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
174	0.02825	0.531	b2154	yeiG	-9.96	0.098977	140 -- 169	15 -- 51	S-formylglutathione hydrolase	_____________139_____________________________________170\n_____________\|_______________________________________\|\n5'-GCU...UACUC____C________________AA______U_________AAAUU...UUC-3'\n______________ACAG_ACAU_______UGAAU__ACGGUA___GAUGAAG\n______________\|\|\|\|_\|\|\|\|_______\|\|\|\|\|__\|\|\|\|\|\|___:\|\|:\|\|\|\n______________UGUC_UGUA_______ACUUA__UGCCAU___UUAUUUC\n3'-UUU...CCAUU_________AGUCUUU_____C_______UAU_______AAUUA...UCG-5'\n_____________\|_______________________________________\|\n_____________52______________________________________14\n	163 -- 169	15 -- 21	-20.0225 kcal/mol	3.74261 kcal/mol	6.32297 kcal/mol	139 170@LB@ \| \|@LB@5'-GCU...UACUC C AA U AAAUU...UUC-3'@LB@ ACAG ACAU UGAAU ACGGUA GAUGAAG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| :\|\|:\|\|\|@LB@ UGUC UGUA ACUUA UGCCAU UUAUUUC@LB@3'-UUU...CCAUU AGUCUUU C UAU AAUUA...UCG-5'@LB@ \| \|@LB@ 52 14@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -20.0225 kcal/mol@LB@Unfolding Energy - mRNA 3.74261 kcal/mol@LB@Unfolding Energy - sRNA 6.32297 kcal/mol@LB@@LB@Position - mRNA 140 -- 169@LB@Position - sRNA 15 -- 51@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 15 -- 21@LB@
125	0.01993	0.5155	b2347	yfdC	-8.10	0.220050	281 -- 291	15 -- 25	putative inner membrane protein	_____________280_________292\n_____________\|___________\|\n5'-GCA...AUAGA___________ACCGA...UCC-3'\n______________AAUAGAUGAAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________UUAUUUAUUUC\n3'-UUU...UGCCA___________AAUUA...UCG-5'\n_____________\|___________\|\n_____________26__________14\n	285 -- 291	15 -- 21	-8.49349 kcal/mol	0.301625 kcal/mol	0.0943905 kcal/mol	280 292@LB@ \| \|@LB@5'-GCA...AUAGA ACCGA...UCC-3'@LB@ AAUAGAUGAAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ UUAUUUAUUUC@LB@3'-UUU...UGCCA AAUUA...UCG-5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -8.49349 kcal/mol@LB@Unfolding Energy - mRNA 0.301625 kcal/mol@LB@Unfolding Energy - sRNA 0.0943905 kcal/mol@LB@@LB@Position - mRNA 281 -- 291@LB@Position - sRNA 15 -- 25@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 15 -- 21@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
171	0.02792	0.531	b2754	ygbF	-9.28	0.134010	284 -- 290	53 -- 59	CRISPR adaptation ssRNA endonuclease	_____________283_____291\n_____________\|_______\|\n5'-UGG...CGUGC_______UAUGU...GUG-3'\n______________AGGGGUA\n______________\|\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	284 -- 290	53 -- 59	-11.8962 kcal/mol	2.55869 kcal/mol	0.0564539 kcal/mol	283 291@LB@ \| \|@LB@5'-UGG...CGUGC UAUGU...GUG-3'@LB@ AGGGGUA@LB@ \|\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -11.8962 kcal/mol@LB@Unfolding Energy - mRNA 2.55869 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 284 -- 290@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 53 -- 59@LB@
127	0.01998	0.5155	b2922	yggE	-8.69	0.172995	232 -- 253	1 -- 26	oxidative stress defense protein	_____________231________________________254\n_____________\|__________________________\|\n5'-GCA...GGCAU________________C_________AGCGC...CCG-3'\n______________UAAUGGGUA___UUAG_GG_GAUGGC\n______________\|\|\|\|:::\|\|___\|\|\|:_\|:_\|\|\|:\|\|\n______________AUUAUUUAU___AAUU_CU_CUAUCG\n3'-UUU...CUGCC_________UUC____A__A______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	234 -- 240	18 -- 24	-12.7828 kcal/mol	3.51669 kcal/mol	0.580494 kcal/mol	231 254@LB@ \| \|@LB@5'-GCA...GGCAU C AGCGC...CCG-3'@LB@ UAAUGGGUA UUAG GG GAUGGC@LB@ \|\|\|\|:::\|\| \|\|\|: \|: \|\|\|:\|\|@LB@ AUUAUUUAU AAUU CU CUAUCG@LB@3'-UUU...CUGCC UUC A A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -12.7828 kcal/mol@LB@Unfolding Energy - mRNA 3.51669 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 232 -- 253@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 18 -- 24@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@
