logoSmall RNA from different tissues of two rat strains.

miR-Intess™


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Composition

miR classification
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Alignments

other hairpins

novel_lenNOK_cloningOK_shortStem_nonpairedHIGH (163 loci)

block1696335 [novel_lenNOK_cloningOK_shortStem_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.230nono0.60/0.7218/25/0.600.5
1.5
10
0
2
0
0
8
3arm
2
nd
0.33
3
102nana
  readsmiRBase family seed
seed------------------------------------------------------------------------CAGAGCA-----------------7novel
seed-------------------------------------------------------------------------AGAGCAG----------------1novel
seed---------------------------------------------------------------------------AGCAGUG--------------1novel
seed-----------------------------------------------------------------------UCAGAGC------------------1novel
  lencloning frequencies
   T1S1T5S1
 -----------------------------------------------------------------------TCAGAGCAGTGGTGAGGGCCC----21-3
 -----------------------------------------------------------------------TCAGAGCAGTGGTGAGGGCCCTT--23-2
 -----------------------------------------------------------------------TCAGAGCAGTGGTGAGGGCCCTTAG25-1
 -----------------------------------------------------------------------TCAGAGCAGTGGTGAGGGC------19-1
 ----------------------------------------------------------------------CTCAGAGCAGTGGTGAGGG-------19-1
 ------------------------------------------------------------------------CAGAGCAGTGGTGAGGGCCCTT--221-
 --------------------------------------------------------------------------GAGCAGTGGTGAGGGCCC----18-1
ratctgagaccctctggtggattggatgtgagttagatgggagaaggaagtggaaagtgaagacacccaggggCTCAGAGCAGTGGTGAGGGCCCTTAG 
 ************************************************************************************************ 
rat(((((.(((((......((((....((((((...((((........................))))..))))))...))))...)))))..)))))0.500 -23.16

ratchromosome:4:164267800:164267895:1intergenic


block1696661 [novel_lenNOK_cloningOK_shortStem_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.226nono0.47/0.5519/20/0.270.0
0.0
7
0
3
0
4
16
5arm
1
nd
0.42
3
113nana
  readsmiRBase family seed
seed-----CCAUGGG------------------------------------------------------------------------------8novel
seed-GCCUCCA----------------------------------------------------------------------------------2novel
seed---CUCCAUG--------------------------------------------------------------------------------1novel
  lencloning frequencies
   T1S2T2S1T5S1
 ----TCCATGGGCTTACAAGCAA-------------------------------------------------------------------191-7
 TGCCTCCATGGGCTTACAAG----------------------------------------------------------------------20--2
 --CCTCCATGGGCTTACAAGCA--------------------------------------------------------------------20-1-
rattgccTCCATGGGCTTACAAGCAAttcctagcatcagtagatacctatatggatggaatgggtagaatgtttcaccagccactaaggtggt 
 ****************************************************************************************** 
rat.(((.((...((((...(((((...((((.((((.((((....))))...))))...)))).....)))))....)))).....)).)))0.720 -22.50

ratchromosome:4:164284436:164284525:1intergenic


novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap (162 loci)

