AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001401

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001401 MtrunA17_Chr4g0050701 32.086 187 102 9 4 176 11 186 1.18e-18 80.5
MsaG001401 MtrunA17_Chr6g0481091 32.500 160 86 7 4 149 6 157 2.13e-18 80.9
MsaG001401 MtrunA17_Chr5g0405211 31.847 157 90 5 4 149 8 158 1.98e-17 79.7
MsaG001401 MtrunA17_Chr4g0056541 33.333 159 83 7 4 148 7 156 3.31e-17 79.3
MsaG001401 MtrunA17_Chr5g0398971 32.184 174 93 8 4 159 7 173 3.86e-17 79.0
MsaG001401 MtrunA17_Chr1g0200561 31.481 162 91 6 1 148 13 168 6.65e-17 78.6
MsaG001401 MtrunA17_Chr8g0372121 28.251 223 138 8 4 210 6 222 1.28e-16 77.4
MsaG001401 MtrunA17_Chr8g0345731 33.088 136 81 4 2 130 22 154 3.10e-16 73.6
MsaG001401 MtrunA17_Chr2g0326361 32.738 168 87 8 4 154 14 172 6.06e-16 75.5
MsaG001401 MtrunA17_Chr2g0318101 30.357 168 101 6 4 164 15 173 8.79e-16 75.1
MsaG001401 MtrunA17_Chr4g0018391 31.214 173 96 7 4 159 7 173 9.59e-16 75.1
MsaG001401 MtrunA17_Chr5g0417791 29.630 162 88 6 4 148 3 155 1.19e-15 73.9
MsaG001401 MtrunA17_Chr5g0400461 27.619 210 126 9 4 194 6 208 1.54e-15 74.3
MsaG001401 MtrunA17_Chr1g0147421 32.298 161 92 6 2 151 25 179 1.97e-15 74.3
MsaG001401 MtrunA17_Chr8g0384721 33.333 162 81 9 4 148 7 158 2.30e-15 73.6
MsaG001401 MtrunA17_Chr7g0263931 31.000 200 99 10 4 186 11 188 3.58e-15 73.2
MsaG001401 MtrunA17_Chr3g0128151 29.762 168 86 9 1 149 19 173 4.01e-15 73.9
MsaG001401 MtrunA17_Chr3g0130731 30.247 162 85 8 4 148 7 157 8.36e-15 72.0
MsaG001401 MtrunA17_Chr4g0047841 33.333 144 80 5 4 138 15 151 9.90e-15 72.0
MsaG001401 MtrunA17_Chr5g0428991 30.357 168 85 9 1 149 22 176 1.09e-14 72.8
MsaG001401 MtrunA17_Chr3g0128111 27.513 189 99 10 7 176 45 214 3.00e-14 69.7
MsaG001401 MtrunA17_Chr8g0359921 30.864 162 86 7 4 149 14 165 7.45e-14 69.7
MsaG001401 MtrunA17_Chr2g0318081 30.000 160 88 8 4 149 16 165 1.10e-13 69.3
MsaG001401 MtrunA17_Chr7g0261411 33.766 154 82 8 4 146 10 154 1.62e-13 68.2
MsaG001401 MtrunA17_Chr2g0309331 30.769 156 92 5 4 148 10 160 2.59e-13 68.2
MsaG001401 MtrunA17_Chr3g0144271 31.788 151 85 7 4 145 23 164 6.38e-13 67.4
MsaG001401 MtrunA17_Chr7g0214071 30.769 156 91 6 4 150 15 162 7.35e-13 65.9
MsaG001401 MtrunA17_Chr8g0361731 27.647 170 92 7 2 148 12 173 8.06e-13 67.0
MsaG001401 MtrunA17_Chr3g0130101 29.630 162 90 7 3 149 6 158 9.59e-13 66.6
