Input and runtime details for job 3202356 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
4	5.758e-05	0.04123	stm3564	livK	-17.90	0.039430	157 -- 215	37 -- 90	leucine ABC transporter subunit substrate-binding protein LivK	_____________156______________________216\n_____________\|________________________\|\n5'-UUU...GCAAA_____A__________________AUGGG...CGA-3'\n______________AAACA_AAC_AUAUAACAUCACGA\n______________\|\|\|\|\|_\|\|\|_\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUGU_UUG_UGUGUUGUAGUGUU\n3'-UUU...UAACG_____G___U______________GGCAU...UCA-5'\n_____________\|________________________\|\n_____________91_______________________36\n	178 -- 184	65 -- 71	-21.8749 kcal/mol	0.694231 kcal/mol	6.38817 kcal/mol	156 216@LB@ \| \|@LB@5'-UUU...GCAAA A AUGGG...CGA-3'@LB@ AAACA AAC AUAUAACAUCACGA@LB@ \|\|\|\|\| \|\|\| \|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUGU UUG UGUGUUGUAGUGUU@LB@3'-UUU...UAACG G U GGCAU...UCA-5'@LB@ \| \|@LB@ 91 36@LB@@LB@@LB@Energy -17.90 kcal/mol@LB@Hybridization Energy -21.8749 kcal/mol@LB@Unfolding Energy - mRNA 0.694231 kcal/mol@LB@Unfolding Energy - sRNA 6.38817 kcal/mol@LB@@LB@Position - mRNA 157 -- 215@LB@Position - sRNA 37 -- 90@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 65 -- 71@LB@
90	0.004161	0.1596	stm1124	putA	-17.89	0.039481	159 -- 201	125 -- 168	trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	_____________158______________________________________________202\n_____________\|________________________________________________\|\n5'-UAA...CGCUA____U___UUA________A_C____A_____________________UGGGA...UAA-3'\n______________ACUA_UGG___GCAGAUAG_G_GAAU__ACAGG_AGU___AGAGGGUA\n______________\|\|\|\|_\|\|\|___:\|\|\|\|:\|\|_\|_:\|\|\|__\|\|\|\|\|_\|\|\|___\|:\|\|\|\|\|\|\n______________UGAU_ACC___UGUCUGUC_C_UUUA__UGUCC_UCA___UUUCCCAU\n3'-UUU...AUUAG___________________C_A____CA_____U___CUU________CAGAG...UCA-5'\n_____________\|________________________________________________\|\n_____________169______________________________________________124\n	195 -- 201	125 -- 131	-33.9858 kcal/mol	7.26317 kcal/mol	8.4265 kcal/mol	158 202@LB@ \| \|@LB@5'-UAA...CGCUA U UUA A C A UGGGA...UAA-3'@LB@ ACUA UGG GCAGAUAG G GAAU ACAGG AGU AGAGGGUA@LB@ \|\|\|\| \|\|\| :\|\|\|\|:\|\| \| :\|\|\| \|\|\|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UGAU ACC UGUCUGUC C UUUA UGUCC UCA UUUCCCAU@LB@3'-UUU...AUUAG C A CA U CUU CAGAG...UCA-5'@LB@ \| \|@LB@ 169 124@LB@@LB@@LB@Energy -17.89 kcal/mol@LB@Hybridization Energy -33.9858 kcal/mol@LB@Unfolding Energy - mRNA 7.26317 kcal/mol@LB@Unfolding Energy - sRNA 8.4265 kcal/mol@LB@@LB@Position - mRNA 159 -- 201@LB@Position - sRNA 125 -- 168@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 125 -- 131@LB@
131	0.006551	0.1774	stm3217	aer	-17.88	0.039631	254 -- 298	36 -- 77	senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506	_____________253____________________________________________________________________________________299\n_____________\|______________________________________________________________________________________\|\n5'-UUU...AAGGC______UGA_____________________ACAAA____AA__AUU____________________UC__G______UUUA_____UAAAG...CCA-3'\n______________GCAGGA___GGUGAAAA_________UCGU_____UAUU__GG____AAUCGCA____AAUUGCGA__CA_AGCAAU____ACAAC\n______________:\|\|\|\|\|___:\|\|\|\|\|\|\|_________\|\|\|:_____\|\|::__\|\|____\|\|\|\|\|\|\|____\|\|\|\|\|\|:\|__\|\|_\|:\|\|\|:____\|\|\|\|\|\n______________UGUCCU___UCACUUUU_________AGCG_____AUGG__CC____UUAGCGU____UUAACGUU__GU_UUGUUG____UGUUG\n3'-UUU...UUACA_________________UCCCAUCAG_____________CA__AGAC_______CUGG________U___G_______________UAGUG...