Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01270.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: 5558
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31


Found at i:531 original size:26 final size:26

Alignment explanation


    Indices: 502--553  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        492 GAAAAGAAGT

                                      
        502 TAGTTATAAACAGTTAACCTCATTTA
          1 TAGTTATAAACAGTTAACCTCATTTA

                                      
        528 TAGTTATAAACAGTTAACCTCATTTA
          1 TAGTTATAAACAGTTAACCTCATTTA

        554 AGTAAACGGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38


Consensus pattern (26 bp):   
TAGTTATAAACAGTTAACCTCATTTA

Found at i:1023 original size:15 final size:16

Alignment explanation


    Indices: 1003--1032  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        993 GCTAGTATTT

                            
       1003 TGGACCTCCA-CTAAG
          1 TGGACCTCCAGCTAAG

                           
       1018 TGGACCTCCAGCTAA
          1 TGGACCTCCAGCTAA

       1033 CGGGGTCACG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20


Consensus pattern (16 bp):   
TGGACCTCCAGCTAAG

Found at i:4350 original size:79 final size:79

Alignment explanation


    Indices: 4214--4371  Score: 237
    Period size: 79  Copynumber: 2.0  Consensus size: 79

       4204 CCTTCAGCCA

                                     *                                       
       4214 CTACCGATACCTGACAGAGCTTGGTTAGTTGTTAGCTTGGATTTCATTGAAGCGTTG-CTCAATT
          1 CTACCGATACCTGACAGAGCTTGGTCAGTTGTTAGCTTGGATTTCATTGAAGCGTTGCCT-AATT

                           
       4278 CAAACAAGAAAAACT
         65 CAAACAAGAAAAACT

                    * *  *                                      *            
       4293 CTACCGATGCTTGGCAGAGCTTGGTCAGTTGTTAGCTTGGATTTCATTGAAGGGTTGCCTAATTC
          1 CTACCGATACCTGACAGAGCTTGGTCAGTTGTTAGCTTGGATTTCATTGAAGCGTTGCCTAATTC

                 *  *     
       4358 AAACATGACAAACT
         66 AAACAAGAAAAACT

       4372 TTATTTTAGT


Statistics
Matches: 71,  Mismatches: 7, Indels: 2
        0.89            0.09        0.03

Matches are distributed among these distances:
  79   69  0.97
  80    2  0.03

ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31


Consensus pattern (79 bp):   
CTACCGATACCTGACAGAGCTTGGTCAGTTGTTAGCTTGGATTTCATTGAAGCGTTGCCTAATTC
AAACAAGAAAAACT

Found at i:5367 original size:24 final size:25

Alignment explanation


    Indices: 5340--5387  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5330 CTAACCTCAT

                                      
       5340 TTAAGT-AAACAGG-GAGTTTTGATC
          1 TTAAGTAAAAC-GGAGAGTTTTGATC

                                    
       5364 TTAAGTAAAACGGAGAGTTTTGAT
          1 TTAAGTAAAACGGAGAGTTTTGAT

       5388 TCTAAGGTTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  24    8  0.36
  25   14  0.64

ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33


Consensus pattern (25 bp):   
TTAAGTAAAACGGAGAGTTTTGATC

Found at i:5393 original size:25 final size:24

Alignment explanation


    Indices: 5340--5387  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5330 CTAACCTCAT

                                    
       5340 TTAAGTAAACAGGGAGTTTTGATC
          1 TTAAGTAAACAGGGAGTTTTGATC

                                     
       5364 TTAAGTAAA-ACGGAGAGTTTTGAT
          1 TTAAGTAAACA-GG-GAGTTTTGAT

       5388 TCTAAGGTTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    1  0.05
  24   11  0.50
  25   10  0.45

ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33


Consensus pattern (24 bp):   
TTAAGTAAACAGGGAGTTTTGATC
Done.