Table S16: Box C/D snoRNAs that were originally denoted as orphan or where solely a predicted target based on single sequence prediction was published. Sequences were taken from Neurospora crassa (Nc_CD xy) [Liu et al.], Saccharomyces cerevisiae (snr4 and snR45) [Piekna-Przybylska et al.], and Aspergillus fumigatus (AM9219xy) [Jöchl et al.]. Initial target predictions that were based on falsely detected box motifs are marked with '∗'

original name	box	published target	aln. pos	snoStrip prediction	ICI_sno	number of interactions	mean mfe	conservation	snoStrip name
Nc_CD_10	D'	25S-3264*	25S-4650	18S-479	1.13	91	-13.15	3..6	CD_10
	D	25S-1039	25S-2066	25S-2066	0.40	37	-13.19	11
Nc_CD_26	D'	U2-183*	U2-246	25S-3836	0.86	52	-23.03	4,6	CD_26
	D	orphan		25S-3941	0.23	25	-15.34	10
Nc_CD_40	D'	25S-2062*	25S-3282	no conserved D' target region					CD_40
	D	orphan		25S-3061	0.78	12	-17.05	11-13
Nc_CD_52	D'	tRNA-Leu-43		no annotated D' box					CD_52
	D	tRNA-Leu-90		25S-2805	0.35	2	-15.30	Ony
Nc_CD_53	D'	orphan		25S-3500	0.71	21	-11.56	11	CD_53
	D	orphan		18S-1554	0.56	16	-11.70	Cap,Hel,15
Nc_CD_54	D'	orphan		U6-70	1.43	39	-18.10	11	CD_54
	D	25S-667	25S-1648	25S-3822	0.11	3	-14.93	Asp,Nfi
Nc_CD_55	D'	orphan		18S-464	1.32	3	-14.20	Neu	CD_55
	D	orphan		18S-1006	1.08	3	-8.97	Neu
snR4	D'	orphan		25S-2578	0.07	3	-12.20	Sac	CD_73
	D	orphan		18S-925	0.12	6	-10.67	Deb,Sac,Asp
snR45	D'	orphan		no annotated D' box					CD_74
	D	orphan		25S-2643	0.57	4	-9.70	Sac
AM921936	D'	orphan		25S-4198	1.58	77	-23.23	3..6	CD_31
	D	orphan		18S-1696	0.15	11	-16.39	Can,Deb,Met
AM921937	D'	orphan		18S-479	1.13	91	-13.15	3..6	CD_10
	D	orphan		25S-2066	0.40	37	-13.19	11
AM921938	D'	orphan		25S-3474	1.19	78	-17.76	3..6	CD_7
	D	orphan		5.8S-150	0.39	37	-10.82	3,6
AM921939	D'	orphan		18S-179	1.09	42	-17.22	11	CD_15
	D	orphan		18S-1401	0.29	17	-11.27	13
AM921940	D'	orphan		no annotated D' box					CD_41
	D	orphan		18S-849	1.21	38	-17.64	11-Sor
AM921941	D'	orphan		18S-630	1.36	89	-17.27	3..6	CD_24
	D	orphan		18S-1478	0.40	40	-9.73	Deb,11
AM921942	D'	orphan		18S-95	0.63	32	-20.45	8-(12,13)	CD_37
	D	orphan		18S-456	1.71	88	-21.52	3,8
AM921944	D'	orphan		18S-1083	1.57	86	-18.64	6	CD_49
	D	orphan		25S-3941	0.07	5	-14.14	Sor
AM921945	D'	orphan		25S-3836	0.86	52	-23.03	4,6	CD_26
	D	orphan		25S-3941	0.23	25	-15.34	10

Conservation of target interactions: 1) Fungi 2) Microsporidia 3) Mucoromycotina 4) Chytridiomycota 5) Blastocladiomycota 6) Dikarya 7) Basidiomycota 8) Asomycota 9) Taphrinomycotina 10) Saccharomycotina 11) Pezizomycotina 12) Dothideomycetes 13) Eurotiomycetes 14) Leotiomycetes 15) Sordariomycetes Deb) Debaryomycetaceae Met) Metschnikowiaceae Sacch) Saccharomyc- etaceae Can) Candida Cap) Capnodiales Asp) Aspergillus Nfi N.fischeri Ony) Onygenales Hel) HelotiaceaeSor) Sordariales Neu) Neurospora 3..6) equals 3,4,5,6 6-15) equals 6 without 15