AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG016443

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016443 MtrunA17_Chr3g0128781 98.397 312 4 1 1 312 1 311 0.0 629
MsaG016443 MtrunA17_Chr5g0432701 52.366 317 131 8 7 312 51 358 3.57e-94 283
MsaG016443 MtrunA17_Chr3g0107491 46.705 349 134 11 7 312 38 377 2.22e-87 266
MsaG016443 MtrunA17_Chr2g0329551 43.056 288 89 10 7 231 72 347 9.01e-51 173
MsaG016443 MtrunA17_Chr6g0463571 48.624 218 87 6 7 201 28 243 6.41e-48 162
MsaG016443 MtrunA17_Chr4g0036071 69.492 118 36 0 90 207 341 458 1.73e-46 164
MsaG016443 MtrunA17_Chr1g0156051 51.923 156 73 1 92 247 370 523 1.21e-29 118
MsaG016443 MtrunA17_Chr2g0316551 46.316 95 51 0 107 201 206 300 3.06e-19 87.0
MsaG016443 MtrunA17_Chr2g0325131 46.809 94 50 0 108 201 190 283 8.42e-18 82.8
MsaG016443 MtrunA17_Chr4g0040891 44.681 94 52 0 108 201 193 286 3.22e-17 80.9
MsaG016443 MtrunA17_Chr1g0202051 31.053 190 119 2 24 213 51 228 4.31e-17 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG016443 AT2G40620.1 51.057 331 98 11 5 288 32 345 9.11e-84 257
MsaG016443 AT1G06850.1 51.082 231 86 4 78 301 116 326 1.52e-68 217
MsaG016443 AT2G31370.5 46.275 255 86 7 7 215 58 307 1.07e-53 180
MsaG016443 AT2G31370.2 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT2G31370.4 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT2G31370.1 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT2G31370.7 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT2G31370.3 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT2G31370.6 46.275 255 86 7 7 215 58 307 1.30e-53 180
MsaG016443 AT1G06070.1 45.200 250 94 6 7 217 73 318 1.28e-51 176
MsaG016443 AT4G38900.2 72.174 115 32 0 92 206 377 491 2.13e-46 164
MsaG016443 AT4G38900.3 72.174 115 32 0 92 206 377 491 2.13e-46 164
MsaG016443 AT1G43700.1 54.070 172 63 4 70 227 142 311 2.47e-46 160
MsaG016443 AT4G38900.1 68.595 121 32 1 92 206 377 497 6.02e-44 158
MsaG016443 AT2G21230.4 57.447 141 59 1 66 206 328 467 3.97e-41 150
MsaG016443 AT2G21230.1 57.447 141 59 1 66 206 328 467 3.97e-41 150
MsaG016443 AT2G21230.3 54.422 147 60 2 66 206 328 473 3.57e-38 142
MsaG016443 AT2G21230.2 55.645 124 54 1 66 189 328 450 5.99e-34 129
MsaG016443 AT1G06850.2 64.835 91 31 1 78 167 116 206 1.59e-31 118
MsaG016443 AT2G12900.1 41.667 96 56 0 109 204 116 211 4.31e-19 85.5
MsaG016443 AT3G58120.1 46.237 93 50 0 109 201 202 294 1.42e-18 85.1
MsaG016443 AT2G42380.2 41.026 117 62 1 108 217 185 301 1.85e-18 84.7
MsaG016443 AT2G12940.1 37.500 112 69 1 92 203 132 242 7.25e-17 79.7
MsaG016443 AT2G13150.1 40.594 101 59 1 101 201 142 241 7.32e-17 79.3
MsaG016443 AT2G42380.5 42.857 84 48 0 107 190 184 267 1.76e-14 72.8
MsaG016443 AT3G58120.2 43.750 80 45 0 109 188 202 281 1.11e-13 70.5
MsaG016443 AT2G21235.1 38.776 98 59 1 109 206 359 455 3.35e-13 70.5
