AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG039628

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039628 MtrunA17_Chr1g0203051 58.759 274 101 2 1 274 1 262 4.88e-104 327
MsaG039628 MtrunA17_Chr1g0203051 58.974 117 48 0 276 392 505 621 1.08e-39 153
MsaG039628 MtrunA17_Chr8g0389811 47.826 138 72 0 65 202 58 195 6.03e-43 152
MsaG039628 MtrunA17_Chr2g0331371 45.736 129 70 0 71 199 35 163 5.88e-31 119
MsaG039628 MtrunA17_Chr2g0287651 31.795 195 129 2 82 273 66 259 2.99e-29 123
MsaG039628 MtrunA17_Chr2g0287651 37.226 137 84 1 271 405 496 632 8.51e-20 93.6
MsaG039628 MtrunA17_Chr2g0308841 39.535 129 78 0 276 404 98 226 1.02e-28 115
MsaG039628 MtrunA17_Chr6g0473421 47.917 96 50 0 71 166 35 130 2.49e-27 107
MsaG039628 MtrunA17_Chr1g0171741 32.719 217 135 5 10 221 52 262 2.72e-27 111
MsaG039628 MtrunA17_Chr1g0172931 43.636 110 62 0 64 173 49 158 1.93e-21 91.3
MsaG039628 MtrunA17_Chr8g0340801 51.389 72 35 0 202 273 1 72 1.51e-20 87.0
MsaG039628 MtrunA17_Chr2g0290391 27.136 199 130 4 103 287 63 260 7.07e-17 84.3
MsaG039628 MtrunA17_Chr1g0198761 34.307 137 80 4 103 230 59 194 1.60e-14 77.0
MsaG039628 MtrunA17_Chr2g0276841 29.167 192 122 7 97 280 76 261 2.48e-14 76.3
MsaG039628 MtrunA17_Chr6g0458391 35.385 130 82 2 276 405 638 765 3.04e-14 75.9
MsaG039628 MtrunA17_Chr6g0458391 24.737 190 113 6 103 266 103 288 5.97e-11 65.5
MsaG039628 MtrunA17_Chr5g0448511 36.364 132 77 3 277 405 270 397 4.17e-14 75.1
MsaG039628 MtrunA17_Chr5g0448761 28.402 169 112 2 250 418 479 638 5.15e-14 75.1
MsaG039628 MtrunA17_Chr5g0448761 28.571 154 108 2 97 248 66 219 4.20e-11 65.9
MsaG039628 MtrunA17_Chr7g0228061 42.391 92 41 3 481 561 4 94 1.54e-13 66.6
MsaG039628 MtrunA17_Chr3g0118611 28.994 169 105 3 277 438 374 534 4.51e-12 68.9
MsaG039628 MtrunA17_Chr7g0258861 28.025 157 111 2 105 261 24 178 1.21e-11 65.9
MsaG039628 MtrunA17_Chr5g0440451 33.333 135 79 5 277 406 477 605 3.65e-11 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039628 AT5G28530.1 29.442 197 122 5 103 284 67 261 4.25e-19 91.7
MsaG039628 AT5G28530.3 29.442 197 122 5 103 284 67 261 5.45e-19 91.3
MsaG039628 AT5G28530.2 29.442 197 122 5 103 284 67 261 5.45e-19 91.3
