Secondary structure and small RNA-seq evidence for dme-mir-4

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548779-15548889 -	AAT---------------ATTATGGAGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTTTCCGGTCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droSim1	chr2R:14254213-14254323 -	AAT---------------ATTCTGTGGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCCGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droSec1	super_1:13063508-13063618 -	AAT---------------ATTCTGTGGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCCGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droYak2	chr2R:13623899-13624012 +	CAG---------------ATACTGGGGCAGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC--------------------ATTAC
droEre2	scaffold_4845:9749030-9749140 -	AAG---------------ATACTGTAGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATCAGCAGCACC-----------------------AA
droAna3	scaffold_13266:9731502-9731641 +	AATAATAT----AC-----CAATATAAAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCAATTGCGGCGCTTATTAACAAGAATTTCAAATGTGAC
dp4	chr3:12677403-12677511 -	TA-----------------CCTTATTGTGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTTGCAGCACT-----------------------AC
droPer1	super_2:8906155-8906263 +	TA-----------------CCTTATTGTGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTTGCAGCACT-----------------------AC
droWil1	scaffold_180701:1651595-1651704 -	AAC---------------CAAATGGC-GGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTATCGCCAGT-----------------------TT
droVir3	scaffold_12875:4112289-4112408 +	ATATA--T----ATCTATATCATATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATAAGCAGCGGC-----------------------TA
droMoj3	scaffold_6496:20936612-20936737 -	AAAGAAAACAAAATCTATATCGTATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATAAGCAGCGCC-----------------------TA
droGri2	scaffold_5621:2961-3084 +	ATCGA--------TCTATGTTTTATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATACGCAGCGATTAT-----------------ATAGT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548779-15548889 -	AAT---------------ATTATGGAGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTTTCCGGTCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droSim1	chr2R:14254213-14254323 -	AAT---------------ATTCTGTGGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCCGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droSec1	super_1:13063508-13063618 -	AAT---------------ATTCTGTGGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCCGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC-----------------------AC
droYak2	chr2R:13623899-13624012 +	CAG---------------ATACTGGGGCAGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACC--------------------ATTAC
droEre2	scaffold_4845:9749030-9749140 -	AAG---------------ATACTGTAGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATCAGCAGCACC-----------------------AA
droAna3	scaffold_13266:9731502-9731641 +	AATAATAT----AC-----CAATATAAAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCAATTGCGGCGCTTATTAACAAGAATTTCAAATGTGAC
dp4	chr3:12677403-12677511 -	TA-----------------CCTTATTGTGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTTGCAGCACT-----------------------AC
droPer1	super_2:8906155-8906263 +	TA-----------------CCTTATTGTGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTTGCAGCACT-----------------------AC
droWil1	scaffold_180701:1651595-1651704 -	AAC---------------CAAATGGC-GGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTATCGCCAGT-----------------------TT
droVir3	scaffold_12875:4112289-4112408 +	ATATA--T----ATCTATATCATATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATAAGCAGCGGC-----------------------TA
droMoj3	scaffold_6496:20936612-20936737 -	AAAGAAAACAAAATCTATATCGTATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATAAGCAGCGCC-----------------------TA
droGri2	scaffold_5621:2961-3084 +	ATCGA--------TCTATGTTTTATAGAGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATACGCAGCGATTAT-----------------ATAGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AATATTCTGTGGCGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGACTTTTCCGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTAGCAGCACCAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................................................ATAAAGCTAGACAACCATTGAA..........................	22	1	3737.00	3737	3737
...............................................................ATAAAGCTAGACAACCATTGA...........................	21	1	3243.00	3243	3243
...............................................................ATAAAGCTAGACAACCATTGAAG.........................	23	1	489.00	489	489
...............................................................ATAAAGCTAGACAACCATTG............................	20	1	297.00	297	297
................................................................TAAAGCTAGACAACCATTGAAG.........................	22	1	92.00	92	92
............................CTTTGGTCGTCCAGCCTTAGGTGA...........................................................	24	1	64.00	64	64
............................CTTTGGTCGTCCAGCCTTAGGT.............................................................	22	1	17.00	17	17
...........................TCTTTGGTCGTCCAGCCTTAGGTGA...........................................................	25	1	15.00	15	15
...........................TCTTTGGTCGTCCAGCCTTAG...............................................................	21	1	15.00	15	15
................................................................TAAAGCTAGACAACCATTGAA..........................	21	1	14.00	14	14
...........................TCTTTGGTCGTCCAGCCTTAGG..............................................................	22	1	14.00	14	14
............................CTTTGGTCGTCCAGCCTTAGGTG............................................................	23	1	11.00	11	11
...........................TCTTTGGTCGTCCAGCCTTAGGTG............................................................	24	1	10.00	10	10
...........................TCTTTGGTCGTCCAGCCTTAGGT.............................................................	23	1	7.00	7	7
..............................................................CATAAAGCTAGACAACCATTGAA..........................	23	1	6.00	6	6
................................................................TAAAGCTAGACAACCATTGA...........................	20	1	5.00	5	5
..............................................................CATAAAGCTAGACAACCATTGA...........................	22	1	5.00	5	5
...............................................................ATAAAGCTAGACAACCATTGAAGT........................	24	1	5.00	5	5
................................................................TAAAGCTAGACAACCATTGAAGT........................	23	1	5.00	5	5
...............................................................ATAAAGCTAGACAACCATT.............................	19	1	4.00	4	4
............................CTTTGGTCGTCCAGCCTTAGG..............................................................	21	1	3.00	3	3
.............................TTTGGTCGTCCAGCCTTAGGTGA...........................................................	23	1	2.00	2	2
...........................TCTTTGGTCGTCCAGCCTTA................................................................	20	1	1.00	1	1
.....................................................................................GTTCGTTGTGGCATTAGCAGCA....	22	1	1.00	1	1

