miR-Intess™

other hairpins

novel_lenNOK_cloningOK_shortStem_loopOverlap_bulgeHIGH (1 loci)

novel_lenNOK_cloningOK_shortStem_loopOverlap_randfoldOK_nonpairedHIGH (1 loci)

block2667106 [novel_lenNOK_cloningOK_shortStem_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

no

0.002

no

no

0.44/0.47

18/19/0.00

0.0

0.0

9

0

3

0

2

-1

5arm_loop

1

nd

0.39

3

11

3

na

na

		reads	miRBase family seed
seed	---AUCAAAC------------------------------------	11	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2
	--GATCAAACAACCAGGTCA--------------------------	18	4	5	1
	--GATCAAACAACCAGGTCAC-------------------------	19	1	-	-
rat	ggGATCAAACAACCAGGTCAccattagacacaggttgagggtcccc
	**********************************************
rat	((((((...(((((..(((.......)))...)))))..)))))).	1.000 -19.00

rat

chromosome:X:14383870:14383915:-1

intergenic

novel_lenNOK_cloningOK_shortStem_mirtron (1 loci)

block485701 [novel_lenNOK_cloningOK_shortStem_mirtron]

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

0.024

no

no

0.53/0.56

18/19/0.00

0.0

0.1

14

0

8

0

1

32

5arm

1

3

0.26

3

14

8

na

na

		reads	miRBase family seed
seed	--GAGGUAG-------------------------------------------------------------------------------------------------------	14	let-7a/7b/7c/7d/7e/7f/7i/miR-98
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S1	T4S2	T5S2
	-TGAGGTAGGCTGGGTACA---------------------------------------------------------------------------------------------	18	1	1	3	2	2	1	1	1
	-TGAGGTAGGCTGGGTACAA--------------------------------------------------------------------------------------------	19	-	-	-	1	-	1	-	-
rat	tTGAGGTAGGCTGGGTACAAgagaaaggaggcctgcaggggagatgtggaggacacccctttaccgttcccttactctgacaggtctcccacgactttgctatcaactttga
	****************************************************************************************************************
	>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000031427 ENSRNOG00000018399 LOC691478
	>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024978 ENSRNOG00000018399 LOC691478
rat	(((((((.((...((((.(((.....(((((((((((((((((..(((((((.....)))))))..))))).....))).))))))))).....))))))).)).)))))))	0.970 -40.50

rat

chromosome:15:33646730:33646841:1

Same_strand|Boundary_coding|ENSRNOT00000031427|ENSRNOG00000018399 ## ENSRNOG00000018399|protein_coding|LOC691478|

novel_lenNOK_cloningOK_shortStem_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block863441 [novel_lenNOK_cloningOK_shortStem_mirtron_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

no

0.007

no

no

0.55/0.61

18/22/0.65

0.0

1.0

12

0

6

0

1

15

3arm

2

0

0.43

4

20

6

na

na

		reads	miRBase family seed
seed	------------------------------------------------------GCCCUCU---------------	20	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S2	T5S2
	-----------------------------------------------------TGCCCTCTCCTTCTCTCCTAG--	21	4	2	1	1	-	-
	-----------------------------------------------------TGCCCTCTCCTTCTCTCC-----	18	3	1	-	-	-	1
	-----------------------------------------------------TGCCCTCTCCTTCTCTCCTAGT-	22	3	1	-	-	-	-
	-----------------------------------------------------TGCCCTCTCCTTCTCTCCT----	19	1	-	-	-	1	-
	-----------------------------------------------------TGCCCTCTCCTTCTCTCCTA---	20	-	-	-	-	1	-
rat	gctggaacaggtgtggccggagggaggggtagggtgtgcctaccctccttcaaTGCCCTCTCCTTCTCTCCTAGTg
	****************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>	ENSRNOT00000032613 ENSRNOG00000023150 Gpi
rat	((((((..(((...(((..((((((.(((((((.....)))))))))))))...)))....)))....))).))).	0.990 -33.70

