AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001449

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001449 MtrunA17_Chr1g0163181 74.066 455 86 5 1 440 1 438 0.0 671
MsaG001449 MtrunA17_Chr1g0163201 71.096 429 67 5 20 438 18 399 0.0 566
MsaG001449 MtrunA17_Chr1g0163251 53.039 362 119 4 1 345 1 328 1.12e-119 354
MsaG001449 MtrunA17_Chr1g0163151 66.932 251 51 2 185 432 1 222 3.06e-113 331
MsaG001449 MtrunA17_Chr1g0163111 66.270 252 60 5 185 433 1 230 9.21e-108 318
MsaG001449 MtrunA17_Chr1g0163261 43.438 320 140 5 1 307 1 292 1.93e-81 253
MsaG001449 MtrunA17_Chr1g0163231 44.904 314 126 8 1 300 1 281 5.11e-79 247
MsaG001449 MtrunA17_Chr1g0163191 74.860 179 25 2 1 179 1 159 8.92e-78 238
MsaG001449 MtrunA17_Chr1g0171611 44.762 315 113 8 1 300 1 269 1.78e-75 237
MsaG001449 MtrunA17_Chr1g0163241 59.322 177 36 3 1 176 7 148 2.98e-58 188
MsaG001449 MtrunA17_Chr6g0476171 34.672 274 141 6 166 431 2 245 6.51e-42 149
MsaG001449 MtrunA17_Chr1g0162151 36.255 251 108 6 185 429 1 205 3.77e-39 140
MsaG001449 MtrunA17_Chr1g0208771 27.409 467 261 16 20 430 12 456 2.59e-38 144
MsaG001449 MtrunA17_Chr1g0163131 32.333 300 184 10 5 297 19 306 2.83e-37 138
MsaG001449 MtrunA17_Chr1g0163131 38.750 160 81 7 289 433 151 308 9.76e-21 92.4
MsaG001449 MtrunA17_Chr8g0390841 25.726 482 280 15 14 430 48 516 1.44e-36 140
MsaG001449 MtrunA17_Chr7g0233561 31.988 322 180 11 9 308 18 322 6.88e-35 132
MsaG001449 MtrunA17_Chr3g0131891 31.399 293 176 8 14 298 28 303 2.21e-32 125
MsaG001449 MtrunA17_Chr1g0163091 43.182 132 70 1 185 311 1 132 2.99e-32 120
MsaG001449 MtrunA17_Chr7g0233541 31.959 291 173 9 21 298 2 280 5.91e-31 120
MsaG001449 MtrunA17_Chr7g0233521 32.281 285 163 9 21 298 2 263 6.52e-31 120
MsaG001449 MtrunA17_Chr1g0163101 48.246 114 56 2 14 127 26 136 1.40e-28 110
MsaG001449 MtrunA17_Chr7g0233531 32.867 286 160 10 21 298 2 263 2.58e-27 110
MsaG001449 MtrunA17_Chr3g0103171 27.143 280 181 8 20 296 5 264 2.07e-25 104
MsaG001449 MtrunA17_Chr1g0162161 42.727 110 60 2 21 130 4 110 4.44e-25 100
MsaG001449 MtrunA17_Chr1g0163071 25.243 309 201 7 21 310 2 299 6.57e-25 104
MsaG001449 MtrunA17_Chr1g0163121 45.536 112 58 2 19 130 9 117 7.28e-25 99.8
MsaG001449 MtrunA17_Chr3g0103181 25.256 293 188 8 9 296 12 278 2.87e-24 101
MsaG001449 MtrunA17_Chr4g0067431 27.362 307 193 9 9 296 15 310 3.95e-24 102
