AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG042264


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042264 MtrunA17_Chr8g0350761 84.200 481 33 3 1 443 1 476 0.0 814
MsaG042264 MtrunA17_Chr4g0067981 31.295 278 152 7 20 287 33 281 9.43e-28 116
MsaG042264 MtrunA17_Chr7g0275401 28.114 281 183 5 21 299 8 271 1.39e-26 108
MsaG042264 MtrunA17_Chr8g0376881 31.102 254 155 9 20 272 27 261 4.28e-26 110
MsaG042264 MtrunA17_Chr3g0123131 30.620 258 153 8 20 272 15 251 4.41e-26 110
MsaG042264 MtrunA17_Chr1g0161431 30.739 257 157 5 20 272 13 252 1.58e-25 109
MsaG042264 MtrunA17_Chr3g0137101 28.125 256 164 6 21 272 11 250 1.08e-23 103
MsaG042264 MtrunA17_Chr2g0294911 28.253 269 171 5 20 287 31 278 1.06e-22 100
MsaG042264 MtrunA17_Chr4g0074401 28.016 257 167 5 20 275 19 258 1.37e-22 100
MsaG042264 MtrunA17_Chr4g0074411 26.923 260 161 4 21 275 21 256 3.88e-22 99.4
MsaG042264 MtrunA17_Chr1g0149841 28.352 261 153 6 21 272 8 243 5.89e-22 98.2
MsaG042264 MtrunA17_Chr7g0275891 25.510 294 172 7 21 292 8 276 1.23e-19 89.7
MsaG042264 MtrunA17_Chr1g0149851 27.046 281 168 6 21 283 8 269 1.15e-18 88.6
MsaG042264 MtrunA17_Chr4g0009851 26.482 253 140 6 21 272 14 221 1.58e-18 85.9
MsaG042264 MtrunA17_Chr4g0009901 24.906 265 151 7 20 283 12 229 1.25e-17 82.8
MsaG042264 MtrunA17_Chr2g0304841 30.252 119 82 1 21 139 21 138 2.24e-13 72.4
MsaG042264 MtrunA17_Chr6g0456631 34.426 122 76 3 20 139 11 130 7.84e-13 66.6
MsaG042264 MtrunA17_Chr8g0391911 25.758 264 150 7 20 269 11 242 5.31e-12 65.9
MsaG042264 MtrunA17_Chr3g0134481 30.328 122 84 1 21 142 11 131 6.16e-12 64.3
MsaG042264 MtrunA17_Chr7g0256551 36.090 133 61 5 24 134 11 141 8.27e-12 65.1
MsaG042264 MtrunA17_Chr8g0383961 32.258 124 80 2 22 142 18 140 9.80e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042264 AT3G16857.1 27.473 273 185 6 20 285 35 301 2.14e-25 109
MsaG042264 AT3G16857.2 27.473 273 185 6 20 285 35 301 2.61e-25 109
MsaG042264 AT2G25180.1 27.586 261 151 6 21 272 16 247 3.28e-23 102
MsaG042264 AT1G67710.1 28.897 263 152 8 20 272 9 246 6.20e-22 98.6
MsaG042264 AT4G31920.1 25.781 256 156 4 21 275 16 238 4.19e-21 96.3
MsaG042264 AT5G58080.1 27.138 269 171 8 5 272 2 246 1.22e-19 92.0
MsaG042264 AT3G16857.3 25.847 236 162 6 57 285 2 231 1.01e-17 86.3
MsaG042264 AT1G49190.1 26.277 274 173 10 20 286 32 283 1.57e-17 84.7
