miR-Intess™

other hairpins

novel_multiarm_loopOverlap_randfoldOK_nonpairedHIGH (1 loci)

novel_multiarm_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block95151 [novel_multiarm_loopOverlap_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

0.010

no

no

0.41/0.48

21/22/1.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

34 40

-3 -10

5arm_loop 5arm_loop_3arm

1 1

nd nd

0.38 0.64

4 10

2

2

na

na

		reads	miRBase family seed
seed	-----------------------------------------UGGAUAA---------------------------------------------------------------	1	novel
seed	-----------------------------------CAUCACU---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	----------------------------------GCATCACTGGATAAACACTGG--------------------------------------------------------	21	1	-
	----------------------------------------CTGGATAAACACTGGAATGGAT-------------------------------------------------	22	-	1
rat	cagtgcctaggcacatgttagtcactcactgcccGCATCACTGGATAAACACTGGAATGGATgtgtcaataaagtgatgaggacacaaggaccatgtgggcccttggtact
	***************************************************************************************************************
rat	.((((((.(((((((((...(((.((...((.((.(((((((..((..((((..........))))..))..))))))).)).))..)))))))))))...))).))))))	1.000 -38.10

rat

chromosome:10:89480934:89481044:1

intergenic

novel_multiarm_nonpairedHIGH_bulgeHIGH (1 loci)

sblock1950 [novel_multiarm_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

0.285

no

no

0.22/0.52

23/23/1.00

0.0 0.0

0.0 0.0

1 1

0 0

1 1

0 0

27 5

6 28

5arm 3arm

1 1

nd nd

0.35 0.39

4 8

2

2

na

na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------AGAGUGU--------------------	1	novel
seed	----------------------------GUGUAAU---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	----------------------------------------------------------------------------------------TAGAGTGTGGGGAGAAGTGTGTG-----	23	-	1
	---------------------------TGTGTAATGTTTATTTCTTTTCT------------------------------------------------------------------	23	1	-
rat	gggacctcctcatcctttgctcggtttTGTGTAATGTTTATTTCTTTTCTatgacttaaaagttgcattgaggaaaataaaatgctcaTAGAGTGTGGGGAGAAGTGTGTGtgcct
	********************************************************************************************************************
rat	((.((((((((((.....((((.....((.(((...(((((((((((.....((((....)))).....))))))).)))).))).))..))))))))))))........)).)).	0.510 -25.90

rat

chromosome:1:128298873:128298988:1

intergenic

novel_multiarm_shortStem (1 loci)

sblock609 [novel_multiarm_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

no

0.086

no

no

0.39/0.47

18/20/0.75

0.0 0.0

0.0 0.0

1 6

0 0

1 1

0 0

37 3

-1 31

5arm_loop 3arm

1 2

nd nd

0.42 0.10

3 1

8

1

na

na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------UCCAGCC---------------	7	novel
seed	--------------------------------------AAGAGAC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------------------------ATCCAGCCTAATGTAAGAAG---	20	6
	------------------------------------------------------------------------------------------ATCCAGCCTAATGTAAGA-----	18	1
	-------------------------------------TAAGAGACAGAGACGAGGA---------------------------------------------------------	19	1
rat	tgactctgtacagagcaagatttaggcaggatgagtctaagagacagagacgaggaagtcccagtcattgaggtctatttgcttacaggaATCCAGCCTAATGTAAGAAGtca
	*****************************************************************************************************************
rat	.((((((.((((.........((((((.((((((((.....((((.(((((..((....))..))).))...))))....))))......)))).))))))))))))).))).	0.460 -29.30

rat

chromosome:1:102017983:102018095:-1

intergenic

novel_multiarm_shortStem_5varHIGH_loopOverlap_nonpairedHIGH_bulgeHIGH (1 loci)

block881563 [novel_multiarm_shortStem_5varHIGH_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

