Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
11	0.0003561	0.1063	b3857	mobA	-16.95	0.002119	239 -- 276	15 -- 59	molybdopterin-guanine dinucleotide synthase	_____________238_______________________________________________277\n_____________\|_________________________________________________\|\n5'-UCC...CUGGC___C______GC___________________G_____C___________GAUUG...AAC-3'\n______________AGG_GGUAAA__CAGAC__________GAAU_GGCGG__GUAGAUAAAG\n______________\|\|\|_\|\|\|\|\|\|__\|\|\|\|\|__________\|\|\|\|_\|:\|\|\|__:\|\|:\|\|\|\|\|\|\n______________UCC_CCAUUU__GUCUG__________CUUA_CUGCC__UAUUUAUUUC\n3'-UUU...CUUUA_________________UAAGUCUUUA__________AU__________AAUUA...UCG-5'\n_____________\|_________________________________________________\|\n_____________60________________________________________________14\n	270 -- 276	15 -- 21	-31.2728 kcal/mol	7.99479 kcal/mol	6.32587 kcal/mol	238 277@LB@ \| \|@LB@5'-UCC...CUGGC C GC G C GAUUG...AAC-3'@LB@ AGG GGUAAA CAGAC GAAU GGCGG GUAGAUAAAG@LB@ \|\|\| \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|:\|\|\| :\|\|:\|\|\|\|\|\|@LB@ UCC CCAUUU GUCUG CUUA CUGCC UAUUUAUUUC@LB@3'-UUU...CUUUA UAAGUCUUUA AU AAUUA...UCG-5'@LB@ \| \|@LB@ 60 14@LB@@LB@@LB@Energy -16.95 kcal/mol@LB@Hybridization Energy -31.2728 kcal/mol@LB@Unfolding Energy - mRNA 7.99479 kcal/mol@LB@Unfolding Energy - sRNA 6.32587 kcal/mol@LB@@LB@Position - mRNA 239 -- 276@LB@Position - sRNA 15 -- 59@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 15 -- 21@LB@
12	0.000426	0.1165	b2331	smrB	-16.71	0.002472	163 -- 205	16 -- 57	putative DNA endonuclease	_____________162____________________________________________206\n_____________\|______________________________________________\|\n5'-UCA...GAGUC________UGUA___AAA________A______A____________AAAGA...GAC-3'\n______________GGGUAAAC____GGA___UUAGAAAU_GA_GAC___GAUAAAUGAA\n______________\|\|\|\|\|\|\|\|____:\|\|___\|:\|\|\|\|\|\|_:\|_\|\|\|___:\|\|\|\|\|\|:\|\|\n______________CCCAUUUG____UCU___AGUCUUUA_UU_CUG___UUAUUUAUUU\n3'-UUU...UUAUC_______________GUA________C__A___CCA__________CAAUU...UCG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________15\n	199 -- 205	16 -- 22	-27.8577 kcal/mol	4.82255 kcal/mol	6.32306 kcal/mol	162 206@LB@ \| \|@LB@5'-UCA...GAGUC UGUA AAA A A AAAGA...GAC-3'@LB@ GGGUAAAC GGA UUAGAAAU GA GAC GAUAAAUGAA@LB@ \|\|\|\|\|\|\|\| :\|\| \|:\|\|\|\|\|\| :\| \|\|\| :\|\|\|\|\|\|:\|\|@LB@ CCCAUUUG UCU AGUCUUUA UU CUG UUAUUUAUUU@LB@3'-UUU...UUAUC GUA C A CCA CAAUU...UCG-5'@LB@ \| \|@LB@ 58 15@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -27.8577 kcal/mol@LB@Unfolding Energy - mRNA 4.82255 kcal/mol@LB@Unfolding Energy - sRNA 6.32306 kcal/mol@LB@@LB@Position - mRNA 163 -- 205@LB@Position - sRNA 16 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
13	0.0005091	0.1286	b2062	wza	-15.65	0.004784	187 -- 207	5 -- 27	colanic acid export protein; outer membrane auxillary lipoprotein	_____________186_____________________208\n_____________\|_______________________\|\n5'-AAA...CCAAA____________C__________AAUCC...GCA-3'\n______________GUGAUAAAUAAA___AAUGAUGA\n______________\|\|:\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAUUAUUUAUUU___UUACUACU\n3'-UUU...ACUGC____________CAA________AUCG-5'\n_____________\|_______________________\|\n_____________28______________________4\n	201 -- 207	5 -- 11	-18.4073 kcal/mol	2.04721 kcal/mol	0.709121 kcal/mol	186 208@LB@ \| \|@LB@5'-AAA...CCAAA C AAUCC...GCA-3'@LB@ GUGAUAAAUAAA AAUGAUGA@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAUUAUUUAUUU UUACUACU@LB@3'-UUU...ACUGC CAA AUCG-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -18.4073 kcal/mol@LB@Unfolding Energy - mRNA 2.04721 kcal/mol@LB@Unfolding Energy - sRNA 0.709121 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
