Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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	Additional homologs
161	0.00773	0.1668	b0945	pyrD	-11.84	0.111523	258 -- 300	33 -- 77	dihydro-orotate oxidase FMN-linked		_____________257____________________________________________300\n_____________\|______________________________________________\|\n5'-UGU...CUCAU___U____UUUU________A__CC__A____A_______ACG____-3'\n______________GAG_UUAC____CAGCAAUU_CG__GU_UUAC_____GGA___CCGU\n______________:\|\|_:\|\|\|____\|\|\|\|\|\|\|\|_\|\|__\|\|_\|:\|\|_____\|\|\|___\|\|:\|\n______________UUC_GAUG____GUCGUUAA_GC__CA_AGUG_____CCU___GGUA\n3'-UUU...CCCGU___U____UGU____________AA__A____AGUCC___AAA____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________78______________________________________________32\n	271 -- 277	59 -- 65	-22.2972 kcal/mol	5.63827 kcal/mol	4.81602 kcal/mol	257 300@LB@ \| \|@LB@5'-UGU...CUCAU U UUUU A CC A A ACG -3'@LB@ GAG UUAC CAGCAAUU CG GU UUAC GGA CCGU@LB@ :\|\| :\|\|\| \|\|\|\|\|\|\|\| \|\| \|\| \|:\|\| \|\|\| \|\|:\|@LB@ UUC GAUG GUCGUUAA GC CA AGUG CCU GGUA@LB@3'-UUU...CCCGU U UGU AA A AGUCC AAA CGAAU...GCA-5'@LB@ \| \|@LB@ 78 32@LB@@LB@@LB@Energy -11.84 kcal/mol@LB@Hybridization Energy -22.2972 kcal/mol@LB@Unfolding Energy - mRNA 5.63827 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 33 -- 77@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 59 -- 65@LB@
29	0.0004091	0.04965	b0958	sulA	-15.92	0.011809	212 -- 243	48 -- 76	SOS cell division inhibitor		_____________211______________________________244\n_____________\|________________________________\|\n5'-AUA...ACUUC____________UC__UC_____C___C____CCGCA...UCA-3'\n______________AGGCUAUGCACA__GU__UUCGU_GUU_UCAU\n______________\|\|:\|\|\|::\|\|\|\|__\|:__\|\|\|\|\|_\|\|\|_\|\|\|:\n______________UCUGAUGUGUGU__CG__AAGCA_CAA_AGUG\n3'-UUU...CCGUU________________UU_____A________AGUCC...GCA-5'\n_____________\|________________________________\|\n_____________77_______________________________47\n	217 -- 223	65 -- 71	-24.9625 kcal/mol	5.35271 kcal/mol	3.68714 kcal/mol	211 244@LB@ \| \|@LB@5'-AUA...ACUUC UC UC C C CCGCA...UCA-3'@LB@ AGGCUAUGCACA GU UUCGU GUU UCAU@LB@ \|\|:\|\|\|::\|\|\|\| \|: \|\|\|\|\| \|\|\| \|\|\|:@LB@ UCUGAUGUGUGU CG AAGCA CAA AGUG@LB@3'-UUU...CCGUU UU A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -24.9625 kcal/mol@LB@Unfolding Energy - mRNA 5.35271 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 212 -- 243@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 65 -- 71@LB@
130	0.005881	0.1577	b0965	yccU	-10.68	0.186123	93 -- 125	46 -- 74	putative CoA-binding protein		_____________92________________________________126\n_____________\|_________________________________\|\n5'-UCA...UACUU___A________A__UAU___CCGC________UCAUU...UGA-3'\n______________ACU_ACAUAUAG_CA___UUC____UUUUGCUC\n______________\|\|\|_\|\|\|:\|:\|\|_\|\|___\|\|\|____\|\|\|::\|\|\|\n______________UGA_UGUGUGUC_GU___AAG____AAAGUGAG\n3'-UUU...GUUUC_______________U_____CAAC________UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________45\n	119 -- 125	46 -- 52	-18.0647 kcal/mol	3.65669 kcal/mol	3.72594 kcal/mol	92 126@LB@ \| \|@LB@5'-UCA...UACUU A A UAU CCGC UCAUU...UGA-3'@LB@ ACU ACAUAUAG CA UUC UUUUGCUC@LB@ \|\|\| \|\|\|:\|:\|\| \|\| \|\|\| \|\|\|::\|\|\|@LB@ UGA UGUGUGUC GU AAG AAAGUGAG@LB@3'-UUU...GUUUC U CAAC UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.0647 kcal/mol@LB@Unfolding Energy - mRNA 3.65669 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 93 -- 125@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 46 -- 52@LB@