rat

chromosome:1:86665063:86665138:-1

Same_strand|Boundary_coding|ENSRNOT00000032613|ENSRNOG00000023150 ## ENSRNOG00000023150|protein_coding|Gpi|glucose phosphate isomerase [Source:RefSeq_peptide;Acc:NP_997475]

novel_lenNOK_gcHIGH_5varHIGH_loopOverlap_nonpairedHIGH (1 loci)

block2349910 [novel_lenNOK_gcHIGH_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

no

0.166

no

no

1.00/1.00

18/19/0.00

2.2

1.8

4

0

3

0

15

-4

5arm_loop

2

nd

0.37

3

4

3

na

na

		reads	miRBase family seed
seed	--------------------CGGGCGG--------------------------------------	2	novel
seed	-----------------GGGCGGG-----------------------------------------	1	novel
seed	----------------GGGGCGG------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T4S1	T4S2
	-------------------GCGGGCGGGGCCGGGGGC----------------------------	18	1	-	1
	---------------CGGGGCGGGCGGGGCCGGG-------------------------------	19	-	1	-
	----------------GGGGCGGGCGGGGCCGGGG------------------------------	19	1	-	-
rat	gcggtacatgaagtcCGGGGCGGGCGGGGCCGGGGGCggggactggcctggccgcaggggccgcg
	*****************************************************************
rat	(((((........(((...((.(((.(((((((.........))))))).))))).)))))))).	0.830 -33.20

rat

chromosome:8:106197792:106197856:-1

intergenic ## {Repeats: dust 106197820 106197839 0 class=dust,GC_rich 34 56 -1 class=Low_complexity,GC_rich 1 56 -1 class=Low_complexity} ## {SimpF: 1 Eponine}

novel_lenNOK_gcHIGH_5varHIGH_loopOverlap_randfoldOK (1 loci)

block1013754 [novel_lenNOK_gcHIGH_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

no

0.006

no

no

0.79/0.94

18/20/0.25

2.2

2.2

4

0

3

0

14

-3

5arm_loop

1

nd

0.28

3

4

3

na

na

		reads	miRBase family seed
seed	-----------------CUCCGCC----------------------------------------	1	novel
seed	-------------------CCGCCCG--------------------------------------	1	novel
seed	------------------UCCGCCC---------------------------------------	1	novel
seed	---------------UUCUCCG------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1
	----------------TCTCCGCCCGGCCGCCGCC-----------------------------	19	1	-	-
	-----------------CTCCGCCCGGCCGCCGCCCT---------------------------	20	-	1	-
	------------------TCCGCCCGGCCGCCGCCC----------------------------	18	-	1	-
	--------------ATTCTCCGCCCGGCCGCCG-------------------------------	19	-	-	1
rat	acccagtgtgcattATTCTCCGCCCGGCCGCCGCCCTcagcgcggcggcgcgggcccacttggg
	****************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000013733 ENSRNOG00000010087 Zfp143
rat	.(((((.(((...........(((((((((((((.......)))))))).))))).))))))))	0.990 -35.20

rat

chromosome:1:167704379:167704442:1

Same_strand|Intronic_non-coding|ENSRNOT00000013733|ENSRNOG00000010087 ## ENSRNOG00000010087|protein_coding|Zfp143|Zinc finger protein 143 (Zfp-143). [Source:UniProtKB/Swiss-Prot;Acc:Q5XIU2] ## {Repeats: GC_rich 1 38 1 class=Low_complexity,GC_rich 1 18 1 class=Low_complexity} ## {SimpF: oe = 0.72 1 CpG}

novel_lenNOK_gcHIGH_5varHIGH_nonpairedHIGH (1 loci)

block1414730 [novel_lenNOK_gcHIGH_5varHIGH_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