MsaG039628 AT5G28530.4 33.094 139 90 2 103 239 67 204 9.33e-19 90.5
MsaG039628 AT5G28530.5 33.094 139 90 2 103 239 67 204 1.02e-18 90.1
MsaG039628 AT1G10240.2 28.495 186 119 7 103 280 60 239 8.45e-14 74.7
MsaG039628 AT1G10240.1 28.495 186 119 7 103 280 60 239 8.45e-14 74.7
MsaG039628 AT2G27110.2 29.771 131 91 1 278 408 453 582 1.64e-12 70.9
MsaG039628 AT2G27110.1 29.771 131 91 1 278 408 453 582 1.64e-12 70.9
MsaG039628 AT2G27110.3 29.771 131 91 1 278 408 308 437 2.11e-12 70.5
MsaG039628 AT4G38180.1 26.022 269 175 8 30 287 13 268 4.77e-12 69.3
MsaG039628 AT4G38180.1 31.061 132 90 1 277 408 507 637 7.41e-12 68.9
MsaG039628 AT4G38170.1 32.558 129 86 1 277 405 272 399 7.71e-11 65.1

Find 111 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTGAACTATTAGCATTT+TGG 0.162179 7:-91242697 None:intergenic
TGAATGCTCTTGCAAGAAAT+TGG 0.233397 7:+91242553 MsaT039628.1:CDS
ATTCAAATGTTAATCGTTCT+TGG 0.236261 7:-91242535 None:intergenic
CCTCCACATATTCCACATTT+AGG 0.243012 7:-91243013 None:intergenic
CAACTAGACGATCCGGAAAA+TGG 0.297337 7:-91241029 None:intergenic
ATAAAAGTCTTGTTCATGAT+TGG 0.343920 7:-91243095 None:intergenic
CGTTCCATCACAACAGATTC+CGG 0.349478 7:-91242641 None:intergenic
TGCAAGAAATTGGAGACATT+TGG 0.353006 7:+91242563 MsaT039628.1:CDS
AAAATCTAGGATATTCAAAA+AGG 0.354570 7:+91241469 MsaT039628.1:CDS
CTTTGAGAAAATTAATTTCA+AGG 0.360382 7:+91240978 MsaT039628.1:CDS
ATTCCTACGACACGTATCTA+TGG 0.360811 7:+91241417 MsaT039628.1:CDS
TCGAATGTGAGCAACAAAAC+TGG 0.360815 7:+91240654 MsaT039628.1:CDS
AACTAGTAGGTGTGGGTGTA+TGG 0.373550 7:+91241224 MsaT039628.1:CDS
TTTATAATGATAACGAAGAT+TGG 0.374615 7:+91243113 MsaT039628.1:CDS
GATAACATCTTTAGCACGTT+TGG 0.378115 7:-91242669 None:intergenic
CCTAAGCTTCTTCCTGTCTC+TGG 0.383822 7:-91242905 None:intergenic
GGTTGTGTGCACGGATTTGC+TGG 0.387480 7:+91241075 MsaT039628.1:CDS
AAGACTGAGTTTCTTCTTGA+CGG 0.400617 7:-91243066 None:intergenic
TAGGTAATCCGCAGCGGCTT+AGG 0.401304 7:+91242924 MsaT039628.1:CDS
GCGGATTATGCATCTTCCTT+TGG 0.402484 7:+91242308 MsaT039628.1:CDS
CATGAACATAAGAAAATTGC+CGG 0.402534 7:+91242622 MsaT039628.1:CDS
AGACATTGGAATCATTCAAC+AGG 0.413806 7:+91242852 MsaT039628.1:CDS
GACGCGTACAATTCGATGTA+TGG 0.424856 7:+91240913 MsaT039628.1:CDS
