Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
125	0.006333	0.1774	stm3094	yggJ	-12.37	0.297521	35 -- 55	69 -- 89	putative cytoplasmic protein	_____________34____________________56\n_____________\|_____________________\|\n5'-GCG...GCCAA__________UUUU_______UGGGA...AGA-3'\n______________CAAACGCAGC____UAACGUC\n______________\|\|\|\|\|:\|\|:\|____:\|\|\|:\|\|\n______________GUUUGUGUUG____GUUGUAG\n3'-UUU...UUAAC__________UUGU_______UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________90____________________68\n	49 -- 55	69 -- 75	-19.7914 kcal/mol	1.34113 kcal/mol	4.32311 kcal/mol	34 56@LB@ \| \|@LB@5'-GCG...GCCAA UUUU UGGGA...AGA-3'@LB@ CAAACGCAGC UAACGUC@LB@ \|\|\|\|\|:\|\|:\| :\|\|\|:\|\|@LB@ GUUUGUGUUG GUUGUAG@LB@3'-UUU...UUAAC UUGU UGUUG...UCA-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -19.7914 kcal/mol@LB@Unfolding Energy - mRNA 1.34113 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 35 -- 55@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
50	0.001812	0.1291	stm3207	ygiH	-15.41	0.101358	70 -- 101	63 -- 93	acyl-phosphate--glycerol-3-phosphate O-acyltransferase	_____________69___________________________________102\n_____________\|____________________________________\|\n5'-UAU...CGAAA_____UCUAU__________U_______________UGCCU...CGC-3'\n______________GUUGC_____AAAUACAAUA_C____CAUCACGACC\n______________:\|\|\|\|_____\|\|\|:\|\|\|\|:\|_\|____\|\|\|\|\|\|:\|\|\|\n______________UAACG_____UUUGUGUUGU_G____GUAGUGUUGG\n3'-UUU...CUGGU____________________U_UGUU__________CAUUC...UCA-5'\n_____________\|____________________________________\|\n_____________94___________________________________62\n	95 -- 101	63 -- 69	-25.69 kcal/mol	1.94006 kcal/mol	8.62086 kcal/mol	69 102@LB@ \| \|@LB@5'-UAU...CGAAA UCUAU U UGCCU...CGC-3'@LB@ GUUGC AAAUACAAUA C CAUCACGACC@LB@ :\|\|\|\| \|\|\|:\|\|\|\|:\| \| \|\|\|\|\|\|:\|\|\|@LB@ UAACG UUUGUGUUGU G GUAGUGUUGG@LB@3'-UUU...CUGGU U UGUU CAUUC...UCA-5'@LB@ \| \|@LB@ 94 62@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -25.69 kcal/mol@LB@Unfolding Energy - mRNA 1.94006 kcal/mol@LB@Unfolding Energy - sRNA 8.62086 kcal/mol@LB@@LB@Position - mRNA 70 -- 101@LB@Position - sRNA 63 -- 93@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 63 -- 69@LB@
161	0.008343	0.1845	stm3321	yhbH	-14.15	0.160801	194 -- 246	48 -- 88	ribosomal subunit interface protein	_____________193______________________247\n_____________\|________________________\|\n5'-GAU...AAGGA______UAU_____U_________CGGAC...GGA-3'\n______________AGACAC___GCAGC_CAAUAUCAC\n______________\|:\|\|\|\|___:\|\|:\|_\|\|\|:\|\|\|\|\|\n______________UUUGUG___UGUUG_GUUGUAGUG\n3'-UUU...UAACG______U_______U_________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________89_______________________47\n	211 -- 217	67 -- 73	-22.4132 kcal/mol	2.65406 kcal/mol	5.48747 kcal/mol	193 247@LB@ \| \|@LB@5'-GAU...AAGGA UAU U CGGAC...GGA-3'@LB@ AGACAC GCAGC CAAUAUCAC@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|:\|\|\|\|\|@LB@ UUUGUG UGUUG GUUGUAGUG@LB@3'-UUU...UAACG U U UUGGC...UCA-5'@LB@ \| \|@LB@ 89 47@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -22.4132 kcal/mol@LB@Unfolding Energy - mRNA 2.65406 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 194 -- 246@LB@Position - sRNA 48 -- 88@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 67 -- 73@LB@