block496457 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.225nono0.56/0.7818/22/0.403.0
6.8
0.7
5.4
3
17
0
0
3
7
0
0
27
36
-3
-20
5arm_loop
3arm_loop
1
1
nd
nd
0.14
0.32
2
6
2080-3
  readsmiRBase family seed
seed     --------------------------------------------CCGAGUC-----------------------------------------------------------------     7novel
seed     -----------------------------------------CAGCCGA--------------------------------------------------------------------     2novel
seed     ---------------------------------------GGCAGCC----------------------------------------------------------------------     2novel
seed     --------------------------------UGGAGCC-----------------------------------------------------------------------------     1novel
seed     -----------------------------------------------AGUCGGA--------------------------------------------------------------     1novel
seed     ---------------------------------------------CGAGUCG----------------------------------------------------------------     1novel
seed     --------------------------------------------------CGGAUUG-----------------------------------------------------------     1novel
seed     ----------------------------GGAGUGG---------------------------------------------------------------------------------     1novel
seed     ---------------------------------GGAGCCG----------------------------------------------------------------------------     1novel
seed     ---------------------------------------------------GGAUUGA----------------------------------------------------------     1novel
seed     -------------------------------------CCGGCAG------------------------------------------------------------------------     1novel
seed     ----------------------------------------------GAGUCGG---------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T2S1T2S2T3S2T4S1T4S2T5S1T5S2
      -------------------------------------------GCCGAGTCGGATTGAGCT-------------------------------------------------------     181----1--
      -------------------------------------------GCCGAGTCGGATTGAGCTGC-----------------------------------------------------     201-1-----
      -------------------------------------------GCCGAGTCGGATTGAGCTG------------------------------------------------------     19-1-1----
      --------------------------------------CGGCAGCCGAGTCGGATTG-----------------------------------------------------------     19------1-
      --------------------------------TGGAGCCGGCAGCCGAGTC-----------------------------------------------------------------     19-------1
      --------------------------------------CGGCAGCCGAGTCGGATTGAG---------------------------------------------------------     21-------1
      ---------------------------------------------CGAGTCGGATTGAGCTGC-----------------------------------------------------     18--1-----
      ---------------------------AGGAGTGGAGCCGGCAGCCGAG-------------------------------------------------------------------     22-----1--
      ------------------------------------GCCGGCAGCCGAGTCGGATTG-----------------------------------------------------------     211-------
      ----------------------------------------GCAGCCGAGTCGGATTGAG---------------------------------------------------------     19--1-----
      --------------------------------------------------CGGATTGAGCTGCTGCAGA-----------------------------------------------     19--1-----
      ----------------------------------------------GAGTCGGATTGAGCTGCTGCAG------------------------------------------------     22-----1--
      -------------------------------------------------TCGGATTGAGCTGCTGCA-------------------------------------------------     18-------1
      -------------------------------------------GCCGAGTCGGATTGAGCTGCT----------------------------------------------------     21-1------
      ----------------------------------------GCAGCCGAGTCGGATTGAGCTG------------------------------------------------------     22------1-
      --------------------------------------------CCGAGTCGGATTGAGCTGC-----------------------------------------------------     19-------1
      -------------------------------GTGGAGCCGGCAGCCGAG-------------------------------------------------------------------     18----1---
rat     gcgctggggccgggcggcctcctctagAGGAGTGGAGCCGGCAGCCGAGTCGGATTGAGCTGCTGCAGAcgccaggccactccagccagcactgccgttttcacgccccggctgca      
      ********************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000001363 ENSRNOG00000001030 Tsc22d1
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ENSRNOT00000058206 ENSRNOG00000001030 Tsc22d1
rat     ((((((((((.(((((((..........(((((((.((((((((((((......))).))))))).....))....)))))))..........)))))))....)))))))).)).     0.550 -54.25

ratchromosome:15:57499543:57499658:1Same_strand|Intronic_coding|ENSRNOT00000001363|ENSRNOG00000001030 ## Same_strand|Boundary_non-coding|ENSRNOT00000001360|ENSRNOG00000001030 ## ENSRNOG00000001030|protein_coding|Tsc22d1|TSC22 domain family protein 1 (Transforming growth factor beta-1- induced transcript 4 protein) (Regulatory protein TSC-22) (TGFB- stimulated clone 22 homolog). [Source:UniProtKB/Swiss-Prot;Acc:P62501]


block770017 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.213nono0.36/0.4219/25/0.445.7
1.3
4.4
3.1
9
7
0
0
1
2
0
0
18
9
-17
-2
5arm_loop_3arm
3arm
1
1
nd
nd
0.37
0.25
5
3
16230
  readsmiRBase family seed
seed---------------------------------------------AGAGAAA----------------------------3novel
seed-----------------------------------------------AGAAACU--------------------------3novel
seed-----------------------CUGUUUA--------------------------------------------------2novel
seed-------------------------GUUUAUG------------------------------------------------2novel
seed-------------------GCUUCUG------------------------------------------------------2novel
seed----------------------UCUGUUU---------------------------------------------------1novel
seed------------------------------------------ACCAGAG-------------------------------1novel
seed--------------------------------CUGUGGA-----------------------------------------1novel
seed----------------------------------GUGGAAA---------------------------------------1novel
  lencloning frequencies
   T2S2T5S1
 --------------------------------------------CAGAGAAACTTTGAGGTAA-----------------1912
 ----------------------TCTGTTTATGCTGTGGAAA---------------------------------------19-2
 ----------------------------------------------GAGAAACTTTGAGGTAAAGGTCT-----------23-2
 ------------------TGCTTCTGTTTATGCTGTGGAAA---------------------------------------23-2
 -------------------------------GCTGTGGAAATACCAGAGAAACTT-------------------------24-1
 -----------------------------------------TACCAGAGAAACTTTGAGGT-------------------20-1
 ------------------------TGTTTATGCTGTGGAAATACCAGAG-------------------------------25-1
 ------------------------TGTTTATGCTGTGGAAATACCAG---------------------------------23-1
 ---------------------------------TGTGGAAATACCAGAGAAA----------------------------19-1
 ---------------------TTCTGTTTATGCTGTGGAA----------------------------------------19-1
 ----------------------------------------------GAGAAACTTTGAGGTAAAGGTCTAA---------25-1
rattaagctttgcatggtgggTGCTTCTGTTTATGCTGTGGAAATACCAGAGAAACTTTGAGGTAAAGGTCTAAgggtggctt 
 ******************************************************************************** 
rat.(((((.....(((....((((((.((((...((.(((.....))).))))))...)))))).....))).....)))))0.660 -17.30