163	0.02649	0.526	b3156	yhbS	-11.68	0.043230	178 -- 217	16 -- 53	GNAT family putative N-acetyltransferase	_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-CCG...AAACC______________U_______CC___C____UC_______AAUUC...AUC-3'\n______________AAACAGACA_UCGG_AGGUGAA__AUG_UAAU__GAGUAGA\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|_\|::\|\|\|\|__\|:\|_\|\|\|\|__:\|:\|\|:\|\n______________UUUGUCUGU_AGUC_UUUACUU__UGC_AUUA__UUUAUUU\n3'-UUU...CCCCA_________A____________AC___C_____________CAAUU...UCG-5'\n_____________\|_________________________________________\|\n_____________54________________________________________15\n	211 -- 217	16 -- 22	-26.1463 kcal/mol	8.14596 kcal/mol	6.32252 kcal/mol	177 218@LB@ \| \|@LB@5'-CCG...AAACC U CC C UC AAUUC...AUC-3'@LB@ AAACAGACA UCGG AGGUGAA AUG UAAU GAGUAGA@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| \|::\|\|\|\| \|:\| \|\|\|\| :\|:\|\|:\|@LB@ UUUGUCUGU AGUC UUUACUU UGC AUUA UUUAUUU@LB@3'-UUU...CCCCA A AC C CAAUU...UCG-5'@LB@ \| \|@LB@ 54 15@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -26.1463 kcal/mol@LB@Unfolding Energy - mRNA 8.14596 kcal/mol@LB@Unfolding Energy - sRNA 6.32252 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 16 -- 53@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 16 -- 22@LB@
30	0.002455	0.2686	b4551	yheV	-11.67	0.043500	186 -- 213	38 -- 63	DUF2387 family putative metal-binding protein	_____________185__________________________214\n_____________\|____________________________\|\n5'-AUC...AAUUU______A_______G_U____A__C___AACGU...UUG-3'\n______________GAGUAG_GGGUAAA_A_GGCA_UC_GAA\n______________:\|:\|\|\|_\|\|\|\|\|\|\|_\|_\|:\|\|_\|\|_\|\|\|\n______________UUUAUC_CCCAUUU_U_CUGU_AG_CUU\n3'-UUU...CCAAC______________G______A__U___UACUU...UCG-5'\n_____________\|____________________________\|\n_____________64___________________________37\n	193 -- 199	51 -- 57	-22.6178 kcal/mol	4.69416 kcal/mol	6.25833 kcal/mol	185 214@LB@ \| \|@LB@5'-AUC...AAUUU A G U A C AACGU...UUG-3'@LB@ GAGUAG GGGUAAA A GGCA UC GAA@LB@ :\|:\|\|\| \|\|\|\|\|\|\| \| \|:\|\| \|\| \|\|\|@LB@ UUUAUC CCCAUUU U CUGU AG CUU@LB@3'-UUU...CCAAC G A U UACUU...UCG-5'@LB@ \| \|@LB@ 64 37@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -22.6178 kcal/mol@LB@Unfolding Energy - mRNA 4.69416 kcal/mol@LB@Unfolding Energy - sRNA 6.25833 kcal/mol@LB@@LB@Position - mRNA 186 -- 213@LB@Position - sRNA 38 -- 63@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
48	0.005342	0.3653	b3380	yhfW	-15.20	0.006283	218 -- 233	1 -- 15	phosphopentomutase-related metalloenzyme superfamily protein	_____________217______________234\n_____________\|________________\|\n5'-CUC...GUGGU________U_______UUUGG...GUG-3'\n______________GUUAGUGA_UGAUAGC\n______________\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________CAAUUACU_ACUAUCG\n3'-UUU...UAUUU________________-5'\n_____________\|_______________\|\n_____________16______________1\n	227 -- 233	1 -- 7	-17.7091 kcal/mol	2.46465 kcal/mol	0.0474282 kcal/mol	217 234@LB@ \| \|@LB@5'-CUC...GUGGU U UUUGG...GUG-3'@LB@ GUUAGUGA UGAUAGC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAAUUACU ACUAUCG@LB@3'-UUU...UAUUU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -17.7091 kcal/mol@LB@Unfolding Energy - mRNA 2.46465 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 1 -- 7@LB@
144	0.02445	0.526	b3441	yhhY	-11.04	0.059403	187 -- 218	22 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________186________________________________219\n_____________\|__________________________________\|\n5'-CCC...CCCCA__GA_____A______________GAUA______CGCCA...UGC-3'\n______________AA__GGACA___AGGAAUGAGUGA____GUAAUA\n______________\|\|__:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|____\|\|\|\|\|\|\n______________UU__UCUGU___UCUUUACUUACU____CAUUAU\n3'-UUU...CCCCA__UG_____AAG____________GC________UUAUU...UCG-5'\n_____________\|__________________________________\|\n_____________54_________________________________21\n	202 -- 208	30 -- 36	-22.9472 kcal/mol	5.59747 kcal/mol	6.31329 kcal/mol	186 219@LB@ \| \|@LB@5'-CCC...CCCCA GA A GAUA CGCCA...UGC-3'@LB@ AA GGACA AGGAAUGAGUGA GUAAUA@LB@ \|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\| \|\|\|\|\|\|@LB@ UU UCUGU UCUUUACUUACU CAUUAU@LB@3'-UUU...CCCCA UG AAG GC UUAUU...UCG-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.9472 kcal/mol@LB@Unfolding Energy - mRNA 5.59747 kcal/mol@LB@Unfolding Energy - sRNA 6.31329 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 30 -- 36@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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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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