AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1385150

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1385150 MtrunA17_Chr5g0403201 95.628 183 6 2 1 181 3 185 4.94e-128 357
Msa1385150 MtrunA17_Chr8g0373921 61.326 181 61 3 1 181 1 172 2.87e-73 218
Msa1385150 MtrunA17_Chr5g0403191 68.932 103 30 1 81 181 1 103 1.55e-47 150
Msa1385150 MtrunA17_Chr2g0295371 33.520 179 97 5 3 181 8 164 5.09e-32 113
Msa1385150 MtrunA17_Chr4g0072781 38.462 156 91 3 26 181 23 173 9.84e-32 112
Msa1385150 MtrunA17_Chr4g0049191 43.357 143 72 6 40 181 25 159 1.01e-28 104
Msa1385150 MtrunA17_Chr4g0049151 36.313 179 91 7 5 181 7 164 3.85e-28 103
Msa1385150 MtrunA17_Chr2g0281271 36.879 141 81 5 43 181 10 144 3.47e-26 98.2
Msa1385150 MtrunA17_Chr2g0280281 35.294 170 93 7 13 181 5 158 3.98e-26 97.8
Msa1385150 MtrunA17_Chr2g0280291 32.961 179 98 6 5 181 277 435 3.06e-25 100
Msa1385150 MtrunA17_Chr2g0280291 36.364 132 77 3 43 174 28 152 3.37e-22 92.4
Msa1385150 MtrunA17_Chr4g0072791 32.374 139 92 1 43 181 70 206 1.18e-22 90.1
Msa1385150 MtrunA17_Chr2g0280351 32.450 151 87 7 38 181 26 168 3.82e-22 87.8
Msa1385150 MtrunA17_Chr2g0280311 32.886 149 86 6 38 181 26 165 3.88e-21 85.1
Msa1385150 MtrunA17_Chr2g0280331 31.111 180 100 8 8 181 4 165 1.03e-19 81.3
Msa1385150 MtrunA17_Chr1g0181941 35.915 142 82 4 42 180 72 207 1.15e-19 82.4
Msa1385150 MtrunA17_Chr2g0280321 31.818 176 103 8 10 181 1 163 3.83e-19 79.7
Msa1385150 MtrunA17_Chr2g0280301 43.011 93 49 3 89 181 47 135 1.35e-18 77.8
Msa1385150 MtrunA17_Chr2g0280341 28.492 179 104 8 8 181 178 337 1.69e-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
Msa1385150 AT5G66590.1 56.497 177 68 2 13 181 10 185 1.22e-62 192
Msa1385150 AT4G33720.1 41.429 140 75 3 42 181 31 163 2.65e-31 111
Msa1385150 AT5G57625.1 34.911 169 94 6 24 181 44 207 2.00e-29 108
Msa1385150 AT4G31470.1 40.000 140 78 4 42 181 52 185 4.45e-29 106
Msa1385150 AT4G25790.1 37.143 140 83 4 42 181 76 210 1.88e-28 105
Msa1385150 AT2G19990.1 37.853 177 104 4 5 181 6 176 2.61e-27 101
Msa1385150 AT3G19690.1 38.732 142 78 5 42 181 27 161 7.06e-27 100
Msa1385150 AT2G14610.1 35.057 174 100 7 8 181 1 161 2.83e-26 98.6
Msa1385150 AT5G26130.1 36.806 144 78 5 42 181 32 166 4.31e-26 98.2
Msa1385150 AT1G01310.1 38.571 140 78 5 43 181 87 219 6.56e-26 99.8