14	0.0005823	0.1358	b4348	hsdS	-17.02	0.002033	190 -- 210	27 -- 58	specificity determinant for hsdM and hsdR	_____________189______________________________211\n_____________\|________________________________\|\n5'-CUG...UUGGU________________________________GGAAA...UAA-3'\n______________GGGGUGA__________AGGAAUGAGUG_CGG\n______________\|\|\|\|\|:\|__________\|\|:\|\|\|\|\|:\|\|_\|\|\|\n______________CCCCAUU__________UCUUUACUUAC_GCC\n3'-UUU...UUUAU_______UGUCUGUAAG___________U___AUUAU...UCG-5'\n_____________\|________________________________\|\n_____________59_______________________________26\n	190 -- 196	52 -- 58	-27.0928 kcal/mol	3.78881 kcal/mol	6.28755 kcal/mol	189 211@LB@ \| \|@LB@5'-CUG...UUGGU GGAAA...UAA-3'@LB@ GGGGUGA AGGAAUGAGUG CGG@LB@ \|\|\|\|\|:\| \|\|:\|\|\|\|\|:\|\| \|\|\|@LB@ CCCCAUU UCUUUACUUAC GCC@LB@3'-UUU...UUUAU UGUCUGUAAG U AUUAU...UCG-5'@LB@ \| \|@LB@ 59 26@LB@@LB@@LB@Energy -17.02 kcal/mol@LB@Hybridization Energy -27.0928 kcal/mol@LB@Unfolding Energy - mRNA 3.78881 kcal/mol@LB@Unfolding Energy - sRNA 6.28755 kcal/mol@LB@@LB@Position - mRNA 190 -- 210@LB@Position - sRNA 27 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 52 -- 58@LB@
15	0.0006204	0.1358	b0652	gltL	-11.66	0.043639	269 -- 295	1 -- 25	glutamate/aspartate ABC transporter ATPase	_____________268_________________________296\n_____________\|___________________________\|\n5'-CUC...ACCGA______A____GCGA____________UUGCG-3'\n______________AGUGAA_AAAG____AGUGGUGGUGGU\n______________\|:\|:\|\|_\|\|\|\|____\|:\|\|:\|\|:\|:\|:\n______________UUAUUU_UUUC____UUACUACUAUCG\n3'-UUU...UGCCA______A____AA______________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	289 -- 295	1 -- 7	-17.2962 kcal/mol	5.52495 kcal/mol	0.112205 kcal/mol	268 296@LB@ \| \|@LB@5'-CUC...ACCGA A GCGA UUGCG-3'@LB@ AGUGAA AAAG AGUGGUGGUGGU@LB@ \|:\|:\|\| \|\|\|\| \|:\|\|:\|\|:\|:\|:@LB@ UUAUUU UUUC UUACUACUAUCG@LB@3'-UUU...UGCCA A AA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -17.2962 kcal/mol@LB@Unfolding Energy - mRNA 5.52495 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 269 -- 295@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
16	0.0008012	0.1482	b2011	sbcB	-16.25	0.003318	186 -- 217	24 -- 52	exodeoxyribonuclease I; exonuclease I	_____________185______________________________218\n_____________\|________________________________\|\n5'-CCU...GAAAU_______UUAACCUAAU_______________GCAAC...CCA-3'\n______________AACGGAU__________GAUGAAUGACGGUAA\n______________\|\|\|:\|\|:__________:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUGUCUG__________UUACUUACUGCCAUU\n3'-UUU...CCCAU_______UAAGUCU__________________AUUUA...UCG-5'\n_____________\|________________________________\|\n_____________53_______________________________23\n	211 -- 217	24 -- 30	-27.0341 kcal/mol	4.49086 kcal/mol	6.2974 kcal/mol	185 218@LB@ \| \|@LB@5'-CCU...GAAAU UUAACCUAAU GCAAC...CCA-3'@LB@ AACGGAU GAUGAAUGACGGUAA@LB@ \|\|\|:\|\|: :\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUGUCUG UUACUUACUGCCAUU@LB@3'-UUU...CCCAU UAAGUCU AUUUA...UCG-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -27.0341 kcal/mol@LB@Unfolding Energy - mRNA 4.49086 kcal/mol@LB@Unfolding Energy - sRNA 6.2974 kcal/mol@LB@@LB@Position - mRNA 186 -- 217@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 24 -- 30@LB@
17	0.000872	0.1482	b3940	metL	-12.03	0.036099	191 -- 199	51 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________190_______200\n_____________\|_________\|\n5'-ACG...AAACA_________AAUGA...GCA-3'\n______________AGGGGUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	193 -- 199	51 -- 57	-13.5839 kcal/mol	1.01846 kcal/mol	0.532875 kcal/mol	190 200@LB@ \| \|@LB@5'-ACG...AAACA AAUGA...GCA-3'@LB@ AGGGGUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.5839 kcal/mol@LB@Unfolding Energy - mRNA 1.01846 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