no

0.420

no

no

0.89/0.91

18/22/0.14

1.1

2.0

7

0

6

0

11

26

5arm

1

nd

0.37

3

7

6

na

na

		reads	miRBase family seed
seed	-------------CAAGGCG--------------------------------------------------------------------------------------------------	3	novel
seed	------------CCAAGGC---------------------------------------------------------------------------------------------------	2	novel
seed	--------------AAGGCGC-------------------------------------------------------------------------------------------------	1	novel
seed	---------------AGGCGCG------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T4S2	T5S1
	------------CCAAGGCGCGGCCCCGCC----------------------------------------------------------------------------------------	18	1	1	-	-	1	-
	-----------GCCAAGGCGCGGCCCCGCCCCC-------------------------------------------------------------------------------------	22	-	-	-	-	1	-
	-------------CAAGGCGCGGCCCCGCCCC--------------------------------------------------------------------------------------	19	-	-	1	-	-	-
	-----------GCCAAGGCGCGGCCCCGC-----------------------------------------------------------------------------------------	18	-	-	-	1	-	-
	--------------AAGGCGCGGCCCCGCCCCC-------------------------------------------------------------------------------------	19	-	-	-	-	-	1
rat	agggggcgcccGCCAAGGCGCGGCCCCGCCCCCccggaggcggcggtggtggcagtcggctgaaacccgggccacagctgccgggccgcgggggccgccgagcgacgggaggacctct
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009852 ENSRNOG00000007514
rat	(((((...((((.....((.((((...((((((.(((...(((((((.(((((...(((.......))).))))).)))))))..))).)))))).)))).))..))))....)))))	0.890 -67.70

rat

chromosome:3:142715392:142715509:-1

Same_strand|Intronic_non-coding|ENSRNOT00000009852|ENSRNOG00000007514 ## ENSRNOG00000007514|protein_coding|| ## {Repeats: GC_rich 14 36 -1 class=Low_complexity,GC_rich 1 45 -1 class=Low_complexity} ## {SimpF: oe = 0.85 0 CpG}

novel_lenNOK_gcHIGH_5varHIGH_nonpairedHIGH_bulgeHIGH (1 loci)

block2660337 [novel_lenNOK_gcHIGH_5varHIGH_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

0.818

no

no

1.00/1.00

18/23/0.33

1.3

2.0

3

0

3

0

8

3

5arm

3

nd

0.50

4

3

3

na

na

		reads	miRBase family seed
seed	-----------CCCGCGC------------------------------------------------------------	2	novel
seed	---------CCCCCGC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T4S1
	----------CCCCGCGCCCCCCGCCCC--------------------------------------------------	18	-	1	1
	--------GCCCCCGCGCCCCCCGCCCCCCC-----------------------------------------------	23	1	-	-
rat	ttattagtGCCCCCGCGCCCCCCGCCCCCCCcgctctcccgcgcccctcctgcgacccccggtgcgcttgtatgagtg
	******************************************************************************
rat	.((((.((((...((((((...(((......(((......)))........)))......))))))...)))).))))	0.480 -16.74

rat

chromosome:X:8004931:8005008:-1

intergenic ## {Repeats: trf 31 52 0 class=trf,GC_rich 4 26 -1 class=Low_complexity,GC_rich 1 26 -1 class=Low_complexity,dust 8004978 8004999 0 class=dust}

novel_lenNOK_gcHIGH_5varHIGH_randfoldOK (1 loci)

block21815 [novel_lenNOK_gcHIGH_5varHIGH_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

no

0.001

no

no

0.67/1.00

18/21/0.33

2.3

3.7

3

0

3

0

34

0

5arm

1

nd

0.10

2

3

3

na

na

		reads	miRBase family seed
seed	-----------------------------------------GGGGGGG---------------------------------------------------------------	1	novel
seed	------------------------------------UUUUCGG--------------------------------------------------------------------	1	novel
seed	-----------------------------------UUUUUCG---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T4S1
	----------------------------------TTTTTTCGGGGGGGCCCC-----------------------------------------------------------	18	-	1	-
	-----------------------------------TTTTTCGGGGGGGCCCCCCCC-------------------------------------------------------	21	-	-	1
	----------------------------------------CGGGGGGGCCCCCCCCCCC----------------------------------------------------	19	1	-	-
rat	gggggggggggggggatataacnngggaggggtgTTTTTTCGGGGGGGCCCCCCCCCCCaaaaagggggggggaaaaattttccccggaaaaattttttttttttccccca
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057682 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057681 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003133 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057680 ENSRNOG00000002277 NCOR1_RAT
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057679 ENSRNOG00000002277 NCOR1_RAT
rat	(((((..((..(((((.................(((((((((((((((..(((((((((.....)))))))))......))))))))))))))))))))..))..))))).	0.960 -56.62

