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
41	0.0008963	0.07693	b1378	pfo	-13.27	0.055135	136 -- 164	58 -- 78	pyruvate-flavodoxin oxidoreductase		_____________135___________________________165\n_____________\|_____________________________\|\n5'-GCU...AAUUG_________UACUGGGC____________CGUGC...CAG-3'\n______________AAAGAUUAC________GCGCAGCAAUUU\n______________\|\|\|\|\|:\|\|\|________:\|:\|\|\|\|\|\|\|\|:\n______________UUUCUGAUG________UGUGUCGUUAAG\n3'-UUU...ACCCG_____________________________CAACA...GCA-5'\n_____________\|_____________________________\|\n_____________79____________________________57\n	158 -- 164	58 -- 64	-22.0871 kcal/mol	5.50788 kcal/mol	3.31018 kcal/mol	135 165@LB@ \| \|@LB@5'-GCU...AAUUG UACUGGGC CGUGC...CAG-3'@LB@ AAAGAUUAC GCGCAGCAAUUU@LB@ \|\|\|\|\|:\|\|\| :\|:\|\|\|\|\|\|\|\|:@LB@ UUUCUGAUG UGUGUCGUUAAG@LB@3'-UUU...ACCCG CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -22.0871 kcal/mol@LB@Unfolding Energy - mRNA 5.50788 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 136 -- 164@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 58 -- 64@LB@
110	0.004806	0.1538	b1429	tehA	-12.16	0.096068	32 -- 62	44 -- 75	potassium-tellurite ethidium and proflavin transporter		_____________31_________________________________63\n_____________\|__________________________________\|\n5'-AAU...UUCCU___A__UAAA_________C___UC_________ACGAU...UUU-3'\n______________GAU_AC____GGC___UCG_UGU__UUCACUUAG\n______________\|\|:_\|\|____:\|\|___\|\|\|_\|\|\|__\|\|\|\|\|\|:\|\|\n______________CUG_UG____UCG___AGC_ACA__AAGUGAGUC\n3'-UUU...CGUUU___A__UGUG___UUA___A______________CCCUA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________43\n	56 -- 62	44 -- 50	-20.5577 kcal/mol	4.26011 kcal/mol	4.13839 kcal/mol	31 63@LB@ \| \|@LB@5'-AAU...UUCCU A UAAA C UC ACGAU...UUU-3'@LB@ GAU AC GGC UCG UGU UUCACUUAG@LB@ \|\|: \|\| :\|\| \|\|\| \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UG UCG AGC ACA AAGUGAGUC@LB@3'-UUU...CGUUU A UGUG UUA A CCCUA...GCA-5'@LB@ \| \|@LB@ 76 43@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -20.5577 kcal/mol@LB@Unfolding Energy - mRNA 4.26011 kcal/mol@LB@Unfolding Energy - sRNA 4.13839 kcal/mol@LB@@LB@Position - mRNA 32 -- 62@LB@Position - sRNA 44 -- 75@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 44 -- 50@LB@
35	0.0005607	0.05638	b1434	ydcN	-11.45	0.133710	242 -- 253	62 -- 74	putative DNA-binding transcriptional regulator	b1508 b1299	_____________241___________254\n_____________\|_____________\|\n5'-CGG...AAACA_____________GCGCG...CUA-3'\n______________ACUACGC_CAGCA\n______________\|\|\|\|\|:\|_\|\|\|\|\|\n______________UGAUGUG_GUCGU\n3'-UUU...GUUUC_______U_____UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	242 -- 248	68 -- 74	-17.054 kcal/mol	2.36402 kcal/mol	3.24359 kcal/mol	241 254@LB@ \| \|@LB@5'-CGG...AAACA GCGCG...CUA-3'@LB@ ACUACGC CAGCA@LB@ \|\|\|\|\|:\| \|\|\|\|\|@LB@ UGAUGUG GUCGU@LB@3'-UUU...GUUUC U UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -17.054 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 68 -- 74@LB@