dp4

TACCTT--ATTGTGGTTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTCTCTGATCATAAAGCTAGACAACCATTGAAGTTCGTTGTGGCATTTGCAGCACTAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............................................................ATAAAGCTAGACAACCATTGAA..........................	22	1	3994.00	3994	3994	0
...............................................................ATAAAGCTAGACAACCATTGA...........................	21	1	2063.00	2063	2063	0
...............................................................ATAAAGCTAGACAACCATTGAAG.........................	23	1	636.00	636	636	0
................................................................TAAAGCTAGACAACCATTGAAG.........................	22	1	227.00	227	227	0
...............................................................ATAAAGCTAGACAACCATTG............................	20	1	225.00	225	225	0
............................CTTTGGTCGTCCAGCCTTAGGTGA...........................................................	24	1	222.00	222	222	0
................................................................TAAAGCTAGACAACCATTGAAGT........................	23	1	105.00	105	105	0
...............................................................ATAAAGCTAGACAACCATTGAAGT........................	24	1	66.00	66	66	0
...........................TCTTTGGTCGTCCAGCCTTAGGTGA...........................................................	25	1	58.00	58	58	0
...........................TCTTTGGTCGTCCAGCCTTAGG..............................................................	22	1	32.00	32	32	0
............................CTTTGGTCGTCCAGCCTTAGGT.............................................................	22	1	29.00	29	29	0
................................................................TAAAGCTAGACAACCATTGAA..........................	21	1	24.00	24	24	0
...........................TCTTTGGTCGTCCAGCCTTAG...............................................................	21	1	24.00	24	24	0
............................CTTTGGTCGTCCAGCCTTAGGTG............................................................	23	1	21.00	21	21	0
...........................TCTTTGGTCGTCCAGCCTTAGGT.............................................................	23	1	14.00	14	14	0
...........................TCTTTGGTCGTCCAGCCTTAGGTG............................................................	24	1	8.00	8	8	0
................................................................TAAAGCTAGACAACCATTGA...........................	20	1	8.00	8	8	0
...............................................................ATAAAGCTAGACAACCATT.............................	19	1	7.00	7	7	0
............................CTTTGGTCGTCCAGCCTTAGG..............................................................	21	1	6.00	6	6	0
.............................TTTGGTCGTCCAGCCTTAGGTGA...........................................................	23	1	6.00	6	6	0
.........TTGTGGTTGCAATTAGTTT...................................................................................	19	1	5.00	5	5	0
..............................................................CATAAAGCTAGACAACCATTGA...........................	22	1	4.00	4	4	0
.................................................................AAAGCTAGACAACCATTGAAGT........................	22	1	4.00	4	4	0
..................................................................AAGCTAGACAACCATTGAAGT........................	21	1	4.00	4	4	0
..............................................................CATAAAGCTAGACAACCATTGAA..........................	23	1	3.00	3	3	0
............................CTTTGGTCGTCCAGCCTTAG...............................................................	20	1	3.00	3	3	0
..................................................................AAGCTAGACAACCATTGAA..........................	19	1	2.00	2	2	0
..........TGTGGTTGCAATTAGTTT...................................................................................	18	1	2.00	2	2	0
.....T--ATTGTGGTTGCAATTAGTTT...................................................................................	21	1	2.00	2	2	0
..................................................................AAGCTAGACAACCATTGA...........................	18	1	1.00	1	1	0