MsaG001449 MtrunA17_Chr6g0476181 41.600 125 66 3 21 144 2 120 2.87e-23 95.9
MsaG001449 MtrunA17_Chr1g0163081 40.909 110 62 2 21 130 6 112 1.37e-22 93.6
MsaG001449 MtrunA17_Chr1g0163221 28.912 294 174 9 14 296 20 289 1.72e-21 95.5
MsaG001449 MtrunA17_Chr7g0233571 30.804 224 139 7 1 215 1 217 2.53e-21 92.0
MsaG001449 MtrunA17_Chr3g0103151 37.815 119 68 3 9 123 12 128 8.17e-20 86.3
MsaG001449 MtrunA17_Chr1g0163141 42.000 100 57 1 17 116 7 105 1.50e-19 86.3
MsaG001449 MtrunA17_Chr3g0103191 31.548 168 105 5 9 168 12 177 7.24e-19 85.9
MsaG001449 MtrunA17_Chr5g0419201 34.074 135 82 2 14 141 25 159 5.23e-18 82.0
MsaG001449 MtrunA17_Chr1g0163161 42.105 95 52 2 33 127 1 92 9.15e-18 79.7
MsaG001449 MtrunA17_Chr6g0467351 35.000 120 70 3 13 124 23 142 3.49e-15 74.7
MsaG001449 MtrunA17_Chr1g0154041 23.659 317 191 10 17 286 27 339 3.93e-14 74.3
MsaG001449 MtrunA17_Chr4g0033961 36.634 101 58 2 7 101 4 104 3.24e-13 71.2
MsaG001449 MtrunA17_Chr1g0162441 34.234 111 66 3 7 110 5 115 1.34e-12 69.3
MsaG001449 MtrunA17_Chr5g0419211 32.632 95 63 1 219 312 10 104 5.66e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001449 AT3G18990.2 26.023 342 200 10 7 301 4 339 5.15e-22 97.4
MsaG001449 AT3G18990.1 26.254 339 197 10 7 298 4 336 9.24e-22 96.3

Find 74 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATTAGCTGTGCTTCTTTA+AGG 0.068553 1:-20248487 None:intergenic
TTTGCAAAGCCTTTCAAATA+TGG 0.180110 1:-20250701 MsaT001449.1:CDS
AAATATCTTGGAGTTGAAAA+TGG 0.201158 1:-20248686 MsaT001449.1:CDS
TATTTCTCCACATATTTCTT+TGG 0.248757 1:+20250836 None:intergenic
TTCATCAACTGATTTGATAT+TGG 0.261684 1:+20250595 None:intergenic
CATTAACAGCTTCAGATCTT+AGG 0.270045 1:+20249988 None:intergenic
AGAAATATGTGGAGAAATAT+TGG 0.281812 1:-20250832 MsaT001449.1:CDS
TGGAGAGTAATGGTGATATT+TGG 0.287546 1:-20250745 MsaT001449.1:CDS
TTAATGGAACTACAACAATA+AGG 0.294713 1:-20249795 MsaT001449.1:CDS
GTGTTTGATGTTTCAATTGT+AGG 0.300485 1:-20248517 MsaT001449.1:CDS
CTCTTAACTTTCAAATTCAT+TGG 0.314459 1:-20250674 MsaT001449.1:CDS
ATAGTAACATTGAATGAAAT+TGG 0.319993 1:+20249625 None:intergenic
TTAGGAAACTTAAGGAATAT+AGG 0.322895 1:+20250794 None:intergenic
AGAAAACCTAGTGATTTCTT+TGG 0.323706 1:+20249577 None:intergenic
AGAGCAATACCCTTTACTTT+TGG 0.331691 1:+20249386 None:intergenic
