[BEGIN]

REFERENCE HAIRPIN
***********************************************************************************************************
ID                 : mmu-mir-28
DESCRIPTION        : mmu-mir-28 MI0000690 Mus musculus miR-28 stem-loop
CHROMOSOME         : 16
SPAN               : 24827941 - 24828026
LENGTH             : 86
SEQUENCE           : GGTCCCTACCTTCAAGGAGCTCACAGTCTATTGAGTTGCCTTTCTGATTCTCCCACTAGATTGTGAGCTGCTGGAGGGCAGGCACT
OVERHANG THRESHOLD : 40%
***********************************************************************************************************


TARGET
******************************
CATEGORY   : MATURE
ID         : mmu-miR-28
ACCID      : MI0000690
PARENT     : mmu-mir-28
CHROMOSOME : 16
START      : 24827941
STOP       : 24828026
OFFSET     : 14..35
SEQUENCE   : AAGGAGCTCACAGTCTATTGAG
STRAND     : +
******************************


TARGET
******************************
CATEGORY   : MATURESTAR
ID         : mmu-miR-28*
ACCID      : MI0000690
PARENT     : mmu-mir-28
CHROMOSOME : 16
START      : 24827941
STOP       : 24828026
OFFSET     : 54..75
SEQUENCE   : CACTAGATTGTGAGCTGCTGGA
STRAND     : +
******************************



*** MATURE ***
______________________________________________________________________________________
GGTCCCTACCTTCAAGGAGCTCACAGTCTATTGAGTTGCCTTTCTGATTCTCCCACTAGATTGTGAGCTGCTGGAGGGCAGGCACT REF                  16                   24827941 - 24828026  
             AAGGAGCTCACAGTCTATTGAG                                                    MATURE               16                   24827955 - 24828061  mmu-miR-28           +                    
                                                     CACTAGATTGTGAGCTGCTGGA            MATURESTAR           16                   24827995 - 24828101  mmu-miR-28*          +                    
______________________________________________________________________________________

