Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01103.M1

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: 3594
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30


Found at i:568 original size:30 final size:30

Alignment explanation


    Indices: 519--598  Score: 117
    Period size: 30  Copynumber: 2.7  Consensus size: 30

        509 CACCTGTTAG

                *    *   *                 
        519 TTCACCGCCTCCATCATCACAACCTTCCCC-
          1 TTCAACGCCACCACCATCACAACC-TCCCCT

                                          
        549 TTCAACGCCACCACCATCACAACCTCCCCT
          1 TTCAACGCCACCACCATCACAACCTCCCCT

                                
        579 TTCAACGCCACCACCATCAC
          1 TTCAACGCCACCACCATCAC

        599 GATCTCCACC


Statistics
Matches: 46,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  29    5  0.11
  30   41  0.89

ACGTcount: A:0.25, C:0.53, G:0.04, T:0.19


Consensus pattern (30 bp):   
TTCAACGCCACCACCATCACAACCTCCCCT

Found at i:656 original size:36 final size:36

Alignment explanation


    Indices: 584--656  Score: 94
    Period size: 36  Copynumber: 2.0  Consensus size: 36

        574 CCCCTTTCAA

                           * *        *         
        584 CGCCACCACCATCACGATCTCCACCACCAAATCCAC
          1 CGCCACCACCATCACAAACTCCACCAACAAATCCAC

                                  *              
        620 CGCCACCACCATCACAAACTCCGCCAACAGAA-CCAC
          1 CGCCACCACCATCACAAACTCCACCAACA-AATCCAC

             
        656 C
          1 C

        657 AAATTCCCGT


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  36   30  0.94
  37    2  0.06

ACGTcount: A:0.33, C:0.52, G:0.07, T:0.08


Consensus pattern (36 bp):   
CGCCACCACCATCACAAACTCCACCAACAAATCCAC

Found at i:2254 original size:15 final size:16

Alignment explanation


    Indices: 2224--2257  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       2214 GAGGTAGATT

                            
       2224 AACCAAAAGAAAAAAG
          1 AACCAAAAGAAAAAAG

                     *      
       2240 AACCAAAA-TAAAAAG
          1 AACCAAAAGAAAAAAG

               
       2255 AAC
          1 AAC

       2258 AAGGAGAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    9  0.53
  16    8  0.47

ACGTcount: A:0.74, C:0.15, G:0.09, T:0.03


Consensus pattern (16 bp):   
AACCAAAAGAAAAAAG
Done.