primers4clades job (26e8c759)
_runmode : primers
_gencode : universal
_evaluation :
_cluster distance metric : protein
_Tm : 55
_amplicon_length : 200 , 500
_email : youremail@email.com
_FASTA sequence file : Ca2.fst
Clustering sequences...
# number of sequences read = 8
# number of recognised taxa = 1
# input sequences seem to be aligned
# computing distance matrix...
# multiple alignment FASTA file
# alignment stats: length = 510 %gaps = 0.00 %constant = 92.0
# mean distance = 0.03258
# max distance = 0.06065 ( 001 <=> 005 )
# min distance = 0.01013 ( 002 <=> 008 )
# NJ tree with cluster labels :
+004__0 [Bombyx_mori]_Seq4_...
+-1
+-2 +005__0 [Bombyx_mori]_Seq5_...
! !
! +006__0 [Bombyx_mori]_Seq6_...
!
! +003__0 [Bombyx_mori]_Seq3_...
3-4
! ! +007__0 [Bombyx_mori]_Seq7_...
! +-5
! ! +002__0 [Bombyx_mori]_Seq2_...
! +-6
! +008__0 [Bombyx_mori]_Seq8_...
!
+-001__0 [Bombyx_mori]_Seq1_...
Calculating primers, results will be shortly emailed...
You might return or wait for your results to appear here.
# largest cluster (0) selected, please use runmode 'cluster sequences' to make your own selection
# input sequences seem to be aligned
## table redundancy vs amplicons stats:
# input_derived_4e6be5b3 redundancy = 0.93 amplicons = 4
# Bombyx_mori redundancy = 0.93 amplicons = 4
# evaluating primers...
# primer evaluation TAB file
# min quality for phylogenetic evaluations = 50%
# ranking pairs of primers...
download
## Amplicon 1 codon_usage_table = input_derived_4e6be5b3 :
GATAATTATGATTTAAAAGAAGAATTAggnaarggngc 5'->3' N 13 81 (aligned residues)
gataattacgatcttaaagaagaacttgggaagggagc >001 [Bombyx mori] Seq1
gataactacgacctaaaagaagaattaggaaaaggagc >002 [Bombyx mori] Seq2
gacaactatgaacttaaggaagaattaggcaagggcgc >003 [Bombyx mori] Seq3
gacaattacgaccttaaggaagaattaggaaagggagc >004 [Bombyx mori] Seq4
gataactatgaccttaaagaagaacttggaaaaggagc >005 [Bombyx mori] Seq5
gataactacgatttgaaagaagaattaggcaaaggagc >006 [Bombyx mori] Seq6
gataattatgatctgaaagaagaattaggaaaaggtgc >007 [Bombyx mori] Seq7
gataattatgatcttaaagaagaattgggaaagggcgc >008 [Bombyx mori] Seq8
..?..?..?..??.?..?......?.?..?.....?..
GATAATTATGATTTAAAAGAAGAATTAggvaargghgc codeh_corr 26e8c759_intronless_cluster_01_N13
GATAATTATGATTTAAAAGAAGAATTAggvaargghgc relax_corr 26e8c759_intronless_cluster_01_N13
gayaaytaygahytdaargaagaaytdggvaargghgc degen_corr 26e8c759_intronless_cluster_01_N13
TCAAAAACTAAATAGTGAAAGTGTtcytcytgdat 5'->3' C 13 81 (aligned residues)
tcaaaaacgaggtagtgaaaatgttcctcttgaat >001 [Bombyx mori] Seq1
tcaaatacgaggtaatgaaaatgttcttcttgaat >002 [Bombyx mori] Seq2
tcaaagacaaggtaatggcaatgttcttcttgaat >003 [Bombyx mori] Seq3
tcaaatacgagatagtggaagtgttcttcctgaat >004 [Bombyx mori] Seq4
tcgaaaacgagataatggaaatgttcttcttgtat >005 [Bombyx mori] Seq5
tcaaatacgaggtagtgaaaatgttcttcttgaat >006 [Bombyx mori] Seq6
tcaaataccaaataatgaaaatgctcttcttgaat >007 [Bombyx mori] Seq7
tcgaaaacaaggtaatgaaaatgttcctcttgaat >008 [Bombyx mori] Seq8
..?..?..?.??..?..??.?..?........?..
