AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG028887

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028887 MtrunA17_Chr5g0438091 97.449 196 5 0 1 196 1 196 1.49e-144 400
MsaG028887 MtrunA17_Chr3g0129071 63.025 238 43 8 1 195 1 236 6.15e-84 248
MsaG028887 MtrunA17_Chr5g0432451 59.052 232 55 7 1 195 1 229 1.96e-71 216
MsaG028887 MtrunA17_Chr2g0311601 63.964 111 40 0 36 146 10 120 4.63e-49 157
MsaG028887 MtrunA17_Chr5g0437571 60.504 119 47 0 34 152 1 119 6.13e-49 157
MsaG028887 MtrunA17_Chr3g0114061 67.619 105 34 0 35 139 4 108 5.86e-48 154
MsaG028887 MtrunA17_Chr4g0043421 62.727 110 41 0 29 138 5 114 1.69e-47 153
MsaG028887 MtrunA17_Chr4g0058651 62.385 109 41 0 38 146 10 118 9.36e-45 147
MsaG028887 MtrunA17_Chr7g0227511 62.617 107 40 0 36 142 8 114 1.56e-44 145
MsaG028887 MtrunA17_Chr3g0106101 55.645 124 50 1 37 155 5 128 1.15e-43 144
MsaG028887 MtrunA17_Chr3g0117121 59.091 110 45 0 37 146 8 117 6.57e-43 142
MsaG028887 MtrunA17_Chr6g0449641 60.577 104 41 0 36 139 6 109 9.04e-43 140
MsaG028887 MtrunA17_Chr5g0402611 60.748 107 42 0 36 142 5 111 2.45e-42 144
MsaG028887 MtrunA17_Chr3g0115431 59.813 107 43 0 36 142 6 112 2.77e-42 141
MsaG028887 MtrunA17_Chr4g0030001 55.263 114 50 1 38 150 23 136 4.92e-42 140
MsaG028887 MtrunA17_Chr6g0449651 57.009 107 46 0 36 142 64 170 6.53e-41 137
MsaG028887 MtrunA17_Chr3g0113891 59.804 102 41 0 36 137 11 112 1.54e-40 136
MsaG028887 MtrunA17_Chr3g0097221 55.963 109 48 0 36 144 4 112 6.26e-40 137
MsaG028887 MtrunA17_Chr1g0200201 54.955 111 50 0 40 150 73 183 6.85e-40 135
MsaG028887 MtrunA17_Chr7g0245871 62.745 102 37 1 39 139 27 128 1.30e-39 135
MsaG028887 MtrunA17_Chr8g0353981 43.590 156 88 0 36 191 4 159 8.40e-39 132
MsaG028887 MtrunA17_Chr5g0437401 55.660 106 47 0 36 141 8 113 9.01e-39 131
MsaG028887 MtrunA17_Chr7g0260971 53.333 105 48 1 36 139 11 115 1.64e-36 126
MsaG028887 MtrunA17_Chr7g0225111 53.333 105 49 0 40 144 6 110 4.64e-36 122
MsaG028887 MtrunA17_Chr8g0351701 47.794 136 65 3 39 168 23 158 4.57e-35 123
MsaG028887 MtrunA17_Chr5g0444351 46.457 127 65 1 40 166 6 129 2.35e-34 119
MsaG028887 MtrunA17_Chr8g0351721 50.435 115 56 1 39 152 18 132 3.56e-34 120
MsaG028887 MtrunA17_Chr1g0184281 53.465 101 46 1 39 138 15 115 4.57e-34 120
MsaG028887 MtrunA17_Chr6g0460951 49.107 112 56 1 38 148 39 150 1.78e-33 119
MsaG028887 MtrunA17_Chr7g0261031 53.398 103 45 2 38 138 7 108 2.19e-32 116
MsaG028887 MtrunA17_Chr1g0184271 53.922 102 44 2 39 138 12 112 3.47e-32 116
MsaG028887 MtrunA17_Chr5g0435641 50.505 99 48 1 38 135 6 104 3.00e-30 109
MsaG028887 MtrunA17_Chr8g0374601 47.115 104 55 0 39 142 26 129 2.11e-29 110
MsaG028887 MtrunA17_Chr7g0245861 54.444 90 38 2 39 125 12 101 2.99e-27 100
