Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
81	0.02893	0.29	ct_185	zwf	-6.95	0.147965	38 -- 47	51 -- 60	glucose-6-phosphate 1-dehydrogenase	_____________37_________48\n_____________\|__________\|\n5'-AAG...GCCUG__________AUCGU...UUU-3'\n______________UCCUCCCUGU\n______________\|\|\|:\|\|\|\|\|\|\n______________AGGGGGGACA\n3'-UUU...ACUGA__________CAUGU...GAA-5'\n_____________\|__________\|\n_____________61_________50\n	41 -- 47	51 -- 57	-17.9011 kcal/mol	1.87917 kcal/mol	9.07545 kcal/mol	37 48@LB@ \| \|@LB@5'-AAG...GCCUG AUCGU...UUU-3'@LB@ UCCUCCCUGU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGGGGGGACA@LB@3'-UUU...ACUGA CAUGU...GAA-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -17.9011 kcal/mol@LB@Unfolding Energy - mRNA 1.87917 kcal/mol@LB@Unfolding Energy - sRNA 9.07545 kcal/mol@LB@@LB@Position - mRNA 38 -- 47@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 51 -- 57@LB@
126	0.05087	0.3262	ct_474	N/A	-6.92	0.149609	150 -- 156	15 -- 21		_____________149_____157\n_____________\|_______\|\n5'-AAA...ACGAA_______GUAUA...UAU-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	150 -- 156	15 -- 21	-10.3963 kcal/mol	2.28336 kcal/mol	1.18845 kcal/mol	149 157@LB@ \| \|@LB@5'-AAA...ACGAA GUAUA...UAU-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -6.92 kcal/mol@LB@Hybridization Energy -10.3963 kcal/mol@LB@Unfolding Energy - mRNA 2.28336 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 150 -- 156@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 15 -- 21@LB@
135	0.05472	0.3262	ct_283	N/A	-6.89	0.152000	262 -- 284	14 -- 35		_____________261______________________285\n_____________\|________________________\|\n5'-UAC...GUUUA_____CU________GC_______UGUUU...UUG-3'\n______________UCGGA__AGUUA_UC__UGGCGUU\n______________\|\|:\|\|__\|\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________AGUCU__UCGAU_AG__ACCGCAA\n3'-UUU...AUCUC____________A__GU_______UCUUA...GAA-5'\n_____________\|________________________\|\n_____________36_______________________13\n	278 -- 284	14 -- 20	-19.9844 kcal/mol	4.64246 kcal/mol	8.44936 kcal/mol	261 285@LB@ \| \|@LB@5'-UAC...GUUUA CU GC UGUUU...UUG-3'@LB@ UCGGA AGUUA UC UGGCGUU@LB@ \|\|:\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ AGUCU UCGAU AG ACCGCAA@LB@3'-UUU...AUCUC A GU UCUUA...GAA-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -19.9844 kcal/mol@LB@Unfolding Energy - mRNA 4.64246 kcal/mol@LB@Unfolding Energy - sRNA 8.44936 kcal/mol@LB@@LB@Position - mRNA 262 -- 284@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 14 -- 20@LB@
141	0.05655	0.3262	ct_645	N/A	-6.85	0.155161	266 -- 276	17 -- 28		_____________265__________277\n_____________\|____________\|\n5'-GAG...GUUCU____________UGCCA...AGU-3'\n______________UUGUUCC_UGGC\n______________:\|:\|\|\|\|_\|\|\|\|\n______________GAUAAGG_ACCG\n3'-UUU...UCUUC_______U____CAAUC...GAA-5'\n_____________\|____________\|\n_____________29___________16\n	266 -- 272	22 -- 28	-12.7306 kcal/mol	1.25811 kcal/mol	4.62088 kcal/mol	265 277@LB@ \| \|@LB@5'-GAG...GUUCU UGCCA...AGU-3'@LB@ UUGUUCC UGGC@LB@ :\|:\|\|\|\| \|\|\|\|@LB@ GAUAAGG ACCG@LB@3'-UUU...UCUUC U CAAUC...GAA-5'@LB@ \| \|@LB@ 29 16@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -12.7306 kcal/mol@LB@Unfolding Energy - mRNA 1.25811 kcal/mol@LB@Unfolding Energy - sRNA 4.62088 kcal/mol@LB@@LB@Position - mRNA 266 -- 276@LB@Position - sRNA 17 -- 28@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 22 -- 28@LB@
172	0.07285	0.3448	ct_090	lcrD	-6.84	0.155915	81 -- 102	18 -- 39	low calcium response protein D	_____________80______________________103\n_____________\|_______________________\|\n5'-AUU...GGAAA___________U________GA_ACCAC...UGU-3'\n______________AGAGUU_GAAG_UUAUUCCA__G\n______________\|\|\|\|\|:_\|\|\|\|_:\|\|\|\|\|\|\|__\|\n______________UCUCAG_CUUC_GAUAAGGU__C\n3'-UUU...UGUGA______U_____________AC_GCAAU...GAA-5'\n_____________\|_______________________\|\n_____________40______________________17\n	93 -- 99	21 -- 27	-20.344 kcal/mol	3.91171 kcal/mol	9.59078 kcal/mol	80 103@LB@ \| \|@LB@5'-AUU...GGAAA U GA ACCAC...UGU-3'@LB@ AGAGUU GAAG UUAUUCCA G@LB@ \|\|\|\|\|: \|\|\|\| :\|\|\|\|\|\|\| \|@LB@ UCUCAG CUUC GAUAAGGU C@LB@3'-UUU...UGUGA U AC GCAAU...GAA-5'@LB@ \| \|@LB@ 40 17@LB@@LB@@LB@Energy -6.84 kcal/mol@LB@Hybridization Energy -20.344 kcal/mol@LB@Unfolding Energy - mRNA 3.91171 kcal/mol@LB@Unfolding Energy - sRNA 9.59078 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 18 -- 39@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 21 -- 27@LB@