rat

chromosome:10:48508474:48508584:-1

Same_strand|Boundary_non-coding|ENSRNOT00000003120|ENSRNOG00000002277 ## Same_strand|Intronic_coding|ENSRNOT00000057680|ENSRNOG00000002277 ## ENSRNOG00000002277|protein_coding|NCOR1_RAT|Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:Q9WUB5] ## {Repeats: dust 48508526 48508536 0 class=dust}

novel_lenNOK_gcHIGH_cloningHIGH_multiarm_randfoldOK_bulgeHIGH (1 loci)

sblock4037 [novel_lenNOK_gcHIGH_cloningHIGH_multiarm_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

no

0.008

no

no

0.61/0.95

18/26/0.65

0.0 0.0 0.0

0.0 1.5 0.6

1 4 17

0 0 0

1 4 10

0 0 0

40 48 26

-4 -11 6

5arm_loop_3arm 5arm_loop_3arm 3arm

1 1 1

nd nd nd

0.38 0.50 0.27

4 4 4

62

10

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CCCGGGG-------------------------------------------	40	novel
seed	-------------------------------------------------------------------GCCCGGG--------------------------------------------	6	novel
seed	-------------------------------------------------GGACGGC--------------------------------------------------------------	4	novel
seed	----------------------------------------------------------------------CGGGGCU-----------------------------------------	3	novel
seed	--------------------------------------------------------------------------GCUGCGC-------------------------------------	3	novel
seed	-----------------------------------------------------------------------GGGGCUG----------------------------------------	2	novel
seed	---------------------------------------------------------------------CCGGGGC------------------------------------------	2	novel
seed	-----------------------------------------GGCCCGG----------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------GGGCUGC---------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGACAAA---------------------------	24	-	-	2	3	-	1	-	1	-	4
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGACAAAG--------------------------	25	1	-	-	1	1	2	-	-	2	-
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGACAA----------------------------	23	-	-	1	1	2	1	-	1	-	-
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGAC------------------------------	21	-	-	-	1	-	1	1	1	-	1
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGA---------------------------------	18	-	1	-	1	1	-	-	1	-	-
	------------------------------------------------GGGACGGCGGCCGTGCCCAG--------------------------------------------------	20	-	1	-	-	-	-	-	1	1	-
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAG--------------------------------	19	-	-	-	-	1	-	-	-	1	1
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGACA-----------------------------	22	-	-	-	1	-	-	-	2	-	-
	------------------------------------------------------------------AGCCCGGGGCTGCGCGAGAGA-------------------------------	21	-	-	-	-	-	-	-	1	1	-
	-------------------------------------------------------------------GCCCGGGGCTGCGCGAGAGA-------------------------------	20	-	-	-	1	-	-	-	-	-	-
	-----------------------------------------------------------------------GGGGCTGCGCGAGAGACAAAGC-------------------------	22	-	-	-	1	-	-	-	-	-	-
	------------------------------------------------------------------AGCCCGGGGCTGCGCGAG----------------------------------	18	-	-	-	-	-	-	1	-	-	-
	----------------------------------------CGGCCCGGGGGACGGCGGCCG---------------------------------------------------------	21	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------------GGCTGCGCGAGAGACAAA---------------------------	18	1	-	-	-	-	-	-	-	-	-
	---------------------------------------------------------------------CCGGGGCTGCGCGAGAGA-------------------------------	18	-	-	1	-	-	-	-	-	-	-
	---------------------------------------------------------------------CCGGGGCTGCGCGAGAGACA-----------------------------	20	-	-	-	-	-	-	-	1	-	-
	---------------------------------------------------------------------CCGGGGCTGCGCGAGAGACAAAG--------------------------	23	-	-	-	1	-	-	-	-	-	-
	----------------------------------------------------------------------CGGGGCTGCGCGAGAGAC------------------------------	18	-	1	-	-	-	-	-	-	-	-
	------------------------------------------------------------------AGCCCGGGGCTGCGCGAGAGACAAAG--------------------------	26	-	-	-	-	-	1	-	-	-	-
	------------------------------------------------------------------AGCCCGGGGCTGCGCGAGA---------------------------------	19	-	-	1	-	-	-	-	-	-	-
	----------------------------------------------------------------------CGGGGCTGCGCGAGAGACAAA---------------------------	21	-	-	-	1	-	-	-	-	-	-
	-------------------------------------------------------------------------GGCTGCGCGAGAGACAAAG--------------------------	19	-	-	-	-	-	-	1	-	-	-
	--------------------------------------------------------------------CCCGGGGCTGCGCGAGAGAC------------------------------	20	-	-	-	1	-	-	-	-	-	-
	--------------------------------------------------------------------CCCGGGGCTGCGCGAGAGACAA----------------------------	22	-	-	1	-	-	-	-	-	-	-
	------------------------------------------------GGGACGGCGGCCGTGCCC----------------------------------------------------	18	-	-	-	-	1	-	-	-	-	-
	-------------------------------------------------------------------------GGCTGCGCGAGAGACAAAGC-------------------------	20	-	-	1	-	-	-	-	-	-	-
	------------------------------------------------------------------AGCCCGGGGCTGCGCGAGAGACA-----------------------------	23	-	-	-	-	-	-	-	-	-	1
rat	gctcccggcggccagaacagaggggtagagcagttctccgcggcccgggggacggcggccgtgcccaGCCCGGGGCTGCGCGAGAGACAAAGccctctctgctgtccgacccgggcgc
	**********************************************************************************************************************
rat	((.((((((((.(((..(((((((((.......(((((((((((((.(((...((((....))))...))).)))))))).))))).....)))).)))))))).)))..))))).))	1.000 -68.00