TCAAAAACTAAATAGTGAAAGTGTtcytcytgwat codeh_corr 26e8c759_intronless_cluster_01_C81
TCAAAAACTAAATAGTGAAAGtgytcytcytgwat relax_corr 26e8c759_intronless_cluster_01_C81
tcraadacvarrtartgrmartgytcytcytgwat degen_corr 26e8c759_intronless_cluster_01_C81
# primer pair quality = 80%
# expected PCR product length (nt) = 207
# fwd: minTm = 52.2 maxTm = 56.5
# rev: minTm = 52.6 maxTm = 55.3
# quality warnings:
# fwd fulldeg (31104 >= 193)
# rev fulldeg (18432 >= 193)
#--
# phylogenetic amplicon evaluation:
# subs.model = TIMIG
# alpha = 0.43
# mean aLRT = 0.66 median aLRT = 0.76
# amplicon FASTA file
# aLRT likelihood tree (newick)
# end_of_amplicon
## Amplicon 2 codon_usage_table = input_derived_4e6be5b3 :
AGAATCTGTTCACCACTGTcaycayaaygg 5'->3' N 122 188 (aligned residues)
agaatcagtacaccactgccaccataatgg >001 [Bombyx mori] Seq1
agaatctgtccaccactgtcatcacaatgg >002 [Bombyx mori] Seq2
agaatctgtccatcactgtcaccataatgg >003 [Bombyx mori] Seq3
ggaatctgttcatcattgccatcataatgg >004 [Bombyx mori] Seq4
ggaatccgtgcaccattgtcaccacaatgg >005 [Bombyx mori] Seq5
ggaatccgtacatcattgtcaccacaatgg >006 [Bombyx mori] Seq6
ggagtcagtgcatcactgccaccataatgg >007 [Bombyx mori] Seq7
tgaatctgtacaccattgtcaccataatgg >008 [Bombyx mori] Seq8
?..?..?..?..?..?..?........!..
AGAATCTGTTCACCACTGTcaycayaatgg codeh_corr 26e8c759_intronless_cluster_02_N122
AGAATCTGTTCACcaytgycaycayaatgg relax_corr 26e8c759_intronless_cluster_02_N122
dgartchgtncaycaytgycaycayaatgg degen_corr 26e8c759_intronless_cluster_02_N122
AATATCAACTGGTTTACCATATggytcyttytt 5'->3' C 122 188 (aligned residues)
aatatctactggcttaccgtaaggctctttttt >001 [Bombyx mori] Seq1
aatgtctacgggctttccgtacggctctttttt >002 [Bombyx mori] Seq2
tatatccactggtttaccataaggttccttttt >003 [Bombyx mori] Seq3
aatatctacgggctttccataaggctctttctt >004 [Bombyx mori] Seq4
aatatccactggcttgccgtaaggttctttttt >005 [Bombyx mori] Seq5
tatatcaactggtttgccataaggttctttttt >006 [Bombyx mori] Seq6
aatatctactggtttgccgtatggctccttctt >007 [Bombyx mori] Seq7
gatatctactggtttaccgtatggttctttttt >008 [Bombyx mori] Seq8
?..?..?..?..?..?..?..?...........