no

0.136

no

no

0.45/0.50

19/22/0.83

0.0 2.8

0.0 2.8

1 5

0 0

1 1

0 0

28 1

-16 -3

5arm_loop_3arm 3arm

1 1

nd nd

0.35 0.32

4 4

6

2

na

na

		reads	miRBase family seed
seed	------------------------------------------GGCAGAU-----------------	2	novel
seed	----------------------------------GACUUGA-------------------------	1	novel
seed	---------------------------------------------AGAUCUC--------------	1	novel
seed	-----------------------------CAGGUGA------------------------------	1	miR-125a
seed	---------------------------------------GAAGGCA--------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	-----------------------------------------AGGCAGATCTCAGACAAGGT-----	20	-	2
	--------------------------------------------CAGATCTCAGACAAGGTTCTG-	21	-	1
	---------------------------------TGACTTGAAGGCAGATCTCAGA-----------	22	-	1
	--------------------------------------TGAAGGCAGATCTCAGACA---------	19	-	1
	----------------------------TCAGGTGACTTGAAGGCAGA------------------	20	1	-
rat	cctagcattcatgtaactggtttggcttTCAGGTGACTTGAAGGCAGATCTCAGACAAGGTTCTGg
	******************************************************************
	----------------------------------------------------------------------------	ENSRNOT00000016427 ENSRNOG00000012031 St8sia2
rat	.((((...((.(((....((((((.((((.((....)).)))).))))))....))).))..))))	0.980 -20.20

rat

chromosome:1:129022515:129022580:-1

Opposite_strand|Intronic_coding|ENSRNOT00000016427|ENSRNOG00000012031 ## ENSRNOG00000012031|protein_coding|St8sia2|Alpha-2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Sialyltransferase X) (STX). [Source:UniProtKB/Swiss-Prot;Acc:Q07977]

novel_rep_cloningOK_mirtron (1 loci)

block437500 [novel_rep_cloningOK_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

0.104

no

LTR/MaLR

0.57/0.61

19/23/0.75

0.1

1.6

12

0

7

0

14

0

3arm

1

0

0.21

2

12

7

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------GAGCCCU-------------------------------	11	novel
seed	---------------------------------------------------------------UGAGCCC--------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1
	---------------------------------------------------------------TGAGCCCTCCACATCTG--ACCAG---------------	22	-	1	-	-	1	2	-
	---------------------------------------------------------------TGAGCCCTCCACATCTG--ACCAGA--------------	23	-	-	3	-	-	-	-
	---------------------------------------------------------------TGAGCCCTCCACATCTG--AC------------------	19	1	-	-	-	-	-	2
	--------------------------------------------------------------CTGAGCCCTCCACATCTG--ACCAG---------------	23	-	-	-	-	-	1	-
	---------------------------------------------------------------TGAGCCCTCCACATCTG--ACCA----------------	21	-	-	-	1	-	-	-
rat	CAGTAAGCTTGGTGCTGTAGCAGAGGCAGCTGTGGTAGGCTTCCTCAATCTCCTCAGTAATGCTGAGCCCTCCACATCTG--ACCAGATGCGGCTGCTGCTG
mouse	C--CAGGCTAGGAGTGGTACTA-----------------------------CCTACAGAAAACTGAGCCCTCCACATCAGTCATC-----------------
	*   * *** ** *  ***  *                             ***    **  **************** *  * *
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++  +++++>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000012235 ENSRNOG00000008964 Tep1
rat	((((.(((.....((((((.....(((((.(((((..(((.............((((.....)))))))..))))).)))  .))...)))))).)))))))	0.710 -34.41
mouse	.  ..((((.((.((((.....                             .((.(((....)))))....)))).))))))...	0.972 -11.90

rat	chromosome:15:26824204:26824303:-1	Same_strand|Boundary_non-coding|ENSRNOT00000051389|ENSRNOG00000008964 ## Same_strand|Boundary_coding|ENSRNOT00000012235|ENSRNOG00000008964 ## ENSRNOG00000008964|protein_coding|Tep1|Telomerase protein component 1 (rTLP1) (Telomerase-associated protein 1) (Telomerase protein 1) (p240) (p230) (p80 telomerase homolog). [Source:UniProtKB/Swiss-Prot;Acc:O08653]
mouse	chromosome:7:119889823:119889962:1	Same_strand|Intronic_coding|ENSMUST00000106638|ENSMUSG00000055320|protein_coding|TEA domain family member 1 Gene [Source:MGI Symbol;Acc:MGI:101876] ## Same_strand|Intronic_non-coding|ENSMUST00000084705|ENSMUSG00000055320|protein_coding|TEA domain family member 1 Gene [Source:MGI Symbol;Acc:MGI:101876] ## {Repeats: MTC -1 class=LTR/MaLR}

novel_rep_cloningOK_multiarm_DicerNOK_loopOverlap (1 loci)

sblock5731 [novel_rep_cloningOK_multiarm_DicerNOK_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