ratchromosome:19:15927859:15927938:-1intergenic


block782410 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.473nono0.42/0.7018/23/0.505.2
1.2
0.0
0.0
0.0
2.0
0.0
7.1
2.2
0.0
0.0
0.0
1.0
0.0
12
4
1
1
1
5
2
0
0
0
0
0
0
0
2
2
1
1
1
2
1
0
0
0
0
0
0
0
8
27
28
23
17
8
5
-12
-17
-10
-4
2
7
16
5arm_loop
3arm_loop
3arm_loop
3arm_loop
3arm
3arm
3arm
1
1
1
1
1
1
1
16
35
46
51
57
63
69
0.11
0.79
0.62
0.60
0.50
0.43
0.17
1
14
9
7
7
6
2
262015
  readsmiRBase family seed
seed     -------------ACAGCUG----------------------------------------------------------------     3novel
seed     --------------------------------------------------------ACACUUG---------------------     2novel
seed     ---------GAUGACA--------------------------------------------------------------------     2novel
seed     -------------------------------------------------------AACACUU----------------------     2novel
seed     ----------------------------CCCCAGA-------------------------------------------------     2novel
seed     --------------------------------------------------------------GGUUCGU---------------     2novel
seed     --------------CAGCUGC---------------------------------------------------------------     1novel
seed     ------------------------------CCAGAGA-----------------------------------------------     1novel
seed     -------------------------------CAGAGAU----------------------------------------------     1novel
seed     -----------------------------------------------------GGAACAC------------------------     1novel
seed     ------------------------------------AUUGCAA-----------------------------------------     1novel
seed     ------------------------------------------------UAUGUGG-----------------------------     1novel
seed     -------------------GCCCAAA----------------------------------------------------------     1novel
seed     ---------------------CCAAAGC--------------------------------------------------------     1novel
seed     ------------GACAGCU-----------------------------------------------------------------     1novel
seed     ----------------GCUGCCC-------------------------------------------------------------     1novel
seed     --------------------CCCAAAG---------------------------------------------------------     1novel
seed     -----------UGACAGC------------------------------------------------------------------     1novel
seed     ------------------------------------------AACGGCU-----------------------------------     1novel
  lencloning frequencies
   T2S1T2S2
      ------------GACAGCTGCCCAAAGCCCC-----------------------------------------------------     1911
      -------------------------------------------------------------TGGTTCGTTATCGCTGCC-----     182-
      ------------------------------------------------------GAACACTTGGTTCGTTATC-----------     1911
      ---------------AGCTGCCCAAAGCCCCCAGAGA-----------------------------------------------     22-1
      -------------ACAGCTGCCCAAAGCCCCCAG--------------------------------------------------     21-1
      ---------------------------CCCCCAGAGATTGCAAAC---------------------------------------     181-
      -------------------------------------------------------AACACTTGGTTCGTTATCGCT--------     211-
      --------AGATGACAGCTGCCCAAAG---------------------------------------------------------     19-1
      --------AGATGACAGCTGCCCAAA----------------------------------------------------------     18-1
      -----------------------------CCCAGAGATTGCAAACGGCT-----------------------------------     20-1
      ----------ATGACAGCTGCCCAAAGCCCC-----------------------------------------------------     211-
      ------------------------------CCAGAGATTGCAAACGGCT-----------------------------------     19-1
      ---------------------------CCCCCAGAGATTGCAAACG--------------------------------------     191-
      ----------------------------------------------------TGGAACACTTGGTTCGTTATCG----------     221-
      -------------------------------------------------------AACACTTGGTTCGTTATCGC---------     201-
      -----------TGACAGCTGCCCAAAGCCC------------------------------------------------------     191-
      -----------------------------------------AAACGGCTATGTGGAACACT-----------------------     201-
      --------------------CCCAAAGCCCCCAGAGATTG--------------------------------------------     20-1
      ------------GACAGCTGCCCAAAGCCCCC----------------------------------------------------     20-1
      -------------------GCCCAAAGCCCCCAGAGA-----------------------------------------------     181-
      -----------------------------------------------CTATGTGGAACACTTGGTTC-----------------     201-
      -----------------------------------GATTGCAAACGGCTATGTGGA----------------------------     21-1
      ------------------TGCCCAAAGCCCCCAGAGATTGC-------------------------------------------     231-
rat     ctcttggcAGATGACAGCTGCCCAAAGCCCCCAGAGATTGCAAACGGCTATGTGGAACACTTGGTTCGTTATCGCTGCCgacag      
      ************************************************************************************      
 +++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000050989 ENSRNOG00000014964 Hp
 +++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000020197 ENSRNOG00000014964 Hp
rat     ((.((((((((((((((((.((((.((((................)))).)).)).......)))).))))))..)))))).))     0.480 -21.09

