Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00600.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, 935

Length: 1559
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30


Found at i:1156 original size:33 final size:33

Alignment explanation


    Indices: 1094--1261  Score: 180
    Period size: 33  Copynumber: 5.1  Consensus size: 33

       1084 TATCTTCAGC

                            *        *        
       1094 CCACCATCA-TACTCCACTCCTTCCGGCTCGTAT
          1 CCACCA-CAGTACTCCGCTCCTTCCAGCTCGTAT

                *         *    *             
       1127 CCACTACAGTACTCTGCTCTTTCCAGCTCGTAT
          1 CCACCACAGTACTCCGCTCCTTCCAGCTCGTAT

                                    *         
       1160 CCACCACCA-TACTCCGCTCCTTCTAGCTCGTAT
          1 CCACCA-CAGTACTCCGCTCCTTCCAGCTCGTAT

                   *               *     *   
       1193 CCACCACCGTACTCCGCTCCTTCTAGCTCATAT
          1 CCACCACAGTACTCCGCTCCTTCCAGCTCGTAT

                          *         **        
       1226 CCACCACCA-TACTTCGCTCCTTCTGGCTCGTAT
          1 CCACCA-CAGTACTCCGCTCCTTCCAGCTCGTAT

               
       1259 CCA
          1 CCA

       1262 TCGACATTCT


Statistics
Matches: 116,  Mismatches: 15, Indels: 8
        0.83            0.11        0.06

Matches are distributed among these distances:
  32    3  0.03
  33  110  0.95
  34    3  0.03

ACGTcount: A:0.18, C:0.43, G:0.10, T:0.29


Consensus pattern (33 bp):   
CCACCACAGTACTCCGCTCCTTCCAGCTCGTAT

Found at i:1172 original size:66 final size:66

Alignment explanation


    Indices: 1094--1312  Score: 242
    Period size: 66  Copynumber: 3.3  Consensus size: 66

       1084 TATCTTCAGC

                  *                *             *              *            
       1094 CCACCATCATACTCCACTCCTTCCGGCTCGTATCCACTACAGTACTCTGCTCTTTCCAGCTCGTA
          1 CCACCACCATACTCCACTCCTTCTGGCTCGTATCCACCACAGTACTCTGCTCCTTCCAGCTCGTA

             
       1159 T
         66 T

                           *        *               *      *        *     *  
       1160 CCACCACCATACTCCGCTCCTTCTAGCTCGTATCCACCACCGTACTCCGCTCCTTCTAGCTCATA
          1 CCACCACCATACTCCACTCCTTCTGGCTCGTATCCACCACAGTACTCTGCTCCTTCCAGCTCGTA

             
       1225 T
         66 T

                         * *                      *     *    *     *  *   *  
       1226 CCACCACCATACTTCGCTCCTTCTGGCTCGTATCCATCGACA-TTCTCTACTCCTCCCGGCTTGT
          1 CCACCACCATACTCCACTCCTTCTGGCTCGTATCCA-CCACAGTACTCTGCTCCTTCCAGCTCGT

              
       1290 AT
         65 AT

               *          *      
       1292 CCATCACCATACTCTACTCCT
          1 CCACCACCATACTCCACTCCT

       1313 CCAGAGTCGT


Statistics
Matches: 126,  Mismatches: 26, Indels: 2
        0.82            0.17        0.01

Matches are distributed among these distances:
  66  123  0.98
  67    3  0.02

ACGTcount: A:0.18, C:0.43, G:0.10, T:0.30


Consensus pattern (66 bp):   
CCACCACCATACTCCACTCCTTCTGGCTCGTATCCACCACAGTACTCTGCTCCTTCCAGCTCGTA
T

Found at i:1279 original size:33 final size:33

Alignment explanation


    Indices: 1101--1314  Score: 130
    Period size: 33  Copynumber: 6.5  Consensus size: 33

       1091 AGCCCACCAT

                   *      *                   
       1101 CATACTCCACTCCTTCCGGCTCGTATCCA-CTA-
          1 CATACTCTACTCCTCCCGGCTCGTATCCATC-AC

                     *   * *  *           *   
       1133 CAGTACTCTGCTCTTTCCAGCTCGTATCCACCAC
          1 CA-TACTCTACTCCTCCCGGCTCGTATCCATCAC

                   **     * **           *   
       1167 CATACTCCGCTCCTTCTAGCTCGTATCCACCAC
          1 CATACTCTACTCCTCCCGGCTCGTATCCATCAC

             *     **     * **    *      *   
       1200 CGTACTCCGCTCCTTCTAGCTCATATCCACCAC
          1 CATACTCTACTCCTCCCGGCTCGTATCCATCAC

                     *     * *                 
       1233 CATACT-TCGCTCCTTCTGGCTCGTATCCATCGA-
          1 CATACTCT-ACTCCTCCCGGCTCGTATCCATC-AC

               *                 *           
       1266 CATTCTCTACTCCTCCCGGCTTGTATCCATCAC
          1 CATACTCTACTCCTCCCGGCTCGTATCCATCAC

                            
       1299 CATACTCTACTCCTCC
          1 CATACTCTACTCCTCC

       1315 AGAGTCGTAT


Statistics
Matches: 155,  Mismatches: 20, Indels: 13
        0.82            0.11        0.07

Matches are distributed among these distances:
  32    3  0.02
  33  147  0.95
  34    5  0.03

ACGTcount: A:0.17, C:0.43, G:0.10, T:0.30


Consensus pattern (33 bp):   
CATACTCTACTCCTCCCGGCTCGTATCCATCAC

Found at i:1325 original size:33 final size:33

Alignment explanation


    Indices: 1250--1325  Score: 93
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       1240 CGCTCCTTCT

                               *            *
       1250 GGCTCGTATCCATCGACATTCTCTACTCCTCCC
          1 GGCTCGTATCCATCGACATACTCTACTCCTCCA

                *                             
       1283 GGCTTGTATCCATC-ACCATACTCTACTCCTCCA
          1 GGCTCGTATCCATCGA-CATACTCTACTCCTCCA

                       
       1316 GAG-TCGTATC
          1 G-GCTCGTATC

       1326 TACCGTCGTT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  32    1  0.03
  33   35  0.95
  34    1  0.03

ACGTcount: A:0.18, C:0.38, G:0.13, T:0.30


Consensus pattern (33 bp):   
GGCTCGTATCCATCGACATACTCTACTCCTCCA
Done.