miR-Intess™

other hairpins

miRNAunknown_rep_Multihit_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

miRNAunknown_rep_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (1 loci)

block1487614 (miRNA) [miRNAunknown_rep_Multihit_shortStem_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

0.120

no

SINE,SINE/Alu

0.55/0.55

22/22/1.00

0.0

0.0

2

0

1

0

0

21

5arm

237

nd

0.41

4

2

1

na

na

		reads	miRBase family seed
seed	-CCUCGAA----------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T3S1
	GCCTCGAACTCACAGAGATCTG--------------------------------------------------------------------	22	2
rat	GCCTCGAACTCACAGAGATCTGcctgcctcttcctcctgagtgcccaccatgcttggcagagggaggttcgttttaagaagtgataggca
	******************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<................................................................	ENSRNOT00000063391 ENSRNOG00000041638
rat	((((...(((....(((((..((((.(((((.((......(((.....)))....)).))))).))))..)))))....)))...)))).	0.970 -28.70

rat

chromosome:3:115150678:115150767:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000063391|ENSRNOG00000041638 ## ENSRNOG00000041638|miRNA|| ## {Repeats: B1_Mur3 56 78 -1 class=SINE/Alu,B1_Mur3 -8 141 -1 class=SINE}

miRNAunknown_rep_Multihit_shortStem_randfoldOK (1 loci)

block407146 (miRNA) [miRNAunknown_rep_Multihit_shortStem_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

0.002

no

SINE

0.62/0.62

21/21/1.00

0.0

0.0

1

0

1

0

3

3

3arm

237

nd

0.24

3

1

1

na

na

		reads	miRBase family seed
seed	-----------------------------------GCGCACA----------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------GGCGCACACACACACACACAC---	21	1
rat	tgtgcacgtgcatgtgtgtgcgcgcgcgcacgcgGGCGCACACACACACACACACaca
	**********************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000062922 ENSRNOG00000041169
rat	.(((...(((..(((((((((((.(((....))).)))))))))))..)))...))).	1.000 -34.80

rat

chromosome:14:68960870:68960927:1

Opposite_strand|Exonic_non-coding|ENSRNOT00000062922|ENSRNOG00000041169 ## ENSRNOG00000041169|miRNA|| ## {Repeats: trf 37 53 0 class=trf,dust 68960944 68960960 0 class=dust,B3A 2 178 1 class=SINE,(CG)n 64 68 1 class=Simple_repeat,(CA)n 1 53 1 class=Simple_repeat,(CA)n 1 17 1 class=Simple_repeat}

miRNAunknown_rep_Multihit_shortStem_randfoldOK_bulgeHIGH (1 loci)

block1050339 (miRNA) [miRNAunknown_rep_Multihit_shortStem_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

LINE,LINE/L1

0.45/0.45

22/22/1.00

0.0

0.0

2

0

1

0

4

34

3arm

285

nd

0.18

4

2

1

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------CACACAG------------------	2	novel
		len	cloning frequencies
			T2S1
	----------------------------------------------------------------------------------------------ACACACAGAAACACACACACAC----	22	2
rat	acgtagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatacaatacatacacatacaacacaacacatacacagacatacACACACAGAAACACACACACACatgg
	************************************************************************************************************************
	..............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........................	ENSRNOT00000063114 ENSRNOG00000041361
rat	.(((.((((((((((((((((((((((((.(((((((((((.(((((((((((.......))))))))))).....))))))))))).))))))))))))....))))))))))))))).	1.000 -73.20

rat

chromosome:1:252303030:252303149:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000063114|ENSRNOG00000041361 ## ENSRNOG00000041361|miRNA|| ## {Repeats: Lx9 5708 5976 1 class=LINE,trf 1 22 0 class=trf,Lx9 5750 5772 1 class=LINE/L1,trf 2 24 0 class=trf,dust 252303087 252303109 0 class=dust}

miRNAunknown_rep_cloningHIGH_Multihit_shortStem (1 loci)

block2346185 (miRNA) [miRNAunknown_rep_cloningHIGH_Multihit_shortStem]