AATATCAACTGGTTTACCATATggytcyttytt codeh_corr 26e8c759_intronless_cluster_02_C188
AATATCAACTGGTTTACCAtahggytcyttytt relax_corr 26e8c759_intronless_cluster_02_C188
datrtchackggyttdccrtahggytcyttytt degen_corr 26e8c759_intronless_cluster_02_C188
# primer pair quality = 80%
# expected PCR product length (nt) = 201
# fwd: minTm = 58.1 maxTm = 61.7
# rev: minTm = 54.5 maxTm = 57.8
# quality warnings:
# fwd fulldeg (2304 >= 193)
# rev fulldeg (10368 >= 193)
#--
# phylogenetic amplicon evaluation:
# subs.model = TrNIG
# alpha = 0.56
# mean aLRT = 0.52 median aLRT = 0.79
# amplicon FASTA file
# aLRT likelihood tree (newick)
# end_of_amplicon
## Amplicon 3 codon_usage_table = input_derived_4e6be5b3 :
TGAAGTTCAAGGTGATCAAcargcntggtt 5'->3' N 163 283 (aligned residues)
tgaagtgcaaggagaacagcaggcctggtt >001 [Bombyx mori] Seq1
cgaggtgcaaggagaccagcaagcatggtt >002 [Bombyx mori] Seq2
cgaagttcaaggagatcaacaagcatggtt >003 [Bombyx mori] Seq3
tgaagtccaaggtgaacaacaagcgtggtt >004 [Bombyx mori] Seq4
cgaagttcaaggggaccagcaagcgtggtt >005 [Bombyx mori] Seq5
tgaagtccaaggtgatcaacaagcatggtt >006 [Bombyx mori] Seq6
agaagtgcaaggtgaccaacaggcgtggtt >007 [Bombyx mori] Seq7
tgaagtacaaggcgaccagcaagcttggtt >008 [Bombyx mori] Seq8
?..?..?.....?..?..?...........
TGAAGTTCAAGGTGATCAAcargcntggtt codeh_corr 26e8c759_intronless_cluster_03_N163
TGAAGTTCAAGGTGATcarcargcntggtt relax_corr 26e8c759_intronless_cluster_03_N163
hgargtncaaggngahcarcargcntggtt degen_corr 26e8c759_intronless_cluster_03_N163
CTTTAAACAATCAACAGTTTCTtgnckrtgcat 5'->3' C 163 283 (aligned residues)
cttcaagcagtccacagtctcctgcctgtgcat >001 [Bombyx mori] Seq1
cttcaagcaatccactgtttcttgcctgtgcat >002 [Bombyx mori] Seq2
tttcaaacaatccacagtttcctgtctatgcat >003 [Bombyx mori] Seq3
cttcaagcaatccacagtctcctgtctgtgcat >004 [Bombyx mori] Seq4
tttcaaacagtctacagtctcctggcggtgcat >005 [Bombyx mori] Seq5
cttcaagcagtccactgtttcctgtctatgcat >006 [Bombyx mori] Seq6
cttcaagcagtctactgtctcttgtctgtgcat >007 [Bombyx mori] Seq7
cttcaaacagtccacggtctcttgcctgtgcat >008 [Bombyx mori] Seq8
?..!..?..?..?..?..?..?..?........
CTTCAAACAATCAACAGTTTCTtgbckrtgcat codeh_corr 26e8c759_intronless_cluster_03_C283
CTTCAAACAATCAACAGTTtcytgbckrtgcat relax_corr 26e8c759_intronless_cluster_03_C283
yttcaarcartcyacdgtytcytgbckrtgcat degen_corr 26e8c759_intronless_cluster_03_C283
# primer pair quality = 80%
# expected PCR product length (nt) = 363
# fwd: minTm = 60.1 maxTm = 63.0
# rev: minTm = 56.8 maxTm = 61.9
# quality warnings:
# fwd fulldeg (4608 >= 193)
# rev fulldeg (2304 >= 193)
#--
# phylogenetic amplicon evaluation:
# subs.model = TIMIG
# alpha = 0.25
# mean aLRT = 0.46 median aLRT = 0.42
# amplicon FASTA file
# aLRT likelihood tree (newick)
# end_of_amplicon
## Amplicon 4 codon_usage_table = Bombyx_mori :
GACCTGAAAGAAGAACTGggnaarggngc 5'->3' N 16 172 (aligned residues)
gatcttaaagaagaacttgggaagggagc >001 [Bombyx mori] Seq1
gacctaaaagaagaattaggaaaaggagc >002 [Bombyx mori] Seq2
gaacttaaggaagaattaggcaagggcgc >003 [Bombyx mori] Seq3
gaccttaaggaagaattaggaaagggagc >004 [Bombyx mori] Seq4
gaccttaaagaagaacttggaaaaggagc >005 [Bombyx mori] Seq5
gatttgaaagaagaattaggcaaaggagc >006 [Bombyx mori] Seq6
gatctgaaagaagaattaggaaaaggtgc >007 [Bombyx mori] Seq7
gatcttaaagaagaattgggaaagggcgc >008 [Bombyx mori] Seq8
..??.?..?......?.?..?.....?..
