(136 letters)

Database: hairpin_length.fa 
           18,432 sequences; 1,887,117 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

mdm-MIR399d_MI0023108_137                                             109   2e-25
mdm-MIR399j_MI0023114_123                                              50   2e-07
osa-MIR399d_MI0001056_Oryza_sativa_miR399d_stem-loop_286               50   2e-07
sbi-MIR399d_MI0001543_Sorghum_bicolor_miR399d_stem-loop_205            50   2e-07
csi-MIR399d_MI0016711_Citrus_sinensis_miR399d_stem-loop_130            46   3e-06
vvi-MIR399b_MI0006574_Vitis_vinifera_miR399b_stem-loop_117             46   3e-06
csi-MIR399b_MI0016713_Citrus_sinensis_miR399b_stem-loop_168            46   3e-06
ath-MIR399b_MI0001021_Arabidopsis_thaliana_miR399b_stem-loop_135       46   3e-06
aly-MIR399b_MI0014589_Arabidopsis_lyrata_miR399b_stem-loop_154         46   3e-06
mtr-MIR399l_MI0005606_Medicago_truncatula_miR399l_stem-loop_79         44   1e-05
zma-MIR399j_MI0013236_Zea_mays_miR399j_stem-loop_175                   44   1e-05
mtr-MIR399p_MI0005634_Medicago_truncatula_miR399p_stem-loop_79         44   1e-05
mdm-MIR399i_MI0023113_114                                              44   1e-05
ghr-MIR399c_MI0013556_Gossypium_hirsutum_miR399c_stem-loop_74          44   1e-05
aqc-MIR399_MI0012098_Aquilegia_caerulea_miR399_stem-loop_98            42   4e-05
sbi-MIR399i_MI0001850_Sorghum_bicolor_miR399i_stem-loop_121            42   4e-05
osa-MIR399j_MI0001062_Oryza_sativa_miR399j_stem-loop_106               42   4e-05
zma-MIR399e_MI0001806_Zea_mays_miR399e_stem-loop_124                   42   4e-05
vvi-MIR399c_MI0007960_Vitis_vinifera_miR399c_stem-loop_82              42   4e-05
sly-MIR399_MI0009979_Solanum_lycopersicum_miR399_stem-loop_71          40   2e-04
rco-MIR399a_MI0013422_Ricinus_communis_miR399a_stem-loop_93            40   2e-04
zma-MIR399i_MI0013235_Zea_mays_miR399i_stem-loop_91                    40   2e-04
vun-MIR399a_MI0019576_Vigna_unguiculata_miR399a_stem-loop_83           40   2e-04
ath-MIR399c_MI0001022_Arabidopsis_thaliana_miR399c_stem-loop_114       40   2e-04
tcc-MIR399i_MI0017527_Theobroma_cacao_miR399i_stem-loop_157            40   2e-04
aly-MIR399c_MI0014590_Arabidopsis_lyrata_miR399c_stem-loop_125         40   2e-04
pvu-MIR399a_MI0010706_Phaseolus_vulgaris_miR399a_stem-loop_223         40   2e-04
mtr-MIR399g_MI0005588_Medicago_truncatula_miR399g_stem-loop_104        40   2e-04
ptc-MIR399i_MI0002346_Populus_trichocarpa_miR399i_stem-loop_108        40   2e-04
ptc-MIR399l_MI0002349_Populus_trichocarpa_miR399l_stem-loop_109        38   6e-04
tcc-MIR399a_MI0017519_Theobroma_cacao_miR399a_stem-loop_136            38   6e-04
vvi-MIR399i_MI0007963_Vitis_vinifera_miR399i_stem-loop_122             38   6e-04

>mdm-MIR399d_MI0023108_137
          Length = 137

 Score =  109 bits (55), Expect = 2e-25
 Identities = 118/137 (86%), Gaps = 9/137 (6%)
 Strand = Plus / Plus

                                                                       
Query: 6   tgagcgaattagttgtagggcctctctccagtggcaggaaatataaatggtcatg----- 60
           ||||||||||||||||||||| |||||||  ||||||||||||| ||||||||||     
Sbjct: 1   tgagcgaattagttgtagggcttctctccgatggcaggaaatattaatggtcatgaatca 60

                                                                       
Query: 61  -gg--gcatggattttc-tgttctctcgtgagctataacctgccaaaggagagttgccct 116
            ||  |||||||||||  ||||||||| |||| ||| |||||||||||||||||||||||
Sbjct: 61  tggaagcatggatttttgtgttctctcatgagttatgacctgccaaaggagagttgccct 120

                            
Query: 117 tcgactgcttctgctta 133
            ||||||||| ||||||
Sbjct: 121 acgactgcttttgctta 137


>mdm-MIR399j_MI0023114_123
          Length = 123

 Score = 50.1 bits (25), Expect = 2e-07
 Identities = 31/33 (93%)
 Strand = Plus / Plus

                                            
Query: 94  acctgccaaaggagagttgcccttcgactgctt 126
           ||||||||||||||||||||||| ||| |||||
Sbjct: 80  acctgccaaaggagagttgccctgcgattgctt 112


