Skip to content

Instantly share code, notes, and snippets.

@meren

meren/gen_primer_match_report.py

Last active June 19, 2020 23:57
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save meren/54d36c7b80e0bcb6e65bf663db5e5bf6 to your computer and use it in GitHub Desktop.
Save meren/54d36c7b80e0bcb6e65bf663db5e5bf6 to your computer and use it in GitHub Desktop.
Download ZIP
Generate a report for primer matching statistics (here you will find the Python program, two example input files (nifH gene primers and full-length nifH genes), and an example terminal output). You will need to have anvi'o installed on your system to run it. For questions: meren at uchicago.edu or tdelmont at uchicago.edu.
Raw
gen_primer_match_report.py
# run this script like this:
#
# python gen_primer_match_report.py primers.txt sequences.txt
#
# it will generate a report file called `primer_matches_report.txt`
#
# example primers file (TAB-delimited, no spaces):
#
# name pair direction sequence
# PolF P1 F TGCGAYCCSAARGCBGACTC
# PolR P1 R ATSGCCATCATYTCRCCGGA
# Ueda19F P2 F GCIWTYTAYGGIAARGGIGG
# Ueda407R P2 R AAICCRCCRCAIACIACRTC
# F2 P3 F TGYGAYCCIAAIGCIGA
# R6 P3 R GCCATCATYTCICCIGA
# IGK3 P4 F GCIWTHTAYGGIAARGGIGGIATHGGIAA
# DVV P4 R ATIGCRAAICCICCRCAIACIACRTC
# nifH1 P5 F ADNGCCATCATYTCNCC
# nifH2 P5 R TGYGAYCCNAARGCNGA
# NifH4 P6 F TTYTAYGGNAARGGNGG
# NifH3 P6 R ATRTTRTTNGCNGCRTA
#
# example sequences file:
# >HBD01_TARA_PSW_MAG_00013
# ATGAGAAAAGTAGCAATTTACGGAAAAGGCGGCATTGGAAAGTCCACCA (...)
# >HBD02_TARA_PSW_MAG_00026
# ATGAGAAAGATAGCTATTTACGGAAAAGGCGGTATCGGCAAATCCACTA (...)
# >HBD03_TARA_ION_MAG_00014
# ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGT (...)
# >HBD04_TARA_PON_MAG_00023
# ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGT (...)
# >HBD05_TARA_PSE_MAG_00116
# ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGT (...)
# >HBD06_TARA_ANW_MAG_00006
# ATGGCAATGCGTCAATGTGCAATTTACGGAAAAGGCGGCATCGGTAAGT (...)
# >HBD07_TARA_ANW_MAG_00019
# ATGGCAATGCGTCAATGTGCAATTTACGGGAAAGGCGGCATCGGTAAGT (...)
# >HBD08_TARA_PSW_MAG_00130
# ATGCGTAAGGTTGCTATCTACGGTAAAGGCGGTATCGGCAAGTCCACCA (...)
# >HBD09_TARA_PSW_MAG_00018
# ATGAGAAAAGTCGCTATCTACGGTAAAGGCGGAATCGGCAAGTCGACCA (...)
# >PSE_Id-346185
# ATGGAACGAATAGCGGTCTACGGGAAAGGGGGAATTGGGAAATCCACTT (...)
# >PSE_Id-1140575
# ATGGTAACCACACTCGAACCGGAAACGGAAAAGAAGACGGAAAAGGCAA (...)
# >PSE_Id-2620196
# ATGAAGAAATTAGCTATTTATGGCAAGGGTGGCATTGGTAAATCCACTA (...)
# >PSE_Id-3785694
# ATGTCACTTCGTCAAATCGCCTTCTACGGCAAGGGCGGCATCGGCAAGT (...)
# >PSE_Id-6292875
# ATGAAGAGGTTAGCCATATATGGCAAAGGAGGAATCGGTAAATCCACAA (...)
# >PON_Id-1645572
# ATGCGTAAGATCGCCATTTACGGAAAGGGGGGGATCGGCAAGAGCACCA (...)
# >PON_Id-3217614
# ATGCGGCGTTCGATGGCCTTTTATGGAAAAGGGGGAGTGGGTAAATCGA (...)
# >PON_Id-3596173
# ATGAGAAAGATTGCGATTTACGGTAAAGGCGGAATTGGAAAATCAACCA (...)
# >RED_Id-2330111
# ATGCATAAGATTGCGGTATATGGAAAAGGTGGAATTGGGAAATCTACGA (...)
import sys
try:
import anvio.utils as u
except:
print("Sorry, this little script requires anvi'o to be installed on your system :(")
sys.exit()
import anvio.fastalib as f
import anvio.terminal as terminal
run = terminal.Run(width=60)
primers = u.get_TAB_delimited_file_as_dictionary(sys.argv[1])
fasta = f.SequenceSource(sys.argv[2])
report = {}
# go through each sequence in the FASTA file, and find matches
while next(fasta):
report[fasta.id] = {}
fasta.close()
valid_bases = ['A', 'T', 'C', 'G']
SLC_to_nt = {'R': '[A,G]',
'Y': '[C,T]',
'M': '[A,C]',
'K': '[G,T]',
'S': '[G,C]',
'W': '[A,T]',
'H': '[A,C,T]',
'B': '[G,C,T]',
'V': '[A,C,G]',
'D': '[A,G,T]',
'N': '[A,C,G,T]',
'I': '[A,C,G,T]',
}
# expand primers by converting degenerate bases into regular expresions
for primer_name in primers:
primers[primer_name]['sequence_orig'] = primers[primer_name]['sequence']
for SLC in SLC_to_nt:
primers[primer_name]['sequence'] = primers[primer_name]['sequence'].replace(SLC, SLC_to_nt[SLC])
for primer_name in primers:
ps = primers[primer_name]['sequence']
# the following state machine goes from regex to all possible combinations
expant, pos = [''], 0
while 1:
if ps[pos] in valid_bases:
for i in range(0, len(expant)):
expant[i] += ps[pos]
pos += 1
elif ps[pos] == '.':
new_stuff = []
for i in range(0, len(expant)):
for base in valid_bases:
new_stuff.append(expant[i] + base)
expant = new_stuff
pos += 1
elif ps[pos] == '[':
start = pos
end = pos
while ps[end] != ']':
end += 1
bases = ps[start+1:end].split(',')
new_stuff = []
for i in range(0, len(expant)):
for base in bases:
new_stuff.append(expant[i] + base)
expant = new_stuff
pos = end + 1
else:
