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
119	0.005328	0.1553	b3417	malP	-6.58	0.680720	220 -- 257	42 -- 71	maltodextrin phosphorylase	_____________219____________________________________258\n_____________\|______________________________________\|\n5'-ACA...UUUUA___AUA________CAG_AAGCGC______G____U__CAGCG...GCC-3'\n______________ACG___AGCAAUUU___G______UUUCAC_UCAG_GG\n______________\|\|:___\|\|\|\|\|\|\|:___\|______\|\|\|\|\|\|_\|\|\|\|_\|\|\n______________UGU___UCGUUAAG___C______AAAGUG_AGUC_CC\n3'-UUU...UCUGA___GUG________CAA_____________________CUAAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________41\n	227 -- 233	58 -- 64	-19.6486 kcal/mol	8.3321 kcal/mol	4.73391 kcal/mol	219 258@LB@ \| \|@LB@5'-ACA...UUUUA AUA CAG AAGCGC G U CAGCG...GCC-3'@LB@ ACG AGCAAUUU G UUUCAC UCAG GG@LB@ \|\|: \|\|\|\|\|\|\|: \| \|\|\|\|\|\| \|\|\|\| \|\|@LB@ UGU UCGUUAAG C AAAGUG AGUC CC@LB@3'-UUU...UCUGA GUG CAA CUAAA...GCA-5'@LB@ \| \|@LB@ 72 41@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.6486 kcal/mol@LB@Unfolding Energy - mRNA 8.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.73391 kcal/mol@LB@@LB@Position - mRNA 220 -- 257@LB@Position - sRNA 42 -- 71@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 58 -- 64@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@
199	0.01026	0.1776	b2324	mnmC	-11.15	0.152427	29 -- 45	45 -- 74	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme	_____________28_____________________________46\n_____________\|______________________________\|\n5'-GCU...UAAUC______________________________AUACC...ACG-3'\n______________ACUGCAC_____________GUUUCAUUCA\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|:\|\|\|\n______________UGAUGUG_____________CAAAGUGAGU\n3'-UUU...GUUUC_______UGUCGUUAAGCAA__________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	39 -- 45	45 -- 51	-17.885 kcal/mol	2.99426 kcal/mol	3.74056 kcal/mol	28 46@LB@ \| \|@LB@5'-GCU...UAAUC AUACC...ACG-3'@LB@ ACUGCAC GUUUCAUUCA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UGAUGUG CAAAGUGAGU@LB@3'-UUU...GUUUC UGUCGUUAAGCAA CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -17.885 kcal/mol@LB@Unfolding Energy - mRNA 2.99426 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 29 -- 45@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 45 -- 51@LB@
84	0.003656	0.1509	b0827	moeA	-7.84	0.503176	157 -- 203	32 -- 75	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________156_______________________________________________204\n_____________\|_________________________________________________\|\n5'-AUU...UUUCU_______AUA___A______AUU___CC____G____A_U_________GAAUU...UAC-3'\n______________GAC_AUA___GGC_AAUUCG___UUG__UC_C_CAGG_G_GUUUUCAUG\n______________\|\|\|_\|:\|___:\|\|_\|\|\|\|\|\|___\|\|\|__\|\|_\|_\|\|\|\|_\|_:\|\|\|:\|\|\|\|\n______________CUG_UGU___UCG_UUAAGC___AAC__AG_G_GUCC_C_UAAAGGUAC\n3'-UUU...CGUUU___A___GUG________________AA__U_A______C_________GAAUA...GCA-5'\n_____________\|_________________________________________________\|\n_____________76________________________________________________31\n	197 -- 203	32 -- 38	-28.9008 kcal/mol	13.8106 kcal/mol	7.24967 kcal/mol	156 204@LB@ \| \|@LB@5'-AUU...UUUCU AUA A AUU CC G A U GAAUU...UAC-3'@LB@ GAC AUA GGC AAUUCG UUG UC C CAGG G GUUUUCAUG@LB@ \|\|\| \|:\| :\|\| \|\|\|\|\|\| \|\|\| \|\| \| \|\|\|\| \| :\|\|\|:\|\|\|\|@LB@ CUG UGU UCG UUAAGC AAC AG G GUCC C UAAAGGUAC@LB@3'-UUU...CGUUU A GUG AA U A C GAAUA...GCA-5'@LB@ \| \|@LB@ 76 31@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -28.9008 kcal/mol@LB@Unfolding Energy - mRNA 13.8106 kcal/mol@LB@Unfolding Energy - sRNA 7.24967 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 32 -- 75@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 32 -- 38@LB@
