Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g02667.F2

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, 822

Length: 1370
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34


Found at i:1184 original size:19 final size:17

Alignment explanation


    Indices: 1158--1216  Score: 57
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       1148 CTATATAATA

                             
       1158 TTTTAGTTTTCTTCTAT
          1 TTTTAGTTTTCTTCTAT

                            *    
       1175 TTTTAAAG-TTTCTATATAAT
          1 TTTT--AGTTTTCT-TCT-AT

                              
       1195 ATTTTAGTTTTCTTCTAT
          1 -TTTTAGTTTTCTTCTAT

                
       1213 TTTT
          1 TTTT

       1217 TTGGTAAAAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 12
        0.71            0.04        0.25

Matches are distributed among these distances:
  17    8  0.24
  18    7  0.21
  19    8  0.24
  20    7  0.21
  21    4  0.12

ACGTcount: A:0.20, C:0.08, G:0.05, T:0.66


Consensus pattern (17 bp):   
TTTTAGTTTTCTTCTAT

Found at i:1190 original size:38 final size:38

Alignment explanation


    Indices: 1139--1216  Score: 156
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       1129 TTTGGTCTTG

                                                  
       1139 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
          1 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT

                                                  
       1177 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
          1 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT

              
       1215 TT
          1 TT

       1217 TTGGTAAAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   40  1.00

ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62


Consensus pattern (38 bp):   
TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT

Found at i:1218 original size:19 final size:19

Alignment explanation


    Indices: 1158--1218  Score: 61
    Period size: 19  Copynumber: 3.2  Consensus size: 19

       1148 CTATATAATA

                               
       1158 TTTTAGTTTTCTTCTATTT
          1 TTTTAGTTTTCTTCTATTT

              **          *  * *
       1177 TTAAAG-TTTCTATATAATA
          1 TTTTAGTTTTCT-TCTATTT

                               
       1196 TTTTAGTTTTCTTCTATTT
          1 TTTTAGTTTTCTTCTATTT

                
       1215 TTTT
          1 TTTT

       1219 GGTAAAAAGT


Statistics
Matches: 30,  Mismatches: 10, Indels: 4
        0.68            0.23        0.09

Matches are distributed among these distances:
  18    5  0.17
  19   20  0.67
  20    5  0.17

ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67


Consensus pattern (19 bp):   
TTTTAGTTTTCTTCTATTT
Done.