logoC.briggsae small RNAs

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cbr-mir-790

cbr-mir-790

Cloning frequencies
absoluteAF16
cbr-mir-790 5arm6
normalizedAF16
cbr-mir-790 5arm0.016
cbr-mir-790 relative cloning frequencies

block2187 (miRBase cbr-mir-790-1) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-790-10.002nono0.65/0.6820/22/1.000.0
0.8
5
0
1
0
16
3
5arm
2
nd
0.14
1
61nana
Clusters
Located in cluster 5: cbr-mir-790, cbr-mir-790
Families
Member of family miR-790/791 (seed UUGGCAC): cbr-mir-790, cbr-mir-790
block2187 hairpin
  readsmiRBase family seed
seed     -----------------UUGGCA---C----------------------------------------------------------------------------     6miR-790/791
  lencloning frequencies
   AF16
cbr-miR-790     ----------------CTTGGCA---CTCGCGAACACCGCG--------------------------------------------------------------     223
      ----------------CTTGGCA---CTCGCGAACACCG----------------------------------------------------------------     202
      ----------------CTTGGCA---CTCGCGAACACCGC---------------------------------------------------------------     211
cbriggsae     AAGTCCCTTCCGATTGCTTGGCA---CTCGCGAACACCGCGATCACTTCCAATATCGATCCGCGGAGTTAGCCA-GTGTCAACCAAATGGATGTTTGAGACTT      
cremanei     ----------------CTTGGCA---CTCGCGAACACCGCGATCTTATCAGATA---AATCGCGGAGTTAGCCG-GTGGCAAC--------------------      
celegans     --GTCCCTTCAGCCGGCTTGGCA---CTCGCGAACACCGCGATTTC----ACTTATAACTCGCGGCGTTAGCTCTGTGTCAAACCGGC---------------      
cbrenneri     ----------------CTTGGCA---CTCGCGAACACCGCGATCTAACTGTATA---AATCGCGGCGTTAGCTC-GTGGCAAA--------------------      
cjaponica     ----------------CTTGGCA---CTCGCGAACACCGCGCTTCACAACTAAAAGATGTCGCGGCGTTGGCTTGGTGCCAAA--------------------      
ppacificus     ----------------CTTGGCACAGCTAAAAAATACCG-ATTCTCTGAAAATTTGAAATCTGGGGTTCTTAAGGGTGCTGATG-------------------      
                      *******   **    ** ****   *                 *  **  *       ***   *                           
 ++++++++++++++++++++++++++++   ++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++NM_066961
cbriggsae     (((((.(.((((.(((.((((((   ((.((.(((.((((((((............))).))))).))).)).) ))))))).))).)))).....).)))))     1.000 -36.50
cremanei                     .(((.((   ((.((.(((.(((((((.((((...)))   )))))))).))).)).) ))).))).                         1.000 -24.70
celegans       .........(((((.((((((   (..((.(((.((((((....    .........)))))).))).))...))))))).)))))                    1.000 -34.42
cbrenneri                     .(((.((   (..((.(((.(((((((.((......))   .))))))).))).)).. ))).))).                         1.000 -23.70
cjaponica                     .((((((   ((.((.(((.(((((..((..........))...))))).))).))..)))))))).                         1.000 -28.00
ppacificus                     .(((((((..((.((.((..((( (((.((.........)))))).))..)).)).)).)))))))..                        0.999 -12.60

cbriggsaechromosome:chrIV:8548022:8548120:-1Same_strand|Intronic_non-coding|NM_066961|W09D10.4 ## {Repeats: no} ## {MIR: cbr-mir-790-1}
cremaneichromosome:chrUn:101798598:101798736:1intergenic
celeganschromosome:chrIV:5566400:5566478:1intergenic ## {MIR: cel-mir-790}
cbrennerichromosome:chrUn:156782538:156782676:1intergenic
cjaponicachromosome:chrUn:34737964:34738102:1intergenic
ppacificuschromosome:chrUn:159875557:159875695:1Same_strand|Intronic_coding|NM_066967


