AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0715840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0715840 MtrunA17_Chr5g0403201 95.082 183 7 2 1 181 3 185 6.22e-127 354
Msa0715840 MtrunA17_Chr8g0373921 64.497 169 58 2 13 181 6 172 3.78e-73 218
Msa0715840 MtrunA17_Chr5g0403191 68.932 103 30 1 81 181 1 103 1.28e-47 150
Msa0715840 MtrunA17_Chr2g0295371 34.831 178 97 6 6 181 4 164 8.83e-32 113
Msa0715840 MtrunA17_Chr4g0072781 38.462 156 91 3 26 181 23 173 1.01e-31 112
Msa0715840 MtrunA17_Chr4g0049191 43.357 143 72 6 40 181 25 159 9.11e-29 104
Msa0715840 MtrunA17_Chr4g0049151 36.464 181 92 7 3 181 5 164 2.04e-28 103
Msa0715840 MtrunA17_Chr2g0280281 35.294 170 93 7 13 181 5 158 3.50e-26 97.8
Msa0715840 MtrunA17_Chr2g0281271 36.879 141 81 5 43 181 10 144 3.74e-26 98.2
Msa0715840 MtrunA17_Chr2g0280291 32.961 179 98 6 5 181 277 435 3.16e-25 100
Msa0715840 MtrunA17_Chr2g0280291 36.364 132 77 3 43 174 28 152 4.36e-22 92.0
Msa0715840 MtrunA17_Chr4g0072791 32.374 139 92 1 43 181 70 206 1.14e-22 90.1
Msa0715840 MtrunA17_Chr2g0280351 32.450 151 87 7 38 181 26 168 3.82e-22 87.8
Msa0715840 MtrunA17_Chr2g0280311 32.886 149 86 6 38 181 26 165 4.60e-21 84.7
Msa0715840 MtrunA17_Chr2g0280331 31.111 180 100 8 8 181 4 165 9.35e-20 81.6
Msa0715840 MtrunA17_Chr1g0181941 36.170 141 81 4 43 180 73 207 1.07e-19 82.4
Msa0715840 MtrunA17_Chr2g0280321 31.818 176 103 8 10 181 1 163 3.30e-19 80.1
Msa0715840 MtrunA17_Chr2g0280301 43.011 93 49 3 89 181 47 135 1.69e-18 77.4
Msa0715840 MtrunA17_Chr2g0280341 28.492 179 104 8 8 181 178 337 1.90e-14 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0715840 AT5G66590.1 56.497 177 68 2 13 181 10 185 1.31e-62 192
Msa0715840 AT4G33720.1 41.429 140 75 3 42 181 31 163 2.70e-31 111
Msa0715840 AT5G57625.1 33.166 199 99 7 12 181 14 207 1.92e-29 108
Msa0715840 AT4G31470.1 40.000 140 78 4 42 181 52 185 3.91e-29 106
Msa0715840 AT4G25790.1 37.143 140 83 4 42 181 76 210 1.96e-28 105
Msa0715840 AT2G19990.1 37.853 177 104 4 5 181 6 176 2.63e-27 101
Msa0715840 AT3G19690.1 38.732 142 78 5 42 181 27 161 7.78e-27 100
Msa0715840 AT2G14610.1 35.057 174 100 7 8 181 1 161 2.80e-26 98.6
Msa0715840 AT5G26130.1 36.806 144 78 5 42 181 32 166 4.45e-26 98.2
Msa0715840 AT1G01310.1 38.571 140 78 5 43 181 87 219 6.92e-26 99.8