CCTAGTGATTTCTTTGGCTT+TGG 0.332979 1:+20249583 None:intergenic
CTGGTCCTTTGAGTTTGCTT+TGG 0.341746 1:+20250410 None:intergenic
TAGGAAACTTAAGGAATATA+GGG 0.346499 1:+20250795 None:intergenic
TGTTCTCTTGAAAACTCATT+TGG 0.346666 1:+20249829 None:intergenic
AATATCTTGGAGTTGAAAAT+GGG 0.359463 1:-20248685 MsaT001449.1:CDS
TAATGGAACTACAACAATAA+GGG 0.368234 1:-20249794 MsaT001449.1:CDS
ACTTTCTTCACCTTCTTCAA+TGG 0.380996 1:+20250472 None:intergenic
TCATGATTCATAAACTCCTT+TGG 0.383485 1:+20248709 None:intergenic
TATGAATCATGAAAATATCT+TGG 0.394934 1:-20248698 MsaT001449.1:CDS
ATAGTTTATTTCTAAAGTAT+TGG 0.406626 1:+20250619 None:intergenic
CCTTAAAGAAGCACAGCTAA+TGG 0.407485 1:+20248487 None:intergenic
CAACGCCGTTAGGAAACTTA+AGG 0.408115 1:+20250786 None:intergenic
GTGGTGGATGGAAAATATTC+AGG 0.420444 1:-20249705 MsaT001449.1:CDS
AAAGAATGCAAAGTGGAGAT+TGG 0.431700 1:-20248580 MsaT001449.1:CDS
AAATATTATGAGAGTCTTTG+TGG 0.437608 1:-20248637 MsaT001449.1:CDS
AGTCTTTGTGGCTGTAAGTT+CGG 0.438865 1:-20248625 MsaT001449.1:CDS
AAGATGATCCTATGAAAATC+TGG 0.438926 1:+20251000 None:intergenic
CAAACTCAAAGGACCAGAAA+TGG 0.451853 1:-20250404 MsaT001449.1:CDS
TTAACTTTCAAATTCATTGG+TGG 0.475675 1:-20250671 MsaT001449.1:CDS
AGGAGCCATCCAAAAGTAAA+GGG 0.477165 1:-20249395 MsaT001449.1:intron
TAGGAGCCATCCAAAAGTAA+AGG 0.478853 1:-20249396 MsaT001449.1:CDS
CAAAGTGGCCATGGTAAAGA+AGG 0.488314 1:-20250021 MsaT001449.1:CDS
TGAAAATGGGGAGAAAATCA+TGG 0.492046 1:-20248672 MsaT001449.1:CDS
TGACATTATAACTTCAAAAG+AGG 0.495408 1:+20249959 None:intergenic
TGTGGCTGTAAGTTCGGTAA+AGG 0.504977 1:-20248619 MsaT001449.1:CDS
AAGACATTGGCGGAACATCT+AGG 0.506064 1:-20249415 MsaT001449.1:CDS
GCTGTAAGTTCGGTAAAGGT+TGG 0.518813 1:-20248615 MsaT001449.1:CDS
AAGAGATATCCATATTTGAA+AGG 0.520085 1:+20250692 None:intergenic
AATGGCAAGAGAAAATTCTC+AGG 0.523324 1:-20250386 MsaT001449.1:intron
GACATTATAACTTCAAAAGA+GGG 0.525934 1:+20249960 None:intergenic
GAAGGAGCACAAGACATTCA+AGG 0.537945 1:-20248960 MsaT001449.1:CDS
AATATCAAATCAGTTGATGA+AGG 0.540855 1:-20250593 MsaT001449.1:CDS
GATGAGGAAGCCATTGAAGA+AGG 0.544836 1:-20250482 MsaT001449.1:CDS
CCAAAGCCAAAGAAATCACT+AGG 0.556666 1:-20249583 MsaT001449.1:intron
CAATAAGGGTTGGTAATGAA+AGG 0.558627 1:-20249780 MsaT001449.1:CDS
TACAGAAGGTCGTGATGTGA+AGG 0.563378 1:-20248978 MsaT001449.1:intron
