AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG033552

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033552 MtrunA17_Chr7g0235151 74.699 83 21 0 3 85 70 152 4.26e-35 132
MsaG033552 MtrunA17_Chr1g0151541 52.033 123 54 2 174 296 652 769 1.01e-34 133
MsaG033552 MtrunA17_Chr8g0392871 48.649 111 56 1 186 296 736 845 1.35e-29 118
MsaG033552 MtrunA17_Chr1g0191171 45.690 116 62 1 181 296 681 795 1.34e-28 115
MsaG033552 MtrunA17_Chr6g0482711 43.103 116 65 1 181 296 652 766 2.21e-26 108
MsaG033552 MtrunA17_Chr2g0294351 37.719 114 70 1 183 296 460 572 1.51e-22 97.8
MsaG033552 MtrunA17_Chr1g0179331 35.802 162 96 3 142 296 503 663 4.86e-22 96.3
MsaG033552 MtrunA17_Chr5g0427651 38.686 137 81 2 162 296 619 754 1.61e-21 94.7
MsaG033552 MtrunA17_Chr3g0132791 39.259 135 79 2 164 296 628 761 2.05e-20 91.7
MsaG033552 MtrunA17_Chr4g0068411 37.719 114 70 1 183 296 454 566 1.09e-19 89.4
MsaG033552 MtrunA17_Chr4g0061541 53.846 65 30 0 4 68 75 139 6.86e-18 82.8
MsaG033552 MtrunA17_Chr5g0406251 42.574 101 57 1 195 295 301 400 4.28e-17 81.3
MsaG033552 MtrunA17_Chr5g0397931 35.965 114 72 1 183 296 417 529 2.26e-16 79.3
MsaG033552 MtrunA17_Chr4g0043211 52.381 63 30 0 4 66 71 133 2.81e-16 78.6
MsaG033552 MtrunA17_Chr7g0219091 28.643 199 115 4 4 175 58 256 2.28e-15 75.9
MsaG033552 MtrunA17_Chr1g0171451 32.500 120 78 2 179 296 404 522 8.54e-15 74.7
MsaG033552 MtrunA17_Chr2g0325851 35.455 110 68 2 188 295 556 664 1.12e-13 71.2
MsaG033552 MtrunA17_Chr4g0041201 32.203 118 77 2 180 295 538 654 2.04e-13 70.5
MsaG033552 MtrunA17_Chr1g0211611 37.963 108 66 1 188 295 300 406 2.29e-13 70.1
MsaG033552 MtrunA17_Chr3g0143531 34.951 103 66 1 193 295 29 130 2.14e-12 66.2
MsaG033552 MtrunA17_Chr1g0202101 35.246 122 74 2 174 295 272 388 1.23e-11 65.1
MsaG033552 MtrunA17_Chr4g0075541 30.345 145 91 4 160 295 54 197 2.79e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG033552 AT5G11850.1 49.593 123 57 2 174 296 598 715 9.03e-31 122
MsaG033552 AT1G18160.1 46.552 116 61 1 181 296 707 821 2.54e-30 120
MsaG033552 AT1G18160.2 46.552 116 61 1 181 296 707 821 2.93e-30 120
MsaG033552 AT1G73660.1 46.491 114 60 1 183 296 742 854 3.48e-30 120
MsaG033552 AT1G08720.1 46.552 116 61 1 181 296 661 775 4.01e-28 114
MsaG033552 AT1G08720.2 46.552 116 61 1 181 296 661 775 4.05e-28 114
MsaG033552 AT3G06620.1 39.655 116 69 1 181 296 486 600 5.82e-23 99.4
MsaG033552 AT3G06640.1 38.793 116 70 1 181 296 438 552 7.86e-22 95.9
