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	Additional homologs
91	0.01489	0.5059	b3805	hemC	-12.98	0.021909	168 -- 195	24 -- 52	hydroxymethylbilane synthase		_____________167___________________________196\n_____________\|_____________________________\|\n5'-AAA...GUUAG_______CA_____UGAU___________CAAGC...GCC-3'\n______________GAUGGAC___CGGA____AAUGACGGUAA\n______________:\|::\|\|\|___\|:\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG___GUCU____UUACUGCCAUU\n3'-UUU...CCCAU_______UAA____UUAC___________AUUUA...UCG-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	189 -- 195	24 -- 30	-23.6136 kcal/mol	4.33145 kcal/mol	6.2974 kcal/mol	167 196@LB@ \| \|@LB@5'-AAA...GUUAG CA UGAU CAAGC...GCC-3'@LB@ GAUGGAC CGGA AAUGACGGUAA@LB@ :\|::\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG GUCU UUACUGCCAUU@LB@3'-UUU...CCCAU UAA UUAC AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -23.6136 kcal/mol@LB@Unfolding Energy - mRNA 4.33145 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 24 -- 30@LB@
92	0.01497	0.5059	b1902	ftnB	-10.62	0.072498	12 -- 36	1 -- 25	ferritin B putative ferrous iron reservoir		_____________11________________________37\n_____________\|_________________________\|\n5'-UGA...GUAAA____U_____C________UUA___AUUUU...AAC-3'\n______________AAUA_AUAAA_UUGAUGAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|:\|\|\|\|\|___\|\|\|\n______________UUAU_UAUUU_AAUUACUA___UCG\n3'-UUU...UGCCA____U_____C________CUA___-5'\n_____________\|________________________\|\n_____________26_______________________1\n	24 -- 30	7 -- 13	-13.6335 kcal/mol	2.89836 kcal/mol	0.112205 kcal/mol	11 37@LB@ \| \|@LB@5'-UGA...GUAAA U C UUA AUUUU...AAC-3'@LB@ AAUA AUAAA UUGAUGAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|:\|\|\|\|\| \|\|\|@LB@ UUAU UAUUU AAUUACUA UCG@LB@3'-UUU...UGCCA U C CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -13.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.89836 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 12 -- 36@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 7 -- 13@LB@
93	0.0151	0.5059	b1675	ydhZ	-8.81	0.164498	185 -- 226	5 -- 54	uncharacterized protein		_____________184________________________________________________227\n_____________\|__________________________________________________\|\n5'-CUU...CAUGA___________AA____UG___AAU___AC____________________ACUGU...AGC-3'\n______________UAAAUAGGUAU__AGAA__GGA___CGG____AAA_AGAG_____GAUGA\n______________\|\|\|\|:\|\|::\|\|__\|\|\|\|__\|:\|___\|\|\|____\|\|\|_\|:\|\|_____\|\|\|\|\|\n______________AUUUGUCUGUA__UCUU__CUU___GCC____UUU_UUUC_____CUACU\n3'-UUU...UCCCC___________AG____UA___ACU___AUUA___A____AAUUA_____AUCG-5'\n_____________\|__________________________________________________\|\n_____________55_________________________________________________4\n	186 -- 192	47 -- 53	-19.2855 kcal/mol	4.14282 kcal/mol	6.33746 kcal/mol	184 227@LB@ \| \|@LB@5'-CUU...CAUGA AA UG AAU AC ACUGU...AGC-3'@LB@ UAAAUAGGUAU AGAA GGA CGG AAA AGAG GAUGA@LB@ \|\|\|\|:\|\|::\|\| \|\|\|\| \|:\| \|\|\| \|\|\| \|:\|\| \|\|\|\|\|@LB@ AUUUGUCUGUA UCUU CUU GCC UUU UUUC CUACU@LB@3'-UUU...UCCCC AG UA ACU AUUA A AAUUA AUCG-5'@LB@ \| \|@LB@ 55 4@LB@@LB@@LB@Energy -8.81 kcal/mol@LB@Hybridization Energy -19.2855 kcal/mol@LB@Unfolding Energy - mRNA 4.14282 kcal/mol@LB@Unfolding Energy - sRNA 6.33746 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 5 -- 54@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
94	0.01566	0.5059	b3918	cdh	-10.38	0.081442	225 -- 238	1 -- 14	CDP-diacylglycerol phosphotidylhydrolase		_____________224____________239\n_____________\|______________\|\n5'-AUU...UUUUU______________UAUCG...CAU-3'\n______________UUGGUGAUGAUAGU\n______________\|\|::\|\|\|\|\|\|\|\|\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	232 -- 238	1 -- 7	-16.1883 kcal/mol	5.76383 kcal/mol	0.0473494 kcal/mol	224 239@LB@ \| \|@LB@5'-AUU...UUUUU UAUCG...CAU-3'@LB@ UUGGUGAUGAUAGU@LB@ \|\|::\|\|\|\|\|\|\|\|\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.1883 kcal/mol@LB@Unfolding Energy - mRNA 5.76383 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 225 -- 238@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 1 -- 7@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@
