miR-Intess™

other hairpins

novel_cloningHIGH_nonpairedHIGH_bulgeHIGH (11 loci)

block1739441 [novel_cloningHIGH_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

no

0.466

no

no

0.52/0.58

18/22/0.77

0.0

0.0

29

0

9

0

10

26

3arm

1

nd

0.35

4

56

9

na

na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------CCCUGAG----------------------	56	miR-125a/125b/351
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------------------------------------------------------------TCCCTGAGACCCTACCATGT----------	20	11	18	1	2	-	1	4	1	2
	-----------------------------------------------------------------------------------TCCCTGAGACCCTACCATG-----------	19	2	3	-	-	-	-	1	1	2
	-----------------------------------------------------------------------------------TCCCTGAGACCCTACCAT------------	18	1	-	1	-	1	-	1	-	-
	-----------------------------------------------------------------------------------TCCCTGAGACCCTACCATGTT---------	21	1	1	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------------TCCCTGAGACCCTACCATGTTC--------	22	-	-	-	-	-	-	1	-	-
rat	gactggaggtgtgggctatttaggggaaggggtagtcactgatgtccagcaggagtccttgaaaggcaaagcccactacagcaTCCCTGAGACCCTACCATGTtcctcttctc
	*****************************************************************************************************************
	........................................................................................................>>>>>>>>>>>>>>>>>>>	ENSRNOT00000017903 ENSRNOG00000013320 RGD1561916_predicted
rat	((..(((((.((((......(((((..(((((((((..((..((((...((((....))))...)))).))...))))).....))))....)))))))))...)))))..))	0.650 -33.40

rat

chromosome:5:58937589:58937701:-1

Same_strand|Boundary_non-coding|ENSRNOT00000017903|ENSRNOG00000013320 ## ENSRNOG00000013320|protein_coding|RGD1561916_predicted|

block1973138 [novel_cloningHIGH_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

no

0.078

no

no

0.26/0.35

19/24/0.97

0.0

1.0

53

0

5

0

9

9

5arm

1

nd

0.33

4

67

5

na

na

		reads	miRBase family seed
seed	----------CAGAACA------------------------------------------------------------------------------	63	novel
seed	------------GAACACA----------------------------------------------------------------------------	2	novel
seed	---------GCAGAAC-------------------------------------------------------------------------------	1	novel
seed	-------AUGCAGA---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T4S2	T5S1
	---------GCAGAACACATAGTTAAAAGATGT--------------------------------------------------------------	24	-	1	1	-	35
	---------GCAGAACACATAGTTAAAAGA-----------------------------------------------------------------	21	1	-	-	-	18
	---------GCAGAACACATAGTTAAAAGAT----------------------------------------------------------------	22	1	-	-	-	2
	---------GCAGAACACATAGTTAAAAGATG---------------------------------------------------------------	23	-	-	-	-	2
	--------TGCAGAACACATAGTTAAAAGA-----------------------------------------------------------------	22	1	-	-	-	-
	---------GCAGAACACATAGTTAAAA-------------------------------------------------------------------	19	-	-	-	1	-
	---------GCAGAACACATAGTTAAAAG------------------------------------------------------------------	20	-	-	-	-	1
	-----------AGAACACATAGTTAAAAGATGT--------------------------------------------------------------	22	-	-	-	-	1
	-----------AGAACACATAGTTAAAAGA-----------------------------------------------------------------	19	-	-	-	-	1
	------TATGCAGAACACATAGTTAAAAGA-----------------------------------------------------------------	24	-	-	-	-	1
rat	cacatatatGCAGAACACATAGTTAAAAGATGTaagagtttatgctatttttcctggactctgttccatttacccgtgttacgtctgcactgtgt
	***********************************************************************************************
rat	.(((((..((((((..((((.((....(((((..((((((((............))))))))....)))))))..))))....)))))).)))))	0.870 -19.80

rat

chromosome:6:122564680:122564774:-1

intergenic

block2420435 [novel_cloningHIGH_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

