Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
146	0.01679	0.3828	b2699	recA	-5.90	0.590167	190 -- 206	40 -- 58	DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP-dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor		_____________189_________________207\n_____________\|___________________\|\n5'-UGC...CAUGA___GA____A_________AUCGA...ACC-3'\n______________CAG__GUAA___AAUGGCU\n______________\|\|\|__\|:\|\|___\|\|\|\|\|\|:\n______________GUC__CGUU___UUACCGG\n3'-UUU...UUUUA___AC____ACG_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________59__________________39\n	200 -- 206	40 -- 46	-15.424 kcal/mol	3.45581 kcal/mol	6.06808 kcal/mol	189 207@LB@ \| \|@LB@5'-UGC...CAUGA GA A AUCGA...ACC-3'@LB@ CAG GUAA AAUGGCU@LB@ \|\|\| \|:\|\| \|\|\|\|\|\|:@LB@ GUC CGUU UUACCGG@LB@3'-UUU...UUUUA AC ACG GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -15.424 kcal/mol@LB@Unfolding Energy - mRNA 3.45581 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
38	0.00253	0.2088	b3789	rffH	-8.84	0.205897	98 -- 106	51 -- 59	glucose-1-phosphate thymidylyltransferase		_____________97________107\n_____________\|_________\|\n5'-GGC...ACGGU_________UCUGG...UGA-3'\n______________UCAGUGGUA\n______________\|\|\|\|\|\|\|:\|\n______________AGUCACCGU\n3'-UUU...CUUUU_________UACGU...UUG-5'\n_____________\|_________\|\n_____________60________50\n	100 -- 106	51 -- 57	-13.9039 kcal/mol	2.34576 kcal/mol	2.71896 kcal/mol	97 107@LB@ \| \|@LB@5'-GGC...ACGGU UCUGG...UGA-3'@LB@ UCAGUGGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ AGUCACCGU@LB@3'-UUU...CUUUU UACGU...UUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.9039 kcal/mol@LB@Unfolding Energy - mRNA 2.34576 kcal/mol@LB@Unfolding Energy - sRNA 2.71896 kcal/mol@LB@@LB@Position - mRNA 98 -- 106@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 51 -- 57@LB@
142	0.01646	0.3828	b2248	rhmR	-12.12	0.041559	199 -- 228	39 -- 72	putative DNA-binding transcriptional regulator for the rhm operon	b4299	_____________198________________________________229\n_____________\|__________________________________\|\n5'-UUU...GUCCA________________A______A__UCCC____UGACA...ACA-3'\n______________GUAUGUUGGA__AUCA___GCAA_GU____GCCC\n______________:\|\|\|\|\|\|\|\|\|__\|\|\|\|___\|\|\|\|_\|:____\|\|\|\|\n______________UAUACAACCU__UAGU___CGUU_CG____CGGG\n3'-UUU...AAAAA__________UU____CAC____A__UUAC____UUGUC...UUG-5'\n_____________\|__________________________________\|\n_____________73_________________________________38\n	202 -- 208	63 -- 69	-27.9384 kcal/mol	8.52428 kcal/mol	7.29447 kcal/mol	198 229@LB@ \| \|@LB@5'-UUU...GUCCA A A UCCC UGACA...ACA-3'@LB@ GUAUGUUGGA AUCA GCAA GU GCCC@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|: \|\|\|\|@LB@ UAUACAACCU UAGU CGUU CG CGGG@LB@3'-UUU...AAAAA UU CAC A UUAC UUGUC...UUG-5'@LB@ \| \|@LB@ 73 38@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -27.9384 kcal/mol@LB@Unfolding Energy - mRNA 8.52428 kcal/mol@LB@Unfolding Energy - sRNA 7.29447 kcal/mol@LB@@LB@Position - mRNA 199 -- 228@LB@Position - sRNA 39 -- 72@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 63 -- 69@LB@
