Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
75	0.007778	0.3458	b0766	ybhA	-9.49	0.341100	208 -- 245	124 -- 172	pyridoxal phosphate (PLP) phosphatase	_____________207___________________________246\n_____________\|_____________________________\|\n5'-GAA...UGGAA_______UG________________U___UCUCG...GCG-3'\n______________UACGCCA__AC_CA__CACGCGUGA_UGC\n______________\|\|\|:\|\|\|__\|\|_\|\|__\|\|\|:\|:\|\|\|_\|\|\|\n______________AUGUGGU__UG_GU__GUGUGUACU_ACG\n3'-UUU...CUAAA_______UA__A__CA_____________UCCGU...UAG-5'\n_____________\|_____________________________\|\n_____________173___________________________123\n	195 -- 201	182 -- 188	-28.0817 kcal/mol	7.23992 kcal/mol	7.72227 kcal/mol	207 246@LB@ \| \|@LB@5'-GAA...UGGAA UG U UCUCG...GCG-3'@LB@ UACGCCA AC CA CACGCGUGA UGC@LB@ \|\|\|:\|\|\| \|\| \|\| \|\|\|:\|:\|\|\| \|\|\|@LB@ AUGUGGU UG GU GUGUGUACU ACG@LB@3'-UUU...CUAAA UA A CA UCCGU...UAG-5'@LB@ \| \|@LB@ 173 123@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -28.0817 kcal/mol@LB@Unfolding Energy - mRNA 7.23992 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 208 -- 245@LB@Position - sRNA 124 -- 172@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 182 -- 188@LB@
119	0.013	0.3575	b0801	ybiC	-16.26	0.015008	158 -- 253	108 -- 187	putative dehydrogenase	_____________157____________________________________________________________________________________________254\n_____________\|______________________________________________________________________________________________\|\n5'-GCU...AUAAA_____AA__AA______ACAUAAA_____________CAU_____A__________G_UUUGAUGCUCAGAC_____________UA_______UGUAU...UUG-3'\n______________AAUAC__CA__CACAUA_______CAGG__AGUUAAC____GGAA__GUGGUCAUC_C______________GCUGCA_CAGUUU__UUCAGGC\n______________\|\|\|\|\|__\|\|__\|\|\|\|:\|_______\|\|\|\|__\|\|\|:\|\|\|____:\|\|\|__\|:\|\|\|\|\|\|\|_\|______________:\|\|\|\|\|_\|\|\|\|::__\|\|\|\|:\|\|\n______________UUAUG__GU__GUGUGU_______GUCC__UCAGUUG____UCUU__CGCCAGUAG_G______________UGACGU_GUCAGG__AAGUUCG\n3'-UUU...UGUGG_____A___CA______ACUAC______GU_______AAAG____AA_________G_____________________A_______________UACCA...UAG-5'\n_____________\|______________________________________________________________________________________________\|\n_____________188____________________________________________________________________________________________107\n	247 -- 253	108 -- 114	-56.5044 kcal/mol	18.8914 kcal/mol	26.5178 kcal/mol	157 254@LB@ \| \|@LB@5'-GCU...AUAAA AA AA ACAUAAA CAU A G UUUGAUGCUCAGAC UA UGUAU...UUG-3'@LB@ AAUAC CA CACAUA CAGG AGUUAAC GGAA GUGGUCAUC C GCUGCA CAGUUU UUCAGGC@LB@ \|\|\|\|\| \|\| \|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|\|\| \| :\|\|\|\|\| \|\|\|\|:: \|\|\|\|:\|\|@LB@ UUAUG GU GUGUGU GUCC UCAGUUG UCUU CGCCAGUAG G UGACGU GUCAGG AAGUUCG@LB@3'-UUU...UGUGG A CA ACUAC GU AAAG AA G A UACCA...UAG-5'@LB@ \| \|@LB@ 188 107@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -56.5044 kcal/mol@LB@Unfolding Energy - mRNA 18.8914 kcal/mol@LB@Unfolding Energy - sRNA 26.5178 kcal/mol@LB@@LB@Position - mRNA 158 -- 253@LB@Position - sRNA 108 -- 187@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 108 -- 114@LB@