97	0.004509	0.1538	b0465	mscK	-15.00	0.020897	217 -- 248	49 -- 74	mechanosensitive channel protein intermediate conductance K+ regulated	_____________216______________________________249\n_____________\|________________________________\|\n5'-CGA...CCAGU______AACGAU_______U______U_____GCAUU...CGC-3'\n______________AUUACA______CACGGCA_UUUGUU_UUUCA\n______________\|:\|\|\|\|______\|\|\|:\|\|\|_\|\|:\|\|\|_\|\|\|\|\|\n______________UGAUGU______GUGUCGU_AAGCAA_AAAGU\n3'-UUU...GUUUC___________________U______C_____GAGUC...GCA-5'\n_____________\|________________________________\|\n_____________75_______________________________48\n	229 -- 235	62 -- 68	-21.8954 kcal/mol	3.22234 kcal/mol	3.67122 kcal/mol	216 249@LB@ \| \|@LB@5'-CGA...CCAGU AACGAU U U GCAUU...CGC-3'@LB@ AUUACA CACGGCA UUUGUU UUUCA@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|:\|\|\| \|\|\|\|\|@LB@ UGAUGU GUGUCGU AAGCAA AAAGU@LB@3'-UUU...GUUUC U C GAGUC...GCA-5'@LB@ \| \|@LB@ 75 48@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.8954 kcal/mol@LB@Unfolding Energy - mRNA 3.22234 kcal/mol@LB@Unfolding Energy - sRNA 3.67122 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 49 -- 74@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 62 -- 68@LB@
139	0.006425	0.1605	b0924	mukB	-11.72	0.118276	203 -- 227	45 -- 75	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________202_____________________________228\n_____________\|_______________________________\|\n5'-UGG...AUAAU_____A_________A_______________CUGAC...CUG-3'\n______________GAUUG_ACGCGGUAA_______UUUCGCUCA\n______________\|\|:\|:_\|\|:\|:\|:\|\|_______\|\|\|\|:\|\|\|\|\n______________CUGAU_UGUGUCGUU_______AAAGUGAGU\n3'-UUU...CGUUU_____G_________AAGCAAC_________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	221 -- 227	45 -- 51	-22.3255 kcal/mol	6.8688 kcal/mol	3.74078 kcal/mol	202 228@LB@ \| \|@LB@5'-UGG...AUAAU A A CUGAC...CUG-3'@LB@ GAUUG ACGCGGUAA UUUCGCUCA@LB@ \|\|:\|: \|\|:\|:\|:\|\| \|\|\|\|:\|\|\|\|@LB@ CUGAU UGUGUCGUU AAAGUGAGU@LB@3'-UUU...CGUUU G AAGCAAC CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -22.3255 kcal/mol@LB@Unfolding Energy - mRNA 6.8688 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 45 -- 51@LB@
98	0.004518	0.1538	b2193	narP	-14.47	0.028569	155 -- 204	31 -- 74	response regulator in two-component regulatory system with NarQ	_____________154________________________________________________205\n_____________\|__________________________________________________\|\n5'-UUG...CCAAC_______UCAA___UAA______UAAUAAAAC______A__CUA______CUGAA...AAG-3'\n______________GCUACGC____ACA___UGAUUC_________CUCAGG_GA___CUAUGC\n______________:\|\|\|\|:\|____\|\|\|___::\|\|\|\|_________\|\|\|\|\|\|_\|\|___\|:\|\|\|\|\n______________UGAUGUG____UGU___GUUAAG_________GAGUCC_CU___GGUACG\n3'-UUU...GUUUC______________C________CAACAAAGU______C__AAA______AAUAU...GCA-5'\n_____________\|__________________________________________________\|\n_____________75_________________________________________________30\n	155 -- 161	68 -- 74	-27.903 kcal/mol	6.17297 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UUG...CCAAC UCAA UAA UAAUAAAAC A CUA CUGAA...AAG-3'@LB@ GCUACGC ACA UGAUUC CUCAGG GA CUAUGC@LB@ :\|\|\|\|:\| \|\|\| ::\|\|\|\| \|\|\|\|\|\| \|\| \|:\|\|\|\|@LB@ UGAUGUG UGU GUUAAG GAGUCC CU GGUACG@LB@3'-UUU...GUUUC C CAACAAAGU C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -27.903 kcal/mol@LB@Unfolding Energy - mRNA 6.17297 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 68 -- 74@LB@