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

0.339

no

SINE

0.60/0.68

18/22/0.94

0.0

0.0

236

0

10

0

4

2

3arm

252

nd

0.23

3

390

10

na

na

		reads	miRBase family seed
seed	-------------------------------------------------GGCUGGA------------------	323	novel
seed	-----------------------------------------------------GGAGAGA--------------	59	miR-185
seed	------------------------------------------------------GAGAGAU-------------	3	novel
seed	---------------------------------------------------CUGGAGA----------------	3	novel
seed	----------------------------------------------------UGGAGAG---------------	1	novel
seed	--------------------------------------------------GCUGGAG-----------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	------------------------------------------------GGGCTGGAGAGATGGCTCAGCC----	22	8	8	1	6	4	35	1	1	23	236
	----------------------------------------------------TGGAGAGATGGCTCAGCCGT--	20	4	2	4	1	6	8	2	-	6	7
	----------------------------------------------------TGGAGAGATGGCTCAGCC----	18	-	2	-	4	-	2	2	2	-	1
	----------------------------------------------------TGGAGAGATGGCTCAGCCG---	19	-	1	2	-	1	2	-	-	-	-
	--------------------------------------------------GCTGGAGAGATGGCTCAGCC----	20	-	-	-	-	-	-	-	-	-	3
	-----------------------------------------------------GGAGAGATGGCTCAGCCGT--	19	-	1	-	-	1	-	-	-	1	-
	---------------------------------------------------CTGGAGAGATGGCTCAGCC----	19	-	-	-	1	-	-	-	-	-	-
	-------------------------------------------------GGCTGGAGAGATGGCTCAGCC----	21	-	-	-	-	-	-	-	-	-	1
rat	ctgatgaaatctgagcttcgttgagacccagtaagagaaagccacatcGGGCTGGAGAGATGGCTCAGCCgtta
	**************************************************************************
	............>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054639 ENSRNOG00000036532
rat	.(((((....((((((..((((.....(((((..((..........))..)))))...)))))))))).)))))	0.880 -18.90

rat

chromosome:8:101498572:101498645:-1

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

miRNAunknown_rep_cloningHIGH_multiarm_DicerOK_loopOverlap_randfoldOK (1 loci)

sblock6353 (miRNA) [miRNAunknown_rep_cloningHIGH_multiarm_DicerOK_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

