Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
164	0.007775	0.1668	b2097	fbaB	-9.67	0.277966	247 -- 265	48 -- 68	fructose-bisphosphate aldolase class I	_____________246___________________266\n_____________\|_____________________\|\n5'-AAU...CCUUU_______C________A_G__AAUUC...AUG-3'\n______________UACAGCA___CGUUGU_U_AC\n______________:\|\|\|\|\|\|___\|\|\|\|\|\|_\|_\|\|\n______________GUGUCGU___GCAACA_A_UG\n3'-UUU...GAUGU_______UAA______A_G__AGUCC...GCA-5'\n_____________\|_____________________\|\n_____________69____________________47\n	247 -- 253	62 -- 68	-18.0796 kcal/mol	4.78239 kcal/mol	3.63277 kcal/mol	246 266@LB@ \| \|@LB@5'-AAU...CCUUU C A G AAUUC...AUG-3'@LB@ UACAGCA CGUUGU U AC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \| \|\|@LB@ GUGUCGU GCAACA A UG@LB@3'-UUU...GAUGU UAA A G AGUCC...GCA-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -18.0796 kcal/mol@LB@Unfolding Energy - mRNA 4.78239 kcal/mol@LB@Unfolding Energy - sRNA 3.63277 kcal/mol@LB@@LB@Position - mRNA 247 -- 265@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 62 -- 68@LB@
65	0.002677	0.1417	b0584	fepA	-11.47	0.132508	209 -- 249	37 -- 78	ferrienterobactin outer membrane transporter	_____________208___________________________________________250\n_____________\|_____________________________________________\|\n5'-GAA...AACAA___________U_CCU___C________G____A__U________AUGGG...ACG-3'\n______________GAAGAUU_CAU_C___GGC___UUGUUG__UCA_UC_GGGGAUUU\n______________:\|\|\|\|:\|_\|\|:_\|___:\|\|___\|:\|\|\|\|__\|\|\|_\|\|_\|\|\|\|\|\|\|\|\n______________UUUCUGA_GUG_G___UCG___AGCAAC__AGU_AG_CCCCUAAA\n3'-UUU...ACCCG_______U___U_______UUA______AA___G__U________GGUAC...GCA-5'\n_____________\|_____________________________________________\|\n_____________79____________________________________________36\n	243 -- 249	37 -- 43	-30.6633 kcal/mol	14.4176 kcal/mol	4.77973 kcal/mol	208 250@LB@ \| \|@LB@5'-GAA...AACAA U CCU C G A U AUGGG...ACG-3'@LB@ GAAGAUU CAU C GGC UUGUUG UCA UC GGGGAUUU@LB@ :\|\|\|\|:\| \|\|: \| :\|\| \|:\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UUUCUGA GUG G UCG AGCAAC AGU AG CCCCUAAA@LB@3'-UUU...ACCCG U U UUA AA G U GGUAC...GCA-5'@LB@ \| \|@LB@ 79 36@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -30.6633 kcal/mol@LB@Unfolding Energy - mRNA 14.4176 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 209 -- 249@LB@Position - sRNA 37 -- 78@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 37 -- 43@LB@
95	0.004386	0.1538	b1083	flgL	-11.72	0.118200	146 -- 194	40 -- 76	flagellar hook-filament junction protein	_____________145_________________________________________________195\n_____________\|___________________________________________________\|\n5'-UUG...UCUGC____G___A______________AUGCGCUGAUUAACA______A______GAUAA...GUA-3'\n______________AGAC_GCA_AC_GCGAUUU_UUG_______________UUCGCU_AGGGGA\n______________\|\|\|\|_:\|\|_\|\|_\|\|:\|\|\|:_\|\|\|_______________\|\|\|:\|\|_\|\|\|\|\|\|\n______________UCUG_UGU_UG_CGUUAAG_AAC_______________AAGUGA_UCCCCU\n3'-UUU...CCGUU____A___G__U_______C___A____________________G______AAAGG...GCA-5'\n_____________\|___________________________________________________\|\n_____________77__________________________________________________39\n	157 -- 163	58 -- 64	-28.9648 kcal/mol	12.4692 kcal/mol	4.77843 kcal/mol	145 195@LB@ \| \|@LB@5'-UUG...UCUGC G A AUGCGCUGAUUAACA A GAUAA...GUA-3'@LB@ AGAC GCA AC GCGAUUU UUG UUCGCU AGGGGA@LB@ \|\|\|\| :\|\| \|\| \|\|:\|\|\|: \|\|\| \|\|\|:\|\| \|\|\|\|\|\|@LB@ UCUG UGU UG CGUUAAG AAC AAGUGA UCCCCU@LB@3'-UUU...CCGUU A G U C A G AAAGG...GCA-5'@LB@ \| \|@LB@ 77 39@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -28.9648 kcal/mol@LB@Unfolding Energy - mRNA 12.4692 kcal/mol@LB@Unfolding Energy - sRNA 4.77843 kcal/mol@LB@@LB@Position - mRNA 146 -- 194@LB@Position - sRNA 40 -- 76@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 58 -- 64@LB@