ratchromosome:19:39445419:39445502:-1Same_strand|Boundary_coding|ENSRNOT00000020197|ENSRNOG00000014964 ## ENSRNOG00000014964|protein_coding|Hp|Haptoglobin precursor (Liver regeneration-related protein LRRG173) [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]. [Source:UniProtKB/Swiss-Prot;Acc:P06866]


block868123 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.806nono0.39/0.5818/24/0.172.6
2.5
2.5
2.2
30
10
0
0
6
5
0
0
18
14
-18
-2
5arm_loop_3arm
3arm
1
1
nd
nd
0.33
0.22
5
2
40940
  readsmiRBase family seed
seed     ----------------------------------CAGCUUG---------------------------------------     15novel
seed     --------------------------------CGCAGCU-----------------------------------------     3novel
seed     ----------------------------------------------GAUUACA---------------------------     3novel
seed     -----------------------------------AGCUUGU--------------------------------------     3novel
seed     --------------------------UCAGUUC-----------------------------------------------     2novel
seed     ---------------------------------------UGUGGAA----------------------------------     2novel
seed     -------------------GAUUGAC------------------------------------------------------     2novel
seed     ---------------------------------GCAGCUU----------------------------------------     2novel
seed     -----------------------GACUCAG--------------------------------------------------     1novel
seed     --------------------------------------------AAGAUUA-----------------------------     1novel
seed     -----------------------------------------------AUUACAU--------------------------     1novel
seed     -------------------------------UCGCAGC------------------------------------------     1novel
seed     -----------------------------------------UGGAAGA--------------------------------     1novel
seed     ----------------------------AGUUCGC---------------------------------------------     1novel
seed     ------------------------------------------------UUACAUG-------------------------     1novel
seed     ---------------------------------------------AGAUUAC----------------------------     1novel
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S2T5S1T5S2
      ---------------------------------GCAGCTTGTGGAAGATTAC----------------------------     19--3222-21
      ---------------------------------------------AGATTACATGCGAGACCCC----------------     1912-------
      -------------------------------TCGCAGCTTGTGGAAGAT-------------------------------     18----2---1
      ----------------------------------CAGCTTGTGGAAGATTAC----------------------------     18-----1--1
      ---------------------------------GCAGCTTGTGGAAGATTA-----------------------------     18--2------
      --------------------------------------TTGTGGAAGATTACATGC------------------------     18----11---
      -------------------------CTCAGTTCGCAGCTTGTGG------------------------------------     19----2----
      ------------------AGATTGACTCAGTTCGCAGCT-----------------------------------------     21---1-----
      --------------------------------CGCAGCTTGTGGAAGATTAC----------------------------     20----1----
      ---------------------------------GCAGCTTGTGGAAGATTACA---------------------------     20-----1---
      ----------------------------------CAGCTTGTGGAAGATTACA---------------------------     19-----1---
      -------------------------------------------GAAGATTACATGCGAGACC------------------     19------1--
      --------------------------------CGCAGCTTGTGGAAGATTACA---------------------------     21----1----
      ---------------------------CAGTTCGCAGCTTGTGGAAGA--------------------------------     21-------1-
      ----------------------------------------GTGGAAGATTACATGCGAGACCCC----------------     24------1--
      -----------------------------------------------ATTACATGCGAGACCCCGC--------------     19----1----
      ------------------AGATTGACTCAGTTCGCA--------------------------------------------     18----1----
      ----------------------TGACTCAGTTCGCAGCTTGTG-------------------------------------     21--------1
      ------------------------------TTCGCAGCTTGTGGAAGA--------------------------------     18-------1-
      --------------------------------------------AAGATTACATGCGAGACC------------------     18----1----
      ----------------------------------------------GATTACATGCGAGACCCC----------------     18-----1---
rat     gggtgatcgtgttggcgcAGATTGACTCAGTTCGCAGCTTGTGGAAGATTACATGCGAGACCCCGCgcgactccgcatcc      
      ********************************************************************************      
 ...................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000044788 ENSRNOG00000020938 Myd116
rat     (((((.((((((.((((((...(((.((..(((((.....))))).)))))..))))....)).)))))).....)))))     0.480 -22.30