no

0.652

no

no

0.35/0.40

18/24/0.97

0.0

0.0

116

0

6

0

14

7

5arm

1

nd

0.48

5

151

6

na

na

		reads	miRBase family seed
seed	---------------CGUUUUA----------------------------------------------------------	149	novel
seed	----------------GUUUUAC---------------------------------------------------------	1	novel
seed	-------------UCCGUUU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T4S2	T5S1	T5S2
	--------------CCGTTTTACACAAGGTTTTGA---------------------------------------------	21	7	4	4	2	116	1
	--------------CCGTTTTACACAAGGTTTTG----------------------------------------------	20	-	-	-	-	5	-
	--------------CCGTTTTACACAAGGTTTTGATG-------------------------------------------	23	-	-	-	-	4	-
	--------------CCGTTTTACACAAGGTTTT-----------------------------------------------	19	-	2	-	-	1	-
	--------------CCGTTTTACACAAGGTTT------------------------------------------------	18	-	-	-	-	2	-
	--------------CCGTTTTACACAAGGTTTTGATGA------------------------------------------	24	-	-	-	-	1	-
	---------------CGTTTTACACAAGGTTTTGA---------------------------------------------	20	-	-	-	-	1	-
	------------TTCCGTTTTACACAAGGTTTTGA---------------------------------------------	23	-	-	-	-	1	-
rat	gagtggtatcatttCCGTTTTACACAAGGTTTTGAtgaaggtttgatgttcatggttctgtaatgagggatggtgttcta
	********************************************************************************
rat	.((...(((((((((((((....((.(((.....(((((.((...)).)))))...))))))))).)))))))))..)).	0.790 -11.60

rat

chromosome:8:72092184:72092263:1

intergenic

block1041625 [novel_cloningHIGH_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

no

0.036

no

no

0.50/0.58

18/24/0.85

0.0

0.0

56

0

10

0

9

16

3arm

1

nd

0.32

5

113

10

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------AGACCUU-----------------------	109	novel
seed	----------------------------------------------------------------------GACCUUG----------------------	2	novel
seed	-----------------------------------------------------------------GUGCAGA---------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACCTGT---------	22	3	7	22	17	4	10	1	2	-	1
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACCTG----------	21	1	4	5	4	-	1	-	1	-	-
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACC------------	19	2	2	2	1	-	1	-	-	-	2
	--------------------------------------------------------------------CAGACCTTGGTGTCCAAC-------------	18	-	-	-	6	-	-	-	-	-	-
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACCT-----------	20	1	1	3	-	-	-	-	-	-	-
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACCTGTTT-------	24	-	-	-	3	-	-	-	-	-	-
	---------------------------------------------------------------------AGACCTTGGTGTCCAACCTGT---------	21	-	-	-	-	-	2	-	-	-	-
	--------------------------------------------------------------------CAGACCTTGGTGTCCAACCTGTT--------	23	-	-	-	1	-	-	-	-	1	-
	----------------------------------------------------------------TGTGCAGACCTTGGTGTCCAAC-------------	22	-	-	-	-	-	1	-	-	-	-
	----------------------------------------------------------------TGTGCAGACCTTGGTGTC-----------------	18	-	-	-	-	-	1	-	-	-	-
rat	aggcacttagaacgctcagaggtcctgacaggaaggagatcaaagcttgcaggagctttctgcctgtgCAGACCTTGGTGTCCAACCTGTttgtgctta
	***************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000020809 ENSRNOG00000015491 Rcl1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048910 ENSRNOG00000015491 Rcl1
rat	((((((.(((.(((((..(((((.((((((((.((((......(((((....))))))))).))))).))))))))))))).....)))...)))))).	0.690 -33.40

rat

chromosome:1:232781306:232781404:1

Same_strand|Intronic_coding|ENSRNOT00000020809|ENSRNOG00000015491 ## ENSRNOG00000015491|protein_coding|Rcl1|RNA terminal phosphate cyclase-like 1 [Source:RefSeq_peptide;Acc:NP_001013170]

block425882 [novel_cloningHIGH_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

no

0.055

no

no

0.42/0.46

21/24/1.00

0.0

0.0

44

0

4

0

5

20

5arm

1

nd

0.33

4

53

4

na

na

		reads	miRBase family seed
seed	------ACACUGU---------------------------------------------------------------	52	novel
seed	---GGCACAC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T4S2	T5S1	T5S2
	-----CACACTGTCAACAATGAACAG--------------------------------------------------	21	1	1	44	3
	-----CACACTGTCAACAATGAACAGCAA-----------------------------------------------	24	-	-	2	-
	-----CACACTGTCAACAATGAACAGCA------------------------------------------------	23	-	-	1	-
	--TGGCACACTGTCAACAATGAACAG--------------------------------------------------	24	-	-	1	-
rat	tctggCACACTGTCAACAATGAACAGcaagccccaactctttcttacaaataggatggtgttcttgatagttcaga
	****************************************************************************
rat	(((((...((((((((....(((((.((.............(((((....))))))).))))))))))))))))))	0.880 -16.81