for i in range(0, len(expant)):
expant[i] += ps[pos]
pos += 1
if pos == len(ps):
break
else:
continue
fasta = f.SequenceSource(sys.argv[2])
run.warning(None, header='%s :: %s (%d combinations)' % (primer_name, primers[primer_name]['sequence_orig'], len(expant)))
while next(fasta):
hit = False
for e in expant:
index = fasta.seq.find(e)
if index > -1:
run.info(fasta.id, 'Hit for %s at %d' % (e, index), mc="green")
hit = True
break
if not hit:
for e in expant:
index = fasta.seq.find(u.rev_comp(e))
if index > -1:
run.info(fasta.id, 'Hit for %s at %d [R]' % (e, index), mc="green")
hit = True
break
if not hit:
run.info(fasta.id, 'No hit', mc="red")
report[fasta.id][primer_name] = hit
fasta.close()
u.store_dict_as_TAB_delimited_file(report, 'primer_matches_report.txt')
Raw
nifH_genes.fa
>HBD01_TARA_PSW_MAG_00013
ATGAGAAAAGTAGCAATTTACGGAAAAGGCGGCATTGGAAAGTCCACCACCACTCAGAACACTGTCGCCGGTTTGGCGGAAATGGGCCGCAAGGTCATGGTCGTCGGCTGTGATCCCAAAGCCGACTCCACCCGCCTGTTGCTCGGTGGTCTGGCTCAGAAGTCCGTTCTCGATACCCTTCGTGAAGAGGGCGAGGATGTGGAACTCGAAGATATCCGTAAGCCCGGATTCGGTGGAACCTGGTGTGTTGAGTCCGGTGGCCCGGAACCCGGTGTCGGTTGTGCCGGTCGCGGAATCATCACTTCCATCAACATGCTCGAATCCCTCGGCGCCTACGAAGAGTCCGAAGGCCTTGATTACGCCTTCTACGACGTCCTCGGTGACGTTGTCTGCGGTGGGTTTGCCATGCCGATTCGTGATGGCAAGGCCCAGGAGATCTACATCGTCTGTTCCGGCGAGATGATGGCCATGTATGCGGCCAACAACATCTGCAAAGGTATCATGAAATATGCCGAATCCGGTGGCGTCCGCCTTGGTGGTCTGATCTGTAACTCCCGTAATACCGACCGTGAAGCGGACCTGATCACCGAGCTTGCCTCTAAACTCGGCACCCAGATGATCTACTTCGTGCCCCGTGACAACGACGTCCAGCGCGCAGAGATCAACCGTAAAACCGTCATCGAATGGGATGGTTCCGTGAATCAGGCCAACGAGTACCGCGGACTGGCCAAAGCCATCGATGAAAACGAAATGTTTGTCATTCCTACCCCACTGGAAATCGAAGACCTGGAACAGCTGCTGCTGGACTACGGCATCATGGAAGCTGCCTAG
>HBD02_TARA_PSW_MAG_00026
ATGAGAAAGATAGCTATTTACGGAAAAGGCGGTATCGGCAAATCCACTACAACCCAGAACACTGTTGCAGGGCTTGTGGAGGCAGGTAAAAAAATCATGGTCGTAGGCTGTGATCCCAAAGCAGACTCCACCCGCCTCCTGCTCAACGGCCTGGCCCAGAAAACCGTCCTGGACACCTTAAGGGATGAGGGGGAGGATGTGCTGCTGGAAGATGTCAGAAAACAGGGGTACGGCGGTACCCTCTGCACCGAATCCGGTGGCCCGGAACCCGGCGTGGGTTGTGCCGGCCGCGGTATCATCACCTCCATCAACCTCCTGGAGCAGCTCGGTGCCTACTCCGAAGACCAGGAACTGGACTACGTATTCTATGACGTTCTGGGCGACGTTGTCTGCGGCGGTTTTGCCATGCCCATCCGTGAAGGAAAGGCCCAGGAAATCTATATTGTTGTTTCCGGCGAGATGATGGCCATGTATGCGGCCAACAATATCTGTAAGGGTATCGTGAAATTCGCCCAGTCCGGCGGCGTTCGCCTGGGCGGCCTGATCTGCAACTCCCGGAAGGTGGACAACGAACGGGCCATGATTGAAGTCCTTGCCCAGAAACTGGGGACCCAGATGATCCACTTCGTTCCCAGGGACAACATGGTTCAGCACGCGGAGATCAACAGGAAAACGGTTATCGATTTTGCCCCGGAACACACACAGGCCGACGAATACAGGGCACTTGCCAAAAAGATTGATGAAAACGAAATGTTTGTCATCCCCACCCCCCTTGAAATCGAAGAACTCGAGGCCCTCCTGATTGAATACGGCATCGCCGCTTAA
>HBD03_TARA_ION_MAG_00014
ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGTCCACTACCACCCAGAACCTGGTTGCTGCTCTGGCAGAATCCGGTAAAAAAGTAATGATCGTGGGTTGTGACCCAAAAGCAGACTCAACCCGTCTGATCCTGCACTCAAAAGCTCAGAACACCATCATGGAAATGGCTGCTGAAGCCGGCACCGTGGAAGATCTGGAACTGGAAGATGTACTGAAAGCCGGTTACGGCGATATCCGTTGTGTTGAATCCGGTGGTCCAGAGCCAGGCGTAGGTTGCGCTGGTCGTGGTGTTATCACCGCCATTAACTTCCTGGAAGAAGAAGGCGCATACGAAGACGATCTGGATTTCGTATTCTACGACGTACTGGGTGACGTTGTGTGTGGTGGTTTCGCGATGCCTATCCGTGAAAACAAAGCACAGGAAATTTACATCGTATGTTCCGGTGAAATGATGGCTATGTACGCAGCCAACAACATTTCCAAAGGTATTGTGAAATACGCAAACTCCGGCGGTGTTCGTCTGGCGGGTCTGATCTGTAACTCTCGTAACACTGACCGTGAAGACGAGCTGATCATGGCTCTGGCTGCCAAACTGGGCACTCAGATGATCCACTTCGTTCCACGTGACAACGTGGTACAGCGTGCAGAAATCCGTCGTATGACAGTAATCGAATACGATCCTTCTGCTAACCAGGCTGACGAATACCGTCAACTGGCTTCAAAAATTGTTGCCAACGAAAAGTTTGTGATTCCAACGCCTATCACTATGGATGAGCTGGAAGAGCTGCTGATGGAATTCGGCATCATGGACGAAGAAGACATGAGCATTGTAGGTAAAACTGCAGCTGAAGAATAA
>HBD04_TARA_PON_MAG_00023
ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGTCCACTACCACCCAGAACCTGGTTGCTGCTCTGGCAGAATCCGGTAAAAAAGTAATGATCGTGGGTTGTGACCCAAAAGCAGACTCAACCCGTCTGATCCTGCACTCAAAAGCTCAGAACACCATCATGGAAATGGCTGCTGAAGCCGGCACCGTGGAAGATCTGGAACTGGAAGATGTACTGAAAGCCGGTTACGGCGATATCCGTTGTGTTGAATCCGGTGGTCCAGAGCCAGGCGTAGGTTGCGCTGGTCGTGGTGTTATCACCGCCATTAACTTCCTGGAAGAAGAAGGCGCATACGAAGACGATCTGGATTTCGTATTCTACGACGTACTGGGTGACGTTGTGTGTGGTGGTTTCGCGATGCCTATCCGTGAAAACAAAGCACAGGAAATTTACATCGTATGTTCCGGTGAAATGATGGCTATGTACGCAGCCAACAACATTTCCAAAGGTATTGTGAAATACGCAAACTCCGGCGGTGTTCGTCTGGCGGGTCTGATCTGTAACTCTCGTAACACTGACCGTGAAGACGAGCTGATCATGGCTCTGGCTGCCAAACTGGGCACTCAGATGATCCACTTCGTTCCACGTGACAACGTGGTACAGCGTGCAGAAATCCGTCGTATGACAGTAATCGAATACGATCCTTCTGCTAACCAGGCTGACGAATACCGTCAACTGGCTTCAAAAATTGTTGCCAACGAAAAGTTTGTGATTCCAACGCCTATCACTATGGATGAGCTGGAAGAGCTGCTGATGGAATTCGGCATCATGGACGAAGAAGACATGAGCATTGTAGGTAAAACTGCAGCTGAAGAATAA
>HBD05_TARA_PSE_MAG_00116