96	0.01578	0.5059	b3283	yrdD	-12.59	0.027007	10 -- 20	2 -- 12	ssDNA-binding protein function unknown		_____________9___________21\n_____________\|___________\|\n5'-AAC...CGUGA___________AGCGA...UUG-3'\n______________AAUGGUGAUAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________UUACUACUAUC\n3'-UUU...UUCAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	14 -- 20	2 -- 8	-13.6612 kcal/mol	1.03146 kcal/mol	0.0386655 kcal/mol	9 21@LB@ \| \|@LB@5'-AAC...CGUGA AGCGA...UUG-3'@LB@ AAUGGUGAUAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ UUACUACUAUC@LB@3'-UUU...UUCAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -13.6612 kcal/mol@LB@Unfolding Energy - mRNA 1.03146 kcal/mol@LB@Unfolding Energy - sRNA 0.0386655 kcal/mol@LB@@LB@Position - mRNA 10 -- 20@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 2 -- 8@LB@
97	0.01584	0.5059	b0116	lpd	-10.63	0.072174	157 -- 204	5 -- 49	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase		_____________156_______________________________________________205\n_____________\|_________________________________________________\|\n5'-CCG...CUGAA_____A_____U____CC_C___A________UAUA___GUC_______GUACU...UAA-3'\n______________AGACG__CGGG_AUGA__G_CGG_GAUAAAUA____GAG___AUGAUGA\n______________\|\|\|\|:__\|:\|:_\|\|\|\|__\|_\|\|\|_:\|\|\|\|\|\|\|____:\|\|___\|\|\|\|\|\|\|\n______________UCUGU__GUCU_UACU__C_GCC_UUAUUUAU____UUC___UACUACU\n3'-UUU...AUUUG_____AA____U____UA_U___A_______________AAU_______AUCG-5'\n_____________\|_________________________________________________\|\n_____________50________________________________________________4\n	198 -- 204	5 -- 11	-27.6335 kcal/mol	10.6788 kcal/mol	6.32229 kcal/mol	156 205@LB@ \| \|@LB@5'-CCG...CUGAA A U CC C A UAUA GUC GUACU...UAA-3'@LB@ AGACG CGGG AUGA G CGG GAUAAAUA GAG AUGAUGA@LB@ \|\|\|\|: \|:\|: \|\|\|\| \| \|\|\| :\|\|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|@LB@ UCUGU GUCU UACU C GCC UUAUUUAU UUC UACUACU@LB@3'-UUU...AUUUG AA U UA U A AAU AUCG-5'@LB@ \| \|@LB@ 50 4@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -27.6335 kcal/mol@LB@Unfolding Energy - mRNA 10.6788 kcal/mol@LB@Unfolding Energy - sRNA 6.32229 kcal/mol@LB@@LB@Position - mRNA 157 -- 204@LB@Position - sRNA 5 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome		_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@LB@
99	0.01587	0.5059	b2155	cirA	-12.92	0.022646	275 -- 290	1 -- 16	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter		_____________274______________291\n_____________\|________________\|\n5'-GGA...UUAGC___C____________GAAAC...UGG-3'\n______________GGU_GAUGAUGAUGGC\n______________:\|\|_:\|\|\|\|\|\|\|\|:\|\|\n______________UCA_UUACUACUAUCG\n3'-UUU...UUAUU___A____________-5'\n_____________\|_______________\|\n_____________17______________1\n	284 -- 290	1 -- 7	-19.8516 kcal/mol	6.87927 kcal/mol	0.0492804 kcal/mol	274 291@LB@ \| \|@LB@5'-GGA...UUAGC C GAAAC...UGG-3'@LB@ GGU GAUGAUGAUGGC@LB@ :\|\| :\|\|\|\|\|\|\|\|:\|\|@LB@ UCA UUACUACUAUCG@LB@3'-UUU...UUAUU A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -19.8516 kcal/mol@LB@Unfolding Energy - mRNA 6.87927 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 1 -- 7@LB@
100	0.01591	0.5059	b0531	sfmC	-11.86	0.039421	211 -- 227	6 -- 22	putative periplasmic pilus chaperone	b4316	_____________210_______________228\n_____________\|_________________\|\n5'-AAU...GACUA___________U_____CUCAU...GUA-3'\n______________AAAUAAAGUUA_UGAUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUAUUUCAAU_ACUAC\n3'-UUU...CAUUA___________U_____UAUCG-5'\n_____________\|_________________\|\n_____________23________________5\n	215 -- 221	12 -- 18	-15.888 kcal/mol	3.9302 kcal/mol	0.0976382 kcal/mol	210 228@LB@ \| \|@LB@5'-AAU...GACUA U CUCAU...GUA-3'@LB@ AAAUAAAGUUA UGAUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUAUUUCAAU ACUAC@LB@3'-UUU...CAUUA U UAUCG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -15.888 kcal/mol@LB@Unfolding Energy - mRNA 3.9302 kcal/mol@LB@Unfolding Energy - sRNA 0.0976382 kcal/mol@LB@@LB@Position - mRNA 211 -- 227@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 12 -- 18@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)

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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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