151	0.007209	0.1668	b0968	yccX	-9.35	0.311742	266 -- 274	62 -- 70	weak acylphosphatase		_____________265_______275\n_____________\|_________\|\n5'-GGC...UACAC_________CGAAG...CCG-3'\n______________CACACAGUA\n______________\|\|\|\|\|\|\|:\|\n______________GUGUGUCGU\n3'-UUU...CUGAU_________UAAGC...GCA-5'\n_____________\|_________\|\n_____________71________61\n	268 -- 274	62 -- 68	-13.335 kcal/mol	0.836274 kcal/mol	3.14945 kcal/mol	265 275@LB@ \| \|@LB@5'-GGC...UACAC CGAAG...CCG-3'@LB@ CACACAGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ GUGUGUCGU@LB@3'-UUU...CUGAU UAAGC...GCA-5'@LB@ \| \|@LB@ 71 61@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -13.335 kcal/mol@LB@Unfolding Energy - mRNA 0.836274 kcal/mol@LB@Unfolding Energy - sRNA 3.14945 kcal/mol@LB@@LB@Position - mRNA 266 -- 274@LB@Position - sRNA 62 -- 70@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 62 -- 68@LB@
106	0.004704	0.1538	b0995	torR	-15.76	0.013096	243 -- 292	33 -- 70	response regulator in two-component regulatory system with TorS		_____________242_________________________________________________293\n_____________\|___________________________________________________\|\n5'-CCA...UUACC__G_________ACAAUCCUAC__________A__GGUAUACC________UACGGCGA-3'\n______________CA_GC_GCGAUU__________UUCACUCAGG_GG________GUUUCCGU\n______________\|\|_:\|_\|\|:\|\|\|__________\|\|\|\|\|\|\|\|\|\|_\|\|________:\|\|\|\|\|:\|\n______________GU_UG_CGUUAA__________AAGUGAGUCC_CC________UAAAGGUA\n3'-UUU...CUGAU__G__U______GCAACA_________________________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________71__________________________________________________32\n	286 -- 292	33 -- 39	-31.2367 kcal/mol	10.6838 kcal/mol	4.7924 kcal/mol	242 293@LB@ \| \|@LB@5'-CCA...UUACC G ACAAUCCUAC A GGUAUACC UACGGCGA-3'@LB@ CA GC GCGAUU UUCACUCAGG GG GUUUCCGU@LB@ \|\| :\| \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\|\|:\|@LB@ GU UG CGUUAA AAGUGAGUCC CC UAAAGGUA@LB@3'-UUU...CUGAU G U GCAACA CGAAU...GCA-5'@LB@ \| \|@LB@ 71 32@LB@@LB@@LB@Energy -15.76 kcal/mol@LB@Hybridization Energy -31.2367 kcal/mol@LB@Unfolding Energy - mRNA 10.6838 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 243 -- 292@LB@Position - sRNA 33 -- 70@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 33 -- 39@LB@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
156	0.007591	0.1668	b1044	ymdA	-16.39	0.008687	226 -- 252	46 -- 73	uncharacterized protein		_____________225__________________________253\n_____________\|____________________________\|\n5'-UGA...CUCUC______U____________U________UUAUU...UUU-3'\n______________UUAUGC_CGGCAGUUUGUU_UUUC_CUU\n______________:\|\|::\|_\|:\|\|\|:\|\|:\|\|\|_\|\|\|\|_\|\|:\n______________GAUGUG_GUCGUUAAGCAA_AAAG_GAG\n3'-UUU...UUUCU______U____________C____U___UCCCC...GCA-5'\n_____________\|____________________________\|\n_____________74___________________________45\n	236 -- 242	57 -- 63	-24.6333 kcal/mol	4.51706 kcal/mol	3.72492 kcal/mol	225 253@LB@ \| \|@LB@5'-UGA...CUCUC U U UUAUU...UUU-3'@LB@ UUAUGC CGGCAGUUUGUU UUUC CUU@LB@ :\|\|::\| \|:\|\|\|:\|\|:\|\|\| \|\|\|\| \|\|:@LB@ GAUGUG GUCGUUAAGCAA AAAG GAG@LB@3'-UUU...UUUCU U C U UCCCC...GCA-5'@LB@ \| \|@LB@ 74 45@LB@@LB@@LB@Energy -16.39 kcal/mol@LB@Hybridization Energy -24.6333 kcal/mol@LB@Unfolding Energy - mRNA 4.51706 kcal/mol@LB@Unfolding Energy - sRNA 3.72492 kcal/mol@LB@@LB@Position - mRNA 226 -- 252@LB@Position - sRNA 46 -- 73@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 57 -- 63@LB@
