Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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_000913 Escherichia coli str. K-12 substr. MG1655

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
116	0.01846	0.5155	b3349	slyD	-11.19	0.055067	245 -- 274	8 -- 47	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________244______________________________________275\n_____________\|________________________________________\|\n5'-UGU...CAGGU____A__________________UGUU_____________GUCUC...ACU-3'\n______________ACGU_CAGAA______GACGGUG________GGUUGAUGA\n______________\|\|:\|_\|\|\|\|\|______\|\|\|\|\|\|:________:\|\|\|:\|\|\|\|\n______________UGUA_GUCUU______CUGCCAU________UCAAUUACU\n3'-UUU...UUGUC____A_____UACUUA_______UAUUUAUU_________ACUAUCG-5'\n_____________\|________________________________________\|\n_____________48_______________________________________7\n	268 -- 274	8 -- 14	-23.1983 kcal/mol	5.6913 kcal/mol	6.31565 kcal/mol	244 275@LB@ \| \|@LB@5'-UGU...CAGGU A UGUU GUCUC...ACU-3'@LB@ ACGU CAGAA GACGGUG GGUUGAUGA@LB@ \|\|:\| \|\|\|\|\| \|\|\|\|\|\|: :\|\|\|:\|\|\|\|@LB@ UGUA GUCUU CUGCCAU UCAAUUACU@LB@3'-UUU...UUGUC A UACUUA UAUUUAUU ACUAUCG-5'@LB@ \| \|@LB@ 48 7@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -23.1983 kcal/mol@LB@Unfolding Energy - mRNA 5.6913 kcal/mol@LB@Unfolding Energy - sRNA 6.31565 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 8 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 8 -- 14@LB@
178	0.02931	0.5406	b3858	yihD	-11.25	0.053413	186 -- 232	8 -- 55	DUF1040 protein YihD	_____________185__________________________________________________233\n_____________\|____________________________________________________\|\n5'-AUA...CAAGA_____G_________CUAU______UAA____UC______________U___ACUCC...CGA-3'\n______________GUAAG_AG_CA_UCA____GAAAUG____ACG____UGAAUGAAGUUA_UGA\n______________\|\|\|\|:_\|\|_\|\|_\|\|\|____\|\|\|\|\|\|____\|\|\|____\|:\|\|\|:\|\|\|\|\|\|_\|\|\|\n______________CAUUU_UC_GU_AGU____CUUUAC____UGC____AUUUAUUUCAAU_ACU\n3'-UUU...AUCCC_____G__U__A_____________UUAC___CAUU____________U___ACUAUCG-5'\n_____________\|____________________________________________________\|\n_____________56___________________________________________________7\n	222 -- 228	12 -- 18	-26.8405 kcal/mol	9.25239 kcal/mol	6.33488 kcal/mol	185 233@LB@ \| \|@LB@5'-AUA...CAAGA G CUAU UAA UC U ACUCC...CGA-3'@LB@ GUAAG AG CA UCA GAAAUG ACG UGAAUGAAGUUA UGA@LB@ \|\|\|\|: \|\| \|\| \|\|\| \|\|\|\|\|\| \|\|\| \|:\|\|\|:\|\|\|\|\|\| \|\|\|@LB@ CAUUU UC GU AGU CUUUAC UGC AUUUAUUUCAAU ACU@LB@3'-UUU...AUCCC G U A UUAC CAUU U ACUAUCG-5'@LB@ \| \|@LB@ 56 7@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -26.8405 kcal/mol@LB@Unfolding Energy - mRNA 9.25239 kcal/mol@LB@Unfolding Energy - sRNA 6.33488 kcal/mol@LB@@LB@Position - mRNA 186 -- 232@LB@Position - sRNA 8 -- 55@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 12 -- 18@LB@
188	0.03165	0.5492	b3247	rng	-10.28	0.085420	187 -- 220	10 -- 64	ribonuclease G	_____________186_____________________________________________________221\n_____________\|_______________________________________________________\|\n5'-GUU...CGUGA_________A____________________________C_______U________AAACG...CGC-3'\n______________GAAA_AGGG_UAAAC________________AUGACGG___UGAAU___GUUAGU\n______________\|\|\|\|_\|\|\|\|_\|\|\|\|\|________________\|\|\|\|\|\|\|___\|:\|\|\|___\|\|\|\|:\|\n______________CUUU_UCCC_AUUUG________________UACUGCC___AUUUA___CAAUUA\n3'-UUU...GCCAA____A____C_____UCUGUAAGUCUUUACU_______AUU_____UUU______CUACU...UCG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________9\n	