miR-Intess™

confident novel miRNAs

novel_cloningOK_randfoldOK (12 loci)

block15416_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block15416_novel 3arm	1	0	5	2	4	1	0	0	2	4
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block15416_novel 3arm	0.000	0	0.000	0.000	0.000	0.000	0	0	0.000	0.000

block15416 [novel_cloningOK_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

0.53/0.58

18/24/0.89

0.2

1.4

19

0

7

0

20

5

3arm

1

nd

0.06

1

19

7

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------CCCAUCU-----------------------------------	15	novel
seed	------------------------------------------------------------------UCCCAUC------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T5S1	T5S2
	------------------------------------------------------------------TCCCATCTTCTCAGAGCCACGAC--------------------	23	-	2	1	1	-	1	1
	------------------------------------------------------------------TCCCATCTTCTCAGAGCCAC-----------------------	20	-	1	-	2	-	1	1
	-----------------------------------------------------------------CTCCCATCTTCTCAGAGCCAC-----------------------	21	1	-	-	-	1	-	1
	------------------------------------------------------------------TCCCATCTTCTCAGAGCCACG----------------------	21	-	1	-	1	-	-	-
	------------------------------------------------------------------TCCCATCTTCTCAGAGCC-------------------------	18	-	1	-	-	-	-	-
	------------------------------------------------------------------TCCCATCTTCTCAGAGCCA------------------------	19	-	-	1	-	-	-	-
	-----------------------------------------------------------------CTCCCATCTTCTCAGAGCCACGAC--------------------	24	-	-	-	-	-	-	1
rat	AGAGCTGCCCACGGCTTTATTTATGAGTCTGGCTTTGAGAAGCTGGGGAGAGGTAACCTGCTTC-CTCCCATCTTCTCAGAGCCACGACTCAAGAAGAAAAGGGTGCTC
mouse	---------------------------TGTGGCTTTGAGGAGTTGGGAAGAGGTAACCCACTTCTCTCCCATCTTCTCCGAGCCATGA---------------------
	* ********** ** **** **********  **** ************* ****** **
rat	.((((.((((....((((.....(((((((((((((((((((.((((..(((((.....))))) ..)))).))))))))))))).)))))).))))....))))))))	1.000 -58.40
mouse	.(((((((.((((((.(((((((((((.....)))))).))))).)))))).)))))))..	1.000 -33.60

rat	chromosome:10:35815151:35815258:-1	intergenic
mouse	chromosome:11:50069432:50069579:-1	Same_strand|Exonic_non-coding|ENSMUST00000102771|ENSMUSG00000050567|protein_coding|mastermind like 1 (Drosophila) Gene [Source:MGI (curated);Acc:Maml1-001]

block82617_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block82617_novel 3arm	3	1	0	0	5	2	0	2	0	8
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block82617_novel 3arm	0.000	0.000	0	0	0.000	0.000	0	0.000	0	0.001

block82617 [novel_cloningOK_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

0.71/0.75

18/22/0.95

0.0

0.4

14

0

6

0

28

6

3arm

1

nd

0.24

2

21

6

na

na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------CAGGGCC-----------------------------------------	20	novel
seed	--------------------------------------------------------------------------------CCAGGGC------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S2	T5S2
	--------------------------------------------------------------------------------CCAGGGCCTGTCTCCCCTCCT----------------------------	21	2	-	2	1	1	5
	--------------------------------------------------------------------------------CCAGGGCCTGTCTCCCCTCC-----------------------------	20	-	1	3	1	1	2
	--------------------------------------------------------------------------------CCAGGGCCTGTCTCCCCT-------------------------------	18	-	-	-	-	-	1
	-------------------------------------------------------------------------------CCCAGGGCCTGTCTCCCCTCCT----------------------------	22	1	-	-	-	-	-
rat	------------TGGTGCTTCAGCCCTGGCCCCTGGGGGGAGCAGGTCTCGGGGTTATCAAGGGCTGGAAAT--GTGATCCCAGGGCCTGTCTCCCCTCCTGGGCAGGGCGGACATGCCTTGGTGCCAG
human	GGTGCCTCCAATTGGTGCTTCAGCCCTGGCCCCTGTGGGGAACAGGTCTTGGGGTCATGAAGGGCTGGAAACAAGTGACCCCAGGGCCTGTCTCCCTTCTTGGGTAGGGCAGACATGCCTTGGTGCC--
mouse	--------------------------------CTGGGGGGAGCAGGTCTCGGGGTTATCAAGGGCTGGAAAC--ACGATCCCAGGGCCTGTCTCCCCTCCT----------------------------
	*** ***** ******* ***** ** ************     ** ***************** ** *
rat	(((..((((.(((((.((((..((((((((((((((..((((((((..............  ))))))))..)))))).))))))))..))))))))).))........))..))).	0.750 -64.54
human	((..((.......((((..((.(((((.((((....((((((((((((((((((((((.......((....)).))))))))))))))))).)))))....))))))))).))..))))..))..))	0.923 -69.70
mouse	..((((((((((((((..((((((.........((....)  ).))))))..)))))).))))))))..	0.938 -36.80

