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: http://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	Additional homologs
95	0.004301	0.1596	stm4114	pflD	-11.77	0.360092	46 -- 100	34 -- 88	formate C-acetyltransferase	stm0843	_____________45_____________________101\n_____________\|______________________\|\n5'-UUU...CGGUA_______C______________GAACA...AGA-3'\n______________AAACGCG_CGACGC__CAUUAU\n______________\|\|\|\|:\|:_\|:\|\|:\|__\|\|\|:\|:\n______________UUUGUGU_GUUGUG__GUAGUG\n3'-UUU...UAACG_______U______UU______UUGGC...UCA-5'\n_____________\|______________________\|\n_____________89_____________________33\n	46 -- 52	82 -- 88	-16.7675 kcal/mol	5.49067 kcal/mol	5.48747 kcal/mol	45 101@LB@ \| \|@LB@5'-UUU...CGGUA C GAACA...AGA-3'@LB@ AAACGCG CGACGC CAUUAU@LB@ \|\|\|\|:\|: \|:\|\|:\| \|\|\|:\|:@LB@ UUUGUGU GUUGUG GUAGUG@LB@3'-UUU...UAACG U UU UUGGC...UCA-5'@LB@ \| \|@LB@ 89 33@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -16.7675 kcal/mol@LB@Unfolding Energy - mRNA 5.49067 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 46 -- 100@LB@Position - sRNA 34 -- 88@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 82 -- 88@LB@
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA		_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@LB@
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I		_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
97	0.004849	0.1728	stm0832	ybiF	-11.58	0.382043	25 -- 72	45 -- 91	threonine/homoserine exporter RhtA		_____________24______________________73\n_____________\|_______________________\|\n5'-GGC...GCGCG_________________U_____CAGAU...CGU-3'\n______________UGC_GGCGCGAUA_CAU__CAUC\n______________\|\|\|_::\|:\|:\|:\|_\|\|:__\|\|\|\|\n______________ACG_UUGUGUUGU_GUG__GUAG\n3'-UUU...GGUUA___U_________U___UU____UGUUG...UCA-5'\n_____________\|_______________________\|\n_____________92______________________44\n	30 -- 36	79 -- 85	-16.3644 kcal/mol	3.58897 kcal/mol	4.34303 kcal/mol	24 73@LB@ \| \|@LB@5'-GGC...GCGCG U CAGAU...CGU-3'@LB@ UGC GGCGCGAUA CAU CAUC@LB@ \|\|\| ::\|:\|:\|:\| \|\|: \|\|\|\|@LB@ ACG UUGUGUUGU GUG GUAG@LB@3'-UUU...GGUUA U U UU UGUUG...UCA-5'@LB@ \| \|@LB@ 92 44@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.3644 kcal/mol@LB@Unfolding Energy - mRNA 3.58897 kcal/mol@LB@Unfolding Energy - sRNA 4.34303 kcal/mol@LB@@LB@Position - mRNA 25 -- 72@LB@Position - sRNA 45 -- 91@LB@Position Seed - mRNA 30 -- 36@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@
77	0.003608	0.1596	stm4473	yjgM	-11.12	0.437983	252 -- 285	42 -- 82	GNAT family N-acetyltransferase		_____________251________________286\n_____________\|__________________\|\n5'-AUU...CGCCG________CC___C____AUGCC...ACG-3'\n______________AAUCACUA___GC_GACA\n______________\|\|\|\|\|\|\|\|___:\|_\|\|\|\|\n______________UUAGUGAU___UG_CUGU\n3'-UUU...UGUAA________ACC__U____CCCAU...UCA-5'\n_____________\|__________________\|\n_____________83_________________41\n	240 -- 246	165 -- 171	-13.0222 kcal/mol	3.39479 kcal/mol	3.49149 kcal/mol	251 286@LB@ \| \|@LB@5'-AUU...CGCCG CC C AUGCC...ACG-3'@LB@ AAUCACUA GC GACA@LB@ \|\|\|\|\|\|\|\| :\| \|\|\|\|@LB@ UUAGUGAU UG CUGU@LB@3'-UUU...UGUAA ACC U CCCAU...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -13.0222 kcal/mol@LB@Unfolding Energy - mRNA 3.39479 kcal/mol@LB@Unfolding Energy - sRNA 3.49149 kcal/mol@LB@@LB@Position - mRNA 252 -- 285@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 165 -- 171@LB@