61	0.002486	0.1417	b1487	ddpA	-13.46	0.049908	168 -- 192	43 -- 71	D D-dipeptide ABC transporter periplasmic binding protein		_____________167___________________________193\n_____________\|_____________________________\|\n5'-UCA...CCCUG________________CAG____A_____AAACU...UGA-3'\n______________GCACACAGCA___CGU____UUA_UCAGG\n______________:\|\|\|\|\|\|\|\|\|___\|\|\|____\|:\|_\|\|\|\|\|\n______________UGUGUGUCGU___GCA____AGU_AGUCC\n3'-UUU...UCUGA__________UAA___ACAA___G_____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	171 -- 177	62 -- 68	-25.043 kcal/mol	7.26137 kcal/mol	4.32409 kcal/mol	167 193@LB@ \| \|@LB@5'-UCA...CCCUG CAG A AAACU...UGA-3'@LB@ GCACACAGCA CGU UUA UCAGG@LB@ :\|\|\|\|\|\|\|\|\| \|\|\| \|:\| \|\|\|\|\|@LB@ UGUGUGUCGU GCA AGU AGUCC@LB@3'-UUU...UCUGA UAA ACAA G CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -25.043 kcal/mol@LB@Unfolding Energy - mRNA 7.26137 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 168 -- 192@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 62 -- 68@LB@
99	0.004523	0.1538	b1516	lsrB	-10.33	0.215118	8 -- 28	39 -- 59	autoinducer 2-binding protein		_____________7______________________29\n_____________\|______________________\|\n____5'-ACCGCCA___CG___________U_____AUUUG...UUC-3'\n______________UUG__GUUUUAUU_AG_GGGAU\n______________\|:\|__\|\|\|\|:\|:\|_\|\|_\|\|\|\|\|\n______________AGC__CAAAGUGA_UC_CCCUA\n3'-UUU...CGUUA___AA________G________AAGGU...GCA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	14 -- 20	47 -- 53	-16.4048 kcal/mol	3.58309 kcal/mol	2.49358 kcal/mol	7 29@LB@ \| \|@LB@ 5'-ACCGCCA CG U AUUUG...UUC-3'@LB@ UUG GUUUUAUU AG GGGAU@LB@ \|:\| \|\|\|\|:\|:\| \|\| \|\|\|\|\|@LB@ AGC CAAAGUGA UC CCCUA@LB@3'-UUU...CGUUA AA G AAGGU...GCA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -16.4048 kcal/mol@LB@Unfolding Energy - mRNA 3.58309 kcal/mol@LB@Unfolding Energy - sRNA 2.49358 kcal/mol@LB@@LB@Position - mRNA 8 -- 28@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 47 -- 53@LB@
186	0.009502	0.1776	b1631	rsxG	-12.74	0.072174	210 -- 253	41 -- 74	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex		_____________209____________________________________________254\n_____________\|______________________________________________\|\n5'-CUG...UGAAA_____CCGAAA________UUA_____G______AUUUG___C___UUCAA...CGA-3'\n______________ACUAU______ACACGGCA___CGUUG___CGCU_____CAG_GGG\n______________\|\|\|\|:______\|\|\|\|:\|\|\|___\|\|\|\|\|___\|:\|\|_____\|\|\|_\|\|\|\n______________UGAUG______UGUGUCGU___GCAAC___GUGA_____GUC_CCC\n3'-UUU...GUUUC___________________UAA_____AAA________________UAAAG...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________40\n	222 -- 228	62 -- 68	-28.539 kcal/mol	11.0247 kcal/mol	4.77133 kcal/mol	209 254@LB@ \| \|@LB@5'-CUG...UGAAA CCGAAA UUA G AUUUG C UUCAA...CGA-3'@LB@ ACUAU ACACGGCA CGUUG CGCU CAG GGG@LB@ \|\|\|\|: \|\|\|\|:\|\|\| \|\|\|\|\| \|:\|\| \|\|\| \|\|\|@LB@ UGAUG UGUGUCGU GCAAC GUGA GUC CCC@LB@3'-UUU...GUUUC UAA AAA UAAAG...GCA-5'@LB@ \| \|@LB@ 75 40@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.539 kcal/mol@LB@Unfolding Energy - mRNA 11.0247 kcal/mol@LB@Unfolding Energy - sRNA 4.77133 kcal/mol@LB@@LB@Position - mRNA 210 -- 253@LB@Position - sRNA 41 -- 74@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 62 -- 68@LB@
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase		_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@LB@