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________78_____________________________________________________________________________________35\n	89 -- 95	99 -- 105	-43.6348 kcal/mol	13.4466 kcal/mol	20.9633 kcal/mol	253 299@LB@ \| \|@LB@5'-UUU...AAGGC UGA ACAAA AA AUU UC G UUUA UAAAG...CCA-3'@LB@ GCAGGA GGUGAAAA UCGU UAUU GG AAUCGCA AAUUGCGA CA AGCAAU ACAAC@LB@ :\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|\| \|:\|\|\|: \|\|\|\|\|@LB@ UGUCCU UCACUUUU AGCG AUGG CC UUAGCGU UUAACGUU GU UUGUUG UGUUG@LB@3'-UUU...UUACA UCCCAUCAG CA AGAC CUGG U G UAGUG...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -43.6348 kcal/mol@LB@Unfolding Energy - mRNA 13.4466 kcal/mol@LB@Unfolding Energy - sRNA 20.9633 kcal/mol@LB@@LB@Position - mRNA 254 -- 298@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 99 -- 105@LB@
31	0.0007673	0.08814	stm0403	yajB	-17.88	0.039643	23 -- 70	41 -- 90	ACP phosphodiesterase	_____________22_____________71\n_____________\|______________\|\n5'-CCC...GGGUA_______AU_____AUUCG...AUU-3'\n______________GUGGGCA__CAGGG\n______________:\|\|\|:\|\|__\|\|\|\|\|\n______________UACCUGU__GUCCC\n3'-UUU...AGUGA_______CU_____AUUUA...UCA-5'\n_____________\|______________\|\n_____________91_____________40\n	57 -- 63	159 -- 165	-19.6891 kcal/mol	4.4153 kcal/mol	3.13232 kcal/mol	22 71@LB@ \| \|@LB@5'-CCC...GGGUA AU AUUCG...AUU-3'@LB@ GUGGGCA CAGGG@LB@ :\|\|\|:\|\| \|\|\|\|\|@LB@ UACCUGU GUCCC@LB@3'-UUU...AGUGA CU AUUUA...UCA-5'@LB@ \| \|@LB@ 91 40@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -19.6891 kcal/mol@LB@Unfolding Energy - mRNA 4.4153 kcal/mol@LB@Unfolding Energy - sRNA 3.13232 kcal/mol@LB@@LB@Position - mRNA 23 -- 70@LB@Position - sRNA 41 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 159 -- 165@LB@
6	7.515e-05	0.04123	stm0665	gltI	-17.87	0.039793	157 -- 199	35 -- 81	glutamate/aspartate transporter	_____________156__________________200\n_____________\|____________________\|\n5'-CGA...UGCAG____UA______U_______GCUAU...CUG-3'\n______________GCAA__ACAACA_CACAAUA\n______________\|\|\|\|__\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________CGUU__UGUUGU_GUGUUGU\n3'-UUU...GUUAA____UG______U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________82___________________34\n	170 -- 176	71 -- 77	-19.9204 kcal/mol	1.29616 kcal/mol	3.80671 kcal/mol	156 200@LB@ \| \|@LB@5'-CGA...UGCAG UA U GCUAU...CUG-3'@LB@ GCAA ACAACA CACAAUA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CGUU UGUUGU GUGUUGU@LB@3'-UUU...GUUAA UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -17.87 kcal/mol@LB@Hybridization Energy -19.9204 kcal/mol@LB@Unfolding Energy - mRNA 1.29616 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 157 -- 199@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 71 -- 77@LB@
