Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter		_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@LB@
22	0.0001652	0.02641	b3566	xylF	-9.94	0.047349	202 -- 240	1 -- 33	D-xylose transporter subunit		_____________201_____________________________________241\n_____________\|_______________________________________\|\n5'-CGA...CACCA_____AUAA________C__CUCAC______C____C__UCCUG...AUG-3'\n______________UGAAA____AGAACAUU_UA_____CCUUUG_ACCU_AC\n______________\|\|\|\|\|____\|\|\|\|\|\|\|:_\|\|_____\|\|\|:\|\|_\|\|\|:_\|\|\n______________ACUUU____UCUUGUAG_AU_____GGAGAC_UGGG_UG\n3'-AUU...UCCAG_____CUA_________A_____________A____A__-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	212 -- 218	18 -- 24	-22.447 kcal/mol	3.48977 kcal/mol	9.04529 kcal/mol	201 241@LB@ \| \|@LB@5'-CGA...CACCA AUAA C CUCAC C C UCCUG...AUG-3'@LB@ UGAAA AGAACAUU UA CCUUUG ACCU AC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|: \|\| \|\|\|:\|\| \|\|\|: \|\|@LB@ ACUUU UCUUGUAG AU GGAGAC UGGG UG@LB@3'-AUU...UCCAG CUA A A A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -22.447 kcal/mol@LB@Unfolding Energy - mRNA 3.48977 kcal/mol@LB@Unfolding Energy - sRNA 9.04529 kcal/mol@LB@@LB@Position - mRNA 202 -- 240@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 18 -- 24@LB@
23	0.0001777	0.02687	b0774	bioA	-12.72	0.005870	209 -- 228	5 -- 24	7 8-diaminopelargonic acid synthase PLP-dependent		_____________208___________________229\n_____________\|_____________________\|\n5'-ACG...ACAAC____G________________AACGC...AAG-3'\n______________GGAC_AUCUUGCCUUUG_ACC\n______________\|:\|\|_\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUUG_UAGAAUGGAGAC_UGG\n3'-AUU...UCUAU_________________A___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	219 -- 225	9 -- 15	-24.4474 kcal/mol	3.74608 kcal/mol	8.01095 kcal/mol	208 229@LB@ \| \|@LB@5'-ACG...ACAAC G AACGC...AAG-3'@LB@ GGAC AUCUUGCCUUUG ACC@LB@ \|:\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUUG UAGAAUGGAGAC UGG@LB@3'-AUU...UCUAU A GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -24.4474 kcal/mol@LB@Unfolding Energy - mRNA 3.74608 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 9 -- 15@LB@
24	0.0002009	0.02687	b1487	ddpA	-9.43	0.065911	261 -- 269	48 -- 56	D D-dipeptide ABC transporter periplasmic binding protein		_____________260_______270\n_____________\|_________\|\n5'-UCA...AUUUC_________CACGC...UGA-3'\n______________CCGGUUGCG\n______________\|\|\|:\|\|:\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	263 -- 269	48 -- 54	-13.2683 kcal/mol	2.26031 kcal/mol	1.55919 kcal/mol	260 270@LB@ \| \|@LB@5'-UCA...AUUUC CACGC...UGA-3'@LB@ CCGGUUGCG@LB@ \|\|\|:\|\|:\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2683 kcal/mol@LB@Unfolding Energy - mRNA 2.26031 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 261 -- 269@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 48 -- 54@LB@
25	0.0002052	0.02687	b0885	aat	-14.70	0.000956	173 -- 191	42 -- 59	leucyl/phenylalanyl-tRNA-protein transferase		_____________172_________________192\n_____________\|___________________\|\n5'-CGU...UGAAC_______C___________UUUGC...UUA-3'\n______________GAUCCGA_UUGCGUGGAGU\n______________:\|\|\|\|\|\|_\|\|:\|\|\|\|:\|\|\|\n______________UUAGGCU_AAUGCACUUCA\n3'-AUU...UCGGU___________________UUUUC...AUG-5'\n_____________\|___________________\|\n_____________60__________________41\n	185 -- 191	42 -- 48	-23.9715 kcal/mol	6.00825 kcal/mol	3.27976 kcal/mol	172 192@LB@ \| \|@LB@5'-CGU...UGAAC C UUUGC...UUA-3'@LB@ GAUCCGA UUGCGUGGAGU@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|:\|\|\|@LB@ UUAGGCU AAUGCACUUCA@LB@3'-AUU...UCGGU UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -23.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.00825 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 173 -- 191@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 42 -- 48@LB@
