| RED | =100 % Complementary sequence |
| . | =Identical residue |
| blue alphabets | =mismatch |
| _ | =Gap |
| Acc number | miRNA | Start | Alignment | End | % Identity |
| Query | 1 | cctccgga | 8 | ||
| MIMAT0017775 | esi-miR3459-5p | 8 | ........ | 1 | 100 |
| MIMAT0017775 | esi-miR3459-5p | 1 | __...... | 6 | 75 |
| MIMAT0026552 | hcmv-miR-UL112-5p | 1 | ........ | 8 | 100 |
| MIMAT0026552 | hcmv-miR-UL112-5p | 8 | __...... | 3 | 75 |
| MIMAT0030107 | bdi-miR5181c-5p | 1 | ......._ | 7 | 87 |
| MIMAT0025828 | gga-miR-6557-5p | 7 | ......._ | 1 | 87 |
| MIMAT0017749 | esi-miR3466-5p | 8 | _....... | 2 | 87 |
| MIMAT0017749 | esi-miR3466-5p | 2 | __...... | 7 | 75 |
| MIMAT0035753 | bfv-miR-BF1-5p | 8 | ......a. | 1 | 87 |
| MIMAT0037042 | ssc-miR-9824-5p | 8 | ......__ | 3 | 75 |
| MIMAT0035538 | bdi-miR5174f | 1 | ......__ | 6 | 75 |
| MIMAT0035104 | efu-miR-9340 | 6 | __...... | 1 | 75 |
| MIMAT0035104 | efu-miR-9340 | 1 | __...... | 6 | 75 |
| MIMAT0031711 | bbe-miR-4904-5p | 8 | _......_ | 3 | 75 |
| MIMAT0030105 | bdi-miR5174d-5p | 3 | ......__ | 8 | 75 |
| MIMAT0030103 | bdi-miR5174c-5p | 3 | ......__ | 8 | 75 |
| MIMAT0029854 | mmu-miR-3569-5p | 7 | ......__ | 2 | 75 |
| MIMAT0028292 | mml-miR-7176-5p | 8 | _......_ | 3 | 75 |
| MIMAT0025566 | bta-miR-6530 | 8 | ......__ | 3 | 75 |
| MIMAT0025341 | pde-miR949b | 2 | _......_ | 7 | 75 |
| MIMAT0024877 | osa-miR6254 | 3 | _......_ | 8 | 75 |
| MIMAT0022108 | pti-miR5475 | 7 | ......__ | 2 | 75 |
| MIMAT0020499 | bfl-miR-4904-5p | 8 | _......_ | 3 | 75 |
| MIMAT0019032 | hsa-miR-4497 | 1 | _......_ | 6 | 75 |
| MIMAT0017982 | hsa-miR-3605-3p | 1 | ......__ | 6 | 75 |
| MIMAT0016297 | sja-miR-3488 | 2 | _......_ | 7 | 75 |
| MIMAT0016091 | ppy-miR-658 | 8 | ......__ | 3 | 75 |
| MIMAT0015935 | ppy-miR-510 | 3 | _......_ | 8 | 75 |
| MIMAT0015576 | bmo-miR-3382-3p | 3 | ......__ | 8 | 75 |
| MIMAT0014707 | hsv2-miR-H24 | 1 | _......_ | 6 | 75 |
| MIMAT0015376 | hsv2-miR-H9-5p | 8 | ......__ | 3 | 75 |
| MIMAT0013966 | bhv1-miR-B5 | 8 | ......__ | 3 | 75 |
| MIMAT0012714 | hvt-miR-H4-5p | 8 | ......__ | 3 | 75 |
| MIMAT0011837 | bta-miR-2316 | 2 | _......_ | 7 | 75 |
| MIMAT0010033 | mtr-miR1510a-3p | 6 | ......__ | 1 | 75 |
| MIMAT0009829 | nve-miR-2051-3p | 8 | _......_ | 3 | 75 |
| MIMAT0009362 | bta-miR-658 | 8 | ......__ | 3 | 75 |
| MIMAT0008307 | ptr-miR-658 | 8 | ......__ | 3 | 75 |
| MIMAT0007957 | ptr-miR-1203 | 7 | _......_ | 2 | 75 |
| MIMAT0007348 | hsa-miR-1470 | 3 | ......__ | 8 | 75 |
| MIMAT0005783 | pbi-miR-510 | 3 | _......_ | 8 | 75 |
| MIMAT0005766 | mml-miR-510-5p | 3 | _......_ | 8 | 75 |
| MIMAT0005757 | ssy-miR-510 | 3 | _......_ | 8 | 75 |
| MIMAT0005866 | hsa-miR-1203 | 7 | _......_ | 2 | 75 |
| MIMAT0005365 | tae-miR1130a | 1 | ......__ | 6 | 75 |
| MIMAT0005048 | ppt-miR166l | 6 | __...... | 1 | 75 |
| MIMAT0005048 | ppt-miR166l | 1 | __...... | 6 | 75 |
| MIMAT0005047 | ppt-miR166k | 6 | __...... | 1 | 75 |
| MIMAT0005047 | ppt-miR166k | 1 | __...... | 6 | 75 |
| MIMAT0005046 | ppt-miR166j | 6 | __...... | 1 | 75 |
| MIMAT0005046 | ppt-miR166j | 1 | __...... | 6 | 75 |
| MIMAT0005009 | pta-miR949 | 2 | _......_ | 7 | 75 |
| MIMAT0004000 | sme-miR-184-3p | 8 | ......__ | 3 | 75 |
| MIMAT0019084 | rlcv-miR-rL1-1-3p | 1 | _......_ | 6 | 75 |
| MIMAT0003336 | hsa-miR-658 | 8 | ......__ | 3 | 75 |
