miR-Intess™

other hairpins

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK (1 loci)

block1082416 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

LTR/ERVK

0.21/0.21

19/19/0.00

0.0

0.0

1

0

1

0

43

-2

5arm_loop

278

nd

0.16

3

1

1

na

na

		reads	miRBase family seed
seed	--------------------------------------------GUGUGUA---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------------------TGTGTGTATATATATGTAT----------------------------------------------------------	19	1
rat	tgtatatatctctctctaatatatatatgtatatatgtatgtgTGTGTGTATATATATGTATatacatatatatatatatacacatacatatatacatatacatacacatacatatatat
	************************************************************************************************************************
	...............................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063255 ENSRNOG00000041502
rat	.((((((((..........(((.(((((((((((((((((((((((((((((((((((((....))))))))))))))))))))))))))))))))))))).))).......))))))))	0.950 -50.63

rat

chromosome:20:40980425:40980544:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063255|ENSRNOG00000041502 ## ENSRNOG00000041502|miRNA|| ## {Repeats: dust 40980483 40980502 0 class=dust,trf 90 109 0 class=trf,RMER12 782 801 1 class=LTR/ERVK,RMER12 1232 1251 -1 class=LTR/ERVK,(TA)n 2 153 -1 class=Simple_repeat}

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH (1 loci)

block1677488 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK_bulgeHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

SINE,SINE/B2

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

43

-4

5arm_loop_3arm

250

nd

0.21

4

1

1

na

na

		reads	miRBase family seed
seed	--------------------------------------------UGUGUGU---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------------------------------GTGTGTGTGTGTGTGCATC----------------------------------------------------------	19	1
rat	aatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtGTGTGTGTGTGTGTGCATCtatacacatacatgcatgcatacatgcatacatacatgcatacattatacacacatat
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000007552 ENSRNOG00000005686 Suclg2
	..................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...................	ENSRNOT00000063158 ENSRNOG00000041405
rat	.(((((((((((((((((((((((((((((((((((((((((((((((((((((((((....))))))))))))))))))))))))))))))))))))))))))))).))))))))))))	1.000 -80.10

rat

chromosome:4:130200893:130201012:1

Opposite_strand|Intronic_coding|ENSRNOT00000007552|ENSRNOG00000005686 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063158|ENSRNOG00000041405 ## ENSRNOG00000041405|miRNA|| ## ENSRNOG00000005686|protein_coding|Suclg2|Suclg2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q68FT4] ## {Repeats: (TG)n 41 56 1 class=Simple_repeat,dust 130200895 130200910 0 class=dust,(TG)n 1 56 1 class=Simple_repeat,B3 166 169 1 class=SINE/B2,trf 1 16 0 class=trf,B3 173 203 1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH (1 loci)

block1484099 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_loopOverlap_randfoldOK_nonpairedHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

SINE,SINE/Alu

0.42/0.42

19/19/0.00

0.0

0.0

1

0

1

0

34

-4

3arm_loop

53

nd

0.37

3

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------UGAUGGC---------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------------------------------------ATGATGGCACATGCCTTTA----------------------------------	19	1
rat	actttaccctcctatctttacctcttgagtgtgaagattacaggtacagccaggcaATGATGGCACATGCCTTTAattccagcactcaggaggcagaggcaggtgaagt
	*************************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......	ENSRNOT00000063199 ENSRNOG00000041446
rat	((((((((..(((.......((((((((((((...(((((.(((((..((((........))))...))))).)))))...))))))))))))...)))..))))))))	1.000 -47.40

rat

chromosome:3:108081189:108081297:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063199|ENSRNOG00000041446 ## ENSRNOG00000041446|miRNA|| ## {Repeats: B1_Rn 9 28 1 class=SINE/Alu,B1_Rn 1 148 1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_shortStem_bulgeHIGH (1 loci)

block2441699 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_shortStem_bulgeHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.061