78	0.003218	0.1452	b1641	slyB	-13.21	0.056987	203 -- 235	43 -- 75	outer membrane lipoprotein		_____________202_________________________________236\n_____________\|___________________________________\|\n5'-CCG...UCAAU_____A___________G_________AUGG____UCUGU...AAG-3'\n______________GAUUA_ACGC_GU_AUU_GUUGUUUCA____UAGG\n______________\|\|:\|\|_\|\|:\|_\|:_\|\|\|_\|\|\|\|\|\|\|\|\|____:\|\|\|\n______________CUGAU_UGUG_CG_UAA_CAACAAAGU____GUCC\n3'-UUU...CGUUU_____G____U__U___G_________GA______CCUAA...GCA-5'\n_____________\|___________________________________\|\n_____________76__________________________________42\n	221 -- 227	49 -- 55	-26.1882 kcal/mol	8.63028 kcal/mol	4.35266 kcal/mol	202 236@LB@ \| \|@LB@5'-CCG...UCAAU A G AUGG UCUGU...AAG-3'@LB@ GAUUA ACGC GU AUU GUUGUUUCA UAGG@LB@ \|\|:\|\| \|\|:\| \|: \|\|\| \|\|\|\|\|\|\|\|\| :\|\|\|@LB@ CUGAU UGUG CG UAA CAACAAAGU GUCC@LB@3'-UUU...CGUUU G U U G GA CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.1882 kcal/mol@LB@Unfolding Energy - mRNA 8.63028 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 203 -- 235@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 49 -- 55@LB@
160	0.007693	0.1668	b1671	ydhX	-11.21	0.148807	210 -- 235	39 -- 74	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________209__________________________________236\n_____________\|____________________________________\|\n5'-CAC...CCUUC___CG________________________U______GGGAA...AGG-3'\n______________ACU__ACGCA__AAUUUGU________UC_GGGGAU\n______________\|\|\|__\|\|:\|\|__\|\|\|\|:\|\|________\|\|_\|\|\|\|\|\|\n______________UGA__UGUGU__UUAAGCA________AG_CCCCUA\n3'-UUU...GUUUC___UG_____CG_______ACAAAGUG__U______AAGGU...GCA-5'\n_____________\|____________________________________\|\n_____________75___________________________________38\n	220 -- 226	56 -- 62	-21.5478 kcal/mol	5.56457 kcal/mol	4.77831 kcal/mol	209 236@LB@ \| \|@LB@5'-CAC...CCUUC CG U GGGAA...AGG-3'@LB@ ACU ACGCA AAUUUGU UC GGGGAU@LB@ \|\|\| \|\|:\|\| \|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ UGA UGUGU UUAAGCA AG CCCCUA@LB@3'-UUU...GUUUC UG CG ACAAAGUG U AAGGU...GCA-5'@LB@ \| \|@LB@ 75 38@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -21.5478 kcal/mol@LB@Unfolding Energy - mRNA 5.56457 kcal/mol@LB@Unfolding Energy - sRNA 4.77831 kcal/mol@LB@@LB@Position - mRNA 210 -- 235@LB@Position - sRNA 39 -- 74@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 56 -- 62@LB@
153	0.007486	0.1668	b1732	katE	-14.34	0.030774	245 -- 275	42 -- 74	catalase HPII heme d-containing		_____________244___________________________________276\n_____________\|_____________________________________\|\n5'-UGG...UCACC________AUUC______AG__AA_____________AUGGA...ACG-3'\n______________ACUACACG____CAGCGA__CG_______AC_CGGGG\n______________\|\|\|\|\|\|\|:____\|\|\|\|:\|__\|\|_______\|\|_\|:\|\|\|\n______________UGAUGUGU____GUCGUU__GC_______UG_GUCCC\n3'-UUU...GUUUC__________________AA__AACAAAG__A_____CUAAA...GCA-5'\n_____________\|_____________________________________\|\n_____________75____________________________________41\n	246 -- 252	67 -- 73	-24.7059 kcal/mol	5.60497 kcal/mol	4.7632 kcal/mol	244 276@LB@ \| \|@LB@5'-UGG...UCACC AUUC AG AA AUGGA...ACG-3'@LB@ ACUACACG CAGCGA CG AC CGGGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| \|\| \|\| \|:\|\|\|@LB@ UGAUGUGU GUCGUU GC UG GUCCC@LB@3'-UUU...GUUUC AA AACAAAG A CUAAA...GCA-5'@LB@ \| \|@LB@ 75 41@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.7059 kcal/mol@LB@Unfolding Energy - mRNA 5.60497 kcal/mol@LB@Unfolding Energy - sRNA 4.7632 kcal/mol@LB@@LB@Position - mRNA 245 -- 275@LB@Position - sRNA 42 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 67 -- 73@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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