AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG027366

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG027366 MtrunA17_Chr5g0422431 97.065 443 13 0 1 443 1 443 0.0 893
MsaG027366 MtrunA17_Chr1g0198751 62.947 475 136 9 2 439 4 475 0.0 569
MsaG027366 MtrunA17_Chr1g0198741 51.672 329 110 8 114 440 8 289 4.55e-94 286
MsaG027366 MtrunA17_Chr7g0227071 54.425 226 79 3 6 219 5 218 9.72e-83 263
MsaG027366 MtrunA17_Chr2g0282871 49.402 251 117 4 34 274 27 277 4.76e-76 240
MsaG027366 MtrunA17_Chr4g0046431 58.081 198 80 2 36 230 44 241 3.37e-75 238
MsaG027366 MtrunA17_Chr8g0389661 59.162 191 68 3 36 218 27 215 9.11e-73 237
MsaG027366 MtrunA17_Chr8g0367761 60.556 180 68 2 36 212 44 223 2.47e-72 229
MsaG027366 MtrunA17_Chr4g0040541 55.330 197 83 2 32 223 19 215 2.21e-68 219
MsaG027366 MtrunA17_Chr2g0324961 55.446 202 86 2 32 229 20 221 6.78e-64 208
MsaG027366 MtrunA17_Chr6g0484441 30.168 179 107 6 58 233 5 168 2.37e-14 73.9
MsaG027366 MtrunA17_Chr1g0147421 30.978 184 104 10 58 234 27 194 1.98e-11 65.5
MsaG027366 MtrunA17_Chr7g0261411 29.878 164 91 7 58 215 10 155 9.65e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG027366 AT1G25580.1 56.897 464 165 10 1 444 1 449 4.51e-175 498
MsaG027366 AT3G01600.1 55.856 222 91 4 5 224 4 220 4.60e-79 250
MsaG027366 AT5G14490.2 51.613 248 109 5 5 250 4 242 7.61e-78 244
MsaG027366 AT5G14490.4 51.613 248 109 5 5 250 4 242 1.14e-77 246
MsaG027366 AT5G14490.1 51.613 248 109 5 5 250 7 245 1.61e-77 246
MsaG027366 AT5G14490.3 51.613 248 109 5 5 250 7 245 2.69e-77 245
MsaG027366 AT4G29230.3 59.375 192 67 3 36 218 28 217 3.29e-74 240
MsaG027366 AT4G29230.1 59.375 192 67 3 36 218 28 217 1.50e-73 240
MsaG027366 AT4G29230.2 59.375 192 66 3 36 218 28 216 2.38e-73 239
MsaG027366 AT4G28500.1 51.556 225 103 4 5 223 2 226 5.59e-72 230
MsaG027366 AT1G28470.1 55.612 196 81 2 34 223 48 243 1.29e-70 226
MsaG027366 AT5G56620.3 55.385 195 74 4 36 218 22 215 7.88e-68 223
MsaG027366 AT5G56620.2 55.385 195 74 4 36 218 22 215 9.53e-68 222
MsaG027366 AT5G56620.1 55.385 195 74 4 36 218 22 215 1.45e-67 221
MsaG027366 AT3G18400.1 30.588 170 95 8 58 221 5 157 7.84e-14 72.8
MsaG027366 AT1G01720.1 26.754 228 131 10 58 272 7 211 6.31e-13 69.7
MsaG027366 AT3G12910.1 31.544 149 86 5 61 206 24 159 2.26e-11 65.1
MsaG027366 AT1G02220.1 31.250 160 90 6 59 215 4 146 2.68e-11 65.5
MsaG027366 AT1G33060.2 29.341 167 96 7 57 216 23 174 5.11e-11 65.5
MsaG027366 AT1G33060.1 29.341 167 96 7 57 216 23 174 5.56e-11 65.1

Find 99 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAATAGTATGCTGACAATT+TGG 0.134743 5:+43461336 None:intergenic
CTTCTTCCACAGAGCAATTA+AGG 0.224693 5:-43459968 MsaT027366.1:CDS
GGATCAAATTTGACACCTTT+TGG 0.259342 5:+43460239 None:intergenic
TGAACCCCATTCAAGATTAC+TGG 0.283602 5:+43459859 None:intergenic
GAAAAGCTGAGAAAACTAAT+TGG 0.286732 5:-43459786 MsaT027366.1:CDS
CAAGATAGCTTTATAGCATT+TGG 0.294737 5:-43458043 MsaT027366.1:CDS
TTTGTGTTTATATAGGAATT+TGG 0.295109 5:-43458070 MsaT027366.1:intron
TGCTTCATTGTTTGACAACT+TGG 0.305195 5:-43457914 MsaT027366.1:CDS
CATCTGATCAGGAGGTAATT+TGG 0.312766 5:-43460217 MsaT027366.1:CDS
GGCTCAGGAGTCACAGATTT+GGG 0.319343 5:+43459598 None:intergenic
CAATAGTATGCTGACAATTT+GGG 0.324090 5:+43461337 None:intergenic
CCAACAGCAGCAAGTCAAAC+TGG 0.324794 5:-43459689 MsaT027366.1:CDS
AGGCTCAGGAGTCACAGATT+TGG 0.328067 5:+43459597 None:intergenic
CCTTTCTATTTATGCTCAGC+TGG 0.332701 5:-43458273 MsaT027366.1:CDS
ACATTTGACTCTACATTTGA+AGG 0.342814 5:+43458197 None:intergenic
GACGTCCGCTGGCACAAAAC+TGG 0.357268 5:-43459892 MsaT027366.1:CDS
TCTGTTGGATTCACAACAAC+TGG 0.369929 5:-43458384 MsaT027366.1:CDS
AAAATACATGATCAGGATTT+GGG 0.372286 5:-43459916 MsaT027366.1:CDS
ATCTTGAATGGGGTTCAAAA+AGG 0.388213 5:-43459853 MsaT027366.1:CDS
ATTGTTGCTTCAATAGCTTC+AGG 0.390657 5:+43459643 None:intergenic
GCAATTAAGGCTTATAATAC+TGG 0.394443 5:-43459955 MsaT027366.1:CDS
CAAACAATGAAGCAACAGTT+AGG 0.403441 5:+43457923 None:intergenic
TTTCTATATGCAGACCATCT+TGG 0.411265 5:-43461458 MsaT027366.1:intron
ATATCCTTCTTCAGATGCTC+TGG 0.424976 5:+43458248 None:intergenic
GTCACAGATTTGGGAGTAAC+CGG 0.426136 5:+43459607 None:intergenic
TCATCTTTACCATCTCTAGT+AGG 0.429288 5:+43458317 None:intergenic
CTAAGCCAGTAATCTTGAAT+GGG 0.433717 5:-43459864 MsaT027366.1:CDS
CAGTATTCGGATGTAGATCT+AGG 0.435339 5:-43459559 MsaT027366.1:CDS
CAAATTTGATCCATCTGATC+AGG 0.442832 5:-43460228 MsaT027366.1:CDS
AGGAACAGAAGAGGATGAAA+AGG 0.451744 5:-43459743 MsaT027366.1:CDS
ACTAAGCCAGTAATCTTGAA+TGG 0.454048 5:-43459865 MsaT027366.1:CDS
GCAAGTCAAACTGGGTGATA+AGG 0.457369 5:-43459680 MsaT027366.1:CDS
AGGTTTACCTGGGGAATGGC+GGG 0.461494 5:+43459526 None:intergenic
TGCATCGGGAGCATGTGATC+TGG 0.461888 5:-43461397 MsaT027366.1:CDS
AGGATTTGGGTGACGTCCGC+TGG 0.463363 5:-43459903 MsaT027366.1:CDS
AAAAGCTGAGAAAACTAATT+GGG 0.463490 5:-43459785 MsaT027366.1:CDS
CTTTCTATTTATGCTCAGCT+GGG 0.463607 5:-43458272 MsaT027366.1:CDS
GCCTCCTCAGATGAATTGTC+TGG 0.464452 5:-43458594 MsaT027366.1:CDS
GGAGTTTCGACTAAGTCAAT+TGG 0.465851 5:-43458156 MsaT027366.1:intron
GAGTGGCCTGGTTTGCCAAA+AGG 0.477697 5:-43460254 MsaT027366.1:CDS
TTTAAGGTTTACCTGGGGAA+TGG 0.481491 5:+43459522 None:intergenic
TCAAGTCTCTCCTCTATGGC+GGG 0.485338 5:-43462152 None:intergenic
TGAAGCAACAATCACTAAAG+TGG 0.486754 5:-43459632 MsaT027366.1:CDS
CATAAATAGAAAGGCTGGGT+TGG 0.487379 5:+43458282 None:intergenic
ATTGAAAATAATCCTGATGA+TGG 0.487705 5:-43458437 MsaT027366.1:CDS
AACAATCACTAAAGTGGATC+CGG 0.490246 5:-43459626 MsaT027366.1:CDS
GCTTCATTGTTTGACAACTT+GGG 0.492584 5:-43457913 MsaT027366.1:CDS
ACTCATCCTCAAAACTTGCC+AGG 0.498733 5:-43460098 MsaT027366.1:intron
CTGAGCATAAATAGAAAGGC+TGG 0.499400 5:+43458277 None:intergenic
CTGACAATTTGGGCAAGCCT+TGG 0.506059 5:+43461347 None:intergenic
GTTATGCATCAATATCATCT+AGG 0.507798 5:-43459763 MsaT027366.1:CDS
ATTACTCTTGAAGTGAATGA+TGG 0.508345 5:-43460131 MsaT027366.1:CDS
CCAGTTTGACTTGCTGCTGT+TGG 0.516424 5:+43459689 None:intergenic
TATATGCAGACCATCTTGGC+TGG 0.517331 5:-43461454 MsaT027366.1:intron
AAGGTTTACCTGGGGAATGG+CGG 0.521012 5:+43459525 None:intergenic
ATGTCAGGTGTTAAGCAAGA+TGG 0.522325 5:-43460003 MsaT027366.1:intron
AATGAAAATAATGCTGATGA+TGG 0.526709 5:-43458488 MsaT027366.1:CDS
GTTCTGTATATGAGTAGTGC+AGG 0.531845 5:-43459814 MsaT027366.1:CDS
TTGCTTGCAAAATGTGGTGT+TGG 0.532555 5:-43460191 MsaT027366.1:CDS
TTTGCTTGCTCTTCACAATG+AGG 0.533963 5:+43458560 None:intergenic
CAATTTGGGCAAGCCTTGGT+AGG 0.534551 5:+43461351 None:intergenic
GTAGAAACTGAACATAATGA+AGG 0.537204 5:-43458521 MsaT027366.1:CDS
TAGTGAATCACAAAATCTGT+TGG 0.540122 5:-43458399 MsaT027366.1:CDS
ACTCTACATTTGAAGGCTCA+AGG 0.543494 5:+43458204 None:intergenic
TACCATCTCTAGTAGGAGAC+TGG 0.544929 5:+43458324 None:intergenic
CCAGCTGAGCATAAATAGAA+AGG 0.555486 5:+43458273 None:intergenic
TAATTGCTCTGTGGAAGAAG+TGG 0.556020 5:+43459971 None:intergenic
GTTGTAAGGTTGTAAAAGAG+TGG 0.556602 5:-43460271 MsaT027366.1:intron
CAAATTACCTCCTGATCAGA+TGG 0.556689 5:+43460218 None:intergenic
AACTCATCAACGAAAGGATG+AGG 0.560139 5:+43460158 None:intergenic
GGGACCAGAGCATCTGAAGA+AGG 0.564286 5:-43458252 MsaT027366.1:CDS
AGACACACCCGCCATTCCCC+AGG 0.573342 5:-43459533 MsaT027366.1:intron
TGTAGAGAATGACACACCTT+CGG 0.575337 5:-43458177 MsaT027366.1:CDS
AGCCAGTCTCCTACTAGAGA+TGG 0.577237 5:-43458326 MsaT027366.1:CDS
ATTATGTTCAGTTTCTACCA+TGG 0.577859 5:+43458526 None:intergenic
TCCAGACAATTCATCTGAGG+AGG 0.583627 5:+43458593 None:intergenic
CAAGTCTCTCCTCTATGGCG+GGG 0.593225 5:-43462151 None:intergenic
AAGGTTGTAAAAGAGTGGCC+TGG 0.594766 5:-43460266 MsaT027366.1:CDS
AGCAAAAGATGATCTATCCA+TGG 0.596236 5:-43458543 MsaT027366.1:CDS
ATGCAGACCATCTTGGCTGG+TGG 0.599205 5:-43461451 MsaT027366.1:intron
ATGATAAACTCATCAACGAA+AGG 0.599805 5:+43460152 None:intergenic
CAACAGCAGCAAGTCAAACT+GGG 0.602243 5:-43459688 MsaT027366.1:CDS
TATATGAGTAGTGCAGGAGG+AGG 0.609676 5:-43459808 MsaT027366.1:CDS
TGGCACTTGCTTGCAAAATG+TGG 0.618127 5:-43460197 MsaT027366.1:CDS
TAGAAACTGAACATAATGAA+GGG 0.620128 5:-43458520 MsaT027366.1:CDS
TCATCCAGACAATTCATCTG+AGG 0.620597 5:+43458590 None:intergenic
GTGATCTGGAAAATGTTACA+TGG 0.621927 5:-43461383 MsaT027366.1:CDS
TGAGCATAAATAGAAAGGCT+GGG 0.624006 5:+43458278 None:intergenic
ACAGAAGAGGATGAAAAGGA+TGG 0.629598 5:-43459739 MsaT027366.1:CDS
ATTTGATCCATCTGATCAGG+AGG 0.636045 5:-43460225 MsaT027366.1:CDS
AATTGCTCTGTGGAAGAAGT+GGG 0.639626 5:+43459972 None:intergenic
ATATCATCTAGGAACAGAAG+AGG 0.646141 5:-43459752 MsaT027366.1:CDS
ATGGAAAAGCAATCCTACCA+AGG 0.655385 5:-43461364 MsaT027366.1:CDS
CTGTATATGAGTAGTGCAGG+AGG 0.660155 5:-43459811 MsaT027366.1:CDS
AGGCTTATAATACTGGCACT+CGG 0.668317 5:-43459948 MsaT027366.1:CDS
TATAAGCCTTAATTGCTCTG+TGG 0.669172 5:+43459962 None:intergenic
TAAGCCAGTAATCTTGAATG+GGG 0.669245 5:-43459863 MsaT027366.1:CDS
TGACTTAGTCGAAACTCCGA+AGG 0.670660 5:+43458161 None:intergenic
TATAGCATTTGGTTACAACA+AGG 0.688806 5:-43458032 MsaT027366.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 43457894 43462159 43457894 ID=MsaG027366
Chr5 mRNA 43457894 43462159 43457894 ID=MsaT027366.1;Parent=MsaG027366
Chr5 exon 43457894 43457950 43457894 ID=MsaT027366.1.exon7;Parent=MsaT027366.1
Chr5 CDS 43457894 43457950 43457894 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43458033 43458077 43458033 ID=MsaT027366.1.exon6;Parent=MsaT027366.1
Chr5 CDS 43458033 43458077 43458033 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43458157 43458615 43458157 ID=MsaT027366.1.exon5;Parent=MsaT027366.1
Chr5 CDS 43458157 43458615 43458157 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43459534 43460018 43459534 ID=MsaT027366.1.exon4;Parent=MsaT027366.1
Chr5 CDS 43459534 43460018 43459534 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43460099 43460285 43460099 ID=MsaT027366.1.exon3;Parent=MsaT027366.1
Chr5 CDS 43460099 43460285 43460099 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43461326 43461467 43461326 ID=MsaT027366.1.exon2;Parent=MsaT027366.1
Chr5 CDS 43461326 43461467 43461326 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Chr5 exon 43462152 43462159 43462152 ID=MsaT027366.1.exon1;Parent=MsaT027366.1
Chr5 CDS 43462152 43462159 43462152 ID=cds.MsaT027366.1;Parent=MsaT027366.1
Gene Sequence

>MsaT027366.1

ATGGCGGGACCATCTTGGCTGGTGGACAAAAGCAGAATTGCAACCAAAATAAAAAGTGCATCGGGAGCATGTGATCTGGAAAATGTTACATGGAAAAGCAATCCTACCAAGGCTTGCCCAAATTGTCAGCATACTATTGACAATAGTGATGTTGTAAAAGAGTGGCCTGGTTTGCCAAAAGGTGTCAAATTTGATCCATCTGATCAGGAGGTAATTTGGCACTTGCTTGCAAAATGTGGTGTTGGAAATTCAAAACCTCATCCTTTCGTTGATGAGTTTATCATTACTCTTGAAGTGAATGATGGAATTTGTTACACTCATCCTCAAAACTTGCCAGGTGTTAAGCAAGATGGAAATGCATCCCACTTCTTCCACAGAGCAATTAAGGCTTATAATACTGGCACTCGGAAGCGCCGAAAAATACATGATCAGGATTTGGGTGACGTCCGCTGGCACAAAACTGGAAGAACTAAGCCAGTAATCTTGAATGGGGTTCAAAAAGGCTGTAAAAAGATTATGGTTCTGTATATGAGTAGTGCAGGAGGAGGAAAAGCTGAGAAAACTAATTGGGTTATGCATCAATATCATCTAGGAACAGAAGAGGATGAAAAGGATGGCGAGTTTGTTATCTCTAAAGTGTTTTACCAACAGCAGCAAGTCAAACTGGGTGATAAGGATGAACAAGATATTCCTGAAGCTATTGAAGCAACAATCACTAAAGTGGATCCGGTTACTCCCAAATCTGTGACTCCTGAGCCTCCTTATAGTGAAAAACAGTATTCGGATGTAGATCTAGGACAAGACACACCCGCCATTCCCCAGCCTCCTCAGATGAATTGTCTGGATGAAATTCAACCTCATTGTGAAGAGCAAGCAAAAGATGATCTATCCATGGTAGAAACTGAACATAATGAAGGGACAGATAATAATGAAAATAATGCTGATGATGGCCAAAAATGGTGTGAAGGAACAGATAATATTGAAAATAATCCTGATGATGGCCAAAAATGGTGGGATAGTGAATCACAAAATCTGTTGGATTCACAACAACTGGTTGACGCATTGTCATTGTGTGATGATTTACTTCGTAGCCAGTCTCCTACTAGAGATGGTAAAGATGAAGAACAAAAGAACCAACCCAGCCTTTCTATTTATGCTCAGCTGGGACCAGAGCATCTGAAGAAGGATATTGAAGACTGTCAAAATCTCGTCCTTGAGCCTTCAAATGTAGAGTCAAATGTAGAGAATGACACACCTTCGGAGTTTCGACTAAGTCAATTGGAATTTGGTTCACAAGATAGCTTTATAGCATTTGGTTACAACAAGGCAAACCTAACTGTTGCTTCATTGTTTGACAACTTGGGCTGTAATTTTTGGCAGTGA
Protein sequence

>MsaT027366.1

MAGPSWLVDKSRIATKIKSASGACDLENVTWKSNPTKACPNCQHTIDNSDVVKEWPGLPKGVKFDPSDQEVIWHLLAKCGVGNSKPHPFVDEFIITLEVNDGICYTHPQNLPGVKQDGNASHFFHRAIKAYNTGTRKRRKIHDQDLGDVRWHKTGRTKPVILNGVQKGCKKIMVLYMSSAGGGKAEKTNWVMHQYHLGTEEDEKDGEFVISKVFYQQQQVKLGDKDEQDIPEAIEATITKVDPVTPKSVTPEPPYSEKQYSDVDLGQDTPAIPQPPQMNCLDEIQPHCEEQAKDDLSMVETEHNEGTDNNENNADDGQKWCEGTDNIENNPDDGQKWWDSESQNLLDSQQLVDALSLCDDLLRSQSPTRDGKDEEQKNQPSLSIYAQLGPEHLKKDIEDCQNLVLEPSNVESNVENDTPSEFRLSQLEFGSQDSFIAFGYNKANLTVASLFDNLGCNFWQ*