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
131	0.006551	0.1774	stm3217	aer	-17.88	0.039631	254 -- 298	36 -- 77	senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506	_____________253____________________________________________________________________________________299\n_____________\|______________________________________________________________________________________\|\n5'-UUU...AAGGC______UGA_____________________ACAAA____AA__AUU____________________UC__G______UUUA_____UAAAG...CCA-3'\n______________GCAGGA___GGUGAAAA_________UCGU_____UAUU__GG____AAUCGCA____AAUUGCGA__CA_AGCAAU____ACAAC\n______________:\|\|\|\|\|___:\|\|\|\|\|\|\|_________\|\|\|:_____\|\|::__\|\|____\|\|\|\|\|\|\|____\|\|\|\|\|\|:\|__\|\|_\|:\|\|\|:____\|\|\|\|\|\n______________UGUCCU___UCACUUUU_________AGCG_____AUGG__CC____UUAGCGU____UUAACGUU__GU_UUGUUG____UGUUG\n3'-UUU...UUACA_________________UCCCAUCAG_____________CA__AGAC_______CUGG________U___G_______________UAGUG...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________78_____________________________________________________________________________________35\n	89 -- 95	99 -- 105	-43.6348 kcal/mol	13.4466 kcal/mol	20.9633 kcal/mol	253 299@LB@ \| \|@LB@5'-UUU...AAGGC UGA ACAAA AA AUU UC G UUUA UAAAG...CCA-3'@LB@ GCAGGA GGUGAAAA UCGU UAUU GG AAUCGCA AAUUGCGA CA AGCAAU ACAAC@LB@ :\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|\| \|:\|\|\|: \|\|\|\|\|@LB@ UGUCCU UCACUUUU AGCG AUGG CC UUAGCGU UUAACGUU GU UUGUUG UGUUG@LB@3'-UUU...UUACA UCCCAUCAG CA AGAC CUGG U G UAGUG...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -43.6348 kcal/mol@LB@Unfolding Energy - mRNA 13.4466 kcal/mol@LB@Unfolding Energy - sRNA 20.9633 kcal/mol@LB@@LB@Position - mRNA 254 -- 298@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 99 -- 105@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@
12	0.0002098	0.05681	stm3344	rpsI	-21.57	0.009451	131 -- 172	57 -- 102	30S ribosomal protein S9	_____________130__________________________173\n_____________\|____________________________\|\n5'-GUG...GGCAA__________C________CA_______CAAGU...GUU-3'\n______________CGAGCACAAC_ACGCGGCA__GCAACCG\n______________\|:\|:\|\|\|\|\|\|_\|\|:\|::\|\|__:\|\|\|\|\|\|\n______________GUUUGUGUUG_UGUGUUGU__UGUUGGC\n3'-UUU...UUAAC__________U________AG_______AUUCG...UCA-5'\n_____________\|____________________________\|\n_____________103__________________________56\n	161 -- 167	62 -- 68	-36.1701 kcal/mol	9.00411 kcal/mol	8.61223 kcal/mol	130 173@LB@ \| \|@LB@5'-GUG...GGCAA C CA CAAGU...GUU-3'@LB@ CGAGCACAAC ACGCGGCA GCAACCG@LB@ \|:\|:\|\|\|\|\|\| \|\|:\|::\|\| :\|\|\|\|\|\|@LB@ GUUUGUGUUG UGUGUUGU UGUUGGC@LB@3'-UUU...UUAAC U AG AUUCG...UCA-5'@LB@ \| \|@LB@ 103 56@LB@@LB@@LB@Energy -21.57 kcal/mol@LB@Hybridization Energy -36.1701 kcal/mol@LB@Unfolding Energy - mRNA 9.00411 kcal/mol@LB@Unfolding Energy - sRNA 8.61223 kcal/mol@LB@@LB@Position - mRNA 131 -- 172@LB@Position - sRNA 57 -- 102@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 62 -- 68@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@