GACCTGAAAGAAGAACTGggvaargghgc codeh_corr 26e8c759_intronless_cluster_01_N16
GACCTGAAAGAAGAACTGggvaargghgc relax_corr 26e8c759_intronless_cluster_01_N16
gahytdaargaagaaytdggvaargghgc degen_corr 26e8c759_intronless_cluster_01_N16
CCAGGTGTACCAGCGaanccraacca 5'->3' C 16 172 (aligned residues)
cctggtgttccagcaaatccaaacca >001 [Bombyx mori] Seq1
cccggagtgcctgcgaatccaaacca >002 [Bombyx mori] Seq2
ccgggtgtacctgcgaatccgaacca >003 [Bombyx mori] Seq3
cctggagtaccagcaaagccaaacca >004 [Bombyx mori] Seq4
ccaggagtaccagcaaatccgaacca >005 [Bombyx mori] Seq5
ccaggggtaccggcaaatccaaacca >006 [Bombyx mori] Seq6
ccaggagtaccagcgaaaccgaacca >007 [Bombyx mori] Seq7
ccaggagtacctgcaaaaccaaacca >008 [Bombyx mori] Seq8
..?..?..?..?..?..?........
CCAGGTGTACCAGCGaadccraacca codeh_corr 26e8c759_intronless_cluster_01_C172
CCAGGTGTACCAgcraadccraacca relax_corr 26e8c759_intronless_cluster_01_C172
ccnggdgtdccdgcraadccraacca degen_corr 26e8c759_intronless_cluster_01_C172
# primer pair quality = 80%
# expected PCR product length (nt) = 471
# fwd: minTm = 62.0 maxTm = 67.5
# rev: minTm = 65.5 maxTm = 68.8
# quality warnings:
# fwd fulldeg (3888 >= 193)
# rev fulldeg (1296 >= 193)
#--
# phylogenetic amplicon evaluation:
# subs.model = TIMIG
# alpha = 0.24
# mean aLRT = 0.49 median aLRT = 0.57
# amplicon FASTA file
# aLRT likelihood tree (newick)
# end_of_amplicon
## Amplicon 5 codon_usage_table = Bombyx_mori :
ACGACTACCCTTCACCTgartgggayac 5'->3' N 232 320 (aligned residues)
atgattatccttctcctgagtgggacac >001 [Bombyx mori] Seq1
atgactacccctccccagagtgggacac >002 [Bombyx mori] Seq2
atgattatccgtctcctgagtgggatac >003 [Bombyx mori] Seq3
atgattacccatcacctgaatgggatac >004 [Bombyx mori] Seq4
atgattacccgtcaccggaatgggacac >005 [Bombyx mori] Seq5
acgattacccatctcccgaatgggatac >006 [Bombyx mori] Seq6
acgattatccctctcctgaatgggatac >007 [Bombyx mori] Seq7
atgattatccatcacccgagtgggatac >008 [Bombyx mori] Seq8
.?..?..?..?..?..?...........
