Input and runtime details for job 8257533 (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 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

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_003210 Listeria monocytogenes EGD-e

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
93	0.02416	0.6733	lmo2042	N/A	-17.13	0.038629	149 -- 196	158 -- 206	cell division protein MraZ	_____________148_____________________________________________197\n_____________\|_______________________________________________\|\n5'-UUU...GCGAA_________________UAAAG_____AUGU____AA__________UCUAA...CCC-3'\n______________GUGGGG___AGAUGUGG______UGGU____AUGA__GUGGGUGAAG\n______________:\|\|:\|\|___\|\|\|::\|\|:______:\|\|:____\|\|\|\|__:\|\|::\|\|\|\|:\n______________UACUCC___UCUGUACU______GCCG____UACU__UACUUACUUU\n3'-GUU...UGCCC______GUA________UGAUGU____GU______C___________UGUUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________207_____________________________________________157\n	190 -- 196	158 -- 164	-27.738 kcal/mol	5.20754 kcal/mol	13.9391 kcal/mol	148 197@LB@ \| \|@LB@5'-UUU...GCGAA UAAAG AUGU AA UCUAA...CCC-3'@LB@ GUGGGG AGAUGUGG UGGU AUGA GUGGGUGAAG@LB@ :\|\|:\|\| \|\|\|::\|\|: :\|\|: \|\|\|\| :\|\|::\|\|\|\|:@LB@ UACUCC UCUGUACU GCCG UACU UACUUACUUU@LB@3'-GUU...UGCCC GUA UGAUGU GU C UGUUU...GGA-5'@LB@ \| \|@LB@ 207 157@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -27.738 kcal/mol@LB@Unfolding Energy - mRNA 5.20754 kcal/mol@LB@Unfolding Energy - sRNA 13.9391 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 158 -- 206@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 158 -- 164@LB@
87	0.02294	0.6733	lmo2765	N/A	-17.07	0.039744	188 -- 213	176 -- 199	PTS cellbiose transporter subunit IIA	_____________187_________________214\n_____________\|___________________\|\n5'-UUA...UAGAC________A__________GUUAU...AUU-3'\n______________AUGA_AUG_AAUGGAAACA\n______________\|\|\|\|_\|\|\|_\|\|\|\|:\|\|\|\|\|\n______________UACU_UAC_UUACUUUUGU\n3'-GUU...CCGGU____C______________UUAUU...GGA-5'\n_____________\|___________________\|\n_____________200_________________175\n	212 -- 218	155 -- 161	-13.3886 kcal/mol	2.47541 kcal/mol	0.935542 kcal/mol	187 214@LB@ \| \|@LB@5'-UUA...UAGAC A GUUAU...AUU-3'@LB@ AUGA AUG AAUGGAAACA@LB@ \|\|\|\| \|\|\| \|\|\|\|:\|\|\|\|\|@LB@ UACU UAC UUACUUUUGU@LB@3'-GUU...CCGGU C UUAUU...GGA-5'@LB@ \| \|@LB@ 200 175@LB@@LB@@LB@Energy -17.07 kcal/mol@LB@Hybridization Energy -13.3886 kcal/mol@LB@Unfolding Energy - mRNA 2.47541 kcal/mol@LB@Unfolding Energy - sRNA 0.935542 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 176 -- 199@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 155 -- 161@LB@