172	0.009395	0.1945	stm3373	mreC	-15.91	0.084075	179 -- 229	45 -- 87	rod shape-determining protein MreC	_____________178____________230\n_____________\|______________\|\n5'-UGA...UGUUA_____AG_______CAUUC...GGA-3'\n______________AUGGA__AGACGGG\n______________\|\|\|\|\|__\|\|\|\|:\|\|\n______________UACCU__UCUGUCC\n3'-UUU...AGUGA_____G________CAUUU...UCA-5'\n_____________\|______________\|\n_____________88_____________44\n	21 -- 27	153 -- 159	-16.2478 kcal/mol	4.60826 kcal/mol	2.82582 kcal/mol	178 230@LB@ \| \|@LB@5'-UGA...UGUUA AG CAUUC...GGA-3'@LB@ AUGGA AGACGGG@LB@ \|\|\|\|\| \|\|\|\|:\|\|@LB@ UACCU UCUGUCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 88 44@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -16.2478 kcal/mol@LB@Unfolding Energy - mRNA 4.60826 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 179 -- 229@LB@Position - sRNA 45 -- 87@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 153 -- 159@LB@
176	0.009613	0.1945	stm3378	N/A	-14.56	0.138793	155 -- 243	45 -- 125	sulfoxide reductase heme-binding subunit YedZ	_____________154_______________________________________________________________________________________244\n_____________\|_________________________________________________________________________________________\|\n5'-UGU...AAUGA____GCU_____GU____C_____CAAU_______AGAAUUU____G____U___________A____G_______U____________UUGUC...GUG-3'\n______________AGUC___UCGCU__AUCG_GGUCU____UUGCGGG_______UUAA_UGCG__C_UGACAGCA_AACA__AUAACC___GGCUAAAAGU\n______________\|\|\|\|___\|\|\|\|\|__\|:\|\|_\|\|\|\|\|____\|:\|\|:\|:_______::\|\|_\|\|\|:__\|_::\|\|\|:\|\|_\|\|\|\|__\|:\|\|\|\|___:\|\|:\|\|\|\|\|:\n______________UCAG___AGCGA__UGGC_CCAGA____AGCGUCU_______GGUU_ACGU__G_GUUGUUGU_UUGU__UGUUGG___UCGGUUUUCG\n3'-UUU...UCCCA__________________A_____CUU___________________A____UU_U________G____AG______CAU__________GGUAG...UCA-5'\n_____________\|_________________________________________________________________________________________\|\n_____________126_______________________________________________________________________________________44\n	209 -- 215	76 -- 82	-59.1156 kcal/mol	19.0244 kcal/mol	31.7466 kcal/mol	154 244@LB@ \| \|@LB@5'-UGU...AAUGA GCU GU C CAAU AGAAUUU G U A G U UUGUC...GUG-3'@LB@ AGUC UCGCU AUCG GGUCU UUGCGGG UUAA UGCG C UGACAGCA AACA AUAACC GGCUAAAAGU@LB@ \|\|\|\| \|\|\|\|\| \|:\|\| \|\|\|\|\| \|:\|\|:\|: ::\|\| \|\|\|: \| ::\|\|\|:\|\| \|\|\|\| \|:\|\|\|\| :\|\|:\|\|\|\|\|:@LB@ UCAG AGCGA UGGC CCAGA AGCGUCU GGUU ACGU G GUUGUUGU UUGU UGUUGG UCGGUUUUCG@LB@3'-UUU...UCCCA A CUU A UU U G AG CAU GGUAG...UCA-5'@LB@ \| \|@LB@ 126 44@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -59.1156 kcal/mol@LB@Unfolding Energy - mRNA 19.0244 kcal/mol@LB@Unfolding Energy - sRNA 31.7466 kcal/mol@LB@@LB@Position - mRNA 155 -- 243@LB@Position - sRNA 45 -- 125@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 76 -- 82@LB@
23	0.0005914	0.08814	stm3466	crp	-13.97	0.171291	272 -- 288	36 -- 50	transcriptional regulator Crp	_____________271_______________________________289\n_____________\|_________________________________\|\n5'-ACG...CGAAA______CUAAA________________C_____UAAUA...AGG-3'\n______________GCUAUG_____ACAGACA____AGAUG_UACAG\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|____\|:\|\|\|_\|\|\|\|\|\n______________UGAUAC_____UGUCUGU____UUUAC_AUGUC\n3'-UUU...AUUAG______C___________CCCA___________CUUCA...UCA-5'\n_____________\|_________________________________\|\n_____________51________________________________35\n	