Msa1385150 AT2G14580.1 34.078 179 95 7 8 181 1 161 7.21e-26 97.4
Msa1385150 AT4G33710.1 35.570 149 89 4 34 181 24 166 4.11e-25 95.9
Msa1385150 AT3G09590.1 34.752 141 88 3 41 181 50 186 2.26e-24 94.4
Msa1385150 AT4G30320.1 36.879 141 81 5 42 181 28 161 3.55e-24 93.2
Msa1385150 AT4G25780.1 30.286 175 120 1 7 181 18 190 9.52e-24 92.8
Msa1385150 AT5G02730.1 36.691 139 84 4 43 181 59 193 6.32e-23 91.3
Msa1385150 AT1G50050.2 30.682 176 102 4 6 181 7 162 2.30e-22 88.6
Msa1385150 AT4G33730.1 36.620 142 79 5 42 181 40 172 4.64e-22 88.2
Msa1385150 AT1G50060.1 31.818 176 99 5 6 181 7 161 6.33e-22 87.4
Msa1385150 AT1G50050.1 29.940 167 97 4 6 172 7 153 5.60e-18 78.6
Msa1385150 AT4G07820.1 32.143 140 86 5 42 181 30 160 1.45e-17 75.9
Msa1385150 AT2G19970.1 32.090 134 84 4 42 171 36 166 5.67e-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 tig0020715:-68791 None:intergenic
CCGTTACCAAAGAAACAAAA+TGG 0.291931 tig0020715:+68475 Msa1385150:CDS
CACTCCTCCACCGCTTTGCT+TGG 0.328916 tig0020715:-68575 None:intergenic
GGTGAAAGAGGCGGCGGTGC+TGG 0.351459 tig0020715:-68347 None:intergenic
GGCTCTGGAATGGTGGCTGC+TGG 0.366573 tig0020715:-68326 None:intergenic
GTGTGATTCTAAGAACTCTT+TGG 0.373119 tig0020715:-68375 None:intergenic
AGAGGCGGCGGTGCTGGCTC+TGG 0.382556 tig0020715:-68341 None:intergenic
CACCGCTTTGCTTGGCGTTA+CGG 0.389629 tig0020715:-68567 None:intergenic
AATACGGTGGTAATCAGCTT+TGG 0.400182 tig0020715:+68528 Msa1385150:CDS
GATCCACCTGGTAATGTCAT+TGG 0.411135 tig0020715:+68761 Msa1385150:CDS
CGGCGGTGCTGGCTCTGGAA+TGG 0.427147 tig0020715:-68336 None:intergenic
GGAGGAGTGGGTGAAGGAGA+AGG 0.432515 tig0020715:+68589 Msa1385150:CDS
ATACGGTGGTAATCAGCTTT+GGG 0.450022 tig0020715:+68529 Msa1385150:CDS
GGCTGCTGGTCTTGCAGCGG+TGG 0.470758 tig0020715:-68312 None:intergenic
AACTTAACAAGCAGCAAATA+CGG 0.475426 tig0020715:+68512 Msa1385150:CDS
TCTAAGAACTCTTTGGCTGC+TGG 0.478483 tig0020715:-68368 None:intergenic
CTCTCTCCAATGACATTACC+AGG 0.478858 tig0020715:-68767 None:intergenic
AACGCCAAGCAAAGCGGTGG+AGG 0.488991 tig0020715:+68571 Msa1385150:CDS
TCTTTGGCTGCTGGTGAAAG+AGG 0.499730 tig0020715:-68359 None:intergenic
CAAGCAAAGCGGTGGAGGAG+TGG 0.503440 tig0020715:+68576 Msa1385150:CDS
GTGTTCACAAGCTACTTGTA+CGG 0.507221 tig0020715:+68703 Msa1385150:CDS
AAGCAAAGCGGTGGAGGAGT+GGG 0.513160 tig0020715:+68577 Msa1385150:CDS
