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
96	0.03475	0.2959	ct_548	N/A	-8.10	0.081484	276 -- 282	54 -- 60		_____________275_____283\n_____________\|_______\|\n5'-ACA...UGCUC_______ACUAU...AAU-3'\n______________UCCCCCC\n______________\|\|\|\|\|\|\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	276 -- 282	54 -- 60	-15.7273 kcal/mol	1.19056 kcal/mol	6.44182 kcal/mol	275 283@LB@ \| \|@LB@5'-ACA...UGCUC ACUAU...AAU-3'@LB@ UCCCCCC@LB@ \|\|\|\|\|\|\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -15.7273 kcal/mol@LB@Unfolding Energy - mRNA 1.19056 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 54 -- 60@LB@
145	0.05831	0.3298	ct_635	N/A	-5.11	0.346704	276 -- 282	53 -- 59		_____________275_____283\n_____________\|_______\|\n5'-AUC...UCGAA_______UUGGA...CUG-3'\n______________CCCUCCU\n______________\|\|\|:\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	276 -- 282	53 -- 59	-11.2032 kcal/mol	0.619026 kcal/mol	5.47887 kcal/mol	275 283@LB@ \| \|@LB@5'-AUC...UCGAA UUGGA...CUG-3'@LB@ CCCUCCU@LB@ \|\|\|:\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -11.2032 kcal/mol@LB@Unfolding Energy - mRNA 0.619026 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 53 -- 59@LB@
142	0.0566	0.3262	ct_284	N/A	-6.95	0.147726	278 -- 292	18 -- 30	phospholipase D	_____________277_____________293\n_____________\|_______________\|\n5'-AUC...ACUAU_________GG____AGACAAAA-3'\n______________AGCUAUUCC__AUGG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UCGAUAAGG__UACC\n3'-UUU...AGUCU_______________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________31______________17\n	280 -- 286	22 -- 28	-16.5616 kcal/mol	4.87795 kcal/mol	4.73403 kcal/mol	277 293@LB@ \| \|@LB@5'-AUC...ACUAU GG AGACAAAA-3'@LB@ AGCUAUUCC AUGG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCGAUAAGG UACC@LB@3'-UUU...AGUCU GCAAU...GAA-5'@LB@ \| \|@LB@ 31 17@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -16.5616 kcal/mol@LB@Unfolding Energy - mRNA 4.87795 kcal/mol@LB@Unfolding Energy - sRNA 4.73403 kcal/mol@LB@@LB@Position - mRNA 278 -- 292@LB@Position - sRNA 18 -- 30@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 22 -- 28@LB@
114	0.04665	0.3262	ct_848	N/A	-8.83	0.054442	279 -- 286	79 -- 86		_____________278______287\n_____________\|________\|\n5'-CAA...CUGCA________UGAGA...CAC-3'\n______________ACGGCUGA\n______________\|\|\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	280 -- 286	79 -- 85	-11.4013 kcal/mol	1.46996 kcal/mol	1.09752 kcal/mol	278 287@LB@ \| \|@LB@5'-CAA...CUGCA UGAGA...CAC-3'@LB@ ACGGCUGA@LB@ \|\|\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -11.4013 kcal/mol@LB@Unfolding Energy - mRNA 1.46996 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 279 -- 286@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 79 -- 85@LB@
196	0.08741	0.3657	ct_698	N/A	-4.23	0.486304	280 -- 292	22 -- 34	tRNA modification GTPase	_____________279___________293\n_____________\|_____________\|\n5'-AAA...CGGAC____U________UAUUUCUG-3'\n______________CGGA_GCUAUUUC\n______________\|:\|\|_\|\|\|\|\|\|:\|\n______________GUCU_CGAUAAGG\n3'-UUU...UCUCA____U________UACCG...GAA-5'\n_____________\|_____________\|\n_____________35____________21\n	285 -- 291	23 -- 29	-13.8571 kcal/mol	4.89721 kcal/mol	4.72608 kcal/mol	279 293@LB@ \| \|@LB@5'-AAA...CGGAC U UAUUUCUG-3'@LB@ CGGA GCUAUUUC@LB@ \|:\|\| \|\|\|\|\|\|:\|@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -4.23 kcal/mol@LB@Hybridization Energy -13.8571 kcal/mol@LB@Unfolding Energy - mRNA 4.89721 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 280 -- 292@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 23 -- 29@LB@
