| Hoxa3 | P02831 | Mir3079-201 | ENSMUST00000175428 | 90 nt | BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm44469-201 | ENSMUST00000198558 | 79 nt | BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Traj49-202 | ENSMUST00000199452 | 62 nt | APPRIS P1 BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm44602-201 | ENSMUST00000205948 | 132 nt | BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm25899-201 | ENSMUST00000082672 | 141 nt | BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Fam46d-201 | ENSMUST00000101292 | 2995 nt | APPRIS P1 TSL 1 (best) BASIC | 1.01 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm24342-201 | ENSMUST00000103907 | 104 nt | BASIC | 1 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm38323-201 | ENSMUST00000192450 | 210 nt | BASIC | 1 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Mir30a-201 | ENSMUST00000083471 | 71 nt | BASIC | 1 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm24252-201 | ENSMUST00000083700 | 132 nt | BASIC | 1 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm14884-201 | ENSMUST00000120456 | 196 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm22485-201 | ENSMUST00000157990 | 109 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm23340-201 | ENSMUST00000158955 | 123 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm26158-201 | ENSMUST00000158973 | 119 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm27974-201 | ENSMUST00000183415 | 105 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm27993-201 | ENSMUST00000184362 | 85 nt | BASIC | 0.99 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm11694-201 | ENSMUST00000118637 | 159 nt | BASIC | 0.98 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm22466-201 | ENSMUST00000175278 | 69 nt | BASIC | 0.98 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Mir344-201 | ENSMUST00000083634 | 95 nt | BASIC | 0.98 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Snora2b-201 | ENSMUST00000084005 | 137 nt | BASIC | 0.98 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm37824-201 | ENSMUST00000193430 | 3236 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Snord69-201 | ENSMUST00000104024 | 80 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm22544-201 | ENSMUST00000104349 | 127 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Mir1904-201 | ENSMUST00000122702 | 80 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm24549-201 | ENSMUST00000158647 | 139 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm42533-201 | ENSMUST00000196247 | 157 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | AC116319.1-201 | ENSMUST00000227765 | 222 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Mir196b-201 | ENSMUST00000083509 | 85 nt | BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Zfp654-201 | ENSMUST00000052588 | 4741 nt | APPRIS P3 TSL 1 (best) BASIC | 0.97 | □□□□□ -2.25 | | |
| Hoxa3 | P02831 | Gm22786-201 | ENSMUST00000104086 | 122 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23482-201 | ENSMUST00000104172 | 122 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25496-201 | ENSMUST00000104430 | 120 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm22565-201 | ENSMUST00000175540 | 69 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir7091-201 | ENSMUST00000184075 | 79 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir6985-201 | ENSMUST00000184641 | 61 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23301-201 | ENSMUST00000082713 | 65 nt | BASIC | 0.96 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Tex15-201 | ENSMUST00000009772 | 8405 nt | APPRIS P1 TSL 1 (best) BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm6272-201 | ENSMUST00000121256 | 171 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm22706-201 | ENSMUST00000157907 | 112 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25768-201 | ENSMUST00000158570 | 98 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm26363-201 | ENSMUST00000158866 | 83 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23917-201 | ENSMUST00000175256 | 98 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25693-201 | ENSMUST00000175443 | 85 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm42506-201 | ENSMUST00000202009 | 150 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm45197-201 | ENSMUST00000205288 | 151 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | AC160962.3-201 | ENSMUST00000225914 | 112 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm22980-201 | ENSMUST00000082608 | 70 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm26062-201 | ENSMUST00000083379 | 107 nt | BASIC | 0.95 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23661-201 | ENSMUST00000122630 | 87 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm24290-201 | ENSMUST00000157634 | 96 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm24942-201 | ENSMUST00000158328 | 114 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25600-201 | ENSMUST00000158357 | 106 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm24129-201 | ENSMUST00000158537 | 97 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25618-201 | ENSMUST00000179484 | 107 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23344-201 | ENSMUST00000083818 | 68 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25629-201 | ENSMUST00000084001 | 107 nt | BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Vmn1r75-202 | ENSMUST00000226622 | 6638 nt | APPRIS P2 BASIC | 0.94 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | B230307C23Rik-201 | ENSMUST00000113729 | 192 nt | TSL 5 BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm26253-201 | ENSMUST00000122493 | 103 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm26089-201 | ENSMUST00000157898 | 107 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir15a-201 | ENSMUST00000175266 | 84 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | AC160550.1-201 | ENSMUST00000228659 | 181 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir219a-2-201 | ENSMUST00000083551 | 97 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm26109-201 | ENSMUST00000083970 | 70 nt | BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Olfr805-203 | ENSMUST00000216794 | 3199 nt | APPRIS P1 TSL 5 BASIC | 0.93 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Olfr832-202 | ENSMUST00000218385 | 4435 nt | APPRIS P1 TSL 5 BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm22030-201 | ENSMUST00000116942 | 63 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23853-201 | ENSMUST00000158375 | 104 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25014-201 | ENSMUST00000158401 | 103 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25715-201 | ENSMUST00000158627 | 125 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Scarna3a-201 | ENSMUST00000158911 | 140 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | BC050972-201 | ENSMUST00000168475 | 526 nt | TSL 3 BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm27419-201 | ENSMUST00000184576 | 109 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm44458-201 | ENSMUST00000196594 | 143 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm42891-201 | ENSMUST00000199340 | 281 nt | TSL 5 BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm24527-201 | ENSMUST00000082920 | 107 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Olfr1100-202 | ENSMUST00000117211 | 2937 nt | APPRIS P1 TSL 5 BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Zfp813-ps-201 | ENSMUST00000186652 | 2506 nt | BASIC | 0.92 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir450b-201 | ENSMUST00000102095 | 82 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23900-201 | ENSMUST00000157569 | 108 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Mir7663-201 | ENSMUST00000183950 | 61 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | AC140930.2-201 | ENSMUST00000221803 | 109 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25635-201 | ENSMUST00000082675 | 131 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm25337-201 | ENSMUST00000083723 | 104 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm23347-201 | ENSMUST00000083823 | 82 nt | BASIC | 0.91 | □□□□□ -2.26 | | |
| Hoxa3 | P02831 | Gm24777-201 | ENSMUST00000157644 | 107 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm24399-201 | ENSMUST00000157869 | 74 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Mir100-201 | ENSMUST00000175270 | 80 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Mir6381-201 | ENSMUST00000183426 | 87 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm26202-201 | ENSMUST00000082910 | 65 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm24099-201 | ENSMUST00000083384 | 107 nt | BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Olfr307-203 | ENSMUST00000217494 | 4515 nt | APPRIS P1 TSL 5 BASIC | 0.9 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm25393-201 | ENSMUST00000157336 | 285 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm26133-201 | ENSMUST00000157363 | 100 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm24009-201 | ENSMUST00000157734 | 93 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm21954-201 | ENSMUST00000179544 | 51 nt | APPRIS P1 TSL 5 BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm44211-201 | ENSMUST00000204867 | 145 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | mt-Tn-201 | ENSMUST00000082399 | 71 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm23244-201 | ENSMUST00000083375 | 92 nt | BASIC | 0.89 | □□□□□ -2.27 | | |
| Hoxa3 | P02831 | Gm5581-201 | ENSMUST00000072940 | 2550 nt | BASIC | 0.88 | □□□□□ -2.27 | | |