AGCTACTTGTACGGGTAAGA+AGG 0.523085 tig0020715:+68712 Msa1385150:CDS
CGGTGGACGAGACAAGGAGC+AGG 0.524492 tig0020715:-68295 None:intergenic
CGGTGCTGGCTCTGGAATGG+TGG 0.525884 tig0020715:-68333 None:intergenic
GCTTGGCGTTACGGCTGCTG+CGG 0.526234 tig0020715:-68558 None:intergenic
AGCTTCTCGCTCCATTGAAG+TGG 0.547634 tig0020715:-68428 None:intergenic
TAGGTGTTGAGCCACTTCAA+TGG 0.550994 tig0020715:+68417 Msa1385150:CDS
GGTGGTAATCAGCTTTGGGC+GGG 0.552262 tig0020715:+68533 Msa1385150:CDS
GCTGCTGGTGAAAGAGGCGG+CGG 0.563476 tig0020715:-68353 None:intergenic
AGTGTGGCTAGAGAGAAGAG+AGG 0.565171 tig0020715:-68269 None:intergenic
CGTTACCAAAGAAACAAAAT+GGG 0.569158 tig0020715:+68476 Msa1385150:CDS
TGTTCACAAGCTACTTGTAC+GGG 0.570283 tig0020715:+68704 Msa1385150:CDS
AGCGGTGGAGGAGTGGGTGA+AGG 0.573564 tig0020715:+68583 Msa1385150:CDS
TTGCAGCGGTGGACGAGACA+AGG 0.573762 tig0020715:-68301 None:intergenic
CGGTGGTAATCAGCTTTGGG+CGG 0.593924 tig0020715:+68532 Msa1385150:CDS
ATTTGTTTCTATGATCCACC+TGG 0.608612 tig0020715:+68749 Msa1385150:CDS
GACAAGGAGCAGGGATAGTG+TGG 0.609020 tig0020715:-68285 None:intergenic
TGGAAGAAATCAGTACAACT+TGG 0.618139 tig0020715:+68680 Msa1385150:CDS
GGTGGCTGCTGGTCTTGCAG+CGG 0.618405 tig0020715:-68315 None:intergenic
TTGGCTGCTGGTGAAAGAGG+CGG 0.629160 tig0020715:-68356 None:intergenic
GTGTTTATACGCAAGTTGTG+TGG 0.629612 tig0020715:+68660 Msa1385150:CDS
GGAAGAAATCAGTACAACTT+GGG 0.648064 tig0020715:+68681 Msa1385150:CDS
CGTAACGCCAAGCAAAGCGG+TGG 0.663476 tig0020715:+68568 Msa1385150:CDS
AACAAAGCAAGAGCTGAAGT+AGG 0.671065 tig0020715:+68398 Msa1385150:CDS
GGTGGACGAGACAAGGAGCA+GGG 0.673917 tig0020715:-68294 None:intergenic
AGCCGTAACGCCAAGCAAAG+CGG 0.678151 tig0020715:+68565 Msa1385150:CDS
TGTGTTGCGAATCATGAGTG+TGG 0.721846 tig0020715:+68638 Msa1385150:CDS
TTAACAAGCAGCAAATACGG+TGG 0.752196 tig0020715:+68515 Msa1385150:CDS
TCTCCAATGACATTACCAGG+TGG 0.762082 tig0020715:-68764 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CCATTTTGTTTCTTTGGTAA+CGG - tig0020715:68478-68497 None:intergenic 30.0%
CGTTACCAAAGAAACAAAAT+GGG + tig0020715:68476-68495 Msa1385150:CDS 30.0%
AACTTAACAAGCAGCAAATA+CGG + tig0020715:68512-68531 Msa1385150:CDS 30.0%
! GTGTGATTCTAAGAACTCTT+TGG - tig0020715:68378-68397 None:intergenic 35.0%
CCGTTACCAAAGAAACAAAA+TGG + tig0020715:68475-68494 Msa1385150:CDS 35.0%
