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
61	0.008575	0.4523	b3464	ftsY	-13.38	0.017655	71 -- 119	2 -- 50	Signal Recognition Particle (SRP) receptor	_____________70__________________________________________________120\n_____________\|___________________________________________________\|\n5'-CCC...UCCGC______ACACAUACUUGCA_______AU______U________________ACUAU...CGG-3'\n______________CAGAUA_____________GGCGGUG__GUGAAU_AAGUUAA__GUGAUAG\n______________\|\|\|\|:\|_____________\|:\|\|\|\|:__:\|:\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________GUCUGU_____________CUGCCAU__UAUUUA_UUCAAUU__UACUAUC\n3'-UUU...CAUUU______AAGUCUUUACUUA_______________U_______AC_______G-5'\n_____________\|___________________________________________________\|\n_____________51__________________________________________________1\n	113 -- 119	2 -- 8	-30.4135 kcal/mol	10.695 kcal/mol	6.33478 kcal/mol	70 120@LB@ \| \|@LB@5'-CCC...UCCGC ACACAUACUUGCA AU U ACUAU...CGG-3'@LB@ CAGAUA GGCGGUG GUGAAU AAGUUAA GUGAUAG@LB@ \|\|\|\|:\| \|:\|\|\|\|: :\|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ GUCUGU CUGCCAU UAUUUA UUCAAUU UACUAUC@LB@3'-UUU...CAUUU AAGUCUUUACUUA U AC G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -30.4135 kcal/mol@LB@Unfolding Energy - mRNA 10.695 kcal/mol@LB@Unfolding Energy - sRNA 6.33478 kcal/mol@LB@@LB@Position - mRNA 71 -- 119@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 2 -- 8@LB@
21	0.001002	0.1516	b4045	yjbJ	-13.25	0.018991	259 -- 290	28 -- 62	stress-induced protein UPF0337 family	_____________258__________________________________291\n_____________\|____________________________________\|\n5'-CGU...AGAGC_______C_____U___CGAU________U______AUCAU...AAG-3'\n______________AAUGGGG__AAAC_GAC_______GAUGA_AUGACG\n______________\|\|\|:\|\|\|__\|\|\|\|_\|\|\|_______:\|\|\|\|_\|\|\|\|\|\|\n______________UUAUCCC__UUUG_CUG_______UUACU_UACUGC\n3'-UUU...CAACU_______CA____U___UAAGUCU____________CAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________63___________________________________27\n	259 -- 265	56 -- 62	-23.7721 kcal/mol	4.22826 kcal/mol	6.29418 kcal/mol	258 291@LB@ \| \|@LB@5'-CGU...AGAGC C U CGAU U AUCAU...AAG-3'@LB@ AAUGGGG AAAC GAC GAUGA AUGACG@LB@ \|\|\|:\|\|\| \|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|\|@LB@ UUAUCCC UUUG CUG UUACU UACUGC@LB@3'-UUU...CAACU CA U UAAGUCU CAUUA...UCG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.7721 kcal/mol@LB@Unfolding Energy - mRNA 4.22826 kcal/mol@LB@Unfolding Energy - sRNA 6.29418 kcal/mol@LB@@LB@Position - mRNA 259 -- 290@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 56 -- 62@LB@
29	0.00201	0.2275	b1479	maeA	-13.16	0.019904	170 -- 200	29 -- 59	malate dehydrogenase decarboxylating NAD-requiring; malic enzyme	_____________169_________________________________201\n_____________\|___________________________________\|\n5'-UAG...CCCCC___________________AAAAA___________AUGGA...GCA-3'\n______________AGGG____AUGGAUAUUCA_____GAGUGAGUGAC\n______________\|\|\|\|____\|::\|\|:\|\|\|\|\|_____:\|:\|\|\|:\|\|\|\|\n______________UCCC____UGUCUGUAAGU_____UUUACUUACUG\n3'-UUU...CUUUA____CAUU___________C_______________CCAUU...UCG-5'\n_____________\|___________________________________\|\n_____________60__________________________________28\n	194 -- 200	29 -- 35	-27.1811 kcal/mol	7.73175 kcal/mol	6.28641 kcal/mol	169 201@LB@ \| \|@LB@5'-UAG...CCCCC AAAAA AUGGA...GCA-3'@LB@ AGGG AUGGAUAUUCA GAGUGAGUGAC@LB@ \|\|\|\| \|::\|\|:\|\|\|\|\| :\|:\|\|\|:\|\|\|\|@LB@ UCCC UGUCUGUAAGU UUUACUUACUG@LB@3'-UUU...CUUUA CAUU C CCAUU...UCG-5'@LB@ \| \|@LB@ 60 28@LB@@LB@@LB@Energy -13.16 kcal/mol@LB@Hybridization Energy -27.1811 kcal/mol@LB@Unfolding Energy - mRNA 7.73175 kcal/mol@LB@Unfolding Energy - sRNA 6.28641 kcal/mol@LB@@LB@Position - mRNA 170 -- 200@LB@Position - sRNA 29 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 29 -- 35@LB@