CCAGAGACAGGAAGAAGCTT+AGG 0.436591 7:+91242905 MsaT039628.1:CDS
CATACACAAAACCATGGAAA+TGG 0.443226 7:+91242814 MsaT039628.1:CDS
CTTGGACAGTGGCTCTTGTT+CGG 0.451115 7:+91240855 MsaT039628.1:CDS
ACCCTAGAGATGACATTCAT+TGG 0.451440 7:+91242498 MsaT039628.1:CDS
TTTGTTGTGGGTCCAGAGAC+AGG 0.453635 7:+91242893 MsaT039628.1:CDS
TGTGGAATATGTGGAGGAAA+GGG 0.458368 7:+91243019 MsaT039628.1:CDS
ATGAAAGCAATGAGAAATGC+TGG 0.465180 7:+91241393 MsaT039628.1:CDS
GTGTTCCTCGGATGATGATA+TGG 0.470919 7:+91240888 MsaT039628.1:CDS
CAGTTTCGATGATGAATTTG+CGG 0.474720 7:+91240939 MsaT039628.1:CDS
AACTACGTATGTTATGTTTG+TGG 0.474919 7:+91242739 MsaT039628.1:CDS
TGCATTTCGAGTTGAAGAAT+CGG 0.477767 7:-91242966 None:intergenic
TGTTTGTGGAGCGTTGTAAG+AGG 0.478007 7:+91242753 MsaT039628.1:CDS
CGAATGTGAGCAACAAAACT+GGG 0.478717 7:+91240655 MsaT039628.1:CDS
TGAACAACACACTGAGACAT+TGG 0.486156 7:+91242838 MsaT039628.1:CDS
AACAATTCAAGGAGAGGGAG+AGG 0.489995 7:+91241505 MsaT039628.1:CDS
ATGCTAATAGTTCAAGTCAC+CGG 0.492201 7:+91242702 MsaT039628.1:CDS
TCACTCATCTTTCTATGTGC+AGG 0.492964 7:-91241354 None:intergenic
GTGTTGTTCAACCATTTCCA+TGG 0.494823 7:-91242825 None:intergenic
GTTGATGAGATGTTTGTTGT+GGG 0.500261 7:+91242881 MsaT039628.1:CDS
AACAGCTACGATATGTTCAC+AGG 0.501838 7:-91242591 None:intergenic
GTCCAATGAATGTCATCTCT+AGG 0.502363 7:-91242500 None:intergenic
AATGTACAATGAACAATTCA+AGG 0.507358 7:+91241494 MsaT039628.1:CDS
CGACAAGCTCTCTCCAATAC+AGG 0.511257 7:-91242416 None:intergenic
GCCTTTGTTTGTCATAGAGA+AGG 0.513837 7:+91241147 MsaT039628.1:CDS
CAGCTGCAAAACAGTATACA+AGG 0.514991 7:+91242372 MsaT039628.1:CDS
GAGAGCACAAGCCAACTAGT+AGG 0.519908 7:+91241211 MsaT039628.1:CDS
TCGTTGTAAAATCGAAGAAA+AGG 0.521997 7:+91242436 MsaT039628.1:CDS
TTGAATGCAACTAGACGATC+CGG 0.524208 7:-91241036 None:intergenic
AGTTGATGAGATGTTTGTTG+TGG 0.524352 7:+91242880 MsaT039628.1:CDS
AATATGTACGGTTGTGTGCA+CGG 0.528502 7:+91241066 MsaT039628.1:CDS
TATTGACATTCCTTGCATCC+CGG 0.536602 7:-91241173 None:intergenic
ATGTGGAATATGTGGAGGAA+AGG 0.540284 7:+91243018 MsaT039628.1:CDS
CACAAGCCAACTAGTAGGTG+TGG 0.542797 7:+91241216 MsaT039628.1:CDS
TCCAATGAATGTCATCTCTA+GGG 0.545127 7:-91242499 None:intergenic