TGGAAGAAATCAGTACAACT+TGG + tig0020715:68680-68699 Msa1385150:CDS 35.0%
GGAAGAAATCAGTACAACTT+GGG + tig0020715:68681-68700 Msa1385150:CDS 35.0%
!! ATTTGTTTCTATGATCCACC+TGG + tig0020715:68749-68768 Msa1385150:CDS 35.0%
AACAAAGCAAGAGCTGAAGT+AGG + tig0020715:68398-68417 Msa1385150:CDS 40.0%
!! CGCAACCCATTTTGTTTCTT+TGG - tig0020715:68484-68503 None:intergenic 40.0%
TTAACAAGCAGCAAATACGG+TGG + tig0020715:68515-68534 Msa1385150:CDS 40.0%
AATACGGTGGTAATCAGCTT+TGG + tig0020715:68528-68547 Msa1385150:CDS 40.0%
ATACGGTGGTAATCAGCTTT+GGG + tig0020715:68529-68548 Msa1385150:CDS 40.0%
GTGTTTATACGCAAGTTGTG+TGG + tig0020715:68660-68679 Msa1385150:CDS 40.0%
GTGTTCACAAGCTACTTGTA+CGG + tig0020715:68703-68722 Msa1385150:CDS 40.0%
TGTTCACAAGCTACTTGTAC+GGG + tig0020715:68704-68723 Msa1385150:CDS 40.0%
TCTAAGAACTCTTTGGCTGC+TGG - tig0020715:68371-68390 None:intergenic 45.0%
!! TAGGTGTTGAGCCACTTCAA+TGG + tig0020715:68417-68436 Msa1385150:CDS 45.0%
TGTGTTGCGAATCATGAGTG+TGG + tig0020715:68638-68657 Msa1385150:CDS 45.0%
AGCTACTTGTACGGGTAAGA+AGG + tig0020715:68712-68731 Msa1385150:CDS 45.0%
! GATCCACCTGGTAATGTCAT+TGG + tig0020715:68761-68780 Msa1385150:CDS 45.0%
TCTCCAATGACATTACCAGG+TGG - tig0020715:68767-68786 None:intergenic 45.0%
CTCTCTCCAATGACATTACC+AGG - tig0020715:68770-68789 None:intergenic 45.0%
AGTGTGGCTAGAGAGAAGAG+AGG - tig0020715:68272-68291 None:intergenic 50.0%
TCTTTGGCTGCTGGTGAAAG+AGG - tig0020715:68362-68381 None:intergenic 50.0%
AGCTTCTCGCTCCATTGAAG+TGG - tig0020715:68431-68450 None:intergenic 50.0%
GACAAGGAGCAGGGATAGTG+TGG - tig0020715:68288-68307 None:intergenic 55.0%
TTGGCTGCTGGTGAAAGAGG+CGG - tig0020715:68359-68378 None:intergenic 55.0%
!! CGGTGGTAATCAGCTTTGGG+CGG + tig0020715:68532-68551 Msa1385150:CDS 55.0%
!! GGTGGTAATCAGCTTTGGGC+GGG + tig0020715:68533-68552 Msa1385150:CDS 55.0%
AGCCGTAACGCCAAGCAAAG+CGG + tig0020715:68565-68584 Msa1385150:CDS 55.0%
CACCGCTTTGCTTGGCGTTA+CGG - tig0020715:68570-68589 None:intergenic 55.0%
AAGCAAAGCGGTGGAGGAGT+GGG + tig0020715:68577-68596 Msa1385150:CDS 55.0%
GGTGGACGAGACAAGGAGCA+GGG - tig0020715:68297-68316 None:intergenic 60.0%
TTGCAGCGGTGGACGAGACA+AGG - tig0020715:68304-68323 None:intergenic 60.0%
CGTAACGCCAAGCAAAGCGG+TGG + tig0020715:68568-68587 Msa1385150:CDS 60.0%