21 -- 27	155 -- 161	-20.3438 kcal/mol	4.64329 kcal/mol	5.58455 kcal/mol	271 289@LB@ \| \|@LB@5'-ACG...CGAAA CUAAA C UAAUA...AGG-3'@LB@ GCUAUG ACAGACA AGAUG UACAG@LB@ :\|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|@LB@ UGAUAC UGUCUGU UUUAC AUGUC@LB@3'-UUU...AUUAG C CCCA CUUCA...UCA-5'@LB@ \| \|@LB@ 51 35@LB@@LB@@LB@Energy -13.97 kcal/mol@LB@Hybridization Energy -20.3438 kcal/mol@LB@Unfolding Energy - mRNA 4.64329 kcal/mol@LB@Unfolding Energy - sRNA 5.58455 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 36 -- 50@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 155 -- 161@LB@
147	0.007823	0.1845	stm3477	cysG	-15.08	0.114738	192 -- 245	61 -- 111	uroporphyrinogen-III C-methyltransferase	_____________191____________________________________________246\n_____________\|______________________________________________\|\n5'-UCC...UAAGG___AAU____________U____CU___UUUUGU____U_______CGCGA...AAG-3'\n______________GGU____GUCGUGGACCA_UUGC__AUA______CAAU_ACGCGAC\n______________\|\|\|____:\|\|\|::\|\|\|\|\|_\|\|\|\|__\|:\|______\|\|\|:_\|\|:\|:\|\|\n______________CCA____UAGCGUCUGGU_AACG__UGU______GUUG_UGUGUUG\n3'-UUU...UGGCA___GACU___________U____UU_____________U_______UAGUG...UCA-5'\n_____________\|______________________________________________\|\n_____________112____________________________________________60\n	230 -- 236	72 -- 78	-36.0085 kcal/mol	10.6439 kcal/mol	13.6111 kcal/mol	191 246@LB@ \| \|@LB@5'-UCC...UAAGG AAU U CU UUUUGU U CGCGA...AAG-3'@LB@ GGU GUCGUGGACCA UUGC AUA CAAU ACGCGAC@LB@ \|\|\| :\|\|\|::\|\|\|\|\| \|\|\|\| \|:\| \|\|\|: \|\|:\|:\|\|@LB@ CCA UAGCGUCUGGU AACG UGU GUUG UGUGUUG@LB@3'-UUU...UGGCA GACU U UU U UAGUG...UCA-5'@LB@ \| \|@LB@ 112 60@LB@@LB@@LB@Energy -15.08 kcal/mol@LB@Hybridization Energy -36.0085 kcal/mol@LB@Unfolding Energy - mRNA 10.6439 kcal/mol@LB@Unfolding Energy - sRNA 13.6111 kcal/mol@LB@@LB@Position - mRNA 192 -- 245@LB@Position - sRNA 61 -- 111@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 72 -- 78@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@
36	0.00125	0.1215	stm3523	glpR	-16.55	0.065942	207 -- 266	37 -- 89	DeoR/GlpR family transcriptional regulator	_____________206________________267\n_____________\|__________________\|\n5'-UUG...UGAAA__________________GCGAU...CGC-3'\n______________CAAACACAACGGCAUGAC\n______________\|\|\|\|\|\|\|\|\|\|::\|\|::\|\|\n______________GUUUGUGUUGUUGUGUUG\n3'-UUU...UUAAC__________________UAGUG...UCA-5'\n_____________\|__________________\|\n_____________90_________________36\n	218 -- 224	72 -- 78	-24.6143 kcal/mol	5.8046 kcal/mol	3.79561 kcal/mol	206 267@LB@ \| \|@LB@5'-UUG...UGAAA GCGAU...CGC-3'@LB@ CAAACACAACGGCAUGAC@LB@ \|\|\|\|\|\|\|\|\|\|::\|\|::\|\|@LB@ GUUUGUGUUGUUGUGUUG@LB@3'-UUU...UUAAC UAGUG...UCA-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -16.55 kcal/mol@LB@Hybridization Energy -24.6143 kcal/mol@LB@Unfolding Energy - mRNA 5.8046 kcal/mol@LB@Unfolding Energy - sRNA 3.79561 kcal/mol@LB@@LB@Position - mRNA 207 -- 266@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 72 -- 78@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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