17	0.003987	0.1836	ct_843	rs15	-6.01	0.232273	282 -- 295	22 -- 34	30S ribosomal protein S15	_____________281____________296\n_____________\|______________\|\n5'-AGG...AUGUG____UU________GACUG-3'\n______________CAGA__GCUAUUCU\n______________\|\|\|\|__\|\|\|\|\|\|\|:\n______________GUCU__CGAUAAGG\n3'-UUU...UCUCA____U_________UACCG...GAA-5'\n_____________\|______________\|\n_____________35_____________21\n	288 -- 294	23 -- 29	-14.3687 kcal/mol	3.62939 kcal/mol	4.72608 kcal/mol	281 296@LB@ \| \|@LB@5'-AGG...AUGUG UU GACUG-3'@LB@ CAGA GCUAUUCU@LB@ \|\|\|\| \|\|\|\|\|\|\|:@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -6.01 kcal/mol@LB@Hybridization Energy -14.3687 kcal/mol@LB@Unfolding Energy - mRNA 3.62939 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 23 -- 29@LB@
69	0.02639	0.29	ct_745	hemG	-5.84	0.251832	282 -- 296	21 -- 34	protoporphyrinogen oxidase	_____________281_____________297\n_____________\|_______________\|\n5'-UUU...AUGUG___CU_U________GAAA-3'\n______________CAG__G_CUAUUCUA\n______________\|\|\|__\|_\|\|\|\|\|\|:\|\n______________GUC__C_GAUAAGGU\n3'-UUU...UCUCA___UU__________ACCGC...GAA-5'\n_____________\|_______________\|\n_____________35______________20\n	290 -- 296	21 -- 27	-11.5957 kcal/mol	1.02702 kcal/mol	4.73132 kcal/mol	281 297@LB@ \| \|@LB@5'-UUU...AUGUG CU U GAAA-3'@LB@ CAG G CUAUUCUA@LB@ \|\|\| \| \|\|\|\|\|\|:\|@LB@ GUC C GAUAAGGU@LB@3'-UUU...UCUCA UU ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -11.5957 kcal/mol@LB@Unfolding Energy - mRNA 1.02702 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 282 -- 296@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 21 -- 27@LB@
28	0.007489	0.2199	ct_755	groEL_3	-5.45	0.299165	283 -- 296	17 -- 33	chaperonin GroEL	_____________282_______________297\n_____________\|_________________\|\n5'-CAC...AGUAA_________________CCCG-3'\n______________AGGGGU___UUUAUGGC\n______________\|\|::\|:___\|::\|\|\|\|\|\n______________UCUUCG___AGGUACCG\n3'-UUU...CUCAG______AUA________CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	290 -- 296	17 -- 23	-13.7025 kcal/mol	3.27337 kcal/mol	4.97804 kcal/mol	282 297@LB@ \| \|@LB@5'-CAC...AGUAA CCCG-3'@LB@ AGGGGU UUUAUGGC@LB@ \|\|::\|: \|::\|\|\|\|\|@LB@ UCUUCG AGGUACCG@LB@3'-UUU...CUCAG AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.45 kcal/mol@LB@Hybridization Energy -13.7025 kcal/mol@LB@Unfolding Energy - mRNA 3.27337 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 283 -- 296@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 17 -- 23@LB@
128	0.05098	0.3262	ct_279	nqr3	-7.28	0.125274	283 -- 291	51 -- 59	Na(+)-translocating NADH-quinone reductase subunit C	_____________282_______292\n_____________\|_________\|\n5'-CCG...UGGUA_________CUUCU...UGU-3'\n______________CCCUCCUGU\n______________\|\|\|:\|\|\|\|\|\n______________GGGGGGACA\n3'-UUU...CUGAA_________CAUGU...GAA-5'\n_____________\|_________\|\n_____________60________50\n	285 -- 291	51 -- 57	-15.9842 kcal/mol	0.606269 kcal/mol	8.10291 kcal/mol	282 292@LB@ \| \|@LB@5'-CCG...UGGUA CUUCU...UGU-3'@LB@ CCCUCCUGU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGGGGACA@LB@3'-UUU...CUGAA CAUGU...GAA-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -15.9842 kcal/mol@LB@Unfolding Energy - mRNA 0.606269 kcal/mol@LB@Unfolding Energy - sRNA 8.10291 kcal/mol@LB@@LB@Position - mRNA 283 -- 291@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
150	0.06394	0.3424	ct_208	gseA	-4.42	0.454874	290 -- 300	19 -- 29	3-deoxy-D-manno-octulosonic acid transferase	_____________289________300\n_____________\|__________\|\n5'-UUG...AAAGU___U_______-3'\n______________GUU_UUCCAUG\n______________\|:\|_\|\|\|\|\|\|\|\n______________CGA_AAGGUAC\n3'-UUU...GUCUU___U_______CGCAA...GAA-5'\n_____________\|___________\|\n_____________30__________18\n	294 -- 300	19 -- 25	-10.2082 kcal/mol	1.1238 kcal/mol	4.66719 kcal/mol	289 300@LB@ \| \|@LB@5'-UUG...AAAGU U -3'@LB@ GUU UUCCAUG@LB@ \|:\| \|\|\|\|\|\|\|@LB@ CGA AAGGUAC@LB@3'-UUU...GUCUU U CGCAA...GAA-5'@LB@ \| \|@LB@ 30 18@LB@@LB@@LB@Energy -4.42 kcal/mol@LB@Hybridization Energy -10.2082 kcal/mol@LB@Unfolding Energy - mRNA 1.1238 kcal/mol@LB@Unfolding Energy - sRNA 4.66719 kcal/mol@LB@@LB@Position - mRNA 290 -- 300@LB@Position - sRNA 19 -- 29@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 19 -- 25@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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