Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03436.P2

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: 13206
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2852 original size:30 final size:31

Alignment explanation


    Indices: 2802--2862  Score: 115
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       2792 GGTATGTGTA

                                           
       2802 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG
          1 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG

                                           
       2833 AGTTTAGGAGAGG-AAAAAAATATTTCTCTG
          1 AGTTTAGGAGAGGAAAAAAAATATTTCTCTG

       2863 TATTGAATTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   17  0.57
  31   13  0.43

ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30


Consensus pattern (31 bp):   
AGTTTAGGAGAGGAAAAAAAATATTTCTCTG

Found at i:4503 original size:42 final size:42

Alignment explanation


    Indices: 4444--4532  Score: 151
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       4434 TCCTAATTGG

                   *                           *      
       4444 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
          1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA

                                                      
       4486 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA
          1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA

            *    
       4528 TAAAA
          1 GAAAA

       4533 ATACTCCTAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29


Consensus pattern (42 bp):   
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAAA

Found at i:4579 original size:19 final size:18

Alignment explanation


    Indices: 4557--4596  Score: 55
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       4547 TGAATAAAAC

                                
       4557 TTATCTACCTAA-ATAAGAT
          1 TTATCTACC-AATATAA-AT

                              
       4576 TTATCTACCAATATAAAT
          1 TTATCTACCAATATAAAT

               
       4594 TTA
          1 TTA

       4597 AAATATATAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  18    7  0.35
  19   13  0.65

ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40


Consensus pattern (18 bp):   
TTATCTACCAATATAAAT

Found at i:8440 original size:42 final size:42

Alignment explanation


    Indices: 8393--8481  Score: 151
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       8383 TCCTAATTTG

                                               *      
       8393 GAAAATAGTTCACTTATTCTAATAAACTACTAAAATATAAAA
          1 GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA

                       *                              
       8435 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
          1 GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA

            *    
       8477 TAAAA
          1 GAAAA

       8482 ATATTCCTAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29


Consensus pattern (42 bp):   
GAAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAA

Found at i:8502 original size:43 final size:42

Alignment explanation


    Indices: 8394--8503  Score: 98
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       8384 CCTAATTTGG

                      *  * * *                *      *
       8394 AAAATAGTTCACTTATTCTAATAAACTACTAAAATATAAAAG
          1 AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAAA

                         * * *                         
       8436 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
          1 AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAA-A

                                       
       8479 AAAATA-TT-CCTAGAATATGAATAAA
          1 AAAATAGTTCCCT-GAATAT-AATAAA

       8504 ACTTATCTAC


Statistics
Matches: 59,  Mismatches: 6, Indels: 5
        0.84            0.09        0.07

Matches are distributed among these distances:
  41    3  0.05
  42   44  0.75
  43   12  0.20

ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30


Consensus pattern (42 bp):   
AAAATAGTTCCCTGAATATAATAAACTACTAAAAGATAAAAA

Found at i:8528 original size:19 final size:18

Alignment explanation


    Indices: 8506--8545  Score: 71
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       8496 TGAATAAAAC

                               
       8506 TTATCTACCTAAATAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       8525 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

               
       8543 TTA
          1 TTA

       8546 AAATATATAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40


Consensus pattern (18 bp):   
TTATCTACCTAAATAAAT
Done.