Msa0715840 AT2G14580.1 34.078 179 95 7 8 181 1 161 7.37e-26 97.4
Msa0715840 AT4G33710.1 35.570 149 89 4 34 181 24 166 3.35e-25 95.9
Msa0715840 AT3G09590.1 34.752 141 88 3 41 181 50 186 2.14e-24 94.4
Msa0715840 AT4G30320.1 36.879 141 81 5 42 181 28 161 3.59e-24 93.2
Msa0715840 AT4G25780.1 30.286 175 120 1 7 181 18 190 9.62e-24 92.8
Msa0715840 AT5G02730.1 36.691 139 84 4 43 181 59 193 6.26e-23 91.3
Msa0715840 AT1G50050.2 30.682 176 102 4 6 181 7 162 2.23e-22 88.6
Msa0715840 AT4G33730.1 37.143 140 77 5 44 181 42 172 4.04e-22 88.2
Msa0715840 AT1G50060.1 31.818 176 99 5 6 181 7 161 6.46e-22 87.4
Msa0715840 AT1G50050.1 30.058 173 99 5 2 172 1 153 6.55e-18 78.6
Msa0715840 AT4G07820.1 32.143 140 86 5 42 181 30 160 1.32e-17 76.3
Msa0715840 AT2G19970.1 32.090 134 84 4 42 171 36 166 5.92e-14 67.0

Find 50 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACATTATCACCAATCAAAA+TGG 0.284930 5_1:+9045788 None:intergenic
CCGTTACCAAAGAAACAAAA+TGG 0.291931 5_1:-9046104 Msa0715840:CDS
CACTCCTCCACCGCTTTGCT+TGG 0.328916 5_1:+9046004 None:intergenic
GGCTCTGGAATGGTGGCTGC+TGG 0.366573 5_1:+9046253 None:intergenic
GTGTGATTCTAAGAACTCTT+TGG 0.373119 5_1:+9046204 None:intergenic
GGTGAAAGAGGTGGCGGTGC+TGG 0.383260 5_1:+9046232 None:intergenic
CACCGCTTTGCTTGGCGTTA+CGG 0.389629 5_1:+9046012 None:intergenic
AATACGGTGGTAATCAGCTT+TGG 0.400182 5_1:-9046051 Msa0715840:CDS
AGAGGTGGCGGTGCTGGCTC+TGG 0.401513 5_1:+9046238 None:intergenic
GATCCACCTGGTAATGTCAT+TGG 0.411135 5_1:-9045818 Msa0715840:CDS
GGAGGAGTGGGTGAAGGAGA+AGG 0.432515 5_1:-9045990 Msa0715840:CDS
TGGCGGTGCTGGCTCTGGAA+TGG 0.441663 5_1:+9046243 None:intergenic
ATACGGTGGTAATCAGCTTT+GGG 0.450022 5_1:-9046050 Msa0715840:CDS
GGCTGCTGGTCTTGCAGCGG+TGG 0.470758 5_1:+9046267 None:intergenic
AACTTAACAAGCAGCAAATA+CGG 0.475426 5_1:-9046067 Msa0715840:CDS
TCTAAGAACTCTTTGGCTGC+TGG 0.478483 5_1:+9046211 None:intergenic
CTCTCTCCAATGACATTACC+AGG 0.478858 5_1:+9045812 None:intergenic
AACGCCAAGCAAAGCGGTGG+AGG 0.488991 5_1:-9046008 Msa0715840:CDS
CAAGCAAAGCGGTGGAGGAG+TGG 0.503440 5_1:-9046003 Msa0715840:CDS
TCTTTGGCTGCTGGTGAAAG+AGG 0.505288 5_1:+9046220 None:intergenic
GTGTTCACAAGCTACTTGTA+CGG 0.507221 5_1:-9045876 Msa0715840:CDS
AAGCAAAGCGGTGGAGGAGT+GGG 0.513160 5_1:-9046002 Msa0715840:CDS