169	0.008352	0.1723	b1222	narX	-15.18	0.018797	58 -- 74	61 -- 75	sensory histidine kinase in two-component regulatory system with NarL	_____________57________________75\n_____________\|_________________\|\n5'-AAA...AAAGC_____AC__________AUAAG...CUG-3'\n______________GACUA__CACACGGCAA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________CUGAU__GUGUGUCGUU\n3'-UUU...CGUUU_________________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________76________________60\n	68 -- 74	61 -- 67	-20.5903 kcal/mol	2.1582 kcal/mol	3.25399 kcal/mol	57 75@LB@ \| \|@LB@5'-AAA...AAAGC AC AUAAG...CUG-3'@LB@ GACUA CACACGGCAA@LB@ \|\|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGAU GUGUGUCGUU@LB@3'-UUU...CGUUU AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -20.5903 kcal/mol@LB@Unfolding Energy - mRNA 2.1582 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 58 -- 74@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 61 -- 67@LB@
182	0.009082	0.1747	b3998	nfi	-11.38	0.137700	53 -- 76	45 -- 75	endonuclease V; deoxyinosine 3' endonuclease	_____________52______________________________77\n_____________\|_______________________________\|\n5'-UGG...GUAGC________UU_________________G___CGGCG...GAG-3'\n______________GACUAUAC___GCAG______GUUUCG_UCA\n______________\|\|\|\|\|:\|\|___\|\|\|:______\|\|\|\|\|:_\|\|\|\n______________CUGAUGUG___CGUU______CAAAGU_AGU\n3'-UUU...CGUUU________UGU____AAGCAA______G___CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	54 -- 60	68 -- 74	-21.6188 kcal/mol	6.49773 kcal/mol	3.74078 kcal/mol	52 77@LB@ \| \|@LB@5'-UGG...GUAGC UU G CGGCG...GAG-3'@LB@ GACUAUAC GCAG GUUUCG UCA@LB@ \|\|\|\|\|:\|\| \|\|\|: \|\|\|\|\|: \|\|\|@LB@ CUGAUGUG CGUU CAAAGU AGU@LB@3'-UUU...CGUUU UGU AAGCAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.38 kcal/mol@LB@Hybridization Energy -21.6188 kcal/mol@LB@Unfolding Energy - mRNA 6.49773 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 53 -- 76@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 68 -- 74@LB@
117	0.005152	0.155	b2235	nrdB	-9.05	0.346139	190 -- 222	48 -- 77	ribonucleoside-diphosphate reductase 1 beta subunit ferritin-like protein	_____________189_______________________________223\n_____________\|_________________________________\|\n5'-UCC...CCAAC_____AC__U_______UAUACCACCU______AGACG...AAU-3'\n______________AGGAC__AC_CAUGGCA__________UUUCAC\n______________\|:\|\|\|__\|\|_\|\|::\|\|\|__________\|\|\|\|\|\|\n______________UUCUG__UG_GUGUCGU__________AAAGUG\n3'-UUU...CCCGU_____A___U_______UAAGCAAC________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________78________________________________47\n	200 -- 206	62 -- 68	-18.188 kcal/mol	5.45206 kcal/mol	3.68729 kcal/mol	189 223@LB@ \| \|@LB@5'-UCC...CCAAC AC U UAUACCACCU AGACG...AAU-3'@LB@ AGGAC AC CAUGGCA UUUCAC@LB@ \|:\|\|\| \|\| \|\|::\|\|\| \|\|\|\|\|\|@LB@ UUCUG UG GUGUCGU AAAGUG@LB@3'-UUU...CCCGU A U UAAGCAAC AGUCC...GCA-5'@LB@ \| \|@LB@ 78 47@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -18.188 kcal/mol@LB@Unfolding Energy - mRNA 5.45206 kcal/mol@LB@Unfolding Energy - sRNA 3.68729 kcal/mol@LB@@LB@Position - mRNA 190 -- 222@LB@Position - sRNA 48 -- 77@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@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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