>osa-MIR399d_MI0001056_Oryza_sativa_miR399d_stem-loop_286
          Length = 286

 Score = 50.1 bits (25), Expect = 2e-07
 Identities = 28/29 (96%)
 Strand = Plus / Plus

                                        
Query: 95  cctgccaaaggagagttgcccttcgactg 123
           |||||||||||||||||||||| ||||||
Sbjct: 254 cctgccaaaggagagttgccctgcgactg 282


>sbi-MIR399d_MI0001543_Sorghum_bicolor_miR399d_stem-loop_205
          Length = 205

 Score = 50.1 bits (25), Expect = 2e-07
 Identities = 28/29 (96%)
 Strand = Plus / Plus

                                        
Query: 95  cctgccaaaggagagttgcccttcgactg 123
           |||||||||||||||||||||| ||||||
Sbjct: 164 cctgccaaaggagagttgccctgcgactg 192


>csi-MIR399d_MI0016711_Citrus_sinensis_miR399d_stem-loop_130
          Length = 130

 Score = 46.1 bits (23), Expect = 3e-06
 Identities = 29/31 (93%)
 Strand = Plus / Plus

                                          
Query: 97  tgccaaaggagagttgcccttcgactgcttc 127
           ||||||||||||||||||||  |||||||||
Sbjct: 100 tgccaaaggagagttgccctgtgactgcttc 130


>vvi-MIR399b_MI0006574_Vitis_vinifera_miR399b_stem-loop_117
          Length = 117

 Score = 46.1 bits (23), Expect = 3e-06
 Identities = 29/31 (93%)
 Strand = Plus / Plus

                                          
Query: 97  tgccaaaggagagttgcccttcgactgcttc 127
           ||||||||||||||||||||  |||||||||
Sbjct: 87  tgccaaaggagagttgccctgtgactgcttc 117


>csi-MIR399b_MI0016713_Citrus_sinensis_miR399b_stem-loop_168
          Length = 168

 Score = 46.1 bits (23), Expect = 3e-06
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 94  acctgccaaaggagagttgccct 116
           |||||||||||||||||||||||
Sbjct: 122 acctgccaaaggagagttgccct 144



 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 32/36 (88%)
 Strand = Plus / Plus

                                              
Query: 8  agcgaattagttgtagggcctctctccagtggcagg 43
          ||||| ||||||||||||| |||||||  |||||||
Sbjct: 10 agcgatttagttgtagggcttctctcctttggcagg 45


>ath-MIR399b_MI0001021_Arabidopsis_thaliana_miR399b_stem-loop_135
          Length = 135

 Score = 46.1 bits (23), Expect = 3e-06
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 94  acctgccaaaggagagttgccct 116
           |||||||||||||||||||||||
Sbjct: 102 acctgccaaaggagagttgccct 124


>aly-MIR399b_MI0014589_Arabidopsis_lyrata_miR399b_stem-loop_154
          Length = 154

 Score = 46.1 bits (23), Expect = 3e-06
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 94  acctgccaaaggagagttgccct 116
           |||||||||||||||||||||||
Sbjct: 103 acctgccaaaggagagttgccct 125


>mtr-MIR399l_MI0005606_Medicago_truncatula_miR399l_stem-loop_79
          Length = 79

 Score = 44.1 bits (22), Expect = 1e-05
 Identities = 25/26 (96%)
 Strand = Plus / Plus

                                     
Query: 91  ataacctgccaaaggagagttgccct 116
           ||||| ||||||||||||||||||||
Sbjct: 48  ataacttgccaaaggagagttgccct 73


>zma-MIR399j_MI0013236_Zea_mays_miR399j_stem-loop_175
          Length = 175

 Score = 44.1 bits (22), Expect = 1e-05
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                 
Query: 95  cctgccaaaggagagttgccct 116
           ||||||||||||||||||||||
Sbjct: 152 cctgccaaaggagagttgccct 173


>mtr-MIR399p_MI0005634_Medicago_truncatula_miR399p_stem-loop_79
          Length = 79

 Score = 44.1 bits (22), Expect = 1e-05
 Identities = 25/26 (96%)
 Strand = Plus / Plus

                                     
Query: 91  ataacctgccaaaggagagttgccct 116
           ||||| ||||||||||||||||||||
Sbjct: 48  ataacttgccaaaggagagttgccct 73


>mdm-MIR399i_MI0023113_114
          Length = 114

 Score = 44.1 bits (22), Expect = 1e-05
 Identities = 28/30 (93%)
 Strand = Plus / Plus

                                         
Query: 97  tgccaaaggagagttgcccttcgactgctt 126
           |||||||||||||||||||| ||| |||||
Sbjct: 78  tgccaaaggagagttgccctgcgattgctt 107


>ghr-MIR399c_MI0013556_Gossypium_hirsutum_miR399c_stem-loop_74
          Length = 74

 Score = 44.1 bits (22), Expect = 1e-05
 Identities = 25/26 (96%)
 Strand = Plus / Plus