MsaG001401 MtrunA17_Chr4g0054791 30.435 161 91 9 4 149 6 160 1.17e-12 66.2
MsaG001401 MtrunA17_Chr4g0060931 31.250 160 86 8 4 148 17 167 1.26e-12 66.2
MsaG001401 MtrunA17_Chr1g0201021 34.074 135 72 5 6 132 21 146 2.27e-12 65.9
MsaG001401 MtrunA17_Chr1g0197351 31.515 165 87 6 4 149 42 199 2.49e-12 65.5
MsaG001401 MtrunA17_Chr8g0345671 30.128 156 84 8 4 145 11 155 9.96e-12 63.5
MsaG001401 MtrunA17_Chr3g0091921 32.298 161 85 9 3 148 15 166 1.63e-11 62.8
MsaG001401 MtrunA17_Chr4g0038751 28.947 152 92 6 6 148 17 161 2.41e-11 62.0
MsaG001401 MtrunA17_Chr3g0131911 28.144 167 92 7 4 150 14 172 2.93e-11 61.2
MsaG001401 MtrunA17_Chr6g0453451 28.994 169 93 9 4 154 20 179 3.53e-11 62.0
MsaG001401 MtrunA17_Chr2g0312321 30.247 162 86 8 4 150 11 160 3.65e-11 61.6
MsaG001401 MtrunA17_Chr8g0384201 28.750 160 88 7 6 149 8 157 4.99e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001401 AT4G36160.1 31.977 172 98 6 4 162 10 175 1.81e-19 86.3
MsaG001401 AT4G36160.3 31.977 172 98 6 4 162 10 175 1.81e-19 86.3
MsaG001401 AT4G36160.2 31.977 172 98 6 4 162 14 179 1.92e-19 86.3
MsaG001401 AT2G18060.3 32.164 171 98 6 4 162 9 173 4.10e-19 85.1
MsaG001401 AT2G18060.1 32.164 171 98 6 4 162 9 173 4.10e-19 85.1
MsaG001401 AT5G62380.2 31.034 203 110 8 4 192 7 193 1.07e-18 84.0
MsaG001401 AT5G62380.1 31.034 203 110 8 4 192 7 193 1.07e-18 84.0
MsaG001401 AT3G17730.1 32.500 160 86 8 4 149 6 157 1.96e-18 81.6
MsaG001401 AT2G24430.2 33.962 159 86 6 2 148 14 165 7.62e-17 78.2
MsaG001401 AT2G24430.1 33.962 159 86 6 2 148 14 165 7.62e-17 78.2
MsaG001401 AT1G71930.2 31.410 156 90 5 4 148 9 158 9.23e-17 78.2
MsaG001401 AT1G71930.1 31.410 156 90 5 4 148 9 158 9.23e-17 78.2
MsaG001401 AT1G12260.2 32.704 159 84 7 4 148 7 156 1.70e-16 77.4
MsaG001401 AT5G64530.1 31.443 194 99 7 4 176 3 183 2.65e-16 74.7
MsaG001401 AT1G12260.1 32.704 159 84 7 4 148 7 156 3.37e-16 77.0
MsaG001401 AT1G76420.1 33.951 162 78 9 4 148 22 171 3.41e-16 76.6
MsaG001401 AT1G62700.1 31.447 159 86 6 4 148 7 156 8.89e-16 75.9
MsaG001401 AT1G62700.2 31.447 159 86 6 4 148 7 156 8.89e-16 75.9
MsaG001401 AT1G54330.1 30.769 156 91 6 4 149 6 154 1.68e-15 74.3
MsaG001401 AT3G10490.1 31.250 160 89 6 4 149 27 179 1.72e-15 73.6
MsaG001401 AT4G27410.3 29.213 178 87 8 4 151 14 182 1.32e-14 72.0
MsaG001401 AT3G10490.2 31.250 160 89 6 4 149 27 179 2.10e-14 72.0