LINE,LINE/CR1

0.33/0.50

18/25/0.83

0.4 0.0

0.5 0.0

1960 2153

0 0

10 10

0 0

31 17

-1 2

5arm_loop 3arm

1 1

nd nd

0.19 0.23

2 3

8744

10

3

2

		reads	miRBase family seed
seed	----------------------------------------------------------------------ACCUGUU-------------------------------	3406	novel
seed	--------------------------------UACAGUU---------------------------------------------------------------------	2249	novel
seed	---------------------------------ACAGUUG--------------------------------------------------------------------	1355	novel
seed	---------------------------------------------------------------------AACCUGU--------------------------------	1236	novel
seed	----------------------------------CAGUUGU-------------------------------------------------------------------	341	novel
seed	-----------------------------------------------------------------------CCUGUUG------------------------------	70	novel
seed	-------------------------------AUACAGU----------------------------------------------------------------------	47	novel
seed	------------------------------------------------------------------------CUGUUGA-----------------------------	27	novel
seed	--------------------------------------------------------------------UAACCUG---------------------------------	10	novel
seed	-----------------------------GGAUACA------------------------------------------------------------------------	2	novel
seed	-------------------------------------UUGUUCA----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	---------------------------------------------------------------------AACCTGTTGAACAACTGAACCC-----------------	22	1418	735	23	26	42	52	42	33	88	57
	-------------------------------ATACAGTTGTTCAACCAGTTAC-------------------------------------------------------	22	539	506	10	20	26	27	11	18	75	47
	--------------------------------------------------------------------TAACCTGTTGAACAACTGAACCC-----------------	23	381	246	14	15	23	32	15	17	50	49
	--------------------------------TACAGTTGTTCAACCAGTTACT------------------------------------------------------	22	355	199	2	14	18	23	9	19	34	22
	-------------------------------ATACAGTTGTTCAACCAGT----------------------------------------------------------	19	171	129	5	5	13	7	2	3	12	13
	--------------------------------TACAGTTGTTCAACCAGTTAC-------------------------------------------------------	21	190	70	2	4	7	10	7	13	22	12
	---------------------------------------------------------------------AACCTGTTGAACAACTGA---------------------	18	150	86	3	1	6	8	2	3	14	3
	-------------------------------ATACAGTTGTTCAACCAG-----------------------------------------------------------	18	115	81	1	7	5	9	4	9	11	9
	---------------------------------------------------------------------AACCTGTTGAACAACTGAACC------------------	21	140	68	1	2	4	7	3	5	5	6
	-------------------------------ATACAGTTGTTCAACCAGTT---------------------------------------------------------	20	116	62	6	4	3	4	2	6	7	5
	---------------------------------ACAGTTGTTCAACCAGTTACT------------------------------------------------------	21	98	64	2	3	3	4	6	10	14	8
	---------------------------------------------------------------------AACCTGTTGAACAACTGAAC-------------------	20	91	41	2	-	2	1	2	8	7	6
	--------------------------------TACAGTTGTTCAACCAGT----------------------------------------------------------	18	78	45	1	3	4	7	-	2	5	4
	--------------------------------------------------------------------TAACCTGTTGAACAACTGAACC------------------	22	61	35	1	1	3	2	2	4	9	7
	--------------------------------TACAGTTGTTCAACCAGTT---------------------------------------------------------	19	61	44	1	3	1	1	1	3	6	2
	--------------------------------------------------------------------TAACCTGTTGAACAACTGA---------------------	19	63	31	1	3	2	3	3	2	11	4
	---------------------------------------------------------------------AACCTGTTGAACAACTGAACCCA----------------	23	54	27	1	1	2	5	2	4	13	14
	-------------------------------ATACAGTTGTTCAACCAGTTACT------------------------------------------------------	23	42	45	1	2	2	3	1	3	6	2
	---------------------------------ACAGTTGTTCAACCAGTTAC-------------------------------------------------------	20	53	16	-	-	-	-	4	3	4	4
	---------------------------------------------------------------------AACCTGTTGAACAACTGAA--------------------	19	54	17	-	-	-	1	-	1	3	4
	--------------------------------------------------------------------TAACCTGTTGAACAACTG----------------------	18	35	23	2	1	-	2	-	2	1	3
	----------------------------------------------------------------------ACCTGTTGAACAACTGAACCC-----------------	21	33	8	2	-	2	2	-	-	-	-
	--------------------------------TACAGTTGTTCAACCAGTTA--------------------------------------------------------	20	18	13	2	1	2	1	1	-	1	-