ACGACTACCCTTCACCTgartgggayac codeh_corr 26e8c759_intronless_cluster_02_N232
ACGACTACCCTTCAccngartgggayac relax_corr 26e8c759_intronless_cluster_02_N232
aygaytayccntchccngartgggayac degen_corr 26e8c759_intronless_cluster_02_N232
TGAACCGTCACCCTTTttrttnacnat 5'->3' C 232 320 (aligned residues)
agatccatcactctttttattaaccat >001 [Bombyx mori] Seq1
agaaccgtccccttttttgttaactat >002 [Bombyx mori] Seq2
cgatccatcgccttttttattaaccat >003 [Bombyx mori] Seq3
tgatccttcacttttcttgttaaccat >004 [Bombyx mori] Seq4
agaaccatcacctttcttattaaccat >005 [Bombyx mori] Seq5
tgaaccatcacctttcttattgaccat >006 [Bombyx mori] Seq6
cgatccatcaccttttttgttgaccat >007 [Bombyx mori] Seq7
tgacccatctccttttttgttcaccat >008 [Bombyx mori] Seq8
?..?..?..?.??..?.....?..?..
TGAACCGTCACCCTTTttrttvacyat codeh_corr 26e8c759_intronless_cluster_02_C320
TGAACCGTCACCCttyttrttvacyat relax_corr 26e8c759_intronless_cluster_02_C320
hgahccdtcncyyttyttrttvacyat degen_corr 26e8c759_intronless_cluster_02_C320
# primer pair quality = 80%
# expected PCR product length (nt) = 267
# fwd: minTm = 62.1 maxTm = 65.5
# rev: minTm = 56.1 maxTm = 62.5
# quality warnings:
# fwd fulldeg (1536 >= 193)
# rev fulldeg (10368 >= 193)
#--
# phylogenetic amplicon evaluation:
# subs.model = TVMI
# alpha = 0
# mean aLRT = 0.75 median aLRT = 0.81
# amplicon FASTA file
# aLRT likelihood tree (newick)
# end_of_amplicon
## Amplicon 6 codon_usage_table = Bombyx_mori :
AAACAGTGGACTGCCTGAAraarttyaayg 5'->3' N 287 370 (aligned residues)
agactgtggactgcttgaagaagttcaatg >001 [Bombyx mori] Seq1
aaacagtggattgcttgaagaaattcaatg >002 [Bombyx mori] Seq2
aaactgtggattgtttgaaaaaattcaatg >003 [Bombyx mori] Seq3
agactgtggattgcttgaagaaattcaatg >004 [Bombyx mori] Seq4
agactgtagactgtttgaaaaagttcaatg >005 [Bombyx mori] Seq5
aaacagtggactgcttgaagaaattcaacg >006 [Bombyx mori] Seq6
agacagtagactgcttgaagaaattcaatg >007 [Bombyx mori] Seq7
agaccgtggactgtttgaagaaattcaatg >008 [Bombyx mori] Seq8
.?..?..?..?..?!..........!....
AAACAGTGGACTGCTTGAAraarttcaayg codeh_corr 26e8c759_intronless_cluster_03_N287
AAACAGTGGACtgyttgaaraarttcaayg relax_corr 26e8c759_intronless_cluster_03_N287
arachgtrgaytgyttgaaraarttcaayg degen_corr 26e8c759_intronless_cluster_03_N287
TCACCTCTAGCTTTACCGAATswrtcngcytt 5'->3' C 287 370 (aligned residues)
tctcctcttgtttttccaaacgaatctgcttt >001 [Bombyx mori] Seq1
tcaccgcgagctttgccgaaggaatcagcttt >002 [Bombyx mori] Seq2
tcgccccgagcttttccaaacgagtccgcttt >003 [Bombyx mori] Seq3
tcgcctcgagcttttccaaaagaatcagcttt >004 [Bombyx mori] Seq4
tcgccgcgagcttttccaaacgaatctgcctt >005 [Bombyx mori] Seq5
tcacctcgagcctttccgaatgagtctgcttt >006 [Bombyx mori] Seq6
tcgccacgcgcttttccaaaagagtctgcttt >007 [Bombyx mori] Seq7
tcaccacgagctttaccgaatgaatcagcttt >008 [Bombyx mori] Seq8
..?..?.??.??..?..?..?!!...?.....
