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
181	0.07898	0.3587	ct_186	devB	-5.59	0.281766	201 -- 207	80 -- 86	6-phosphogluconolactonase	_____________200_____208\n_____________\|_______\|\n5'-GAA...UAUAC_______CCCUU...CAG-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	201 -- 207	80 -- 86	-9.11344 kcal/mol	2.46127 kcal/mol	1.06449 kcal/mol	200 208@LB@ \| \|@LB@5'-GAA...UAUAC CCCUU...CAG-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -9.11344 kcal/mol@LB@Unfolding Energy - mRNA 2.46127 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
182	0.07944	0.3588	ct_320	nusG	-7.37	0.119406	230 -- 236	81 -- 87	transcription termination/antitermination protein NusG	_____________229_____237\n_____________\|_______\|\n5'-AAC...GUUUU_______CAAGA...UUA-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	230 -- 236	81 -- 87	-10.814 kcal/mol	2.34788 kcal/mol	1.09752 kcal/mol	229 237@LB@ \| \|@LB@5'-AAC...GUUUU CAAGA...UUA-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -10.814 kcal/mol@LB@Unfolding Energy - mRNA 2.34788 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 230 -- 236@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 81 -- 87@LB@
183	0.08019	0.3602	ct_648	N/A	-7.31	0.122948	212 -- 231	14 -- 34		_____________211___________________232\n_____________\|_____________________\|\n5'-ACU...GUAAG________UAAG_________UAUGU...UUA-3'\n______________UAGAAGCU_____AUGGUGUU\n______________:\|\|\|\|\|\|\|_____\|\|\|\|:\|\|\|\n______________GUCUUCGA_____UACCGCAA\n3'-UUU...UCUCA________UAAGG________UCUUA...GAA-5'\n_____________\|_____________________\|\n_____________35____________________13\n	225 -- 231	14 -- 20	-20.6397 kcal/mol	4.879 kcal/mol	8.44924 kcal/mol	211 232@LB@ \| \|@LB@5'-ACU...GUAAG UAAG UAUGU...UUA-3'@LB@ UAGAAGCU AUGGUGUU@LB@ :\|\|\|\|\|\|\| \|\|\|\|:\|\|\|@LB@ GUCUUCGA UACCGCAA@LB@3'-UUU...UCUCA UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -20.6397 kcal/mol@LB@Unfolding Energy - mRNA 4.879 kcal/mol@LB@Unfolding Energy - sRNA 8.44924 kcal/mol@LB@@LB@Position - mRNA 212 -- 231@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 14 -- 20@LB@
184	0.0822	0.363	ct_497	dnaB	-7.07	0.138978	138 -- 179	3 -- 57	replicative DNA helicase	_____________137________________________________________________________180\n_____________\|__________________________________________________________\|\n5'-ACG...AUAUU_____A_____CCU________CCG____G_________UU_________________CAUAA...GUG-3'\n______________CCCCU___UAC___AAC_CUGG____AGA_AGCU__UCC____________UACCAAC\n______________\|\|\|\|\|___\|\|\|___\|\|\|_\|\|:\|____\|\|\|_\|\|\|\|__\|\|\|____________\|\|\|\|\|\|\|\n______________GGGGA___AUG___UUG_GAUC____UCU_UCGA__AGG____________AUGGUUG\n3'-UUU...GAAGG_____CAC___U_____U____UCAG________UA___UACCGCAAUCUU_______AA-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________2\n	173 -- 179	3 -- 9	-29.7257 kcal/mol	6.10481 kcal/mol	16.5501 kcal/mol	137 180@LB@ \| \|@LB@5'-ACG...AUAUU A CCU CCG G UU CAUAA...GUG-3'@LB@ CCCCU UAC AAC CUGG AGA AGCU UCC UACCAAC@LB@ \|\|\|\|\| \|\|\| \|\|\| \|\|:\| \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ GGGGA AUG UUG GAUC UCU UCGA AGG AUGGUUG@LB@3'-UUU...GAAGG CAC U U UCAG UA UACCGCAAUCUU AA-5'@LB@ \| \|@LB@ 58 2@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -29.7257 kcal/mol@LB@Unfolding Energy - mRNA 6.10481 kcal/mol@LB@Unfolding Energy - sRNA 16.5501 kcal/mol@LB@@LB@Position - mRNA 138 -- 179@LB@Position - sRNA 3 -- 57@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 3 -- 9@LB@
185	0.083	0.363	ct_260	N/A	-8.27	0.074080	87 -- 93	53 -- 59		_____________86______94\n_____________\|_______\|\n5'-GUU...CCCCC_______CCCAU...UCA-3'\n______________CCCCCCU\n______________\|\|\|\|\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	87 -- 93	53 -- 59	-14.3095 kcal/mol	0.558947 kcal/mol	5.47887 kcal/mol	86 94@LB@ \| \|@LB@5'-GUU...CCCCC CCCAU...UCA-3'@LB@ CCCCCCU@LB@ \|\|\|\|\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -14.3095 kcal/mol@LB@Unfolding Energy - mRNA 0.558947 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 87 -- 93@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 53 -- 59@LB@