0.145

no

SINE,SINE/MIR

0.45/0.60

18/24/0.81

0.0 0.0 0.0 0.0 0.0

0.7 0.0 0.0 0.0 0.0

11 1 1 7 5

0 0 0 0 0

6 1 1 2 1

0 0 0 0 0

2 10 23 28 6

9 4 -7 -14 -2

5arm 5arm 5arm_loop_3arm 5arm_loop_3arm 3arm_loop

1 1 1 1 1

nd nd nd nd nd

0.33 0.30 0.56 0.30 0.20

4 4 6 6 2

47

6

-7

-12

		reads	miRBase family seed
seed	---CCAUACG------------------------------------------------------	18	novel
seed	-----------------------------GCAUUGG----------------------------	14	novel
seed	---------------------------------------AGAUGUC------------------	5	novel
seed	-CUCCAUA--------------------------------------------------------	4	novel
seed	----------------------------UGCAUUG-----------------------------	2	miR-33
seed	-------ACGUCCU--------------------------------------------------	1	novel
seed	-----------CCUCUCA----------------------------------------------	1	novel
seed	--UCCAUAC-------------------------------------------------------	1	novel
seed	------------------------GCCUUGC---------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T4S2	T5S1	T5S2
	----------------------------TGCATTGGGGTAGATGTCAG----------------	20	2	-	-	-	7	-
	--TCCATACGTCCTCTCAAGCCC-----------------------------------------	21	-	1	1	1	4	-
	--TCCATACGTCCTCTCAAGCCCTG---------------------------------------	23	-	2	-	-	5	-
	--------------------------------------TAGATGTCAGGGAACTTGAC------	20	-	-	-	-	5	-
	TCTCCATACGTCCTCTCAA---------------------------------------------	19	-	-	1	-	-	1
	----------------------------TGCATTGGGGTAGATGTCAGG---------------	21	-	-	-	-	2	-
	----------------------------TGCATTGGGGTAGATGTCAGGGA-------------	23	-	-	-	-	2	-
	---------------------------TTGCATTGGGGTAGATGTCAG----------------	21	-	-	-	-	2	-
	-CTCCATACGTCCTCTCAAG--------------------------------------------	19	-	-	-	-	1	-
	TCTCCATACGTCCTCTCAAG--------------------------------------------	20	-	-	-	-	1	-
	TCTCCATACGTCCTCTCA----------------------------------------------	18	1	-	-	-	-	-
	--TCCATACGTCCTCTCAAGCCCT----------------------------------------	22	-	-	1	-	-	-
	--TCCATACGTCCTCTCAAG--------------------------------------------	18	-	-	1	-	-	-
	-----------------------TGCCTTGCATTGGGGTAG-----------------------	18	-	-	-	-	1	-
	--TCCATACGTCCTCTCAAGC-------------------------------------------	19	-	-	-	-	1	-
	------TACGTCCTCTCAAGCCCTG---------------------------------------	19	-	-	-	-	-	1
	--TCCATACGTCCTCTCAAGCCCTGC--------------------------------------	24	-	-	-	-	1	-
	----------------------------TGCATTGGGGTAGATGTCA-----------------	19	-	-	-	-	1	-
	----------TCCTCTCAAGCCCTGCCTTG----------------------------------	20	-	-	-	-	1	-
rat	tcTCCATACGTCCTCTCAAGCCCTGcctTGCATTGGGGTAGATGTCAGGGAACTTGACggaggt
	****************************************************************
rat	.......((.(((..((((((((((....(((((......))))))))))..))))).))).))	0.720 -19.70

rat

chromosome:19:15929418:15929481:-1

intergenic ## {Repeats: MIR 94 112 -1 class=SINE/MIR,MIR 59 112 -1 class=SINE}

novel_rep_lenNOK_cloningHIGH_randfoldOK (1 loci)

block1751068 [novel_rep_lenNOK_cloningHIGH_randfoldOK]