83	0.02274	0.6733	lmo1752	N/A	-17.06	0.039898	184 -- 210	151 -- 173	lmo1752	_____________183___________211\n_____________\|_____________\|\n5'-CUA...CAAGA_____________CGAUA...CAG-3'\n______________AAUGAGGUGAAUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\n______________UUACUCUACUUAC\n3'-GUU...GCCGG_____________UUUUG...GGA-5'\n_____________\|_____________\|\n_____________174___________150\n	190 -- 196	161 -- 167	-16.9304 kcal/mol	1.40294 kcal/mol	0.838004 kcal/mol	183 211@LB@ \| \|@LB@5'-CUA...CAAGA CGAUA...CAG-3'@LB@ AAUGAGGUGAAUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|@LB@ UUACUCUACUUAC@LB@3'-GUU...GCCGG UUUUG...GGA-5'@LB@ \| \|@LB@ 174 150@LB@@LB@@LB@Energy -17.06 kcal/mol@LB@Hybridization Energy -16.9304 kcal/mol@LB@Unfolding Energy - mRNA 1.40294 kcal/mol@LB@Unfolding Energy - sRNA 0.838004 kcal/mol@LB@@LB@Position - mRNA 184 -- 210@LB@Position - sRNA 151 -- 173@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 161 -- 167@LB@
120	0.03214	0.6968	lmo0368	N/A	-17.05	0.040150	163 -- 213	95 -- 164		_____________162______________________________________________214\n_____________\|________________________________________________\|\n5'-UGC...AAUGA_____A_____AA_______AGGGA___G______G_______A____AUUUG...UUC-3'\n______________AAGCA___GUC__UGAUUAG_____GCC_AUUUUA_UGGAAGA_UGGG\n______________\|\|:\|\|___\|\|\|__\|\|\|:\|\|\|_____\|\|\|_\|\|\|:\|\|_\|\|\|\|\|\|\|_\|\|\|:\n______________UUUGU___CAG__ACUGAUC_____CGG_UAAGAU_ACCUUCU_ACCU\n3'-GUU...ACAGA_____CUA____________AA_____________A____________AUGUG...GGA-5'\n_____________\|________________________________________________\|\n_____________165______________________________________________94\n	202 -- 208	99 -- 105	-32.1999 kcal/mol	10.9316 kcal/mol	9.49359 kcal/mol	162 214@LB@ \| \|@LB@5'-UGC...AAUGA A AA AGGGA G G A AUUUG...UUC-3'@LB@ AAGCA GUC UGAUUAG GCC AUUUUA UGGAAGA UGGG@LB@ \|\|:\|\| \|\|\| \|\|\|:\|\|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:@LB@ UUUGU CAG ACUGAUC CGG UAAGAU ACCUUCU ACCU@LB@3'-GUU...ACAGA CUA AA A AUGUG...GGA-5'@LB@ \| \|@LB@ 165 94@LB@@LB@@LB@Energy -17.05 kcal/mol@LB@Hybridization Energy -32.1999 kcal/mol@LB@Unfolding Energy - mRNA 10.9316 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 163 -- 213@LB@Position - sRNA 95 -- 164@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 99 -- 105@LB@
102	0.02619	0.6733	lmo1799	N/A	-17.02	0.040600	38 -- 69	171 -- 207	peptidoglycan binding protein	_____________37______________70\n_____________\|_______________\|\n5'-CUA...AAAAC__G____________UUGGC...UGG-3'\n______________GA_GGGA_GGGGCAU\n______________:\|_\|\|\|\|_\|:\|\|\|\|\|\n______________UU_CCCU_CUCCGUA\n3'-GUU...ACGUA__G____A_______UCUGU...GGA-5'\n_____________\|_______________\|\n_____________208_____________170\n	45 -- 51	193 -- 199	-19.1902 kcal/mol	1.80232 kcal/mol	8.95053 kcal/mol	37 70@LB@ \| \|@LB@5'-CUA...AAAAC G UUGGC...UGG-3'@LB@ GA GGGA GGGGCAU@LB@ :\| \|\|\|\| \|:\|\|\|\|\|@LB@ UU CCCU CUCCGUA@LB@3'-GUU...ACGUA G A UCUGU...GGA-5'@LB@ \| \|@LB@ 208 170@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -19.1902 kcal/mol@LB@Unfolding Energy - mRNA 1.80232 kcal/mol@LB@Unfolding Energy - sRNA 8.95053 kcal/mol@LB@@LB@Position - mRNA 38 -- 69@LB@Position - sRNA 171 -- 207@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 193 -- 199@LB@