MsaG033552 AT3G06640.2 38.793 116 70 1 181 296 438 552 8.03e-22 95.9
MsaG033552 AT3G06640.3 38.793 116 70 1 181 296 438 552 8.03e-22 95.9
MsaG033552 AT5G49470.3 38.596 114 69 1 183 296 485 597 1.03e-21 95.5
MsaG033552 AT5G49470.7 38.596 114 69 1 183 296 358 470 1.12e-21 95.5
MsaG033552 AT5G49470.5 38.596 114 69 1 183 296 485 597 1.13e-21 95.5
MsaG033552 AT5G49470.4 38.596 114 69 1 183 296 459 571 1.18e-21 95.5
MsaG033552 AT5G49470.6 38.596 114 69 1 183 296 485 597 1.23e-21 95.5
MsaG033552 AT5G49470.1 38.596 114 69 1 183 296 198 310 1.41e-21 94.7
MsaG033552 AT1G67890.1 38.596 114 69 1 183 296 481 593 1.75e-21 95.1
MsaG033552 AT3G06630.4 39.474 114 68 1 183 296 428 540 1.79e-21 94.7
MsaG033552 AT3G06630.3 39.474 114 68 1 183 296 428 540 1.79e-21 94.7
MsaG033552 AT3G06630.5 39.474 114 68 1 183 296 428 540 1.79e-21 94.7
MsaG033552 AT3G06630.6 39.474 114 68 1 183 296 344 456 1.92e-21 94.7
MsaG033552 AT1G67890.3 38.596 114 69 1 183 296 481 593 2.04e-21 94.7
MsaG033552 AT1G67890.2 38.596 114 69 1 183 296 481 593 2.04e-21 94.7
MsaG033552 AT3G06630.1 39.474 114 68 1 183 296 428 540 2.17e-21 94.7
MsaG033552 AT3G06630.7 39.474 114 68 1 183 296 428 540 2.21e-21 94.7
MsaG033552 AT3G06630.2 39.474 114 68 1 183 296 428 540 2.25e-21 94.7
MsaG033552 AT1G67890.4 38.596 114 69 1 183 296 353 465 2.27e-21 94.4
MsaG033552 AT5G03730.2 30.570 193 114 5 121 296 470 659 5.43e-21 93.6
MsaG033552 AT5G03730.1 30.570 193 114 5 121 296 470 659 5.43e-21 93.6
MsaG033552 AT4G23050.1 38.596 114 69 1 183 296 461 573 5.29e-20 90.5
MsaG033552 AT4G23050.2 38.596 114 69 1 183 296 462 574 5.65e-20 90.5
MsaG033552 AT3G25150.1 52.941 68 32 0 3 70 74 141 6.83e-20 89.7
MsaG033552 AT4G24480.2 35.714 140 84 3 159 296 642 777 7.86e-20 90.1
MsaG033552 AT3G25150.2 52.941 68 32 0 3 70 173 240 8.20e-20 89.7
MsaG033552 AT4G24480.3 35.714 140 84 3 159 296 642 777 8.62e-20 90.1
MsaG033552 AT4G24480.1 34.483 145 84 4 159 296 642 782 4.81e-18 84.7
MsaG033552 AT4G35780.1 40.476 126 70 2 170 295 277 397 5.55e-18 84.3
MsaG033552 AT2G17700.1 39.370 127 72 2 170 296 271 392 2.03e-17 82.8
MsaG033552 AT5G60980.2 50.746 67 33 0 4 70 71 137 1.32e-16 80.1
MsaG033552 AT5G60980.3 50.746 67 33 0 4 70 71 137 1.32e-16 80.1
MsaG033552 AT5G60980.4 50.746 67 33 0 4 70 71 137 1.33e-16 80.1
MsaG033552 AT5G60980.1 50.746 67 33 0 4 70 71 137 1.33e-16 80.1
MsaG033552 AT4G38470.3 38.136 118 68 2 178 295 283 395 3.13e-16 79.0