95	0.004386	0.1538	b1083	flgL	-11.72	0.118200	146 -- 194	40 -- 76	flagellar hook-filament junction protein		_____________145_________________________________________________195\n_____________\|___________________________________________________\|\n5'-UUG...UCUGC____G___A______________AUGCGCUGAUUAACA______A______GAUAA...GUA-3'\n______________AGAC_GCA_AC_GCGAUUU_UUG_______________UUCGCU_AGGGGA\n______________\|\|\|\|_:\|\|_\|\|_\|\|:\|\|\|:_\|\|\|_______________\|\|\|:\|\|_\|\|\|\|\|\|\n______________UCUG_UGU_UG_CGUUAAG_AAC_______________AAGUGA_UCCCCU\n3'-UUU...CCGUU____A___G__U_______C___A____________________G______AAAGG...GCA-5'\n_____________\|___________________________________________________\|\n_____________77__________________________________________________39\n	157 -- 163	58 -- 64	-28.9648 kcal/mol	12.4692 kcal/mol	4.77843 kcal/mol	145 195@LB@ \| \|@LB@5'-UUG...UCUGC G A AUGCGCUGAUUAACA A GAUAA...GUA-3'@LB@ AGAC GCA AC GCGAUUU UUG UUCGCU AGGGGA@LB@ \|\|\|\| :\|\| \|\| \|\|:\|\|\|: \|\|\| \|\|\|:\|\| \|\|\|\|\|\|@LB@ UCUG UGU UG CGUUAAG AAC AAGUGA UCCCCU@LB@3'-UUU...CCGUU A G U C A G AAAGG...GCA-5'@LB@ \| \|@LB@ 77 39@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -28.9648 kcal/mol@LB@Unfolding Energy - mRNA 12.4692 kcal/mol@LB@Unfolding Energy - sRNA 4.77843 kcal/mol@LB@@LB@Position - mRNA 146 -- 194@LB@Position - sRNA 40 -- 76@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 58 -- 64@LB@
195	0.009901	0.1776	b1098	tmk	-15.44	0.015998	201 -- 230	41 -- 71	thymidylate kinase		_____________200_____________________________231\n_____________\|_______________________________\|\n5'-UAA...AAAAA___________GUAUAUCG______G_____CUGGA...GCG-3'\n______________AUGCGCAGUAA_________UCAUU_AGGGG\n______________\|::\|:\|\|\|:\|\|_________\|\|\|:\|_\|\|\|\|\|\n______________UGUGUGUCGUU_________AGUGA_UCCCC\n3'-UUU...UCUGA___________AAGCAACAA_____G_____UAAAG...GCA-5'\n_____________\|_______________________________\|\n_____________72______________________________40\n	205 -- 211	61 -- 67	-28.5877 kcal/mol	8.40445 kcal/mol	4.74226 kcal/mol	200 231@LB@ \| \|@LB@5'-UAA...AAAAA GUAUAUCG G CUGGA...GCG-3'@LB@ AUGCGCAGUAA UCAUU AGGGG@LB@ \|::\|:\|\|\|:\|\| \|\|\|:\| \|\|\|\|\|@LB@ UGUGUGUCGUU AGUGA UCCCC@LB@3'-UUU...UCUGA AAGCAACAA G UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -28.5877 kcal/mol@LB@Unfolding Energy - mRNA 8.40445 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 201 -- 230@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 61 -- 67@LB@
127	0.005686	0.1575	b1176	minC	-17.54	0.003902	3 -- 40	35 -- 74	inhibitor of FtsZ ring polymerization		_____________2________________________________________41\n_____________\|________________________________________\|\n_________5'-AA_G_____________GG____A__G__A_____U______UAAGC...AAG-3'\n______________A_UACG_ACGGCAAU__GUUG_UU_AC__AGGG_AUUUUU\n______________\|_\|\|\|:_\|\|:\|\|\|\|\|__\|\|\|\|_\|\|_\|\|__\|\|\|\|_\|\|\|\|::\n______________U_AUGU_UGUCGUUA__CAAC_AA_UG__UCCC_UAAAGG\n3'-UUU...GUUUC_G____G________AG____A__G__AG____C______UACGA...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________34\n	10 -- 16	60 -- 66	-29.7113 kcal/mol	7.37167 kcal/mol	4.80541 kcal/mol	2 41@LB@ \| \|@LB@ 5'-AA G GG A G A U UAAGC...AAG-3'@LB@ A UACG ACGGCAAU GUUG UU AC AGGG AUUUUU@LB@ \| \|\|\|: \|\|:\|\|\|\|\| \|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|::@LB@ U AUGU UGUCGUUA CAAC AA UG UCCC UAAAGG@LB@3'-UUU...GUUUC G G AG A G AG C UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -29.7113 kcal/mol@LB@Unfolding Energy - mRNA 7.37167 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 3 -- 40@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 60 -- 66@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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