21	0.0001827	0.02926	b1937	fliE	-13.91	0.039102	192 -- 221	38 -- 77	flagellar basal-body component	_____________191________________________________________222\n_____________\|__________________________________________\|\n5'-CUG...UCCGG_____GAGA___U_______A_____________________GAAGG...GUU-3'\n______________GAGAC____AUG_CAGCGAU_____________CAGGGGAUU\n______________:\|\|\|\|____\|::_\|\|\|\|:\|\|_____________\|\|\|\|\|\|\|\|\|\n______________UUCUG____UGU_GUCGUUA_____________GUCCCCUAA\n3'-UUU...CCCGU_____AUG____________AGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________37\n	215 -- 221	38 -- 44	-25.7557 kcal/mol	7.06678 kcal/mol	4.77969 kcal/mol	191 222@LB@ \| \|@LB@5'-CUG...UCCGG GAGA U A GAAGG...GUU-3'@LB@ GAGAC AUG CAGCGAU CAGGGGAUU@LB@ :\|\|\|\| \|:: \|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UUCUG UGU GUCGUUA GUCCCCUAA@LB@3'-UUU...CCCGU AUG AGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 78 37@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -25.7557 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 4.77969 kcal/mol@LB@@LB@Position - mRNA 192 -- 221@LB@Position - sRNA 38 -- 77@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
69	0.002809	0.1417	b1925	fliS	-16.42	0.008504	133 -- 153	57 -- 74	flagellar protein potentiates polymerization	_____________132___________________154\n_____________\|_____________________\|\n5'-UUA...CAGCA_____UUA_____________AAAAC...AUG-3'\n______________GCUAC___ACGCAGCAGUUCG\n______________:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|\|\n______________UGAUG___UGUGUCGUUAAGC\n3'-UUU...GUUUC_____________________AACAA...GCA-5'\n_____________\|_____________________\|\n_____________75____________________56\n	147 -- 153	57 -- 63	-25.0139 kcal/mol	5.019 kcal/mol	3.57148 kcal/mol	132 154@LB@ \| \|@LB@5'-UUA...CAGCA UUA AAAAC...AUG-3'@LB@ GCUAC ACGCAGCAGUUCG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\|\|@LB@ UGAUG UGUGUCGUUAAGC@LB@3'-UUU...GUUUC AACAA...GCA-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.0139 kcal/mol@LB@Unfolding Energy - mRNA 5.019 kcal/mol@LB@Unfolding Energy - sRNA 3.57148 kcal/mol@LB@@LB@Position - mRNA 133 -- 153@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 57 -- 63@LB@
174	0.008627	0.1745	b1926	fliT	-7.57	0.540698	180 -- 211	31 -- 53	putative flagellar synthesis and assembly chaperone	_____________179______________________________212\n_____________\|________________________________\|\n5'-GUG...CCUUC___G_______ACCCAGUCU___GAA______ACCGC...UCA-3'\n______________UUU_AUUCAGG_________GAU___CCAUGC\n______________\|\|\|_\|:\|\|\|\|\|_________\|\|\|___\|\|\|\|\|\|\n______________AAA_UGAGUCC_________CUA___GGUACG\n3'-UUU...GCAAC___G_______C___________AA_______AAUAU...GCA-5'\n_____________\|________________________________\|\n_____________54_______________________________30\n	184 -- 190	43 -- 49	-18.5651 kcal/mol	6.60729 kcal/mol	4.38339 kcal/mol	179 212@LB@ \| \|@LB@5'-GUG...CCUUC G ACCCAGUCU GAA ACCGC...UCA-3'@LB@ UUU AUUCAGG GAU CCAUGC@LB@ \|\|\| \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AAA UGAGUCC CUA GGUACG@LB@3'-UUU...GCAAC G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -18.5651 kcal/mol@LB@Unfolding Energy - mRNA 6.60729 kcal/mol@LB@Unfolding Energy - sRNA 4.38339 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
147	0.006785	0.1624	b1920	fliY	-15.06	0.020217	159 -- 198	40 -- 75	cystine transporter subunit	_____________158______________________________________199\n_____________\|________________________________________\|\n5'-CCA...ACAAU____C_____U____ACAGACAUAACAA_________U__AUAUG...UGC-3'\n______________GGCU_UACAC_GCAA_____________CAUUCGGGG_GA\n______________\|:\|\|_:\|\|\|\|_\|\|\|\|_____________\|\|:\|\|:\|\|\|_\|\|\n______________CUGA_GUGUG_CGUU_____________GUGAGUCCC_CU\n3'-UUU...CGUUU____U_____U____AAGCAACAAA_______________AAAGG...GCA-5'\n_____________\|________________________________________\|\n_____________76_______________________________________39\n	189 -- 195	42 -- 48	-27.6268 kcal/mol	7.79206 kcal/mol	4.77786 kcal/mol	158 199@LB@ \| \|@LB@5'-CCA...ACAAU C U ACAGACAUAACAA U AUAUG...UGC-3'@LB@ GGCU UACAC GCAA CAUUCGGGG GA@LB@ \|:\|\| :\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\| \|\|@LB@ CUGA GUGUG CGUU GUGAGUCCC CU@LB@3'-UUU...CGUUU U U AAGCAACAAA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -27.6268 kcal/mol@LB@Unfolding Energy - mRNA 7.79206 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 159 -- 198@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 42 -- 48@LB@