rat

chromosome:15:250225:250300:-1

intergenic

block880984 [novel_cloningHIGH_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

no

0.249

no

no

0.42/0.44

18/23/0.90

0.0 0.0

0.0 0.0

67 2

0 0

4 1

0 0

9 6

8 13

3arm 3arm

1 1

nd nd

0.57 0.63

8 11

83

4

na

na

		reads	miRBase family seed
seed	---------------------------------------------------GCAAUAG----------------------	79	novel
seed	--------------------------------------------------------AGUGGUC-----------------	2	novel
seed	-------------------------------------------------CUGCAAU------------------------	1	novel
seed	----------------------------------------------------CAAUAGU---------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T5S1
	--------------------------------------------------TGCAATAGTGGTCACTACACA---------	21	5	1	1	67
	--------------------------------------------------TGCAATAGTGGTCACTACA-----------	19	-	-	-	4
	-------------------------------------------------------TAGTGGTCACTACACAACT------	19	-	-	-	2
	--------------------------------------------------TGCAATAGTGGTCACTAC------------	18	-	-	-	1
	------------------------------------------------TCTGCAATAGTGGTCACTACACA---------	23	-	-	-	1
	---------------------------------------------------GCAATAGTGGTCACTACA-----------	18	-	-	-	1
rat	agctgacttccatgtcactaatccagagaacaccaggactcgttggtgtcTGCAATAGTGGTCACTACACAacttccagc
	********************************************************************************
rat	.((((.......((((((((...((((...((((((......))))))))))...)))))).))............))))	0.440 -16.81

rat

chromosome:1:128999354:128999433:-1

intergenic

block1093575 [novel_cloningHIGH_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

no

0.546

no

no

0.41/0.55

18/25/0.81

0.0

0.0

42

0

9

0

23

0

5arm_loop_3arm

1

nd

0.40

4

85

9

na

na

		reads	miRBase family seed
seed	------------------------GCAUUCA-------------------------------------------------------	47	novel
seed	----------------------CUGCAUU---------------------------------------------------------	11	miR-20a*
seed	-----------------AGCCUCU--------------------------------------------------------------	10	novel
seed	----------------------------UCAAAAC---------------------------------------------------	6	novel
seed	--------------GUCAGCC-----------------------------------------------------------------	5	novel
seed	------------------GCCUCUG-------------------------------------------------------------	2	novel
seed	-------------------CCUCUGC------------------------------------------------------------	2	novel
seed	-----------GCUGUCA--------------------------------------------------------------------	1	novel
seed	----------------CAGCCUC---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------TGCATTCAAAACGCCAACAG-------------------------------------------	20	2	-	-	1	-	-	-	42	1
	---------------------TCTGCATTCAAAACGCCAACAG-------------------------------------------	22	-	-	-	-	-	-	-	10	-
	----------------CAGCCTCTGCATTCAAAAC---------------------------------------------------	19	1	-	-	-	-	-	-	8	-
	-------------TGTCAGCCTCTGCATTCAAAAC---------------------------------------------------	22	-	-	1	-	1	-	-	3	-
	---------------------------TTCAAAACGCCAACAGCATTCTGAC----------------------------------	25	-	1	-	-	-	-	-	2	-
	------------------GCCTCTGCATTCAAAACGCC------------------------------------------------	20	-	1	-	-	-	-	-	1	-
	-----------------AGCCTCTGCATTCAAAACG--------------------------------------------------	19	-	-	-	-	-	1	-	1	-
	---------------------------TTCAAAACGCCAACAGCATTCT-------------------------------------	22	-	-	-	-	-	-	1	1	-
	---------------TCAGCCTCTGCATTCAAAAC---------------------------------------------------	20	-	-	-	-	-	-	-	-	1
	---------------------------TTCAAAACGCCAACAGCA-----------------------------------------	18	-	-	-	-	-	-	-	1	-
	----------TGCTGTCAGCCTCTGCATTCAAA-----------------------------------------------------	23	-	-	-	-	-	-	-	1	-
	----------------CAGCCTCTGCATTCAAAACGCC------------------------------------------------	22	-	-	-	-	-	-	-	1	-
	---------------------TCTGCATTCAAAACGCCAAC---------------------------------------------	20	-	-	-	-	-	-	1	-	-
	-----------------------TGCATTCAAAACGCCAAC---------------------------------------------	18	-	-	1	-	-	-	-	-	-
rat	ggtccaacattgctgtcagcctcTGCATTCAAAACGCCAACAGcattctgacgtccgaattgcggaggggaagtgagtatgctgcc
	**************************************************************************************
rat	(((.((...(((((.((..(((((((((((...(((....(((....))).)))..)))).))))))).)))))))...))..)))	0.980 -21.70

