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
140	0.01495	0.3575	b2415	ptsH	-9.89	0.288161	112 -- 122	24 -- 34	phosphohistidinoprotein-hexose phosphotransferase component of PTS system (Hpr)	_____________111____________123\n_____________\|______________\|\n5'-UUG...CAAUA_____UA_______ACCGC...UUA-3'\n______________CAGGC__AAGUCGA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\n______________GUCCG__UUCAGUU\n3'-UUU...ACUAC______________GAAAG...UAG-5'\n_____________\|______________\|\n_____________35_____________23\n	138 -- 144	150 -- 156	-14.4294 kcal/mol	3.35524 kcal/mol	6.54796 kcal/mol	111 123@LB@ \| \|@LB@5'-UUG...CAAUA UA ACCGC...UUA-3'@LB@ CAGGC AAGUCGA@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ GUCCG UUCAGUU@LB@3'-UUU...ACUAC GAAAG...UAG-5'@LB@ \| \|@LB@ 35 23@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -14.4294 kcal/mol@LB@Unfolding Energy - mRNA 3.35524 kcal/mol@LB@Unfolding Energy - sRNA 6.54796 kcal/mol@LB@@LB@Position - mRNA 112 -- 122@LB@Position - sRNA 24 -- 34@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 150 -- 156@LB@
109	0.01201	0.3575	b1096	pabC	-8.08	0.578936	115 -- 139	144 -- 163	4-amino-4-deoxychorismate lyase component of para-aminobenzoate synthase multienzyme complex	_____________114____________140\n_____________\|______________\|\n5'-GUU...GUGUA_______CG_____GGUGG...ACG-3'\n______________ACUCCUU__GCUUC\n______________\|\|:\|\|:\|__\|\|\|\|\|\n______________UGGGGGA__CGAAG\n3'-UUU...CCCCG_______A______UAG-5'\n_____________\|______________\|\n_____________164____________143\n	29 -- 35	10 -- 16	-15.037 kcal/mol	0.971533 kcal/mol	6.96912 kcal/mol	114 140@LB@ \| \|@LB@5'-GUU...GUGUA CG GGUGG...ACG-3'@LB@ ACUCCUU GCUUC@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGGGGGA CGAAG@LB@3'-UUU...CCCCG A UAG-5'@LB@ \| \|@LB@ 164 143@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -15.037 kcal/mol@LB@Unfolding Energy - mRNA 0.971533 kcal/mol@LB@Unfolding Energy - sRNA 6.96912 kcal/mol@LB@@LB@Position - mRNA 115 -- 139@LB@Position - sRNA 144 -- 163@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 10 -- 16@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@
150	0.01679	0.3749	b3550	yiaC	-14.78	0.030008	125 -- 180	123 -- 174	GNAT family putative N-acetyltransferase	_____________124_______________________________________________181\n_____________\|_________________________________________________\|\n5'-AAU...UCUGU_____CU_______G_C________U___G___GA______________GGCUG...GGC-3'\n______________UACUC__UUAUGCA_G_AUGUGGGC_GGU_AAU__UCA____UGUGGUU\n______________\|\|\|\|\|__\|:\|::\|\|_\|_\|\|\|::\|\|\|_:\|\|_\|\|:__\|\|\|____\|\|:\|\|\|:\n______________AUGAG__AGUGUGU_C_UACGUCCG_UCA_UUG__AGU____ACGCCAG\n3'-UUU...UGGUU_____UC_______A__________U___G___AA___CUUA_______UAGGG...UAG-5'\n_____________\|_________________________________________________\|\n_____________175_______________________________________________122\n	134 -- 140	167 -- 173	-39.4647 kcal/mol	14.8163 kcal/mol	12.8033 kcal/mol	124 181@LB@ \| \|@LB@5'-AAU...UCUGU CU G C U G GA GGCUG...GGC-3'@LB@ UACUC UUAUGCA G AUGUGGGC GGU AAU UCA UGUGGUU@LB@ \|\|\|\|\| \|:\|::\|\| \| \|\|\|::\|\|\| :\|\| \|\|: \|\|\| \|\|:\|\|\|:@LB@ AUGAG AGUGUGU C UACGUCCG UCA UUG AGU ACGCCAG@LB@3'-UUU...UGGUU UC A U G AA CUUA UAGGG...UAG-5'@LB@ \| \|@LB@ 175 122@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -39.4647 kcal/mol@LB@Unfolding Energy - mRNA 14.8163 kcal/mol@LB@Unfolding Energy - sRNA 12.8033 kcal/mol@LB@@LB@Position - mRNA 125 -- 180@LB@Position - sRNA 123 -- 174@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 167 -- 173@LB@
183	0.02111	0.3833	b0461	tomB	-12.41	0.091700	125 -- 158	128 -- 160	Hha toxicity attenuator; conjugation-related protein	_____________124_________________________________________159\n_____________\|___________________________________________\|\n5'-UGC...GGAUG________CCCAAA_G_______AUC____C__C____G____UCUGU...AUC-3'\n______________AAUACUCA______A_ACAUGAU____GCA_AG_UUAA_UUUC\n______________\|\|\|\|\|\|\|\|______\|_\|\|\|\|\|\|\|____\|\|\|_\|\|_\|:\|\|_\|\|\|\|\n______________UUAUGAGU______U_UGUACUA____CGU_UC_AGUU_AAAG\n3'-UUU...UGUGG________CAG____G_______CGUC___________G____UCUUA...UAG-5'\n_____________\|___________________________________________\|\n_____________161_________________________________________127\n	224 -- 230	163 -- 169	-23.2008 kcal/mol	3.84731 kcal/mol	8.26055 kcal/mol	124 159@LB@ \| \|@LB@5'-UGC...GGAUG CCCAAA G AUC C C G UCUGU...AUC-3'@LB@ AAUACUCA A ACAUGAU GCA AG UUAA UUUC@LB@ \|\|\|\|\|\|\|\| \| \|\|\|\|\|\|\| \|\|\| \|\| \|:\|\| \|\|\|\|@LB@ UUAUGAGU U UGUACUA CGU UC AGUU AAAG@LB@3'-UUU...UGUGG CAG G CGUC G UCUUA...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -23.2008 kcal/mol@LB@Unfolding Energy - mRNA 3.84731 kcal/mol@LB@Unfolding Energy - sRNA 8.26055 kcal/mol@LB@@LB@Position - mRNA 125 -- 158@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 163 -- 169@LB@
