[BEGIN]

REFERENCE HAIRPIN
**********************************************************************************************************
ID                 : mmu-mir-542
DESCRIPTION        : mmu-mir-542 MI0003522 Mus musculus miR-542 stem-loop
CHROMOSOME         : X
SPAN               : 50402580 - 50402664
LENGTH             : 85
SEQUENCE           : GGATCTCAGACGTCTCGGGGATCATCATGTCACGAGATACCACTGTGCCCTTGTGACAGATTGATAACTGAAAGGTCTGGGAGCC
OVERHANG THRESHOLD : 75%
**********************************************************************************************************


TARGET
******************************
CATEGORY   : MATURE-3P
ID         : mmu-miR-542-3p
ACCID      : MI0003522
PARENT     : mmu-mir-542
CHROMOSOME : X
START      : 50402580
STOP       : 50402664
OFFSET     : 52..73
SEQUENCE   : TGTGACAGATTGATAACTGAAA
STRAND     : -
******************************


TARGET
******************************
CATEGORY   : MATURE-5P
ID         : mmu-miR-542-5p
ACCID      : MI0003522
PARENT     : mmu-mir-542
CHROMOSOME : X
START      : 50402580
STOP       : 50402664
OFFSET     : 14..35
SEQUENCE   : CTCGGGGATCATCATGTCACGA
STRAND     : -
******************************



*** MATURE-3P ***
_____________________________________________________________________________________
GGATCTCAGACGTCTCGGGGATCATCATGTCACGAGATACCACTGTGCCCTTGTGACAGATTGATAACTGAAAGGTCTGGGAGCC REF                  X                    50402580 - 50402664  
                                                   TGTGACAGATTGATAACTGAAA             MATURE-3P            X                    50402632 - 50402737  mmu-miR-542-3p       -                    
             CTCGGGGATCATCATGTCACGA                                                   MATURE-5P            X                    50402594 - 50402699  mmu-miR-542-5p       -                    
_____________________________________________________________________________________

                                                                                 -SEQ-                    -READ-        -CAT-      -TOTAL-       -TOT%-       -REST-      -REST%-        -ACT-       -ACT%-        -VAR-   -MISMATCH-   
....................................................GTGACAGATTGATAACTGA...............   read_198356_7_3_3_0_0_3    MATURE-3P           16        31.37           13        34.21            3        23.08                        19   
....................................................GTGACAGATTGATAACTGAAAGt...........   read_278923_2_2_2_1_0_2    MATURE-3P            9        17.65            6        15.79            3        23.08            t           22   
....................................................GTGACAGATTGATAACTGAAAG............    read_78923_0_5_0_0_2_0    MATURE-3P            7        13.73            5        13.16            2        15.38                        22   
....................................................GTGACAGATTGATAACTGAAA.............   read_243577_1_1_1_0_1_1    MATURE-3P            5         9.80            3         7.89            2        15.38                        21   
....................................................GTGACAGATTGATAACTGAA..............    read_44397_2_1_0_1_0_0    MATURE-3P            4         7.84            3         7.89            1         7.69                        20   
....................................................GTGACAGATTGATAACTGAg..............   read_152458_1_1_0_0_0_0    MATURE-3P            2         3.92            2         5.26            0         0.00            g           19   
......................................................GACAGATTGATAACTGAAAGt...........   read_191808_0_2_0_0_0_0    MATURE-3P            2         3.92            2         5.26            0         0.00            t           20   
....................................................GTGACAGATTGATAACTGAAAGtt..........   read_268396_0_1_0_0_0_0    MATURE-3P            1         1.96            1         2.63            0         0.00           tt           22   
......................................................GACAGATTGATAACTGAAAGta..........    read_25761_1_0_0_0_0_0    MATURE-3P            1         1.96            1         2.63            0         0.00           ta           20   
....................................................GTGACAGATTGATAACTGAAAGa...........   read_340186_0_0_0_0_0_1    MATURE-3P            1         1.96            0         0.00            1         7.69            a           22   
....................................................GTGACAGATTGATAgCTGAA..............   read_211591_1_0_0_0_0_0    MATURE-3P            1         1.96            1         2.63            0         0.00                      14G5   
....................................................GTGACAGATTGATAtCTGAAA.............   read_312689_1_0_0_0_0_0    MATURE-3P            1         1.96            1         2.63            0         0.00                      14T6   
....................................................GTGACAGATTGATAACTGAAAa............   read_201032_0_0_0_1_0_0    MATURE-3P            1         1.96            0         0.00            1         7.69            a           21   
                                                                                                                                ----------                ----------                ----------   
                                                                                                                                        51                        38                        13                                          
                                                                                                                                                             (74.51)                   (25.49)                                       




*** MATURE-5P ***
_____________________________________________________________________________________
GGATCTCAGACGTCTCGGGGATCATCATGTCACGAGATACCACTGTGCCCTTGTGACAGATTGATAACTGAAAGGTCTGGGAGCC REF                  X                    50402580 - 50402664  
                                                   TGTGACAGATTGATAACTGAAA             MATURE-3P            X                    50402632 - 50402737  mmu-miR-542-3p       -                    
             CTCGGGGATCATCATGTCACGA                                                   MATURE-5P            X                    50402594 - 50402699  mmu-miR-542-5p       -                    
_____________________________________________________________________________________

                                                                                 -SEQ-                    -READ-        -CAT-      -TOTAL-       -TOT%-       -REST-      -REST%-        -ACT-       -ACT%-        -VAR-   -MISMATCH-   
..............TCGGGGATCATCATGTCACGA...................................................   read_138948_4_0_0_2_0_0    MATURE-5P            6        46.15            4        80.00            2        25.00                        21   
..............TCGGGGATCATCATGTCACG....................................................   read_183943_1_0_0_1_1_1    MATURE-5P            4        30.77            1        20.00            3        37.50                        20   
..............TCGGGGATCATCATGTCACGAGt.................................................   read_381950_0_0_0_0_0_1    MATURE-5P            1         7.69            0         0.00            1        12.50            t           22   
..............TCGGGGATCATCATGTCAC.....................................................   read_159509_0_0_0_1_0_0    MATURE-5P            1         7.69            0         0.00            1        12.50                        19   
..............TCGGGGATCATCATGTCA......................................................   read_322438_0_0_0_0_1_0    MATURE-5P            1         7.69            0         0.00            1        12.50                        18   
                                                                                                                                ----------                ----------                ----------   
                                                                                                                                        13                         5                         8                                          
                                                                                                                                                             (38.46)                   (61.54)                                       




((( SUMMARY )))

          -CAT-          -REST-           -ACT-         -TOTAL-        -TOTAL%-
     ----------      ----------      ----------      ----------      ----------
      MATURE-3P              38              13              51          79.69%
      MATURE-5P               5               8              13          20.31%
                     ----------      ----------      ----------                
                             43              21              64                



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