Hairpin parameters

miRNA

randfold

RNA

rep

GC min/max

len min/max/mir_range

5'var

3'var

reads

reads edited

libs

libs edited

base distance

loop distance

position

locations

exon distance

unpaired

max bulge

total reads

total libs

dicer

drosha

no

0.006

no

SINE/MIR

0.63/0.67

18/21/0.00

0.0

0.4

1771

0

10

0

19

2

5arm

1

nd

0.21

3

2008

10

na

na

		reads	miRBase family seed
seed	--------------------UGGCCCU----------------------------------------------------------------------	2008	miR-328
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-------------------CTGGCCCTCTCTGGGGTA------------------------------------------------------------	18	1004	53	16	3	49	8	59	22	1	7
	-------------------CTGGCCCTCTCTGGGGTAT-----------------------------------------------------------	19	767	5	2	-	5	2	-	2	-	1
	-------------------CTGGCCCTCTCTGGGGTATG----------------------------------------------------------	20	1	-	-	-	-	-	-	-	-	-
	-------------------CTGGCCCTCTCTGGGGTATGG---------------------------------------------------------	21	1	-	-	-	-	-	-	-	-	-
rat	GCACACTTCAGACTCATTTCTGGCCCTCTCTGGGGTATGGTGCCTTTATTCCTTTGCCTTCAGAGAGGGATGAGTGATTTCTTAAAATGTCTGTGCA
human	-------------------CTGGCCCTCTCTGGG-----------------CCTCAGCTTCCTGGAAGGCTGAGGGGGT--------------GGCG
	***************                 * *   ****   ** ** **** *  *               **
rat	((((.....((((((((((....((((((((((((((.((..........))..))))).)))))))))..))))))...........)))))))).	0.500 -34.00
human	...(((((((((.((                 ((((((....)))..))))).)))))).              ))).	1.000 -24.50

rat	chromosome:5:79241045:79241141:-1	intergenic
human	chromosome:9:131400069:131400205:1	intergenic ## {Repeats: MIR3 1 class=SINE/MIR} ## {SimpF: rank = 2 1 FirstEF,rank = 1 1 FirstEF,rank = 3 1 FirstEF}

novel_rep_lenNOK_multiarm_DicerOK_randfoldOK (1 loci)

sblock5586 [novel_rep_lenNOK_multiarm_DicerOK_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

LTR/MaLR

0.43/0.52

18/21/0.67

1.0 0.0

0.5 0.0

2 1

0 0

2 1

0 0

8 9

24 27

5arm 3arm

1 1

nd nd

0.05 0.05

1 1

3

2

1

1

		reads	miRBase family seed
seed	---------GUUAGCC--------------------------------------------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------------------------------------------------------GAUUUGG----------------------	1	novel
seed	-----------UAGCCGG------------------------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	------------------------------------------------------------------------------------------------------------------AGATTTGGAACTGGCTAACAC---------	21	1	-
	----------TTAGCCGGTCCCAAATCT--------------------------------------------------------------------------------------------------------------------	18	1	-
	--------TGTTAGCCGGTCCCAAATCTG-------------------------------------------------------------------------------------------------------------------	21	-	1
rat	ATCTTTAGTGTTAGCCGGTCCCAAATCTGTAAACTGTTTTAATATTTTTTAAAGATTTAAATTTAAATTAAA---------------TATTAAAACAGTTCA-----------CAGATTTGGAACTGGCTAACACTACTGGGTC
human	-----TAA-ATTACTCAGTCTCAGATACTTTTACAGCAGTGCAAATGGATGAACACAGAAAATTAGTATCAAGGAGTTGTGTATCACTATTAAGGTACCTGAAAATGAAGAAGCAGATTTGGAACTGGGTAACAAG--------
	**   ***  * *** ** **   *  ** *   *   * *   * ** *   *** ***   * **               ******   *  * *           *************** *****
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++               +++++++++++++++           ++++++++++++++++++++++++++++++++++++	ENSRNOT00000023763 ENSRNOG00000017453 Ptpn2
rat	((((.((((((((((((((.((((((((((.((((((((((((((((((((((........))))))..)))               ))))))))))))).)           ))))))))).))))))))))))))..)))).	1.000 -59.00
human	... .(((((((((..(((((.(((((.((.((((((.(((((.(((((((((....((......))....)))))).))))))))...)))).))....)).)))))...)))))..)))))))))....	1.000 -35.10

rat	chromosome:18:64241350:64241467:-1	Same_strand|Intronic_coding|ENSRNOT00000023763|ENSRNOG00000017453 ## ENSRNOG00000017453|protein_coding|Ptpn2|Tyrosine-protein phosphatase non-receptor type 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase PTP-S). [Source:UniProtKB/Swiss-Prot;Acc:P35233]
human	chromosome:2:40691389:40691546:-1	Same_strand|Boundary_non-coding|ENST00000394999|ENSG00000183023|protein_coding|Sodium/calcium exchanger 1 Precursor (Na(+)/Ca(2+)-exchange protein 1) [Source:UniProtKB/Swiss-Prot;Acc:P32418] ## Same_strand|Intronic_non-coding|ENST00000405269|ENSG00000183023|protein_coding|Sodium/calcium exchanger 1 Precursor (Na(+)/Ca(2+)-exchange protein 1) [Source:UniProtKB/Swiss-Prot;Acc:P32418] ## {Repeats: MSTB-int 1 class=LTR/MaLR,MSTB 1 class=LTR/MaLR}

novel_rep_multiarm_DicerOK_loopOverlap_randfoldOK (1 loci)