50	0.005695	0.3739	b1086	rluC	-13.13	0.020232	139 -- 168	28 -- 55	23S rRNA pseudouridine(955 2504 2580) synthase	_____________138____________________________169\n_____________\|______________________________\|\n5'-UCC...CAAAA_______UAA____AG_A____________CGAAU...UAC-3'\n______________GUAAAUA___GCAU__A_AAAUGAGUGGCG\n______________\|\|\|\|\|:\|___:\|\|\|__\|_\|\|\|\|\|\|:\|\|:\|\|\n______________CAUUUGU___UGUA__U_UUUACUUACUGC\n3'-UUU...AUCCC_______C______AG_C____________CAUUA...UCG-5'\n_____________\|______________________________\|\n_____________56_____________________________27\n	161 -- 167	29 -- 35	-21.8911 kcal/mol	2.47099 kcal/mol	6.28725 kcal/mol	138 169@LB@ \| \|@LB@5'-UCC...CAAAA UAA AG A CGAAU...UAC-3'@LB@ GUAAAUA GCAU A AAAUGAGUGGCG@LB@ \|\|\|\|\|:\| :\|\|\| \| \|\|\|\|\|\|:\|\|:\|\|@LB@ CAUUUGU UGUA U UUUACUUACUGC@LB@3'-UUU...AUCCC C AG C CAUUA...UCG-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -21.8911 kcal/mol@LB@Unfolding Energy - mRNA 2.47099 kcal/mol@LB@Unfolding Energy - sRNA 6.28725 kcal/mol@LB@@LB@Position - mRNA 139 -- 168@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 29 -- 35@LB@
78	0.01113	0.4523	b2678	proW	-13.08	0.020853	190 -- 200	49 -- 59	glycine betaine/proline ABC transporter permease	_____________189_________201\n_____________\|___________\|\n5'-GUU...CGUGA___________AUGGC...ACG-3'\n______________GGGGGUAAAUA\n______________:\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUGU\n3'-UUU...CUUUA___________CUGUA...UCG-5'\n_____________\|___________\|\n_____________60__________48\n	194 -- 200	49 -- 55	-15.0309 kcal/mol	1.22377 kcal/mol	0.730523 kcal/mol	189 201@LB@ \| \|@LB@5'-GUU...CGUGA AUGGC...ACG-3'@LB@ GGGGGUAAAUA@LB@ :\|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUGU@LB@3'-UUU...CUUUA CUGUA...UCG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -15.0309 kcal/mol@LB@Unfolding Energy - mRNA 1.22377 kcal/mol@LB@Unfolding Energy - sRNA 0.730523 kcal/mol@LB@@LB@Position - mRNA 190 -- 200@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 49 -- 55@LB@
79	0.01117	0.4523	b1593	ynfK	-13.04	0.021217	188 -- 210	1 -- 21	putative dethiobiotin synthetase	_____________187_____________________211\n_____________\|_______________________\|\n5'-CAC...AUAAC________________CUGA___GUUUC...CGG-3'\n______________GGUGGAGUUAGUGAUG____AGC\n______________::\|::\|\|\|\|\|:\|\|\|\|\|____\|\|\|\n______________UUAUUUCAAUUACUAC____UCG\n3'-UUU...AUUAU________________UA_____-5'\n_____________\|______________________\|\n_____________22_____________________1\n	197 -- 203	6 -- 12	-19.4081 kcal/mol	6.29658 kcal/mol	0.0669945 kcal/mol	187 211@LB@ \| \|@LB@5'-CAC...AUAAC CUGA GUUUC...CGG-3'@LB@ GGUGGAGUUAGUGAUG AGC@LB@ ::\|::\|\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ UUAUUUCAAUUACUAC UCG@LB@3'-UUU...AUUAU UA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 6.29658 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
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@