no

SINE

0.53/0.53

19/19/0.00

0.0

0.0

1

0

1

0

2

13

5arm

256

nd

0.26

4

1

1

na

na

		reads	miRBase family seed
seed	---UGAGCCU---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--GTGAGCCTAGCCTTTAACG----------------------------------------------------	19	1
rat	ttGTGAGCCTAGCCTTTAACGgctgagccatctctccagcccgatgtggctttctcttactgggtctcaacga
	*************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000054639 ENSRNOG00000036532
rat	((((((((((((....(((.((..(((((((.((........)).))))))).)).)))))))).)))).)))	0.400 -21.80

rat

chromosome:8:101498556:101498628:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054639|ENSRNOG00000036532 ## ENSRNOG00000036532|miRNA|| ## {Repeats: B4 -245 47 -1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block320237 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

LINE,LINE/L1

0.56/0.56

25/25/0.00

0.0

0.0

1

0

1

0

1

31

3arm

203

nd

0.32

4

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------ACACACA------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------------------------------------------------------------CACACACACACACACACACAGCCAC-	25	1
rat	gtggcatatatgtatgtatgtatgtatgtatgtatgtatgtatgtatgtatgtatgtatacacacacacacacacacacacacacacacacaCACACACACACACACACACAGCCACc
	**********************************************************************************************************************
	............>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>......................	ENSRNOT00000063143 ENSRNOG00000041390
rat	(((((.....(((.(((.(((.(((.(((.(((.(((.(((.(((.(((.(((.(((....))).))).))).))).))).))).))).))).))).))).))).)))....))))).	1.000 -35.80

rat

chromosome:13:82820465:82820582:1

Same_strand|Boundary_non-coding|ENSRNOT00000063143|ENSRNOG00000041390 ## ENSRNOG00000041390|miRNA|| ## {Repeats: trf 1 21 0 class=trf,dust 82820524 82820544 0 class=dust,(CA)n 34 54 1 class=Simple_repeat,L1_Rat3 6095 6536 1 class=LINE,(CA)n 2 54 1 class=Simple_repeat,L1_Rat3 6101 6105 1 class=LINE/L1}

miRNAunknown_rep_lenNOK_cloningHIGH_randfoldOK (1 loci)

block2159208 (miRNA) [miRNAunknown_rep_lenNOK_cloningHIGH_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

LINE,LINE/L2

0.61/0.72

18/24/0.67

0.0

2.1

5512

0

10

0

29

3

3arm

1

nd

0.05

1

8144

10

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------CGCCCUU--------------------------------------------	8093	novel
seed	--------------------------------------------------------------------ACGCCCU---------------------------------------------	44	novel
seed	----------------------------------------------------------------------GCCCUUC-------------------------------------------	3	novel
seed	-----------------------------------------------------------------------CCCUUCC------------------------------------------	2	novel
seed	--------------------------------------------------------------------------UUCCCCC---------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCTTCAC-----------------------------	23	1231	921	146	126	185	72	75	74	142	101
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCTTC-------------------------------	21	735	619	91	64	134	42	38	53	58	33
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTC----------------------------------	18	564	473	79	52	44	29	24	24	47	37
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCT---------------------------------	19	545	424	57	55	57	33	25	33	65	33
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCTTCA------------------------------	22	60	60	15	13	18	9	10	11	6	1
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCTT--------------------------------	20	77	57	17	6	14	2	2	8	12	2
	--------------------------------------------------------------------ACGCCCTTCCCCCCCTTCTTCACC----------------------------	24	26	10	2	5	4	1	-	2	3	-
	-------------------------------------------------------------------AACGCCCTTCCCCCCCTTCTTC-------------------------------	22	5	4	1	-	3	-	-	1	1	1
	-------------------------------------------------------------------AACGCCCTTCCCCCCCTTC----------------------------------	19	7	5	-	-	-	-	-	-	1	-
	-------------------------------------------------------------------AACGCCCTTCCCCCCCTTCT---------------------------------	20	4	-	2	1	-	-	-	-	1	-
	-------------------------------------------------------------------AACGCCCTTCCCCCCCTTCTTCAC-----------------------------	24	4	-	-	-	2	-	-	-	-	-
	-------------------------------------------------------------------------CTTCCCCCCCTTCTTCAC-----------------------------	18	1	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------CGCCCTTCCCCCCCTTCTTC-------------------------------	20	1	1	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------GCCCTTCCCCCCCTTCTTCAC-----------------------------	21	-	1	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------CGCCCTTCCCCCCCTTCTTCAC-----------------------------	22	-	-	-	-	-	-	-	1	-	-
	----------------------------------------------------------------------GCCCTTCCCCCCCTTCTTC-------------------------------	19	1	-	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------AACGCCCTTCCCCCCCTT-----------------------------------	18	1	-	-	-	-	-	-	-	-	-
rat	tcttgctgctccgattcttgtttgcatggggaggagggaggggatgggccaagttccctatgcctggaACGCCCTTCCCCCCCTTCTTCACctggcgaactcctactcgtccttcaagac
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042070 ENSRNOG00000031269 RGD1304694
	.................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...............................	ENSRNOT00000063245 ENSRNOG00000041492
rat	(((((......(((.....((((((..(((((((((((.(((((.((((...(((((........))))))))).)))))))))))))).))..))))))......))).....))))).	0.990 -54.70