MsaG042264 AT2G01760.1 35.537 121 76 2 20 139 9 128 5.12e-15 77.0
MsaG042264 AT5G49240.1 23.864 264 154 6 21 269 41 272 9.98e-15 75.1
MsaG042264 AT2G40970.1 34.074 135 72 3 219 351 103 222 5.18e-12 66.2
MsaG042264 AT2G27070.1 25.091 275 175 10 19 272 13 277 1.69e-11 66.6
MsaG042264 AT4G00760.1 29.064 203 135 5 40 238 1 198 2.28e-11 65.5

Find 101 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTAGACCAATTGCATTT+TGG 0.197316 8:+19546705 None:intergenic
CTATGATCTCATAGGGAAAA+TGG 0.221957 8:-19547105 MsaT042264.1:CDS
ATATCACGGGCTCTTGGTTT+TGG 0.233266 8:-19546920 MsaT042264.1:CDS
GAGTGCCTCAAACTATTTAC+AGG 0.272286 8:-19546372 MsaT042264.1:intron
GTTGTCCGGAGTCACCTTTC+AGG 0.273076 8:-19545828 MsaT042264.1:CDS
ATTCTTCTTCTCACAGATAA+TGG 0.274227 8:+19547175 None:intergenic
TGATTTACATATGAAGTTCT+TGG 0.275930 8:-19546564 MsaT042264.1:CDS
ATAGTTTGAGGCACTCTCTT+TGG 0.318103 8:+19546379 None:intergenic
TTCATGGATGGTTGGCATTT+GGG 0.333819 8:+19546746 None:intergenic
ATTCATGGATGGTTGGCATT+TGG 0.334762 8:+19546745 None:intergenic
ATGGAAATCTATGATCTCAT+AGG 0.353225 8:-19547113 MsaT042264.1:CDS
AAAACCAAGAGCCCGTGATA+TGG 0.366143 8:+19546922 None:intergenic
AGATCCTTCGGATCGGCATC+TGG 0.369128 8:+19545916 None:intergenic
ACCCTTCCACATTCATAATC+TGG 0.374739 8:+19546405 None:intergenic
TATATCATTGTGCGTGCGCT+CGG 0.375322 8:-19545459 MsaT042264.1:CDS
TGGCTTTCTAAAACACCATT+TGG 0.375414 8:+19546895 None:intergenic
CTTCTTTCACTTGGATATGA+AGG 0.378032 8:-19547617 MsaT042264.1:intron
CAATGACTGTTGTTTCATAT+CGG 0.387086 8:+19546825 None:intergenic
GCATCTGTCAGATGTGATTA+TGG 0.389198 8:-19546780 MsaT042264.1:CDS
CACGCACAATGATATATTAC+TGG 0.397475 8:+19545466 None:intergenic
TCCTCAGCTTCGCCGCTGAC+TGG 0.399441 8:+19547720 None:intergenic
AAACCATTCTCCTGTATTCA+TGG 0.400145 8:+19546730 None:intergenic
CTCCTGCATTCAAAGATGGT+TGG 0.406146 8:+19546681 None:intergenic
TGGTTGGCATTTGGGACCCT+TGG 0.407552 8:+19546754 None:intergenic
TTTCTGATCTACATGACCTT+TGG 0.412759 8:-19546865 MsaT042264.1:CDS
CAAAATGCAATTGGTCTAGA+AGG 0.418166 8:-19546704 MsaT042264.1:CDS
GACTTTGCTGTTCCAATGGC+AGG 0.429908 8:+19545791 None:intergenic
CCTTCCATATCACGGGCTCT+TGG 0.439741 8:-19546926 MsaT042264.1:CDS
ATAACTCAGTACTCCTGAAC+AGG 0.440547 8:-19546607 MsaT042264.1:CDS
CAGTACTCCTGAACAGGAAA+AGG 0.443080 8:-19546601 MsaT042264.1:CDS