	-------------------------------ATACAGTTGTTCAACCAGTTA--------------------------------------------------------	21	16	11	-	-	1	3	-	1	4	1
	--------------------------------------------------------------------TAACCTGTTGAACAACTGAAC-------------------	21	19	8	-	2	-	-	1	1	1	4
	--------------------------------------------------------------------TAACCTGTTGAACAACTGAA--------------------	20	12	9	-	1	-	2	-	-	3	2
	---------------------------------ACAGTTGTTCAACCAGTTA--------------------------------------------------------	19	10	6	-	-	-	-	-	-	-	-
	---------------------------------ACAGTTGTTCAACCAGTTACTA-----------------------------------------------------	22	6	8	-	-	-	-	-	-	1	-
	------------------------------GATACAGTTGTTCAACCAGTTAC-------------------------------------------------------	23	6	6	-	-	-	-	-	1	2	-
	---------------------------------ACAGTTGTTCAACCAGTT---------------------------------------------------------	18	2	8	2	-	-	-	-	-	1	1
	------------------------------GATACAGTTGTTCAACCAGTT---------------------------------------------------------	21	5	5	-	-	-	2	-	-	-	1
	----------------------------------------------------------------------ACCTGTTGAACAACTGAACCCA----------------	22	5	6	-	-	-	-	1	-	1	-
	--------------------------------TACAGTTGTTCAACCAGTTACTA-----------------------------------------------------	23	5	4	-	-	-	-	-	1	1	1
	--------------------------------------------------------------------TAACCTGTTGAACAACTGAACCCA----------------	24	3	1	-	-	1	-	2	-	2	3
	-----------------------------------------------------------------------CCTGTTGAACAACTGAACCCA----------------	21	5	6	-	-	-	-	-	-	-	1
	---------------------------------------------------------------------AACCTGTTGAACAACTGAACCCAA---------------	24	2	-	-	2	-	-	-	-	3	2
	------------------------------GATACAGTTGTTCAACCAGT----------------------------------------------------------	20	7	1	-	-	-	1	-	-	-	-
	-----------------------------------------------------------------------CCTGTTGAACAACTGAACCC-----------------	20	3	3	-	-	-	1	-	-	-	1
	-------------------------------------------------------------------GTAACCTGTTGAACAACTGAACC------------------	23	4	1	-	-	-	-	-	-	1	-
	------------------------------GATACAGTTGTTCAACCAG-----------------------------------------------------------	19	1	4	-	-	-	-	-	-	-	-
	------------------------------GATACAGTTGTTCAACCA------------------------------------------------------------	18	3	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CCTGTTGAACAACTGAACCCAA---------------	22	1	3	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------ACCTGTTGAACAACTGAACC------------------	20	1	2	-	-	-	-	-	-	-	-
	-------------------------------------------------------------------GTAACCTGTTGAACAACTGA---------------------	20	1	-	-	-	-	1	-	-	1	-
	----------------------------------------------------------------------ACCTGTTGAACAACTGAACCCAA---------------	23	-	3	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------ACCTGTTGAACAACTGAAC-------------------	19	1	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CCTGTTGAACAACTGAACC------------------	19	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------------------------------ACCTGTTGAACAACTGAA--------------------	18	2	-	-	-	-	-	-	-	-	-
	----------------------------TGGATACAGTTGTTCAACCAGT----------------------------------------------------------	22	1	-	-	-	-	-	-	-	-	-
	----------------------------TGGATACAGTTGTTCAACCAGTT---------------------------------------------------------	23	-	-	-	1	-	-	-	-	-	-
	------------------------------GATACAGTTGTTCAACCAGTTA--------------------------------------------------------	22	-	-	-	-	-	-	-	-	-	1
	---------------------------------------------------------------------AACCTGTTGAACAACTGAACCCAAA--------------	25	-	1	-	-	-	-	-	-	-	-
	------------------------------------GTTGTTCAACCAGTTACT------------------------------------------------------	18	-	-	-	-	-	-	-	-	1	-
	-------------------------------------------------------------------GTAACCTGTTGAACAACT-----------------------	18	-	1	-	-	-	-	-	-	-	-
	-----------------------------------------------------------------------CCTGTTGAACAACTGAAC-------------------	18	1	-	-	-	-	-	-	-	-	-
rat	gccaatctccctagtaatctgtactctttggATACAGTTGTTCAACCAGTTACtaatctaactaattgtAACCTGTTGAACAACTGAACCCaaagggtgcaaagttgg
	************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015138 ENSRNOG00000011099 NM_001113328.1
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........	ENSRNOT00000062187 ENSRNOG00000040434
rat	.(((((.............((((((((((((...((((((((((((..(((((..............)))))..))))))))))))...))))))))))))..)))))	0.530 -39.90