MsaG028887 MtrunA17_Chr8g0374591 41.739 115 64 1 39 150 8 122 3.81e-27 100
MsaG028887 MtrunA17_Chr6g0460941 45.161 93 50 1 35 126 3 95 1.56e-26 97.4
MsaG028887 MtrunA17_Chr6g0452691 39.806 103 61 1 32 133 2 104 2.91e-25 96.7
MsaG028887 MtrunA17_Chr8g0374581 46.667 105 55 1 39 142 8 112 2.91e-25 97.8
MsaG028887 MtrunA17_Chr4g0059901 37.705 122 76 0 36 157 7 128 9.01e-25 97.4
MsaG028887 MtrunA17_Chr6g0452671 38.235 102 63 0 35 136 7 108 1.08e-23 93.2
MsaG028887 MtrunA17_Chr6g0452661 37.755 98 60 1 40 136 10 107 6.97e-22 89.7
MsaG028887 MtrunA17_Chr4g0040831 35.185 108 68 1 40 147 16 121 3.53e-21 86.7
MsaG028887 MtrunA17_Chr2g0330201 39.048 105 62 2 36 139 16 119 8.24e-21 87.4
MsaG028887 MtrunA17_Chr8g0342351 35.780 109 68 2 36 143 9 116 3.19e-20 85.5
MsaG028887 MtrunA17_Chr5g0439111 34.579 107 66 2 34 136 1 107 1.33e-19 83.2
MsaG028887 MtrunA17_Chr4g0055441 35.714 98 62 1 40 136 3 100 2.41e-19 80.5
MsaG028887 MtrunA17_Chr2g0326041 62.000 50 19 0 38 87 32 81 6.35e-18 75.1
MsaG028887 MtrunA17_Chr2g0326051 50.746 67 33 0 84 150 5 71 1.18e-16 72.8
MsaG028887 MtrunA17_Chr4g0046201 32.955 88 59 0 38 125 5 92 5.56e-14 68.6
MsaG028887 MtrunA17_Chr8g0337271 27.891 147 99 2 40 185 11 151 1.96e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028887 AT2G40470.1 73.054 167 34 4 1 157 1 166 1.72e-71 216
MsaG028887 AT2G40470.2 79.851 134 24 1 27 157 8 141 4.49e-67 204
MsaG028887 AT2G30340.1 62.424 165 49 2 1 152 1 165 4.60e-67 206
MsaG028887 AT2G30340.2 74.797 123 31 0 30 152 44 166 4.29e-65 201
MsaG028887 AT2G30130.1 66.990 103 34 0 37 139 6 108 7.32e-46 150
MsaG028887 AT1G31320.1 60.345 116 46 0 36 151 10 125 8.65e-46 149
MsaG028887 AT5G63090.4 53.285 137 61 1 37 170 9 145 2.28e-43 143
MsaG028887 AT5G63090.3 53.285 137 61 1 37 170 9 145 2.28e-43 143
MsaG028887 AT5G63090.2 53.285 137 61 1 37 170 9 145 2.28e-43 143
MsaG028887 AT5G63090.1 53.285 137 61 1 37 170 9 145 2.28e-43 143
MsaG028887 AT3G27650.1 60.748 107 42 0 36 142 36 142 2.97e-43 142
MsaG028887 AT5G66870.1 55.072 138 57 3 36 173 4 136 9.59e-43 145
MsaG028887 AT1G07900.1 54.867 113 51 0 38 150 32 144 4.95e-42 140
MsaG028887 AT1G16530.1 50.704 142 63 3 23 162 3 139 8.02e-42 139
MsaG028887 AT2G28500.1 54.867 113 51 0 38 150 54 166 1.81e-41 140
MsaG028887 AT2G23660.2 57.944 107 45 0 36 142 2 108 6.97e-41 140
MsaG028887 AT2G23660.3 57.944 107 45 0 36 142 2 108 6.97e-41 140
MsaG028887 AT2G23660.1 57.944 107 45 0 36 142 2 108 6.97e-41 140
MsaG028887 AT1G65620.1 61.468 109 42 0 35 143 5 113 1.58e-40 137
MsaG028887 AT1G65620.4 61.468 109 42 0 35 143 5 113 1.58e-40 137
MsaG028887 AT1G65620.3 61.468 109 42 0 35 143 5 113 1.58e-40 137
MsaG028887 AT1G65620.5 61.468 109 42 0 35 143 5 113 1.58e-40 137
