Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00188.N1

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, 989

Length: 1649
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32


Found at i:66 original size:6 final size:6

Alignment explanation


    Indices: 57--90  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

         47 ATCCTCCTAC

                                                   
         57 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCT
          1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCT

         91 GTTCTGCCCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (6 bp):   
TCCTCT

Found at i:941 original size:30 final size:30

Alignment explanation


    Indices: 907--991  Score: 145
    Period size: 30  Copynumber: 2.9  Consensus size: 30

        897 AAAACCCTAG

                                          
        907 CCACCTTGCCTCCCACTTGCACCTACTCCA
          1 CCACCTTGCCTCCCACTTGCACCTACTCCA

                                  *       
        937 CCACCTTGCCTCCCACTTGCACTTACTCCA
          1 CCACCTTGCCTCCCACTTGCACCTACTCCA

                    *                 
        967 CCACCTTGTC-CCCACTTGCACCTAC
          1 CCACCTTGCCTCCCACTTGCACCTAC

        992 ACCATCAAAT


Statistics
Matches: 52,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  29   14  0.27
  30   38  0.73

ACGTcount: A:0.16, C:0.52, G:0.07, T:0.25


Consensus pattern (30 bp):   
CCACCTTGCCTCCCACTTGCACCTACTCCA

Found at i:1511 original size:3 final size:3

Alignment explanation


    Indices: 1482--1571  Score: 71
    Period size: 3  Copynumber: 29.7  Consensus size: 3

       1472 GAGCTTTGTT

                                      *     *                           
       1482 TTA TT- TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA

                               *      *                                   
       1525 TTA TTA TTA TTA TTTC TTA CATA TATA TTA TTA TT- TATA TTA TTA TT
          1 TTA TTA TTA TTA -TTA TTA -TTA T-TA TTA TTA TTA T-TA TTA TTA TT

       1572 GTATTATATA


Statistics
Matches: 70,  Mismatches: 8, Indels: 18
        0.73            0.08        0.19

Matches are distributed among these distances:
   2    6  0.09
   3   55  0.79
   4    9  0.13

ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Done.