rat

chromosome:2:40714094:40714201:1

Same_strand|Exonic_non-coding|ENSRNOT00000062187|ENSRNOG00000040434 ## Same_strand|Intronic_coding|ENSRNOT00000015138|ENSRNOG00000011099 ## ENSRNOG00000040434|miRNA|| ## ENSRNOG00000011099|protein_coding|NM_001113328.1|phosphodiesterase 4D, cAMP specific (Pde4d), transcript variant 1, mRNA [Source:RefSeq_dna;Acc:NM_001113328] ## {Repeats: L3 3438 3465 -1 class=LINE/CR1,L3 3477 3504 -1 class=LINE/CR1,L3 -901 3588 -1 class=LINE}

miRNAunknown_rep_cloningOK_Multihit_loopOverlap (1 loci)

block2266514 (miRNA) [miRNAunknown_rep_cloningOK_Multihit_loopOverlap]

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

0.049

no

SINE

0.60/0.63

19/20/0.82

0.0

0.0

35

0

9

0

6

-2

5arm_loop

256

nd

0.30

3

49

9

na

na

		reads	miRBase family seed
seed	-------GGAGAGA--------------------------------------------------------------	46	miR-185
seed	--------GAGAGAU-------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T5S1	T5S2
	------TGGAGAGATGGCTCAGCCGT--------------------------------------------------	20	4	2	4	1	6	8	2	6	7
	------TGGAGAGATGGCTCAGCCG---------------------------------------------------	19	-	1	2	-	1	2	-	-	-
	-------GGAGAGATGGCTCAGCCGT--------------------------------------------------	19	-	1	-	-	1	-	-	1	-
rat	ttgggcTGGAGAGATGGCTCAGCCGTtaaaggctaggctcacaaccaaatatataagaaagcatcctcctttctag
	****************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>..........................	ENSRNOT00000054622 ENSRNOG00000036515
rat	.((((..((((.((((((..((((......))))..)).......................))))))))..)))).	0.570 -21.00

rat

chromosome:7:135934912:135934987:1

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

miRNAunknown_rep_cloningOK_Multihit_loopOverlap_nonpairedHIGH (1 loci)

block2429515 (miRNA) [miRNAunknown_rep_cloningOK_Multihit_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

0.118

no

SINE,SINE/Alu

0.60/0.68

18/20/0.70

0.0 0.0 0.0

0.0 0.0 0.0

5 1 1

0 0 0

4 1 1

0 0 0

36 30 25

-12 -5 1

3arm_loop 3arm_loop 3arm

254 261 271

nd nd nd

0.65 0.42 0.39

11 4 3

10

5

na

na

		reads	miRBase family seed
seed	------------------------------------------------CCCUCUG------------------------------------------------	8	novel
seed	-------------------------------------------------------------AGGCUGG-----------------------------------	1	novel
seed	-------------------------------------------------------UAGACCA-----------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T5S1
	-----------------------------------------------TCCCTCTGTAGACCAGGCTG------------------------------------	20	1	-	-	1	5
	-----------------------------------------------TCCCTCTGTAGACCAGGC--------------------------------------	18	-	1	-	-	-
	------------------------------------------------------------CAGGCTGGCCTCGAACTC-------------------------	18	-	-	1	-	-
	------------------------------------------------------GTAGACCAGGCTGGCCTCG------------------------------	19	-	-	-	-	1
rat	gctttttgagacagggtttctctatgtagtcctggctgtcctggaatTCCCTCTGTAGACCAGGCTGgcctcgaactcacagggatctgtctgccttctaagt
	*******************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037650 ENSRNOG00000025332 Cd109
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037665 ENSRNOG00000025332 Cd109
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000037657 ENSRNOG00000025332 Cd109
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057088 ENSRNOG00000025332 Cd109
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057087 ENSRNOG00000025332 Cd109
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........	ENSRNOT00000063257 ENSRNOG00000041504
rat	........(((((((...(((((.((...((..((((..(((((...............)))))..))))..))...)).))))))))))))...........	0.990 -30.56