rat	chromosome:10:64476780:64476894:1	intergenic
human	chromosome:17:24100871:24100997:1	Same_strand|Exonic_non-coding|ENST00000262395|ENSG00000076604|protein_coding|TNF receptor-associated factor 4 (Cysteine-rich domain associated with RING and Traf domains protein 1)(Malignant 62)(RING finger protein 83) [Source:UniProtKB/Swiss-Prot;Acc:Q9BUZ4] ## Same_strand|Boundary_non-coding|ENST00000394925|ENSG00000076604|protein_coding|TNF receptor-associated factor 4 (Cysteine-rich domain associated with RING and Traf domains protein 1)(Malignant 62)(RING finger protein 83) [Source:UniProtKB/Swiss-Prot;Acc:Q9BUZ4]
mouse	chromosome:11:77973121:77973275:-1	Same_strand|Exonic_non-coding|ENSMUST00000017530|ENSMUSG00000017386|protein_coding|Tnf receptor associated factor 4 Gene [Source:MGI (curated);Acc:Traf4-001]

block747712_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block747712_novel 5arm	0	3	0	0	3	3	0	2	1	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block747712_novel 5arm	0	0.000	0	0	0.000	0.000	0	0.000	0.000	0

block747712 [novel_cloningOK_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

0.60/0.64

18/22/0.83

0.0

1.0

12

0

5

0

31

0

5arm

1

nd

0.29

3

12

5

na

na

Families

Member of family novel50 (seed CUGCCUG): block747712_novel, block393982_cand, block2527225_cand

		reads	miRBase family seed
seed	--------------------------------CUGCCUG------------------------------------------------------------------------	12	novel
		len	cloning frequencies
			T1S2	T3S1	T3S2	T4S2	T5S1
	-------------------------------TCTGCCTGGTGTGAAGCCCTG-----------------------------------------------------------	21	-	2	-	2	1
	-------------------------------TCTGCCTGGTGTGAAGCCCT------------------------------------------------------------	20	3	-	-	-	-
	-------------------------------TCTGCCTGGTGTGAAGCCCTGC----------------------------------------------------------	22	-	1	1	-	-
	-------------------------------TCTGCCTGGTGTGAAGCC--------------------------------------------------------------	18	-	-	1	-	-
	-------------------------------TCTGCCTGGTGTGAAGCCC-------------------------------------------------------------	19	-	-	1	-	-
rat	aggcacaaccaccaggagtgttcggccggcgTCTGCCTGGTGTGAAGCCCTGCtctaccgtctgcatggctcctcactgggcaggcgccgctgggcccgtagtggtcagct
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000019351 ENSRNOG00000013774 Lmnb1
rat	.(((...(((((..((...((((((.(((((((((((..(((...((((.(((..........))).))))...)))..)))))))))))))))))))...)))))..)))	1.000 -60.20

rat

chromosome:18:52499001:52499111:1

Same_strand|Intronic_coding|ENSRNOT00000019351|ENSRNOG00000013774 ## ENSRNOG00000013774|protein_coding|Lmnb1|Lamin-B1. [Source:UniProtKB/Swiss-Prot;Acc:P70615]

block1137124_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1137124_novel 5arm	2	0	0	0	11	0	0	2	3	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1137124_novel 5arm	0.000	0	0	0	0.001	0	0	0.000	0.000	0.000

block1137124 [novel_cloningOK_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