rat

chromosome:20:5540893:5540978:1

intergenic

block1099946 [novel_cloningHIGH_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

no

0.065

no

no

0.42/0.48

19/25/0.86

0.0 1.4

0.0 2.7

26 7

0 0

8 3

0 0

14 0

15 28

3arm 3arm

2 2

nd nd

0.58 0.42

6 4

57

8

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------ACCGUAU------------------------------	46	novel
seed	------------------------------------------------------------------------------------------------CACUUCC-----------------	4	novel
seed	------------------------------------------------------------------------------------CCGUAUU-----------------------------	2	novel
seed	----------------------------------------------------------------------------------------------------UCCACAU-------------	1	novel
seed	---------------------------------------------------------------------------------------UAUUGUC--------------------------	1	novel
seed	-------------------------------------------------------------------------------------------------ACUUCCA----------------	1	novel
seed	------------------------------------------------------------------------------------------UGUCCUC-----------------------	1	novel
seed	-----------------------------------------------------------------------------------------------------CCACAUU------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S1	T5S1	T5S2
	----------------------------------------------------------------------------------TACCGTATTGTCCTCACTTCCACA--------------	24	4	1	1	2	1	-	26	1
	----------------------------------------------------------------------------------TACCGTATTGTCCTCACTTCCAC---------------	23	1	-	-	-	-	-	4	-
	-----------------------------------------------------------------------------------------------TCACTTCCACATTTGCCAA------	19	-	-	1	-	-	-	2	-
	----------------------------------------------------------------------------------TACCGTATTGTCCTCACTTCC-----------------	21	-	1	-	-	-	-	1	-
	----------------------------------------------------------------------------------TACCGTATTGTCCTCACTT-------------------	19	-	-	-	-	-	-	2	-
	-----------------------------------------------------------------------------------ACCGTATTGTCCTCACTTCCACA--------------	23	2	-	-	-	-	-	-	-
	--------------------------------------------------------------------------------------GTATTGTCCTCACTTCCACA--------------	20	-	-	-	-	-	-	1	-
	------------------------------------------------------------------------------------------------CACTTCCACATTTGCCAAGAG---	21	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------------TACCGTATTGTCCTCACTTC------------------	20	-	-	-	-	-	1	-	-
	---------------------------------------------------------------------------------------------------TTCCACATTTGCCAAGAGA--	19	1	-	-	-	-	-	-	-
	-----------------------------------------------------------------------------------------TTGTCCTCACTTCCACATT------------	19	-	-	-	-	-	-	1	-
	-----------------------------------------------------------------------------------------------TCACTTCCACATTTGCCAAGAGAGA	25	-	-	-	-	-	-	1	-
	----------------------------------------------------------------------------------------------------TCCACATTTGCCAAGAGAGA	20	-	-	-	-	-	-	1	-
rat	tttttactgtatttactgggggtggagaaangaaggaagtgaaanctatagttggatgcaatttgtggttgcagccggccgcTACCGTATTGTCCTCACTTCCACAtttgccaagagaga
	************************************************************************************************************************
rat	(((((...(((.....(((..(((..((......((.((((.........(((((.((((((.....)))))).))))))))).))......))..)))..)))....)))...))))).	0.990 -32.70

rat

chromosome:20:13210445:13210564:1

intergenic

novel_cloningOK_5varHIGH_loopOverlap (11 loci)

block97516 [novel_cloningOK_5varHIGH_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

