Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
33	0.0002072	0.02212	b2101	yegW	-12.62	0.023301	188 -- 205	37 -- 56	putative DNA-binding transcriptional regulator		_____________187__________________206\n_____________\|____________________\|\n5'-CGG...CCGGC_____A______________ACAAG...AAA-3'\n______________AGGAA__AAGACAA_AUGGA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCCUU__UUCUGUU_UACCU\n3'-UUU...UUUUU_____CA_______A_____CGCGU...ACG-5'\n_____________\|____________________\|\n_____________57___________________36\n	194 -- 200	43 -- 49	-17.4469 kcal/mol	1.13054 kcal/mol	3.6645 kcal/mol	187 206@LB@ \| \|@LB@5'-CGG...CCGGC A ACAAG...AAA-3'@LB@ AGGAA AAGACAA AUGGA@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCCUU UUCUGUU UACCU@LB@3'-UUU...UUUUU CA A CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -17.4469 kcal/mol@LB@Unfolding Energy - mRNA 1.13054 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 43 -- 49@LB@
45	0.0004696	0.03623	b4035	malK	-9.83	0.120497	188 -- 201	44 -- 57	maltose ABC transportor ATPase		_____________187____________202\n_____________\|______________\|\n5'-CGC...UUACA_______A______UGGCG...UGU-3'\n______________AAGGGAG_AGGGCA\n______________\|\|\|\|:\|\|_\|:\|:\|\|\n______________UUCCUUC_UUCUGU\n3'-UUU...GUUUU_______A______UAUAC...ACG-5'\n_____________\|______________\|\n_____________58_____________43\n	188 -- 194	51 -- 57	-14.5332 kcal/mol	2.95068 kcal/mol	1.74831 kcal/mol	187 202@LB@ \| \|@LB@5'-CGC...UUACA A UGGCG...UGU-3'@LB@ AAGGGAG AGGGCA@LB@ \|\|\|\|:\|\| \|:\|:\|\|@LB@ UUCCUUC UUCUGU@LB@3'-UUU...GUUUU A UAUAC...ACG-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.5332 kcal/mol@LB@Unfolding Energy - mRNA 2.95068 kcal/mol@LB@Unfolding Energy - sRNA 1.74831 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
111	0.003511	0.1114	b0077	ilvI	-11.05	0.061087	188 -- 206	36 -- 52	acetolactate synthase 3 large subunit		_____________187_________________207\n_____________\|___________________\|\n5'-AAA...CAAAC__________GCC______AUGUU...UUU-3'\n______________AGUGAGGCAG___AUGGAG\n______________\|\|\|:\|\|:\|\|:___\|\|\|\|\|\|\n______________UCAUUCUGUU___UACCUC\n3'-UUU...UUCCU__________A________GCGUU...ACG-5'\n_____________\|___________________\|\n_____________53__________________35\n	191 -- 197	43 -- 49	-19.2253 kcal/mol	4.72052 kcal/mol	3.43382 kcal/mol	187 207@LB@ \| \|@LB@5'-AAA...CAAAC GCC AUGUU...UUU-3'@LB@ AGUGAGGCAG AUGGAG@LB@ \|\|\|:\|\|:\|\|: \|\|\|\|\|\|@LB@ UCAUUCUGUU UACCUC@LB@3'-UUU...UUCCU A GCGUU...ACG-5'@LB@ \| \|@LB@ 53 35@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -19.2253 kcal/mol@LB@Unfolding Energy - mRNA 4.72052 kcal/mol@LB@Unfolding Energy - sRNA 3.43382 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 36 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
126	0.004539	0.1258	b0546	ybcM	-11.00	0.062763	188 -- 220	45 -- 91	DLP12 prophage; putative DNA-binding transcriptional regulator	b1499 b0564 b3515 b4116 b0566 b3516	_____________187_____________________________________________221\n_____________\|_______________________________________________\|\n5'-GCU...AUAAA___G__UGA__GUA_________A_______________________UAACU...GUC-3'\n______________GUA_GG___GA___UGCUG_GCA______________GAGGUAAGAC\n______________\|\|\|_\|:___:\|___\|\|\|\|:_\|\|\|______________\|\|:\|\|\|\|\|\|\|\n______________CAU_CU___UU___ACGAU_CGU______________CUUCAUUCUG\n3'-UUU...CGCAG___G__UAG__AAC_____A___CAUUAAGUUUUUUC__________UUAUA...ACG-5'\n_____________\|_______________________________________________\|\n_____________92______________________________________________44\n	214 -- 220	45 -- 51	-23.4531 kcal/mol	6.72952 kcal/mol	5.72765 kcal/mol	187 221@LB@ \| \|@LB@5'-GCU...AUAAA G UGA GUA A UAACU...GUC-3'@LB@ GUA GG GA UGCUG GCA GAGGUAAGAC@LB@ \|\|\| \|: :\| \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|\|\|@LB@ CAU CU UU ACGAU CGU CUUCAUUCUG@LB@3'-UUU...CGCAG G UAG AAC A CAUUAAGUUUUUUC UUAUA...ACG-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -23.4531 kcal/mol@LB@Unfolding Energy - mRNA 6.72952 kcal/mol@LB@Unfolding Energy - sRNA 5.72765 kcal/mol@LB@@LB@Position - mRNA 188 -- 220@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 45 -- 51@LB@