0.47/0.50

19/22/0.84

0.0

0.0

13

0

5

0

19

9

5arm

1

nd

0.18

2

19

5

na

na

		reads	miRBase family seed
seed	--------------------CUGGCCC-------------------------------------------------------------------------------	19	novel
		len	cloning frequencies
			T1S1	T3S1	T4S2	T5S1	T5S2
	-------------------TCTGGCCCATCTCTTTAGACCT-----------------------------------------------------------------	22	-	10	2	3	-
	-------------------TCTGGCCCATCTCTTTAGA--------------------------------------------------------------------	19	2	-	-	-	1
	-------------------TCTGGCCCATCTCTTTAGAC-------------------------------------------------------------------	20	-	1	-	-	-
rat	acaccaagtgctcataactTCTGGCCCATCTCTTTAGACCTaattgtttatattttgaaaggtgagggggctggagagatggctcagaggttaggagcactatgtg
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000025506 ENSRNOG00000018746 NP_001099874.1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000025445 ENSRNOG00000018746 NP_001099874.1
rat	.(((..(((((((.(((((((((..((((((((((((.(((.((..((((.....))))..)).)))...))))))))))))..))))))))).)))))))..)))	1.000 -52.70

rat

chromosome:2:31616024:31616129:-1

Same_strand|Intronic_coding|ENSRNOT00000025506|ENSRNOG00000018746 ## ENSRNOG00000018746|protein_coding|NP_001099874.1|solute carrier family 30 (zinc transporter), member 5 [Source:RefSeq_peptide;Acc:NP_001099874]

block1961412_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1961412_novel 3arm	0	0	0	0	3	2	0	0	9	6
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block1961412_novel 3arm	0	0	0	0	0.000	0.000	0	0	0.001	0.000

block1961412 [novel_cloningOK_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

0.002

no

no

0.47/0.53

19/23/0.85

0.2

0.3

11

0

4

0

12

2

3arm

1

nd

0.13

2

20

4

na

na

Families

Member of family novel54 (seed AGAAGCC): block1961412_novel, block78279_cand, block941731_cand

		reads	miRBase family seed
seed	--------------------------------------------------------GAAGCCU---------------------------	13	novel
seed	-------------------------------------------------------AGAAGCC----------------------------	6	novel
seed	---------------------------------------------------------AAGCCUA--------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2	T5S1	T5S2
	-------------------------------------------------------AGAAGCCTAAGTCTGCTCTGAC-------------	22	1	-	4	2
	-------------------------------------------------------AGAAGCCTAAGTCTGCTCTGACT------------	23	-	1	3	-
	------------------------------------------------------GAGAAGCCTAAGTCTGCTCTGAC-------------	23	1	-	1	2
	------------------------------------------------------GAGAAGCCTAAGTCTGCTC-----------------	19	-	-	1	1
	-------------------------------------------------------AGAAGCCTAAGTCTGCTCTGA--------------	21	-	1	-	-
	-------------------------------------------------------AGAAGCCTAAGTCTGCTCT----------------	19	-	-	-	1
	--------------------------------------------------------GAAGCCTAAGTCTGCTCTGACT------------	22	1	-	-	-
rat	gctgaaccctccttcccagcctagagcaggcttaactctttcctccctgcctagGAGAAGCCTAAGTCTGCTCTGACTaaagaggccagc
	******************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005990 ENSRNOG00000004309 Actn1_v3
rat	((((...((((.((...((..(((((((((((((.((.((((((........))))))))..))))))))))))).)))).)))).))))	0.990 -32.20

rat

chromosome:6:103141587:103141676:-1

Same_strand|Boundary_non-coding|ENSRNOT00000040528|ENSRNOG00000004309 ## Same_strand|Intronic_non-coding|ENSRNOT00000005990|ENSRNOG00000004309 ## ENSRNOG00000004309|protein_coding|Actn1_v3|Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin-1) (F-actin cross-linking protein). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z1P2]

block2309589_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2309589_novel 3arm	1	0	2	2	4.500	6.500	0	2	0	4
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2309589_novel 3arm	0.000	0	0.000	0.000	0.000	0.000	0	0.000	0	0.000

block2309589 [novel_cloningOK_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