ATGGCTATGCGTCAATGCGCCATTTATGGCAAAGGCGGTATCGGTAAGTCTACCACCACTCAGAACCTGGTGGCTGCTCTGGCAGAAGCCGGTAAAAAAGTAATGATCGTGGGTTGTGACCCGAAAGCAGACTCAACCCGTCTGATCCTGCACTCAAAAGCTCAGAACACCATCATGGAAATGGCTGCAGAAGCCGGCACCGTGGAAGATCTGGAACTGGAAGATGTACTGAAAACCGGTTACGGCGATATCCGTTGTGTTGAATCCGGTGGTCCTGAGCCAGGTGTTGGTTGTGCAGGTCGTGGTGTAATCACTGCGATCAACTTCCTCGAAGAGGAAGGTGCCTACGAAGACGATATCGATTTCGTTTTCTACGACGTACTGGGTGACGTTGTGTGTGGTGGTTTCGCGATGCCTATCCGTGAAAACAAAGCACAGGAAATTTACATCGTATGTTCTGGTGAAATGATGGCTATGTATGCAGCCAACAACATTTCCAAAGGTATTGTGAAATACGCCAACTCAGGCGGTGTACGTCTGGCAGGTCTGATCTGTAACTCACGTAACACTGACCGTGAAGACGAGCTGATCGAAGCACTGGCTGCCAAACTGGGCACCCAGATGATTCACTTCGTTCCTCGTGACAACGTGGTACAGCGTGCAGAGATCCGTCGTATGACCTGTATTGAGTACGATCCTTCTGCTAACCAGTCCGATGAATACCGTCAACTGGCTCAGAAAATCATCGATAACAAGAAGTTGGTTATCCCAACTCCCTGCACCATGGATGAACTGGAAGAGCTGCTGATGGAATTCGGCATCATGGACGAAGAAGATATGAGCGTTGTAGGTAAAACTGCCGCTGAACTGGAAGGCTGA
>HBD06_TARA_ANW_MAG_00006
ATGGCAATGCGTCAATGTGCAATTTACGGAAAAGGCGGCATCGGTAAGTCAACGACTACTCAGAACCTGGTTGCTGCCCTGGCAGAAGCGGGTAAGAAAGTAATGATCGTGGGCTGTGATCCTAAAGCAGACTCCACTCGTCTGATTCTTCACTCCAAAGCACAGAACACCATCATGGAAATGGCTGCTGAAGCCGGCACCGTGGAAGATCTGGAACTGGAAGATGTATTAAAAGCCGGTTACGGCGACATCCGCTGTGTTGAATCCGGTGGCCCGGAGCCAGGTGTTGGATGTGCCGGTCGCGGTGTAATCACTGCAATCAACTTCCTGGAAGAGGAAGGTGCATATGAAGATGACCTGGACTTCGTATTCTACGATGTACTGGGTGATGTTGTATGCGGTGGCTTTGCTATGCCGATCCGTGAAAACAAAGCGCAGGAAATCTACATTGTGGTATCCGGCGAAATGATGGCGATGTATGCCGCCAATAACATTTCCAAGGGTATCGTGAAATACGCCAATTCCGGCGGTGTTCGTCTGGCTGGCCTGATCTGTAACTCACGTAACACAGATCGTGAAGACGAGCTGATCGAAGCTCTGGCTGCCAAGCTCGGCACTCAGATGATCCACTTCATCCCACGAGACAATGTTGTACAGCGTGCTGAGATTCGCCGTATGACCGTCATCGAGTATGACCCTAACGCCGGTCAGGCCGATGAGTATCGTGCTCTTGCCAACAAAATCATCAACAACGAAAAGCTGGTCATTCCAGAGCCTTGCACCATGGATGAGCTGGAAGAGTTGCTGATGGAATTCGGCATCATGGATGAAGAAGACCTGAGCATCGTAGGTAAAACTGCGGCTGACGAAGCCTAA
>HBD07_TARA_ANW_MAG_00019
ATGGCAATGCGTCAATGTGCAATTTACGGGAAAGGCGGCATCGGTAAGTCAACCACCACTCAGAATCTGGTGGCTGCTCTGGCGGAAGCTGGCAAAAAAGTGATGATCGTGGGCTGCGATCCCAAGGCGGACTCCACTCGACTGATTCTTCACTCCAAAGCGCAAAACACCATCATGGAAATGGCTGCCGAAGCCGGTACCGTGGAAGACCTGGAGCTGGAAGATGTGTTGAAAGCCGGTTACGGCGACATTCGCTGTGTAGAGTCTGGTGGTCCGGAGCCGGGCGTAGGCTGCGCCGGTCGCGGTGTTATCACTGCCATTAACTTCCTGGAAGAGGAAGGTGCCTACGAGGAAGACCTGGACTTCGTATTCTATGACGTACTGGGCGACGTGGTGTGTGGTGGTTTTGCCATGCCTATCCGCGAAAACAAAGCTCAGGAAATCTACATCGTGGTATCCGGAGAAATGATGGCCATGTATGCGGCCAACAACATTTCCAAGGGTATCGTGAAGTACGCCAACTCCGGCGGTGTGCGTCTGGCTGGTCTGATCTGTAACTCTCGTAATACCGACCGTGAAGACGAACTGATCGAAGCCCTGGCTGCCAAGCTGGGAACCCAGATGGTCCACTTCATCCCCCGTGACAATGTGGTTCAGCGTGCGGAAATCCGTCGTATGACCGTCATTGAATACGATCCCGCAGCCAAGCAGGCTGATGAGTATCGCACTCTGGCTCAAAAGGTTATCGATAACGAAAAACTGGTAATCCCTGAGCCCTGCACCATGGATGAGCTGGAAGAGCTGCTGATGGAATTCGGCATCATGGAAGAAGAAGATATGAGTATCGTAGGTAAAACCGCTGCTGACGAGGCTGTTGCCTAA
>HBD08_TARA_PSW_MAG_00130
ATGCGTAAGGTTGCTATCTACGGTAAAGGCGGTATCGGCAAGTCCACCACCACACAGAACACAGTTGCTGCTCTGGCAGAAATGGGCAAGAAGGTCATGGTCGTCGGTTGCGACCCCAAGGCTGACTCCACCCGCTTGCTGCTGGGCGGCTTGGCTCAGAAGTCGGTGCTTGACACCATTCGTGATGAAGGTGAAGACATCGAACTTGACGACATCCGTCGCGACGGCTTCGGCAGCTGCAAGTGCGTCGAATCCGGTGGCCCGGAACCCGGCGTCGGTTGTGCAGGTCGTGGGATCATCACCTCGATCAACATGCTCGAACAACTCGGTGCCTACGATGAGTCCGAGGAATTGGACTACGCGTTTTACGACGTGCTCGGCGACGTGGTGTGCGGCGGTTTCGCCATGCCCATCCGTCAGGGTAAAGCCCAGGAAATTTACATCGTCTGCTCCGGTGAAATGATGGCCATGTATGCTGCCAACAACATCTGCAAAGGCATCATGAAATTTGCCGAGTCCGGCGGCGTGCGTCTTGGTGGTCTGATCTGTAACAGCCGTAACGTCGACAATGAATCGGAAATGATTCAGGAATTCGCCAAGCGTCTGGGCACCCAGATGATTCACTTCGTGCCCCGTGACAATGACGTGCAGCGTGCGGAAATCCGCAAGATGACCGTCATCGACTGGAACCCCGAAGCACCCCAGGCTGACGAATATCGCACCCTGGCCCGCAACATCGACAACAACGAACTGTTCGTCATTCCCAAGCCGCTGGAAATCGAAGAACTCGAAAGCCTGCTGCTTGAATACGGTCTGCTCGAAGCAGCGTAA
>HBD09_TARA_PSW_MAG_00018
ATGAGAAAAGTCGCTATCTACGGTAAAGGCGGAATCGGCAAGTCGACCACCACACAAAACACAGTCGCTGCACTGGCGGAGATGGGTAAGAAGGTTTTGGTCGTCGGTTGCGACCCCAAGGCCGACTCCACCCGTTTGCTTCTGGGCGGTCTGTCACAGAAGTCCGTGCTGGATACCATTCGTGATGAAGGTGAAGACATTGAACTTGAAGACATCCGCCGCGGTGGGTTTGGCAGTTGCCAATGCGTTGAGTCCGGTGGCCCAGAACCTGGGGTAGGCTGTGCAGGCCGCGGGATCATCACCTCGATTAACATGCTCGAACAACTCGGTGCCTATGAAGAATCCGAAGAACTCGACTACGCATTTTATGACGTGCTCGGCGACGTGGTCTGTGGCGGTTTCGCCATGCCGATTCGTCAAGGTAAAGCCCAGGAAATTTACATCGTCTGTTCCGGTGAAATGATGGCCATGTATGCAGCCAACAACATCTGCAAAGGCATCATGAAATTCGCAGAGTCCGGCGGTGTGCGACTGGGCGGCCTGATCTGCAACAGCCGTAACGTCGACAACGAAAAAGAAATGATCGAAGAATTCGCCAAACGCCTGGGCACGAAAATGGTTCACTTCGTTCCCCGAGACAATGACGTGCAGCGTGCGGAAATCCGCAAGAAAACCGTCATCGAATGGAACCCCGAAGCGCCCCAGGCCAACGAATACCGTGCCTTGGCTCGGAACATCGACAACAACGAAATGTTCGTCGTGCCCAAGCCCATGGAAATCGAAGAACTCGAAAGCCTGCTCATGGAATTCGGTCTGCTCGAAGCCGTAGGCTAA
>PSE_Id-346185