ATATTCCTTAAGTTTCCTAA+CGG 0.565521 1:-20250791 MsaT001449.1:CDS
AAGTGATGAATCAAGTGATG+AGG 0.567308 1:-20250498 MsaT001449.1:CDS
AGGTAGTAACAAAGTGGCCA+TGG 0.577811 1:-20250030 MsaT001449.1:CDS
ACTTACAAAGAAATAGCCAT+TGG 0.583056 1:+20249926 None:intergenic
AATATTGTATGGGTGGTGGA+TGG 0.587908 1:-20249717 MsaT001449.1:CDS
GAGTAATGAGAGTTCAGATG+AGG 0.591415 1:-20250441 MsaT001449.1:CDS
GAGGGTTCCAAAGAAATATG+TGG 0.594786 1:-20250843 MsaT001449.1:CDS
GTTGTAAAGAAGCAAGACAT+TGG 0.594884 1:-20249428 MsaT001449.1:CDS
GGAACTACAACAATAAGGGT+TGG 0.596420 1:-20249790 MsaT001449.1:CDS
GTATCTGCAGTGTGTACCAA+AGG 0.598126 1:-20248725 MsaT001449.1:intron
ATGTCACAATCTTACGCCAA+TGG 0.605717 1:-20249942 MsaT001449.1:CDS
GGTTGGTAATGAAAGGAGTG+TGG 0.605745 1:-20249773 MsaT001449.1:CDS
GTAAAGAAGCAAGACATTGG+CGG 0.609258 1:-20249425 MsaT001449.1:CDS
GTAAATTCGAGATGATTCAA+CGG 0.615228 1:-20249651 MsaT001449.1:CDS
TATGTGGAGAAATATTGGAA+AGG 0.617787 1:-20250827 MsaT001449.1:CDS
ATTCATGAAAGAATGCAAAG+TGG 0.625279 1:-20248587 MsaT001449.1:CDS
TTTCGTGAAGAACAAAACCC+CGG 0.628138 1:-20248936 MsaT001449.1:intron
ATATCTTGGAGTTGAAAATG+GGG 0.639227 1:-20248684 MsaT001449.1:CDS
GGTGCTGAAGACACAGAAGA+GGG 0.652982 1:-20250572 MsaT001449.1:CDS
AAATACCAAAGCAAACTCAA+AGG 0.654830 1:-20250415 MsaT001449.1:CDS
AGGTGCTGAAGACACAGAAG+AGG 0.658114 1:-20250573 MsaT001449.1:CDS
GGAGTGTGGAAGTGAGTGTG+AGG 0.659449 1:-20249759 MsaT001449.1:CDS
CTTGGCAGGTAGTAACAAAG+TGG 0.671173 1:-20250036 MsaT001449.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 20248489 20251040 20248489 ID=MsaG001449
Chr1 mRNA 20248489 20251040 20248489 ID=MsaT001449.1;Parent=MsaG001449
Chr1 exon 20248489 20248737 20248489 ID=MsaT001449.1.exon7;Parent=MsaT001449.1
Chr1 CDS 20248489 20248737 20248489 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20248937 20248995 20248937 ID=MsaT001449.1.exon6;Parent=MsaT001449.1
Chr1 CDS 20248937 20248995 20248937 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20249396 20249482 20249396 ID=MsaT001449.1.exon5;Parent=MsaT001449.1
Chr1 CDS 20249396 20249482 20249396 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20249584 20249857 20249584 ID=MsaT001449.1.exon4;Parent=MsaT001449.1
Chr1 CDS 20249584 20249857 20249584 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20249932 20250050 20249932 ID=MsaT001449.1.exon3;Parent=MsaT001449.1