18	0.0008759	0.1482	b3626	waaR	-11.62	0.044565	224 -- 238	11 -- 25	lipopolysaccharide 1 2-glucosyltransferase; UDP-glucose:(glucosyl)LPS alpha-1 2-glucosyltransferase	_____________223_____________239\n_____________\|_______________\|\n5'-UGG...AUAGA_______________AGCCU...GUG-3'\n______________GAUAGAUAAAGUUAA\n______________:\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________UUAUUUAUUUCAAUU\n3'-UUU...UGCCA_______________ACUAC...UCG-5'\n_____________\|_______________\|\n_____________26______________10\n	232 -- 238	11 -- 17	-12.9968 kcal/mol	1.27318 kcal/mol	0.10636 kcal/mol	223 239@LB@ \| \|@LB@5'-UGG...AUAGA AGCCU...GUG-3'@LB@ GAUAGAUAAAGUUAA@LB@ :\|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ UUAUUUAUUUCAAUU@LB@3'-UUU...UGCCA ACUAC...UCG-5'@LB@ \| \|@LB@ 26 10@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -12.9968 kcal/mol@LB@Unfolding Energy - mRNA 1.27318 kcal/mol@LB@Unfolding Energy - sRNA 0.10636 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 11 -- 25@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
19	0.0008973	0.1482	b3964	yijD	-17.08	0.001951	152 -- 223	2 -- 55	DUF1422 family inner membrane protein	_____________151______________________________________________________________________224\n_____________\|________________________________________________________________________\|\n5'-ACU...UCGCC______A___GAAAACCGCAAU_____CG_______UGAAG____A________AC___CA___CAA_____AGGUA...UGC-3'\n______________GUGAAC_AGA____________UAUUC__GGAAAUG_____GACG_GUAAUGAA__AAG__AAU___GAUAG\n______________\|\|:\|\|\|_\|\|\|____________:\|\|\|\|__:\|\|\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|__\|\|\|__\|\|\|___\|\|\|\|\|\n______________CAUUUG_UCU____________GUAAG__UCUUUAC_____CUGC_CAUUAUUU__UUC__UUA___CUAUC\n3'-UUU...AUCCC____________________________________UUA_______________AU___AA___CUA_____G-5'\n_____________\|________________________________________________________________________\|\n_____________56_______________________________________________________________________1\n	199 -- 205	20 -- 26	-31.4266 kcal/mol	8.00944 kcal/mol	6.33752 kcal/mol	151 224@LB@ \| \|@LB@5'-ACU...UCGCC A GAAAACCGCAAU CG UGAAG A AC CA CAA AGGUA...UGC-3'@LB@ GUGAAC AGA UAUUC GGAAAUG GACG GUAAUGAA AAG AAU GAUAG@LB@ \|\|:\|\|\| \|\|\| :\|\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\| \|\|\| \|\|\| \|\|\|\|\|@LB@ CAUUUG UCU GUAAG UCUUUAC CUGC CAUUAUUU UUC UUA CUAUC@LB@3'-UUU...AUCCC UUA AU AA CUA G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -17.08 kcal/mol@LB@Hybridization Energy -31.4266 kcal/mol@LB@Unfolding Energy - mRNA 8.00944 kcal/mol@LB@Unfolding Energy - sRNA 6.33752 kcal/mol@LB@@LB@Position - mRNA 152 -- 223@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 20 -- 26@LB@
20	0.0009027	0.1482	b2696	csrA	-13.42	0.017327	268 -- 280	48 -- 60	pleiotropic regulatory protein for carbon source metabolism	_____________267___________281\n_____________\|_____________\|\n5'-CGG...AGUUU__________G__CAACC...GCG-3'\n______________UAGGGGUAAA_GG\n______________\|\|\|\|\|\|\|\|\|\|_:\|\n______________AUCCCCAUUU_UC\n3'-UUU...ACUUU__________G__UGUAA...UCG-5'\n_____________\|_____________\|\n_____________61____________47\n	271 -- 277	51 -- 57	-17.9026 kcal/mol	2.43021 kcal/mol	2.05446 kcal/mol	267 281@LB@ \| \|@LB@5'-CGG...AGUUU G CAACC...GCG-3'@LB@ UAGGGGUAAA GG@LB@ \|\|\|\|\|\|\|\|\|\| :\|@LB@ AUCCCCAUUU UC@LB@3'-UUU...ACUUU G UGUAA...UCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -17.9026 kcal/mol@LB@Unfolding Energy - mRNA 2.43021 kcal/mol@LB@Unfolding Energy - sRNA 2.05446 kcal/mol@LB@@LB@Position - mRNA 268 -- 280@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 51 -- 57@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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