sblock9812 [novel_rep_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

no

0.001

no

LINE/L1

0.58/0.64

20/25/0.80

0.2 0.0

2.0 0.0

4 1

0 0

3 1

0 0

13 11

-1 2

5arm_loop 3arm

1 1

nd nd

0.15 0.23

2 3

5

4

3

1

		reads	miRBase family seed
seed	---------------GGCCUGG---------------------------------------------------------------	3	novel
seed	-----------------------------------------------------AGACUGG-------------------------	1	novel
seed	--------------AGGCCUG----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T4S2
	--------------AGGCCTGGTCAGGCAG-----TTCT----------------------------------------------	20	2	-	-	-
	--------------AGGCCTGGTCAGGCAG-----TTCTGTCT------------------------------------------	24	-	-	1	-
	-------------CAGGCCTGGTCAGGCAG-----TTCTGTCT------------------------------------------	25	-	-	-	1
	----------------------------------------------------CAGACTGGCAGACCAGGCTCCA-----------	22	-	1	-	-
rat	CTGCTTTGGGGCTCAGGCCTGGTCAGGCAG-----TTCTGTCTATTCCCTGACAGACTGGCAGACCAGGCTCCAGGCACTGCGGT
mouse	-------------TAGGCCTGGTCAGGCAGACCTCTGCTATATTTGTGCTAGGTGCCT--CAGACCAGCCTA-------------
	****************     * ** * * *   **    * **  ******** **
	+++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016493 ENSRNOG00000012204 AU040320
rat	((((...((.(((..(((((((((..((((     .((((((........)))))))).)).)))))))))...))).)))))).	1.000 -36.40
mouse	((((.((((((((((..((((..((.........)).))))))))  ..))))))))))	0.988 -24.60

rat	chromosome:5:146167641:146167720:1	Same_strand|Intronic_non-coding|ENSRNOT00000016493|ENSRNOG00000012204 ## ENSRNOG00000012204|protein_coding|AU040320|Uncharacterized protein KIAA0319-like [Source:UniProtKB/Swiss-Prot;Acc:Q8K135]
mouse	chromosome:9:7260830:7260886:1	intergenic ## {Repeats: Lx3C -1 class=LINE/L1}

novel_rep_shortStem_mirtron_randfoldOK (1 loci)

block2523200 [novel_rep_shortStem_mirtron_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

0.010

no

LTR/MaLR

0.55/0.55

22/22/1.00

0.0

0.0

1

0

1

0

4

9

3arm

1

2

0.18

1

1

1

na

na

		reads	miRBase family seed
seed	----------------------------------------------------------------CUCUCAC--------------------	1	novel
		len	cloning frequencies
			T5S2
	---------------------------------------------------------------TCTCTCACCACCTCTCTTCC--TC----	22	1
rat	GT-----GCAGGGGTGGGGCAGGAGGAAGGGAGAGCTGAGCCTGTTTCCTCAGCA----GAGCTCTCTCACCACCTCTCTTCC--TCAGCA
human	GCTTCAAGCAGAGCTGGATCTGGGGG--------TTTGAAACTG--TCATCAGGATCTGGGACTCTCTCACCACCTCTCTGCTTGTTGGC-
	*      **** * ***  * ** **          ***  ***  ** **** *    *  ****************** *   *  **
	+++++++     ++++++++++++++++++++++++++++++++++++++++++++++++    ++++++++++++++++++++++++  ++++>>>>>>>	ENSRNOT00000035277 ENSRNOG00000014182 Tns
rat	.(     ((.((((.((((.(((.((..(((((((((..((.((......)))).    .))))))))).)).))))))).))  )).)))	1.000 -36.80
human	(((.(((((((((.(((....(((((        ((.((..(((  ....)))..))...)))))))...)))...)))))))))..)))	0.997 -31.10

rat	chromosome:9:73306060:73306139:-1	Same_strand|Boundary_non-coding|ENSRNOT00000019092|ENSRNOG00000014182 ## Same_strand|Intronic_coding|ENSRNOT00000035277|ENSRNOG00000014182 ## ENSRNOG00000014182|protein_coding|Tns|Tensin (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q62783]
human	chromosome:5:171715850:171715929:-1	Same_strand|Intronic_coding|ENST00000311601|ENSG00000174705|protein_coding|SH3 and PX domain-containing protein 2B (Adapter protein HOFI) [Source:UniProtKB/Swiss-Prot;Acc:A1X283] ## {Repeats: MLT1K -1 class=LTR/MaLR}

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other hairpins:

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