65	0.01641	0.6733	lmo0040	N/A	-17.01	0.040772	52 -- 100	171 -- 220	agmatine deiminase	_____________51______________101\n_____________\|_______________\|\n5'-GUC...AAUAG____A__________GGGAC...CUG-3'\n______________GAGG_GAAUGAGGAU\n______________\|\|\|:_\|\|\|\|\|\|::\|:\n______________CUCU_CUUACUUUUG\n3'-GUU...GGUUA____A__________UUUAU...GGA-5'\n_____________\|_______________\|\n_____________221_____________170\n	196 -- 202	156 -- 162	-15.5399 kcal/mol	0.994344 kcal/mol	0.916023 kcal/mol	51 101@LB@ \| \|@LB@5'-GUC...AAUAG A GGGAC...CUG-3'@LB@ GAGG GAAUGAGGAU@LB@ \|\|\|: \|\|\|\|\|\|::\|:@LB@ CUCU CUUACUUUUG@LB@3'-GUU...GGUUA A UUUAU...GGA-5'@LB@ \| \|@LB@ 221 170@LB@@LB@@LB@Energy -17.01 kcal/mol@LB@Hybridization Energy -15.5399 kcal/mol@LB@Unfolding Energy - mRNA 0.994344 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 52 -- 100@LB@Position - sRNA 171 -- 220@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 156 -- 162@LB@
45	0.0103	0.599	lmo0066	N/A	-17.00	0.040990	179 -- 207	157 -- 199	toxin	_____________178___________208\n_____________\|_____________\|\n5'-AAA...AGGCC_____________AAGUC...AUU-3'\n______________AGAUGAAUGAAAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCUACUUACUUUU\n3'-GUU...GUUAC_____________GUUUA...GGA-5'\n_____________\|_____________\|\n_____________200___________156\n	201 -- 207	157 -- 163	-14.7839 kcal/mol	1.76886 kcal/mol	0.884237 kcal/mol	178 208@LB@ \| \|@LB@5'-AAA...AGGCC AAGUC...AUU-3'@LB@ AGAUGAAUGAAAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCUACUUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -14.7839 kcal/mol@LB@Unfolding Energy - mRNA 1.76886 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 179 -- 207@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
142	0.03693	0.6968	lmo2586	N/A	-16.96	0.041696	196 -- 266	151 -- 227	formate dehydrogenase subunit alpha	_____________195______267\n_____________\|________\|\n5'-UUU...GUGGC________UGGUG...AUC-3'\n______________GCGGGAUG\n______________:\|\|\|\|\|\|\|\n______________UGCCCUAC\n3'-GUU...CGUAU________UCCGU...GGA-5'\n_____________\|________\|\n_____________228______150\n	240 -- 246	199 -- 205	-13.0644 kcal/mol	3.68871 kcal/mol	0.331032 kcal/mol	195 267@LB@ \| \|@LB@5'-UUU...GUGGC UGGUG...AUC-3'@LB@ GCGGGAUG@LB@ :\|\|\|\|\|\|\|@LB@ UGCCCUAC@LB@3'-GUU...CGUAU UCCGU...GGA-5'@LB@ \| \|@LB@ 228 150@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -13.0644 kcal/mol@LB@Unfolding Energy - mRNA 3.68871 kcal/mol@LB@Unfolding Energy - sRNA 0.331032 kcal/mol@LB@@LB@Position - mRNA 196 -- 266@LB@Position - sRNA 151 -- 227@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 199 -- 205@LB@
