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
31	0.009434	0.2502	ct_824	N/A	-6.02	0.231369	20 -- 32	21 -- 33	Zn-dependent peptidase	_____________19____________33\n_____________\|_____________\|\n5'-GUC...UUUUA________G____GUAUG...CCG-3'\n______________GGAAGCUA_UCUA\n______________:\|\|\|\|\|\|\|_\|\|:\|\n______________UCUUCGAU_AGGU\n3'-UUU...CUCAG________A____ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	21 -- 27	26 -- 32	-13.8347 kcal/mol	3.08274 kcal/mol	4.73034 kcal/mol	19 33@LB@ \| \|@LB@5'-GUC...UUUUA G GUAUG...CCG-3'@LB@ GGAAGCUA UCUA@LB@ :\|\|\|\|\|\|\| \|\|:\|@LB@ UCUUCGAU AGGU@LB@3'-UUU...CUCAG A ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -13.8347 kcal/mol@LB@Unfolding Energy - mRNA 3.08274 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 26 -- 32@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@
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@
179	0.07718	0.3544	ct_781	lysS	-5.99	0.234962	194 -- 201	79 -- 86	lysine--tRNA ligase	_____________193______202\n_____________\|________\|\n5'-AAA...AAAGG________UGUCU...AUC-3'\n______________ACGGUUGA\n______________\|\|\|\|:\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	195 -- 201	79 -- 85	-9.06205 kcal/mol	1.97593 kcal/mol	1.09752 kcal/mol	193 202@LB@ \| \|@LB@5'-AAA...AAAGG UGUCU...AUC-3'@LB@ ACGGUUGA@LB@ \|\|\|\|:\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -9.06205 kcal/mol@LB@Unfolding Energy - mRNA 1.97593 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 194 -- 201@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 79 -- 85@LB@
87	0.03104	0.29	ct_437	fusA	-5.85	0.250219	118 -- 125	79 -- 86	elongation factor G	_____________117______126\n_____________\|________\|\n5'-AUC...AUCGC________AGCAA...UCU-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	119 -- 125	79 -- 85	-8.84241 kcal/mol	1.89322 kcal/mol	1.09752 kcal/mol	117 126@LB@ \| \|@LB@5'-AUC...AUCGC AGCAA...UCU-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.85 kcal/mol@LB@Hybridization Energy -8.84241 kcal/mol@LB@Unfolding Energy - mRNA 1.89322 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 79 -- 85@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@
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@
104	0.03845	0.3036	ct_860	N/A	-5.72	0.265250	231 -- 258	29 -- 56	type III secretion system translocator CopD2	_____________230__________________________259\n_____________\|____________________________\|\n5'-AGU...CACUA____CAU________A___CAA______AGCAG...CCA-3'\n______________CCUU___UACAAACA_UAG___CAGGAG\n______________\|\|:\|___\|\|\|\|\|\|\|\|_\|\|\|___\|\|\|:\|\|\n______________GGGA___AUGUUUGU_AUC___GUCUUC\n3'-UUU...AAGGG____CAC________G___UCA______GAUAA...GAA-5'\n_____________\|____________________________\|\n_____________57___________________________28\n	239 -- 245	42 -- 48	-21.1219 kcal/mol	3.33524 kcal/mol	12.064 kcal/mol	230 259@LB@ \| \|@LB@5'-AGU...CACUA CAU A CAA AGCAG...CCA-3'@LB@ CCUU UACAAACA UAG CAGGAG@LB@ \|\|:\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GGGA AUGUUUGU AUC GUCUUC@LB@3'-UUU...AAGGG CAC G UCA GAUAA...GAA-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -21.1219 kcal/mol@LB@Unfolding Energy - mRNA 3.33524 kcal/mol@LB@Unfolding Energy - sRNA 12.064 kcal/mol@LB@@LB@Position - mRNA 231 -- 258@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 42 -- 48@LB@
146	0.05858	0.3298	ct_655	kdsA	-5.70	0.267824	236 -- 245	48 -- 57	2-dehydro-3-deoxyphosphooctonate aldolase	_____________235________246\n_____________\|__________\|\n5'-GCU...GCAGG__________AUUGA...CUC-3'\n______________CCCUUGUGUA\n______________\|\|\|:\|\|\|\|\|\|\n______________GGGGACACAU\n3'-UUU...GAAGG__________GUUUG...GAA-5'\n_____________\|__________\|\n_____________58_________47\n	237 -- 243	50 -- 56	-16.3498 kcal/mol	3.37377 kcal/mol	7.27486 kcal/mol	235 246@LB@ \| \|@LB@5'-GCU...GCAGG AUUGA...CUC-3'@LB@ CCCUUGUGUA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GGGGACACAU@LB@3'-UUU...GAAGG GUUUG...GAA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -5.70 kcal/mol@LB@Hybridization Energy -16.3498 kcal/mol@LB@Unfolding Energy - mRNA 3.37377 kcal/mol@LB@Unfolding Energy - sRNA 7.27486 kcal/mol@LB@@LB@Position - mRNA 236 -- 245@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 50 -- 56@LB@
143	0.05698	0.3262	ct_451	cdsA	-5.69	0.268983	146 -- 169	3 -- 34	phosphatidate cytidylyltransferase	_____________145______________________________170\n_____________\|________________________________\|\n5'-GAC...CUUGC_______G___AAAAC________________AACGA...GUA-3'\n______________UAGAAGC_AUU_____________AUACCAAC\n______________:\|\|\|\|\|\|_\|\|\|_____________\|\|\|\|\|\|\|\|\n______________GUCUUCG_UAA_____________UAUGGUUG\n3'-UUU...UCUCA_______A___GGUACCGCAAUCU________AA-5'\n_____________\|________________________________\|\n_____________35_______________________________2\n	163 -- 169	3 -- 9	-16.5797 kcal/mol	2.2962 kcal/mol	8.59197 kcal/mol	145 170@LB@ \| \|@LB@5'-GAC...CUUGC G AAAAC AACGA...GUA-3'@LB@ UAGAAGC AUU AUACCAAC@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUCUUCG UAA UAUGGUUG@LB@3'-UUU...UCUCA A GGUACCGCAAUCU AA-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -16.5797 kcal/mol@LB@Unfolding Energy - mRNA 2.2962 kcal/mol@LB@Unfolding Energy - sRNA 8.59197 kcal/mol@LB@@LB@Position - mRNA 146 -- 169@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 3 -- 9@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)

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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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