21	0.001755	0.2633	b3037	ygiB	-10.05	0.269263	126 -- 141	3 -- 15	DUF1190 family protein	_____________125______________142\n_____________\|________________\|\n5'-AAA...UUCUU_______CUC______AUUUC...UGC-3'\n______________CCCCCUU___GCUUCA\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GGGGGAA___CGAAGU\n3'-UUU...CCCGU________________AG-5'\n_____________\|________________\|\n_____________16_______________2\n	126 -- 132	9 -- 15	-20.0074 kcal/mol	1.89647 kcal/mol	7.00663 kcal/mol	125 142@LB@ \| \|@LB@5'-AAA...UUCUU CUC AUUUC...UGC-3'@LB@ CCCCCUU GCUUCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GGGGGAA CGAAGU@LB@3'-UUU...CCCGU AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -20.0074 kcal/mol@LB@Unfolding Energy - mRNA 1.89647 kcal/mol@LB@Unfolding Energy - sRNA 7.00663 kcal/mol@LB@@LB@Position - mRNA 126 -- 141@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 9 -- 15@LB@
17	0.001014	0.2007	b4032	malG	-14.09	0.041561	127 -- 139	193 -- 205	maltose transporter subunit	_____________126___________140\n_____________\|_____________\|\n5'-CGU...UCUUC_____________CGCUG...UGG-3'\n______________CUGCUGGUGGGUG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________GACGACCGCCCAC\n3'-UUU...UAUUA_____________UAAAA...UAG-5'\n_____________\|_____________\|\n_____________206___________192\n	132 -- 138	194 -- 200	-26.9183 kcal/mol	7.69341 kcal/mol	9.06058 kcal/mol	126 140@LB@ \| \|@LB@5'-CGU...UCUUC CGCUG...UGG-3'@LB@ CUGCUGGUGGGUG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ GACGACCGCCCAC@LB@3'-UUU...UAUUA UAAAA...UAG-5'@LB@ \| \|@LB@ 206 192@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -26.9183 kcal/mol@LB@Unfolding Energy - mRNA 7.69341 kcal/mol@LB@Unfolding Energy - sRNA 9.06058 kcal/mol@LB@@LB@Position - mRNA 127 -- 139@LB@Position - sRNA 193 -- 205@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@LB@
8	0.0005643	0.1842	b2557	purL	-10.01	0.273478	129 -- 143	111 -- 124	phosphoribosylformyl-glycineamide synthetase	_____________128______________144\n_____________\|________________\|\n5'-AGG...UUGGG________AA______AAGAC...UUU-3'\n______________UACACCGA__GCUUAG\n______________\|\|\|\|\|\|:\|__:\|\|:\|\|\n______________AUGUGGUU__UGAGUC\n3'-UUU...CUAAA________A_______AGUGU...UAG-5'\n_____________\|________________\|\n_____________125______________110\n	172 -- 178	181 -- 187	-14.8421 kcal/mol	1.97129 kcal/mol	3.669 kcal/mol	128 144@LB@ \| \|@LB@5'-AGG...UUGGG AA AAGAC...UUU-3'@LB@ UACACCGA GCUUAG@LB@ \|\|\|\|\|\|:\| :\|\|:\|\|@LB@ AUGUGGUU UGAGUC@LB@3'-UUU...CUAAA A AGUGU...UAG-5'@LB@ \| \|@LB@ 125 110@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -14.8421 kcal/mol@LB@Unfolding Energy - mRNA 1.97129 kcal/mol@LB@Unfolding Energy - sRNA 3.669 kcal/mol@LB@@LB@Position - mRNA 129 -- 143@LB@Position - sRNA 111 -- 124@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 181 -- 187@LB@
50	0.004849	0.3217	b1079	flgH	-12.97	0.070541	130 -- 141	23 -- 34	flagellar protein of basal-body outer-membrane L ring	_____________129____________________142\n_____________\|______________________\|\n5'-ACU...CGAUC__A_____CA____________ACUCU...GGG-3'\n______________AG_UGCUG__AAAACUGACGCA\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________UC_ACGAC__UUUUGACUGCGU\n3'-UUU...UUUUA________UA____________ACCCC...UAG-5'\n_____________\|______________________\|\n_____________35_____________________22\n	135 -- 141	23 -- 29	-26.3449 kcal/mol	4.56982 kcal/mol	12.5314 kcal/mol	129 142@LB@ \| \|@LB@5'-ACU...CGAUC A CA ACUCU...GGG-3'@LB@ AG UGCUG AAAACUGACGCA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UC ACGAC UUUUGACUGCGU@LB@3'-UUU...UUUUA UA ACCCC...UAG-5'@LB@ \| \|@LB@ 35 22@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -26.3449 kcal/mol@LB@Unfolding Energy - mRNA 4.56982 kcal/mol@LB@Unfolding Energy - sRNA 12.5314 kcal/mol@LB@@LB@Position - mRNA 130 -- 141@LB@Position - sRNA 23 -- 34@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 23 -- 29@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase	_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 7 -- 13@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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