ratchromosome:1:95997047:95997126:-1Same_strand|Boundary_non-coding|ENSRNOT00000028415|ENSRNOG00000020938 ## ENSRNOG00000020938|protein_coding|Myd116|myeloid differentiation primary response gene 116 [Source:RefSeq_peptide;Acc:NP_598230] ## {SimpF: 1 Eponine}


block1060596 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.099nono0.33/0.7018/25/0.410.0
0.0
0.0
5.1
0.0
0.0
0.0
3.4
1
2
1
14
0
0
0
0
1
2
1
4
0
0
0
0
8
14
19
16
0
-4
-11
-22
5arm
5arm_loop
5arm_loop
3arm_loop
1
1
1
1
nd
nd
nd
nd
0.25
0.44
0.65
0.58
2
5
12
5
22402
  readsmiRBase family seed
seed---------------------------------------ACAAACC----------------------------9novel
seed--------------------------GGAAAAU-----------------------------------------5novel
seed----------------------------------AGACUAC---------------------------------2novel
seed---------------GGCACAG----------------------------------------------------2novel
seed------------------------------------ACUACAA-------------------------------2novel
seed--------------------AGCACUG-----------------------------------------------1novel
seed---------GCAGCUG----------------------------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T2S2T5S1
 --------------------------------------TACAAACCAGACTGGCTGG-----------------19-115
 -------------------------TGGAAAATTAGACTACAAACCAGAC------------------------25---3
 --------------TGGCACAGCACTGGAAAA------------------------------------------181--1
 -----------------------------------GACTACAAACCAGACTGGCTG------------------21---2
 --------------------------------------TACAAACCAGACTGGCTGGG----------------20---2
 -------------------------TGGAAAATTAGACTACAAACC----------------------------21---2
 -------------------CAGCACTGGAAAATTAGACT-----------------------------------20---1
 ---------------------------------TAGACTACAAACCAGACTGG---------------------20---1
 --------GGCAGCTGGCACAGCACTGG----------------------------------------------20---1
 ---------------------------------TAGACTACAAACCAGACTGGCTGGG----------------251---
ratgggccccaggcagctggcacagcacTGGAAAATTAGACTACAAACCAGACTGGCTGGGcttccagcagctccca 
 ************************************************************************** 
rat(((.....(((.(((((..((((.((((................))))....)))).....))))).)))))).0.730 -23.49