TCACCTCTAGCTTTACCGAATgartchgcytt codeh_corr 26e8c759_intronless_cluster_03_C370
TCACCTCTAGCTTTACCGAATgartchgcytt relax_corr 26e8c759_intronless_cluster_03_C370
tcdccnckhgyyttdccraangartchgcytt degen_corr 26e8c759_intronless_cluster_03_C370
# primer pair quality = 80%
# expected PCR product length (nt) = 252
# fwd: minTm = 56.9 maxTm = 60.5
# rev: minTm = 59.5 maxTm = 63.4
# quality warnings:
# fwd fulldeg (384 >= 193)
# rev fulldeg (82944 >= 193)
#--
# phylogenetic evaluation skipped (max runtime 300s)
# end_of_amplicon
## Amplicon 7 codon_usage_table = Bombyx_mori :
CGCTATCAACAACGGTgaytayganac 5'->3' N 399 467 (aligned residues)
tgctattaataacggcgattatgaaac >001 [Bombyx mori] Seq1
tgctataaataacggcgattatgatac >002 [Bombyx mori] Seq2
tgcaatcaataatggtgattacgacac >003 [Bombyx mori] Seq3
cgctattaacaatggcgactatgagac >004 [Bombyx mori] Seq4
cgcaatcaataatggcgactacgacac >005 [Bombyx mori] Seq5
tgctattaataacggagactatgaaac >006 [Bombyx mori] Seq6
cgctattaacaacggtgattacgatac >007 [Bombyx mori] Seq7
tgcaattaataacggtgattatgaaac >008 [Bombyx mori] Seq8
?..?..?..?..?..?...........
CGCTATCAACAACGGTgaytayganac codeh_corr 26e8c759_intronless_cluster_04_N399
CGCTATCAACAACGGTgaytayganac relax_corr 26e8c759_intronless_cluster_04_N399
ygcwathaayaaygghgaytayganac degen_corr 26e8c759_intronless_cluster_04_N399
TGATTGTGTCACGCACacrtangcdat 5'->3' C 399 467 (aligned residues)
actttgtgtgacgcatacgtacgctat >001 [Bombyx mori] Seq1
actttgtgttacgcagacatatgctat >002 [Bombyx mori] Seq2
gctttgtgttacgcagacgtatgctat >003 [Bombyx mori] Seq3
actttgtgtaacacacacatatgcaat >004 [Bombyx mori] Seq4
gctctgtgtaacgcacacataagctat >005 [Bombyx mori] Seq5
actctgcgttacacacacgtaagctat >006 [Bombyx mori] Seq6
actctgtgtcacgcatacatatgctat >007 [Bombyx mori] Seq7
actttgtgttacgcatacgtatgcgat >008 [Bombyx mori] Seq8
?!!?..?..?..?..?.....?.....
