[EMBOSS] Why tfscan generate duplicate results?

[Tao Zhu]

tfscan from emboss 6.5.7.0

My input sequence is an intron sequence from Arabidopsis thaliana(in
attached files: test.fasta)

I run:

$ tfscan -sequence test.fasta -menu P -mismatch 0 -outfile test.out

the result is:

########################################
# Program: tfscan
# Rundate: Fri  3 Aug 2012 08:55:50
# Commandline: tfscan
#    -sequence test.fasta
#    -menu P
#    -mismatch 0
#    -outfile test.out
# Report_format: seqtable
# Report_file: test.out
########################################

#=======================================
#
# Sequence: Atha     from: 1   to: 3388
# HitCount: 20
#=======================================

  Start     End  Strand Accession Factor
               Sequence
   3108    3114       + R03715
               ggttaat
   3108    3114       + R03715
               ggttaat
   2482    2488       + R03710
               gaaagaa
   3354    3359       + R02731    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   2185    2190       + R02731    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   1008    1013       + R02731    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   1261    1266       + R02731    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. gagata
   3354    3359       + R02729    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   2185    2190       + R02729    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   1008    1013       + R02729    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatctc
   2726    2731       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
    989     994       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
    223     228       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
   2726    2731       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
    989     994       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
    223     228       + R02728    T00627; NIT2;Quality: 2; Species:
Neurospora crassa. tatcta
   2876    2879       + R01203
               ctcc
   2449    2452       + R01203
               ctcc
   2141    2144       + R01203
               ctcc
   2877    2883       + R01202
               tccacct

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Reported_sequences: 1
# Reported_hitcount: 20
#---------------------------------------

It could be seen that there exists duplicate items: for example,
3108-3114, +, appear and be counted twice. Why so?

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn

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