                                     
Query: 92  taacctgccaaaggagagttgccctt 117
           ||||||||||||||||||||| ||||
Sbjct: 49  taacctgccaaaggagagttggcctt 74


>aqc-MIR399_MI0012098_Aquilegia_caerulea_miR399_stem-loop_98
          Length = 98

 Score = 42.1 bits (21), Expect = 4e-05
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 96  ctgccaaaggagagttgccct 116
           |||||||||||||||||||||
Sbjct: 71  ctgccaaaggagagttgccct 91


>sbi-MIR399i_MI0001850_Sorghum_bicolor_miR399i_stem-loop_121
          Length = 121

 Score = 42.1 bits (21), Expect = 4e-05
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 96  ctgccaaaggagagttgccct 116
           |||||||||||||||||||||
Sbjct: 81  ctgccaaaggagagttgccct 101


>osa-MIR399j_MI0001062_Oryza_sativa_miR399j_stem-loop_106
          Length = 106

 Score = 42.1 bits (21), Expect = 4e-05
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 96  ctgccaaaggagagttgccct 116
           |||||||||||||||||||||
Sbjct: 75  ctgccaaaggagagttgccct 95


>zma-MIR399e_MI0001806_Zea_mays_miR399e_stem-loop_124
          Length = 124

 Score = 42.1 bits (21), Expect = 4e-05
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 96  ctgccaaaggagagttgccct 116
           |||||||||||||||||||||
Sbjct: 84  ctgccaaaggagagttgccct 104


>vvi-MIR399c_MI0007960_Vitis_vinifera_miR399c_stem-loop_82
          Length = 82

 Score = 42.1 bits (21), Expect = 4e-05
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 96  ctgccaaaggagagttgccct 116
           |||||||||||||||||||||
Sbjct: 51  ctgccaaaggagagttgccct 71


>sly-MIR399_MI0009979_Solanum_lycopersicum_miR399_stem-loop_71
          Length = 71

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 51  tgccaaaggagagttgccct 70


>rco-MIR399a_MI0013422_Ricinus_communis_miR399a_stem-loop_93
          Length = 93

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 68  tgccaaaggagagttgccct 87


>zma-MIR399i_MI0013235_Zea_mays_miR399i_stem-loop_91
          Length = 91

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 70  tgccaaaggagagttgccct 89


>vun-MIR399a_MI0019576_Vigna_unguiculata_miR399a_stem-loop_83
          Length = 83

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 58  tgccaaaggagagttgccct 77


>ath-MIR399c_MI0001022_Arabidopsis_thaliana_miR399c_stem-loop_114
          Length = 114

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 84  tgccaaaggagagttgccct 103


>tcc-MIR399i_MI0017527_Theobroma_cacao_miR399i_stem-loop_157
          Length = 157

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 117 tgccaaaggagagttgccct 136


>aly-MIR399c_MI0014590_Arabidopsis_lyrata_miR399c_stem-loop_125
          Length = 125

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 89  tgccaaaggagagttgccct 108


>pvu-MIR399a_MI0010706_Phaseolus_vulgaris_miR399a_stem-loop_223
          Length = 223

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 89  tgccaaaggagagttgccct 108


>mtr-MIR399g_MI0005588_Medicago_truncatula_miR399g_stem-loop_104
          Length = 104

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                   
Query: 92  taacctgccaaaggagagttgccc 115
           ||||||||||||||||| ||||||
Sbjct: 74  taacctgccaaaggagatttgccc 97


>ptc-MIR399i_MI0002346_Populus_trichocarpa_miR399i_stem-loop_108
          Length = 108

 Score = 40.1 bits (20), Expect = 2e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 97  tgccaaaggagagttgccct 116
           ||||||||||||||||||||
Sbjct: 79  tgccaaaggagagttgccct 98


>ptc-MIR399l_MI0002349_Populus_trichocarpa_miR399l_stem-loop_109
          Length = 109

 Score = 38.2 bits (19), Expect = 6e-04
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 98  gccaaaggagagttgccct 116
           |||||||||||||||||||
Sbjct: 82  gccaaaggagagttgccct 100


>tcc-MIR399a_MI0017519_Theobroma_cacao_miR399a_stem-loop_136
          Length = 136

 Score = 38.2 bits (19), Expect = 6e-04
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 91  ataacctgccaaaggagag 109
           |||||||||||||||||||
Sbjct: 47  ataacctgccaaaggagag 29



 Score = 38.2 bits (19), Expect = 6e-04
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 98  gccaaaggagagttgccct 116
           |||||||||||||||||||
Sbjct: 97  gccaaaggagagttgccct 115


>vvi-MIR399i_MI0007963_Vitis_vinifera_miR399i_stem-loop_122
          Length = 122

 Score = 38.2 bits (19), Expect = 6e-04
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 98  gccaaaggagagttgccct 116
           |||||||||||||||||||
Sbjct: 93  gccaaaggagagttgccct 111


BLASTN 2.2.20 [Feb-08-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.