Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00375.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, 866

Length: 1444
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30


Found at i:29 original size:19 final size:19

Alignment explanation


    Indices: 2--57  Score: 60
    Period size: 18  Copynumber: 3.0  Consensus size: 19

          1 C

                               
          2 CAATCAAACAATCTTCCGT
          1 CAATCAAACAATCTTCCGT

                *    **    * * 
         21 CAATTAAACCCT-TTTCTT
          1 CAATCAAACAATCTTCCGT

                               
         39 CAATCAAACAATCTTCCGT
          1 CAATCAAACAATCTTCCGT

         58 TAATTAAACC


Statistics
Matches: 26,  Mismatches: 10, Indels: 2
        0.68            0.26        0.05

Matches are distributed among these distances:
  18   13  0.50
  19   13  0.50

ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32


Consensus pattern (19 bp):   
CAATCAAACAATCTTCCGT

Found at i:47 original size:18 final size:18

Alignment explanation


    Indices: 20--80  Score: 52
    Period size: 18  Copynumber: 3.3  Consensus size: 18

         10 CAATCTTCCG

                 *            
         20 TCAATTAAACCCTTTTCT
          1 TCAATCAAACCCTTTTCT

                      **    *   
         38 TCAATCAAACAATCTTCCGT
          1 TCAATCAAACCCT-TTTC-T

                 *            
         58 T-AATTAAACCCTTTTCT
          1 TCAATCAAACCCTTTTCT

                  
         75 TCAATC
          1 TCAATC

         81 TTCAACTAAT


Statistics
Matches: 31,  Mismatches: 9, Indels: 6
        0.67            0.20        0.13

Matches are distributed among these distances:
  17    2  0.06
  18   16  0.52
  19   11  0.35
  20    2  0.06

ACGTcount: A:0.31, C:0.28, G:0.02, T:0.39


Consensus pattern (18 bp):   
TCAATCAAACCCTTTTCT

Found at i:52 original size:37 final size:37

Alignment explanation


    Indices: 2--80  Score: 149
    Period size: 37  Copynumber: 2.1  Consensus size: 37

          1 C

                                                 
          2 CAATCAAACAATCTTCCGTCAATTAAACCCTTTTCTT
          1 CAATCAAACAATCTTCCGTCAATTAAACCCTTTTCTT

                               *                 
         39 CAATCAAACAATCTTCCGTTAATTAAACCCTTTTCTT
          1 CAATCAAACAATCTTCCGTCAATTAAACCCTTTTCTT

                 
         76 CAATC
          1 CAATC

         81 TTCAACTAAT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  37   41  1.00

ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35


Consensus pattern (37 bp):   
CAATCAAACAATCTTCCGTCAATTAAACCCTTTTCTT
Done.