151	0.06398	0.3424	ct_647	N/A	-6.81	0.158308	265 -- 281	12 -- 34		_____________264_____________________282\n_____________\|_______________________\|\n5'-UAU...UGCAA_______________________CGUCA...AGG-3'\n______________UAGGAGC______AUGGUGUUGG\n______________:\|\|:\|\|\|______\|\|\|\|:\|\|\|:\|\n______________GUCUUCG______UACCGCAAUC\n3'-UUU...UCUCA_______AUAAGG__________UUAUG...GAA-5'\n_____________\|_______________________\|\n_____________35______________________11\n	274 -- 280	13 -- 19	-18.8273 kcal/mol	3.44317 kcal/mol	8.57325 kcal/mol	264 282@LB@ \| \|@LB@5'-UAU...UGCAA CGUCA...AGG-3'@LB@ UAGGAGC AUGGUGUUGG@LB@ :\|\|:\|\|\| \|\|\|\|:\|\|\|:\|@LB@ GUCUUCG UACCGCAAUC@LB@3'-UUU...UCUCA AUAAGG UUAUG...GAA-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -18.8273 kcal/mol@LB@Unfolding Energy - mRNA 3.44317 kcal/mol@LB@Unfolding Energy - sRNA 8.57325 kcal/mol@LB@@LB@Position - mRNA 265 -- 281@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 13 -- 19@LB@
113	0.04597	0.3262	ct_841	ftsH	-6.80	0.159029	200 -- 207	80 -- 87	ATP-dependent zinc metalloprotease FtsH	_____________199______208\n_____________\|________\|\n5'-GGU...AGUUU________AAGAU...UUC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.6438 kcal/mol	2.74436 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GGU...AGUUU AAGAU...UUC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.80 kcal/mol@LB@Hybridization Energy -10.6438 kcal/mol@LB@Unfolding Energy - mRNA 2.74436 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
15	0.003628	0.1836	ct_134	N/A	-6.77	0.161910	221 -- 229	80 -- 88		_____________220_______230\n_____________\|_________\|\n5'-CAA...UGUGU_________CGAUG...UUC-3'\n______________AUACGGUUA\n______________\|\|\|\|\|\|:\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	223 -- 229	80 -- 86	-9.99522 kcal/mol	2.13198 kcal/mol	1.09753 kcal/mol	220 230@LB@ \| \|@LB@5'-CAA...UGUGU CGAUG...UUC-3'@LB@ AUACGGUUA@LB@ \|\|\|\|\|\|:\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -9.99522 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 221 -- 229@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 80 -- 86@LB@
129	0.0523	0.3262	ct_872	pmpH	-6.76	0.162049	85 -- 103	18 -- 34	outer membrane protein PmpH	_____________84__________________104\n_____________\|___________________\|\n5'-AGA...CAAUA_______A___GG______AAGAU...AUG-3'\n______________UAGAAGU_UAU__CCAUGG\n______________:\|\|\|\|\|:_\|\|\|__\|\|\|\|\|\|\n______________GUCUUCG_AUA__GGUACC\n3'-UUU...UCUCA___________A_______GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	85 -- 91	28 -- 34	-16.9306 kcal/mol	5.18888 kcal/mol	4.97803 kcal/mol	84 104@LB@ \| \|@LB@5'-AGA...CAAUA A GG AAGAU...AUG-3'@LB@ UAGAAGU UAU CCAUGG@LB@ :\|\|\|\|\|: \|\|\| \|\|\|\|\|\|@LB@ GUCUUCG AUA GGUACC@LB@3'-UUU...UCUCA A GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -16.9306 kcal/mol@LB@Unfolding Energy - mRNA 5.18888 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 85 -- 103@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 28 -- 34@LB@
70	0.02698	0.29	ct_381	artJ	-6.76	0.162330	168 -- 194	31 -- 57	arginine ABC transporter substrate-binding protein ArtJ	_____________167__________________________195\n_____________\|____________________________\|\n5'-AUU...UAUAG______CC__UA__C_____________GUGAG...GUG-3'\n______________UCCCUG__GU__GA_CAUU_GAGUCGGA\n______________:\|\|\|\|\|__\|\|__:\|_\|\|:\|_\|\|\|\|\|:\|\|\n______________GGGGAC__CA__UU_GUGA_CUCAGUCU\n3'-UUU...GAAGG______A___UG__U____U________UCGAU...GAA-5'\n_____________\|____________________________\|\n_____________58___________________________30\n	188 -- 194	31 -- 37	-25.975 kcal/mol	9.18513 kcal/mol	10.0297 kcal/mol	167 195@LB@ \| \|@LB@5'-AUU...UAUAG CC UA C GUGAG...GUG-3'@LB@ UCCCUG GU GA CAUU GAGUCGGA@LB@ :\|\|\|\|\| \|\| :\| \|\|:\| \|\|\|\|\|:\|\|@LB@ GGGGAC CA UU GUGA CUCAGUCU@LB@3'-UUU...GAAGG A UG U U UCGAU...GAA-5'@LB@ \| \|@LB@ 58 30@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -25.975 kcal/mol@LB@Unfolding Energy - mRNA 9.18513 kcal/mol@LB@Unfolding Energy - sRNA 10.0297 kcal/mol@LB@@LB@Position - mRNA 168 -- 194@LB@Position - sRNA 31 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@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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