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
46	0.00512	0.3601	b2012	yeeD	-13.46	0.016912	185 -- 206	3 -- 23	putative TusA family sulfurtransferase	_____________184____________________207\n_____________\|______________________\|\n5'-GAU...CAAAU__________G___A_______AUUAA...UAG-3'\n______________UAAGUAAGGU_UAA_GAUGGUG\n______________\|\|\|:\|\|\|:\|\|_\|\|\|_\|\|\|\|:\|:\n______________AUUUAUUUCA_AUU_CUACUAU\n3'-UUU...CCAUU______________A_______CG-5'\n_____________\|______________________\|\n_____________24_____________________2\n	200 -- 206	3 -- 9	-15.4658 kcal/mol	1.89879 kcal/mol	0.104738 kcal/mol	184 207@LB@ \| \|@LB@5'-GAU...CAAAU G A AUUAA...UAG-3'@LB@ UAAGUAAGGU UAA GAUGGUG@LB@ \|\|\|:\|\|\|:\|\| \|\|\| \|\|\|\|:\|:@LB@ AUUUAUUUCA AUU CUACUAU@LB@3'-UUU...CCAUU A CG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -15.4658 kcal/mol@LB@Unfolding Energy - mRNA 1.89879 kcal/mol@LB@Unfolding Energy - sRNA 0.104738 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 3 -- 9@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@
136	0.02238	0.526	b1883	cheB	-10.46	0.078180	185 -- 206	1 -- 23	fused chemotaxis regulator: protein-glutamate methylesterase in two-component regulatory system with CheA	_____________184______________________207\n_____________\|________________________\|\n5'-GGG...UGCGC_________A____C_________AAAAU...CGA-3'\n______________UAAGUAAGG_UUAA_GAUGA__GC\n______________\|\|\|:\|\|\|:\|_\|\|\|\|_\|\|\|\|\|__\|\|\n______________AUUUAUUUC_AAUU_CUACU__CG\n3'-UUU...CCAUU______________A_____AU__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	187 -- 193	15 -- 21	-15.1436 kcal/mol	4.57462 kcal/mol	0.105066 kcal/mol	184 207@LB@ \| \|@LB@5'-GGG...UGCGC A C AAAAU...CGA-3'@LB@ UAAGUAAGG UUAA GAUGA GC@LB@ \|\|\|:\|\|\|:\| \|\|\|\| \|\|\|\|\| \|\|@LB@ AUUUAUUUC AAUU CUACU CG@LB@3'-UUU...CCAUU A AU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -15.1436 kcal/mol@LB@Unfolding Energy - mRNA 4.57462 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 15 -- 21@LB@
16	0.0008012	0.1482	b2011	sbcB	-16.25	0.003318	186 -- 217	24 -- 52	exodeoxyribonuclease I; exonuclease I	_____________185______________________________218\n_____________\|________________________________\|\n5'-CCU...GAAAU_______UUAACCUAAU_______________GCAAC...CCA-3'\n______________AACGGAU__________GAUGAAUGACGGUAA\n______________\|\|\|:\|\|:__________:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG__________UUACUUACUGCCAUU\n3'-UUU...CCCAU_______UAAGUCU__________________AUUUA...UCG-5'\n_____________\|________________________________\|\n_____________53_______________________________23\n	211 -- 217	24 -- 30	-27.0341 kcal/mol	4.49086 kcal/mol	6.2974 kcal/mol	185 218@LB@ \| \|@LB@5'-CCU...GAAAU UUAACCUAAU GCAAC...CCA-3'@LB@ AACGGAU GAUGAAUGACGGUAA@LB@ \|\|\|:\|\|: :\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG UUACUUACUGCCAUU@LB@3'-UUU...CCCAU UAAGUCU AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -27.0341 kcal/mol@LB@Unfolding Energy - mRNA 4.49086 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 186 -- 217@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 24 -- 30@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@