MsaG033552 AT4G38470.1 38.136 118 68 2 178 295 283 395 3.66e-16 79.0
MsaG033552 AT4G38470.2 38.136 118 68 2 178 295 283 395 4.04e-16 79.0
MsaG033552 AT2G31010.1 33.051 118 76 2 180 295 510 626 7.24e-14 72.4
MsaG033552 AT2G31010.2 33.051 118 76 2 180 295 510 626 7.24e-14 72.4
MsaG033552 AT5G48650.1 28.767 219 114 8 4 188 72 282 8.31e-14 71.6
MsaG033552 AT3G58640.1 32.203 118 77 2 180 295 544 660 9.86e-14 72.0
MsaG033552 AT3G58640.2 32.203 118 77 2 180 295 544 660 9.86e-14 72.0
MsaG033552 AT5G49470.2 34.737 95 61 1 183 277 482 575 1.67e-12 68.2
MsaG033552 AT1G62400.1 32.283 127 76 5 174 295 75 196 4.53e-11 63.5

Find 62 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCATATGACTTCTTCAATT+TGG 0.127781 6:-93041005 None:intergenic
TTCAGATATGTTGATGAAAA+TGG 0.160277 6:+93040736 MsaT033552.1:CDS
CTGGACCCTGGGAATCTTGC+TGG 0.282007 6:-93041295 None:intergenic
GGCTGTTTCCACAGTCATTA+TGG 0.285014 6:-93041274 None:intergenic
TTAAAGAAGTGCACAACATT+AGG 0.299689 6:-93042361 None:intergenic
GCATATGACTTCTTCAATTT+GGG 0.321329 6:-93041004 None:intergenic
CTATTCTGTCAACCTTCTTT+CGG 0.321731 6:+93040876 MsaT033552.1:CDS
AAAGAGCCTGATGTTGATAT+TGG 0.346345 6:+93040763 MsaT033552.1:CDS
CTGCACATCAAGTTTAAAAT+CGG 0.348129 6:-93042707 None:intergenic
TCTGTCACAATACATAAATA+TGG 0.382518 6:-93042400 None:intergenic
AATTCGTTGTCTTGGTCATC+GGG 0.391346 6:+93040620 MsaT033552.1:CDS
GAATTCGTTGTCTTGGTCAT+CGG 0.392280 6:+93040619 MsaT033552.1:CDS
GATACAGAGGCGATTTATAC+AGG 0.393571 6:+93042671 MsaT033552.1:intron
TTCCTTGCTTCTCTAGAGAA+AGG 0.419220 6:+93040691 MsaT033552.1:CDS
GACAAAAGAATCAGCGGAAT+GGG 0.422303 6:+93041317 MsaT033552.1:CDS
CGAAAGAAGGTTGACAGAAT+AGG 0.436847 6:-93040875 None:intergenic
TGCATCATATTACCATTGTC+AGG 0.439837 6:-93040799 None:intergenic
ACCCTCTTCTGTGAATCATT+AGG 0.451712 6:-93040967 None:intergenic
CATTACAGAATGTTGCAATA+AGG 0.453465 6:+93042175 MsaT033552.1:intron
CTAGCTTAAAGTAAAGAAAG+AGG 0.460440 6:+93041236 MsaT033552.1:intron
TGGTGGGGAATTCGTTGTCT+TGG 0.477522 6:+93040612 MsaT033552.1:CDS
ACAGAAGAGGGTCGATGGAT+TGG 0.486457 6:+93040978 MsaT033552.1:CDS
AACAACAACTTCAACTTCGA+TGG 0.488455 6:+93041340 MsaT033552.1:CDS
CTTGGTCATCGGGTTTATGA+CGG 0.490018 6:+93040630 MsaT033552.1:CDS
TTGGTCATCGGGTTTATGAC+GGG 0.490026 6:+93040631 MsaT033552.1:CDS
AGAACAGAGACTTACAATAG+AGG 0.491201 6:-93041026 None:intergenic
TGCACTAGATCTGTTCAAAT+CGG 0.492647 6:+93042227 MsaT033552.1:CDS
GGAATTTCATCAAGAACCTC+AGG 0.494127 6:-93040946 None:intergenic