0.50/0.55

18/22/0.78

0.0

0.4

14

0

7

0

12

2

3arm

1

nd

0.14

2

23

7

na

na

		reads	miRBase family seed
seed	-------------------------------------------------CAGACAG--------------------------	22	novel
seed	-----------------------------------------------GUCAGAC----------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S2
	------------------------------------------------TCAGACAGCTGAGTCACTCTG-------------	21	-	2	-	2	4	1	2
	------------------------------------------------TCAGACAGCTGAGTCACTC---------------	19	-	-	2	1	-	-	-
	------------------------------------------------TCAGACAGCTGAGTCACTCTGC------------	22	-	-	-	-	2	-	1
	------------------------------------------------TCAGACAGCTGAGTCACTCT--------------	20	1	-	-	1	-	-	1
	------------------------------------------------TCAGACAGCTGAGTCACT----------------	18	-	-	-	1	1	-	-
	----------------------------------------------TGTCAGACAGCTGAGTCACTCT--------------	22	-	-	-	-	-	1	-
rat	GGTGACAGTTTGCAATGTGACTCAGCTATCTGAACAGTCACCCCAATGTCAGACAGCTGAGTCACTCTGCAAATTGTCACCC
human	ATTG---------AATGGGA-GCAGCCAACTGGC---TCATCCACTTGTCAGACAGCTGAGTCATTTGAT------------
	**         **** **  **** * ***     *** **   ****************** *
rat	((((((((((((((..(((((((((((.((((.(((..........))))))).)))))))))))..)))))))))))))).	1.000 -51.00
human	((..         (((((.. .((((...(((((   ..........)))))...))))..)))))..))	0.721 -16.50

rat	chromosome:8:55466026:55466107:-1	intergenic
human	chromosome:2:141965691:141965812:1	Opposite_strand|Intronic_coding|ENST00000389484|ENSG00000168702|protein_coding|Low-density lipoprotein receptor-related protein 1B Precursor (Low-density lipoprotein receptor-related protein-deleted in tumor)(LRP-DIT) [Source:UniProtKB/Swiss-Prot;Acc:Q9NZR2]

block2352273_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2352273_novel 5arm	2	2	0	0	1	1	2	2	0	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2352273_novel 5arm	0.000	0.000	0	0	0.000	0.000	0.000	0.000	0	0.000

block2352273 [novel_cloningOK_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

0.005

no

no

0.42/0.46

19/24/0.83

0.0

1.4

12

0

7

0

29

3

5arm

1

nd

0.14

2

12

7

na

na

		reads	miRBase family seed
seed	------------------------------UAACCCU----------------------------------------------------------------------------------	12	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S2
	-----------------------------ATAACCCTTACCACAGAACCTG--------------------------------------------------------------------	22	-	2	-	-	2	-	-
	-----------------------------ATAACCCTTACCACAGAACCT---------------------------------------------------------------------	21	-	-	-	-	-	2	1
	-----------------------------ATAACCCTTACCACAGAACCTGTC------------------------------------------------------------------	24	2	-	-	1	-	-	-
	-----------------------------ATAACCCTTACCACAGAAC-----------------------------------------------------------------------	19	-	-	1	-	-	-	1
rat	TTCCTCTGAAGCTTTTGTGCCTGGCAGACATAACCCTTACCACAGAACCTGTCAGCAGGA-TGTCACAGGACCTGGGTGAATGGGTTGTGCCTGCCTGTCCTCACCACTGCCAGGGAAG
mouse	-----------------------------ATAACCCTTGCCACAGAAACTGTCAACAGGGCTGTACCAGTACCTGGGCGAGTGGGCTGT------------------------------
	********* ******** ****** ****  ***  *** ******* ** **** ***
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056453 ENSRNOG00000011491 NP_001102246.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015344 ENSRNOG00000011491 NP_001102246.1
rat	((((.(((..((....(((...(((((.(((((((((((((.(((..(((((..((.... .)).)))))..))))))))..)))))))).)))))......)))....))))))))).	0.780 -47.10
mouse	....((((((((.(((..((((...(((....)))..))))..))))))))).)).....	0.804 -21.30