MsaG001401 AT5G46590.1 31.847 157 85 7 4 145 6 155 3.42e-14 70.5
MsaG001401 AT3G10480.2 31.447 159 89 6 4 149 27 178 3.90e-14 71.2
MsaG001401 AT3G10480.1 31.250 160 89 6 4 149 27 179 3.94e-14 71.2
MsaG001401 AT3G49530.2 27.545 167 92 9 1 149 10 165 5.61e-14 70.9
MsaG001401 AT3G49530.1 27.545 167 92 9 1 149 10 165 5.82e-14 70.9
MsaG001401 AT1G32510.1 29.341 167 92 7 3 149 5 165 5.85e-14 69.7
MsaG001401 AT5G39610.1 31.677 161 86 8 4 149 20 171 6.45e-14 69.7
MsaG001401 AT5G64530.2 35.659 129 70 5 4 132 3 118 8.09e-14 67.4
MsaG001401 AT1G77450.1 28.962 183 97 7 4 164 10 181 1.32e-13 68.6
MsaG001401 AT3G18400.1 32.484 157 85 9 4 148 5 152 1.54e-13 68.9
MsaG001401 AT5G04395.1 32.886 149 79 6 4 135 28 172 1.89e-13 67.0
MsaG001401 AT5G22290.1 30.405 148 86 7 6 145 23 161 2.51e-13 68.6
MsaG001401 AT1G26870.1 28.824 170 90 7 2 148 14 175 3.57e-13 68.6
MsaG001401 AT5G24590.2 28.659 164 88 8 4 149 13 165 3.87e-13 68.6
MsaG001401 AT5G61430.1 31.902 163 87 8 4 151 16 169 4.02e-13 67.8
MsaG001401 AT3G29035.1 34.074 135 74 6 4 132 24 149 4.28e-13 67.8
MsaG001401 AT4G35580.2 26.776 183 104 8 1 163 6 178 1.10e-12 67.0
MsaG001401 AT4G35580.3 26.776 183 104 8 1 163 6 178 1.11e-12 67.0
MsaG001401 AT4G35580.1 26.776 183 104 8 1 163 6 178 1.27e-12 67.0
MsaG001401 AT2G43000.1 29.936 157 87 7 6 148 20 167 1.48e-12 65.9
MsaG001401 AT1G33060.2 27.381 168 88 8 1 148 21 174 1.53e-12 66.6
MsaG001401 AT1G33060.1 27.381 168 88 8 1 148 21 174 1.76e-12 66.6
MsaG001401 AT5G46590.2 31.655 139 81 6 4 135 6 137 1.81e-12 65.5
MsaG001401 AT4G10350.1 31.410 156 88 7 4 146 9 158 2.00e-12 65.9
MsaG001401 AT3G10500.1 30.380 158 90 6 4 148 9 159 2.04e-12 66.2
MsaG001401 AT3G15510.1 28.395 162 100 6 10 164 23 175 2.52e-12 65.9
MsaG001401 AT2G33480.1 31.210 157 89 7 4 150 15 162 3.53e-12 64.7
MsaG001401 AT5G04410.1 28.481 158 93 6 4 148 9 159 4.22e-12 65.5
MsaG001401 AT5G50820.1 33.088 136 76 5 4 135 17 141 4.64e-12 63.2
MsaG001401 AT5G07680.1 31.902 163 87 8 4 151 17 170 4.86e-12 64.7
MsaG001401 AT5G07680.2 31.902 163 87 8 4 151 3 156 5.65e-12 64.3
MsaG001401 AT3G12977.1 28.177 181 96 9 4 164 18 184 1.03e-11 63.5
MsaG001401 AT3G04060.1 29.508 183 104 8 4 170 20 193 1.13e-11 63.9
MsaG001401 AT5G18270.2 30.864 162 87 8 4 149 21 173 3.14e-11 62.4
MsaG001401 AT5G18270.1 30.864 162 87 8 4 149 21 173 3.42e-11 62.4
MsaG001401 AT2G46770.1 25.359 209 117 7 4 182 16 215 3.80e-11 62.4