201 -- 207	27 -- 33	-22.7807 kcal/mol	6.16544 kcal/mol	6.33995 kcal/mol	186 221@LB@ \| \|@LB@5'-GUU...CGUGA A C U AAACG...CGC-3'@LB@ GAAA AGGG UAAAC AUGACGG UGAAU GUUAGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|:\|@LB@ CUUU UCCC AUUUG UACUGCC AUUUA CAAUUA@LB@3'-UUU...GCCAA A C UCUGUAAGUCUUUACU AUU UUU CUACU...UCG-5'@LB@ \| \|@LB@ 65 9@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -22.7807 kcal/mol@LB@Unfolding Energy - mRNA 6.16544 kcal/mol@LB@Unfolding Energy - sRNA 6.33995 kcal/mol@LB@@LB@Position - mRNA 187 -- 220@LB@Position - sRNA 10 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 27 -- 33@LB@
18	0.0008759	0.1482	b3626	waaR	-11.62	0.044565	224 -- 238	11 -- 25	lipopolysaccharide 1 2-glucosyltransferase; UDP-glucose:(glucosyl)LPS alpha-1 2-glucosyltransferase	_____________223_____________239\n_____________\|_______________\|\n5'-UGG...AUAGA_______________AGCCU...GUG-3'\n______________GAUAGAUAAAGUUAA\n______________:\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________UUAUUUAUUUCAAUU\n3'-UUU...UGCCA_______________ACUAC...UCG-5'\n_____________\|_______________\|\n_____________26______________10\n	232 -- 238	11 -- 17	-12.9968 kcal/mol	1.27318 kcal/mol	0.10636 kcal/mol	223 239@LB@ \| \|@LB@5'-UGG...AUAGA AGCCU...GUG-3'@LB@ GAUAGAUAAAGUUAA@LB@ :\|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ UUAUUUAUUUCAAUU@LB@3'-UUU...UGCCA ACUAC...UCG-5'@LB@ \| \|@LB@ 26 10@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -12.9968 kcal/mol@LB@Unfolding Energy - mRNA 1.27318 kcal/mol@LB@Unfolding Energy - sRNA 0.10636 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 11 -- 25@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
25	0.00149	0.1957	b4244	pyrI	-16.22	0.003374	188 -- 229	11 -- 59	aspartate carbamoyltransferase regulatory subunit	_____________187_________________________________________________230\n_____________\|___________________________________________________\|\n5'-UUC...CUGUA__________________________CAC___A________UGC_______AGCUA...UCA-3'\n______________AGGGG_AAAUAGA________GAUGA___ACG_UAAUAAAU___AGGUUGA\n______________\|\|\|\|\|_\|\|\|:\|\|\|________:\|\|\|\|___\|\|\|_\|\|\|\|\|\|\|\|___\|:\|\|\|:\|\n______________UCCCC_UUUGUCU________UUACU___UGC_AUUAUUUA___UUCAAUU\n3'-UUU...CUUUA_____A_______GUAAGUCU_____UAC___C________U_________ACUAC...UCG-5'\n_____________\|___________________________________________________\|\n_____________60__________________________________________________10\n	223 -- 229	11 -- 17	-28.8643 kcal/mol	6.31236 kcal/mol	6.33314 kcal/mol	187 230@LB@ \| \|@LB@5'-UUC...CUGUA CAC A UGC AGCUA...UCA-3'@LB@ AGGGG AAAUAGA GAUGA ACG UAAUAAAU AGGUUGA@LB@ \|\|\|\|\| \|\|\|:\|\|\| :\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|:\|@LB@ UCCCC UUUGUCU UUACU UGC AUUAUUUA UUCAAUU@LB@3'-UUU...CUUUA A GUAAGUCU UAC C U ACUAC...UCG-5'@LB@ \| \|@LB@ 60 10@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -28.8643 kcal/mol@LB@Unfolding Energy - mRNA 6.31236 kcal/mol@LB@Unfolding Energy - sRNA 6.33314 kcal/mol@LB@@LB@Position - mRNA 188 -- 229@LB@Position - sRNA 11 -- 59@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 11 -- 17@LB@