MsaG028887 AT1G65620.2 61.468 109 42 0 35 143 5 113 1.58e-40 137
MsaG028887 AT3G11090.1 52.500 120 57 0 36 155 8 127 4.77e-38 129
MsaG028887 AT3G26620.1 55.000 100 45 0 40 139 6 105 4.47e-37 125
MsaG028887 AT3G26660.1 55.000 100 45 0 40 139 6 105 5.20e-37 125
MsaG028887 AT2G42430.1 47.656 128 66 1 29 155 5 132 6.94e-36 126
MsaG028887 AT3G03760.1 51.786 112 53 1 38 148 50 161 6.00e-35 124
MsaG028887 AT4G00210.1 53.922 102 46 1 39 139 11 112 1.05e-33 120
MsaG028887 AT2G31310.1 51.961 102 48 1 38 138 6 107 9.34e-33 116
MsaG028887 AT4G00220.1 55.769 104 45 1 42 144 20 123 1.42e-32 117
MsaG028887 AT3G58190.1 52.941 102 45 2 39 138 11 111 1.89e-32 116
MsaG028887 AT5G06080.1 49.107 112 56 1 38 148 6 117 5.43e-32 114
MsaG028887 AT2G45420.1 50.962 104 50 1 42 144 40 143 8.29e-31 113
MsaG028887 AT2G42440.1 50.485 103 48 2 38 138 6 107 1.75e-30 112
MsaG028887 AT2G45410.1 51.515 99 47 1 42 139 19 117 1.29e-29 108
MsaG028887 AT3G50510.1 41.026 117 69 0 37 153 10 126 1.45e-26 100
MsaG028887 AT3G50510.2 41.026 117 69 0 37 153 10 126 1.45e-26 100
MsaG028887 AT3G47870.1 38.889 108 66 0 36 143 33 140 1.20e-25 101
MsaG028887 AT1G72980.1 40.385 104 62 0 36 139 10 113 1.50e-22 90.9
MsaG028887 AT5G35900.1 37.500 104 65 0 36 139 2 105 5.31e-22 89.4
MsaG028887 AT3G13850.1 33.654 104 69 0 40 143 37 140 8.27e-20 84.7
MsaG028887 AT1G06280.1 46.753 77 41 0 40 116 25 101 1.42e-18 80.1
MsaG028887 AT4G22700.1 39.216 102 51 4 40 132 6 105 1.30e-15 72.0
MsaG028887 AT2G19820.1 33.333 90 59 1 38 126 11 100 4.43e-15 68.9
MsaG028887 AT5G15060.1 38.202 89 49 3 27 110 3 90 8.60e-12 60.8
MsaG028887 AT1G36000.1 30.108 93 63 2 34 125 4 95 2.08e-11 59.3

Find 34 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGAGAAATATGGAGAAAA+AGG 0.233084 5:+70118039 None:intergenic
CTTGCAAATTTAATCAAAAT+AGG 0.235336 5:+70116992 None:intergenic
GCTTCTGTCCACAAAGTCTT+TGG 0.267396 5:-70117997 MsaT028887.1:CDS
TTTCAAAAGGGAAGAATGTT+AGG 0.277293 5:-70118138 MsaT028887.1:CDS
AGGCTAAGAGATCCAGTTTA+TGG 0.306813 5:-70117254 MsaT028887.1:CDS
GCATCTGCTCTTTGATTCTC+TGG 0.341032 5:+70117308 None:intergenic
GGAAGAATGTTAGGTCCTTC+AGG 0.355019 5:-70118129 MsaT028887.1:CDS
GGCTCATGAGGAGAGAAATA+TGG 0.368976 5:+70118030 None:intergenic
GCACCCATGCATCCATAAAC+TGG 0.381798 5:+70117242 None:intergenic
ACTTGAAATTGAGCTATAAC+TGG 0.426496 5:+70117025 None:intergenic
CAACAAGTTCAATCATTACT+AGG 0.447623 5:-70117203 MsaT028887.1:CDS
TGCTGGCACCAAAGACTTTG+TGG 0.448216 5:+70117989 None:intergenic
TAGCAACTTTGAGACGTTGC+TGG 0.449895 5:+70117972 None:intergenic
CAACGTCTCAAAGTTGCTAT+TGG 0.452802 5:-70117968 MsaT028887.1:intron
TAGTTTATGAAGCAAATGTA+AGG 0.466219 5:-70117274 MsaT028887.1:CDS
