**Table S22:** Summary of box H/ACA snoRNAs that were originally denoted as orphan. Sequences were taken from *Neurospora crassa* (Nc_HACA xy) [Liu *et al.*], *Aspergillus fumigatus* (AM921943) [Jöchl *et al.*], and *Schizosaccharomyces pombe* (AJ6320xy) [Li *et al.*]. * Families containing a budding yeast sequence with an experimentally verified target.
original name	number of sequences	hairpin	`snoStrip prediction`	single sequence position	ICI_sno	numver of interactions	mean mfe	conservation	`snoStrip` name
Nc_HACA_7	56	HP1	U4-10	U4-8	0.11	6	-32.04	Pen,Mag,Cha	HACA_7
Nc_HACA_7	56	HP2	25S-3500	25S-2314	1.26	33	-31.30	13,14,15	HACA_7
Nc_HACA_10	3	HP1	U2-54	U2-31	1.02	3	-55.75	Neu	HACA_10
Nc_HACA_10	3	HP2	U6-110	U6-103	1.11	3	-29.85	Neu	HACA_10
Nc_HACA_11	85	HP1	25S-3610	25S-2416	0.56	29	-31.28	10,11	HACA_11*
Nc_HACA_11	85	HP2	U4-66	U4-60	0.15	11	-24.33	13	HACA_11*
Nc_HACA_12	97	cleavage associated snoRNA, S.cerevisiae sce snR30							HACA_12*
Nc_HACA_13	131	HP1	25S-4073	25S-2854	0.34	26	-33.20	3,6-(10,15)	HACA_13*
Nc_HACA_13	131	HP2	U4-46	U4-41	0.37	41	-33.98	10,11-12	HACA_13*
Nc_HACA_16	3	HP1	5.8S-18	5.8S-17	1.04	3	-25.91	-	HACA_16
Nc_HACA_16	3	HP2	25S-2700	25S-1622	1.14	2	-14.8	-	HACA_16
AM921943	101	HP1	5.8S-57	5.8S-54	0.53	36	-27.32	11	HACA_21*
AM921943	101	HP2	25S-3374	25S-2191	1.12	59	-30.75	10,11	HACA_21*
AJ632012	10	HP1	18S-228	18S-207	0.33	3	-38.79	-	HACA_54
AJ632012	10	HP2	25S-3439	25S-2254	1.22	9	-35.36	Schiz,Can,Deb	HACA_54
AJ632013	4	HP1	U2-54	U2-31	0.55	2	-37.51	-	HACA_55
AJ632013	4	HP2	U1-150	U1-135	0.52	2	-25.44	-	HACA_55
AJ632014	1	HP1	25S-290	-	0	1	-29.59	-	HACA_56
AJ632014	1	HP2	-	-	-	-	-	-	HACA_56
AJ632015	1	HP1	25S-1114	25S-329	0.00	1	-15.66	-	HACA_45
AJ632015	1	HP2	25S-1949	25S-955	0.00	1	-7.04	-	HACA_45
AJ632016	68	HP1	U6-79	U6-74	0.12	8	-31.95	13	HACA_53
AJ632016	68	HP2	18S-1302	18S-1175	0.82	45	-43.49	9,11	HACA_53
AJ632017	7	HP1	18S-393	18S-351	0.00	1	-17.98	-	HACA_51
AJ632017	7	HP2	18S-400	18S-358	0.48	2	-26.09	-	HACA_51
AJ632018	95	HP1	25S-1962	25S-966	1.17	62	-31.85	8	HACA_9*
AJ632018	95	HP2	25S-3654	25S-2460	0.16	10	-33.82	-	HACA_9*
AJ632019	1	HP1	18S-651	18S-598	0.00	1	-22.42	-	HACA_49
AJ632019	1	HP2	25S-3930	25S-2713	0.00	1	-26.45	-	HACA_49

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 Schiz) Schizosaccharomyces Can) Candida Pen) Penicillium Mag) Magnaporthales Cha) Chaetomiaceae Neu) Neurospora 3..6) equals 3,4,5,6 6-15) equals 6 without 15