CTTGGAAAGCTCAAGTTGTC+CGG 0.445175 8:-19545842 MsaT042264.1:CDS
GACAGATGCCACACGAAGTC+AGG 0.457217 8:+19546794 None:intergenic
ATAATCTGGAATATTGTCTT+CGG 0.459039 8:+19546419 None:intergenic
CTCCTGTATTCATGGATGGT+TGG 0.460192 8:+19546738 None:intergenic
TATGATCTCATAGGGAAAAT+GGG 0.462257 8:-19547104 MsaT042264.1:CDS
GTTGGTTGTGGATGCTAGTT+CGG 0.466592 8:-19547666 MsaT042264.1:CDS
TTGGAAGCTGTTGAAATAGC+AGG 0.471879 8:-19546545 MsaT042264.1:CDS
AAATCAGCTGTCCCTGCCAT+TGG 0.472311 8:-19545803 MsaT042264.1:CDS
TGAACAGGAAAAGGAAAAGC+TGG 0.472904 8:-19546592 MsaT042264.1:CDS
TGGTTTCGCCAAAATGCAAT+TGG 0.475231 8:-19546713 MsaT042264.1:CDS
AAGTGCAAATGGTAAAGAAC+AGG 0.480421 8:-19546645 MsaT042264.1:CDS
AGATCATAGATTTCCATGTC+TGG 0.480523 8:+19547119 None:intergenic
ATATCATTGTGCGTGCGCTC+GGG 0.484893 8:-19545458 MsaT042264.1:CDS
TGTAGATCAGAAATCTGAAC+TGG 0.485157 8:+19546875 None:intergenic
AAGACTTTCCGAAGTGCAAA+TGG 0.488422 8:-19546656 MsaT042264.1:CDS
TCCAGTCAGCGGCGAAGCTG+AGG 0.492869 8:-19547721 MsaT042264.1:CDS
TGCCAACCATCCATGAATAC+AGG 0.500767 8:-19546740 MsaT042264.1:CDS
ACAAACCTGTAAATAGTTTG+AGG 0.502869 8:+19546367 None:intergenic
TCTGGTGGTAGTGGCGGCAT+AGG 0.521933 8:+19545592 None:intergenic
ATAGGAAGCACCATGCATAA+TGG 0.522991 8:+19545610 None:intergenic
GGCCAACCATCTTTGAATGC+AGG 0.525238 8:-19546683 MsaT042264.1:CDS
TTCCAGATTATGAATGTGGA+AGG 0.529710 8:-19546407 MsaT042264.1:CDS
GAACCTACGTGCTACTGCAA+TGG 0.529949 8:-19546022 MsaT042264.1:CDS
CATTCTCCTGTATTCATGGA+TGG 0.530842 8:+19546734 None:intergenic
AACTCAGCTGTTTACTGATG+AGG 0.532043 8:-19545530 MsaT042264.1:CDS
CGATCCAGATGCCGATCCGA+AGG 0.532999 8:-19545920 MsaT042264.1:CDS
GGAGGTTCAGTTGCCAGACA+TGG 0.533668 8:-19547132 MsaT042264.1:CDS
ACAAAATTACTGAGATCCTT+CGG 0.535642 8:+19545904 None:intergenic
AGGTACCATGGTCCAGTAGC+CGG 0.537071 8:-19547698 MsaT042264.1:CDS
GTTCTTTACCATTTGCACTT+CGG 0.537752 8:+19546648 None:intergenic
TGAGGTTAACCTTGTGCTTG+TGG 0.538862 8:-19547153 MsaT042264.1:CDS
TGGAAATCTATGATCTCATA+GGG 0.539851 8:-19547112 MsaT042264.1:CDS
ACTAGAACTTACTGAAAGAC+GGG 0.545088 8:+19547066 None:intergenic
CGGACAACTTGAGCTTTCCA+AGG 0.549307 8:+19545843 None:intergenic
GCAGGACTTTGCTGTTCCAA+TGG 0.549979 8:+19545787 None:intergenic
TACTAGAACTTACTGAAAGA+CGG 0.553968 8:+19547065 None:intergenic
CTGATGAGGATTTGAAAATG+TGG 0.559224 8:-19545516 MsaT042264.1:CDS
