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
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@
191	0.08461	0.363	ct_112	pepF	-2.97	0.715117	121 -- 127	54 -- 60	oligoendopeptidase F	_____________120_____128\n_____________\|_______\|\n5'-UCU...UCUCU_______ACUGG...AAG-3'\n______________UCCCCUU\n______________\|\|\|\|\|::\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	121 -- 127	54 -- 60	-10.8708 kcal/mol	1.46061 kcal/mol	6.44182 kcal/mol	120 128@LB@ \| \|@LB@5'-UCU...UCUCU ACUGG...AAG-3'@LB@ UCCCCUU@LB@ \|\|\|\|\|::@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -2.97 kcal/mol@LB@Hybridization Energy -10.8708 kcal/mol@LB@Unfolding Energy - mRNA 1.46061 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 54 -- 60@LB@
74	0.02719	0.29	ct_114	N/A	-7.65	0.102976	115 -- 129	17 -- 32		_____________114______________130\n_____________\|________________\|\n5'-AGG...GCGGU______UA________AAAAG...AAA-3'\n______________GGAGCU___CUAUGGC\n______________\|:\|\|\|\|___\|:\|\|\|\|\|\n______________CUUCGA___GGUACCG\n3'-UUU...UCAGU______UAA_______CAAUC...GAA-5'\n_____________\|________________\|\n_____________33_______________16\n	123 -- 129	17 -- 23	-17.2748 kcal/mol	4.65579 kcal/mol	4.96575 kcal/mol	114 130@LB@ \| \|@LB@5'-AGG...GCGGU UA AAAAG...AAA-3'@LB@ GGAGCU CUAUGGC@LB@ \|:\|\|\|\| \|:\|\|\|\|\|@LB@ CUUCGA GGUACCG@LB@3'-UUU...UCAGU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -17.2748 kcal/mol@LB@Unfolding Energy - mRNA 4.65579 kcal/mol@LB@Unfolding Energy - sRNA 4.96575 kcal/mol@LB@@LB@Position - mRNA 115 -- 129@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 17 -- 23@LB@
54	0.02089	0.29	ct_119	incA	-7.14	0.134009	237 -- 243	52 -- 58	inclusion membrane protein A	_____________236_____244\n_____________\|_______\|\n5'-UCC...CAUCU_______CACCU...AGA-3'\n______________CCCCCUG\n______________\|\|\|\|\|\|\|\n______________GGGGGAC\n3'-UUU...UGAAG_______ACAUG...GAA-5'\n_____________\|_______\|\n_____________59______51\n	237 -- 243	52 -- 58	-14.4133 kcal/mol	0.279731 kcal/mol	6.99083 kcal/mol	236 244@LB@ \| \|@LB@5'-UCC...CAUCU CACCU...AGA-3'@LB@ CCCCCUG@LB@ \|\|\|\|\|\|\|@LB@ GGGGGAC@LB@3'-UUU...UGAAG ACAUG...GAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -14.4133 kcal/mol@LB@Unfolding Energy - mRNA 0.279731 kcal/mol@LB@Unfolding Energy - sRNA 6.99083 kcal/mol@LB@@LB@Position - mRNA 237 -- 243@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 52 -- 58@LB@
149	0.06369	0.3424	ct_124	accC	-5.62	0.277702	171 -- 193	17 -- 31	acetyl-CoA carboxylase biotin carboxylase subunit	_____________170_____________________194\n_____________\|_______________________\|\n5'-CUC...GUUCU____________AUAGUUAA___UUAGU...UGG-3'\n______________AAGUUAUUCCGU________GGC\n______________\|\|\|:\|\|\|\|\|\|:\|________\|\|\|\n______________UUCGAUAAGGUA________CCG\n3'-UUU...CAGUC_______________________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________32______________________16\n	176 -- 182	20 -- 26	-15.1557 kcal/mol	4.67447 kcal/mol	4.86101 kcal/mol	170 194@LB@ \| \|@LB@5'-CUC...GUUCU AUAGUUAA UUAGU...UGG-3'@LB@ AAGUUAUUCCGU GGC@LB@ \|\|\|:\|\|\|\|\|\|:\| \|\|\|@LB@ UUCGAUAAGGUA CCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -5.62 kcal/mol@LB@Hybridization Energy -15.1557 kcal/mol@LB@Unfolding Energy - mRNA 4.67447 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