ATGGAACGAATAGCGGTCTACGGGAAAGGGGGAATTGGGAAATCCACTTTCGCCACCAGCGCATCCCTGGTTTTGTCACGCATGGGCAAGCGCGTGCTCCACGTGGGCTGCGACCCCAAACACGACAGCAGCGTGGTCTTGGTTCAAGACCCGTCTCGCTTCCGTACCGTCATGAACAAAGTGTTCGCCGGTGAGGAAGTCTTCGACCCCGAAGACATCATCATGCCCGGTATCGAAGGCATCGACTGCGTCGAATCCGGTGGCCCCGACGCTGGCCGCGGCTGTGGCGGACGCGCCGTCTCTCGCTCATTCGAAGTCTTCGAAGACGTGGAACTGGTCGACGCCGAAAACTACGACGCCGTCATCTACGACGTTCTGGGCGACGTGGTGTGTGGCGGTTTTGCCGCTCCCATGCGTAAATCATCTCGGTCAAAAGTGGTTATCGTCCTCTCCGAAGAACTCATGGCCGCCTACGCTGCCAACCGGATTGCAGCAGCCGTCTCTGAGTTTCACTCCAACGACGTTCGCCTCGCTGGCTTTGTGATCAACCTCAAAAGCAACCAGGCTGACATCCGGCCCATCCAGCGCTTCGCCGAAGCCATCGGCACCCGAATCTTGGGTGTACTCCCTCGCGACCCACTGGTCTGCGAAGCCGAAATGTACCGCCAATGCATCGTGCAATACGCACCGGAAAGCCCGGTCGCCGTGGGTATACAAGCCGTTATCGAAGCCGTGGTTGCCTTGGACCGCACCACGCTCGACGCCCCCAAAGCCCTGCTCGAACAAGACCTGCGACAAATCATGCGCGGCATCACGGCCGAAGAACCGCTACCCAGCCCGCCTCCCATCGAGGCGCGCATCAGTAAAATCACCGAGTGGTCTCAAGTCGGCTGA
>PSE_Id-1140575
ATGGTAACCACACTCGAACCGGAAACGGAAAAGAAGACGGAAAAGGCAATGCGCAAAGTTGCAATCTACGGCAAGGGCGGCATTGGAAAATCCACCACTACACAGAACACGGTCGCTGCCCTGGCAGAGATGGGCAAGAAGGTCATGGTCGTCGGTTGCGACCCCAAGGCCGACTCGACTCGCCTCCTGCTCGGCGGTCTCGCCCAGCGCTCGGTTCTCGACACCCTTCGCGAAGAAGGTGAGGACGTCGAACTCGAAGACATCCGCAGCGGTGGCTTCTGCAACAGCCTCTGCGTGGAGTCCGGCGGTCCCGAGCCCGGCGTTGGTTGTGCCGGTCGCGGTATCATCACTTCCATTAACATGCTCGAGCAGCTCGGCGCTTATGAAGAAGAGCAGGAGCTCGACTACGTCTTCTACGACGTGCTCGGTGACGTGGTCTGCGGCGGCTTCGCCATGCCGATCCGCGAAGGCAAGGCCGAAGAAATCTACATCGTCTGCTCTGGCGAAATGATGGCCATGTACGCCGCCAACAACATCTGCAAGGGTATCCTCAAATTCGCTGAAACTGGTGTCGTCCGCCTCGGCGGCCTCATCTGCAACAGCCGTAACTGCGACCGCGAGGCCGAGATGATCGAGGAGTTCGCCAAGCGCCTGGGTACGCAAATGATCCACTTCGTGCCGCGCGACAACGACGTCCAGCGCGCCGAGATCAACCGCAAGACGGTCATCGACTGGAACCCGGACTGCAAGCAGGCCAATGAGTACCGCACCCTGGCCAAGAACATCGATGCCAACGAACTGAAGGTTATACCGAAGCCGCTCTCCATCGACGAACTCGAGCAGCTCCTCATGGACTACGGTCTGTTCCAGTAA
>PSE_Id-2620196
ATGAAGAAATTAGCTATTTATGGCAAGGGTGGCATTGGTAAATCCACTACGGTTAGCAATTTGTCTGCCGCCTATGCCACATTAGGATACAAGGTGATGCAAATCGGTTGTGATCCAAAAGCCGATTCAACGACAAACCTGACCAAGGGTATTCCTTGTTCCACAGTGCTGGATGTTTTAAGAGAAGATGACGATGCAGAGCTTGAAGATATTGTTACAGTTGGGGATTTAGGCGTCCTATGTGTAGAAGCAGGAGGACCGCTGCCGGGTGTAGGCTGTGCAGGAAGGGGCATAATTACGGCCTTTGAAACATTAGAGGAGCTTGGTGCTTATGAAGCTTATGAGCCAGATATTATTCTCTATGATGTACTAGGTGATGTGGTTTGCGGTGGTTTTGCTATGCCATTACGTGGCGGTTATGCAGACGAGGTTTGTATCGTTACATCTGGAGAGATGATGTCCCTCTACGCAGCTTCCAACATATCAACAGCGGTTAACAACTTCAAAAGAAAGGGATATGCAAAATTAAGAGGACTAATACTCAACAAGAAAAATATAGAGGATGAAGAAATACTTGTTGAAAAAGCAGCTAAAGAGATAGGAACAAATGTATTATACACCCTTGATAGATGCCCATTGGTTCAAAAAGCCGAAAGCCAGGGCAAGACAGTTGTAAGTGCATTTCCTGACAGTAGCATGGCTAAGGCTTATTTGGATTTAGCACAGCTTTTAATTACGGATAATGAGGTTATGACATGA
>PSE_Id-3785694
ATGTCACTTCGTCAAATCGCCTTCTACGGCAAGGGCGGCATCGGCAAGTCCACCACCTCGCAGAATACCCTCGCCGCGCTCGCCGACCTCGGCCAGCGCATCCTCATCGTCGGCTGCGATCCCAAGGCCGACTCCACCCGCCTGATGCTGCACGCCAAGGCCCAGGACACCATCCTTTCGCTCGCCGCCGAAGCCGGCTCGGTCGAGGACCTCGAGCTCGAGGACGTGATGAAGATCGGCTACAAGGACATCCGCTGCGTTGAATCGGGCGGTCCCGAGCCGGGCGTCGGCTGCGCCGGTCGCGGTGTTATCACCTCGATCAACTTCCTGGAGGAAGAAGGCGCCTACGACGACATTGACTACGTCTCCTACGACGTGCTCGGCGACGTCGTCTGCGGCGGCTTCGCGATGCCGATCCGCGAGAACAAGGCTCAGGAAATCTACATCGTCATGTCGGGCGAGATGATGGCCATGTACGCGGCCAACAACATCTCCAAGGGCATTCTCAAGTATGCCAATTCCGGCGGCGTGCGCCTGGGCGGCCTCATCTGCAACGAGCGCCAGACCGACAAGGAACTGGAACTGGCAGAATCGCTCGCCGGCAAGCTGGGCACCTCGCTCATCCACTTCGTGCCGCGCGACAACATCGTGCAGCATGCCGAGCTGCGCCGCATGACGGTGATCGAATATGCGCCTGAAAGCAACCAGGCCAACGAGTACCGCGAGCTGGCCCAGAAGATCCACAACAACTCGGGCAACGGCATCATCCCGACCCCGATCACGATGGACGAACTGGAAGACCTGCTCATGGAGCACGGCATCATGTCGGCCGTCGATGAAAACCAGGTCGGCAAGGCTGCCGAAGTCGCCTGA
>PSE_Id-6292875
ATGAAGAGGTTAGCCATATATGGCAAAGGAGGAATCGGTAAATCCACAACTGTTTCTAACCTATCAGTGGCGTTGACAAAATGTGGATATAGGGTTATGCAAATAGGCTGCGATCCGAAAGCAGATTCAACAAAGAATTTAACAAATGGTATAGGTATAACCACAGTGCTTGATGCATTAAAGGATGGTAAGGAATCCTTAGAGGATTTTGTTGTTATAAGCGATACAGGAGTTATATGTGTAGAAGCTGGAGGGCCTATACCTGGTGTTGGGTGTGCCGGTAGAGGTATAATAAGCGCTTTTGAAAAGCTTGATGAGTTAGATGCCTATTCTATATACAAGCCTGATATAGTGTTATATGACGTATTAGGTGATGTGGTTTGTGGTGGATTTGCCATGCCGCTGAGAGGTGGATATGCTGATGAGGTATGTATAGTAACATCCGGTGAGATGATGTCACTATATGCAGCTTCAAACATAGCAAGTGCCGTAAGGAACTTTAAGAATAAGGGATATGCACGACTAAAGGGTCTAATACAAAATAGTAAAAACATAGATAACGAGGATTATCTAGTCGACAAGCTAGCCGATGAAGAAAGTACATCTGTCATTTACAGATTACCTAGAAATCCTATTGTACAAAAGGCTGAAGAGTTCGGAAAGACCGTAGTTGAGATGTATCCAGATTCAGAGATGAGCAAAAACTATATAGCTTTAGCA
>PON_Id-1645572
ATGCGTAAGATCGCCATTTACGGAAAGGGGGGGATCGGCAAGAGCACCATCGCCACTCACCTGGCCGCGGCTTGGGGACAACAGGGGTTGAGAGTGATGTTGGTAGGTTGCGACCCGAAGGCTGACAGCACCGCACCGCTCTTGGGGCGCCGGAGTCCGATTTTGTTAGACGATTACGAGCATATCGTGTCTGATCTTGACACGAATGGCAAGCTGTCAGCCCTGGAGCGCGTCATTGGAGTGGGGTACGCCGGGGTGAGGTGCGTTGAGATCGGCGGCCCCAAGCCAGGCGTGGGTTGTGCCGGCCGAGGCATTAGCCTAGCGCTAGAGTTATTGCAGAAGTTAGGGGCTTTCGAGGCGCTGGATTGCGTTATCTACGACATCCTGGGCGACGTCGTGTGTGGCGGCTTCGCGATGCCGATGCGAATGGGGTTCGCCGAGGAAGTGTACATTGTCACGTCAGGCGAATACGCGGCCCTGTATGCTGCCAACAACATCTGCAAAGGCATTTGTAATATGGGCGCCAAACTCGGCGGAATCATCGGCAACTGCCGGGAACTGCCCGGCGAAGAAAGGCTGATATCCGAGTTTGTCCAGGCGCTCAGCAGTCGCTTAATTGCCTTCGTTCCTCGGTCGCCGGAGTTTCCTCGCTGTGAGCTGCTGCGCAAAACTGTGCTCGAGGTTGTGCCAGAATCTCCGCAGGCGGAGATTGTCAGGTGTTTGAGCCGGGTTATTCTGGACAACTCCCAATTCTCGCAGCTCTCCCCGCTGTCTGAGCAGGATCTGGAAGGCCTAGCCAAGACTCATCTGCTCACCCAGACCCAGGCTCACGATGTAGCTTTGGAGCTCACCCCCTGA