185	0.008022	0.1528	b1813	nudL	-20.51	0.000035	188 -- 228	15 -- 56	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________187____________________________________________229\n_____________\|______________________________________________\|\n5'-CCU...CAACU__A__________________AUAC_________G___________AUUUU...CUG-3'\n______________GG_GAAGUAAGAC___GUGGA____CGUAGC_CU_A_CGCUUGAUG\n______________:\|_\|\|\|\|\|\|\|\|\|\|___:\|\|\|\|____\|\|:\|:\|_\|:_\|_\|\|\|\|\|\|\|:\|\n______________UC_CUUCAUUCUG___UACCU____GCGUUG_GG_U_GCGAACUGC\n3'-UUU...UUUUU_____________UUA_____C_________C__G_A_________AACGU...ACG-5'\n_____________\|______________________________________________\|\n_____________57_____________________________________________14\n	221 -- 227	16 -- 22	-41.758 kcal/mol	7.45502 kcal/mol	13.7937 kcal/mol	187 229@LB@ \| \|@LB@5'-CCU...CAACU A AUAC G AUUUU...CUG-3'@LB@ GG GAAGUAAGAC GUGGA CGUAGC CU A CGCUUGAUG@LB@ :\| \|\|\|\|\|\|\|\|\|\| :\|\|\|\| \|\|:\|:\| \|: \| \|\|\|\|\|\|\|:\|@LB@ UC CUUCAUUCUG UACCU GCGUUG GG U GCGAACUGC@LB@3'-UUU...UUUUU UUA C C G A AACGU...ACG-5'@LB@ \| \|@LB@ 57 14@LB@@LB@@LB@Energy -20.51 kcal/mol@LB@Hybridization Energy -41.758 kcal/mol@LB@Unfolding Energy - mRNA 7.45502 kcal/mol@LB@Unfolding Energy - sRNA 13.7937 kcal/mol@LB@@LB@Position - mRNA 188 -- 228@LB@Position - sRNA 15 -- 56@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 16 -- 22@LB@
199	0.008927	0.1548	b1019	efeB	-11.91	0.036296	188 -- 218	52 -- 88	deferrrochelatase periplasmic		_____________187___________________________________219\n_____________\|_____________________________________\|\n5'-GCC...GGGAC________GC______________________U____AACGG...CUC-3'\n______________UGGAUUAA____GUUAUGCAGUA___UAAAGA__GAA\n______________:\|:\|\|:\|\|____\|:\|\|\|\|\|\|\|\|\|___:\|\|\|:\|__\|\|\|\n______________GCUUAGUU____CGAUACGUCAU___GUUUUU__CUU\n3'-UUU...AGCAU________AACA___________UAA______UC___CAUUC...ACG-5'\n_____________\|_____________________________________\|\n_____________89____________________________________51\n	202 -- 208	66 -- 72	-22.4719 kcal/mol	5.89402 kcal/mol	4.66982 kcal/mol	187 219@LB@ \| \|@LB@5'-GCC...GGGAC GC U AACGG...CUC-3'@LB@ UGGAUUAA GUUAUGCAGUA UAAAGA GAA@LB@ :\|:\|\|:\|\| \|:\|\|\|\|\|\|\|\|\| :\|\|\|:\| \|\|\|@LB@ GCUUAGUU CGAUACGUCAU GUUUUU CUU@LB@3'-UUU...AGCAU AACA UAA UC CAUUC...ACG-5'@LB@ \| \|@LB@ 89 51@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -22.4719 kcal/mol@LB@Unfolding Energy - mRNA 5.89402 kcal/mol@LB@Unfolding Energy - sRNA 4.66982 kcal/mol@LB@@LB@Position - mRNA 188 -- 218@LB@Position - sRNA 52 -- 88@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
37	0.0003128	0.02889	b1107	nagZ	-10.24	0.096497	189 -- 204	38 -- 57	beta N-acetyl-glucosaminidase		_____________188__________________205\n_____________\|____________________\|\n5'-AUU...ACAAU____________________GUCCA...CGC-3'\n______________AAGGA___GAG_CAGUGUGG\n______________\|\|\|\|\|___:\|\|_\|\|:\|:\|\|\|\n______________UUCCU___UUC_GUUAUACC\n3'-UUU...GUUUU_____UCA___U________UCGCG...ACG-5'\n_____________\|____________________\|\n_____________58___________________37\n	198 -- 204	38 -- 44	-15.5747 kcal/mol	1.78066 kcal/mol	3.52446 kcal/mol	188 205@LB@ \| \|@LB@5'-AUU...ACAAU GUCCA...CGC-3'@LB@ AAGGA GAG CAGUGUGG@LB@ \|\|\|\|\| :\|\| \|\|:\|:\|\|\|@LB@ UUCCU UUC GUUAUACC@LB@3'-UUU...GUUUU UCA U UCGCG...ACG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.5747 kcal/mol@LB@Unfolding Energy - mRNA 1.78066 kcal/mol@LB@Unfolding Energy - sRNA 3.52446 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 38 -- 44@LB@