66	0.009484	0.4523	b4034	malE	-12.98	0.021943	73 -- 123	2 -- 55	maltose transporter subunit	_____________72_____________________________________________________124\n_____________\|______________________________________________________\|\n5'-AGG...AUUCU_________G_____CACAAAGC_________GGC______GC__G__G_____AAAGA...UGG-3'\n______________GU_AACAGA_A_UCA_________GACGGUGG___GUAGGG__AA_GA_GAUGG\n______________\|\|_\|\|\|\|\|\|_\|_\|\|\|_________\|\|\|\|\|\|::___:\|\|::\|__\|\|_\|\|_\|\|\|:\|\n______________CA_UUGUCU_U_AGU_________CUGCCAUU___UAUUUC__UU_CU_CUAUC\n3'-UUU...AUCCC__U______G_A___CUUUACUUA________AUU______AA__A__A_____G-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	95 -- 101	24 -- 30	-30.2337 kcal/mol	10.9143 kcal/mol	6.33752 kcal/mol	72 124@LB@ \| \|@LB@5'-AGG...AUUCU G CACAAAGC GGC GC G G AAAGA...UGG-3'@LB@ GU AACAGA A UCA GACGGUGG GUAGGG AA GA GAUGG@LB@ \|\| \|\|\|\|\|\| \| \|\|\| \|\|\|\|\|\|:: :\|\|::\| \|\| \|\| \|\|\|:\|@LB@ CA UUGUCU U AGU CUGCCAUU UAUUUC UU CU CUAUC@LB@3'-UUU...AUCCC U G A CUUUACUUA AUU AA A A G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -30.2337 kcal/mol@LB@Unfolding Energy - mRNA 10.9143 kcal/mol@LB@Unfolding Energy - sRNA 6.33752 kcal/mol@LB@@LB@Position - mRNA 73 -- 123@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 24 -- 30@LB@
32	0.003146	0.3086	b1553	rzpQ	-12.95	0.022283	187 -- 223	23 -- 60	Rz-like protein Qin prophage	_____________186______________________________________224\n_____________\|________________________________________\|\n5'-UAU...CCUGC______AUA______UGAA_____UAUUC___________UUUUC...GUG-3'\n______________UGGGGG___GAACAG____UCAGA________AUGGUGAU\n______________\|:\|\|\|\|___:\|\|\|\|\|____\|\|\|\|\|________\|:\|\|\|:\|\|\n______________AUCCCC___UUUGUC____AGUCU________UGCCAUUA\n3'-UUU...ACUUU______A________UGUA_____UUACUUAC________UUUAU...UCG-5'\n_____________\|________________________________________\|\n_____________61_______________________________________22\n	217 -- 223	23 -- 29	-27.4351 kcal/mol	8.1631 kcal/mol	6.31885 kcal/mol	186 224@LB@ \| \|@LB@5'-UAU...CCUGC AUA UGAA UAUUC UUUUC...GUG-3'@LB@ UGGGGG GAACAG UCAGA AUGGUGAU@LB@ \|:\|\|\|\| :\|\|\|\|\| \|\|\|\|\| \|:\|\|\|:\|\|@LB@ AUCCCC UUUGUC AGUCU UGCCAUUA@LB@3'-UUU...ACUUU A UGUA UUACUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 61 22@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -27.4351 kcal/mol@LB@Unfolding Energy - mRNA 8.1631 kcal/mol@LB@Unfolding Energy - sRNA 6.31885 kcal/mol@LB@@LB@Position - mRNA 187 -- 223@LB@Position - sRNA 23 -- 60@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 23 -- 29@LB@
197	0.03325	0.554	b4139	aspA	-12.92	0.022631	26 -- 66	25 -- 59	aspartate ammonia-lyase	_____________25_________________________________________67\n_____________\|__________________________________________\|\n5'-GAU...AAUUA________AA__C____C__________UCCAG__U______GAAAU...ACU-3'\n______________AGGGGUAA__AC_GACA_UUA_AAGUGA_____AU_ACGGUA\n______________\|\|\|\|\|\|\|\|__\|\|_\|\|\|\|_\|:\|_\|\|:\|\|\|_____\|\|_\|\|\|\|\|\|\n______________UCCCCAUU__UG_CUGU_AGU_UUUACU_____UA_UGCCAU\n3'-UUU...CUUUA____________U____A___C_____________C______UAUUU...UCG-5'\n_____________\|__________________________________________\|\n_____________60_________________________________________24\n	27 -- 33	52 -- 58	-28.0294 kcal/mol	8.80617 kcal/mol	6.29893 kcal/mol	25 67@LB@ \| \|@LB@5'-GAU...AAUUA AA C C UCCAG U GAAAU...ACU-3'@LB@ AGGGGUAA AC GACA UUA AAGUGA AU ACGGUA@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\| \|:\| \|\|:\|\|\| \|\| \|\|\|\|\|\|@LB@ UCCCCAUU UG CUGU AGU UUUACU UA UGCCAU@LB@3'-UUU...CUUUA U A C C UAUUU...UCG-5'@LB@ \| \|@LB@ 60 24@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -28.0294 kcal/mol@LB@Unfolding Energy - mRNA 8.80617 kcal/mol@LB@Unfolding Energy - sRNA 6.29893 kcal/mol@LB@@LB@Position - mRNA 26 -- 66@LB@Position - sRNA 25 -- 59@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 52 -- 58@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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