135	0.03605	0.6968	lmo1003	N/A	-16.96	0.041836	78 -- 154	154 -- 221	phosphotransferase system enzyme I	_____________77_______________________________________________________________________________________155\n_____________\|________________________________________________________________________________________\|\n5'-GUG...CUUAA____AUCA_____________CUCUUG___U___UAA______CU_____UACUAU______U_AA___A_C______AAA_______UUGAA...AAG-3'\n______________AUCA____UGGGCG_UUAUGU______GUA_UGG____AGGCG__GACAU______CUACAC_G__GGU_G_GAUGAA___GAAGCAA\n______________\|\|\|\|____:\|\|\|\|\|_:\|\|\|\|:______:\|\|_:\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|_\|__::\|_\|_\|\|\|\|\|\|___:\|\|:\|\|\|\n______________UAGU____GCCCGC_GAUACG______UAU_GCC____UCCGU__CUGUA______GAUGUG_C__UUA_C_CUACUU___UUUUGUU\n3'-GUU...AACGG____ACAA______G_______________U___CUAC_____AU_____CUU_________C_GG_____U______AC________UAUUA...GGA-5'\n_____________\|________________________________________________________________________________________\|\n_____________222______________________________________________________________________________________153\n	148 -- 154	154 -- 160	-50.8348 kcal/mol	18.1196 kcal/mol	22.592 kcal/mol	77 155@LB@ \| \|@LB@5'-GUG...CUUAA AUCA CUCUUG U UAA CU UACUAU U AA A C AAA UUGAA...AAG-3'@LB@ AUCA UGGGCG UUAUGU GUA UGG AGGCG GACAU CUACAC G GGU G GAUGAA GAAGCAA@LB@ \|\|\|\| :\|\|\|\|\| :\|\|\|\|: :\|\| :\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\| \| ::\| \| \|\|\|\|\|\| :\|\|:\|\|\|@LB@ UAGU GCCCGC GAUACG UAU GCC UCCGU CUGUA GAUGUG C UUA C CUACUU UUUUGUU@LB@3'-GUU...AACGG ACAA G U CUAC AU CUU C GG U AC UAUUA...GGA-5'@LB@ \| \|@LB@ 222 153@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -50.8348 kcal/mol@LB@Unfolding Energy - mRNA 18.1196 kcal/mol@LB@Unfolding Energy - sRNA 22.592 kcal/mol@LB@@LB@Position - mRNA 78 -- 154@LB@Position - sRNA 154 -- 221@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 154 -- 160@LB@
155	0.04112	0.7058	lmo1165	N/A	-16.89	0.043077	88 -- 150	155 -- 206	ethanolamine utilization protein EutE	_____________87_______________________________151\n_____________\|________________________________\|\n5'-AAG...AAUGG____________G___C_______G_______UCCAC...CAA-3'\n______________GGAUUA_GCGGC_GAU_AG_UGGA_GAAGAUA\n______________\|:\|:\|\|_:\|\|\|\|_:\|\|_\|\|_\|\|:\|_\|\|\|:\|:\|\n______________CUUGAU_UGCCG_UUA_UC_ACUU_CUUUUGU\n3'-GUU...CUGUA______G_____G___C__U____A_______UUAUU...GGA-5'\n_____________\|________________________________\|\n_____________207______________________________154\n	144 -- 150	155 -- 161	-24.1777 kcal/mol	5.41964 kcal/mol	9.66922 kcal/mol	87 151@LB@ \| \|@LB@5'-AAG...AAUGG G C G UCCAC...CAA-3'@LB@ GGAUUA GCGGC GAU AG UGGA GAAGAUA@LB@ \|:\|:\|\| :\|\|\|\| :\|\| \|\| \|\|:\| \|\|\|:\|:\|@LB@ CUUGAU UGCCG UUA UC ACUU CUUUUGU@LB@3'-GUU...CUGUA G G C U A UUAUU...GGA-5'@LB@ \| \|@LB@ 207 154@LB@@LB@@LB@Energy -16.89 kcal/mol@LB@Hybridization Energy -24.1777 kcal/mol@LB@Unfolding Energy - mRNA 5.41964 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 88 -- 150@LB@Position - sRNA 155 -- 206@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 155 -- 161@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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