GTGGATGCACAAGAGTCTTA+TGG 0.499964 6:+93040592 MsaT033552.1:CDS
TCCACAGTCATTATGGAGGA+TGG 0.509452 6:-93041267 None:intergenic
TTACCATTGTCAGGAGTGGC+AGG 0.511043 6:-93040790 None:intergenic
GGATATCCAATATCAACATC+AGG 0.515760 6:-93040769 None:intergenic
TTAAACTTGATGTGCAGAAA+CGG 0.524320 6:+93042713 MsaT033552.1:CDS
AAACAGCCAGCAAGATTCCC+AGG 0.527469 6:+93041289 MsaT033552.1:CDS
AGACAAAAGAATCAGCGGAA+TGG 0.528144 6:+93041316 MsaT033552.1:CDS
TCCTAATGATTCACAGAAGA+GGG 0.539960 6:+93040966 MsaT033552.1:CDS
CAATGGTAATATGATGCATA+AGG 0.545366 6:+93040804 MsaT033552.1:CDS
TGTGCAGAAACGGTTGCATA+TGG 0.559493 6:+93042723 MsaT033552.1:CDS
TTGTGACAGAGTTTCTTCCC+AGG 0.561615 6:+93042413 MsaT033552.1:CDS
GATTCACAGAAGAGGGTCGA+TGG 0.562567 6:+93040973 MsaT033552.1:CDS
TTCCTAATGATTCACAGAAG+AGG 0.574976 6:+93040965 MsaT033552.1:CDS
GTCACAATACATAAATATGG+AGG 0.580591 6:-93042397 None:intergenic
AGAATGTTGCAATAAGGATG+TGG 0.582517 6:+93042181 MsaT033552.1:intron
ACAACAACTTCAACTTCGAT+GGG 0.584285 6:+93041341 MsaT033552.1:CDS
TGATCAAGTGTCTGTTCCTG+AGG 0.596922 6:+93040930 MsaT033552.1:CDS
ATTGGCAAGTGTATTAATCG+TGG 0.598029 6:+93041375 MsaT033552.1:CDS
CGAGGAGACTTACATTGTCA+TGG 0.600574 6:-93041596 None:intergenic
CTACAGATTGAGATTATGCG+AGG 0.602525 6:+93042328 MsaT033552.1:intron
TGCACAAGAGTCTTATGGTG+GGG 0.612653 6:+93040597 MsaT033552.1:CDS
AGCCTTTCTCTAGAGAAGCA+AGG 0.613750 6:-93040693 None:intergenic
TATCCTGCCACTCCTGACAA+TGG 0.622322 6:+93040787 MsaT033552.1:CDS
TAATGCAGAGATCGTATCTG+TGG 0.623699 6:+93040573 MsaT033552.1:CDS
CATATTACCATTGTCAGGAG+TGG 0.623868 6:-93040794 None:intergenic
TCACAATACATAAATATGGA+GGG 0.625187 6:-93042396 None:intergenic
ATGCACAAGAGTCTTATGGT+GGG 0.626724 6:+93040596 MsaT033552.1:CDS
TCCATCCTCCATAATGACTG+TGG 0.631778 6:+93041266 MsaT033552.1:CDS
TACAGATTGAGATTATGCGA+GGG 0.632426 6:+93042329 MsaT033552.1:intron
TGTTTCCACAGTCATTATGG+AGG 0.659573 6:-93041271 None:intergenic
GGTCCAGACAAAAGAATCAG+CGG 0.663488 6:+93041311 MsaT033552.1:CDS
AACAGCCAGCAAGATTCCCA+GGG 0.672369 6:+93041290 MsaT033552.1:CDS
GATGCACAAGAGTCTTATGG+TGG 0.692528 6:+93040595 MsaT033552.1:CDS
TGTCATGGCAATCATCAACA+CGG 0.726105 6:-93041581 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 93040404 93042762 93040404 ID=MsaG033552
Chr6 mRNA 93040404 93042762 93040404 ID=MsaT033552.1;Parent=MsaG033552
Chr6 exon 93040404 93040409 93040404 ID=MsaT033552.1.exon1;Parent=MsaT033552.1