199	0.01101	0.197	stm3346	yhcM	-12.83	0.254909	186 -- 228	33 -- 82	cell division protein ZapE	_____________185____________________229\n_____________\|______________________\|\n5'-CAG...UUCAA_G__UA__________UAU___AAGCC...AAA-3'\n______________G_AA__ACAAUAACAU___GCA\n______________\|_\|\|__\|\|\|\|:\|\|\|\|:___:\|\|\n______________C_UU__UGUUGUUGUG___UGU\n3'-UUU...GUUAA_G__UG__________U_____AGUGU...UCA-5'\n_____________\|______________________\|\n_____________83_____________________32\n	193 -- 199	75 -- 81	-14.0954 kcal/mol	2.45302 kcal/mol	3.80671 kcal/mol	185 229@LB@ \| \|@LB@5'-CAG...UUCAA G UA UAU AAGCC...AAA-3'@LB@ G AA ACAAUAACAU GCA@LB@ \| \|\| \|\|\|\|:\|\|\|\|: :\|\|@LB@ C UU UGUUGUUGUG UGU@LB@3'-UUU...GUUAA G UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 83 32@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -14.0954 kcal/mol@LB@Unfolding Energy - mRNA 2.45302 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 186 -- 228@LB@Position - sRNA 33 -- 82@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 75 -- 81@LB@
24	0.000609	0.08814	stm3510	yhgH	-18.34	0.033208	106 -- 153	42 -- 84	DNA utilization protein GntX	_____________105____________________________________154\n_____________\|______________________________________\|\n5'-CCG...UCCGU____________G__G___AUUUCCCUC__________UGCCA...GCG-3'\n______________GCAGCAGCACAA_AU_ACA_________GCCGUAGGUC\n______________:\|\|:\|\|:\|\|\|\|\|_\|\|_\|\|\|_________:\|\|\|\|\|:\|:\|\n______________UGUUGUUGUGUU_UA_UGU_________UGGCAUUCGG\n3'-UUU...GUUUG____________G__G______________________UUUUC...UCA-5'\n_____________\|______________________________________\|\n_____________85_____________________________________41\n	135 -- 141	58 -- 64	-35.7194 kcal/mol	10.0869 kcal/mol	11.5136 kcal/mol	105 154@LB@ \| \|@LB@5'-CCG...UCCGU G G AUUUCCCUC UGCCA...GCG-3'@LB@ GCAGCAGCACAA AU ACA GCCGUAGGUC@LB@ :\|\|:\|\|:\|\|\|\|\| \|\| \|\|\| :\|\|\|\|\|:\|:\|@LB@ UGUUGUUGUGUU UA UGU UGGCAUUCGG@LB@3'-UUU...GUUUG G G UUUUC...UCA-5'@LB@ \| \|@LB@ 85 41@LB@@LB@@LB@Energy -18.34 kcal/mol@LB@Hybridization Energy -35.7194 kcal/mol@LB@Unfolding Energy - mRNA 10.0869 kcal/mol@LB@Unfolding Energy - sRNA 11.5136 kcal/mol@LB@@LB@Position - mRNA 106 -- 153@LB@Position - sRNA 42 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 58 -- 64@LB@
168	0.009144	0.1938	stm3609	yhjE	-18.08	0.036777	202 -- 261	35 -- 91	MFS transporter	_____________201__________________________________262\n_____________\|____________________________________\|\n5'-UAA...UAGUA_______A__C_____________U_____A_____AGGAA...UUG-3'\n______________UGCAAGC_AC_GC__CACAACA_C_CGACC_UGAGC\n______________\|\|\|\|\|:\|_\|\|_:\|__\|\|\|\|\|\|\|_\|_\|:\|\|\|_\|:\|\|\|\n______________ACGUUUG_UG_UG__GUGUUGU_G_GUUGG_AUUCG\n3'-UUU...GGUUA__________U__UU_______A_U_____C_____GUUUU...UCA-5'\n_____________\|____________________________________\|\n_____________92___________________________________34\n	215 -- 221	71 -- 77	-32.2191 kcal/mol	4.27941 kcal/mol	11.5198 kcal/mol	201 262@LB@ \| \|@LB@5'-UAA...UAGUA A C U A AGGAA...UUG-3'@LB@ UGCAAGC AC GC CACAACA C CGACC UGAGC@LB@ \|\|\|\|\|:\| \|\| :\| \|\|\|\|\|\|\| \| \|:\|\|\| \|:\|\|\|@LB@ ACGUUUG UG UG GUGUUGU G GUUGG AUUCG@LB@3'-UUU...GGUUA U UU A U C GUUUU...UCA-5'@LB@ \| \|@LB@ 92 34@LB@@LB@@LB@Energy -18.08 kcal/mol@LB@Hybridization Energy -32.2191 kcal/mol@LB@Unfolding Energy - mRNA 4.27941 kcal/mol@LB@Unfolding Energy - sRNA 11.5198 kcal/mol@LB@@LB@Position - mRNA 202 -- 261@LB@Position - sRNA 35 -- 91@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 71 -- 77@LB@