Chr1 CDS 20249932 20250050 20249932 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20250387 20250864 20250387 ID=MsaT001449.1.exon2;Parent=MsaT001449.1
Chr1 CDS 20250387 20250864 20250387 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Chr1 exon 20250984 20251040 20250984 ID=MsaT001449.1.exon1;Parent=MsaT001449.1
Chr1 CDS 20250984 20251040 20250984 ID=cds.MsaT001449.1;Parent=MsaT001449.1
Gene Sequence

>MsaT001449.1

ATGTCATTTCAATATATTCCAGATTTTCATAGGATCATCTTGCAAGATAAGAAACTTAGGGTTCCAAAGAAATATGTGGAGAAATATTGGAAAGGAATATCAAACCCTATATTCCTTAAGTTTCCTAACGGCGTTGAACAAAAAATATTTTGGGTGGAGAGTAATGGTGATATTTGGTTTCAAAAAAATTGGGAAAATTTTGCAAAGCCTTTCAAATATGGATATCTCTTAACTTTCAAATTCATTGGTGGATCATATTTTAAGGTTAAGATATTTGGTGCCAATACTTTAGAAATAAACTATTCCAATATCAAATCAGTTGATGAAGGTGCTGAAGACACAGAAGAGGGTAAAGAAAGAGATGAATCAAGTGATGATGAAGTCACAAAAGAAGCTCAAGAAAGTGATGAATCAAGTGATGAGGAAGCCATTGAAGAAGGTGAAGAAAGTGATGAAGAGAGTAATGAGAGTTCAGATGAGGTTGAAATACCAAAGCAAACTCAAAGGACCAGAAATGGCAAGAGAAAATTCTCAGGTAGTAACAAAGTGGCCATGGTAAAGAAGGCTAGAAAATGCCTAAGATCTGAAGCTGTTAATGAGAATCCCTCTTTTGAAGTTATAATGTCACAATCTTACGCCAATGGCTATTTCTTTTGGATACCAAATGAGTTTTCAAGAGAACACTTGAAAGATTTTAATGGAACTACAACAATAAGGGTTGGTAATGAAAGGAGTGTGGAAGTGAGTGTGAGGTATTATGATACCCAGAAAAAATATTGTATGGGTGGTGGATGGAAAATATTCAGGCAAAAATATAATTTGCAAGTTGATGATGTTTGTAAATTCGAGATGATTCAACGGAGACCAATTTCATTCAATGTTACTATTACTCGTGCCAAAAACGAACCAAAGCCAAAGAAATCACTAGGTTATAAAAAAGGGGTCTCTTGTGGTAATAGTGTTGTAAAGAAGCAAGACATTGGCGGAACATCTAGGAGCCATCCAAAAGTAAAGGAAGGTCGTGATGTGAAGGAGCACAAGACATTCAAGGTTTTCGTGAAGAACAAAACCCCGTGTGTACCAAAGGAGTTTATGAATCATGAAAATATCTTGGAGTTGAAAATGGGGAGAAAATCATGGTTTGTAAAAGTCAAATATTATGAGAGTCTTTGTGGCTGTAAGTTCGGTAAAGGTTGGAGAAAATTCATGAAAGAATGCAAAGTGGAGATTGGAGATACTTGTCTCTTCAAGTTAATTGATGAAAGAAATTTTGTGTTTGATGTTTCAATTGTAGGAAAGAATCCATTAGCTGTGCTTCTTTAA
Protein sequence

>MsaT001449.1

MSFQYIPDFHRIILQDKKLRVPKKYVEKYWKGISNPIFLKFPNGVEQKIFWVESNGDIWFQKNWENFAKPFKYGYLLTFKFIGGSYFKVKIFGANTLEINYSNIKSVDEGAEDTEEGKERDESSDDEVTKEAQESDESSDEEAIEEGEESDEESNESSDEVEIPKQTQRTRNGKRKFSGSNKVAMVKKARKCLRSEAVNENPSFEVIMSQSYANGYFFWIPNEFSREHLKDFNGTTTIRVGNERSVEVSVRYYDTQKKYCMGGGWKIFRQKYNLQVDDVCKFEMIQRRPISFNVTITRAKNEPKPKKSLGYKKGVSCGNSVVKKQDIGGTSRSHPKVKEGRDVKEHKTFKVFVKNKTPCVPKEFMNHENILELKMGRKSWFVKVKYYESLCGCKFGKGWRKFMKECKVEIGDTCLFKLIDERNFVFDVSIVGKNPLAVLL*