Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00970.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, 943

Length: 1572
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1360 original size:3 final size:3

Alignment explanation


    Indices: 1337--1412  Score: 72
    Period size: 3  Copynumber: 27.0  Consensus size: 3

       1327 CCTGGGCAGT

                     *                           *                         
       1337 AGA AGA ATA AG- AGA A-A A-A AGA AGA ATA AG- AGA AGA AGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA

                 *                *              *     
       1381 AGA AAA AGA AG- AGA AGG AGA AGA AGA ATA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA

       1413 GAAAATGGAA


Statistics
Matches: 59,  Mismatches: 10, Indels: 8
        0.77            0.13        0.10

Matches are distributed among these distances:
   2   10  0.17
   3   49  0.83

ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04


Consensus pattern (3 bp):   
AGA

Found at i:1371 original size:23 final size:23

Alignment explanation


    Indices: 1345--1415  Score: 85
    Period size: 23  Copynumber: 3.1  Consensus size: 23

       1335 GTAGAAGAAT

                    *              
       1345 AAGAGAAAAAAGAAGAATAAGAG
          1 AAGAGAAAGAAGAAGAATAAGAG

                                    
       1368 AAGA-AGAAGAAGAAGAA-AA-AG
          1 AAGAGA-AAGAAGAAGAATAAGAG

                                     
       1389 AAGAGAAGGAGAAGAAGAATAAGAG
          1 AAGAGAA--AGAAGAAGAATAAGAG

              
       1414 AA
          1 AA

       1416 AATGGAAGGA


Statistics
Matches: 41,  Mismatches: 1, Indels: 10
        0.79            0.02        0.19

Matches are distributed among these distances:
  21    7  0.17
  22    4  0.10
  23   24  0.59
  24    2  0.05
  25    4  0.10

ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03


Consensus pattern (23 bp):   
AAGAGAAAGAAGAAGAATAAGAG

Found at i:1374 original size:26 final size:26

Alignment explanation


    Indices: 1351--1404  Score: 72
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       1341 GAATAAGAGA

                    *  *              
       1351 AAAAAGAAGAATAAGAGAAGAAGAAG
          1 AAAAAGAAAAAGAAGAGAAGAAGAAG

              *                 *     
       1377 AAGAAGAAAAAGAAGAGAAGGAGAAG
          1 AAAAAGAAAAAGAAGAGAAGAAGAAG

              
       1403 AA
          1 AA

       1405 GAATAAGAGA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02


Consensus pattern (26 bp):   
AAAAAGAAAAAGAAGAGAAGAAGAAG

Found at i:1375 original size:32 final size:32

Alignment explanation


    Indices: 1337--1417  Score: 112
    Period size: 32  Copynumber: 2.5  Consensus size: 32

       1327 CCTGGGCAGT

                                             
       1337 AGAAGAATAAGAGAAAAAAGAAGA-ATAAGAGA
          1 AGAAGAATAAGAGAAAAAAGAAGAGA-AAGAGA

                   *                    *    
       1369 AGAAGAAGAAGA-AGAAAAAGAAGAGAAGGAGA
          1 AGAAGAATAAGAGA-AAAAAGAAGAGAAAGAGA

                             
       1401 AGAAGAATAAGAGAAAA
          1 AGAAGAATAAGAGAAAA

       1418 TGGAAGGAGA


Statistics
Matches: 43,  Mismatches: 3, Indels: 6
        0.83            0.06        0.12

Matches are distributed among these distances:
  31    1  0.02
  32   40  0.93
  33    2  0.05

ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04


Consensus pattern (32 bp):   
AGAAGAATAAGAGAAAAAAGAAGAGAAAGAGA
Done.