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
39	0.01357	0.2859	ct_401	gltT	-7.80	0.095127	36 -- 47	44 -- 55	sodium:dicarboxylate symport protein	_____________35___________48\n_____________\|____________\|\n5'-UGU...GGUAU____________AAAGG...AUA-3'\n______________CCUGUGUACAGA\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________GGACACAUGUUU\n3'-UUU...AGGGG____________GUGAU...GAA-5'\n_____________\|____________\|\n_____________56___________43\n	41 -- 47	44 -- 50	-17.8988 kcal/mol	2.58215 kcal/mol	7.51272 kcal/mol	35 48@LB@ \| \|@LB@5'-UGU...GGUAU AAAGG...AUA-3'@LB@ CCUGUGUACAGA@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ GGACACAUGUUU@LB@3'-UUU...AGGGG GUGAU...GAA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.8988 kcal/mol@LB@Unfolding Energy - mRNA 2.58215 kcal/mol@LB@Unfolding Energy - sRNA 7.51272 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 44 -- 50@LB@
106	0.04101	0.3134	ct_445	gltX	-7.36	0.119711	199 -- 233	6 -- 32	glutamate--tRNA ligase	_____________198__________________________________234\n_____________\|____________________________________\|\n5'-UUU...GUAGC___U_A________AAA__UAC__________A___CCUUC...CAA-3'\n______________GAA_G_CUG_UCCA___UG___GCGUUAGAGU_GCC\n______________\|\|\|_\|_\|\|:_\|\|\|\|___\|\|___\|\|\|\|\|\|\|\|:\|_:\|\|\n______________CUU_C_GAU_AGGU___AC___CGCAAUCUUA_UGG\n3'-UUU...UCAGU_________A__________________________UUGAA-5'\n_____________\|____________________________________\|\n_____________33___________________________________5\n	220 -- 226	12 -- 18	-22.1489 kcal/mol	6.20636 kcal/mol	8.57923 kcal/mol	198 234@LB@ \| \|@LB@5'-UUU...GUAGC U A AAA UAC A CCUUC...CAA-3'@LB@ GAA G CUG UCCA UG GCGUUAGAGU GCC@LB@ \|\|\| \| \|\|: \|\|\|\| \|\| \|\|\|\|\|\|\|\|:\| :\|\|@LB@ CUU C GAU AGGU AC CGCAAUCUUA UGG@LB@3'-UUU...UCAGU A UUGAA-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -22.1489 kcal/mol@LB@Unfolding Energy - mRNA 6.20636 kcal/mol@LB@Unfolding Energy - sRNA 8.57923 kcal/mol@LB@@LB@Position - mRNA 199 -- 233@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@LB@
60	0.02363	0.29	ct_796	glyQ	-6.44	0.189870	236 -- 248	21 -- 33	glycine--tRNA ligase	_____________235___________249\n_____________\|_____________\|\n5'-UAG...AUGAU__C__________AACUU...AAG-3'\n______________GG_AGCUAUUCUA\n______________:\|_\|\|\|\|\|\|\|\|:\|\n______________UC_UCGAUAAGGU\n3'-UUU...CUCAG__U__________ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	241 -- 247	22 -- 28	-13.5001 kcal/mol	2.33043 kcal/mol	4.73034 kcal/mol	235 249@LB@ \| \|@LB@5'-UAG...AUGAU C AACUU...AAG-3'@LB@ GG AGCUAUUCUA@LB@ :\| \|\|\|\|\|\|\|\|:\|@LB@ UC UCGAUAAGGU@LB@3'-UUU...CUCAG U ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.44 kcal/mol@LB@Hybridization Energy -13.5001 kcal/mol@LB@Unfolding Energy - mRNA 2.33043 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 236 -- 248@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 22 -- 28@LB@
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@LB@
19	0.004244	0.1836	ct_583	gp6D	-9.00	0.049504	83 -- 102	18 -- 35	virulence protein GP6-D	_____________82___________________103\n_____________\|____________________\|\n5'-UAA...CUAUC________CGCUA_______GAAAC...CUC-3'\n______________UCAGAAGC_____UCCAUGG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\|\n______________AGUCUUCG_____AGGUACC\n3'-UUU...AUCUC________AUA_________GCAAU...GAA-5'\n_____________\|____________________\|\n_____________36___________________17\n	96 -- 102	18 -- 24	-22.1713 kcal/mol	8.18904 kcal/mol	4.97803 kcal/mol	82 103@LB@ \| \|@LB@5'-UAA...CUAUC CGCUA GAAAC...CUC-3'@LB@ UCAGAAGC UCCAUGG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGUCUUCG AGGUACC@LB@3'-UUU...AUCUC AUA GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -22.1713 kcal/mol@LB@Unfolding Energy - mRNA 8.18904 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 83 -- 102@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 18 -- 24@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@
22	0.005311	0.1984	ct_111	groES	-5.40	0.305537	269 -- 283	17 -- 33	co-chaperonin GroES	_____________268_______________284\n_____________\|_________________\|\n5'-AGC...GAAGA_____________CU__AAGAG...UUC-3'\n______________AGAAGCU__UCCA__GC\n______________\|\|\|\|\|\|\|__\|\|\|\|__\|\|\n______________UCUUCGA__AGGU__CG\n3'-UUU...CUCAG_______UA____AC__CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	269 -- 275	27 -- 33	-15.094 kcal/mol	4.71335 kcal/mol	4.97804 kcal/mol	268 284@LB@ \| \|@LB@5'-AGC...GAAGA CU AAGAG...UUC-3'@LB@ AGAAGCU UCCA GC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|@LB@ UCUUCGA AGGU CG@LB@3'-UUU...CUCAG UA AC CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -15.094 kcal/mol@LB@Unfolding Energy - mRNA 4.71335 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 269 -- 283@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@LB@
67	0.02533	0.29	ct_395	grpE	-6.02	0.231793	191 -- 203	19 -- 33	stress response protein GrpE	_____________190_____________204\n_____________\|_______________\|\n5'-CCU...CGCUA_______________ACAGA...UAA-3'\n______________AGGAGCUAU__CAUG\n______________\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________UCUUCGAUA__GUAC\n3'-UUU...CUCAG_________AG____CGCAA...GAA-5'\n_____________\|_______________\|\n_____________34______________18\n	192 -- 198	26 -- 32	-14.6636 kcal/mol	3.66894 kcal/mol	4.97702 kcal/mol	190 204@LB@ \| \|@LB@5'-CCU...CGCUA ACAGA...UAA-3'@LB@ AGGAGCUAU CAUG@LB@ \|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UCUUCGAUA GUAC@LB@3'-UUU...CUCAG AG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -14.6636 kcal/mol@LB@Unfolding Energy - mRNA 3.66894 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 26 -- 32@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@
116	0.04833	0.3262	ct_570	gspF	-8.17	0.078365	199 -- 207	80 -- 88	type II secretion system protein F	_____________198_______208\n_____________\|_________\|\n5'-AUC...AGGGG_________GGUUU...CUG-3'\n______________AUAUGGCUA\n______________\|\|\|:\|\|\|\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	201 -- 207	80 -- 86	-11.0443 kcal/mol	1.77912 kcal/mol	1.09753 kcal/mol	198 208@LB@ \| \|@LB@5'-AUC...AGGGG GGUUU...CUG-3'@LB@ AUAUGGCUA@LB@ \|\|\|:\|\|\|\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -11.0443 kcal/mol@LB@Unfolding Energy - mRNA 1.77912 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching