AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG005359

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005359 MtrunA17_Chr1g0207311 70.066 304 22 3 1 252 1 287 8.65e-141 396
MsaG005359 MtrunA17_Chr5g0393721 46.835 316 99 10 1 250 1 313 8.88e-71 220
MsaG005359 MtrunA17_Chr1g0207301 42.857 322 107 7 1 245 51 372 3.18e-60 194
MsaG005359 MtrunA17_Chr3g0134741 51.724 174 71 4 83 245 142 313 1.28e-46 157
MsaG005359 MtrunA17_Chr1g0152651 84.416 77 12 0 160 236 273 349 8.01e-40 141
MsaG005359 MtrunA17_Chr5g0435021 49.451 91 45 1 139 229 197 286 1.23e-23 97.1
MsaG005359 MtrunA17_Chr8g0384141 66.071 56 19 0 170 225 123 178 1.41e-18 82.4
MsaG005359 MtrunA17_Chr3g0134001 62.963 54 20 0 170 223 180 233 8.88e-17 77.8
MsaG005359 MtrunA17_Chr4g0074161 57.576 66 28 0 159 224 204 269 1.60e-16 78.2
MsaG005359 MtrunA17_Chr7g0243041 56.364 55 24 0 168 222 33 87 3.93e-16 73.6
MsaG005359 MtrunA17_Chr1g0190731 52.055 73 35 0 152 224 184 256 1.60e-15 75.1
MsaG005359 MtrunA17_Chr4g0014771 42.857 98 55 1 130 226 87 184 4.78e-13 65.9
MsaG005359 MtrunA17_Chr7g0234761 43.299 97 45 2 138 224 285 381 5.32e-13 68.2
MsaG005359 MtrunA17_Chr1g0193321 47.368 57 30 0 168 224 469 525 1.41e-12 67.0
MsaG005359 MtrunA17_Chr1g0153241 36.620 71 45 0 168 238 92 162 7.86e-12 63.5
MsaG005359 MtrunA17_Chr1g0207321 48.193 83 26 4 16 86 50 127 9.37e-12 60.8
MsaG005359 MtrunA17_Chr3g0095391 40.278 72 38 1 159 230 307 373 2.66e-11 63.2
MsaG005359 MtrunA17_Chr8g0339091 40.449 89 43 2 162 249 292 371 3.55e-11 62.8
MsaG005359 MtrunA17_Chr5g0402031 37.037 81 51 0 170 250 114 194 4.93e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005359 AT2G14760.1 70.248 121 34 1 133 251 207 327 4.33e-50 167
MsaG005359 AT4G33880.1 75.000 104 25 1 141 243 245 348 1.89e-46 158
MsaG005359 AT2G14760.3 63.433 134 34 2 133 251 207 340 1.97e-46 158
MsaG005359 AT5G43175.1 70.103 97 29 0 147 243 118 214 2.30e-43 147
MsaG005359 AT1G27740.1 78.571 84 18 0 160 243 166 249 5.72e-43 147
MsaG005359 AT5G37800.1 53.409 88 40 1 142 229 183 269 3.97e-23 95.9
MsaG005359 AT1G66470.1 60.000 70 27 1 160 229 195 263 1.04e-21 92.0
MsaG005359 AT2G24260.2 52.632 76 36 0 160 235 34 109 1.06e-17 80.1
MsaG005359 AT4G30980.1 57.143 70 30 0 155 224 124 193 2.14e-17 80.5
MsaG005359 AT4G30980.2 57.143 70 30 0 155 224 172 241 2.84e-17 80.5
MsaG005359 AT2G24260.1 60.000 65 26 0 160 224 137 201 3.85e-17 80.1
MsaG005359 AT5G01305.1 53.226 62 29 0 159 220 35 96 6.51e-17 76.3
MsaG005359 AT3G21330.1 58.929 56 23 0 168 223 276 331 7.60e-17 79.3
MsaG005359 AT5G58010.1 55.385 65 29 0 160 224 98 162 1.52e-15 75.1
MsaG005359 AT4G00120.1 46.970 66 34 1 170 235 121 185 1.82e-15 73.2
MsaG005359 AT1G09530.3 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G09530.2 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G09530.5 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G09530.1 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G09530.4 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G09530.6 40.909 66 39 0 168 233 344 409 4.86e-12 65.9
MsaG005359 AT1G73830.1 44.048 84 43 2 162 244 148 228 5.85e-12 64.3
MsaG005359 AT1G73830.2 44.048 84 43 2 162 244 148 228 6.26e-12 64.3
MsaG005359 AT1G18400.2 50.000 64 31 1 162 224 146 209 8.74e-12 63.5
MsaG005359 AT4G09180.1 52.941 68 31 1 160 226 183 250 1.20e-11 63.5
MsaG005359 AT3G23690.1 40.625 96 54 2 130 224 162 255 1.27e-11 64.3
MsaG005359 AT5G50915.1 43.529 85 43 3 162 245 137 217 1.33e-11 63.5
MsaG005359 AT5G50915.2 43.529 85 43 3 162 245 137 217 1.33e-11 63.5
MsaG005359 AT1G18400.1 50.000 64 31 1 162 224 146 209 1.36e-11 63.2
MsaG005359 AT5G48560.1 46.053 76 40 1 150 224 290 365 1.42e-11 64.3
MsaG005359 AT5G48560.2 46.053 76 40 1 150 224 290 365 1.60e-11 64.3
MsaG005359 AT5G50915.3 43.529 85 43 3 162 245 137 217 1.76e-11 63.2
MsaG005359 AT5G50915.4 43.529 85 43 3 162 245 137 217 1.76e-11 63.2
MsaG005359 AT4G00050.2 48.077 52 27 0 177 228 121 172 2.36e-11 63.2
MsaG005359 AT4G36930.1 35.135 74 48 0 168 241 198 271 2.86e-11 63.2
MsaG005359 AT4G00050.1 48.077 52 27 0 177 228 223 274 4.02e-11 62.8
MsaG005359 AT4G00050.3 48.077 52 27 0 177 228 223 274 4.82e-11 62.4
MsaG005359 AT2G20180.7 47.368 57 30 0 168 224 214 270 8.28e-11 62.0
MsaG005359 AT2G20180.1 47.368 57 30 0 168 224 214 270 8.28e-11 62.0
MsaG005359 AT2G20180.5 47.368 57 30 0 168 224 214 270 8.28e-11 62.0
MsaG005359 AT2G20180.4 47.368 57 30 0 168 224 285 341 8.63e-11 62.0
MsaG005359 AT2G20180.6 47.368 57 30 0 168 224 285 341 8.63e-11 62.0
MsaG005359 AT2G20180.2 47.368 57 30 0 168 224 285 341 8.63e-11 62.0
MsaG005359 AT2G20180.3 47.368 57 30 0 168 224 285 341 8.63e-11 62.0

Find 44 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATTTAGTCCTCAATATT+TGG 0.162834 1:-80534302 MsaT005359.1:CDS
TTGCTCATAGAAGCAGATTT+TGG 0.214748 1:+80533981 None:intergenic
CAAATATTGAGGACTAAATT+TGG 0.216033 1:+80534303 None:intergenic
GCTTACAATGGAATGAATAT+TGG 0.254169 1:-80533066 MsaT005359.1:CDS
CCCATTCTTCAGAAATCAAT+TGG 0.299308 1:+80534580 None:intergenic
TTCATTCCATTGTAAGCAAT+TGG 0.326950 1:+80533072 None:intergenic
CCCAATTGATTTCTGAAGAA+TGG 0.332468 1:-80534581 MsaT005359.1:CDS
GAAGCTACCTTTGTTCCATT+TGG 0.350337 1:+80533384 None:intergenic
AATGATAGCATTGATCATAA+AGG 0.357619 1:-80534253 MsaT005359.1:CDS
AAGCTACCTTTGTTCCATTT+GGG 0.369150 1:+80533385 None:intergenic
CCAATTGATTTCTGAAGAAT+GGG 0.373736 1:-80534580 MsaT005359.1:CDS
ATGTTTAGAGCCAGTGAAAC+TGG 0.383865 1:-80534227 MsaT005359.1:CDS
CTACCTAAGTTGGGTGCCTC+AGG 0.386763 1:+80533864 None:intergenic
GAAGAATGGGATTCTCTTAG+TGG 0.394320 1:-80534567 MsaT005359.1:CDS
ATGATAGCATTGATCATAAA+GGG 0.425204 1:-80534252 MsaT005359.1:CDS
TTCATGAATCAGTTCCTTAG+TGG 0.426280 1:-80534519 MsaT005359.1:intron
GGTAGAAAATCAAGAGCAAC+AGG 0.428540 1:-80533846 MsaT005359.1:CDS
CTTCTATCCTCTTCTGAACA+AGG 0.432681 1:+80534166 None:intergenic
TGCAGGTCTTAGAAAACATT+AGG 0.448557 1:-80534019 MsaT005359.1:intron
CCTTTGTTCCATTTGGGACA+AGG 0.453226 1:+80533391 None:intergenic
TTGCAAACCCTTGTCCCAAA+TGG 0.465028 1:-80533399 MsaT005359.1:CDS
CTTTGTTCCATTTGGGACAA+GGG 0.489847 1:+80533392 None:intergenic
ATGTTATCATCCAAATATTG+AGG 0.490926 1:+80534292 None:intergenic
GAACCTGAGGCACCCAACTT+AGG 0.497691 1:-80533867 MsaT005359.1:CDS
AAGATTTAGGAGCTCAATAG+AGG 0.507018 1:-80534119 MsaT005359.1:intron
GCAGCAAGAACCAGTTTCAC+TGG 0.514887 1:+80534217 None:intergenic
TTCTGAACCTTGTTCAGAAG+AGG 0.517904 1:-80534173 MsaT005359.1:CDS
ATGCTCTGTGCATCAGTGGC+AGG 0.521454 1:+80533819 None:intergenic
TCACATGTTGACTCAATTGG+AGG 0.523673 1:-80533915 MsaT005359.1:CDS
TGCTAACAATGAAATGATGA+TGG 0.528083 1:-80534197 MsaT005359.1:CDS
TCTTCAGAAATCAATTGGGC+AGG 0.532125 1:+80534585 None:intergenic
CCATTCTTCAGAAATCAATT+GGG 0.537373 1:+80534581 None:intergenic
TTCTGAGCTCAGAAGATATG+TGG 0.585124 1:-80533104 MsaT005359.1:CDS
TTCTATGAGCAACAATGAAG+AGG 0.588809 1:-80533970 MsaT005359.1:CDS
TATGCTCCAATTGCTTACAA+TGG 0.606083 1:-80533078 MsaT005359.1:CDS
GAAGAGGACTTAATGTGGCA+TGG 0.606487 1:-80533954 MsaT005359.1:CDS
AGATATTAGCACTATGCTTG+AGG 0.620150 1:-80533279 MsaT005359.1:CDS
CCTTGTCCCAAATGGAACAA+AGG 0.623499 1:-80533391 MsaT005359.1:intron
TCTGAGCCTAAAAGAACCTG+AGG 0.648501 1:-80533880 MsaT005359.1:CDS
TAGTGGACAGTACACAGCTG+AGG 0.680277 1:-80534550 MsaT005359.1:CDS
ACAATGAAGAGGACTTAATG+TGG 0.680942 1:-80533959 MsaT005359.1:CDS
ATAAATGCTCTGTGCATCAG+TGG 0.693217 1:+80533815 None:intergenic
TAGTTGTAGAAGAAAAGCTG+AGG 0.699528 1:+80533037 None:intergenic
AGAAAATCAAGAGCAACAGG+TGG 0.715777 1:-80533843 MsaT005359.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 80533032 80534613 80533032 ID=MsaG005359
Chr1 mRNA 80533032 80534613 80533032 ID=MsaT005359.1;Parent=MsaG005359
Chr1 exon 80533032 80533127 80533032 ID=MsaT005359.1.exon6;Parent=MsaT005359.1
Chr1 CDS 80533032 80533127 80533032 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Chr1 exon 80533238 80533303 80533238 ID=MsaT005359.1.exon5;Parent=MsaT005359.1
Chr1 CDS 80533238 80533303 80533238 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Chr1 exon 80533392 80533457 80533392 ID=MsaT005359.1.exon4;Parent=MsaT005359.1
Chr1 CDS 80533392 80533457 80533392 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Chr1 exon 80533809 80534036 80533809 ID=MsaT005359.1.exon3;Parent=MsaT005359.1
Chr1 CDS 80533809 80534036 80533809 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Chr1 exon 80534120 80534328 80534120 ID=MsaT005359.1.exon2;Parent=MsaT005359.1
Chr1 CDS 80534120 80534328 80534120 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Chr1 exon 80534520 80534613 80534520 ID=MsaT005359.1.exon1;Parent=MsaT005359.1
Chr1 CDS 80534520 80534613 80534520 ID=cds.MsaT005359.1;Parent=MsaT005359.1
Gene Sequence

>MsaT005359.1

ATGGAACCTGCCCAATTGATTTCTGAAGAATGGGATTCTCTTAGTGGACAGTACACAGCTGAGGAAGCTGACTTCATGAATCAGTTCCTTAGTGATGCCAAATTTAGTCCTCAATATTTGGATGATAACATAAGTAAACACATAAATAATGATAGCATTGATCATAAAGGGTCATGTTTAGAGCCAGTGAAACTGGTTCTTGCTGCTAACAATGAAATGATGATGGTTTCTGAACCTTGTTCAGAAGAGGATAGAAGCAAAAACATGGAGAACCCTGCAAAAAGATTTAGGAGCTCAATAGAGGTCTTAGAAAACATTAGGAATGTTAAGAAGTGTCCAAAATCTGCTTCTATGAGCAACAATGAAGAGGACTTAATGTGGCATGGCTCCAATAACTGTTTTTCACATGTTGACTCAATTGGAGGAACATCTTCAAATCTGAGCCTAAAAGAACCTGAGGCACCCAACTTAGGTAGAAAATCAAGAGCAACAGGTGGTCCTGCCACTGATGCACAGAGCATTTATGCAAGAAAGAGAAGAGAAAGAATAAATGAAAGATTGAGAATCTTGCAAACCCTTGTCCCAAATGGAACAAAGGTAGATATTAGCACTATGCTTGAGGAAGCTGTCCAATATGTGAAGTTTTTGCAGCATCAAATTAAGCTTCTGAGCTCAGAAGATATGTGGATGTATGCTCCAATTGCTTACAATGGAATGAATATTGGATTAGACCTCAGCTTTTCTTCTACAACTAATTAA
Protein sequence

>MsaT005359.1

MEPAQLISEEWDSLSGQYTAEEADFMNQFLSDAKFSPQYLDDNISKHINNDSIDHKGSCLEPVKLVLAANNEMMMVSEPCSEEDRSKNMENPAKRFRSSIEVLENIRNVKKCPKSASMSNNEEDLMWHGSNNCFSHVDSIGGTSSNLSLKEPEAPNLGRKSRATGGPATDAQSIYARKRRERINERLRILQTLVPNGTKVDISTMLEEAVQYVKFLQHQIKLLSSEDMWMYAPIAYNGMNIGLDLSFSSTTN*