>PON_Id-3217614
ATGCGGCGTTCGATGGCCTTTTATGGAAAAGGGGGAGTGGGTAAATCGACTGTTGTGTCGAATTTGACCACAGCGCTCGCCCATATGGGCCGTCAAGTGTTGCAGGTCGGCTGCGATCCCAAGCGAGACTCAAGCCGCAATCTTGTCAAAGTCTTCCCACCCATCACCTTGATGGAACTGCTTGCCGAAGGTCGAAAAGATCTGGTCCCTGAAGACATCGTCATGGATGGCGGCACCAACATCGACTGCATCGAAGTTGGTGGCCCTAAACCAGGAGTCGGCTGTGCGGGGCGTGGACTTGGGCGTCTTTTCGAAGAGCTTGAGGACATGGAGTTGCTCGAACGCGACTACGACTATGTCTTCTACGACGTGCTCGGTGATGTCGTTTGTGGTGGCTTCGCGGTGCCAATGCGATCAGGCTACGCCGAAGAGGTGTATGTGGTGACCTCTGGCGAGTTCATGAGTCTGTACGCAGCGAACAACATCGCCCGCGGAATCCAAAACTACGCGGAAGATGGTGACGTTCGTATGGGCGGGCTGATCGCCAACGTCAAAGACTTAGAGTACGACAAGCCCTTGATCGAAGCCTTCGCCAAACGAATCGGCACCCACGTGGTGTCGTACTTGGAGTGGAATAAGGTCGTTTATGACGCCGAGCGGCGCCGAACGACTGTGTTGCGACACGCGCCAGAGCACCCCTTCGCCCAACGCTGGTTAGACCTCGCGAAGAATCTTGAGCAGACTCCTCGGCCTCACATCCCGACGCCTATGGCCGACGCCGAACTCGATGTGTTCCTCGAGGAACTCTTTGGATTTAGTGATGCGCCAGCGGCAATAGGCTGTGATGTGTCAGATGCGCCAAAGACCCTGAGTCTGCAGCGTCACTGA
>PON_Id-3596173
ATGAGAAAGATTGCGATTTACGGTAAAGGCGGAATTGGAAAATCAACCACAACACAGAACACGGTTGCCGGTCTCGCTGAAATGGGTAAAAAAGTAATGGTAGTTGGATGTGACCCGAAAGCTGACTCAACCCGTCTGCTTCTGGGTGGTCTGGCACAGAAGACCGTTCTCGACACTCTTCGTGAAGAAGGTGAAGACGTAGAGATTGATGACGTAATCAAACCGGGATACGGCGGCACTCGCTGCGTTGAGTCCGGTGGTCCGGAACCTGGTGTTGGTTGTGCCGGTCGCGGTATCATTACTTCGATCACTCTGTTGGAACAGCTGGGTGCTTATGATGACGAATGGGAACTGGATTACGCTTTCTACGACGTACTTGGTGACGTTGTTTGTGGTGGATTCGCGATGCCTATCCGTGATGGTAAAGCTCAGGAAATCTACATTGTTGTATCCGGCGAAATGATGGCCATGTACGCAGCCAACAACATCTGTAAAGGTATTGTAAAATACGCTGATACCGGTGGTGTTCGTCTCGGTGGTCTGATCTGTAACAGCCGTAAAGTTGACAACGAACGTGAAATGATCGAAGAGCTG
>RED_Id-2330111
ATGCATAAGATTGCGGTATATGGAAAAGGTGGAATTGGGAAATCTACGATTTCATCGCATCTGAGTGCTGTATTTGCAGAAAAGAACTTGAAGGTCTTGCATGTTGGGTGTGATCCGAAACATGACTCAACCATGCGGATTGCCCCAAAGGACGGTGTTCCTACGGTGATCCAGATGCTGAGGGAGAACCCCGGCTGGCTTCGTTCCCGGGCTTTTGTCCAGAAAGGCCGTTTTGGAATTGACCTGGTAGAATGTGGTGGTCCCGAGCCCGGAGCCGGTTGTGGCGGACGTGGTGTGGCCAAGATGTTTGAAATGTTTACGAGCATACGCCTGCTTGAACGAGGGGACTGGGACGTCTCTCTTTTCGATGTTCTTGGTGATGTTGTCTGCGGTGGATTTGCCGCACCCATGCGTCAAGGCTTTGCGGAGAAGGCCTATATCGTATGTTCGGAAGAGTTGATGGCCATGTATGCTGCCAACAACGTCGTGAAGGCGATAACCACCAACGCTGGTAACGGCGTGACGCTCGGTGGAATCATCGCCAATACACGGGATAACGAGAATGGTGGAGAGATACTTCGACTCTTCGCAGAAGCCCTGGGAACACAGGTTGTTGAGTATATACCTCGATCTCCGATCATCCTTGAGGCGGAAGGAGAGATGAAGACGGTAGTGGAATATGATCCGACGGCTCCCATCGTCGATGTCTTCCGTAGTCTGGCAGATAAGATTCTGGCGTACGATCCGAGTGCGGCCTCATTACCCACACCTCTTGAGGATCGTGAATTTAACGACTTTACGGTCGACGCCTTCCGTAAAACGGCATAG
Raw
output.txt
$ python gen_primer_match_report.py primers.txt nifH_genes.fa
PolF (24 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: No hit
HBD02_TARA_PSW_MAG_00026 .....................: No hit
HBD03_TARA_ION_MAG_00014 .....................: No hit
HBD04_TARA_PON_MAG_00023 .....................: No hit
HBD05_TARA_PSE_MAG_00116 .....................: No hit
HBD06_TARA_ANW_MAG_00006 .....................: No hit
HBD07_TARA_ANW_MAG_00019 .....................: Hit for TGCGATCCCAAGGCGGACTC at 114
HBD08_TARA_PSW_MAG_00130 .....................: Hit for TGCGACCCCAAGGCTGACTC at 108
HBD09_TARA_PSW_MAG_00018 .....................: Hit for TGCGACCCCAAGGCCGACTC at 108
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for TGCGACCCCAAGGCCGACTC at 156
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: Hit for TGCGATCCCAAGGCCGACTC at 114
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: No hit
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: No hit
RED_Id-2330111 ...............................: No hit
PolR (8 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for ATGGCCATCATCTCGCCGGA at 450 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for ATGGCCATCATCTCGCCGGA at 450 [R]
HBD03_TARA_ION_MAG_00014 .....................: No hit
HBD04_TARA_PON_MAG_00023 .....................: No hit
HBD05_TARA_PSE_MAG_00116 .....................: No hit
HBD06_TARA_ANW_MAG_00006 .....................: Hit for ATCGCCATCATTTCGCCGGA at 456 [R]
HBD07_TARA_ANW_MAG_00019 .....................: No hit
HBD08_TARA_PSW_MAG_00130 .....................: Hit for ATGGCCATCATTTCACCGGA at 450 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for ATGGCCATCATTTCACCGGA at 450 [R]
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: No hit
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: No hit
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: No hit
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for ATGGCCATCATTTCGCCGGA at 450 [R]
RED_Id-2330111 ...............................: No hit