ratchromosome:20:5510476:5510549:-1intergenic


block1060884 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.851nono0.42/0.7418/26/0.570.8
3.2
1.0
3.6
1.9
2.2
1.9
4.0
10
4
11
5
0
0
0
0
2
2
3
2
0
0
0
0
0
11
13
2
-5
-16
-3
8
5arm_loop
5arm_loop_3arm
3arm
3arm
1
1
1
1
nd
nd
nd
nd
0.26
0.41
0.68
0.42
3
6
13
4
30500
  readsmiRBase family seed
seed-------------------------CAGUCGA------------------------------8novel
seed-CUGUGCC------------------------------------------------------7novel
seed------------------------------------------ACCCGCG-------------3novel
seed---GUGCCUU----------------------------------------------------2novel
seed------------------CACCCCU-------------------------------------2novel
seed-----------------------------CGAGCCU--------------------------2novel
seed------------------------------------CUCCCAA-------------------2miR-150
seed----------------------------UCGAGCC---------------------------1novel
seed-----GCCUUUU--------------------------------------------------1novel
seed------------UGUUCUC-------------------------------------------1novel
seed-------------GUUCUCA------------------------------------------1novel
  lencloning frequencies
   T1S1T2S1T3S2T5S1T5S2
 TCTGTGCCTTTTTGTTCTCACCCCTC------------------------------------26---21
 ------------------------TCAGTCGAGCCTCTCCCAAC------------------20---3-
 -----------------------------------------AACCCGCGTGCAGGCCCA---18--11-
 ------------------------TCAGTCGAGCCTCTCCCAACCC----------------221--1-
 TCTGTGCCTTTTTGTTCTCACCC---------------------------------------23---2-
 ----------------------------TCGAGCCTCTCCCAACCCG---------------19---2-
 ----TGCCTTTTTGTTCTCACCCCT-------------------------------------21---1-
 -----------------TCACCCCTCAGTCGAGCCT--------------------------191----
 -----------------------------------TCTCCCAACCCGCGTGCAGGCCC----23---1-
 ------------------------TCAGTCGAGCCTCTCCCAA-------------------19-1---
 ------------------------TCAGTCGAGCCTCTCCCA--------------------181----
 ------------------------TCAGTCGAGCCTCTCCCAACCCG---------------23---1-
 ------------TGTTCTCACCCCTCAGTCGAGCC---------------------------23---1-
 -----------------------------------TCTCCCAACCCGCGTGCAG--------19---1-
 TCTGTGCCTTTTTGTTCTC-------------------------------------------19---1-
 TCTGTGCCTTTTTGTTCTCACCCC--------------------------------------24---1-
 -----------------TCACCCCTCAGTCGAGCCTC-------------------------201----
 --TGTGCCTTTTTGTTCTCACCCCTC------------------------------------24----1
 --TGTGCCTTTTTGTTCTCACCC---------------------------------------21---1-
 -----------TTGTTCTCACCCCTCAGTCGAG-----------------------------22---1-
 -----------------------------------------AACCCGCGTGCAGGCCCAG--19--1--
 ---------------------------GTCGAGCCTCTCCCAACCCGCG-------------22---1-
ratTCTGTGCCTTTTTGTTCTCACCCCTCAGTCGAGCCTCTCCCAACCCGCGTGCAGGCCCAGgc 
 ************************************************************** 
rat((((.((((...(((.(((((......)).))).............)))...)))).)))).0.490 -9.24

