| Hoxa3 | P02831 | Gm25663-201 | ENSMUST00000157698 | 135 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23267-201 | ENSMUST00000178490 | 132 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23714-201 | ENSMUST00000179259 | 105 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm16976-205 | ENSMUST00000227324 | 226 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Hspe1-ps2-201 | ENSMUST00000051437 | 312 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24410-201 | ENSMUST00000083433 | 107 nt | BASIC | 1.38 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25089-201 | ENSMUST00000102015 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23907-201 | ENSMUST00000104595 | 189 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm14923-201 | ENSMUST00000118270 | 155 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25840-201 | ENSMUST00000177821 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24952-201 | ENSMUST00000177909 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23682-201 | ENSMUST00000178146 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24652-201 | ENSMUST00000178223 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22629-201 | ENSMUST00000178272 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24021-201 | ENSMUST00000178435 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22274-201 | ENSMUST00000178441 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22050-201 | ENSMUST00000178442 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23688-201 | ENSMUST00000178502 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23944-201 | ENSMUST00000178607 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm26283-201 | ENSMUST00000178625 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25452-201 | ENSMUST00000178776 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23286-201 | ENSMUST00000178963 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22640-201 | ENSMUST00000179035 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25984-201 | ENSMUST00000179129 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25585-201 | ENSMUST00000179469 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm26374-201 | ENSMUST00000179737 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24040-201 | ENSMUST00000179786 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25017-201 | ENSMUST00000179805 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm23618-201 | ENSMUST00000179912 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm26284-201 | ENSMUST00000180107 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24570-201 | ENSMUST00000180314 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24654-201 | ENSMUST00000180315 | 79 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm28862-201 | ENSMUST00000188246 | 163 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | CT025689.3-201 | ENSMUST00000223817 | 301 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | AC136457.1-201 | ENSMUST00000224195 | 156 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24494-201 | ENSMUST00000083804 | 81 nt | BASIC | 1.37 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm25610-201 | ENSMUST00000104016 | 129 nt | BASIC | 1.36 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22149-201 | ENSMUST00000104442 | 136 nt | BASIC | 1.36 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24262-201 | ENSMUST00000157431 | 144 nt | BASIC | 1.36 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24222-201 | ENSMUST00000158834 | 93 nt | BASIC | 1.36 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm16307-201 | ENSMUST00000161269 | 210 nt | BASIC | 1.36 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm26080-201 | ENSMUST00000104069 | 131 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm24913-201 | ENSMUST00000157286 | 107 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22665-201 | ENSMUST00000158720 | 275 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Mir6351-201 | ENSMUST00000183826 | 99 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm27365-201 | ENSMUST00000184041 | 177 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | CT485608.2-201 | ENSMUST00000227210 | 291 nt | BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Zfp960-201 | ENSMUST00000127027 | 2667 nt | APPRIS P1 TSL 1 (best) BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Vmn1r78-203 | ENSMUST00000228664 | 8100 nt | APPRIS P1 BASIC | 1.35 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm12086-201 | ENSMUST00000120863 | 228 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm22164-201 | ENSMUST00000158413 | 106 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm16550-201 | ENSMUST00000162550 | 126 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm27265-201 | ENSMUST00000183559 | 77 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Gm28383-201 | ENSMUST00000187563 | 139 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | AL928567.1-201 | ENSMUST00000197891 | 138 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | AC126939.1-201 | ENSMUST00000224943 | 226 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Mir320-201 | ENSMUST00000083594 | 82 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Mir92-2-201 | ENSMUST00000083679 | 91 nt | BASIC | 1.34 | □□□□□ -2.19 | | |
| Hoxa3 | P02831 | Arhgap5-201 | ENSMUST00000110725 | 5197 nt | APPRIS P1 TSL 1 (best) BASIC | 1.34 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm22785-201 | ENSMUST00000104087 | 132 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm22196-201 | ENSMUST00000116865 | 109 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm23838-201 | ENSMUST00000158067 | 162 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25831-201 | ENSMUST00000158924 | 163 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Mir7241-201 | ENSMUST00000184532 | 64 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm35309-201 | ENSMUST00000208337 | 478 nt | TSL 3 BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | AC122769.2-201 | ENSMUST00000227248 | 302 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | mt-Ts2-201 | ENSMUST00000082416 | 59 nt | BASIC | 1.33 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm23060-201 | ENSMUST00000102345 | 109 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25541-201 | ENSMUST00000116888 | 126 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24379-201 | ENSMUST00000122695 | 86 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm23763-201 | ENSMUST00000158345 | 60 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm27248-201 | ENSMUST00000184004 | 166 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm37330-201 | ENSMUST00000192606 | 153 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | 1700112D23Rik-202 | ENSMUST00000193387 | 299 nt | TSL 2 BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm44962-201 | ENSMUST00000206460 | 279 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25815-201 | ENSMUST00000082755 | 107 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm26456-201 | ENSMUST00000082831 | 111 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24406-201 | ENSMUST00000083026 | 128 nt | BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Olfr1431-202 | ENSMUST00000213759 | 3001 nt | APPRIS P1 TSL 5 BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Vmn1r75-203 | ENSMUST00000226855 | 6548 nt | APPRIS P2 BASIC | 1.32 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Mir653-201 | ENSMUST00000102402 | 85 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25879-201 | ENSMUST00000104330 | 107 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24482-201 | ENSMUST00000117005 | 93 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm14882-201 | ENSMUST00000117216 | 218 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm12013-201 | ENSMUST00000121971 | 155 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24509-201 | ENSMUST00000157086 | 101 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25358-201 | ENSMUST00000157189 | 101 nt | BASIC | 1.31 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24894-201 | ENSMUST00000122744 | 118 nt | BASIC | 1.3 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24902-201 | ENSMUST00000158126 | 123 nt | BASIC | 1.3 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm23967-201 | ENSMUST00000175062 | 78 nt | BASIC | 1.3 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm22809-201 | ENSMUST00000082743 | 156 nt | BASIC | 1.3 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Snord96a-201 | ENSMUST00000082791 | 81 nt | BASIC | 1.3 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm22003-201 | ENSMUST00000101885 | 107 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm15115-201 | ENSMUST00000121145 | 264 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm15654-201 | ENSMUST00000152660 | 300 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm25329-201 | ENSMUST00000158041 | 126 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm24174-201 | ENSMUST00000158933 | 111 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm26498-201 | ENSMUST00000177799 | 79 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm22756-201 | ENSMUST00000180118 | 107 nt | BASIC | 1.29 | □□□□□ -2.2 | | |
| Hoxa3 | P02831 | Gm26230-201 | ENSMUST00000180141 | 79 nt | BASIC | 1.29 | □□□□□ -2.2 | | |