, Indels: 7
        0.78            0.16        0.06

Matches are distributed among these distances:
  48   82  0.92
  49    7  0.08

ACGTcount: A:0.48, C:0.18, G:0.32, T:0.02


Consensus pattern (47 bp):   
AAAGGCAGAGCAAAAGACAGAGACAGAGGCAGAAAAAAGACAGAGAC

Found at i:1437 original size:12 final size:12

Alignment explanation


    Indices: 1278--1437  Score: 76
    Period size: 12  Copynumber: 13.3  Consensus size: 12

       1268 AGAAAGAGCA

                       *
       1278 AAAGGCAGAGAT
          1 AAAGGCAGAGAC

             *        * 
       1290 AGAGGCAGAGCC
          1 AAAGGCAGAGAC

             *        * 
       1302 AGAGGCAGA-CC
          1 AAAGGCAGAGAC

                         
       1313 AAAAGGCAGAGAC
          1 -AAAGGCAGAGAC

            **     *    
       1326 GGAGGCACAG-C
          1 AAAGGCAGAGAC

                 *       
       1337 AAAAGACAGAGAC
          1 -AAAGGCAGAGAC

             *   *      
       1350 ACAGGTAGA-AC
          1 AAAGGCAGAGAC

                 *    *  
       1361 AAAAGACAGATAC
          1 -AAAGGCAGAGAC

             *          
       1374 AGAGGCAGAG-C
          1 AAAGGCAGAGAC

                 *       
       1385 AAAAGACAGAGAC
          1 -AAAGGCAGAGAC

             *         *
       1398 AGAGGCAGAGAA
          1 AAAGGCAGAGAC

                *     * 
       1410 AAAGACAGAGCC
          1 AAAGGCAGAGAC

                      * 
       1422 AAAGGCAGAGGC
          1 AAAGGCAGAGAC

                
       1434 AAAG
          1 AAAG

       1438 CAAAAGGCGG


Statistics
Matches: 108,  Mismatches: 32, Indels: 16
        0.69            0.21        0.10

Matches are distributed among these distances:
  11    6  0.06
  12   97  0.90
  13    5  0.05

ACGTcount: A:0.48, C:0.17, G:0.33, T:0.02


Consensus pattern (12 bp):   
AAAGGCAGAGAC

Done.