MsaG016443 AT2G42380.1 37.607 117 55 2 108 217 185 290 3.58e-12 66.2

Find 99 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATTCTATCGGCCAATTTC+AGG 0.184834 3:+97939995 MsaT016443.1:CDS
AACATGGTCCAAACGATCTT+AGG 0.241223 3:+97939865 MsaT016443.1:CDS
TTTGATTTGATTCAGGATTC+TGG 0.271099 3:+97937752 MsaT016443.1:intron
CAATGTCCAGCCCCTGAAAT+TGG 0.281734 3:-97940007 None:intergenic
CACAATTGAGCAAGTTTATC+AGG 0.289271 3:-97937631 None:intergenic
TTTCATTCCCTCTCATCTAA+TGG 0.291764 3:+97939906 MsaT016443.1:CDS
GTTGCGGTGGTGGTGGATCT+TGG 0.360501 3:-97937450 None:intergenic
AGGGGCTGGACATTGGCAAC+AGG 0.370603 3:+97940015 MsaT016443.1:CDS
AAGCTTGAGAATATGAAAAT+TGG 0.377609 3:-97939821 None:intergenic
TGCATGGCCCTAAGATCGTT+TGG 0.389186 3:-97939873 None:intergenic
CCATGCTGATACCTATGGTT+TGG 0.391118 3:+97939791 MsaT016443.1:CDS
AAAGACCTCTTGGCGCGTTT+AGG 0.396524 3:-97937664 None:intergenic
GGTCGAAATCGTCGGGGATT+CGG 0.403638 3:-97937384 None:intergenic
GAGTTTGGATCCGGAATTAT+CGG 0.405371 3:-97937506 None:intergenic
TTTGCATCAAAAGGCGTTGT+TGG 0.405645 3:-97940087 None:intergenic
CGACGATTTCGACCTCGAAA+TGG 0.407698 3:+97937393 MsaT016443.1:CDS
TACATCGATTCCGATAATTC+CGG 0.408499 3:+97937496 MsaT016443.1:CDS
CATGCTGATACCTATGGTTT+GGG 0.409516 3:+97939792 MsaT016443.1:CDS
TTAGTAAAATTTGCATCAAA+AGG 0.417524 3:-97940096 None:intergenic
AAACTGAGGCTGGTGGGGAC+TGG 0.421487 3:-97939931 None:intergenic
ACCCACTTCGTATGATTTGT+CGG 0.426091 3:+97939959 MsaT016443.1:CDS
GATTCTATCGGCCAATTTCA+GGG 0.428325 3:+97939996 MsaT016443.1:CDS
GTGGTGGTGGATCTTGGAAC+TGG 0.429585 3:-97937444 None:intergenic
TATCGGCCAATTTCAGGGGC+TGG 0.448809 3:+97940001 MsaT016443.1:CDS
GATAGGCTCAAGCTTGCTAC+TGG 0.454169 3:+97939756 MsaT016443.1:CDS
ATTGAGATCGACGGTGGAAC+GGG 0.455173 3:-97937348 None:intergenic
CATTGAAGAACGAAGTTGAT+AGG 0.457070 3:+97939739 MsaT016443.1:CDS
ATTTCGAGGTCGAAATCGTC+GGG 0.457489 3:-97937391 None:intergenic
TCTCATGTTCTGATGCCTGA+TGG 0.464397 3:+97940041 MsaT016443.1:CDS
GGCGGTAGGAGAATTGAGTT+TGG 0.473174 3:-97937521 None:intergenic
TAGCTTAGCTTGTTGCTCCA+TGG 0.487772 3:-97938712 None:intergenic
CTGATAAACTTGCTCAATTG+TGG 0.489201 3:+97937632 MsaT016443.1:CDS
ACAGAAACGGAGGGACCATC+AGG 0.491647 3:-97940056 None:intergenic
AGGAGAATTGAGTTTGGATC+CGG 0.498325 3:-97937515 None:intergenic
GGAATTGCTACGGCGGTGAC+CGG 0.499947 3:-97937551 None:intergenic
TCTTCTTCCTTGTTGTCTGA+AGG 0.501718 3:+97937583 MsaT016443.1:CDS
CCAACCCATGCTGATACCTA+TGG 0.503575 3:+97939786 MsaT016443.1:CDS
CAATTTCAGGGGCTGGACAT+TGG 0.506474 3:+97940008 MsaT016443.1:CDS
AGATCAAACTGAGGCTGGTG+GGG 0.510809 3:-97939936 None:intergenic
GTTCCACCGTCGATCTCAAT+CGG 0.512206 3:+97937351 MsaT016443.1:CDS
ATTATCGGAATCGATGTAAG+AGG 0.514373 3:-97937491 None:intergenic
ACATGGTCCAAACGATCTTA+GGG 0.515048 3:+97939866 MsaT016443.1:CDS
TAGATCAAACTGAGGCTGGT+GGG 0.518122 3:-97939937 None:intergenic