block2188 (miRBase cbr-mir-790-2) [miRNAknown_cloningOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-790-20.007nono0.65/0.6820/22/1.000.0
0.8
5
0
1
0
5
2
5arm
2
nd
0.14
1
61nana
Clusters
Located in cluster 5: cbr-mir-790, cbr-mir-790
Families
Member of family miR-790/791 (seed UUGGCAC): cbr-mir-790, cbr-mir-790
block2188 hairpin
  readsmiRBase family seed
seed     -------------------UUGGCAC-------------------------------------------------------------------------------     6miR-790/791
  lencloning frequencies
   AF16
cbr-miR-790     ------------------CTTGGCACTCGCGAACACCG---CG--------------------------------------------------------------     223
      ------------------CTTGGCACTCGCGAACACCG-------------------------------------------------------------------     202
      ------------------CTTGGCACTCGCGAACACCG---C---------------------------------------------------------------     211
cbriggsae     -------------GACTGCTTGGCACTCGCGAACACCG---CGGTCGAA----GTTAC---TCGCGGAGTTAGCCA-GTGTCAACCAGATG--------------      
cremanei     ------------------CTTGGCACTCGCGAACACCG---CGATCTTATCAGATAAA---TCGCGGAGTTAGCCG-GTGGCAACCAGG----------------      
celegans     -------------GCCGGCTTGGCACTCGCGAACACCG---CGATTTCACT-TATAAC---TCGCGGCGTTAGCTCTGTGTCAAACCGGC---------------      
cbrenneri     AAGGTCCCGTTCTACCTGCTTGGCACTCGCGAACACCG---CGATCTAACTGTATAAA---TCGCGGCGTTAGCTC-GTGGCAAACAGGTGATGCTGAAGACTTT      
cjaponica     TCCAGTCCCTCCAAACTGCTTGGCACTCGCGAACACCG---CGCTTCACAACTAAAAGATGTCGCGGCGTTGGCTTGGTGCCAAACAGGATGAGAGTTTGAGA--      
ppacificus     ------------------CTTGGCACAGCTCAAAATCGATTCTCTGAAGCTATGTGAA---TCGGGGTTCTCGAGG-GTGCTGAT--------------------      
                        ********     ** * **   *  *           *    *** **   * *    ***   *                           
 +++++             +++++++++++++++++++++++++   ++++++++    +++++   +++++++++++++++ ++++++++++++++              +++++NM_066961
cbriggsae                  ..(((.((((((((.((.(((.(((   ((((....    ...))   .))))).))).)).) ))))))).)))...                   1.000 -29.30
cremanei                       .(((.((((.((.(((.(((   ((((.((((...)))))   )))))).))).)).) ))).))).....                     1.000 -24.70
celegans                  (((((.(((((((..((.(((.(((   (((....... ......   )))))).))).))...))))))).)))))                    1.000 -34.22
cbrenneri     ((((((..((..((((((.(((.(((..((.(((.(((   ((((.((......)).)   )))))).))).)).. ))).))).))))))..))....))))))     1.000 -38.30
cjaponica     ..(((...(((((..(((.((((((((.((.(((.(((   ((..((..........))...))))).))).))..)))))))).)))..)).))).)))...       1.000 -38.10
ppacificus                       .(((((((..(((((..(((((((.............)))   ))))..))...))). ))))))).                         0.994 -17.52

cbriggsaechromosome:chrIV:8548664:8548730:-1Same_strand|Intronic_non-coding|NM_066961|W09D10.4 ## {Repeats: no} ## {MIR: cbr-mir-790-2}
cremaneichromosome:chrUn:101798609:101798715:1intergenic
celeganschromosome:chrIV:5566409:5566478:1intergenic ## {MIR: cel-mir-790}
cbrennerichromosome:chrUn:156782556:156782653:1intergenic
cjaponicachromosome:chrUn:34737982:34738081:1intergenic
ppacificuschromosome:chrUn:90815662:90815768:-1Opposite_strand|Intronic_coding|NM_062686


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