1. Supplemental Figures S1-S10 Emanuelsson et al.

2. Figure S1a Number of nts in TARs (placenta) Emanuelsson et al. TAR Generation Threshold (percentile) Number of Nucleotides in TARs

3. Figure S1b Number of nts in TARs (NB4) Emanuelsson et al. TAR Generation Threshold (percentile) Number of Nucleotides in TARs

4. Figure S2a Assessing the performance of different MAS scoring schemes – placenta Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

5. Figure S2b Assessing the performance of different MAS scoring schemes – NB4 Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

6. Figure S3 PPV vs. sensitivity for MAS-N and Affy NB4 data, varying the segmentation threshold from 70 th to 99 th Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

7. Figure S4a sens/PPV vs Gencode; placenta MAS stranded Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

8. Figure S4b sens/PPV vs Gencode; placenta MAS strands merged Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

9. Figure S5a sens/PPV vs Gencode; NB4 MAS stranded Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

10. Figure S5b sens/PPV vs Gencode; NB4 MAS strands merged Emanuelsson et al. sensitivity=tp/(tp+fn) ppv=tp/(tp+fp)

11. Figure S6a Length distribution (percentage) of TARs length (nt) Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Emanuelsson et al.

12. Figure S6b Distribution of number of probes per TAR number of probes number of TARs < Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Emanuelsson et al.

13. Figure S7a Distribution of Exon and Intron Median Scores Placenta MAS-B (red=intron, blue=exon)

14. Figure S7b Distribution of Exon and Intron Median Scores Placenta MAS-N (red=intron, blue=exon)

15. Figure S7c Distribution of Exon and Intron Median Scores Placenta Affy (red=intron, blue=exon)

16. Figure S7d Distribution of Exon and Intron Median Scores NB4 MAS-N (red=intron, blue=exon)

17. Figure S7e Distribution of Exon and Intron Median Scores NB4 Affy (red=intron, blue=exon)

18. 265 67 325 240 108 128 207 701629 684 47 38 175 52 71 85 38 222369 245 33 25 135 32 48 53 26 143262 160 18 22 111 19 42 48 13 106223 121 Figure S8a I III IV II [Total][Exon ovlp] [Conserved region ovlp][Exon and conserved region ovlp] Placenta (MAS and Affy) Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Emanuelsson et al. Overlap of TAR sets (kbp)

19. 455 177 452 632629 Figure S8b 105 86 178 190263 65 58 145 125205 41 50 110 91160 I [Total] III [Exon ovlp] II [Conserved region ovlp] IV [Exon and conserved region ovlp] NB4 (MAS and Affy) Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Overlap of TAR sets (kbp)

20. 104 228 51 64 57 305 267 632 684 28 57 13 32 15 105 94 222190 245 19 44 9 20 14 65 63 143125 160 14 26 6 17 10 50 47 10791 121 Figure S8c 701 I [Total] III [Exon ovlp] II [Conserved region ovlp] IV [Exon and conserved region ovlp] MAS (placenta and NB4) Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Overlap of TAR sets (kbp)

21. 296 333 296 629 Figure S8d 157 212 51 369263 103 159 45 262205 85 138 22 223160 I [Total] III [Exon ovlp] II [Conserved region ovlp] IV [Exon and conserved region ovlp] Affy (placenta and NB4) Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Overlap of TAR sets (kbp)

22. Figure S9a number of exons covered by TAR fraction of exon length covered Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy

23. Figure S9b fraction of exon length covered percentage of 5' exons covered by TAR Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy

24. Figure S9c percentage of 3' exons covered by TAR fraction of exon length covered Emanuelsson et al. Placenta MAS-N Placenta MAS-B Placenta Affy NB4 MAS-N NB4 Affy

25. Figure S10a fraction of TAR length covered percentage of genic and intergenic TARs covered by conserved elements MAS genic TARs MAS intergenic TARs Affymetrix genic TARs Affymetrix intergenic TARs 0- 0.10 0.90- 1.00 80 70 60 50 40 30 20 10 0 90 0.30- 0.40 0.60- 0.70 Placenta Emanuelsson et al.

26. Figure S10b percentage of genic and intergenic TARs covered by conserved elements fraction of TAR length covered MAS genic TARs MAS intergenic TARs Affymetrix genic TARs Affymetrix intergenic TARs 0- 0.10 0.30- 0.40 0.90- 1.00 80 70 60 50 40 30 20 10 0 90 0.60- 0.70 NB4 Emanuelsson et al.