170	0.02787	0.531	b3184	yhbE	-10.77	0.067448	1 -- 31	11 -- 53	EamA family inner membrane putative transporter	______________1__________________________________________32\n______________\|__________________________________________\|\n___________5'-_________GUA_________AUU___________________AGGCC...UGG-3'\n______________AAGCAGACG_____AAGUGAA___CG__________AAGUUAA\n______________\|\|:\|\|\|\|\|:_____\|\|:\|\|\|\|___\|\|__________\|\|\|\|\|\|\|\n______________UUUGUCUGU_____UUUACUU___GC__________UUCAAUU\n3'-UUU...CCCCA_________AAGUC_______ACU__CAUUAUUUAU_______ACUAC...UCG-5'\n_____________\|___________________________________________\|\n_____________54__________________________________________10\n	25 -- 31	11 -- 17	-18.1985 kcal/mol	1.09209 kcal/mol	6.3325 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GUA AUU AGGCC...UGG-3'@LB@ AAGCAGACG AAGUGAA CG AAGUUAA@LB@ \|\|:\|\|\|\|\|: \|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUGUCUGU UUUACUU GC UUCAAUU@LB@3'-UUU...CCCCA AAGUC ACU CAUUAUUUAU ACUAC...UCG-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -18.1985 kcal/mol@LB@Unfolding Energy - mRNA 1.09209 kcal/mol@LB@Unfolding Energy - sRNA 6.3325 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
180	0.02979	0.5424	b4217	ytfK	-6.46	0.400721	35 -- 83	12 -- 56	DUF1107 family protein	_____________34_____________________________________________________84\n_____________\|______________________________________________________\|\n5'-GAA...GCUUC______A____A______________A__U___ACCUUUAG_____A_______UACGC...AAU-3'\n______________GGUAAA_AGAU_AUUC_____UGAAU_AU_GUA________GUAAA_AAAGUUA\n______________\|\|\|\|\|\|_\|\|\|:_\|\|\|\|_____\|\|\|\|\|_\|:_\|\|\|________:\|\|\|\|_\|\|\|\|\|\|\|\n______________CCAUUU_UCUG_UAAG_____ACUUA_UG_CAU________UAUUU_UUUCAAU\n3'-UUU...UAUCC______G_________UCUUU_____C__C________________A_______UACUA...UCG-5'\n_____________\|______________________________________________________\|\n_____________57_____________________________________________________11\n	77 -- 83	12 -- 18	-20.0112 kcal/mol	7.22293 kcal/mol	6.33232 kcal/mol	34 84@LB@ \| \|@LB@5'-GAA...GCUUC A A A U ACCUUUAG A UACGC...AAU-3'@LB@ GGUAAA AGAU AUUC UGAAU AU GUA GUAAA AAAGUUA@LB@ \|\|\|\|\|\| \|\|\|: \|\|\|\| \|\|\|\|\| \|: \|\|\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CCAUUU UCUG UAAG ACUUA UG CAU UAUUU UUUCAAU@LB@3'-UUU...UAUCC G UCUUU C C A UACUA...UCG-5'@LB@ \| \|@LB@ 57 11@LB@@LB@@LB@Energy -6.46 kcal/mol@LB@Hybridization Energy -20.0112 kcal/mol@LB@Unfolding Energy - mRNA 7.22293 kcal/mol@LB@Unfolding Energy - sRNA 6.33232 kcal/mol@LB@@LB@Position - mRNA 35 -- 83@LB@Position - sRNA 12 -- 56@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 12 -- 18@LB@
41	0.004182	0.3349	b3771	ilvD	-12.17	0.033695	175 -- 200	14 -- 53	dihydroxyacid dehydratase	_____________174______________________________________201\n_____________\|________________________________________\|\n5'-GCG...UUACG_________C_________________GA___________AUGCC...GUA-3'\n______________AGACAGACA_______________UGG__GUAAAUAAAGU\n______________\|:\|\|\|\|\|\|\|_______________:\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________UUUGUCUGU_______________GCC__UAUUUAUUUCA\n3'-UUU...CCCCA_________AAGUCUUUACUUACU___AU___________AUUAC...UCG-5'\n_____________\|________________________________________\|\n_____________54_______________________________________13\n	194 -- 200	14 -- 20	-22.054 kcal/mol	3.56189 kcal/mol	6.32552 kcal/mol	174 201@LB@ \| \|@LB@5'-GCG...UUACG C GA AUGCC...GUA-3'@LB@ AGACAGACA UGG GUAAAUAAAGU@LB@ \|:\|\|\|\|\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ UUUGUCUGU GCC UAUUUAUUUCA@LB@3'-UUU...CCCCA AAGUCUUUACUUACU AU AUUAC...UCG-5'@LB@ \| \|@LB@ 54 13@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -22.054 kcal/mol@LB@Unfolding Energy - mRNA 3.56189 kcal/mol@LB@Unfolding Energy - sRNA 6.32552 kcal/mol@LB@@LB@Position - mRNA 175 -- 200@LB@Position - sRNA 14 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 14 -- 20@LB@