MsaG001401 AT1G32870.1 31.579 133 80 5 4 132 10 135 8.34e-11 61.6
MsaG001401 AT1G32870.2 31.579 133 80 5 4 132 10 135 8.46e-11 61.6

Find 45 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATGGTTCTGACTTGATTA+AGG 0.237815 1:+19564467 MsaT001401.1:CDS
GGCATTGTAAGACTGGATTT+TGG 0.240614 1:+19564601 MsaT001401.1:CDS
CCTCCTCAGCTCATCACTTT+TGG 0.293515 1:-19564580 None:intergenic
CCTTGTGTGAGGGAAGAAAA+AGG 0.370691 1:-19564538 None:intergenic
TGAAGGAACTCAACAACTTA+AGG 0.384542 1:+19565012 MsaT001401.1:CDS
GCAATTCAAACGGATCATAT+TGG 0.403266 1:-19564503 None:intergenic
AGGTGATGCATTGCATTTCA+TGG 0.410069 1:+19565075 MsaT001401.1:CDS
AGTCCAGATCCATCCCTCTA+TGG 0.420396 1:-19564919 None:intergenic
CGTTTGAATTGCATCTTGCT+CGG 0.448065 1:+19564514 MsaT001401.1:CDS
AAAACACGGCAAACAACAAA+AGG 0.449123 1:-19564890 None:intergenic
TGGATCTGGACTCTGAATTG+TGG 0.459225 1:+19564930 MsaT001401.1:CDS
CAAACGGATCATATTGGTAC+AGG 0.462188 1:-19564497 None:intergenic
CTGAGGAGGCATTGTAAGAC+TGG 0.469451 1:+19564594 MsaT001401.1:CDS
GAAGGAACTCAACAACTTAA+GGG 0.473282 1:+19565013 MsaT001401.1:CDS
CCGCCATAGAGGGATGGATC+TGG 0.473585 1:+19564916 MsaT001401.1:CDS
GGATCTGGACTCTGAATTGT+GGG 0.473825 1:+19564931 MsaT001401.1:CDS
GAAGAGGTTCAAAATTTCCA+TGG 0.507513 1:+19564450 MsaT001401.1:CDS
TATTCAAAACCTTTATGTGT+TGG 0.520837 1:+19565300 MsaT001401.1:CDS
TCTGATGAGAAGGCGAATGA+AGG 0.523662 1:+19564995 MsaT001401.1:CDS
GATTTGCTTCCACCTGGTGT+TGG 0.532322 1:+19564372 MsaT001401.1:CDS
ACCTTCATCGACATCAGATA+AGG 0.533255 1:-19564954 None:intergenic
AGAACGCAATCAAAACTAGC+TGG 0.537621 1:+19564721 MsaT001401.1:CDS
CGAGCAAGATGCAATTCAAA+CGG 0.545354 1:-19564513 None:intergenic
GTCGATGAAGGTGATGTTGT+TGG 0.547764 1:+19564965 MsaT001401.1:CDS
TGGAGCTGATGACGTGTTGG+TGG 0.553560 1:+19564656 MsaT001401.1:CDS
GCTGTCGAAGACATTACTGT+TGG 0.561036 1:+19564636 MsaT001401.1:CDS
CCAAAAGTGATGAGCTGAGG+AGG 0.564041 1:+19564580 MsaT001401.1:CDS
TAGCAAGGTAGTAGCTAACA+AGG 0.569555 1:-19564416 None:intergenic
GCAATGGATTTGCTTCCACC+TGG 0.569568 1:+19564366 None:intergenic
CAGTAAAACTCCCTTGTGTG+AGG 0.577220 1:-19564549 None:intergenic
AAGGAACTCAACAACTTAAG+GGG 0.586043 1:+19565014 MsaT001401.1:CDS
GCCTTATCTGATGTCGATGA+AGG 0.592468 1:+19564953 MsaT001401.1:CDS
AGTAAAACTCCCTTGTGTGA+GGG 0.603789 1:-19564548 None:intergenic
TGTTGGAGCTGATGACGTGT+TGG 0.619893 1:+19564653 MsaT001401.1:CDS