AGCTACTTGTACGGGTAAGA+AGG 0.523085 5_1:-9045867 Msa0715840:CDS
CGGTGGACGAGACAAGGAGC+AGG 0.524492 5_1:+9046284 None:intergenic
GCTTGGCGTTACGGCTGCTG+CGG 0.526234 5_1:+9046021 None:intergenic
CGGTGCTGGCTCTGGAATGG+TGG 0.535615 5_1:+9046246 None:intergenic
AGCTTCTCGCTCCATTGAAG+TGG 0.547634 5_1:+9046151 None:intergenic
TAGGTGTTGAGCCACTTCAA+TGG 0.550994 5_1:-9046162 Msa0715840:CDS
GGTGGTAATCAGCTTTGGGC+GGG 0.552262 5_1:-9046046 Msa0715840:CDS
AGTGTGGCTAGAGAGAAGAG+AGG 0.565171 5_1:+9046310 None:intergenic
CGTTACCAAAGAAACAAAAT+GGG 0.569158 5_1:-9046103 Msa0715840:CDS
TGTTCACAAGCTACTTGTAC+GGG 0.570283 5_1:-9045875 Msa0715840:CDS
AGCGGTGGAGGAGTGGGTGA+AGG 0.573564 5_1:-9045996 Msa0715840:CDS
TTGCAGCGGTGGACGAGACA+AGG 0.573762 5_1:+9046278 None:intergenic
CGGTGGTAATCAGCTTTGGG+CGG 0.593924 5_1:-9046047 Msa0715840:CDS
GCTGCTGGTGAAAGAGGTGG+CGG 0.597831 5_1:+9046226 None:intergenic
ATTTGTTTCTATGATCCACC+TGG 0.608612 5_1:-9045830 Msa0715840:CDS
GACAAGGAGCAGGGATAGTG+TGG 0.609020 5_1:+9046294 None:intergenic
TGGAAGAAATCAGTACAACT+TGG 0.618139 5_1:-9045899 Msa0715840:CDS
GGTGGCTGCTGGTCTTGCAG+CGG 0.618405 5_1:+9046264 None:intergenic
TTGGCTGCTGGTGAAAGAGG+TGG 0.621563 5_1:+9046223 None:intergenic
GTGTTTATACGCAAGTTGTG+TGG 0.629612 5_1:-9045919 Msa0715840:CDS
GGAAGAAATCAGTACAACTT+GGG 0.648064 5_1:-9045898 Msa0715840:CDS
CGTAACGCCAAGCAAAGCGG+TGG 0.663476 5_1:-9046011 Msa0715840:CDS
AACAAAGCAAGAGCTGAAGT+AGG 0.671065 5_1:-9046181 Msa0715840:CDS
GGTGGACGAGACAAGGAGCA+GGG 0.673917 5_1:+9046285 None:intergenic
AGCCGTAACGCCAAGCAAAG+CGG 0.678151 5_1:-9046014 Msa0715840:CDS
TGTGTTGCGAATCATGAGTG+TGG 0.721846 5_1:-9045941 Msa0715840:CDS
TTAACAAGCAGCAAATACGG+TGG 0.752196 5_1:-9046064 Msa0715840:CDS
TCTCCAATGACATTACCAGG+TGG 0.762082 5_1:+9045815 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CCATTTTGTTTCTTTGGTAA+CGG + chr5_1:9046026-9046045 None:intergenic 30.0%
CGTTACCAAAGAAACAAAAT+GGG - chr5_1:9046024-9046043 Msa0715840:CDS 30.0%
AACTTAACAAGCAGCAAATA+CGG - chr5_1:9046060-9046079 Msa0715840:CDS 30.0%
! GTGTGATTCTAAGAACTCTT+TGG + chr5_1:9045926-9045945 None:intergenic 35.0%
CCGTTACCAAAGAAACAAAA+TGG - chr5_1:9046023-9046042 Msa0715840:CDS 35.0%
TGGAAGAAATCAGTACAACT+TGG - chr5_1:9046228-9046247 Msa0715840:CDS 35.0%