78	0.0282	0.29	ct_131	N/A	-9.30	0.042003	199 -- 219	17 -- 35		_____________198___________________220\n_____________\|_____________________\|\n5'-GAG...UGAAU___U_____GUUC________AUAAA...AAU-3'\n______________UCA_GAAGC____UCCAUGGU\n______________\|\|\|_\|\|\|\|\|____\|\|\|\|\|\|\|:\n______________AGU_CUUCG____AGGUACCG\n3'-UUU...AUCUC_________AUA_________CAAUC...GAA-5'\n_____________\|_____________________\|\n_____________36____________________16\n	213 -- 219	17 -- 23	-20.9121 kcal/mol	6.63751 kcal/mol	4.9781 kcal/mol	198 220@LB@ \| \|@LB@5'-GAG...UGAAU U GUUC AUAAA...AAU-3'@LB@ UCA GAAGC UCCAUGGU@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AGU CUUCG AGGUACCG@LB@3'-UUU...AUCUC AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -20.9121 kcal/mol@LB@Unfolding Energy - mRNA 6.63751 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 199 -- 219@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 17 -- 23@LB@
57	0.02238	0.29	ct_132	N/A	-4.44	0.450895	20 -- 27	53 -- 60		_____________19_______28\n_____________\|________\|\n5'-GAU...AUGGA________AAAAA...ACA-3'\n______________UCUCCCCU\n______________\|\|:\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	21 -- 27	53 -- 59	-12.9803 kcal/mol	2.08802 kcal/mol	6.45136 kcal/mol	19 28@LB@ \| \|@LB@5'-GAU...AUGGA AAAAA...ACA-3'@LB@ UCUCCCCU@LB@ \|\|:\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -4.44 kcal/mol@LB@Hybridization Energy -12.9803 kcal/mol@LB@Unfolding Energy - mRNA 2.08802 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 20 -- 27@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 53 -- 59@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@
132	0.05402	0.3262	ct_150	rl33	-5.54	0.287166	186 -- 205	17 -- 33	50S ribosomal protein L33	_____________185__________________206\n_____________\|____________________\|\n5'-CUC...UCUUG___AAA____CA________CAGCA...UAG-3'\n______________AGA___GGUU__UUCAUGGC\n______________\|\|\|___:\|:\|__\|:\|\|\|\|\|\|\n______________UCU___UCGA__AGGUACCG\n3'-UUU...CUCAG__________UA________CAAUC...GAA-5'\n_____________\|____________________\|\n_____________34___________________16\n	199 -- 205	17 -- 23	-14.3817 kcal/mol	3.85921 kcal/mol	4.97804 kcal/mol	185 206@LB@ \| \|@LB@5'-CUC...UCUUG AAA CA CAGCA...UAG-3'@LB@ AGA GGUU UUCAUGGC@LB@ \|\|\| :\|:\| \|:\|\|\|\|\|\|@LB@ UCU UCGA AGGUACCG@LB@3'-UUU...CUCAG UA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.54 kcal/mol@LB@Hybridization Energy -14.3817 kcal/mol@LB@Unfolding Energy - mRNA 3.85921 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
58	0.02303	0.29	ct_184	N/A	-4.35	0.465673	5 -- 18	18 -- 35	Holliday junction resolvase	_____________4__________________19\n_____________\|__________________\|\n_______5'-ACGU_______AA_________AUUAA...UGC-3'\n______________UUAGAAG______CAUGG\n______________\|:\|\|\|\|\|______\|\|\|\|\|\n______________AGUCUUC______GUACC\n3'-UUU...AUCUC_______GAUAAG_____GCAAU...GAA-5'\n_____________\|__________________\|\n_____________36_________________17\n	5 -- 11	29 -- 35	-12.193 kcal/mol	2.86148 kcal/mol	4.97803 kcal/mol	4 19@LB@ \| \|@LB@ 5'-ACGU AA AUUAA...UGC-3'@LB@ UUAGAAG CAUGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGUCUUC GUACC@LB@3'-UUU...AUCUC GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -12.193 kcal/mol@LB@Unfolding Energy - mRNA 2.86148 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 5 -- 18@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@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