CATAGGTGTGGAAGGTTCAG+AGG 0.545355 7:+91240704 MsaT039628.1:CDS
CGAAGATTGGAACATTCCTA+TGG 0.546117 7:+91243126 MsaT039628.1:CDS
TGCTAATAGTTCAAGTCACC+GGG 0.550074 7:+91242703 MsaT039628.1:CDS
CCGCAGCGGCTTAGGAAAAG+AGG 0.554134 7:+91242932 MsaT039628.1:CDS
TGTTAGATACAGAGAAATAG+AGG 0.558009 7:+91242286 MsaT039628.1:intron
TGAAGCAGTTGAATTTCTGA+AGG 0.558669 7:+91241545 MsaT039628.1:CDS
GAGAAGGTCACCGGGATGCA+AGG 0.560242 7:+91241163 MsaT039628.1:CDS
ACGCGTACAATTCGATGTAT+GGG 0.566673 7:+91240914 MsaT039628.1:CDS
ATACACCCACACCTACTAGT+TGG 0.569760 7:-91241222 None:intergenic
ACAACTGCGGAAGGCAACAT+AGG 0.571663 7:+91240687 MsaT039628.1:CDS
GAAGGCAACACAACTGCGGA+AGG 0.571872 7:+91240678 MsaT039628.1:CDS
TAGTTACAAATGCAGGATCC+CGG 0.574230 7:-91242721 None:intergenic
TTGCAGAACGGTTTCACCAA+AGG 0.574454 7:-91242324 None:intergenic
ACATACGTAGTTACAAATGC+AGG 0.577104 7:-91242728 None:intergenic
ATCGAAGAAAAGGTGTGCAA+TGG 0.584665 7:+91242446 MsaT039628.1:CDS
AAACGGAGCACGCCTAAATG+TGG 0.585711 7:+91243001 MsaT039628.1:CDS
CAATGAACAATTCAAGGAGA+GGG 0.586372 7:+91241500 MsaT039628.1:CDS
ACGCCTAAATGTGGAATATG+TGG 0.588121 7:+91243010 MsaT039628.1:CDS
CGTGTTGTTAAGAACAAGGA+TGG 0.588169 7:+91241108 MsaT039628.1:CDS
ATCCTTGTTCTTAACAACAC+GGG 0.590395 7:-91241106 None:intergenic
ATTGCCGGAATCTGTTGTGA+TGG 0.590987 7:+91242637 MsaT039628.1:CDS
GAAGCAGTTGAATTTCTGAA+GGG 0.598478 7:+91241546 MsaT039628.1:CDS
CATCCTTGTTCTTAACAACA+CGG 0.599878 7:-91241107 None:intergenic
ATTCTACAGGACTTGGACAG+TGG 0.602899 7:+91240844 MsaT039628.1:intron
ATTCTAGTACACGTTGACTA+CGG 0.607905 7:+91241252 MsaT039628.1:CDS
GAAGGCAACATAGGTGTGGA+AGG 0.608992 7:+91240696 MsaT039628.1:CDS
GTGAGCAACAAAACTGGGGA+AGG 0.610958 7:+91240660 MsaT039628.1:CDS
TTTGTCATAGAGAAGGTCAC+CGG 0.614733 7:+91241154 MsaT039628.1:CDS
ATCCCGTGTTGTTAAGAACA+AGG 0.615983 7:+91241104 MsaT039628.1:CDS
CAGCGGCTTAGGAAAAGAGG+TGG 0.616891 7:+91242935 MsaT039628.1:CDS
AAGCAGTTGAATTTCTGAAG+GGG 0.619311 7:+91241547 MsaT039628.1:CDS
GTCACAATCGCGTGTCATGT+CGG 0.624160 7:+91243041 MsaT039628.1:CDS
TGCGGAAGGCAACATAGGTG+TGG 0.624453 7:+91240692 MsaT039628.1:CDS
TTGTCATAGAGAAGGTCACC+GGG 0.626512 7:+91241155 MsaT039628.1:CDS
TGTGGAGCGTTGTAAGAGGA+TGG 0.636202 7:+91242757 MsaT039628.1:CDS