71	0.01035	0.4523	b3365	nirB	-13.52	0.016420	166 -- 211	14 -- 63	nitrite reductase large subunit NAD(P)H-binding	_____________165_________________________________________________212\n_____________\|___________________________________________________\|\n5'-AUC...CGUUA_______C__________AA_________C______AAA______C_____CAGAC...UUA-3'\n______________AGGUAGG_GGU_AAUAGA_____AGAAAU_GA_GGC___AAUGAG_AAAGU\n______________\|::\|\|\|\|_\|\|\|_\|\|:\|\|\|_____\|\|\|\|\|\|_:\|_\|:\|___\|\|\|:\|:_\|\|\|\|\|\n______________UUUAUCC_CCA_UUGUCU_____UCUUUA_UU_CUG___UUAUUU_UUUCA\n3'-UUU...CCAAC___________U______GUAAG______C__A___CCA______A_____AUUAC...UCG-5'\n_____________\|___________________________________________________\|\n_____________64__________________________________________________13\n	166 -- 172	57 -- 63	-27.6903 kcal/mol	7.84168 kcal/mol	6.33269 kcal/mol	165 212@LB@ \| \|@LB@5'-AUC...CGUUA C AA C AAA C CAGAC...UUA-3'@LB@ AGGUAGG GGU AAUAGA AGAAAU GA GGC AAUGAG AAAGU@LB@ \|::\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|\|\|\| :\| \|:\| \|\|\|:\|: \|\|\|\|\|@LB@ UUUAUCC CCA UUGUCU UCUUUA UU CUG UUAUUU UUUCA@LB@3'-UUU...CCAAC U GUAAG C A CCA A AUUAC...UCG-5'@LB@ \| \|@LB@ 64 13@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -27.6903 kcal/mol@LB@Unfolding Energy - mRNA 7.84168 kcal/mol@LB@Unfolding Energy - sRNA 6.33269 kcal/mol@LB@@LB@Position - mRNA 166 -- 211@LB@Position - sRNA 14 -- 63@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 57 -- 63@LB@
95	0.01574	0.5059	b2714	ascG	-10.13	0.091468	184 -- 220	14 -- 55	asc operon transcriptional repressor; prpBC operon repressor	_____________183________________________________________221\n_____________\|__________________________________________\|\n5'-AAA...UGCGU_____G_____________AU_______AC____CUG_____GGCGA...AAG-3'\n______________GUAAA_GGAU_____GAAA__GAUGACG__GAUG___GAAGU\n______________\|\|\|\|\|_:\|\|:_____\|\|\|\|__:\|\|\|\|\|\|__:\|\|:___:\|\|\|\|\n______________CAUUU_UCUG_____CUUU__UUACUGC__UUAU___UUUCA\n3'-UUU...AUCCC_____G____UAAGU____AC_______CA____UUA_____AUUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________56_________________________________________13\n	200 -- 206	28 -- 34	-22.7561 kcal/mol	6.30192 kcal/mol	6.32604 kcal/mol	183 221@LB@ \| \|@LB@5'-AAA...UGCGU G AU AC CUG GGCGA...AAG-3'@LB@ GUAAA GGAU GAAA GAUGACG GAUG GAAGU@LB@ \|\|\|\|\| :\|\|: \|\|\|\| :\|\|\|\|\|\| :\|\|: :\|\|\|\|@LB@ CAUUU UCUG CUUU UUACUGC UUAU UUUCA@LB@3'-UUU...AUCCC G UAAGU AC CA UUA AUUAC...UCG-5'@LB@ \| \|@LB@ 56 13@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -22.7561 kcal/mol@LB@Unfolding Energy - mRNA 6.30192 kcal/mol@LB@Unfolding Energy - sRNA 6.32604 kcal/mol@LB@@LB@Position - mRNA 184 -- 220@LB@Position - sRNA 14 -- 55@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 28 -- 34@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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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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