AACGCCAAGCAAAGCGGTGG+AGG + tig0020715:68571-68590 Msa1385150:CDS 60.0%
CACTCCTCCACCGCTTTGCT+TGG - tig0020715:68578-68597 None:intergenic 60.0%
CAAGCAAAGCGGTGGAGGAG+TGG + tig0020715:68576-68595 Msa1385150:CDS 60.0%
GGAGGAGTGGGTGAAGGAGA+AGG + tig0020715:68589-68608 Msa1385150:CDS 60.0%
CGGTGGACGAGACAAGGAGC+AGG - tig0020715:68298-68317 None:intergenic 65.0%
!! GGTGGCTGCTGGTCTTGCAG+CGG - tig0020715:68318-68337 None:intergenic 65.0%
!! GGCTCTGGAATGGTGGCTGC+TGG - tig0020715:68329-68348 None:intergenic 65.0%
!! CGGTGCTGGCTCTGGAATGG+TGG - tig0020715:68336-68355 None:intergenic 65.0%
GCTGCTGGTGAAAGAGGCGG+CGG - tig0020715:68356-68375 None:intergenic 65.0%
GCTTGGCGTTACGGCTGCTG+CGG - tig0020715:68561-68580 None:intergenic 65.0%
AGCGGTGGAGGAGTGGGTGA+AGG + tig0020715:68583-68602 Msa1385150:CDS 65.0%
!! GGCTGCTGGTCTTGCAGCGG+TGG - tig0020715:68315-68334 None:intergenic 70.0%
!! CGGCGGTGCTGGCTCTGGAA+TGG - tig0020715:68339-68358 None:intergenic 70.0%
GGTGAAAGAGGCGGCGGTGC+TGG - tig0020715:68350-68369 None:intergenic 70.0%
!! AGAGGCGGCGGTGCTGGCTC+TGG - tig0020715:68344-68363 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
tig0020715 gene 68254 68799 68254 ID=Msa1385150;Name=Msa1385150
tig0020715 mRNA 68254 68799 68254 ID=Msa1385150-mRNA-1;Parent=Msa1385150;Name=Msa1385150-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|181
tig0020715 exon 68254 68799 68254 ID=Msa1385150-mRNA-1:exon:9461;Parent=Msa1385150-mRNA-1
tig0020715 CDS 68254 68799 68254 ID=Msa1385150-mRNA-1:cds;Parent=Msa1385150-mRNA-1
Gene Sequence

>Msa1385150

ATGTTACATTATTTTCCTCTCTTCTCTCTAGCCACACTATCCCTGCTCCTTGTCTCGTCCACCGCTGCAAGACCAGCAGCCACCATTCCAGAGCCAGCACCGCCGCCTCTTTCACCAGCAGCCAAAGAGTTCTTAGAATCACACAACAAAGCAAGAGCTGAAGTAGGTGTTGAGCCACTTCAATGGAGCGAGAAGCTAGCAAAAGACACAAGCTTACTAGTCCGTTACCAAAGAAACAAAATGGGTTGCGATTTTGCAAACTTAACAAGCAGCAAATACGGTGGTAATCAGCTTTGGGCGGGTTCCGCAGCAGCCGTAACGCCAAGCAAAGCGGTGGAGGAGTGGGTGAAGGAGAAGGAGTTTTACATTCATGTGAATAATACTTGTGTTGCGAATCATGAGTGTGGTGTTTATACGCAAGTTGTGTGGAAGAAATCAGTACAACTTGGGTGTTCACAAGCTACTTGTACGGGTAAGAAGGAAGCTAGTTTGACTATTTGTTTCTATGATCCACCTGGTAATGTCATTGGAGAGAGTCCATTTTGA
Protein sequence

>Msa1385150

MLHYFPLFSLATLSLLLVSSTAARPAATIPEPAPPPLSPAAKEFLESHNKARAEVGVEPLQWSEKLAKDTSLLVRYQRNKMGCDFANLTSSKYGGNQLWAGSAAAVTPSKAVEEWVKEKEFYIHVNNTCVANHECGVYTQVVWKKSVQLGCSQATCTGKKEASLTICFYDPPGNVIGESPF*