ratchromosome:20:5520262:5520323:-1intergenic


block1092648 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.159nono0.55/0.7118/23/0.223.1
0.0
0.0
0.0
0.0
2.7
0.5
0.0
0.0
0.0
27
2
4
1
2
0
0
0
0
0
8
2
2
1
1
0
0
0
0
0
13
37
41
37
31
-7
-11
-14
-5
0
5arm_loop_3arm
5arm_loop_3arm
5arm_loop_3arm
3arm_loop
3arm
1
1
1
1
1
nd
nd
nd
nd
nd
0.05
0.32
0.39
0.37
0.25
1
6
6
4
2
37820
  readsmiRBase family seed
seed     ------------------------------UGGAGCA-----------------------------------------------------------------     9novel
seed     ------------------------------------------UAGGACG-----------------------------------------------------     5novel
seed     ----------------------------------GCAGCCU-------------------------------------------------------------     3novel
seed     ---------------------------------AGCAGCC--------------------------------------------------------------     3novel
seed     ----------------------------------------------------UGGAGGA-------------------------------------------     2novel
seed     -------------------------UGGAGUG----------------------------------------------------------------------     2novel
seed     --------------------------------------CCUCUAG---------------------------------------------------------     2novel
seed     -----------------------------------CAGCCUC------------------------------------------------------------     2novel
seed     --------------------------GGAGUGG---------------------------------------------------------------------     2novel
seed     ----------------------------AGUGGAG-------------------------------------------------------------------     1novel
seed     -----------------------------GUGGAGC------------------------------------------------------------------     1novel
seed     --------------CCAUUUC---------------------------------------------------------------------------------     1novel
seed     --------------------CGCGCUG---------------------------------------------------------------------------     1novel
seed     -----------------------------------------------CGAGCUG------------------------------------------------     1novel
seed     ------------------------CUGGAGU-----------------------------------------------------------------------     1novel
seed     -------------------------------GGAGCAG----------------------------------------------------------------     1novel
  lencloning frequencies
   T1S1T2S1T2S2T3S1T3S2T4S1T5S1T5S2
      -----------------------------GTGGAGCAGCCTCTAGGAC------------------------------------------------------     19-1-3211-
      -----------------------------------------CTAGGACGAGCTGGAGGA-------------------------------------------     1841------
      ---------------------------------AGCAGCCTCTAGGACGAGC--------------------------------------------------     192---1---
      ---------------------------------------------------CTGGAGGATTGTGCCTACTG-------------------------------     20-2------
      ----------------------------------GCAGCCTCTAGGACGAGC--------------------------------------------------     181--1----
      ------------------------CTGGAGTGGAGCAGCCTCT-----------------------------------------------------------     19----2---
      -------------------------------------GCCTCTAGGACGAGCTGGA----------------------------------------------     19----1---
      -------------GCCATTTCGCGCTGGAGTGGAG-------------------------------------------------------------------     22-------1
      -------------------------------------GCCTCTAGGACGAGCTGG-----------------------------------------------     181-------
      -------------------TCGCGCTGGAGTGGAGCAGCC--------------------------------------------------------------     21--1-----
      --------------------------------GAGCAGCCTCTAGGACGAG---------------------------------------------------     19------1-
      ------------------------------TGGAGCAGCCTCTAGGACG-----------------------------------------------------     19--1-----
      ----------------------------AGTGGAGCAGCCTCTAGGAC------------------------------------------------------     20--1-----
      -----------------------GCTGGAGTGGAGCAGCCTC------------------------------------------------------------     19---1----
      --------------------------------GAGCAGCCTCTAGGACGAGC--------------------------------------------------     20-1------
      -----------------------------GTGGAGCAGCCTCTAGGA-------------------------------------------------------     181-------
      ---------------------------GAGTGGAGCAGCCTCTAGGAC------------------------------------------------------     21---1----
      ----------------------------------------------ACGAGCTGGAGGATTGTGC-------------------------------------     19-----1--
      --------------------------------GAGCAGCCTCTAGGACGA----------------------------------------------------     18-------1
      -------------------------TGGAGTGGAGCAGCCTCTAGGAC------------------------------------------------------     23----1---
      -------------------------TGGAGTGGAGCAGCCTCT-----------------------------------------------------------     18----1---
rat     ggggctcggcggcgccatttcgcgCTGGAGTGGAGCAGCCTCTAGGACGAGCTGGAGGATTGTGCCTACTGacccagagtcttggagcctccgcgggccgcc      
      ******************************************************************************************************      
 .......................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000000535 ENSRNOG00000000461 Brd2
rat     (((((((((.(((.(((....((.(((((((((.(((((((((((......))))))).))))..)))))...)))).))..))).))).)))..)))).))     0.820 -47.80

ratchromosome:20:4864572:4864673:1Same_strand|Boundary_non-coding|ENSRNOT00000000535|ENSRNOG00000000461 ## ENSRNOG00000000461|protein_coding|Brd2|Bromodomain-containing protein 2 (Protein RING3). [Source:UniProtKB/Swiss-Prot;Acc:Q6MGA9] ## {SimpF: 1 Eponine,oe = 0.79 1 CpG}