170	0.009347	0.1945	stm0477	acrR	-17.70	0.042454	229 -- 246	74 -- 91	DNA-binding transcriptional repressor AcrR	_____________228________________247\n_____________\|__________________\|\n5'-AAG...AGCGC__G_______________UCCUG...CGC-3'\n______________UG_AGACACGACAACACA\n______________\|\|_\|:\|\|\|\|:\|\|\|\|\|\|\|\|\n______________AC_UUUGUGUUGUUGUGU\n3'-UUU...GGUUA__G_______________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________92_________________73\n	240 -- 246	74 -- 80	-24.9092 kcal/mol	3.16809 kcal/mol	3.73631 kcal/mol	228 247@LB@ \| \|@LB@5'-AAG...AGCGC G UCCUG...CGC-3'@LB@ UG AGACACGACAACACA@LB@ \|\| \|:\|\|\|\|:\|\|\|\|\|\|\|\|@LB@ AC UUUGUGUUGUUGUGU@LB@3'-UUU...GGUUA G UGUAG...UCA-5'@LB@ \| \|@LB@ 92 73@LB@@LB@@LB@Energy -17.70 kcal/mol@LB@Hybridization Energy -24.9092 kcal/mol@LB@Unfolding Energy - mRNA 3.16809 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 229 -- 246@LB@Position - sRNA 74 -- 91@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 74 -- 80@LB@
123	0.006073	0.1758	stm4355	yjeS	-17.69	0.042665	80 -- 140	31 -- 90	putative Fe-S protein	_____________79______________________________141\n_____________\|_______________________________\|\n_______5'-CGUU______________C________________AGUGU...UUA-3'\n______________GUUGC___CAUGAC_ACACAACA_C_CAGCC\n______________:\|\|\|\|___\|\|::\|\|_\|\|\|\|\|\|\|\|_\|_\|\|:\|\|\n______________UAACG___GUGUUG_UGUGUUGU_G_GUUGG\n3'-UUU...CUGGU_____UUU______U________A_U_____CAUUC...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________30\n	18 -- 24	71 -- 77	-27.2663 kcal/mol	5.13395 kcal/mol	8.62086 kcal/mol	79 141@LB@ \| \|@LB@ 5'-CGUU C AGUGU...UUA-3'@LB@ GUUGC CAUGAC ACACAACA C CAGCC@LB@ :\|\|\|\| \|\|::\|\| \|\|\|\|\|\|\|\| \| \|\|:\|\|@LB@ UAACG GUGUUG UGUGUUGU G GUUGG@LB@3'-UUU...CUGGU UUU U A U CAUUC...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -27.2663 kcal/mol@LB@Unfolding Energy - mRNA 5.13395 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 80 -- 140@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 71 -- 77@LB@
2	2.663e-05	0.04123	stm2355	argT	-17.69	0.042680	144 -- 202	34 -- 91	histidine ABC transporter substrate-binding protein HisJ	_____________143____________________203\n_____________\|______________________\|\n5'-UUA...AAGUC_________________C____AAAAC...AUA-3'\n______________UGCAAACAC_ACAACGC_ACGU\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|\|:\|_\|\|:\|\n______________ACGUUUGUG_UGUUGUG_UGUA\n3'-UUU...GGUUA_________U_______U____GUGUU...UCA-5'\n_____________\|______________________\|\n_____________92_____________________33\n	153 -- 159	75 -- 81	-25.653 kcal/mol	2.98604 kcal/mol	4.21448 kcal/mol	143 203@LB@ \| \|@LB@5'-UUA...AAGUC C AAAAC...AUA-3'@LB@ UGCAAACAC ACAACGC ACGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|:\| \|\|:\|@LB@ ACGUUUGUG UGUUGUG UGUA@LB@3'-UUU...GGUUA U U GUGUU...UCA-5'@LB@ \| \|@LB@ 92 33@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -25.653 kcal/mol@LB@Unfolding Energy - mRNA 2.98604 kcal/mol@LB@Unfolding Energy - sRNA 4.21448 kcal/mol@LB@@LB@Position - mRNA 144 -- 202@LB@Position - sRNA 34 -- 91@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 75 -- 81@LB@