                                                                                  -SEQ-                -READ-        -CAT-      -TOTAL-       -TOT%-       -REST-      -REST%-        -ACT-       -ACT%-        -VAR-   -MISMATCH-   
.............AAGGAGCTCACAGTCTATTGA.....................................................   36927_26_0_0_0_0_73       MATURE           99        25.92           26        16.67           73        32.30                        21   
.............AAGGAGCTCACAGTCTATTG......................................................   30562_40_0_0_0_0_33       MATURE           73        19.11           40        25.64           33        14.60                        20   
.............AAGGAGCTCACAGTCaATTGA.....................................................   32092_14_0_0_0_0_17       MATURE           31         8.12           14         8.97           17         7.52                      15A5   
.............AAGGAGCTCACAGTCcATTGA.....................................................   43039_10_0_0_0_0_14       MATURE           24         6.28           10         6.41           14         6.19                      15C5   
.............AAGGAGCTCACAGTCTATTa......................................................    37842_14_0_0_0_0_9       MATURE           23         6.02           14         8.97            9         3.98                        19   
.............AAGGAGCTCACAGTCTATTGAa....................................................    43976_5_0_0_0_0_15       MATURE           20         5.24            5         3.21           15         6.64                        21   
.............AAGGAGCTCACAGTCgATTGA.....................................................    40788_7_0_0_0_0_13       MATURE           20         5.24            7         4.49           13         5.75                      15G5   
.............AAGGAGCTCACAGTCTATTGAG....................................................     32658_6_0_0_0_0_9       MATURE           15         3.93            6         3.85            9         3.98                        22   
.............AAGGAGCTCACAGTCTATT.......................................................     24448_5_0_0_0_0_7       MATURE           12         3.14            5         3.21            7         3.10                        19   
.............AAGGAGCTCACAGTCTAcTGA.....................................................     43425_2_0_0_0_0_7       MATURE            9         2.36            2         1.28            7         3.10                      17C3   
.............AAGGAGCTCACAGTCTATTGAGT...................................................     29692_4_0_0_0_0_4       MATURE            8         2.09            4         2.56            4         1.77                        23   
.............AAGGAGCTCACAGTCTcTTGAa....................................................     41446_3_0_0_0_0_2       MATURE            5         1.31            3         1.92            2         0.88                      16C4   
.............AAGGAGCTCACAGTCTATTGAGa...................................................     43423_0_0_0_0_0_4       MATURE            4         1.05            0         0.00            4         1.77                        22   
.............AAGGAGCTCACAGTCTtTTGA.....................................................     20923_1_0_0_0_0_2       MATURE            3         0.79            1         0.64            2         0.88                      16T4   
.............AAGGAGCTCACAGTCTATaGA.....................................................     40881_1_0_0_0_0_2       MATURE            3         0.79            1         0.64            2         0.88                      18A2   
.............AAGGAGCTCACAGTCTATTaAG....................................................     33218_1_0_0_0_0_2       MATURE            3         0.79            1         0.64            2         0.88                      19A2   
.............AAGGAGCTCACAGTCTATTGAc....................................................     41833_2_0_0_0_0_1       MATURE            3         0.79            2         1.28            1         0.44                        21   
.............AAGGAGCTCACAGTCTATTGt.....................................................     22244_2_0_0_0_0_1       MATURE            3         0.79            2         1.28            1         0.44                        20   
.............AAGGAGCTCACAGTCTcTTGA.....................................................      7087_1_0_0_0_0_2       MATURE            3         0.79            1         0.64            2         0.88                      16C4   
.............AAGGAGCTCACAGTCTATTt......................................................     14426_2_0_0_0_0_0       MATURE            2         0.52            2         1.28            0         0.00                        19   
.............AAGGAGCTCACAGTCTATaGAGa...................................................      8101_1_0_0_0_0_1       MATURE            2         0.52            1         0.64            1         0.44                      18A3   
.............AAGGAGCTCACAGTCTATTGAaTT..................................................      1786_2_0_0_0_0_0       MATURE            2         0.52            2         1.28            0         0.00                      21A2   
.............AAGGAGCTCACAGTCTATTGtGT...................................................     29187_0_0_0_0_0_2       MATURE            2         0.52            0         0.00            2         0.88                      20T2   
.............AAGGAGCTCACAGTCTATTaAGa...................................................     19303_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                      19A2   
.............AAGGAGCTCACAGTCTAcTGAG....................................................     22791_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                      17C4   
.............AAGGAGCTCACAGTCTATgGAGa...................................................      3462_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                      18G3   
.............AAGGAGCTCACAGTCTATcGAa....................................................     41411_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                      18C2   
.............AAGGAGCTCACAGTCTATTcAG....................................................       523_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                      19C2   
.............AAGGAGCTCACAGTCTATaGAG....................................................     32955_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                      18A3   
.............AAGGAGCTCACAGTCTATcGAt....................................................      6406_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                      18C2   
............CAAGGAGCTCACAGTCTATTt......................................................      5723_0_0_0_0_0_1       MATURE            1         0.26            0         0.00            1         0.44                        20   
.............AAGGAGCTCACAGTCTATTGg.....................................................     13725_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                        20   
.............AAGGAGCTCACAGTCTATTc......................................................     25406_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                        19   
..............AGGAGCTCACAGTCTATTG......................................................     15636_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                        19   
.............AAGGAGCTCACAGTCTATaGAGTT..................................................      4178_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                      18A5   
.............AAGGAGCTCACAGTCTATTGAGTa..................................................     27416_1_0_0_0_0_0       MATURE            1         0.26            1         0.64            0         0.00                        23   
                                                                                                                             ----------                ----------                ----------   
                                                                                                                                    382                       156                       226                                          
                                                                                                                                                          (40.84)                   (59.16)                                       