16	0.0008966	0.1886	b0807	rlmF	-16.29	0.014793	117 -- 160	51 -- 97	23S rRNA m(6)A1618 methyltransferase SAM-dependent	_____________116_____________________________________________161\n_____________\|_______________________________________________\|\n5'-AUU...UUAAG___U_____AA______A_______________U__A_C________UUAUG...UCC-3'\n______________GUU_UGGGG____UGAU_AACGCAGCCAG_AUA_UU_C_CUGUCGCG\n______________\|\|\|_\|\|\|\|:____\|:\|:_\|\|\|\|\|\|:\|\|\|\|_\|:\|_:\|_\|_\|\|\|\|\|\|\|\|\n______________CAA_ACCCU____AUUG_UUGCGUUGGUC_UGU_GA_G_GACAGCGC\n3'-UUU...AUUAG___C_____GCGA____G___________G___U__A_C________CAUUU...UAG-5'\n_____________\|_______________________________________________\|\n_____________98______________________________________________50\n	154 -- 160	51 -- 57	-44.7843 kcal/mol	10.0752 kcal/mol	25.3667 kcal/mol	116 161@LB@ \| \|@LB@5'-AUU...UUAAG U AA A U A C UUAUG...UCC-3'@LB@ GUU UGGGG UGAU AACGCAGCCAG AUA UU C CUGUCGCG@LB@ \|\|\| \|\|\|\|: \|:\|: \|\|\|\|\|\|:\|\|\|\| \|:\| :\| \| \|\|\|\|\|\|\|\|@LB@ CAA ACCCU AUUG UUGCGUUGGUC UGU GA G GACAGCGC@LB@3'-UUU...AUUAG C GCGA G G U A C CAUUU...UAG-5'@LB@ \| \|@LB@ 98 50@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -44.7843 kcal/mol@LB@Unfolding Energy - mRNA 10.0752 kcal/mol@LB@Unfolding Energy - sRNA 25.3667 kcal/mol@LB@@LB@Position - mRNA 117 -- 160@LB@Position - sRNA 51 -- 97@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 51 -- 57@LB@
99	0.01084	0.3575	b0872	hcr	-12.58	0.084706	106 -- 121	192 -- 205	HCP oxidoreductase NADH-dependent	_____________105______________122\n_____________\|________________\|\n5'-UCC...CAGAC__________U_C___ACGAG...AUU-3'\n______________CUGCUGGCGG_G_UGA\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\|\|\n______________GACGACCGCC_C_ACU\n3'-UUU...UAUUA________________AAAAU...UAG-5'\n_____________\|________________\|\n_____________206______________191\n	109 -- 115	196 -- 202	-24.2797 kcal/mol	6.55023 kcal/mol	9.06563 kcal/mol	105 122@LB@ \| \|@LB@5'-UCC...CAGAC U C ACGAG...AUU-3'@LB@ CUGCUGGCGG G UGA@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\|@LB@ GACGACCGCC C ACU@LB@3'-UUU...UAUUA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -24.2797 kcal/mol@LB@Unfolding Energy - mRNA 6.55023 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 106 -- 121@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 196 -- 202@LB@
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase	_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@LB@
114	0.01268	0.3575	b0888	trxB	-13.24	0.061992	5 -- 14	83 -- 92	thioredoxin reductase FAD/NAD(P)-binding	_____________4__________15\n_____________\|__________\|\n_______5'-AACA__________UUCAU...UGC-3'\n______________GGGGCGUUUA\n______________\|\|\|:\|\|:\|\|\|\n______________CCCUGCGAAU\n3'-UUU...CAACA__________UGGUU...UAG-5'\n_____________\|__________\|\n_____________93_________82\n	7 -- 13	84 -- 90	-15.9307 kcal/mol	0.512019 kcal/mol	6.69187 kcal/mol	4 15@LB@ \| \|@LB@ 5'-AACA UUCAU...UGC-3'@LB@ GGGGCGUUUA@LB@ \|\|\|:\|\|:\|\|\|@LB@ CCCUGCGAAU@LB@3'-UUU...CAACA UGGUU...UAG-5'@LB@ \| \|@LB@ 93 82@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -15.9307 kcal/mol@LB@Unfolding Energy - mRNA 0.512019 kcal/mol@LB@Unfolding Energy - sRNA 6.69187 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 83 -- 92@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 84 -- 90@LB@
