Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01749.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, 1000

Length: 3097
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:1374 original size:25 final size:25

Alignment explanation


    Indices: 1346--1419  Score: 68
    Period size: 25  Copynumber: 3.2  Consensus size: 25

       1336 TAGTAGGCAT

                                     
       1346 CTTTATTCTGATTAAGAATTGAATA
          1 CTTTATTCTGATTAAGAATTGAATA

                  *  *      *  * *   
       1371 CTTT-TAC-CATT-AGTA-GGCAT-
          1 CTTTATTCTGATTAAGAATTGAATA

                                     
       1391 CTTTATTCTGATTAAGAATTGAATA
          1 CTTTATTCTGATTAAGAATTGAATA

                
       1416 CTTT
          1 CTTT

       1420 TACCATTAGT


Statistics
Matches: 34,  Mismatches: 10, Indels: 10
        0.63            0.19        0.19

Matches are distributed among these distances:
  20    4  0.12
  21    5  0.15
  22    6  0.18
  23    6  0.18
  24    5  0.15
  25    8  0.24

ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45


Consensus pattern (25 bp):   
CTTTATTCTGATTAAGAATTGAATA

Found at i:1382 original size:23 final size:23

Alignment explanation


    Indices: 1356--1427  Score: 60
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       1346 CTTTATTCTG

                                   
       1356 ATTAAGAATTGAATACTTTTACC
          1 ATTAAGAATTGAATACTTTTACC

                  *  * *         *  *
       1379 ATT-AGTA-GGCAT-CTTTATTCTG
          1 ATTAAGAATTGAATACTTT-TAC-C

                                   
       1401 ATTAAGAATTGAATACTTTTACC
          1 ATTAAGAATTGAATACTTTTACC

                
       1424 ATTA
          1 ATTA

       1428 GTAGGCATCT


Statistics
Matches: 34,  Mismatches: 10, Indels: 10
        0.63            0.19        0.19

Matches are distributed among these distances:
  20    4  0.12
  21    5  0.15
  22    6  0.18
  23   10  0.29
  24    5  0.15
  25    4  0.12

ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42


Consensus pattern (23 bp):   
ATTAAGAATTGAATACTTTTACC

Found at i:1387 original size:45 final size:45

Alignment explanation


    Indices: 1323--1458  Score: 272
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       1313 GCCTTCTATG

                                                         
       1323 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA
          1 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA

                                                         
       1368 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA
          1 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA

                                                         
       1413 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA
          1 ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA

             
       1458 A
          1 A

       1459 CTTATTGGAT


Statistics
Matches: 91,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   91  1.00

ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42


Consensus pattern (45 bp):   
ATACTTTTACCATTAGTAGGCATCTTTATTCTGATTAAGAATTGA
Done.