TGGATTGTTACACTTTAACA+CGG 0.636698 7:-91242786 None:intergenic
AGACCATAGATACGTGTCGT+AGG 0.637536 7:-91241420 None:intergenic
CTTATGCTGAGTTTGCAGAA+CGG 0.641727 7:-91242336 None:intergenic
ACAAGCCAACTAGTAGGTGT+GGG 0.642158 7:+91241217 MsaT039628.1:CDS
AGATTACATACACAAAACCA+TGG 0.642302 7:+91242808 MsaT039628.1:CDS
GACATTGGAATCATTCAACA+GGG 0.648120 7:+91242853 MsaT039628.1:CDS
ACCTTCTCTATGACAAACAA+AGG 0.649933 7:-91241148 None:intergenic
GTCTTCCATATCATCATCCG+AGG 0.656865 7:-91240893 None:intergenic
ACAATGAACAATTCAAGGAG+AGG 0.657945 7:+91241499 MsaT039628.1:CDS
CCTAAATGTGGAATATGTGG+AGG 0.662748 7:+91243013 MsaT039628.1:CDS
ACGTTGACTACGGTAGTGAC+CGG 0.666848 7:+91241262 MsaT039628.1:CDS
ACAGCTACGATATGTTCACA+GGG 0.674772 7:-91242590 None:intergenic
TGGGGAAGGCAACACAACTG+CGG 0.699382 7:+91240674 MsaT039628.1:CDS
AATCTGTTGTGATGGAACGA+TGG 0.702342 7:+91242645 MsaT039628.1:CDS
GAATGTGAGCAACAAAACTG+GGG 0.714038 7:+91240656 MsaT039628.1:CDS
GAAGCTTAGGTAATCCGCAG+CGG 0.717772 7:+91242918 MsaT039628.1:CDS
TAGATACAGAGAAATAGAGG+CGG 0.742799 7:+91242289 MsaT039628.1:intron
TTGACTACGGTAGTGACCGG+TGG 0.749164 7:+91241265 MsaT039628.1:CDS
ACATTGGAATCATTCAACAG+GGG 0.758577 7:+91242854 MsaT039628.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 91240618 91243250 91240618 ID=MsaG039628
Chr7 mRNA 91240618 91243250 91240618 ID=MsaT039628.1;Parent=MsaG039628
Chr7 exon 91240618 91240725 91240618 ID=MsaT039628.1.exon1;Parent=MsaT039628.1
Chr7 CDS 91240618 91240725 91240618 ID=cds.MsaT039628.1;Parent=MsaT039628.1
Chr7 exon 91240853 91241568 91240853 ID=MsaT039628.1.exon2;Parent=MsaT039628.1
Chr7 CDS 91240853 91241568 91240853 ID=cds.MsaT039628.1;Parent=MsaT039628.1
Chr7 exon 91242292 91243147 91242292 ID=MsaT039628.1.exon3;Parent=MsaT039628.1
Chr7 CDS 91242292 91243147 91242292 ID=cds.MsaT039628.1;Parent=MsaT039628.1
Chr7 exon 91243236 91243250 91243236 ID=MsaT039628.1.exon4;Parent=MsaT039628.1
Chr7 CDS 91243236 91243250 91243236 ID=cds.MsaT039628.1;Parent=MsaT039628.1
Gene Sequence

>MsaT039628.1