TCTTTGTGTCACGCACacrtahgcdat codeh_corr 26e8c759_intronless_cluster_04_C467
TCTTTGTGTCACGCACacrtahgcdat relax_corr 26e8c759_intronless_cluster_04_C467
rctytgygtnacrcabacrtahgcdat degen_corr 26e8c759_intronless_cluster_04_C467
# primer pair quality = 80%
# expected PCR product length (nt) = 207
# fwd: minTm = 57.6 maxTm = 62.5
# rev: minTm = 59.4 maxTm = 64.4
# quality warnings:
# fwd fulldeg (2304 >= 193)
# rev fulldeg (3456 >= 193)
#--
# phylogenetic evaluation skipped (max runtime 300s)
# end_of_amplicon
## Amplicon 8 codon_usage_table = input_derived_4e6be5b3 :
CAAGAAACTGTTGATTGTTTGAAraarttyaayg 5'->3' N 286 433 (aligned residues)
caggagactgtggactgcttgaagaagttcaatg >001 [Bombyx mori] Seq1
caagaaacagtggattgcttgaagaaattcaatg >002 [Bombyx mori] Seq2
caggaaactgtggattgtttgaaaaaattcaatg >003 [Bombyx mori] Seq3
caggagactgtggattgcttgaagaaattcaatg >004 [Bombyx mori] Seq4
caggagactgtagactgtttgaaaaagttcaatg >005 [Bombyx mori] Seq5
caggaaacagtggactgcttgaagaaattcaacg >006 [Bombyx mori] Seq6
caagagacagtagactgcttgaagaaattcaatg >007 [Bombyx mori] Seq7
caagagaccgtggactgtttgaagaaattcaatg >008 [Bombyx mori] Seq8
..?..?..?..?..?..?...........!....
CAAGAAACTGTTGATTGTTTGAAraarttcaayg codeh_corr 26e8c759_intronless_cluster_04_N286
CAAGAAACTGTTGATtgyttgaaraarttcaayg relax_corr 26e8c759_intronless_cluster_04_N286
cargarachgtrgaytgyttgaaraarttcaayg degen_corr 26e8c759_intronless_cluster_04_N286
TTGGAGTATTATCAATGAAAAATttrtgraaytc 5'->3' C 286 433 (aligned residues)
tagccgtattatctataaagaatttatggaattc >001 [Bombyx mori] Seq1
tcggtgtgttgtcgataaagaatttatgaaattc >002 [Bombyx mori] Seq2
gcggtgtattgtcaataaagaatttatggaattc >003 [Bombyx mori] Seq3
ttggtgtattatcgatgaaaaacttgtgaaattc >004 [Bombyx mori] Seq4
tcggagtgttatcaataaagaacttgtgaaattc >005 [Bombyx mori] Seq5
taggagtattatcgatgaagaatttatgaaactc >006 [Bombyx mori] Seq6
ccggagtgttgtcaatgaagaatttatggaattc >007 [Bombyx mori] Seq7
ttggcgtgttatcgataaagaacttgtggaactc >008 [Bombyx mori] Seq8
??.??..?..?..?..?..?..?...........
TTGGAGTATTATCAATGAAAAATttrtgraaytc codeh_corr 26e8c759_intronless_cluster_04_C433
TTGGAGTATTATCAATGAAAaayttrtgraaytc relax_corr 26e8c759_intronless_cluster_04_C433
bhgshgtrttrtcdatraaraayttrtgraaytc degen_corr 26e8c759_intronless_cluster_04_C433
# primer pair quality = 60%
# expected PCR product length (nt) = 444
# fwd: minTm = 54.1 maxTm = 57.3
# rev: minTm = 50.3 maxTm = 54.3
# quality warnings:
# fwd fulldeg (768 >= 193)
# fwd hpinpot (0.62 >= 0.61)
# rev fulldeg (41472 >= 193)
# rev hpinpot (0.72 >= 0.61)
#--
# phylogenetic evaluation skipped (max runtime 300s)
# end_of_amplicon
## abbreviations:
# quality = quality estimation [best = 100, worst = 0] %
# crosspot = potential of cross-hybridization [0-1]
# relaxdeg = relaxed (3' extended segment) degeneracy
# fulldeg = full primer degeneracy
# minTm = minimum Tm for the pool of relaxed primers
# maxTm = maximum Tm for the pool of relaxed primers
# hpinpot = potential of primer hairpin [0-1]
# selfpot = potential of primer self-priming [0-1]
# aLRT = approximate likelihood-ratio test [0-1],
# overall confidence on trees built using this amplicon