86	0.009326	0.3575	b0899	ycaM	-11.50	0.140486	23 -- 68	127 -- 173	putative transporter	_____________22_______________________________________________________69\n_____________\|________________________________________________________\|\n5'-AGC...GAACU____GUU______UC_____UUUUUU___UCUU__A__U__C____U_________AAUUU...AUG-3'\n______________UACU___UCACAC____UGC______GUU____CU_UC_GA_UUGC__UUAUUCCA\n______________\|\|\|\|___\|\|\|\|\|\|____\|\|\|______\|\|:____\|\|_\|\|_\|\|_\|\|\|\|__\|:\|\|:\|\|\|\n______________AUGA___AGUGUG____ACG______CAG____GA_AG_CU_AACG__AGUAGGGU\n3'-UUU...UGGUU____GUC______UACU___UCCGUU___UU____A__U__U____CC________GACGU...UAG-5'\n_____________\|________________________________________________________\|\n_____________174______________________________________________________126\n	62 -- 68	127 -- 133	-29.7478 kcal/mol	2.56458 kcal/mol	15.6497 kcal/mol	22 69@LB@ \| \|@LB@5'-AGC...GAACU GUU UC UUUUUU UCUU A U C U AAUUU...AUG-3'@LB@ UACU UCACAC UGC GUU CU UC GA UUGC UUAUUCCA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\| \|\|: \|\| \|\| \|\| \|\|\|\| \|:\|\|:\|\|\|@LB@ AUGA AGUGUG ACG CAG GA AG CU AACG AGUAGGGU@LB@3'-UUU...UGGUU GUC UACU UCCGUU UU A U U CC GACGU...UAG-5'@LB@ \| \|@LB@ 174 126@LB@@LB@@LB@Energy -11.50 kcal/mol@LB@Hybridization Energy -29.7478 kcal/mol@LB@Unfolding Energy - mRNA 2.56458 kcal/mol@LB@Unfolding Energy - sRNA 15.6497 kcal/mol@LB@@LB@Position - mRNA 23 -- 68@LB@Position - sRNA 127 -- 173@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 127 -- 133@LB@
79	0.008119	0.3458	b0945	pyrD	-11.48	0.141710	30 -- 41	191 -- 202	dihydro-orotate oxidase FMN-linked	_____________29______________________42\n_____________\|_______________________\|\n5'-UGU...AGCAA_____________A___GA____CGU-3'\n______________UUACGCCG_UAUU_CAG__ACGC\n______________\|\|\|\|:\|\|:_\|\|:\|_\|\|\|__\|\|:\|\n______________AAUGUGGU_AUGA_GUC__UGUG\n3'-UUU...ACUAA________U________AG____UACUA...UAG-5'\n_____________\|_______________________\|\n_____________203_____________________190\n	277 -- 283	182 -- 188	-20.4941 kcal/mol	3.55802 kcal/mol	4.91485 kcal/mol	29 42@LB@ \| \|@LB@5'-UGU...AGCAA A GA CGU-3'@LB@ UUACGCCG UAUU CAG ACGC@LB@ \|\|\|\|:\|\|: \|\|:\| \|\|\| \|\|:\|@LB@ AAUGUGGU AUGA GUC UGUG@LB@3'-UUU...ACUAA U AG UACUA...UAG-5'@LB@ \| \|@LB@ 203 190@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.4941 kcal/mol@LB@Unfolding Energy - mRNA 3.55802 kcal/mol@LB@Unfolding Energy - sRNA 4.91485 kcal/mol@LB@@LB@Position - mRNA 30 -- 41@LB@Position - sRNA 191 -- 202@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 182 -- 188@LB@
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent	_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@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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