Chr6 CDS 93040404 93040409 93040404 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93040559 93040825 93040559 ID=MsaT033552.1.exon2;Parent=MsaT033552.1
Chr6 CDS 93040559 93040825 93040559 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93040872 93041033 93040872 ID=MsaT033552.1.exon3;Parent=MsaT033552.1
Chr6 CDS 93040872 93041033 93040872 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93041240 93041396 93041240 ID=MsaT033552.1.exon4;Parent=MsaT033552.1
Chr6 CDS 93041240 93041396 93041240 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93041562 93041605 93041562 ID=MsaT033552.1.exon5;Parent=MsaT033552.1
Chr6 CDS 93041562 93041605 93041562 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93042183 93042251 93042183 ID=MsaT033552.1.exon6;Parent=MsaT033552.1
Chr6 CDS 93042183 93042251 93042183 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93042334 93042434 93042334 ID=MsaT033552.1.exon7;Parent=MsaT033552.1
Chr6 CDS 93042334 93042434 93042334 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Chr6 exon 93042678 93042762 93042678 ID=MsaT033552.1.exon8;Parent=MsaT033552.1
Chr6 CDS 93042678 93042762 93042678 ID=cds.MsaT033552.1;Parent=MsaT033552.1
Gene Sequence

>MsaT033552.1

ATGGCTGGTTATAGTGAACTTAATGCAGAGATCGTATCTGTGGATGCACAAGAGTCTTATGGTGGGGAATTCGTTGTCTTGGTCATCGGGTTTATGACGGGAAATGATGACATTAAGCAGAAATTTACTCACTGTTTCTTCCTTGCTTCTCTAGAGAAAGGCTACTTTGTTTTGAATGATATTTTCAGATATGTTGATGAAAATGGAATCAAAGAGCCTGATGTTGATATTGGATATCCTGCCACTCCTGACAATGGTAATATGATGCATAAGTTGCCTATTCTGTCAACCTTCTTTCGGTGTCAAAACCTCAAGTCTACAATCCAGAAAATGATCAAGTGTCTGTTCCTGAGGTTCTTGATGAAATTCCTAATGATTCACAGAAGAGGGTCGATGGATTGGCATCCCAAATTGAAGAAGTCATATGCCTCTATTCTTAAAGTAAAGAAAGAGGTTGCAGTTCCATCCTCCATAATGACTGTGGAAACAGCCAGCAAGATTCCCAGGGTCCAGACAAAAGAATCAGCGGAATGGGAACAACAACTTCAACTTCGATGGGACCATCTTTTTATTGGCAAGTGTATTAATCGTGGTTCTTACAAAGATATTTTCCGTGTTGATGATTGCCATGACAATAATGTTGCAATAAGGATGTGGATAGACGAAGATGTCAATCGTGATGCACTAGATCTGTTCAAATCGGAAATTGAGATTATGCGAGGGCTGAAGCATCCTAATGTTGTGCACTTCTTTAAAGCAATTACTCTCCCTCCATATTTATGTATTGTGACAGAGTTTCTTCCCAGAGGCGATTTATACAGGCTGTTGCATTATTCCGATTTTAAACTTGATGTGCAGAAACGGTTGCATATGGCTCTTGATGTTGTATGA
Protein sequence

>MsaT033552.1

MAGYSELNAEIVSVDAQESYGGEFVVLVIGFMTGNDDIKQKFTHCFFLASLEKGYFVLNDIFRYVDENGIKEPDVDIGYPATPDNGNMMHKLPILSTFFRCQNLKSTIQKMIKCLFLRFLMKFLMIHRRGSMDWHPKLKKSYASILKVKKEVAVPSSIMTVETASKIPRVQTKESAEWEQQLQLRWDHLFIGKCINRGSYKDIFRVDDCHDNNVAIRMWIDEDVNRDALDLFKSEIEIMRGLKHPNVVHFFKAITLPPYLCIVTEFLPRGDLYRLLHYSDFKLDVQKRLHMALDVV*