rat

chromosome:8:83612171:83612273:1

Same_strand|Intronic_coding|ENSRNOT00000037650|ENSRNOG00000025332 ## Opposite_strand|Exonic_non-coding|ENSRNOT00000063257|ENSRNOG00000041504 ## ENSRNOG00000041504|miRNA|| ## ENSRNOG00000025332|protein_coding|Cd109|CD109 antigen Gene [Source:MGI Symbol;Acc:MGI:2445221] ## {Repeats: B1_Mur4 -7 143 -1 class=SINE,B1_Mur4 68 99 -1 class=SINE/Alu}

miRNAunknown_rep_lenNOK_Multihit_loopOverlap (1 loci)

block2367496 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_loopOverlap]

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

0.095

no

SINE,SINE/Alu

0.56/0.56

18/18/0.00

0.0

0.0

1

0

1

0

10

-4

3arm_loop

154

nd

0.28

3

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------CCUGAGU--------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------------------TCCTGAGTGCTGGGATTC----------	18	1
rat	gctggccttgagtttgttgagatccacctgcctctgccTCCTGAGTGCTGGGATTCaaggcatgca
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000026073 ENSRNOG00000019271 RGD1565726_predicted
	...........................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063230 ENSRNOG00000041477
rat	((..((((((((((............((.(((((........))).)).))))))))))))..)).	0.730 -22.40

rat

chromosome:8:126153350:126153415:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063230|ENSRNOG00000041477 ## Same_strand|Intronic_coding|ENSRNOT00000026073|ENSRNOG00000019271 ## Same_strand|Boundary_non-coding|ENSRNOT00000055871|ENSRNOG00000019271 ## ENSRNOG00000019271|protein_coding|RGD1565726_predicted| ## ENSRNOG00000041477|miRNA|| ## {Repeats: B1_Mur1 3 147 -1 class=SINE,B1_Mur1 30 48 -1 class=SINE/Alu}

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_nonpairedHIGH (1 loci)

block2692866 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_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

0.123

no

SINE,SINE/Alu

0.67/0.67

18/18/0.00

0.0

0.0

1

0

1

0

12

-1

5arm_loop

50

nd

0.33

2

1

1

na

na

		reads	miRBase family seed
seed	-------------GCCUUCU-------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	------------TGCCTTCTGGGTGCTGGG---------------------------------------------------	18	1
rat	tccacctgcctcTGCCTTCTGGGTGCTGGGattaaaggcatgcaccaccactgcccagctggtactggtaattttgaagga
	*********************************************************************************
	.....>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063236 ENSRNOG00000041483
rat	......((((..((((..((((((..(((..................)))..))))))..))))..))))...........	0.990 -24.87

rat

chromosome:X:40838610:40838690:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063236|ENSRNOG00000041483 ## ENSRNOG00000041483|miRNA|| ## {Repeats: B1_Rn 31 49 -1 class=SINE/Alu,B1_Rn 1 139 -1 class=SINE}

miRNAunknown_rep_lenNOK_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

block1611731 (miRNA) [miRNAunknown_rep_lenNOK_Multihit_loopOverlap_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

0.711

no

LTR,LTR/ERVL

0.56/0.56

18/18/0.00

0.0

0.0

1

0

1

0

20

-4

3arm_loop

22

nd

0.50

5

1

1

na

na

		reads	miRBase family seed
seed	---------------------------------------UCUCUUC------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------CTCTCTTCTTTGCCTGCC--------------------	18	1
rat	tgctggagacctatgtaaggacattggaagaaggaagaCTCTCTTCTTTGCCTGCCtgccttgtgagactgagcaa
	****************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063268 ENSRNOG00000041515
rat	((((..((..((...(((((.....((...(((((((.....))))))).))......)))))..)).)).)))).	0.780 -16.10

rat

chromosome:4:183448611:183448686:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063268|ENSRNOG00000041515 ## ENSRNOG00000041515|miRNA|| ## {Repeats: MT2_Rat2 306 324 1 class=LTR/ERVL,MT2_Rat2 -3 484 1 class=LTR}

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