ATGGATATTAGTGAAATTCTTGAAATTTTTCAAGTTTCGAATGTGAGCAACAAAACTGGGGAAGGCAACACAACTGCGGAAGGCAACATAGGTGTGGAAGGTTCAGAGGACTTGGACAGTGGCTCTTGTTCGGAGAGTTTTGCGTGTTCCTCGGATGATGATATGGAAGACGCGTACAATTCGATGTATGGGTGCAGTTTCGATGATGAATTTGCGGTTGATTGCACGACTGACTTTGAGAAAATTAATTTCAAGGAATTAAGCTCTGATGAAATTATGATGTACCATTTTCCGGATCGTCTAGTTGCATTCAAGTTTTACAATATGTACGGTTGTGTGCACGGATTTGCTGGTAGAAGATCCCGTGTTGTTAAGAACAAGGATGGCGAAGTTATTCAACAAGCCTTTGTTTGTCATAGAGAAGGTCACCGGGATGCAAGGAATGTCAATAATCATGAAAGAAAAAGAGAGCACAAGCCAACTAGTAGGTGTGGGTGTATGGCAAAAATTCTAGTACACGTTGACTACGGTAGTGACCGGTGGTACATAAAAATGTTTGACGATATTCATAATCACACATTTTTGGATGAGAAGTATGAGGGGATGCTACCTGCACATAGAAAGATGAGTGATTATGACAAATTTCAAATGAAAGCAATGAGAAATGCTGGAATTCCTACGACACGTATCTATGGTCTTTTTGCTTCACAAGCTGGTGGATTCAAAAATCTAGGATATTCAAAAAGGACAATGTACAATGAACAATTCAAGGAGAGGGAGAGGAAGACAACAGATGCAGATGAAGCAGTTGAATTTCTGAAGGGATACAGAGAAATAGAGGCGGATTATGCATCTTCCTTTGGTGAAACCGTTCTGCAAACTCAGCATAAGAGTTTAGAGAAATCAGCTGCAAAACAGTATACAAGGTCAGTTTTCAAGCTTTTTAGGCCTGTATTGGAGAGAGCTTGTCGTTGTAAAATCGAAGAAAAGGTGTGCAATGGTTCCATTTTTAATTATAATGTTTTCAAATACCCTAGAGATGACATTCATTGGACTGTTTCATATTGCCAAGAACGATTAACATTTGAATGCTCTTGCAAGAAATTGGAGACATTTGGTATTCCCTGTGAACATATCGTAGCTGTTTTAGTGTACATGAACATAAGAAAATTGCCGGAATCTGTTGTGATGGAACGATGGACCAAACGTGCTAAAGATGTTATCAATGCCCAAAATGCTAATAGTTCAAGTCACCGGGATCCTGCATTTGTAACTACGTATGTTATGTTTGTGGAGCGTTGTAAGAGGATGGCAAACGCCGTGTTAAAGTGTAACAATCCAGATTACATACACAAAACCATGGAAATGGTTGAACAACACACTGAGACATTGGAATCATTCAACAGGGGTGAAGTTGATGAGATGTTTGTTGTGGGTCCAGAGACAGGAAGAAGCTTAGGTAATCCGCAGCGGCTTAGGAAAAGAGGTGGAGCAGCAGCCGATTCTTCAACTCGAAATGCAAATGCGAAAAAAAAACGGAGCACGCCTAAATGTGGAATATGTGGAGGAAAGGGTCACAATCGCGTGTCATGTCGGTTCCGTCAAGAAGAAACTCAGTCTTCAAATTCCAATCATGAACAAGACTTTTATAATGATAACGAAGATTGGAACATTCCTATGGATGGCTTGAATTAA
Protein sequence

>MsaT039628.1

MDISEILEIFQVSNVSNKTGEGNTTAEGNIGVEGSEDLDSGSCSESFACSSDDDMEDAYNSMYGCSFDDEFAVDCTTDFEKINFKELSSDEIMMYHFPDRLVAFKFYNMYGCVHGFAGRRSRVVKNKDGEVIQQAFVCHREGHRDARNVNNHERKREHKPTSRCGCMAKILVHVDYGSDRWYIKMFDDIHNHTFLDEKYEGMLPAHRKMSDYDKFQMKAMRNAGIPTTRIYGLFASQAGGFKNLGYSKRTMYNEQFKERERKTTDADEAVEFLKGYREIEADYASSFGETVLQTQHKSLEKSAAKQYTRSVFKLFRPVLERACRCKIEEKVCNGSIFNYNVFKYPRDDIHWTVSYCQERLTFECSCKKLETFGIPCEHIVAVLVYMNIRKLPESVVMERWTKRAKDVINAQNANSSSHRDPAFVTTYVMFVERCKRMANAVLKCNNPDYIHKTMEMVEQHTETLESFNRGEVDEMFVVGPETGRSLGNPQRLRKRGGAAADSSTRNANAKKKRSTPKCGICGGKGHNRVSCRFRQEETQSSNSNHEQDFYNDNEDWNIPMDGLN*