90	0.01478	0.5059	b0740	tolB	-11.20	0.054749	186 -- 207	1 -- 21	periplasmic protein	_____________185_____________________208\n_____________\|_______________________\|\n5'-UCC...GUCCA_______GAGAU___________AGGCA...CCG-3'\n______________GAUAAGG_____AUGAUGA_AGC\n______________:\|\|\|\|:\|_____\|\|\|\|\|\|\|_\|\|\|\n______________UUAUUUC_____UACUACU_UCG\n3'-UUU...AUUAU_______AAU_________A___-5'\n_____________\|______________________\|\n_____________22_____________________1\n	198 -- 204	5 -- 11	-16.1118 kcal/mol	4.84175 kcal/mol	0.0669945 kcal/mol	185 208@LB@ \| \|@LB@5'-UCC...GUCCA GAGAU AGGCA...CCG-3'@LB@ GAUAAGG AUGAUGA AGC@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UUAUUUC UACUACU UCG@LB@3'-UUU...AUUAU AAU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -16.1118 kcal/mol@LB@Unfolding Energy - mRNA 4.84175 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 186 -- 207@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
178	0.02931	0.5406	b3858	yihD	-11.25	0.053413	186 -- 232	8 -- 55	DUF1040 protein YihD	_____________185__________________________________________________233\n_____________\|____________________________________________________\|\n5'-AUA...CAAGA_____G_________CUAU______UAA____UC______________U___ACUCC...CGA-3'\n______________GUAAG_AG_CA_UCA____GAAAUG____ACG____UGAAUGAAGUUA_UGA\n______________\|\|\|\|:_\|\|_\|\|_\|\|\|____\|\|\|\|\|\|____\|\|\|____\|:\|\|\|:\|\|\|\|\|\|_\|\|\|\n______________CAUUU_UC_GU_AGU____CUUUAC____UGC____AUUUAUUUCAAU_ACU\n3'-UUU...AUCCC_____G__U__A_____________UUAC___CAUU____________U___ACUAUCG-5'\n_____________\|____________________________________________________\|\n_____________56___________________________________________________7\n	222 -- 228	12 -- 18	-26.8405 kcal/mol	9.25239 kcal/mol	6.33488 kcal/mol	185 233@LB@ \| \|@LB@5'-AUA...CAAGA G CUAU UAA UC U ACUCC...CGA-3'@LB@ GUAAG AG CA UCA GAAAUG ACG UGAAUGAAGUUA UGA@LB@ \|\|\|\|: \|\| \|\| \|\|\| \|\|\|\|\|\| \|\|\| \|:\|\|\|:\|\|\|\|\|\| \|\|\|@LB@ CAUUU UC GU AGU CUUUAC UGC AUUUAUUUCAAU ACU@LB@3'-UUU...AUCCC G U A UUAC CAUU U ACUAUCG-5'@LB@ \| \|@LB@ 56 7@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -26.8405 kcal/mol@LB@Unfolding Energy - mRNA 9.25239 kcal/mol@LB@Unfolding Energy - sRNA 6.33488 kcal/mol@LB@@LB@Position - mRNA 186 -- 232@LB@Position - sRNA 8 -- 55@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 12 -- 18@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding	_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
13	0.0005091	0.1286	b2062	wza	-15.65	0.004784	187 -- 207	5 -- 27	colanic acid export protein; outer membrane auxillary lipoprotein	_____________186_____________________208\n_____________\|_______________________\|\n5'-AAA...CCAAA____________C__________AAUCC...GCA-3'\n______________GUGAUAAAUAAA___AAUGAUGA\n______________\|\|:\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAUUAUUUAUUU___UUACUACU\n3'-UUU...ACUGC____________CAA________AUCG-5'\n_____________\|_______________________\|\n_____________28______________________4\n	201 -- 207	5 -- 11	-18.4073 kcal/mol	2.04721 kcal/mol	0.709121 kcal/mol	186 208@LB@ \| \|@LB@5'-AAA...CCAAA C AAUCC...GCA-3'@LB@ GUGAUAAAUAAA AAUGAUGA@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAUUAUUUAUUU UUACUACU@LB@3'-UUU...ACUGC CAA AUCG-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -18.4073 kcal/mol@LB@Unfolding Energy - mRNA 2.04721 kcal/mol@LB@Unfolding Energy - sRNA 0.709121 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@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@

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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