Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01206.P4

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: 13841
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34


Found at i:669 original size:34 final size:33

Alignment explanation


    Indices: 599--716  Score: 107
    Period size: 34  Copynumber: 3.5  Consensus size: 33

        589 GTCGTTCAGT

                           *     *         *   
        599 TGAAAATTTATTAAATGTACTCTAATTATTTTTCA
          1 TGAAAATTTA-TAAAAGTA-TTTAATTATTTATCA

                                      *       
        634 TGAAAATTTATAAAAGTATTATAATTGTTTATCA
          1 TGAAAATTTATAAAAGTATT-TAATTATTTATCA

                   *      *       *   *       
        668 TG--AATAT-TAAATGTACTTTGATTTTTTATCA
          1 TGAAAATTTATAAAAGTA-TTTAATTATTTATCA

                              
        699 TGAAAATTTATAAAAGTA
          1 TGAAAATTTATAAAAGTA

        717 GTAATTTTTA


Statistics
Matches: 68,  Mismatches: 10, Indels: 11
        0.76            0.11        0.12

Matches are distributed among these distances:
  31   20  0.29
  32    6  0.09
  33    5  0.07
  34   27  0.40
  35   10  0.15

ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46


Consensus pattern (33 bp):   
TGAAAATTTATAAAAGTATTTAATTATTTATCA

Found at i:1322 original size:9 final size:9

Alignment explanation


    Indices: 1308--1356  Score: 53
    Period size: 10  Copynumber: 5.0  Consensus size: 9

       1298 TAGTTTTTTA

                     
       1308 TTTATAATT
          1 TTTATAATT

                   *  
       1317 TTTATAGTTT
          1 TTTATA-ATT

                      
       1327 TTCTATAATT
          1 TT-TATAATT

                      
       1337 TTTATAATAT
          1 TTTATAAT-T

                      
       1347 TTTAATAATT
          1 TTT-ATAATT

       1357 ATTAAACTTG


Statistics
Matches: 34,  Mismatches: 2, Indels: 7
        0.79            0.05        0.16

Matches are distributed among these distances:
   9   12  0.35
  10   13  0.38
  11    9  0.26

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63


Consensus pattern (9 bp):   
TTTATAATT

Found at i:6962 original size:3 final size:3

Alignment explanation


    Indices: 6956--6996  Score: 82
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       6946 TGATGATGAT

                                                                  
       6956 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
          1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA

       6997 CGATGTTATT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00


Consensus pattern (3 bp):   
GAG

Done.