no

0.246

no

no

0.40/0.59

19/23/0.83

6.7

7.4

12

0

2

0

17

-22

3arm_loop

1

nd

0.30

3

12

2

na

na

		reads	miRBase family seed
seed	----------------------------------------------GGGAUUG-----------------------------------	3	novel
seed	-------------------------------------AUUGACG--------------------------------------------	2	novel
seed	----------------------------------------------------GAAGCGC-----------------------------	2	novel
seed	---------------------------------------UGACGCU------------------------------------------	2	novel
seed	---------------------------------------------------UGAAGCG------------------------------	1	novel
seed	-----------------------------------UUAUUGA----------------------------------------------	1	miR-325
seed	----------------------------------------GACGCUG-----------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	------------------------------------TATTGACGCTGGGATTGAAG--------------------------------	20	-	2
	--------------------------------------TTGACGCTGGGATTGAAGCGCAC---------------------------	23	-	2
	---------------------------------------------------TGAAGCGCACGTAAGAATGT-----------------	20	-	2
	----------------------------------TTTATTGACGCTGGGATTGA----------------------------------	20	1	-
	---------------------------------------------TGGGATTGAAGCGCACGTA------------------------	19	-	1
	---------------------------------------TGACGCTGGGATTGAAGCGCAC---------------------------	22	-	1
	--------------------------------------------------TTGAAGCGCACGTAAGAAT-------------------	19	-	1
	---------------------------------------------TGGGATTGAAGCGCACGTAAGAA--------------------	23	-	1
	---------------------------------------------TGGGATTGAAGCGCACGTAA-----------------------	20	-	1
rat	gagaatacgccctgtcacattttttttctctaaaTTTATTGACGCTGGGATTGAAGCGCACGTAAGAATGTaaagaagggcaacttct
	****************************************************************************************
rat	.((((...(((((...((((((((...............((.((((........))))))...)))))))).....)))))...))))	0.610 -18.77

rat

chromosome:10:92629487:92629574:1

intergenic

block1283326 [novel_cloningOK_5varHIGH_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

no

0.483

no

no

0.43/0.50

18/25/0.77

1.4

1.2

23

0

10

0

5

-2

3arm

1

nd

0.28

3

35

10

na

na

		reads	miRBase family seed
seed	-----------------------------------------------AACCUAA------------------	17	novel
seed	----------------------------------------------UAACCUA-------------------	10	novel
seed	-----------------------------------------GGUAUUA------------------------	5	novel
seed	------------------------------------------GUAUUAA-----------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------------------------------TAACCTAAGCTGTGCTCCTAG-----	21	1	-	4	-	3	4	1	1	-	-
	---------------------------------------------TTAACCTAAGCTGTGCTCCT-------	20	-	-	2	1	-	1	-	-	2	-
	----------------------------------------CGGTATTAACCTAAGCTGTGCTCCT-------	25	-	-	2	-	-	1	-	-	-	-
	-----------------------------------------GGTATTAACCTAAGCTGTGCTCCT-------	24	-	-	-	-	1	1	-	-	1	-
	---------------------------------------------TTAACCTAAGCTGTGCTCC--------	19	-	2	-	-	-	-	-	-	-	-
	----------------------------------------CGGTATTAACCTAAGCTGTGCTC---------	23	-	-	-	2	-	-	-	-	-	-
	---------------------------------------------TTAACCTAAGCTGTGCTCCTA------	21	2	-	-	-	-	-	-	-	-	-
	----------------------------------------------TAACCTAAGCTGTGCTCCT-------	19	-	-	1	-	-	-	-	-	-	1
	----------------------------------------------TAACCTAAGCTGTGCTCC--------	18	-	-	-	-	-	1	-	-	-	-
rat	tactgtaattgtatagatcttggcatttaaatatagtactCGGTATTAACCTAAGCTGTGCTCCTAGggtac
	************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015756 ENSRNOG00000011817 LOC688712
rat	((((.((...((((((..(((((......(((((........)))))...)))))))))))...)).)))).	0.750 -11.70

rat

chromosome:2:116169965:116170036:1

Same_strand|Intronic_coding|ENSRNOT00000015756|ENSRNOG00000011817 ## ENSRNOG00000011817|protein_coding|LOC688712|ribosomal protein L22 like 1 [Source:RefSeq_peptide;Acc:NP_001102018]

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other hairpins:

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