rat	chromosome:8:109223934:109224051:-1	Same_strand|Boundary_non-coding|ENSRNOT00000015534|ENSRNOG00000011491 ## Same_strand|Intronic_coding|ENSRNOT00000015344|ENSRNOG00000011491 ## Same_strand|Intronic_non-coding|ENSRNOT00000056453|ENSRNOG00000011491 ## ENSRNOG00000011491|protein_coding|NP_001102246.1|DnaJ (Hsp40) homolog, subfamily C, member 13 [Source:RefSeq_peptide;Acc:NP_001102246]
mouse	chromosome:9:104066692:104066849:-1	Same_strand|Intronic_coding|ENSMUST00000035170|ENSMUSG00000032560|protein_coding|DnaJ (Hsp40) homolog, subfamily C, member 13 Gene [Source:MGI Symbol;Acc:MGI:2676368]

block2704919_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2704919_novel 5arm	3	4	0	0	2	1	0	0	5	3
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2704919_novel 5arm	0.000	0.000	0	0	0.000	0.000	0	0	0.000	0.000

block2704919 [novel_cloningOK_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

0.007

no

no

0.67/0.72

18/22/0.72

0.0

1.8

18

0

6

0

31

2

5arm

1

nd

0.11

1

18

6

na

na

		reads	miRBase family seed
seed	--------------------------------GGGGGCA----------------------------------------------------------------------------------	18	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T5S1	T5S2
	-------------------------------TGGGGGCAGGCCGGATCTAG----------------------------------------------------------------------	20	2	-	1	1	1	2
	-------------------------------TGGGGGCAGGCCGGATCTAGTG--------------------------------------------------------------------	22	-	1	1	-	3	-
	-------------------------------TGGGGGCAGGCCGGATCT------------------------------------------------------------------------	18	1	1	-	-	-	1
	-------------------------------TGGGGGCAGGCCGGATCTA-----------------------------------------------------------------------	19	-	2	-	-	-	-
	-------------------------------TGGGGGCAGGCCGGATCTAGT---------------------------------------------------------------------	21	-	-	-	-	1	-
rat	GGAAGGTGGGTGAGGAGGGCTCCTCAGTCCCTGGGGGCAGGCCGGATCTAGTGGTGACGAGAGAGC-CCTAGATGTGGTCCCTGCGCCCATAGGACAGGTGAGCGCCAGCCCAGACTGGCC
human	-------------------------------AGGGGGCAGGCCGGAGTTGAGGATGATGTTTGATCACCGCAATGTCAGCCGTGAGCC------------GTGCTCC--------CTGGC-
	**************  *   * *** *   ** * **   ****   ** ** ***            * ** **        *****
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059031 ENSRNOG00000004257 Ctps2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000059030 ENSRNOG00000004257 Ctps2
rat	((.((.(((((..((...((((.((.((((.((((.((((((((.((((((.(((.........)) ))))))).)))..))))).))))..)))).)).)))).)).)))))..))..))	0.700 -57.80
human	((((((((((((((.((((.((.((((.....)))))).)))).....)))...)))            .))))))        ))...	0.999 -29.90

rat	chromosome:X:52534661:52534780:-1	Same_strand|Intronic_non-coding|ENSRNOT00000059031|ENSRNOG00000004257 ## Same_strand|Boundary_non-coding|ENSRNOT00000005669|ENSRNOG00000004257 ## Same_strand|Intronic_coding|ENSRNOT00000059030|ENSRNOG00000004257 ## ENSRNOG00000004257|protein_coding|Ctps2|CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2). [Source:UniProtKB/Swiss-Prot;Acc:Q5U2N0]
human	chromosome:5:175070841:175070909:1	intergenic

block2835051_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2835051_novel 3arm	0	1	1	1	3	2	2	0	2	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block2835051_novel 3arm	0	0.000	0.000	0.000	0.000	0.000	0.000	0	0.000	0

block2835051 [novel_cloningOK_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