42	0.002679	0.2088	b1427	rimL	-12.89	0.027177	178 -- 217	11 -- 49	ribosomal-protein-L7/L12-serine acetyltransferase		_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-GAU...ACAAC________AU____U___________GA___AA________AGUAA...CCU-3'\n______________UGC_AUGG__UGAC_GGAGAUAAGAU__CUG__ACGAUAAA\n______________\|\|\|_\|\|\|\|__::\|\|_\|:\|:\|\|\|\|:\|\|__\|\|\|__\|\|:\|\|\|\|\|\n______________ACG_UACC__GUUG_CUUUUAUUUUA__GAC__UGUUAUUU\n3'-UUU...CCGUU___U____GG____U________________AC________CCGUA...UUG-5'\n_____________\|_________________________________________\|\n_____________50________________________________________10\n	211 -- 217	11 -- 17	-27.9575 kcal/mol	3.9779 kcal/mol	11.0867 kcal/mol	177 218@LB@ \| \|@LB@5'-GAU...ACAAC AU U GA AA AGUAA...CCU-3'@LB@ UGC AUGG UGAC GGAGAUAAGAU CUG ACGAUAAA@LB@ \|\|\| \|\|\|\| ::\|\| \|:\|:\|\|\|\|:\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ ACG UACC GUUG CUUUUAUUUUA GAC UGUUAUUU@LB@3'-UUU...CCGUU U GG U AC CCGUA...UUG-5'@LB@ \| \|@LB@ 50 10@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -27.9575 kcal/mol@LB@Unfolding Energy - mRNA 3.9779 kcal/mol@LB@Unfolding Energy - sRNA 11.0867 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 11 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
176	0.02144	0.4097	b0948	rlmL	-6.91	0.434425	184 -- 201	13 -- 33	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent		_____________183___________________202\n_____________\|_____________________\|\n5'-GAC...CUCUU_____________________UGAAU...GUG-3'\n______________AGAGUAAAA___GUGACGAUA\n______________\|:\|:\|\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________UUUUAUUUU___CACUGUUAU\n3'-UUU...UUGUC_________AGA_________UUCCG...UUG-5'\n_____________\|_____________________\|\n_____________34____________________12\n	195 -- 201	13 -- 19	-14.282 kcal/mol	2.4415 kcal/mol	4.9341 kcal/mol	183 202@LB@ \| \|@LB@5'-GAC...CUCUU UGAAU...GUG-3'@LB@ AGAGUAAAA GUGACGAUA@LB@ \|:\|:\|\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ UUUUAUUUU CACUGUUAU@LB@3'-UUU...UUGUC AGA UUCCG...UUG-5'@LB@ \| \|@LB@ 34 12@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -14.282 kcal/mol@LB@Unfolding Energy - mRNA 2.4415 kcal/mol@LB@Unfolding Energy - sRNA 4.9341 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 13 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
94	0.008385	0.3	b1804	rnd	-8.17	0.271836	224 -- 238	41 -- 54	ribonuclease D		_____________223_____________239\n_____________\|_______________\|\n5'-GUC...ACCAC__A_______C____UUCUU...GUA-3'\n______________GG_CGAUGCG_UGGC\n______________\|\|_\|:\|\|\|\|:_\|\|\|\|\n______________CC_GUUACGU_ACCG\n3'-UUU...AGUCA__________U____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	227 -- 233	46 -- 52	-18.0571 kcal/mol	5.99437 kcal/mol	3.89026 kcal/mol	223 239@LB@ \| \|@LB@5'-GUC...ACCAC A C UUCUU...GUA-3'@LB@ GG CGAUGCG UGGC@LB@ \|\| \|:\|\|\|\|: \|\|\|\|@LB@ CC GUUACGU ACCG@LB@3'-UUU...AGUCA U GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -18.0571 kcal/mol@LB@Unfolding Energy - mRNA 5.99437 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 46 -- 52@LB@
86	0.007534	0.2889	b0189	rof	-5.95	0.582576	103 -- 121	40 -- 57	modulator of Rho-dependent transcription termination		_____________102_________________122\n_____________\|___________________\|\n5'-AGG...UUGAA____CUG____A_______GCCGA...GCG-3'\n______________AGUG___AAUG_AAUGGCU\n______________\|\|\|\|___\|\|\|\|_\|\|\|\|\|\|:\n______________UCAC___UUAC_UUACCGG\n3'-UUU...UUUAG____CG_____G_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________58__________________39\n	115 -- 121	40 -- 46	-14.9441 kcal/mol	3.94739 kcal/mol	5.04912 kcal/mol	102 122@LB@ \| \|@LB@5'-AGG...UUGAA CUG A GCCGA...GCG-3'@LB@ AGUG AAUG AAUGGCU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:@LB@ UCAC UUAC UUACCGG@LB@3'-UUU...UUUAG CG G GUUGU...UUG-5'@LB@ \| \|@LB@ 58 39@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -14.9441 kcal/mol@LB@Unfolding Energy - mRNA 3.94739 kcal/mol@LB@Unfolding Energy - sRNA 5.04912 kcal/mol@LB@@LB@Position - mRNA 103 -- 121@LB@Position - sRNA 40 -- 57@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 40 -- 46@LB@
