Table S3.

Probe sets used in this study

Oligonucleotide name	Probe set 1	Probe set 2	Probe set 3	Probe set 4	Probe set 5	Probe set 6	Probe set 7
Eub338	Eub338-Rhodamine Red X	Eub338-Atto 655 dual	Eub338-Alexa 647		Eub338-Atto 655 dual	Eub338-Pacific Blue
Cor633	Cor633-Alexa 488	Cor633-Alexa 488	Cor633-Alexa 610	Cor633-Alexa 647	Cor633-Alexa 488	Cor633-Alexa 610
Str405		Str405-Alexa 514	Str405-Rhodamine Red X	Str405-Alexa 514	Str405-Alexa 514		Str405-Alexa 514
Pg1160		Pg1160-Dy485 XL	Pg1160-Alexa 555	Pg1160-Rhodamine Red X	Pg1160-Texas Red X
Pas111		Pas111-Alexa 555	Pas111-Alexa 488	Pas111-Alexa 488	Pas111-Alexa 555		Pas111-Dy615
Nei1030		Nei1030-Rhodamine Red X			Nei1030-Rhodamine Red X		Nei1030-Atto 633 dual
Cap371		Cap371-Texas Red X					Cap371-Texas Red X
Act476		Act476-Atto 594 dual			Act476-Atto 594 dual	Act476-Alexa 488
Fus714		Fus714-Atto 620 dual	Fus714-Alexa 514		Fus714-Atto 620 dual
Lep568		Lep568-Atto 647N dual			Lep568-Atto 647N dual
Cmat175						Cmat175-Alexa 514
Act692						Act690-Alexa 555
Cor595						Cor595-Rhodamine Red X
Act381						Act382-Alexa 594
Rot491						Rot491-Alexa 647	Rot491-Rhodamine Red X
Prv392							Prv392-Alexa 488
Vei488							Vei488-Alexa 555
Lmir444							Lmir444-Atto 655 dual

For each set, the table lists the probes used (oligonucleotide and fluorophore). Dual indicates that the probe was labeled with the same fluorophore at both 3′ and 5′ ends; if dual is not specified, the probe was labeled only at the 5′ end. Probe set 1 is shown in Fig. 2. Probe set 2 is shown in Figs. 3, 4C, and 5, Upper and Figs. S1 and S2A. Probe set 3 is shown in Fig. 4A and Fig. S2C. Probe set 4 is shown in Fig. 4 B and C. Probe set 5 is shown in Figs. 5, Lower and 6 and Figs. S2B and S4. Probe set 6 is shown in Fig. 7 and Fig. S3. Probe set 7 is shown in Fig. 8.