TCGTCGTGTTGTTGCGGTGG+TGG 0.518420 3:-97937460 None:intergenic
TCGTGTTGTTGCGGTGGTGG+TGG 0.524797 3:-97937457 None:intergenic
TCTCCTACCGCCGCTAATGC+CGG 0.526393 3:+97937532 MsaT016443.1:CDS
CATTTCGAGGTCGAAATCGT+CGG 0.531230 3:-97937392 None:intergenic
TGGGTAGATCAAACTGAGGC+TGG 0.537417 3:-97939941 None:intergenic
ACGGCGGTGACCGGCATTAG+CGG 0.537421 3:-97937542 None:intergenic
AAAATACCGAGTTGAAGCTT+CGG 0.538764 3:+97938682 MsaT016443.1:CDS
CGTTTGGACCATGTTGTGGT+TGG 0.540715 3:-97939857 None:intergenic
GTTATGTGGTTGAGCTTGAA+AGG 0.547036 3:+97937817 MsaT016443.1:CDS
CGGAGAAGCGTCGAAGTCGA+AGG 0.552256 3:-97937419 None:intergenic
ATGAAAATGTTGCATTTGCA+TGG 0.556228 3:-97939889 None:intergenic
GGGGCTGGACATTGGCAACA+GGG 0.559117 3:+97940016 MsaT016443.1:CDS
GATTGAGATCGACGGTGGAA+CGG 0.569204 3:-97937349 None:intergenic
CGGAATCGATGTAAGAGGAA+AGG 0.570255 3:-97937486 None:intergenic
AGGAGATCGTCGTGTTGTTG+CGG 0.570948 3:-97937466 None:intergenic
ATGTATCGGCGGAATTGCTA+CGG 0.574251 3:-97937561 None:intergenic
AGATCGTTTGGACCATGTTG+TGG 0.576424 3:-97939861 None:intergenic
AGAGAGGAAAGCTTGTTATG+TGG 0.577168 3:+97937803 MsaT016443.1:CDS
GACTGGATCCATTAGATGAG+AGG 0.584227 3:-97939914 None:intergenic
AGTCGAAGGGATCCATTTCG+AGG 0.586525 3:-97937405 None:intergenic
TTGGTGCATTCCCAAACCAT+AGG 0.592111 3:-97939802 None:intergenic
CAACAAGGAAGAAGATGTAT+CGG 0.593104 3:-97937575 None:intergenic
CCGCGGCGAGGTCGAAAGAG+AGG 0.593130 3:+97937787 MsaT016443.1:CDS
ACTGGATCCATTAGATGAGA+GGG 0.595904 3:-97939913 None:intergenic
GTAGATCAAACTGAGGCTGG+TGG 0.597370 3:-97939938 None:intergenic
TTCCGACAAATCATACGAAG+TGG 0.598591 3:-97939961 None:intergenic
ATTCTATCGGCCAATTTCAG+GGG 0.601347 3:+97939997 MsaT016443.1:CDS
GAAGCTTCGGTTACAAACCA+TGG 0.603767 3:+97938695 MsaT016443.1:CDS
ATGTTGTGGTTGGTGCATGA+AGG 0.606809 3:-97939847 None:intergenic
CAACAAGCTAAGCTATGTGA+TGG 0.613164 3:+97938720 MsaT016443.1:CDS
TTCGATTCCTTCAGACAACA+AGG 0.616363 3:-97937590 None:intergenic
GGAGAAGCGTCGAAGTCGAA+GGG 0.620947 3:-97937418 None:intergenic
TTGTAACCGAAGCTTCAACT+CGG 0.625038 3:-97938688 None:intergenic
AGATCGTCGTGTTGTTGCGG+TGG 0.629335 3:-97937463 None:intergenic
CTTGGCGCGTTTAGGATCAA+CGG 0.630373 3:-97937656 None:intergenic
CCTCTCTTTCGACCTCGCCG+CGG 0.634132 3:-97937787 None:intergenic
TCCGACAAATCATACGAAGT+GGG 0.636300 3:-97939960 None:intergenic
CCAAACCATAGGTATCAGCA+TGG 0.641882 3:-97939791 None:intergenic
TTCATGCACCAACCACAACA+TGG 0.648904 3:+97939849 MsaT016443.1:CDS
GGTGGATCTTGGAACTGGAG+CGG 0.658797 3:-97937439 None:intergenic
CGAATCGTCAATCCGCGGCG+AGG 0.660871 3:+97937775 MsaT016443.1:CDS
CCATAGGTATCAGCATGGGT+TGG 0.661247 3:-97939786 None:intergenic
CAAACCATAGGTATCAGCAT+GGG 0.662566 3:-97939790 None:intergenic
TTGATCCTAAACGCGCCAAG+AGG 0.666281 3:+97937659 MsaT016443.1:CDS
GCTCAAGCTTGCTACTGGAG+AGG 0.667501 3:+97939761 MsaT016443.1:CDS