197	0.02537	0.4256	b3317	rplB	-11.01	0.074049	182 -- 205	41 -- 62	50S ribosomal subunit protein L2		_____________181______________________206\n_____________\|________________________\|\n5'-GCA...UGAGU_______AG_A_____A_______AGUUG...UGC-3'\n______________AAGUCGG__G_GUAAU_CAAUGGC\n______________\|\|:\|\|:\|__\|_\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUUAGUC__C_CGUUA_GUUACCG\n3'-UUU...AACCU_______A________C_______GGUUG...UUG-5'\n_____________\|________________________\|\n_____________63_______________________40\n	199 -- 205	41 -- 47	-19.8959 kcal/mol	4.6063 kcal/mol	4.27585 kcal/mol	181 206@LB@ \| \|@LB@5'-GCA...UGAGU AG A A AGUUG...UGC-3'@LB@ AAGUCGG G GUAAU CAAUGGC@LB@ \|\|:\|\|:\| \| \|:\|\|\| \|\|\|\|\|\|\|@LB@ UUUAGUC C CGUUA GUUACCG@LB@3'-UUU...AACCU A C GGUUG...UUG-5'@LB@ \| \|@LB@ 63 40@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -19.8959 kcal/mol@LB@Unfolding Energy - mRNA 4.6063 kcal/mol@LB@Unfolding Energy - sRNA 4.27585 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 41 -- 62@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 41 -- 47@LB@
45	0.002879	0.2151	b3319	rplD	-8.41	0.246804	191 -- 204	42 -- 54	50S ribosomal subunit protein L4		_____________190____________205\n_____________\|______________\|\n5'-UCA...CGUAA__A___A_______AAUUA...UUG-3'\n______________GG_GAU_GCAAUGG\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CC_UUA_CGUUACC\n3'-UUU...AGUCA__G___________GGGUU...UUG-5'\n_____________\|______________\|\n_____________55_____________41\n	198 -- 204	42 -- 48	-13.9027 kcal/mol	1.99374 kcal/mol	3.49932 kcal/mol	190 205@LB@ \| \|@LB@5'-UCA...CGUAA A A AAUUA...UUG-3'@LB@ GG GAU GCAAUGG@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CC UUA CGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.9027 kcal/mol@LB@Unfolding Energy - mRNA 1.99374 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
74	0.006275	0.2822	b3298	rpsM	-14.03	0.014091	187 -- 207	39 -- 57	30S ribosomal subunit protein S13		_____________186___________________208\n_____________\|_____________________\|\n5'-GUC...UAAAU___A_G______UA_______GUAUA...UCC-3'\n______________AGU_G_AGUGCA__GUGGCCC\n______________\|\|\|_\|_\|:\|\|\|\|__:\|\|\|\|\|\|\n______________UCA_C_UUACGU__UACCGGG\n3'-UUU...UUUAG___C_G_______________UUGUC...UUG-5'\n_____________\|_____________________\|\n_____________58____________________38\n	201 -- 207	39 -- 45	-23.7565 kcal/mol	4.54468 kcal/mol	5.17956 kcal/mol	186 208@LB@ \| \|@LB@5'-GUC...UAAAU A G UA GUAUA...UCC-3'@LB@ AGU G AGUGCA GUGGCCC@LB@ \|\|\| \| \|:\|\|\|\| :\|\|\|\|\|\|@LB@ UCA C UUACGU UACCGGG@LB@3'-UUU...UUUAG C G UUGUC...UUG-5'@LB@ \| \|@LB@ 58 38@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -23.7565 kcal/mol@LB@Unfolding Energy - mRNA 4.54468 kcal/mol@LB@Unfolding Energy - sRNA 5.17956 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 39 -- 57@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 39 -- 45@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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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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