26	0.0002109	0.02687	b4122	fumB	-13.50	0.002989	276 -- 286	47 -- 57	anaerobic class I fumarate hydratase (fumarase B)	b1612	_____________275_________287\n_____________\|___________\|\n5'-UCC...UCACU___________UAGCG...ACU-3'\n______________UCCGAUUACGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AGGCUAAUGCA\n3'-AUU...GGUUU___________CUUCA...AUG-5'\n_____________\|___________\|\n_____________58__________46\n	280 -- 286	47 -- 53	-16.5827 kcal/mol	1.51899 kcal/mol	1.56839 kcal/mol	275 287@LB@ \| \|@LB@5'-UCC...UCACU UAGCG...ACU-3'@LB@ UCCGAUUACGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AGGCUAAUGCA@LB@3'-AUU...GGUUU CUUCA...AUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -16.5827 kcal/mol@LB@Unfolding Energy - mRNA 1.51899 kcal/mol@LB@Unfolding Energy - sRNA 1.56839 kcal/mol@LB@@LB@Position - mRNA 276 -- 286@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 47 -- 53@LB@
27	0.0002115	0.02687	b2607	trmD	-14.32	0.001383	229 -- 258	48 -- 75	tRNA m(1)G37 methyltransferase SAM-dependent		_____________228____________________________259\n_____________\|______________________________\|\n5'-UCG...GUUUC___________C__G___U_A_________GGGUA...UCC-3'\n______________CUGAAAUGUUC_GC_CAA_U_CCGAUUACG\n______________\|\|:\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|_\|\|\|\|\|\|\|\|\|\n______________GAUUUUAUAAG_CG_GUU_A_GGCUAAUGC\n3'-AUU...CCGCC___________U______U___________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	252 -- 258	48 -- 54	-28.476 kcal/mol	6.50272 kcal/mol	7.67232 kcal/mol	228 259@LB@ \| \|@LB@5'-UCG...GUUUC C G U A GGGUA...UCC-3'@LB@ CUGAAAUGUUC GC CAA U CCGAUUACG@LB@ \|\|:\|\|\|\|:\|\|\| \|\| \|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ GAUUUUAUAAG CG GUU A GGCUAAUGC@LB@3'-AUU...CCGCC U U ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -28.476 kcal/mol@LB@Unfolding Energy - mRNA 6.50272 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 229 -- 258@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 48 -- 54@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor		_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
29	0.0002348	0.02849	b4015	aceA	-10.12	0.041760	186 -- 214	1 -- 27	isocitrate lyase		_____________185____________________________215\n_____________\|______________________________\|\n5'-UUG...UAACU______________ACA__AAA____G___ACAAC...UGA-3'\n______________AUGGAGCAUCU_GC___UG___ACCC_UAC\n______________\|\|:\|\|:\|\|\|\|\|_:\|___\|\|___\|\|\|\|_\|\|\|\n______________UAUCUUGUAGA_UG___AC___UGGG_AUG\n3'-AUU...CUUUC___________A__GAG__A__________-5'\n_____________\|_____________________________\|\n_____________28____________________________1\n	190 -- 196	17 -- 23	-23.282 kcal/mol	5.13768 kcal/mol	8.046 kcal/mol	185 215@LB@ \| \|@LB@5'-UUG...UAACU ACA AAA G ACAAC...UGA-3'@LB@ AUGGAGCAUCU GC UG ACCC UAC@LB@ \|\|:\|\|:\|\|\|\|\| :\| \|\| \|\|\|\| \|\|\|@LB@ UAUCUUGUAGA UG AC UGGG AUG@LB@3'-AUU...CUUUC A GAG A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -23.282 kcal/mol@LB@Unfolding Energy - mRNA 5.13768 kcal/mol@LB@Unfolding Energy - sRNA 8.046 kcal/mol@LB@@LB@Position - mRNA 186 -- 214@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
30	0.0002612	0.03063	b3789	rffH	-9.15	0.078548	244 -- 254	48 -- 58	glucose-1-phosphate thymidylyltransferase		_____________243_________255\n_____________\|___________\|\n5'-GGC...AUUGC___________CGCGG...UGA-3'\n______________AUCCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAGGCUAAUGC\n3'-AUU...CGGUU___________ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	248 -- 254	48 -- 54	-15.7126 kcal/mol	4.98099 kcal/mol	1.55987 kcal/mol	243 255@LB@ \| \|@LB@5'-GGC...AUUGC CGCGG...UGA-3'@LB@ AUCCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAGGCUAAUGC@LB@3'-AUU...CGGUU ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.7126 kcal/mol@LB@Unfolding Energy - mRNA 4.98099 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 244 -- 254@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 48 -- 54@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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