AATATTCCAGATTATGAATG+TGG 0.565218 8:-19546411 MsaT042264.1:CDS
CATCCATGAATACAGGAGAA+TGG 0.569815 8:-19546733 MsaT042264.1:CDS
TCTATCAATACTAGTTATGA+CGG 0.574247 8:-19547222 MsaT042264.1:intron
AGTCAGCGGCGAAGCTGAGG+AGG 0.585284 8:-19547718 MsaT042264.1:CDS
ATGACACTCCTTCCATATCA+CGG 0.589305 8:-19546934 MsaT042264.1:CDS
TCCACACTGCGAATCGCCAA+AGG 0.589805 8:+19546849 None:intergenic
TGACACTCCTTCCATATCAC+GGG 0.590869 8:-19546933 MsaT042264.1:CDS
TCCAGATTATGAATGTGGAA+GGG 0.595446 8:-19546406 MsaT042264.1:CDS
ACTTTGCTGTTCCAATGGCA+GGG 0.595685 8:+19545792 None:intergenic
CCAAGAGCCCGTGATATGGA+AGG 0.596254 8:+19546926 None:intergenic
GGACAACTTGAGCTTTCCAA+GGG 0.606529 8:+19545844 None:intergenic
TCTCGGACTAACAAAAGTCA+AGG 0.607987 8:-19545976 MsaT042264.1:CDS
AGATGTGATTATGGCAACCA+AGG 0.609212 8:-19546771 MsaT042264.1:CDS
ACCTTTGGCGATTCGCAGTG+TGG 0.611049 8:-19546850 MsaT042264.1:CDS
ATGTGGTTATCAACGATTCG+AGG 0.613048 8:-19545499 MsaT042264.1:CDS
TTACACCGGCTACTGGACCA+TGG 0.619788 8:+19547693 None:intergenic
ACAGATAATGGATAATGCAT+CGG 0.619908 8:+19547187 None:intergenic
AGTAGCCGGTGTAAAAGTGT+TGG 0.620685 8:-19547684 MsaT042264.1:CDS
GGTTAACCTTGTGCTTGTGG+AGG 0.621345 8:-19547150 MsaT042264.1:CDS
GATGTGATTATGGCAACCAA+GGG 0.624431 8:-19546770 MsaT042264.1:CDS
GAAGTGTCAAGAATATGCAC+AGG 0.635227 8:+19545880 None:intergenic
GTTGAAATAGCAGGAATCGA+CGG 0.638995 8:-19546536 MsaT042264.1:intron
GTCTGACGAGTTCCAGTCAG+CGG 0.643494 8:-19547732 MsaT042264.1:CDS
GCGAAGCTGAGGAGGTACCA+TGG 0.649372 8:-19547710 MsaT042264.1:CDS
CGGTGTAAAAGTGTTGGTTG+TGG 0.652064 8:-19547678 MsaT042264.1:CDS
AAGCAGTACCTGACTTCGTG+TGG 0.652087 8:-19546802 MsaT042264.1:CDS
ATGTGAATGAATATGTGTCT+CGG 0.664181 8:-19545993 MsaT042264.1:CDS
ACTGAACCTCCACAAGCACA+AGG 0.665135 8:+19547144 None:intergenic
ATTACTGAGATCCTTCGGAT+CGG 0.667987 8:+19545909 None:intergenic
TGTAGACTCACTCGTGCTCG+CGG 0.670245 8:+19545435 None:intergenic
GTTCCATTGCAGTAGCACGT+AGG 0.677485 8:+19546019 None:intergenic
CATGTGCGAACCATTATGCA+TGG 0.704435 8:-19545620 MsaT042264.1:CDS
TATCTGTGAGAAGAAGAATG+AGG 0.710608 8:-19547171 MsaT042264.1:CDS
TCGCACATGTCAAAGCTCAG+CGG 0.744624 8:+19545634 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 19545300 19547759 19545300 ID=MsaG042264
Chr8 mRNA 19545300 19547759 19545300 ID=MsaT042264.1;Parent=MsaG042264