*** MATURESTAR ***
______________________________________________________________________________________
GGTCCCTACCTTCAAGGAGCTCACAGTCTATTGAGTTGCCTTTCTGATTCTCCCACTAGATTGTGAGCTGCTGGAGGGCAGGCACT REF                  16                   24827941 - 24828026  
             AAGGAGCTCACAGTCTATTGAG                                                    MATURE               16                   24827955 - 24828061  mmu-miR-28           +                    
                                                     CACTAGATTGTGAGCTGCTGGA            MATURESTAR           16                   24827995 - 24828101  mmu-miR-28*          +                    
______________________________________________________________________________________

                                                                                  -SEQ-              -READ-        -CAT-      -TOTAL-       -TOT%-       -REST-      -REST%-        -ACT-       -ACT%-        -VAR-   -MISMATCH-   
.....................................................CACTAGATTGTGAGCTGCTGGAt...........   20466_4_0_0_0_0_3   MATURESTAR            7        18.42            4        21.05            3        15.79                        22   
.....................................................CACTAGATTGTGAGCTaCTGGA............   39894_0_0_0_0_0_3   MATURESTAR            3         7.89            0         0.00            3        15.79                      16A5   
.....................................................CACTAGATTGTGAGCTGCTGGAa...........   41290_0_0_0_0_0_3   MATURESTAR            3         7.89            0         0.00            3        15.79                        22   
.....................................................CACTAGATTGTGAGCTGCTaGAa...........   37692_2_0_0_0_0_1   MATURESTAR            3         7.89            2        10.53            1         5.26                      19A2   
..................................................TCgCACTAGATTGTGAGCTGCTGGA............    7134_1_0_0_0_0_1   MATURESTAR            2         5.26            1         5.26            1         5.26                      2G22   
......................................................ACTAGATTGTGAGCTGCTGGAa...........   41688_2_0_0_0_0_0   MATURESTAR            2         5.26            2        10.53            0         0.00                        21   
.....................................................CACTAGATTGTGAGCTGCaGGAa...........    4661_1_0_0_0_0_1   MATURESTAR            2         5.26            1         5.26            1         5.26                      18A3   
......................................................ACTAGATTGTGAGCTGCaGGAt...........   43690_2_0_0_0_0_0   MATURESTAR            2         5.26            2        10.53            0         0.00                      17A3   
.....................................................CACTAGATTGTGAGCTGCcGGA............    7654_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                      18C3   
.......................................................CTAGATTGTGAGCTGCcGGAGt..........   21596_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                      16C4   
.....................................................CACTAGATTGTGAGCTGaTGGAa...........    2726_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                      17A4   
......................................................ACTAGATTGTGAGCTGCTaGAt...........   30394_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                      18A2   
......................................................ACTAGATTGTGAGCTGCTaGAa...........   14051_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                      18A2   
......................................................ACTAGATTGTGAGCTGCaGGAa...........   33341_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                      17A3   
......................................................ACTAGATTGTGAGCTGCTGGAGt..........   10543_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                        22   
.....................................................CACTAGATTGTGAGCTGCTaGA............   29249_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                      19A2   
.....................................................CACTAGATTGTGAGCTGCTGGA............   39320_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                        22   
.....................................................CACTAGATTGTGAGCTcCTGGA............   44113_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                      16C5   
......................................................ACTAGATTGTGAGCTGCcGGAa...........   10224_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                      17C3   
.....................................................CACTAGATTGTGAGCTGCTG..............   25527_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                        20   
.......................................................CTAGATTGTGAGCTGCTGGAGt..........   30570_0_0_0_0_0_1   MATURESTAR            1         2.63            0         0.00            1         5.26                        21   
.......................................................CTAGATTGTGAGCTGCTGGAGa..........   15230_1_0_0_0_0_0   MATURESTAR            1         2.63            1         5.26            0         0.00                        21   
                                                                                                                           ----------                ----------                ----------   
                                                                                                                                   38                        19                        19                                          
                                                                                                                                                        (50.00)                   (50.00)                                       




((( SUMMARY )))

          -CAT-          -REST-           -ACT-         -TOTAL-        -TOTAL%-
     ----------      ----------      ----------      ----------      ----------
         MATURE             156             226             382          90.95%
     MATURESTAR              19              19              38           9.05%
                     ----------      ----------      ----------                
                            175             245             420                



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