159	0.008305	0.1845	stm3625	yhjV	-13.06	0.235438	203 -- 240	55 -- 86	transporter	_____________202________________________241\n_____________\|__________________________\|\n5'-UUA...UAUUU_____________CUCUA________CGACA...UCU-3'\n______________UGGGCAG__GGGG______UGCAGGA\n______________\|\|\|:\|\|\|__:\|\|\|______\|:\|\|\|\|\|\n______________ACCUGUC__UCCC______AUGUCCU\n3'-UUU...GUGAU_______UG____AUUUAC_______UCACU...UCA-5'\n_____________\|__________________________\|\n_____________87_________________________54\n	202 -- 208	139 -- 145	-24.2103 kcal/mol	7.6176 kcal/mol	3.71206 kcal/mol	202 241@LB@ \| \|@LB@5'-UUA...UAUUU CUCUA CGACA...UCU-3'@LB@ UGGGCAG GGGG UGCAGGA@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ ACCUGUC UCCC AUGUCCU@LB@3'-UUU...GUGAU UG AUUUAC UCACU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -13.06 kcal/mol@LB@Hybridization Energy -24.2103 kcal/mol@LB@Unfolding Energy - mRNA 7.6176 kcal/mol@LB@Unfolding Energy - sRNA 3.71206 kcal/mol@LB@@LB@Position - mRNA 203 -- 240@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 139 -- 145@LB@
68	0.003225	0.1596	stm3930	yifK	-15.10	0.113746	177 -- 247	44 -- 93	amino acid permease	_____________176____________________248\n_____________\|______________________\|\n5'-CUU...GAACC_______________UG_G___UUAUG...GCG-3'\n______________GUUGCAAACACGACA__A_GAU\n______________:\|\|\|\|\|\|\|\|\|\|:\|\|\|__\|_:\|:\n______________UAACGUUUGUGUUGU__U_UUG\n3'-UUU...CUGGU_______________UG_G___UAGUG...UCA-5'\n_____________\|______________________\|\n_____________94_____________________43\n	185 -- 191	79 -- 85	-22.6062 kcal/mol	5.26496 kcal/mol	3.80917 kcal/mol	176 248@LB@ \| \|@LB@5'-CUU...GAACC UG G UUAUG...GCG-3'@LB@ GUUGCAAACACGACA A GAU@LB@ :\|\|\|\|\|\|\|\|\|\|:\|\|\| \| :\|:@LB@ UAACGUUUGUGUUGU U UUG@LB@3'-UUU...CUGGU UG G UAGUG...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -22.6062 kcal/mol@LB@Unfolding Energy - mRNA 5.26496 kcal/mol@LB@Unfolding Energy - sRNA 3.80917 kcal/mol@LB@@LB@Position - mRNA 177 -- 247@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 79 -- 85@LB@
154	0.008185	0.1845	stm3738	yigC	-11.16	0.433331	228 -- 246	55 -- 74	similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223	_____________227__________________247\n_____________\|____________________\|\n5'-UAA...ACCUC_____________AC_____AAAUG...UUA-3'\n______________GCA__UACAAUAA__CACAA\n______________\|\|\|__:\|\|\|\|:\|\|__\|\|\|\|\|\n______________CGU__GUGUUGUU__GUGUU\n3'-UUU...GUUAA___UU_______________GUAGU...UCA-5'\n_____________\|____________________\|\n_____________75___________________54\n	27 -- 33	78 -- 84	-12.6647 kcal/mol	0.985902 kcal/mol	3.77104 kcal/mol	227 247@LB@ \| \|@LB@5'-UAA...ACCUC AC AAAUG...UUA-3'@LB@ GCA UACAAUAA CACAA@LB@ \|\|\| :\|\|\|\|:\|\| \|\|\|\|\|@LB@ CGU GUGUUGUU GUGUU@LB@3'-UUU...GUUAA UU GUAGU...UCA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -11.16 kcal/mol@LB@Hybridization Energy -12.6647 kcal/mol@LB@Unfolding Energy - mRNA 0.985902 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 228 -- 246@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 78 -- 84@LB@
173	0.009489	0.1945	stm3985	yigZ	-14.68	0.132642	77 -- 135	33 -- 90	YigZ family protein	_____________76___________________136\n_____________\|____________________\|\n5'-CGA...GUUCA________UU__________GAAAA...ACG-3'\n______________GCAAGCAC__CAAC_UGGCA\n______________\|\|\|\|:\|\|\|__\|\|\|\|_:::\|\|\n______________CGUUUGUG__GUUG_GUUGU\n3'-UUU...GUUAA________UU____U_____AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________32\n	78 -- 84	83 -- 89	-19.4869 kcal/mol	6.86655 kcal/mol	3.80671 kcal/mol	76 136@LB@ \| \|@LB@5'-CGA...GUUCA UU GAAAA...ACG-3'@LB@ GCAAGCAC CAAC UGGCA@LB@ \|\|\|\|:\|\|\| \|\|\|\| :::\|\|@LB@ CGUUUGUG GUUG GUUGU@LB@3'-UUU...GUUAA UU U AGUGU...UCA-5'@LB@ \| \|@LB@ 91 32@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -19.4869 kcal/mol@LB@Unfolding Energy - mRNA 6.86655 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 77 -- 135@LB@Position - sRNA 33 -- 90@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 83 -- 89@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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