13	0.0001005	0.0245	b1921	fliZ	-13.92	0.038869	246 -- 263	63 -- 78	RpoS antagonist; putative regulator of FliA activity	_____________245________________264\n_____________\|__________________\|\n5'-UGC...AUCUU_______UUAA_______CAGAC...AUC-3'\n______________AAAGACU____ACACAGC\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UUUCUGA____UGUGUCG\n3'-UUU...ACCCG_______UG_________UUAAG...GCA-5'\n_____________\|__________________\|\n_____________79_________________62\n	257 -- 263	63 -- 69	-17.8578 kcal/mol	0.69523 kcal/mol	3.24195 kcal/mol	245 264@LB@ \| \|@LB@5'-UGC...AUCUU UUAA CAGAC...AUC-3'@LB@ AAAGACU ACACAGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUCUGA UGUGUCG@LB@3'-UUU...ACCCG UG UUAAG...GCA-5'@LB@ \| \|@LB@ 79 62@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.8578 kcal/mol@LB@Unfolding Energy - mRNA 0.69523 kcal/mol@LB@Unfolding Energy - sRNA 3.24195 kcal/mol@LB@@LB@Position - mRNA 246 -- 263@LB@Position - sRNA 63 -- 78@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 63 -- 69@LB@
53	0.001859	0.1218	b0529	folD	-11.41	0.136116	200 -- 226	61 -- 85	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase	_____________199_________________________227\n_____________\|___________________________\|\n5'-CAA...UCUCU_____CA___________UG_______AACGA...CAC-3'\n______________GAUGG__GCAAAGAUUAU__ACGGUAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|:\|\|\n______________CUACC__CGUUUCUGAUG__UGUCGUU\n3'-UUU...ACCCU__________________UG_______AAGCA...GCA-5'\n_____________\|___________________________\|\n_____________86__________________________60\n	220 -- 226	61 -- 67	-27.4215 kcal/mol	5.77154 kcal/mol	10.2439 kcal/mol	199 227@LB@ \| \|@LB@5'-CAA...UCUCU CA UG AACGA...CAC-3'@LB@ GAUGG GCAAAGAUUAU ACGGUAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:\|\|: \|\|:\|:\|\|@LB@ CUACC CGUUUCUGAUG UGUCGUU@LB@3'-UUU...ACCCU UG AAGCA...GCA-5'@LB@ \| \|@LB@ 86 60@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -27.4215 kcal/mol@LB@Unfolding Energy - mRNA 5.77154 kcal/mol@LB@Unfolding Energy - sRNA 10.2439 kcal/mol@LB@@LB@Position - mRNA 200 -- 226@LB@Position - sRNA 61 -- 85@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 61 -- 67@LB@
126	0.00562	0.157	b3017	ftsP	-15.30	0.017476	190 -- 242	38 -- 84	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)	_____________189____________________________________________________243\n_____________\|______________________________________________________\|\n5'-GAC...UUUAC____A_____U__GU___U____CGG____CAG________GGCAUC_______GCACU...CGC-3'\n______________AUGG_GCAAA_AU__CAC_CAGU____CGU___UUCAUUCA______GGGGAUU\n______________\|\|\|\|_\|\|\|\|\|_\|:__\|\|\|_\|\|\|:____\|\|\|___\|\|\|\|:\|\|\|______\|\|\|\|\|\|\|\n______________UACC_CGUUU_UG__GUG_GUCG____GCA___AAGUGAGU______CCCCUAA\n3'-UUU...CCCUC__________C__AU___U____UUAA___ACA_____________________AGGUA...GCA-5'\n_____________\|______________________________________________________\|\n_____________85_____________________________________________________37\n	236 -- 242	38 -- 44	-40.4092 kcal/mol	11.1124 kcal/mol	13.9994 kcal/mol	189 243@LB@ \| \|@LB@5'-GAC...UUUAC A U GU U CGG CAG GGCAUC GCACU...CGC-3'@LB@ AUGG GCAAA AU CAC CAGU CGU UUCAUUCA GGGGAUU@LB@ \|\|\|\| \|\|\|\|\| \|: \|\|\| \|\|\|: \|\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UACC CGUUU UG GUG GUCG GCA AAGUGAGU CCCCUAA@LB@3'-UUU...CCCUC C AU U UUAA ACA AGGUA...GCA-5'@LB@ \| \|@LB@ 85 37@LB@@LB@@LB@Energy -15.30 kcal/mol@LB@Hybridization Energy -40.4092 kcal/mol@LB@Unfolding Energy - mRNA 11.1124 kcal/mol@LB@Unfolding Energy - sRNA 13.9994 kcal/mol@LB@@LB@Position - mRNA 190 -- 242@LB@Position - sRNA 38 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 38 -- 44@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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