block1204031 [novel_lenNOK_cloningOK_multiarm_DicerNOK_5varHIGH_loopOverlap]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.305nono0.44/0.6818/26/0.3310.6
0.0
0.0
12.4
0.0
0.0
37
6
1
0
0
0
10
3
1
0
0
0
17
47
32
-7
-14
-1
5arm_loop_3arm
5arm_loop_3arm
3arm
2
2
2
14
45
53
0.22
0.37
0.26
2
4
2
461004
  readsmiRBase family seed
seed     --------------------GUUUCCU-------------------------------------------------------------------------------     9novel
seed     -----------------------------------CCGUCCG----------------------------------------------------------------     9novel
seed     ------------------------------------------------UGCGCUC---------------------------------------------------     7novel
seed     ---------------------------------------CCGUCUG------------------------------------------------------------     5novel
seed     ------------------CAGUUUC---------------------------------------------------------------------------------     5novel
seed     ------------------------------------CGUCCGU---------------------------------------------------------------     2novel
seed     --------------------------------UGACCGU-------------------------------------------------------------------     2novel
seed     --------------------------------------------------------CGUGAUG-------------------------------------------     1novel
seed     ----------------------------------ACCGUCC-----------------------------------------------------------------     1novel
seed     ---------------------UUUCCUG------------------------------------------------------------------------------     1novel
seed     -------------------------------GUGACCG--------------------------------------------------------------------     1novel
seed     -------------------------------------------------GCGCUCU--------------------------------------------------     1novel
seed     --------------------------UGGUUGU-------------------------------------------------------------------------     1novel
seed     -----------------------------UUGUGAC----------------------------------------------------------------------     1miR-758
  lencloning frequencies
   T1S1T1S2T2S1T2S2T3S1T3S2T4S1T4S2T5S1T5S2
      -----------------------------------------------TTGCGCTCTCGTGATGTCC----------------------------------------     19----2---4-
      ----------------------------------ACCGTCCGTCTGTTTGCGC-----------------------------------------------------     19--2---111-
      -----------------ACAGTTTCCTGGTTGTGA-----------------------------------------------------------------------     1811------2-
      --------------------------------------TCCGTCTGTTTGCGCTCTCG------------------------------------------------     20----1--2--
      -------------------AGTTTCCTGGTTGTGACCGTC------------------------------------------------------------------     21-----2--1-
      -------------------------------GTGACCGTCCGTCTGTTTGC-------------------------------------------------------     20-----2----
      -------------------AGTTTCCTGGTTGTGACCG--------------------------------------------------------------------     191-1-------
      -------------------AGTTTCCTGGTTGTGACC---------------------------------------------------------------------     18---1----1-
      ----------------------------------ACCGTCCGTCTGTTTGCGCTC---------------------------------------------------     21----2-----
      --------------------------------------TCCGTCTGTTTGCGCTCTC-------------------------------------------------     19----2-----
      --------------------GTTTCCTGGTTGTGACCGTCCGTC--------------------------------------------------------------     24-1--------
      ----------------------------------ACCGTCCGTCTGTTTGCGCTCTCGT-----------------------------------------------     25-----1----
      -----------------------------------CCGTCCGTCTGTTTGCGCTCTCG------------------------------------------------     23----1-----
      ------------------------------TGTGACCGTCCGTCTGTTTG--------------------------------------------------------     20--1-------
      ------------------------------------------------TGCGCTCTCGTGATGTCCG---------------------------------------     19---1------
      ----------------------------GTTGTGACCGTCCGTCTGT-----------------------------------------------------------     19---------1
      -------------------------CTGGTTGTGACCGTCCGTC--------------------------------------------------------------     19---------1
      ---------------------------------GACCGTCCGTCTGTTTGC-------------------------------------------------------     18--------1-
      -------------------------------------------------------TCGTGATGTCCGGCCGTGG--------------------------------     19-1--------
      ----------------------------------ACCGTCCGTCTGTTTGCG------------------------------------------------------     18--------1-
      -----------------------------------CCGTCCGTCTGTTTGCGC-----------------------------------------------------     18--------1-
      -------------------AGTTTCCTGGTTGTGACCGTCCGTCT-------------------------------------------------------------     26----1-----
      -----------------ACAGTTTCCTGGTTGTGAC----------------------------------------------------------------------     19---------1
      -------------------AGTTTCCTGGTTGTGACCGTCC-----------------------------------------------------------------     22--------1-
      -----------------------------------------------TTGCGCTCTCGTGATGTCCG---------------------------------------     20--------1-
rat     ggcgtcggcgttggcgcACAGTTTCCTGGTTGTGACCGTCCGTCTGTTTGCGCTCTCGTGATGTCCggccgtggcaagcaaggaggcaaggcccgcgccaaggcca      
      **********************************************************************************************************      
 ++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>ENSRNOT00000044268 ENSRNOG00000032949 LOC690131
rat     (((...((((.(((.((...(((((((.((..((.(((..((((.....(((....)))))))..))).))..)).....)))))))...)))))))))...))).     0.440 -43.00

ratchromosome:2:191045361:191045466:-1Same_strand|Boundary_non-coding|ENSRNOT00000044268|ENSRNOG00000032949 ## ENSRNOG00000032949|protein_coding|LOC690131|Histone H2A type 1. [Source:UniProtKB/Swiss-Prot;Acc:P02262] ## {SimpF: 1 Eponine,oe = 0.84 -1 CpG}


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