Ueda19F (1024 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for GCAATTTACGGAAAAGGCGG at 12
HBD02_TARA_PSW_MAG_00026 .....................: Hit for GCTATTTACGGAAAAGGCGG at 12
HBD03_TARA_ION_MAG_00014 .....................: Hit for GCCATTTATGGCAAAGGCGG at 18
HBD04_TARA_PON_MAG_00023 .....................: Hit for GCCATTTATGGCAAAGGCGG at 18
HBD05_TARA_PSE_MAG_00116 .....................: Hit for GCCATTTATGGCAAAGGCGG at 18
HBD06_TARA_ANW_MAG_00006 .....................: Hit for GCAATTTACGGAAAAGGCGG at 18
HBD07_TARA_ANW_MAG_00019 .....................: Hit for GCAATTTACGGGAAAGGCGG at 18
HBD08_TARA_PSW_MAG_00130 .....................: Hit for GCTATCTACGGTAAAGGCGG at 12
HBD09_TARA_PSW_MAG_00018 .....................: Hit for GCTATCTACGGTAAAGGCGG at 12
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for GCAATCTACGGCAAGGGCGG at 60
PSE_Id-2620196 ...............................: Hit for GCTATTTATGGCAAGGGTGG at 12
PSE_Id-3785694 ...............................: Hit for GCCTTCTACGGCAAGGGCGG at 18
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: Hit for GCCATTTACGGAAAGGGGGG at 12
PON_Id-3217614 ...............................: Hit for GCCTTTTATGGAAAAGGGGG at 15
PON_Id-3596173 ...............................: Hit for GCGATTTACGGTAAAGGCGG at 12
RED_Id-2330111 ...............................: No hit
Ueda407R (512 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for AACCCACCGCAGACAACGTC at 381 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for AAACCGCCGCAGACAACGTC at 381 [R]
HBD03_TARA_ION_MAG_00014 .....................: Hit for AAACCACCACACACAACGTC at 387 [R]
HBD04_TARA_PON_MAG_00023 .....................: Hit for AAACCACCACACACAACGTC at 387 [R]
HBD05_TARA_PSE_MAG_00116 .....................: Hit for AAACCACCACACACAACGTC at 387 [R]
HBD06_TARA_ANW_MAG_00006 .....................: Hit for AAGCCACCGCATACAACATC at 387 [R]
HBD07_TARA_ANW_MAG_00019 .....................: Hit for AAACCACCACACACCACGTC at 387 [R]
HBD08_TARA_PSW_MAG_00130 .....................: Hit for AAACCGCCGCACACCACGTC at 381 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for AAACCGCCACAGACCACGTC at 381 [R]
PSE_Id-346185 ................................: Hit for AAACCGCCACACACCACGTC at 381 [R]
PSE_Id-1140575 ...............................: Hit for AAGCCGCCGCAGACCACGTC at 429 [R]
PSE_Id-2620196 ...............................: Hit for AAACCACCGCAAACCACATC at 375 [R]
PSE_Id-3785694 ...............................: Hit for AAGCCGCCGCAGACGACGTC at 384 [R]
PSE_Id-6292875 ...............................: Hit for AATCCACCACAAACCACATC at 372 [R]
PON_Id-1645572 ...............................: Hit for AAGCCGCCACACACGACGTC at 390 [R]
PON_Id-3217614 ...............................: Hit for AAGCCACCACAAACGACATC at 378 [R]
PON_Id-3596173 ...............................: Hit for AATCCACCACAAACAACGTC at 381 [R]
RED_Id-2330111 ...............................: Hit for AATCCACCGCAGACAACATC at 378 [R]
F2 (256 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for TGTGATCCCAAAGCCGA at 108
HBD02_TARA_PSW_MAG_00026 .....................: Hit for TGTGATCCCAAAGCAGA at 108
HBD03_TARA_ION_MAG_00014 .....................: Hit for TGTGACCCAAAAGCAGA at 114
HBD04_TARA_PON_MAG_00023 .....................: Hit for TGTGACCCAAAAGCAGA at 114
HBD05_TARA_PSE_MAG_00116 .....................: Hit for TGTGACCCGAAAGCAGA at 114
HBD06_TARA_ANW_MAG_00006 .....................: Hit for TGTGATCCTAAAGCAGA at 114
HBD07_TARA_ANW_MAG_00019 .....................: Hit for TGCGATCCCAAGGCGGA at 114
HBD08_TARA_PSW_MAG_00130 .....................: Hit for TGCGACCCCAAGGCTGA at 108
HBD09_TARA_PSW_MAG_00018 .....................: Hit for TGCGACCCCAAGGCCGA at 108
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for TGCGACCCCAAGGCCGA at 156
PSE_Id-2620196 ...............................: Hit for TGTGATCCAAAAGCCGA at 108
PSE_Id-3785694 ...............................: Hit for TGCGATCCCAAGGCCGA at 114
PSE_Id-6292875 ...............................: Hit for TGCGATCCGAAAGCAGA at 108
PON_Id-1645572 ...............................: Hit for TGCGACCCGAAGGCTGA at 108
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for TGTGACCCGAAAGCTGA at 108
RED_Id-2330111 ...............................: No hit
R6 (32 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for GCCATCATCTCGCCGGA at 450 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for GCCATCATCTCGCCGGA at 450 [R]
HBD03_TARA_ION_MAG_00014 .....................: Hit for GCCATCATTTCACCGGA at 456 [R]
HBD04_TARA_PON_MAG_00023 .....................: Hit for GCCATCATTTCACCGGA at 456 [R]