49	0.0005476	0.03937	b2432	yfeY	-8.84	0.200409	189 -- 199	48 -- 58	RpoE-regulated lipoprotein		_____________188_________200\n_____________\|___________\|\n5'-GCU...UAACC___________CAUGA...ACU-3'\n______________AAAGGAAGUGA\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UUUCCUUCAUU\n3'-UUU...AGUUU___________CUGUU...ACG-5'\n_____________\|___________\|\n_____________59__________47\n	193 -- 199	48 -- 54	-12.8959 kcal/mol	3.31176 kcal/mol	0.745549 kcal/mol	188 200@LB@ \| \|@LB@5'-GCU...UAACC CAUGA...ACU-3'@LB@ AAAGGAAGUGA@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UUUCCUUCAUU@LB@3'-UUU...AGUUU CUGUU...ACG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -12.8959 kcal/mol@LB@Unfolding Energy - mRNA 3.31176 kcal/mol@LB@Unfolding Energy - sRNA 0.745549 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 48 -- 54@LB@
77	0.00185	0.08273	b2325	yfcL	-11.04	0.061434	190 -- 213	35 -- 57	uncharacterized protein		_____________189______________________214\n_____________\|________________________\|\n5'-AAC...ACAAU______AG________CGC_____UUGAA...GCC-3'\n______________GAGGAA__AAGAUGAU___GGAGU\n______________:\|\|\|\|\|__\|\|\|\|::\|\|___\|\|\|\|:\n______________UUCCUU__UUCUGUUA___CCUCG\n3'-UUU...GUUUU______CA________UA______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________58_______________________34\n	199 -- 205	42 -- 48	-19.5886 kcal/mol	4.3321 kcal/mol	4.1846 kcal/mol	189 214@LB@ \| \|@LB@5'-AAC...ACAAU AG CGC UUGAA...GCC-3'@LB@ GAGGAA AAGAUGAU GGAGU@LB@ :\|\|\|\|\| \|\|\|\|::\|\| \|\|\|\|:@LB@ UUCCUU UUCUGUUA CCUCG@LB@3'-UUU...GUUUU CA UA CGUUG...ACG-5'@LB@ \| \|@LB@ 58 34@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -19.5886 kcal/mol@LB@Unfolding Energy - mRNA 4.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 190 -- 213@LB@Position - sRNA 35 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@LB@
107	0.003422	0.1114	b0415	ribE	-10.96	0.064092	190 -- 254	4 -- 58	riboflavin synthase beta chain		_____________189_________________________________________________________________255\n_____________\|___________________________________________________________________\|\n5'-CGG...AACCC________AAAAU_A___U___U_A_________UUGCUAC____GA____C_____C__CA_____AUCGC...GUG-3'\n______________GAAGGAAG_____G_ACA_UAU_G_AGC_UAACG_______CCCG__CGCU__GCGU_GC__UCACC\n______________:\|\|\|\|\|\|\|_____\|_\|\|\|_\|\|\|_\|_\|\|\|_:\|\|\|\|_______\|\|\|:__\|\|\|\|__:\|\|\|_\|\|__\|\|\|\|\|\n______________UUUCCUUC_____C_UGU_AUA_C_UCG_GUUGC_______GGGU__GCGA__UGCA_CG__AGUGG\n3'-UUU...AGUUU________AUU_______U___C_____C________________A_____AC____A__UA_____ACG-5'\n_____________\|___________________________________________________________________\|\n_____________59__________________________________________________________________3\n	191 -- 197	51 -- 57	-41.366 kcal/mol	13.5359 kcal/mol	16.8715 kcal/mol	189 255@LB@ \| \|@LB@5'-CGG...AACCC AAAAU A U U A UUGCUAC GA C C CA AUCGC...GUG-3'@LB@ GAAGGAAG G ACA UAU G AGC UAACG CCCG CGCU GCGU GC UCACC@LB@ :\|\|\|\|\|\|\| \| \|\|\| \|\|\| \| \|\|\| :\|\|\|\| \|\|\|: \|\|\|\| :\|\|\| \|\| \|\|\|\|\|@LB@ UUUCCUUC C UGU AUA C UCG GUUGC GGGU GCGA UGCA CG AGUGG@LB@3'-UUU...AGUUU AUU U C C A AC A UA ACG-5'@LB@ \| \|@LB@ 59 3@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -41.366 kcal/mol@LB@Unfolding Energy - mRNA 13.5359 kcal/mol@LB@Unfolding Energy - sRNA 16.8715 kcal/mol@LB@@LB@Position - mRNA 190 -- 254@LB@Position - sRNA 4 -- 58@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 51 -- 57@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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