Table 2. MapMi homology mapping of P. hawaiensis conserved miRNA to the Daphnia pulex genome.

mirBasemiRNA	Query sequence	Mismatch	Chromosome	start	end	length	MapMi Score
mir-1	TGGAATGTAAAGAAGTATGGAGC	0	scaffold_1	1720882	1720904	23	48.27
mir-2a	TATCACAGCCAGCTTTGATGAGC	0	scaffold_80	241083	241105	23	54.12
mir-12	TGAGTATTACATCAGGTACTGGT	0	scaffold_1	1847883	1847905	23	47.86
mir-34	TGGCAGTGTGGTTAGCTGGT	0	scaffold_4	1242095	1242114	20	52.09
mir-71	TGAAAGACATGGGTAGTGAGATG	0	scaffold_80	240430	240452	23	57.26
mir-79	ATAAAGCTAGGTTACCAAAG	0	scaffold_2	1526251	1526270	20	51.97
mir-92	AATTGCACTCGTCCCGGCCTGT	1	scaffold_38	876194	876215	22	35.05
mir-193	ACTGGCCTGCTAAGTCCCAA	0	scaffold_167	85458	85477	20	46.75
mir-252a	CTAAGTACTGGTGCCGCAGGAG	1	scaffold_285	66066	66087	22	37.02
mir-263b	AATGGCACTGGAAGAATTCAC	0	scaffold_87	475620	475640	21	31.44
mir-263a	CTTGGCACTGGAAGAATTCACA	0	scaffold_87	475817	475838	22	45.22
mir-276	AGGAACTTCATACCGTGCTCTC	0	scaffold_15	755668	755689	22	42.58
mir-279	ATGACTAGATCCACACTC	0	Scaffold_63	523658	523675	18	35.68
mir-307	TCACAACCTCCTTGAGTG	0	Scaffold_47	601105	641122	18	33.14
mir-317	TGAACACAGCTGGTGGTATCTCA	0	scaffold_4	1243963	1243985	23	52.54
mir-745	GAGCTGCCCAGTGAAGGGCA	1	scaffold_63	361999	362018	20	34.70
mir-965	TAAGCGTATGGCTTTTCCCCT	0	scaffold_32	27783	27803	21	48.07
mir-993	GAAGCTCGTTTCTACAGGTATCT	0	scaffold_7	282360	282382	23	49.27
mir-iab-4-5p	ACGTATACTGAATGTATCCTGA	0	scaffold_7	515547	515568	22	44.98
mir-iab-4-3p	CGGTATACCTTCAGTATACGTA	0	scaffold_7	515582	515603	22	42.92
bantam	GAGATCATTGTGAAAGCTGAT	0	scaffold_115	370210	370230	21	44.47
mir-275	TCAGGTACCTGATGTAGCG	1	scaffold_4	1790782	1790800	19	44.53

Table shows the result of MapMi homology mapping to the D. pulex genome with P. hawaiensis sequences annotated by known miRNA from mirBase with a tolerance of a 1 bp mismatch. The mapping position on the D. pulex chromosome corresponding to known miRNA sequences are shown with the calculated MapMi score for the mapping and RNA fold analysis.