HBD05_TARA_PSE_MAG_00116 .....................: Hit for GCCATCATTTCACCAGA at 456 [R]
HBD06_TARA_ANW_MAG_00006 .....................: Hit for GCCATCATTTCGCCGGA at 456 [R]
HBD07_TARA_ANW_MAG_00019 .....................: Hit for GCCATCATTTCTCCGGA at 456 [R]
HBD08_TARA_PSW_MAG_00130 .....................: Hit for GCCATCATTTCACCGGA at 450 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for GCCATCATTTCACCGGA at 450 [R]
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for GCCATCATTTCGCCAGA at 498 [R]
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: Hit for GCCATCATCTCGCCCGA at 453 [R]
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: No hit
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for GCCATCATTTCGCCGGA at 450 [R]
RED_Id-2330111 ...............................: No hit
IGK3 (73728 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for GCAATTTACGGAAAAGGCGGCATTGGAAA at 12
HBD02_TARA_PSW_MAG_00026 .....................: Hit for GCTATTTACGGAAAAGGCGGTATCGGCAA at 12
HBD03_TARA_ION_MAG_00014 .....................: Hit for GCCATTTATGGCAAAGGCGGTATCGGTAA at 18
HBD04_TARA_PON_MAG_00023 .....................: Hit for GCCATTTATGGCAAAGGCGGTATCGGTAA at 18
HBD05_TARA_PSE_MAG_00116 .....................: Hit for GCCATTTATGGCAAAGGCGGTATCGGTAA at 18
HBD06_TARA_ANW_MAG_00006 .....................: Hit for GCAATTTACGGAAAAGGCGGCATCGGTAA at 18
HBD07_TARA_ANW_MAG_00019 .....................: Hit for GCAATTTACGGGAAAGGCGGCATCGGTAA at 18
HBD08_TARA_PSW_MAG_00130 .....................: Hit for GCTATCTACGGTAAAGGCGGTATCGGCAA at 12
HBD09_TARA_PSW_MAG_00018 .....................: Hit for GCTATCTACGGTAAAGGCGGAATCGGCAA at 12
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for GCAATCTACGGCAAGGGCGGCATTGGAAA at 60
PSE_Id-2620196 ...............................: Hit for GCTATTTATGGCAAGGGTGGCATTGGTAA at 12
PSE_Id-3785694 ...............................: Hit for GCCTTCTACGGCAAGGGCGGCATCGGCAA at 18
PSE_Id-6292875 ...............................: Hit for GCCATATATGGCAAAGGAGGAATCGGTAA at 12
PON_Id-1645572 ...............................: Hit for GCCATTTACGGAAAGGGGGGGATCGGCAA at 12
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for GCGATTTACGGTAAAGGCGGAATTGGAAA at 12
RED_Id-2330111 ...............................: No hit
DVV (8192 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for ATGGCAAACCCACCGCAGACAACGTC at 381 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for ATGGCAAAACCGCCGCAGACAACGTC at 381 [R]
HBD03_TARA_ION_MAG_00014 .....................: Hit for ATCGCGAAACCACCACACACAACGTC at 387 [R]
HBD04_TARA_PON_MAG_00023 .....................: Hit for ATCGCGAAACCACCACACACAACGTC at 387 [R]
HBD05_TARA_PSE_MAG_00116 .....................: Hit for ATCGCGAAACCACCACACACAACGTC at 387 [R]
HBD06_TARA_ANW_MAG_00006 .....................: Hit for ATAGCAAAGCCACCGCATACAACATC at 387 [R]
HBD07_TARA_ANW_MAG_00019 .....................: Hit for ATGGCAAAACCACCACACACCACGTC at 387 [R]
HBD08_TARA_PSW_MAG_00130 .....................: Hit for ATGGCGAAACCGCCGCACACCACGTC at 381 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for ATGGCGAAACCGCCACAGACCACGTC at 381 [R]
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for ATGGCGAAGCCGCCGCAGACCACGTC at 429 [R]
PSE_Id-2620196 ...............................: Hit for ATAGCAAAACCACCGCAAACCACATC at 375 [R]
PSE_Id-3785694 ...............................: Hit for ATCGCGAAGCCGCCGCAGACGACGTC at 384 [R]
PSE_Id-6292875 ...............................: Hit for ATGGCAAATCCACCACAAACCACATC at 372 [R]
PON_Id-1645572 ...............................: Hit for ATCGCGAAGCCGCCACACACGACGTC at 390 [R]
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for ATCGCGAATCCACCACAAACAACGTC at 381 [R]
RED_Id-2330111 ...............................: No hit
nifH1 (96 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for ATGGCCATCATCTCGCC at 453 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for ATGGCCATCATCTCGCC at 453 [R]
HBD03_TARA_ION_MAG_00014 .....................: Hit for ATAGCCATCATTTCACC at 459 [R]
HBD04_TARA_PON_MAG_00023 .....................: Hit for ATAGCCATCATTTCACC at 459 [R]
HBD05_TARA_PSE_MAG_00116 .....................: Hit for ATAGCCATCATTTCACC at 459 [R]
HBD06_TARA_ANW_MAG_00006 .....................: Hit for ATCGCCATCATTTCGCC at 459 [R]
HBD07_TARA_ANW_MAG_00019 .....................: Hit for ATGGCCATCATTTCTCC at 459 [R]
HBD08_TARA_PSW_MAG_00130 .....................: Hit for ATGGCCATCATTTCACC at 453 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for ATGGCCATCATTTCACC at 453 [R]
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for ATGGCCATCATTTCGCC at 501 [R]
