Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01745.N4

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: 8332
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:1059 original size:14 final size:14

Alignment explanation


    Indices: 1037--1070  Score: 50
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1027 AATAGAAAAC

                *         
       1037 TTTTCATCACTTTT
          1 TTTTTATCACTTTT

                          
       1051 TTTTTATCACTTTT
          1 TTTTTATCACTTTT

             *    
       1065 TCTTTA
          1 TTTTTA

       1071 GCCTCCGGGC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68


Consensus pattern (14 bp):   
TTTTTATCACTTTT

Found at i:1812 original size:16 final size:17

Alignment explanation


    Indices: 1791--1824  Score: 61
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       1781 AATTAGAGAA

                             
       1791 TTCTATTTAA-TTCTAT
          1 TTCTATTTAATTTCTAT

                             
       1807 TTCTATTTAATTTCTAT
          1 TTCTATTTAATTTCTAT

             
       1824 T
          1 T

       1825 AAATCCATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   10  0.59
  17    7  0.41

ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65


Consensus pattern (17 bp):   
TTCTATTTAATTTCTAT

Found at i:2516 original size:15 final size:15

Alignment explanation


    Indices: 2498--2528  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2488 ATAACTAAAG

                           
       2498 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

                           
       2513 AAAAAATAGATAGAT
          1 AAAAAATAGATAGAT

             
       2528 A
          1 A

       2529 GATGAGAGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19


Consensus pattern (15 bp):   
AAAAAATAGATAGAT

Found at i:8197 original size:26 final size:26

Alignment explanation


    Indices: 8168--8256  Score: 82
    Period size: 23  Copynumber: 3.7  Consensus size: 26

       8158 AAATTACAAG

                   *                  
       8168 TTATTAGCAATTAATATTAATTTATA
          1 TTATTAGTAATTAATATTAATTTATA

                 *  *            **   
       8194 TTATTTGTTATTAATATTAA-GAATA
          1 TTATTAGTAATTAATATTAATTTATA

                            *         
       8219 TTA--AGTAATTAATAAT-ATTTATA
          1 TTATTAGTAATTAATATTAATTTATA

                             
       8242 TTATTA-T-ATTAATAT
          1 TTATTAGTAATTAATAT

       8257 ATTTCGATTT


Statistics
Matches: 49,  Mismatches: 11, Indels: 9
        0.71            0.16        0.13

Matches are distributed among these distances:
  22    1  0.02
  23   23  0.47
  24    1  0.02
  25    7  0.14
  26   17  0.35

ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52


Consensus pattern (26 bp):   
TTATTAGTAATTAATATTAATTTATA

Found at i:8313 original size:15 final size:14

Alignment explanation


    Indices: 8280--8326  Score: 55
    Period size: 15  Copynumber: 3.4  Consensus size: 14

       8270 AATCTATATT

                          
       8280 TCTA-TATTATTTA
          1 TCTATTATTATTTA

                           
       8293 T-T-TTATTATTCTA
          1 TCTATTATTATT-TA

                           
       8306 TCTATTATTATATTA
          1 TCTATTATTAT-TTA

                  
       8321 TCTATT
          1 TCTATT

       8327 TATAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  12    8  0.28
  13    4  0.14
  14    1  0.03
  15   15  0.52
  16    1  0.03

ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64


Consensus pattern (14 bp):   
TCTATTATTATTTA
Done.