TAAATAGAAGAAGGAAGCCT+TGG 0.522625 5:+70117068 None:intergenic
GAGATAGGAAAGAAGAGAGA+GGG 0.526552 5:-70118171 MsaT028887.1:CDS
AGATCCAGTTTATGGATGCA+TGG 0.526865 5:-70117246 MsaT028887.1:CDS
ATTGATACATCATCTGAAGA+AGG 0.534416 5:+70117119 None:intergenic
TTTGAGACGAAGGTGTGCCC+AGG 0.536248 5:-70118067 MsaT028887.1:CDS
GCAAACTTCTGAGGCTCATG+AGG 0.547685 5:+70118018 None:intergenic
ATGCTTGAATGTCCAGAGAA+AGG 0.549398 5:-70118384 None:intergenic
TGAGATAGGAAAGAAGAGAG+AGG 0.549797 5:-70118172 MsaT028887.1:CDS
AATTCATAAATACAAACTCA+TGG 0.552933 5:-70117156 MsaT028887.1:CDS
GAAATTGAGCTATAACTGGT+AGG 0.562061 5:+70117029 None:intergenic
TGTTGTGTGTAAATAGAAGA+AGG 0.566644 5:+70117059 None:intergenic
GATCCAGTTTATGGATGCAT+GGG 0.578062 5:-70117245 MsaT028887.1:CDS
TGGACAGAAGCAAACTTCTG+AGG 0.589514 5:+70118009 None:intergenic
AAAAGCTTGCATGCAGCACA+AGG 0.594669 5:+70118087 None:intergenic
GCATGCAGCACAAGGAGTAG+TGG 0.596320 5:+70118095 None:intergenic
GTGGTATTTAGTGTTCCTGA+AGG 0.618012 5:+70118114 None:intergenic
CACCTTCAACATCACTACCA+AGG 0.661627 5:-70117085 MsaT028887.1:CDS
AGCCTTGGTAGTGATGTTGA+AGG 0.670441 5:+70117083 None:intergenic
CTTGGTAGTGATGTTGAAGG+TGG 0.715413 5:+70117086 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 70117001 70118398 70117001 ID=MsaG028887
Chr5 mRNA 70117001 70118398 70117001 ID=MsaT028887.1;Parent=MsaG028887
Chr5 exon 70117001 70117336 70117001 ID=MsaT028887.1.exon3;Parent=MsaT028887.1
Chr5 CDS 70117001 70117336 70117001 ID=cds.MsaT028887.1;Parent=MsaT028887.1
Chr5 exon 70117969 70118209 70117969 ID=MsaT028887.1.exon2;Parent=MsaT028887.1
Chr5 CDS 70117969 70118209 70117969 ID=cds.MsaT028887.1;Parent=MsaT028887.1
Chr5 exon 70118385 70118398 70118385 ID=MsaT028887.1.exon1;Parent=MsaT028887.1
Chr5 CDS 70118385 70118398 70118385 ID=cds.MsaT028887.1;Parent=MsaT028887.1
Gene Sequence

>MsaT028887.1

ATGTCCAGAGAAAGGGGGAGATTTTTTGATGAGATAGGAAAGAAGAGAGAGGGTGATGATTCTTTTCAAAAGGGAAGAATGTTAGGTCCTTCAGGAACACTAAATACCACTACTCCTTGTGCTGCATGCAAGCTTTTGAGACGAAGGTGTGCCCAGGAATGTCCTTTTTCTCCATATTTCTCTCCTCATGAGCCTCAGAAGTTTGCTTCTGTCCACAAAGTCTTTGGTGCCAGCAACGTCTCAAAGTTGCTATTGGAGGTACCAGAGAATCAAAGAGCAGATGCAGCAAATAGTTTAGTTTATGAAGCAAATGTAAGGCTAAGAGATCCAGTTTATGGATGCATGGGTGCAATTTCATCTTTGCAACAACAAGTTCAATCATTACTAGGTGAACTCAATGCTATAAGAGAAGAAATTCATAAATACAAACTCATGGAAGCTAACATGCTTCCTTCTTCAGATGATGTATCAATTGCTACTCTACCACCTTCAACATCACTACCAAGGCTTCCTTCTTCTATTTACACACAACAAACAAATCCTACCAGTTATAGCTCAATTTCAAGTGATCATATTTCCTATTTTGATTAA
Protein sequence

>MsaT028887.1

MSRERGRFFDEIGKKREGDDSFQKGRMLGPSGTLNTTTPCAACKLLRRRCAQECPFSPYFSPHEPQKFASVHKVFGASNVSKLLLEVPENQRADAANSLVYEANVRLRDPVYGCMGAISSLQQQVQSLLGELNAIREEIHKYKLMEANMLPSSDDVSIATLPPSTSLPRLPSSIYTQQTNPTSYSSISSDHISYFD*