186	0.08332	0.363	ct_811	plsX	-5.83	0.252304	163 -- 171	79 -- 87	phosphate acyltransferase	_____________162_______172\n_____________\|_________\|\n5'-GGC...GUUAU_________GAAGU...AAC-3'\n______________UACGGUUGA\n______________\|\|\|\|\|:\|:\|\n______________AUGCCGAUU\n3'-UUU...CCUCU_________GAGGU...GAA-5'\n_____________\|_________\|\n_____________88________78\n	165 -- 171	79 -- 85	-10.158 kcal/mol	3.22704 kcal/mol	1.09752 kcal/mol	162 172@LB@ \| \|@LB@5'-GGC...GUUAU GAAGU...AAC-3'@LB@ UACGGUUGA@LB@ \|\|\|\|\|:\|:\|@LB@ AUGCCGAUU@LB@3'-UUU...CCUCU GAGGU...GAA-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -5.83 kcal/mol@LB@Hybridization Energy -10.158 kcal/mol@LB@Unfolding Energy - mRNA 3.22704 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 163 -- 171@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 79 -- 85@LB@
187	0.08358	0.363	ct_041	N/A	-5.64	0.274890	141 -- 160	41 -- 59		_____________140__________________161\n_____________\|____________________\|\n5'-UUU...UGCAA________GCA_________CUUAA...CUA-3'\n______________CCCCUUUG___UAUGAACAU\n______________\|\|\|\|::\|\|___\|\|::\|\|\|\|:\n______________GGGGGGAC___AUGUUUGUG\n3'-UUU...CUGAA________AC__________AUCUC...GAA-5'\n_____________\|____________________\|\n_____________60___________________40\n	142 -- 148	52 -- 58	-19.5521 kcal/mol	5.08593 kcal/mol	8.82318 kcal/mol	140 161@LB@ \| \|@LB@5'-UUU...UGCAA GCA CUUAA...CUA-3'@LB@ CCCCUUUG UAUGAACAU@LB@ \|\|\|\|::\|\| \|\|::\|\|\|\|:@LB@ GGGGGGAC AUGUUUGUG@LB@3'-UUU...CUGAA AC AUCUC...GAA-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -5.64 kcal/mol@LB@Hybridization Energy -19.5521 kcal/mol@LB@Unfolding Energy - mRNA 5.08593 kcal/mol@LB@Unfolding Energy - sRNA 8.82318 kcal/mol@LB@@LB@Position - mRNA 141 -- 160@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 52 -- 58@LB@
188	0.08401	0.363	ct_024	N/A	-5.57	0.284242	184 -- 199	20 -- 35	release factor glutamine methyltransferase	_____________183______________200\n_____________\|________________\|\n5'-AGA...GUACA____C________G__CAUGA...AGA-3'\n______________UCGG_AGCUAUUC_GU\n______________\|\|:\|_\|\|\|\|\|\|\|\|_:\|\n______________AGUC_UCGAUAAG_UA\n3'-UUU...AUCUC____U________G__CCGCA...GAA-5'\n_____________\|________________\|\n_____________36_______________19\n	190 -- 196	23 -- 29	-16.0617 kcal/mol	5.57694 kcal/mol	4.91708 kcal/mol	183 200@LB@ \| \|@LB@5'-AGA...GUACA C G CAUGA...AGA-3'@LB@ UCGG AGCUAUUC GU@LB@ \|\|:\| \|\|\|\|\|\|\|\| :\|@LB@ AGUC UCGAUAAG UA@LB@3'-UUU...AUCUC U G CCGCA...GAA-5'@LB@ \| \|@LB@ 36 19@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -16.0617 kcal/mol@LB@Unfolding Energy - mRNA 5.57694 kcal/mol@LB@Unfolding Energy - sRNA 4.91708 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 20 -- 35@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 23 -- 29@LB@
189	0.0841	0.363	ct_792	mutS	-5.18	0.336119	140 -- 151	22 -- 33	DNA mismatch repair protein MutS	_____________139__________152\n_____________\|____________\|\n5'-AUA...ACAUA____C_______CCUAC...AAG-3'\n______________AGAG_CUGUUCC\n______________\|\|\|:_\|\|:\|\|\|\|\n______________UCUU_GAUAAGG\n3'-UUU...CUCAG____C_______UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	145 -- 151	22 -- 28	-12.2041 kcal/mol	2.29966 kcal/mol	4.72509 kcal/mol	139 152@LB@ \| \|@LB@5'-AUA...ACAUA C CCUAC...AAG-3'@LB@ AGAG CUGUUCC@LB@ \|\|\|: \|\|:\|\|\|\|@LB@ UCUU GAUAAGG@LB@3'-UUU...CUCAG C UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -12.2041 kcal/mol@LB@Unfolding Energy - mRNA 2.29966 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 22 -- 28@LB@
190	0.08414	0.363	ct_503	N/A	-6.17	0.215667	244 -- 250	81 -- 87		_____________243_____251\n_____________\|_______\|\n5'-UGG...UUUGU_______UCGCA...CUC-3'\n______________UACGGUU\n______________\|\|\|\|\|:\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	244 -- 250	81 -- 87	-7.94334 kcal/mol	0.67364 kcal/mol	1.09752 kcal/mol	243 251@LB@ \| \|@LB@5'-UGG...UUUGU UCGCA...CUC-3'@LB@ UACGGUU@LB@ \|\|\|\|\|:\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.94334 kcal/mol@LB@Unfolding Energy - mRNA 0.67364 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 244 -- 250@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 81 -- 87@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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