0.39/0.41

18/22/0.75

0.0

1.0

12

0

7

0

28

7

3arm

1

nd

0.14

2

12

7

na

na

Clusters

Located in cluster 87: rno-mir-542, block2835051_novel

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UACCUUG------------------------------------------	12	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T5S1
	----------------------------------------------------------------------TTACCTTGTCCAAAAGCATC------------------------------	20	-	-	1	1	-	2	2
	----------------------------------------------------------------------TTACCTTGTCCAAAAGCATCTC----------------------------	22	-	-	-	2	1	-	-
	----------------------------------------------------------------------TTACCTTGTCCAAAAGCA--------------------------------	18	1	1	-	-	1	-	-
rat	ctgtcagtccacggaggcatcaccagagatgcttctggacaatgggaaaatagatctctagaaattaatgTTACCTTGTCCAAAAGCATCTCtggtgctgccagaagtttatctgttcat
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000046779 ENSRNOG00000037484
rat	.((.(((...((...((((.((((((((((((((.(((((((.((....((.(((........))).))....))))))))).)))))))))))))).))))....))....)))..)).	0.430 -47.70

rat

chromosome:X:139996899:139997018:-1

Opposite_strand|Intronic_coding|ENSRNOT00000046779|ENSRNOG00000037484 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000056740|ENSRNOG00000037484 ## ENSRNOG00000037484|protein_coding||

block182671_novel

Cloning frequencies

absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block182671_novel 5arm	0.500	1	0	0	0	1	0	0	0.500	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
block182671_novel 5arm	0.000	0.000	0	0	0	0.000	0	0	0.000	0

block182671 [novel_cloningOK_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

0.61/0.67

20/23/1.00

0.5

0.7

12

0

4

0

30

2

5arm

2

nd

0.26

2

12

4

na

na

Clusters

Located in cluster 18: block182671_novel, block182672_novel

Families

Member of family novel19 (seed GUCCCCA): block182671_novel, block182671_novel, block182672_novel, block182672_novel, sblock3519_cand

		reads	miRBase family seed
seed	------------------------------------------------------------------GUCCCCA------------------------------------------	3	novel
seed	-------------------------------------------------------------------UCCCCAC-----------------------------------------	3	novel
seed	-------------------------------GUCCCCA-----------------------------------------------------------------------------	3	novel
seed	--------------------------------UCCCCAC----------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T5S1
	-------------------------------GTCCCCACCGTGGTTGCAGA----------------------------------------------------------------	20	-	2	-	-
	------------------------------------------------------------------GTCCCCACCGTGGTTGCAGA-----------------------------	20	-	2	-	-
	-----------------------------------------------------------------TGTCCCCACCGTGGTTGCAGAC----------------------------	22	-	-	1	-
	------------------------------------------------------------------GTCCCCACCGTGGTTGCAGAC----------------------------	21	-	-	-	1
	------------------------------TGTCCCCACCGTGGTTGCAGACA--------------------------------------------------------------	23	1	-	-	-
	------------------------------TGTCCCCACCGTGGTTGCAGAC---------------------------------------------------------------	22	-	-	1	-
	------------------------------TGTCCCCACCGTGGTTGCAGA----------------------------------------------------------------	21	-	-	1	-
	-------------------------------GTCCCCACCGTGGTTGCAGAC---------------------------------------------------------------	21	-	-	-	1
	-----------------------------------------------------------------TGTCCCCACCGTGGTTGCAGACA---------------------------	23	1	-	-	-
	-----------------------------------------------------------------TGTCCCCACCGTGGTTGCAGA-----------------------------	21	-	-	1	-
rat	ccaccatggttgcagacatgtgctacgtgcTGTCCCCACCGTGGTTGCAGACAtgtgctacgtgcTGTCCCCACCGTGGTTGCAGACAtgtgctatgtgctgtccccactgtggt
	*******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001412 ENSRNOG00000001065 Pscd3
rat	((((..(((..(((((((((.((.(((((((((..((((.((((..((((.((((.....))))))))..)))).))))..)))).)))))))))))).))))..)))..)))).	1.000 -57.40

rat

chromosome:12:11178279:11178393:-1

Same_strand|Intronic_coding|ENSRNOT00000001412|ENSRNOG00000001065 ## ENSRNOG00000001065|protein_coding|Pscd3|Cytohesin-3 (PH, SEC7 and coiled-coil domain-containing protein 3) (SEC7 homolog C) (rSec7-3). [Source:UniProtKB/Swiss-Prot;Acc:P97696] ## {Repeats: trf 52 75 0 class=trf}

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confident novel miRNAs:

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