GGAAGAAATCAGTACAACTT+GGG - chr5_1:9046229-9046248 Msa0715840:CDS 35.0%
!! ATTTGTTTCTATGATCCACC+TGG - chr5_1:9046297-9046316 Msa0715840:CDS 35.0%
AACAAAGCAAGAGCTGAAGT+AGG - chr5_1:9045946-9045965 Msa0715840:CDS 40.0%
!! CGCAACCCATTTTGTTTCTT+TGG + chr5_1:9046032-9046051 None:intergenic 40.0%
TTAACAAGCAGCAAATACGG+TGG - chr5_1:9046063-9046082 Msa0715840:CDS 40.0%
AATACGGTGGTAATCAGCTT+TGG - chr5_1:9046076-9046095 Msa0715840:CDS 40.0%
ATACGGTGGTAATCAGCTTT+GGG - chr5_1:9046077-9046096 Msa0715840:CDS 40.0%
GTGTTTATACGCAAGTTGTG+TGG - chr5_1:9046208-9046227 Msa0715840:CDS 40.0%
GTGTTCACAAGCTACTTGTA+CGG - chr5_1:9046251-9046270 Msa0715840:CDS 40.0%
TGTTCACAAGCTACTTGTAC+GGG - chr5_1:9046252-9046271 Msa0715840:CDS 40.0%
TCTAAGAACTCTTTGGCTGC+TGG + chr5_1:9045919-9045938 None:intergenic 45.0%
!! TAGGTGTTGAGCCACTTCAA+TGG - chr5_1:9045965-9045984 Msa0715840:CDS 45.0%
TGTGTTGCGAATCATGAGTG+TGG - chr5_1:9046186-9046205 Msa0715840:CDS 45.0%
AGCTACTTGTACGGGTAAGA+AGG - chr5_1:9046260-9046279 Msa0715840:CDS 45.0%
! GATCCACCTGGTAATGTCAT+TGG - chr5_1:9046309-9046328 Msa0715840:CDS 45.0%
TCTCCAATGACATTACCAGG+TGG + chr5_1:9046315-9046334 None:intergenic 45.0%
CTCTCTCCAATGACATTACC+AGG + chr5_1:9046318-9046337 None:intergenic 45.0%
AGTGTGGCTAGAGAGAAGAG+AGG + chr5_1:9045820-9045839 None:intergenic 50.0%
TCTTTGGCTGCTGGTGAAAG+AGG + chr5_1:9045910-9045929 None:intergenic 50.0%
AGCTTCTCGCTCCATTGAAG+TGG + chr5_1:9045979-9045998 None:intergenic 50.0%
GACAAGGAGCAGGGATAGTG+TGG + chr5_1:9045836-9045855 None:intergenic 55.0%
TTGGCTGCTGGTGAAAGAGG+TGG + chr5_1:9045907-9045926 None:intergenic 55.0%
!! CGGTGGTAATCAGCTTTGGG+CGG - chr5_1:9046080-9046099 Msa0715840:CDS 55.0%
!! GGTGGTAATCAGCTTTGGGC+GGG - chr5_1:9046081-9046100 Msa0715840:CDS 55.0%
AGCCGTAACGCCAAGCAAAG+CGG - chr5_1:9046113-9046132 Msa0715840:CDS 55.0%
CACCGCTTTGCTTGGCGTTA+CGG + chr5_1:9046118-9046137 None:intergenic 55.0%
AAGCAAAGCGGTGGAGGAGT+GGG - chr5_1:9046125-9046144 Msa0715840:CDS 55.0%
GGTGGACGAGACAAGGAGCA+GGG + chr5_1:9045845-9045864 None:intergenic 60.0%
TTGCAGCGGTGGACGAGACA+AGG + chr5_1:9045852-9045871 None:intergenic 60.0%
GCTGCTGGTGAAAGAGGTGG+CGG + chr5_1:9045904-9045923 None:intergenic 60.0%
CGTAACGCCAAGCAAAGCGG+TGG - chr5_1:9046116-9046135 Msa0715840:CDS 60.0%