rat

chromosome:7:122973514:122973633:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063245|ENSRNOG00000041492 ## Same_strand|Intronic_coding|ENSRNOT00000042070|ENSRNOG00000031269 ## ENSRNOG00000041492|miRNA|| ## ENSRNOG00000031269|protein_coding|RGD1304694|Uncharacterized protein C22orf9 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q4G008] ## {Repeats: L2 2961 2986 1 class=LINE/L2,L2 -86 3292 1 class=LINE}

miRNAunknown_rep_lenNOK_cloningOK_Multihit_nonpairedHIGH_bulgeHIGH (1 loci)

block2048700 (miRNA) [miRNAunknown_rep_lenNOK_cloningOK_Multihit_nonpairedHIGH_bulgeHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.161

no

SINE

0.37/0.47

19/19/0.00

0.3

0.3

20

0

10

0

19

2

3arm

255

nd

0.37

4

35

10

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------GGCUCAC-------------------------------	21	novel
seed	--------------------------------------------------------AGGCUCA--------------------------------	5	novel
seed	-------------------------------------------------------UAGGCUC---------------------------------	4	novel
seed	----------------------------------------------------------GCUCACA------------------------------	3	novel
seed	------------------------------------------------------CUAGGCU----------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------AGGCTCACAACCAAATATA--------------------	19	1	1	4	1	1	1	4	3	5	-
	-------------------------------------------------------TAGGCTCACAACCAAATAT---------------------	19	1	-	-	1	1	-	-	-	1	1
	------------------------------------------------------CTAGGCTCACAACCAAATA----------------------	19	-	-	-	-	-	-	1	-	2	1
	---------------------------------------------------------GGCTCACAACCAAATATAT-------------------	19	1	-	-	-	-	-	-	-	2	-
	-----------------------------------------------------GCTAGGCTCACAACCAAAT-----------------------	19	1	-	-	-	-	-	1	-	-	-
rat	ctgagtaagatatactgtacacatgggctggagagatggctcagccgttaaaggCTAGGCTCACAACCAAATATATaagatatactgtacacagt
	***********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000058195 ENSRNOG00000007646 Sipa1l1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000010626 ENSRNOG00000007646 Sipa1l1
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......................	ENSRNOT00000054610 ENSRNOG00000036502
rat	(((.(((..((((..((((....(((..((.......(((..((((......))))..)))..)).)))....))))..))))....))).))).	0.720 -21.00

rat

chromosome:6:106263518:106263612:1

Same_strand|Intronic_coding|ENSRNOT00000010626|ENSRNOG00000007646 ## Same_strand|Exonic_non-coding|ENSRNOT00000054610|ENSRNOG00000036502 ## ENSRNOG00000007646|protein_coding|Sipa1l1|Signal-induced proliferation-associated 1-like protein 1 (SPA-1-like protein p1294). [Source:UniProtKB/Swiss-Prot;Acc:O35412] ## ENSRNOG00000036502|miRNA|| ## {Repeats: B4 2 47 1 class=SINE}

miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH (1 loci)

sblock12804 (miRNA) [miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_nonpairedHIGH]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.019

no

SINE,SINE/Alu

0.47/0.68

18/24/0.23

0.0 5.1 0.0 0.0

0.0 3.9 0.0 0.0

1 10 1 1

0 0 0 0

1 5 1 1

0 0 0 0

19 26 25 20

4 -16 0 6

5arm 5arm_loop_3arm 3arm 3arm

287 290 290 290

nd nd nd nd

0.47 0.39 0.47 0.50

7 3 4 7

13

6

3

0

		reads	miRBase family seed
seed	--------------------------------GUCCUGG------------------------------------------------------	2	novel
seed	---------------------------------------AACUCAC-----------------------------------------------	2	novel
seed	--------------------GUAGCCC------------------------------------------------------------------	1	novel
seed	----------------------------------------ACUCACU----------------------------------------------	1	novel
seed	--------------------------------------------------------AGGCUGG------------------------------	1	novel
seed	-----------------------------GCUGUCC---------------------------------------------------------	1	novel
seed	---------------------------UGGCUGU-----------------------------------------------------------	1	novel
seed	-------------------------------------GGAACUC-------------------------------------------------	1	novel
seed	--------------------------------------------------UAGACCA------------------------------------	1	novel
seed	-------------------------------UGUCCUG-------------------------------------------------------	1	novel
seed	-----------------------------------CUGGAAC---------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T3S1	T3S2	T5S1	T5S2
	--------------------------------------GAACTCACTCTGTAGACC-------------------------------------	18	-	-	-	2	-	-
	----------------------------------CCTGGAACTCACTCTGTAGAC--------------------------------------	21	-	1	-	-	-	-
	--------------------------CTGGCTGTCCTGGAACTC-------------------------------------------------	18	-	1	-	-	-	-
	------------------------------------TGGAACTCACTCTGTAGACC-------------------------------------	20	-	-	-	-	-	1
	----------------------------GGCTGTCCTGGAACTCAC-----------------------------------------------	18	-	-	-	-	-	1
	------------------------------CTGTCCTGGAACTCACTCT--------------------------------------------	19	-	-	-	-	1	-
	---------------------------------------AACTCACTCTGTAGACCAG-----------------------------------	19	-	-	-	1	-	-
	-------------------------------------------------------CAGGCTGGCCTCGAACTC--------------------	18	-	-	1	-	-	-
	-------------------TGTAGCCCTGGCTGTCCTG-------------------------------------------------------	19	1	-	-	-	-	-
	-------------------------------TGTCCTGGAACTCACTCTGTAGAC--------------------------------------	24	1	-	-	-	-	-
	-------------------------------------------------GTAGACCAGGCTGGCCTCG-------------------------	19	-	-	-	-	1	-
	-------------------------------TGTCCTGGAACTCACTCTG-------------------------------------------	19	-	-	-	-	1	-
rat	ttgagacagggtttttctgTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCacagaaactgcttgcctcag
	*********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......	ENSRNOT00000063188 ENSRNOG00000041435
rat	.((((.((((...((((((((.......((((..(((((.((.......))...)))))..)))).......))))))))...)))).)))).	1.000 -33.14

rat

chromosome:X:81947103:81947195:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063188|ENSRNOG00000041435 ## ENSRNOG00000041435|miRNA|| ## {Repeats: B1_Mur4 68 92 -1 class=SINE/Alu,B1_Mur4 83 122 -1 class=SINE/Alu,B1_Mur3 0 149 -1 class=SINE}

miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_randfoldOK (1 loci)

sblock12676 (miRNA) [miRNAunknown_rep_lenNOK_cloningOK_multiarm_DicerNOK_Multihit_5varHIGH_loopOverlap_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.001