rat

chromosome:14:36515862:36515979:-1

intergenic

novel_lenNOK_gcHIGH_cloningOK_5varHIGH_loopOverlap (1 loci)

block1488499 [novel_lenNOK_gcHIGH_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

0.137

no

no

0.89/0.95

18/19/0.00

1.7

2.0

26

0

8

0

38

-5

3arm_loop

1

nd

0.16

1

26

8

na

na

		reads	miRBase family seed
seed	--------------------------------------------------------CCCGCGU-------------------------------------------------	9	novel
seed	-------------------------------------------------------CCCCGCG--------------------------------------------------	8	novel
seed	-----------------------------------------------------CUCCCCG----------------------------------------------------	7	novel
seed	------------------------------------------------------UCCCCGC---------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------------------------------------------CCCCGCGTCCCGCCGCCG---------------------------------------	18	1	-	-	2	-	3	1	1
	----------------------------------------------------CCTCCCCGCGTCCCGCCG------------------------------------------	18	3	2	-	-	-	2	-	-
	------------------------------------------------------TCCCCGCGTCCCGCCGCCG---------------------------------------	19	-	-	3	-	2	-	-	-
	------------------------------------------------------TCCCCGCGTCCCGCCGCC----------------------------------------	18	1	-	-	-	1	1	-	-
	-----------------------------------------------------CTCCCCGCGTCCCGCCGCC----------------------------------------	19	-	2	-	-	-	-	-	-
	-------------------------------------------------------CCCCGCGTCCCGCCGCCGG--------------------------------------	19	-	-	1	-	-	-	-	-
rat	cgtcacctgtcggcggcggccgggaacaggtgcccgcaggcggcgcagcggtCCTCCCCGCGTCCCGCCGCCGGcctccagacctgccctccagccccgccccgttcttgac
	****************************************************************************************************************
rat	.((((......(((((.(((.(((..((((((((.((.(((((.((.((((......)))))).))))))).)))......)))))...))).)))))))).......))))	1.000 -53.22

rat

chromosome:3:116575904:116576015:1

intergenic ## {SimpF: oe = 0.92 0 CpG}

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other hairpins:

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