CCTCCGATTGAGATCGACGG+TGG 0.668695 3:-97937354 None:intergenic
CAAGGAAGAAGATGTATCGG+CGG 0.669677 3:-97937572 None:intergenic
TGACCGGCATTAGCGGCGGT+AGG 0.676875 3:-97937535 None:intergenic
ATGTTGTCAAGTGATTCTAT+CGG 0.677885 3:+97939984 MsaT016443.1:CDS
TATCGGCGGAATTGCTACGG+CGG 0.692611 3:-97937558 None:intergenic
CCACCGTCGATCTCAATCGG+AGG 0.695045 3:+97937354 MsaT016443.1:CDS
GCGGTGACCGGCATTAGCGG+CGG 0.701383 3:-97937539 None:intergenic
GTACCTCCGATTGAGATCGA+CGG 0.703198 3:-97937357 None:intergenic
TTTCGAGGTCGAAATCGTCG+GGG 0.718515 3:-97937390 None:intergenic
TCTGGCGAATCGTCAATCCG+CGG 0.722384 3:+97937770 MsaT016443.1:CDS
GAAGTGGGTAGATCAAACTG+AGG 0.775188 3:-97939945 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 97937337 97940103 97937337 ID=MsaG016443
Chr3 mRNA 97937337 97940103 97937337 ID=MsaT016443.1;Parent=MsaG016443
Chr3 exon 97937337 97937680 97937337 ID=MsaT016443.1.exon1;Parent=MsaT016443.1
Chr3 CDS 97937337 97937680 97937337 ID=cds.MsaT016443.1;Parent=MsaT016443.1
Chr3 exon 97937767 97937899 97937767 ID=MsaT016443.1.exon2;Parent=MsaT016443.1
Chr3 CDS 97937767 97937899 97937767 ID=cds.MsaT016443.1;Parent=MsaT016443.1
Chr3 exon 97938657 97938741 97938657 ID=MsaT016443.1.exon3;Parent=MsaT016443.1
Chr3 CDS 97938657 97938741 97938657 ID=cds.MsaT016443.1;Parent=MsaT016443.1
Chr3 exon 97939727 97940103 97939727 ID=MsaT016443.1.exon4;Parent=MsaT016443.1
Chr3 CDS 97939727 97940103 97939727 ID=cds.MsaT016443.1;Parent=MsaT016443.1
Gene Sequence

>MsaT016443.1

ATGTCGTCGTTCCCGTTCCACCGTCGATCTCAATCGGAGGTACATTTCCGAATCCCCGACGATTTCGACCTCGAAATGGATCCCTTCGACTTCGACGCTTCTCCGCTCCAGTTCCAAGATCCACCACCACCGCAACAACACGACGATCTCCTTTCCTCTTACATCGATTCCGATAATTCCGGATCCAAACTCAATTCTCCTACCGCCGCTAATGCCGGTCACCGCCGTAGCAATTCCGCCGATACATCTTCTTCCTTGTTGTCTGAAGGAATCGAATCTAAGAAAGCTATGTCTCCTGATAAACTTGCTCAATTGTGGACCGTTGATCCTAAACGCGCCAAGAGGATTCTGGCGAATCGTCAATCCGCGGCGAGGTCGAAAGAGAGGAAAGCTTGTTATGTGGTTGAGCTTGAAAGGAAAATTCATACTCTTCAAACTGAAGCAACTACTCTTTCTGCTCAATTAAATCTTTTCCAGAGAGATACAACTGGTCTGTCAAGTGAAAATACCGAGTTGAAGCTTCGGTTACAAACCATGGAGCAACAAGCTAAGCTATGTGATGCTCTAAATGAAGCATTGAAGAACGAAGTTGATAGGCTCAAGCTTGCTACTGGAGAGGTACCAACCCATGCTGATACCTATGGTTTGGGAATGCACCAATTTTCATATTCTCAAGCTTCATCCTTCATGCACCAACCACAACATGGTCCAAACGATCTTAGGGCCATGCAAATGCAACATTTTCATTCCCTCTCATCTAATGGATCCAGTCCCCACCAGCCTCAGTTTGATCTACCCACTTCGTATGATTTGTCGGAAATGTTGTCAAGTGATTCTATCGGCCAATTTCAGGGGCTGGACATTGGCAACAGGGTTTCTCATGTTCTGATGCCTGATGGTCCCTCCGTTTCTGTTAATAAAACCAACAACGCCTTTTGA
Protein sequence

>MsaT016443.1

MSSFPFHRRSQSEVHFRIPDDFDLEMDPFDFDASPLQFQDPPPPQQHDDLLSSYIDSDNSGSKLNSPTAANAGHRRSNSADTSSSLLSEGIESKKAMSPDKLAQLWTVDPKRAKRILANRQSAARSKERKACYVVELERKIHTLQTEATTLSAQLNLFQRDTTGLSSENTELKLRLQTMEQQAKLCDALNEALKNEVDRLKLATGEVPTHADTYGLGMHQFSYSQASSFMHQPQHGPNDLRAMQMQHFHSLSSNGSSPHQPQFDLPTSYDLSEMLSSDSIGQFQGLDIGNRVSHVLMPDGPSVSVNKTNNAF*