AACGCCAAGCAAAGCGGTGG+AGG - chr5_1:9046119-9046138 Msa0715840:CDS 60.0%
CACTCCTCCACCGCTTTGCT+TGG + chr5_1:9046126-9046145 None:intergenic 60.0%
CAAGCAAAGCGGTGGAGGAG+TGG - chr5_1:9046124-9046143 Msa0715840:CDS 60.0%
GGAGGAGTGGGTGAAGGAGA+AGG - chr5_1:9046137-9046156 Msa0715840:CDS 60.0%
CGGTGGACGAGACAAGGAGC+AGG + chr5_1:9045846-9045865 None:intergenic 65.0%
!! GGTGGCTGCTGGTCTTGCAG+CGG + chr5_1:9045866-9045885 None:intergenic 65.0%
!! GGCTCTGGAATGGTGGCTGC+TGG + chr5_1:9045877-9045896 None:intergenic 65.0%
!! CGGTGCTGGCTCTGGAATGG+TGG + chr5_1:9045884-9045903 None:intergenic 65.0%
!! TGGCGGTGCTGGCTCTGGAA+TGG + chr5_1:9045887-9045906 None:intergenic 65.0%
! GGTGAAAGAGGTGGCGGTGC+TGG + chr5_1:9045898-9045917 None:intergenic 65.0%
GCTTGGCGTTACGGCTGCTG+CGG + chr5_1:9046109-9046128 None:intergenic 65.0%
AGCGGTGGAGGAGTGGGTGA+AGG - chr5_1:9046131-9046150 Msa0715840:CDS 65.0%
!! GGCTGCTGGTCTTGCAGCGG+TGG + chr5_1:9045863-9045882 None:intergenic 70.0%
!! AGAGGTGGCGGTGCTGGCTC+TGG + chr5_1:9045892-9045911 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 9045802 9046347 9045802 ID=Msa0715840;Name=Msa0715840
chr5_1 mRNA 9045802 9046347 9045802 ID=Msa0715840-mRNA-1;Parent=Msa0715840;Name=Msa0715840-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|-1|0|1|-1|1|1|0|181
chr5_1 exon 9045802 9046347 9045802 ID=Msa0715840-mRNA-1:exon:3694;Parent=Msa0715840-mRNA-1
chr5_1 CDS 9045802 9046347 9045802 ID=Msa0715840-mRNA-1:cds;Parent=Msa0715840-mRNA-1
Gene Sequence

>Msa0715840

ATGTTAAATTATTTTCCTCTCTTCTCTCTAGCCACACTATCCCTGCTCCTTGTCTCGTCCACCGCTGCAAGACCAGCAGCCACCATTCCAGAGCCAGCACCGCCACCTCTTTCACCAGCAGCCAAAGAGTTCTTAGAATCACACAACAAAGCAAGAGCTGAAGTAGGTGTTGAGCCACTTCAATGGAGCGAGAAGCTAGCAAAAGACACAAGCTTACTAGTCCGTTACCAAAGAAACAAAATGGGTTGCGATTTTGCAAACTTAACAAGCAGCAAATACGGTGGTAATCAGCTTTGGGCGGGTTCCGCAGCAGCCGTAACGCCAAGCAAAGCGGTGGAGGAGTGGGTGAAGGAGAAGGAGTTTTACATTCATGTGAATAATACTTGTGTTGCGAATCATGAGTGTGGTGTTTATACGCAAGTTGTGTGGAAGAAATCAGTACAACTTGGGTGTTCACAAGCTACTTGTACGGGTAAGAAGGAAGCTAGTTTGACTATTTGTTTCTATGATCCACCTGGTAATGTCATTGGAGAGAGTCCATTTTGA
Protein sequence

>Msa0715840

MLNYFPLFSLATLSLLLVSSTAARPAATIPEPAPPPLSPAAKEFLESHNKARAEVGVEPLQWSEKLAKDTSLLVRYQRNKMGCDFANLTSSKYGGNQLWAGSAAAVTPSKAVEEWVKEKEFYIHVNNTCVANHECGVYTQVVWKKSVQLGCSQATCTGKKEASLTICFYDPPGNVIGESPF*