26	0.0006768	0.08814	stm1365	ydiJ	-17.55	0.045121	78 -- 116	57 -- 91	similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017	_____________77_________________________117\n_____________\|__________________________\|\n5'-CUA...AAUGU_________AAUA_____________AACGA...CCA-3'\n______________GAUACAACA____ACGCAACA_CGCA\n______________:\|:\|\|\|\|\|\|____\|\|:\|\|\|\|\|_\|:\|\|\n______________UUGUGUUGU____UGUGUUGU_GUGU\n3'-UUU...AACGU_____________________A____UGGCA...UCA-5'\n_____________\|__________________________\|\n_____________92_________________________56\n	95 -- 101	71 -- 77	-21.9961 kcal/mol	1.97147 kcal/mol	5.98953 kcal/mol	77 117@LB@ \| \|@LB@5'-CUA...AAUGU AAUA AACGA...CCA-3'@LB@ GAUACAACA ACGCAACA CGCA@LB@ :\|:\|\|\|\|\|\| \|\|:\|\|\|\|\| \|:\|\|@LB@ UUGUGUUGU UGUGUUGU GUGU@LB@3'-UUU...AACGU A UGGCA...UCA-5'@LB@ \| \|@LB@ 92 56@LB@@LB@@LB@Energy -17.55 kcal/mol@LB@Hybridization Energy -21.9961 kcal/mol@LB@Unfolding Energy - mRNA 1.97147 kcal/mol@LB@Unfolding Energy - sRNA 5.98953 kcal/mol@LB@@LB@Position - mRNA 78 -- 116@LB@Position - sRNA 57 -- 91@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 71 -- 77@LB@
132	0.006673	0.1774	stm2677	ffh	-17.54	0.045291	232 -- 275	38 -- 86	4.5S-RNP protein	_____________231_________________________________________________________________________________________________276\n_____________\|___________________________________________________________________________________________________\|\n5'-UAG...CAAAA_______UA__U_____CG____UU__CC__________A_A____A___A__G___UACG___C______CU____CC__U____________AA___GGCUU...AAG-3'\n______________ACGGGCA__GU__GUGU__ACAG__GA__AGUGAGAAAG_G_AG_C__GU_UA_CGU____UGA__CGCAG__CCAA__GU__GCAUAACAACA__GAC\n______________\|\|:\|:\|\|__\|\|__:\|\|\|__\|\|\|\|__\|\|__\|\|\|\|\|:\|\|\|\|_\|_\|\|_\|__\|:_\|\|_\|\|\|____\|\|\|__\|\|\|\|\|__\|\|\|\|__\|:__:\|\|:\|\|\|\|\|\|\|__:\|\|\n______________UGUCUGU__CA__UACA__UGUC__CU__UCACUUUUUC_C_UC_G__CG_AU_GCA____ACU__GCGUC__GGUU__CG__UGUGUUGUUGU__UUG\n3'-UUU...AUACC_______CC__UU__________________________C_A__A_AG_____G___CCAG___UA_____U_____AA__UU___________G____UAGUG...UCA-5'\n_____________\|___________________________________________________________________________________________________\|\n_____________87__________________________________________________________________________________________________37\n	110 -- 116	76 -- 82	-60.3799 kcal/mol	23.7315 kcal/mol	24.6218 kcal/mol	231 276@LB@ \| \|@LB@5'-UAG...CAAAA UA U CG UU CC A A A A G UACG C CU CC U AA GGCUU...AAG-3'@LB@ ACGGGCA GU GUGU ACAG GA AGUGAGAAAG G AG C GU UA CGU UGA CGCAG CCAA GU GCAUAACAACA GAC@LB@ \|\|:\|:\|\| \|\| :\|\|\| \|\|\|\| \|\| \|\|\|\|\|:\|\|\|\| \| \|\| \| \|: \|\| \|\|\| \|\|\| \|\|\|\|\| \|\|\|\| \|: :\|\|:\|\|\|\|\|\|\| :\|\|@LB@ UGUCUGU CA UACA UGUC CU UCACUUUUUC C UC G CG AU GCA ACU GCGUC GGUU CG UGUGUUGUUGU UUG@LB@3'-UUU...AUACC CC UU C A A AG G CCAG UA U AA UU G UAGUG...UCA-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -60.3799 kcal/mol@LB@Unfolding Energy - mRNA 23.7315 kcal/mol@LB@Unfolding Energy - sRNA 24.6218 kcal/mol@LB@@LB@Position - mRNA 232 -- 275@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 76 -- 82@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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usability assessment

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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