107	0.00529	0.1728	stm0994	mukB	-11.10	0.440174	5 -- 20	154 -- 167	cell division protein MukB		_____________4_________________________21\n_____________\|_________________________\|\n5'-UGG...UCAGC_______U__________G______AAUAA...CCG-3'\n______________CGGACAG_GG_______A_AGGAAG\n______________\|:\|\|\|\|\|_\|\|_______\|_\|\|\|\|\|\|\n______________GUCUGUC_CC_______U_UCCUUC\n3'-UUU...UACCU__________AUUUACA_G______ACUUU...UCA-5'\n_____________\|_________________________\|\n_____________168_______________________153\n	179 -- 185	154 -- 160	-19.4251 kcal/mol	3.58038 kcal/mol	5.99227 kcal/mol	4 21@LB@ \| \|@LB@5'-UGG...UCAGC U G AAUAA...CCG-3'@LB@ CGGACAG GG A AGGAAG@LB@ \|:\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ GUCUGUC CC U UCCUUC@LB@3'-UUU...UACCU AUUUACA G ACUUU...UCA-5'@LB@ \| \|@LB@ 168 153@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -19.4251 kcal/mol@LB@Unfolding Energy - mRNA 3.58038 kcal/mol@LB@Unfolding Energy - sRNA 5.99227 kcal/mol@LB@@LB@Position - mRNA 5 -- 20@LB@Position - sRNA 154 -- 167@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 154 -- 160@LB@
65	0.003171	0.1596	stm0830	glnH	-11.06	0.446113	180 -- 193	153 -- 165	glutamine ABC transporter substrate-binding protein GlnH		_____________179____________194\n_____________\|______________\|\n5'-AGA...GCCCC_________AA___AAAUG...CGG-3'\n______________GUGGAUAGA__AGG\n______________:\|\|\|\|:\|\|\|__\|\|\|\n______________UACCUGUCU__UCC\n3'-UUU...AGUGA_________G____CAUUU...UCA-5'\n_____________\|______________\|\n_____________166____________152\n	182 -- 188	157 -- 163	-15.2236 kcal/mol	3.11192 kcal/mol	2.82582 kcal/mol	179 194@LB@ \| \|@LB@5'-AGA...GCCCC AA AAAUG...CGG-3'@LB@ GUGGAUAGA AGG@LB@ :\|\|\|\|:\|\|\| \|\|\|@LB@ UACCUGUCU UCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 166 152@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -15.2236 kcal/mol@LB@Unfolding Energy - mRNA 3.11192 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 153 -- 165@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 157 -- 163@LB@
151	0.00796	0.1845	stm2365	folC	-10.71	0.491716	269 -- 300	50 -- 78	bifunctional tetrahydrofolate synthase/dihydrofolate synthase		_____________268__________301\n_____________\|____________\|\n5'-CCG...CGGCG____A_______UCUGA...AGC-3'\n______________CCGG_UCAGGAG\n______________\|\|\|\|_\|\|\|\|\|\|:\n______________GGCC_AGUCCUU\n3'-UUU...AGCAA____G_______CA-5'\n_____________\|____________\|\n_____________79___________49\n	115 -- 121	3 -- 9	-17.3652 kcal/mol	5.30633 kcal/mol	4.72771 kcal/mol	268 301@LB@ \| \|@LB@5'-CCG...CGGCG A UCUGA...AGC-3'@LB@ CCGG UCAGGAG@LB@ \|\|\|\| \|\|\|\|\|\|:@LB@ GGCC AGUCCUU@LB@3'-UUU...AGCAA G CA-5'@LB@ \| \|@LB@ 79 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.3652 kcal/mol@LB@Unfolding Energy - mRNA 5.30633 kcal/mol@LB@Unfolding Energy - sRNA 4.72771 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 50 -- 78@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 3 -- 9@LB@
51	0.001912	0.1324	stm2692	N/A	-10.31	0.546971	162 -- 173	130 -- 141	putative HlyD family secretion protein		_____________161__________174\n_____________\|____________\|\n5'-GUU...CCGUC____________AUGAA...CGU-3'\n______________GGGAGUGGAAAA\n______________\|\|:\|\|\|\|:\|\|\|\|\n______________CCUUCACUUUUU\n3'-UUU...CAUGU____________CCCAU...UCA-5'\n_____________\|____________\|\n_____________142__________129\n	166 -- 172	131 -- 137	-15.3652 kcal/mol	2.02429 kcal/mol	2.83702 kcal/mol	161 174@LB@ \| \|@LB@5'-GUU...CCGUC AUGAA...CGU-3'@LB@ GGGAGUGGAAAA@LB@ \|\|:\|\|\|\|:\|\|\|\|@LB@ CCUUCACUUUUU@LB@3'-UUU...CAUGU CCCAU...UCA-5'@LB@ \| \|@LB@ 142 129@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -15.3652 kcal/mol@LB@Unfolding Energy - mRNA 2.02429 kcal/mol@LB@Unfolding Energy - sRNA 2.83702 kcal/mol@LB@@LB@Position - mRNA 162 -- 173@LB@Position - sRNA 130 -- 141@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 131 -- 137@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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