no

SINE,SINE/Alu

0.50/0.68

18/24/0.36

0.1 3.0 0.0 0.0

0.2 5.2 0.0 0.0

8 4 1 1

0 0 0 0

6 3 1 1

0 0 0 0

18 24 37 18

1 -11 -19 0

5arm 5arm_loop_3arm 5arm_loop_3arm 3arm

265 295 295 295

nd nd nd nd

0.30 0.44 0.59 0.29

3 3 8 3

14

8

-1

1

		reads	miRBase family seed
seed	-------------------AGUUCGA----------------------------------------------------------------	7	novel
seed	-------------------------AGGCCAG----------------------------------------------------------	2	novel
seed	--------------------------------------CUACAGA---------------------------------------------	1	novel
seed	---------------------------------CUGGUCU--------------------------------------------------	1	novel
seed	-------------------------------------------------GUUCCAG----------------------------------	1	novel
seed	--------------------GUUCGAG---------------------------------------------------------------	1	novel
seed	-----------------------------CAGCCUG------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	------------------GAGTTCGAGGCCAGCCTGG-----------------------------------------------------	19	1	2	1	2	-	-	1	-
	------------------------------------------------AGTTCCAGGACAGCCAGGGCTACA------------------	24	-	-	-	-	-	-	1	-
	----------------------------CCAGCCTGGTCTACAGAGTGA-----------------------------------------	21	-	1	-	-	-	-	-	-
	-------------------AGTTCGAGGCCAGCCTGGTC---------------------------------------------------	20	-	-	-	-	1	-	-	-
	--------------------------------CCTGGTCTACAGAGTGAGT---------------------------------------	19	-	-	-	-	-	-	-	1
	------------------------GAGGCCAGCCTGGTCTACAGAGT-------------------------------------------	23	-	-	-	-	-	1	-	-
	------------------------GAGGCCAGCCTGGTCTAC------------------------------------------------	18	-	-	-	-	-	-	-	1
	-------------------------------------TCTACAGAGTGAGTTCCAGGAC-------------------------------	22	-	-	-	-	-	1	-	-
rat	gaggcaagcagtttctgtGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACAcagaaaaaccctgtctca
	******************************************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063188 ENSRNOG00000041435
rat	((((((.....(((((((((((((..(((...(((((.((........))..)))))...))).))))).)))))))).....)))))).	1.000 -38.90

rat

chromosome:X:81947104:81947193:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063188|ENSRNOG00000041435 ## ENSRNOG00000041435|miRNA|| ## {Repeats: B1_Mur4 87 128 1 class=SINE/Alu,B1_Mur3 0 149 1 class=SINE,B1_Mur4 117 141 1 class=SINE/Alu}

miRNAunknown_rep_lenNOK_multiarm_DicerNOK (1 loci)

sblock11060 (miRNA) [miRNAunknown_rep_lenNOK_multiarm_DicerNOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

Ensembl miRNA

0.475

no

SINE

0.50/0.63

18/19/0.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

10 14

13 12

5arm 3arm

2 2

nd nd

0.32 0.22

2 2

2

2

0

0

		reads	miRBase family seed
seed	-------------------------------------------------------------CUUUCUG------------------------	1	novel
seed	-----------UCUCCAG--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	------------------------------------------------------------GCTTTCTGGTTTGGAAGG--------------	18	-	1
	----------CTCTCCAGCCCAAGGAGGA---------------------------------------------------------------	19	1	-
rat	gctgagccatCTCTCCAGCCCAAGGAGGAtgctttcttaaatacgcaaatgatgaggactGCTTTCTGGTTTGGAAGGtgtaatggaaaggc
	********************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..................................................	ENSRNOT00000054622 ENSRNOG00000036515
rat	(((...((((((.((((..((.((((((.....((((((.((......))..))))))...))))))))..)))).))....))))...)))	0.920 -22.30

rat

chromosome:7:135934843:135934934:-1

Opposite_strand|Exonic_non-coding|ENSRNOT00000054622|ENSRNOG00000036515 ## intergenic ## ENSRNOG00000036515|miRNA|| ## {Repeats: B4 2 47 -1 class=SINE}

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