TAACAAGGAGTTCATCAGAA+GGG 0.633655 1:-19564401 None:intergenic
CCTTAATCAAGTCAGAACCA+TGG 0.642289 1:-19564467 None:intergenic
CTGCCAAAAGTGATGAGCTG+AGG 0.648920 1:+19564577 MsaT001401.1:CDS
GGAGCTGATGACGTGTTGGT+GGG 0.656135 1:+19564657 MsaT001401.1:CDS
GGGACGAAACCAACACCAGG+TGG 0.656589 1:-19564381 None:intergenic
GCTGATGCTAGTGCTGAGCA+AGG 0.658942 1:+19565055 MsaT001401.1:CDS
TGGTGACGACTCTGATGAGA+AGG 0.667599 1:+19564985 MsaT001401.1:CDS
CTAACAAGGAGTTCATCAGA+AGG 0.675712 1:-19564402 None:intergenic
GAAGGGACGAAACCAACACC+AGG 0.689839 1:-19564384 None:intergenic
CCAGATCCATCCCTCTATGG+CGG 0.701242 1:-19564916 None:intergenic
AGGAACTCAACAACTTAAGG+GGG 0.701895 1:+19565015 MsaT001401.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 19564369 19565345 19564369 ID=MsaG001401
Chr1 mRNA 19564369 19565345 19564369 ID=MsaT001401.1;Parent=MsaG001401
Chr1 exon 19564369 19564779 19564369 ID=MsaT001401.1.exon1;Parent=MsaT001401.1
Chr1 CDS 19564369 19564779 19564369 ID=cds.MsaT001401.1;Parent=MsaT001401.1
Chr1 exon 19564887 19565117 19564887 ID=MsaT001401.1.exon2;Parent=MsaT001401.1
Chr1 CDS 19564887 19565117 19564887 ID=cds.MsaT001401.1;Parent=MsaT001401.1
Chr1 exon 19565295 19565345 19565295 ID=MsaT001401.1.exon3;Parent=MsaT001401.1
Chr1 CDS 19565295 19565345 19565295 ID=cds.MsaT001401.1;Parent=MsaT001401.1
Gene Sequence

>MsaT001401.1

ATGGATTTGCTTCCACCTGGTGTTGGTTTCGTCCCTTCTGATGAACTCCTTGTTAGCTACTACCTTGCTAACAAAAACAATGAAGAGGTTCAAAATTTCCATGGTTCTGACTTGATTAAGGAGCTAAACCTGTACCAATATGATCCGTTTGAATTGCATCTTGCTCGGTCCTTTTTCTTCCCTCACACAAGGGAGTTTTACTGCTTCACTGCCAAAAGTGATGAGCTGAGGAGGCATTGTAAGACTGGATTTTGGATGCAGATGGGAGCTGTCGAAGACATTACTGTTGGAGCTGATGACGTGTTGGTGGGAAAGAAGTCTCTCTTCTTTTTTTATATAGGAAATTCCCCTCAGAACGCAATCAAAACTAGCTGGACTATGTACGAGTACACTCTTGTTAACAACCCTCATGCTCCTTTTGTTGTTTGCCGTGTTTTTGACCGCCATAGAGGGATGGATCTGGACTCTGAATTGTGGGCCTTATCTGATGTCGATGAAGGTGATGTTGTTGGTGACGACTCTGATGAGAAGGCGAATGAAGGAACTCAACAACTTAAGGGGGTTGGGACTAGTTATAGTGCTGATGCTAGTGCTGAGCAAGGTGATGCATTGCATTTCATGGCTACTCAAGCCACTTTTCAGGTGGCTATTCAAAACCTTTATGTGTTGGTAGTTTTTGTGGTTGATGTTTGA
Protein sequence

>MsaT001401.1

MDLLPPGVGFVPSDELLVSYYLANKNNEEVQNFHGSDLIKELNLYQYDPFELHLARSFFFPHTREFYCFTAKSDELRRHCKTGFWMQMGAVEDITVGADDVLVGKKSLFFFYIGNSPQNAIKTSWTMYEYTLVNNPHAPFVVCRVFDRHRGMDLDSELWALSDVDEGDVVGDDSDEKANEGTQQLKGVGTSYSADASAEQGDALHFMATQATFQVAIQNLYVLVVFVVDV*