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: Hit for ATGGCCATCATCTCGCC at 456 [R]
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: No hit
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for ATGGCCATCATTTCGCC at 453 [R]
RED_Id-2330111 ...............................: No hit
nifH2 (128 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for TGTGATCCCAAAGCCGA at 108
HBD02_TARA_PSW_MAG_00026 .....................: Hit for TGTGATCCCAAAGCAGA at 108
HBD03_TARA_ION_MAG_00014 .....................: Hit for TGTGACCCAAAAGCAGA at 114
HBD04_TARA_PON_MAG_00023 .....................: Hit for TGTGACCCAAAAGCAGA at 114
HBD05_TARA_PSE_MAG_00116 .....................: Hit for TGTGACCCGAAAGCAGA at 114
HBD06_TARA_ANW_MAG_00006 .....................: Hit for TGTGATCCTAAAGCAGA at 114
HBD07_TARA_ANW_MAG_00019 .....................: Hit for TGCGATCCCAAGGCGGA at 114
HBD08_TARA_PSW_MAG_00130 .....................: Hit for TGCGACCCCAAGGCTGA at 108
HBD09_TARA_PSW_MAG_00018 .....................: Hit for TGCGACCCCAAGGCCGA at 108
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for TGCGACCCCAAGGCCGA at 156
PSE_Id-2620196 ...............................: Hit for TGTGATCCAAAAGCCGA at 108
PSE_Id-3785694 ...............................: Hit for TGCGATCCCAAGGCCGA at 114
PSE_Id-6292875 ...............................: Hit for TGCGATCCGAAAGCAGA at 108
PON_Id-1645572 ...............................: Hit for TGCGACCCGAAGGCTGA at 108
PON_Id-3217614 ...............................: No hit
PON_Id-3596173 ...............................: Hit for TGTGACCCGAAAGCTGA at 108
RED_Id-2330111 ...............................: No hit
NifH4 (128 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: No hit
HBD02_TARA_PSW_MAG_00026 .....................: No hit
HBD03_TARA_ION_MAG_00014 .....................: No hit
HBD04_TARA_PON_MAG_00023 .....................: No hit
HBD05_TARA_PSE_MAG_00116 .....................: No hit
HBD06_TARA_ANW_MAG_00006 .....................: No hit
HBD07_TARA_ANW_MAG_00019 .....................: No hit
HBD08_TARA_PSW_MAG_00130 .....................: No hit
HBD09_TARA_PSW_MAG_00018 .....................: No hit
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: No hit
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: Hit for TTCTACGGCAAGGGCGG at 21
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: No hit
PON_Id-3217614 ...............................: Hit for TTTTATGGAAAAGGGGG at 18
PON_Id-3596173 ...............................: No hit
RED_Id-2330111 ...............................: No hit
NifH3 (128 combinations)
===============================================
HBD01_TARA_PSW_MAG_00013 .....................: Hit for ATGTTGTTGGCCGCATA at 471 [R]
HBD02_TARA_PSW_MAG_00026 .....................: Hit for ATATTGTTGGCCGCATA at 471 [R]
HBD03_TARA_ION_MAG_00014 .....................: Hit for ATGTTGTTGGCTGCGTA at 477 [R]
HBD04_TARA_PON_MAG_00023 .....................: Hit for ATGTTGTTGGCTGCGTA at 477 [R]
HBD05_TARA_PSE_MAG_00116 .....................: Hit for ATGTTGTTGGCTGCATA at 477 [R]
HBD06_TARA_ANW_MAG_00006 .....................: Hit for ATGTTATTGGCGGCATA at 477 [R]
HBD07_TARA_ANW_MAG_00019 .....................: Hit for ATGTTGTTGGCCGCATA at 477 [R]
HBD08_TARA_PSW_MAG_00130 .....................: Hit for ATGTTGTTGGCAGCATA at 471 [R]
HBD09_TARA_PSW_MAG_00018 .....................: Hit for ATGTTGTTGGCTGCATA at 471 [R]
PSE_Id-346185 ................................: No hit
PSE_Id-1140575 ...............................: Hit for ATGTTGTTGGCGGCGTA at 519 [R]
PSE_Id-2620196 ...............................: No hit
PSE_Id-3785694 ...............................: Hit for ATGTTGTTGGCCGCGTA at 474 [R]
PSE_Id-6292875 ...............................: No hit
PON_Id-1645572 ...............................: Hit for ATGTTGTTGGCAGCATA at 480 [R]
PON_Id-3217614 ...............................: Hit for ATGTTGTTCGCTGCGTA at 468 [R]
PON_Id-3596173 ...............................: Hit for ATGTTGTTGGCTGCGTA at 471 [R]
RED_Id-2330111 ...............................: No hit
Raw
primers.txt
name pair direction sequence
PolF P1 F TGCGAYCCSAARGCBGACTC
PolR P1 R ATSGCCATCATYTCRCCGGA
Ueda19F P2 F GCIWTYTAYGGIAARGGIGG
Ueda407R P2 R AAICCRCCRCAIACIACRTC
F2 P3 F TGYGAYCCIAAIGCIGA
R6 P3 R GCCATCATYTCICCIGA
IGK3 P4 F GCIWTHTAYGGIAARGGIGGIATHGGIAA
DVV P4 R ATIGCRAAICCICCRCAIACIACRTC
nifH1 P5 F ADNGCCATCATYTCNCC
nifH2 P5 R TGYGAYCCNAARGCNGA
NifH4 P6 F TTYTAYGGNAARGGNGG
NifH3 P6 R ATRTTRTTNGCNGCRTA
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment