| ORF | Name | MIPS complex | Total overlap | Fraction overlap |
| YDR296W | MHR1 | 500.60.10 | 44 | 1.00000 |
| YGR129W | SYF2 | 440.30.10 | 42 | 1.00000 |
| YLR117C | CLF1 | 440.30.10 | 42 | 1.00000 |
| YKL173W | SNU114 | 440.30.10 | 42 | 1.00000 |
| YER029C | SMB1 | 440.30.10 | 42 | 1.00000 |
| YMR240C | CUS1 | 440.30.10 | 42 | 1.00000 |
| YJR050W | ISY1 | 440.30.10 | 42 | 1.00000 |
| YGL127C | SOH1 | 510.40.20 | 21 | 1.00000 |
| YBR102C | EXO84 | 160 | 7 | 1.00000 |
| YGL075C | MPS2 | 270.20.40 | 4 | 1.00000 |
| YKL173W | SNU114 | 440.30.10.10 | 3 | 1.00000 |
| YER029C | SMB1 | 440.30.10.10 | 3 | 1.00000 |
| YLR117C | CLF1 | 440.30.10.10 | 3 | 1.00000 |
| YJR050W | ISY1 | 440.30.10.10 | 3 | 1.00000 |
| YFL017W-A | SMX2 | 440.30.10.10 | 3 | 1.00000 |
| YMR240C | CUS1 | 440.30.10.10 | 3 | 1.00000 |
| YGR129W | SYF2 | 440.30.10.10 | 3 | 1.00000 |
| YER029C | SMB1 | 440.30.10.20 | 2 | 1.00000 |
| YLR117C | CLF1 | 440.30.10.20 | 2 | 1.00000 |
| YMR240C | CUS1 | 440.30.10.20 | 2 | 1.00000 |
| YKL173W | SNU114 | 440.30.10.20 | 2 | 1.00000 |
| YJR050W | ISY1 | 440.30.10.20 | 2 | 1.00000 |
| YBR119W | MUD1 | 440.30.10.20 | 2 | 1.00000 |
| YGR129W | SYF2 | 440.30.10.20 | 2 | 1.00000 |
| YFL017W-A | SMX2 | 440.30.10 | 41 | 0.97619 |
| YMR213W | CEF1 | 440.30.10 | 40 | 0.95238 |
| YPR070W | MED1 | 510.40.20 | 20 | 0.95238 |
| YDR036C | EHD3 | 500.60.20 | 29 | 0.93548 |
| YIL070C | MAM33 | 500.60.20 | 29 | 0.93548 |
| YDR416W | SYF1 | 440.30.10 | 39 | 0.92857 |
| YMR288W | HSH155 | 440.30.10 | 39 | 0.92857 |
| YHR086W | NAM8 | 440.30.10 | 39 | 0.92857 |
| YBR119W | MUD1 | 440.30.10 | 39 | 0.92857 |
| YOR308C | SNU66 | 440.30.10 | 39 | 0.92857 |
| YLR424W | SPP382 | 440.30.10 | 38 | 0.90476 |
| YNR036C | YNR036C | 500.60.20 | 28 | 0.90323 |
| YGR013W | SNU71 | 440.30.10 | 37 | 0.88095 |
| YDR235W | PRP42 | 440.30.10 | 37 | 0.88095 |
| YDL087C | LUC7 | 440.30.10 | 37 | 0.88095 |
| YLR275W | SMD2 | 440.30.10 | 37 | 0.88095 |
| YOR095C | RKI1 | 500.40.20 | 50 | 0.87719 |
| YBR065C | ECM2 | 440.30.10 | 36 | 0.85714 |
| YPR182W | SMX3 | 440.30.10 | 36 | 0.85714 |
| YML114C | TAF8 | 510.70.20 | 10 | 0.83333 |
| YMR223W | UBP8 | 510.190.10.10 | 5 | 0.83333 |
| YMR223W | UBP8 | 230.20.10 | 5 | 0.83333 |
| YOR095C | RKI1 | 500.40000 | 114 | 0.82609 |
| YAL032C | PRP45 | 440.30.10 | 34 | 0.80952 |
| YDL098C | SNU23 | 440.30.10 | 34 | 0.80952 |
| YDR296W | MHR1 | 500.60000 | 61 | 0.80263 |
| YLR074C | BUD20 | 500.40.10 | 65 | 0.80247 |
| YOR095C | RKI1 | 500.40.10 | 64 | 0.79012 |
| YPR131C | NAT3 | 500.40.20 | 45 | 0.78947 |
| YLR438C-A | LSM3 | 440.30.10 | 33 | 0.78571 |
| YPL151C | PRP46 | 440.30.10 | 33 | 0.78571 |
| YPR131C | NAT3 | 500.40000 | 108 | 0.78261 |
| YPR131C | NAT3 | 500.40.10 | 63 | 0.77778 |
| YML114C | TAF8 | 510.70000 | 10 | 0.76923 |
| YDL060W | TSR1 | 500.40.10 | 62 | 0.76543 |
| YCR063W | BUD31 | 440.30.10 | 32 | 0.76190 |
| YDL060W | TSR1 | 500.40000 | 105 | 0.76087 |
| YDL060W | TSR1 | 500.40.20 | 43 | 0.75439 |
| YJR112W | NNF1 | 270.20.40 | 3 | 0.75000 |
| YAL034W-A | MTW1 | 270.20.40 | 3 | 0.75000 |
| YPR082C | DIB1 | 440.30.10 | 31 | 0.73810 |
| YLR074C | BUD20 | 500.40000 | 99 | 0.71739 |
| YBR119W | MUD1 | 440.30.10.10 | 2 | 0.66667 |
| YMR213W | CEF1 | 440.30.10.10 | 2 | 0.66667 |
| YPR082C | DIB1 | 440.30.10.10 | 2 | 0.66667 |
| YMR223W | UBP8 | 510.190.10.20.10 | 10 | 0.62500 |
| YMR223W | UBP8 | 510.190.10.20 | 10 | 0.62500 |
| YGL075C | MPS2 | 480.10000 | 10 | 0.62500 |
| YMR223W | UBP8 | 510.190.10 | 10 | 0.62500 |
| YMR223W | UBP8 | 230.20.20 | 10 | 0.62500 |
| YDR240C | SNU56 | 440.30.10 | 26 | 0.61905 |
| YJL011C | RPC17 | 510.12000 | 8 | 0.61538 |
| YGL127C | SOH1 | 510.40000 | 21 | 0.60000 |
| YLR074C | BUD20 | 500.40.20 | 34 | 0.59649 |
| YMR223W | UBP8 | 230.20000 | 10 | 0.58824 |
| YML049C | RSE1 | 440.30.10 | 24 | 0.57143 |
| YPR070W | MED1 | 510.40000 | 20 | 0.57143 |
| YLR117C | CLF1 | 440.30000 | 44 | 0.55000 |
| YGR129W | SYF2 | 440.30000 | 44 | 0.55000 |
| YKL173W | SNU114 | 440.30000 | 44 | 0.55000 |
| YDR296W | MHR1 | 500.60.20 | 17 | 0.54839 |
| YBL026W | LSM2 | 440.30.10 | 23 | 0.54762 |
| YJR050W | ISY1 | 440.30000 | 43 | 0.53750 |
| YER029C | SMB1 | 440.30000 | 43 | 0.53750 |
| YMR240C | CUS1 | 440.30000 | 43 | 0.53750 |
| YIL070C | MAM33 | 500.60000 | 40 | 0.52632 |
| YMR223W | UBP8 | 230 | 10 | 0.52632 |
| YFL017W-A | SMX2 | 440.30000 | 42 | 0.52500 |
| YPL199C | YPL199C | 500.40.10 | 42 | 0.51852 |
| YMR213W | CEF1 | 440.30000 | 41 | 0.51250 |
| YPL199C | YPL199C | 500.40000 | 70 | 0.50725 |
| YDR416W | SYF1 | 440.30000 | 40 | 0.50000 |
| YBR119W | MUD1 | 440.30000 | 40 | 0.50000 |
| YHR086W | NAM8 | 440.30000 | 40 | 0.50000 |
| YMR288W | HSH155 | 440.30000 | 40 | 0.50000 |
| YOR308C | SNU66 | 440.30000 | 40 | 0.50000 |
| YIR009W | MSL1 | 440.30.10 | 21 | 0.50000 |
| YML114C | TAF8 | 510.190.10 | 8 | 0.50000 |
| YML114C | TAF8 | 510.190.10.20 | 8 | 0.50000 |
| YML114C | TAF8 | 510.190.10.20.10 | 8 | 0.50000 |
| YML114C | TAF8 | 230.20.20 | 8 | 0.50000 |
| YGL225W | VRG4 | 260.30.10 | 4 | 0.50000 |
| YPR070W | MED1 | 230.20.10 | 3 | 0.50000 |
| YPL047W | SGF11 | 230.20.10 | 3 | 0.50000 |
| YPR070W | MED1 | 510.190.10.10 | 3 | 0.50000 |
| YPL047W | SGF11 | 510.190.10.10 | 3 | 0.50000 |
| YPL269W | KAR9 | 270.20.40 | 2 | 0.50000 |
| YOR195W | SLK19 | 270.20.40 | 2 | 0.50000 |