Chr8 exon 19545300 19545322 19545300 ID=MsaT042264.1.exon7;Parent=MsaT042264.1
Chr8 CDS 19545300 19545322 19545300 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19545446 19545679 19545446 ID=MsaT042264.1.exon6;Parent=MsaT042264.1
Chr8 CDS 19545446 19545679 19545446 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19545794 19546061 19545794 ID=MsaT042264.1.exon5;Parent=MsaT042264.1
Chr8 CDS 19545794 19546061 19545794 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19546373 19546446 19546373 ID=MsaT042264.1.exon4;Parent=MsaT042264.1
Chr8 CDS 19546373 19546446 19546373 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19546537 19546974 19546537 ID=MsaT042264.1.exon3;Parent=MsaT042264.1
Chr8 CDS 19546537 19546974 19546537 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19547078 19547230 19547078 ID=MsaT042264.1.exon2;Parent=MsaT042264.1
Chr8 CDS 19547078 19547230 19547078 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Chr8 exon 19547618 19547759 19547618 ID=MsaT042264.1.exon1;Parent=MsaT042264.1
Chr8 CDS 19547618 19547759 19547618 ID=cds.MsaT042264.1;Parent=MsaT042264.1
Gene Sequence

>MsaT042264.1

ATGGAGTCTGACGAGTTCCAGTCAGCGGCGAAGCTGAGGAGGTACCATGGTCCAGTAGCCGGTGTAAAAGTGTTGGTTGTGGATGCTAGTTCGGCATGCCGAACAATTGTATCAAAAATGCTTCTTTCACTTGGATATGAAGTTATGACGGCTTCACTAGCTTCCGATGCATTATCCATTATCTGTGAGAAGAAGAATGAGGTTAACCTTGTGCTTGTGGAGGTTCAGTTGCCAGACATGGAAATCTATGATCTCATAGGGAAAATGGGAGAAAGCTCTAATCTCCCGTCTTTCATTATGACTGCTTATGATGATGACACTCCTTCCATATCACGGGCTCTTGGTTTTGGAGCCAAATGGTGTTTTAGAAAGCCAGTTCAGATTTCTGATCTACATGACCTTTGGCGATTCGCAGTGTGGAACCGATATGAAACAACAGTCATTGAAGCAGTACCTGACTTCGTGTGGCATCTGTCAGATGTGATTATGGCAACCAAGGGTCCCAAATGCCAACCATCCATGAATACAGGAGAATGGTTTCGCCAAAATGCAATTGGTCTAGAAGGCCAACCATCTTTGAATGCAGGAGAAAAGACTTTCCGAAGTGCAAATGGTAAAGAACAGGAATTTCCTGAAAAAGATAACTCAGTACTCCTGAACAGGAAAAGGAAAAGCTGGACTGATGATTTACATATGAAGTTCTTGGAAGCTGTTGAAATAGCAGGAATCGACGCTGGTCCGAAGACAATATTCCAGATTATGAATGTGGAAGGGTTTACCAAAGAGAGTGCCTCAAACTATTTACAGAGATATCGTCAATCTATGAACCTACGTGCTACTGCAATGGAACAGCATGTGAATGAATATGTGTCTCGGACTAACAAAAGTCAAGGAAAACGCCCTCTAGAAAAACAAGTTTTGATCAACGATCCAGATGCCGATCCGAAGGATCTCAGTAATTTTGTGCCTGTGCATATTCTTGACACTTCTGCTACTTTTCTTCCCTTGGAAAGCTCAAGTTGTCCGGAGTCACCTTTCAGGCAAAATCAGCTGTCCCTGCCATTGGAACAGCAAAGAAAACAGTTGAATTTTTCAACACCGCTGAGCTTTGACATGTGCGAACCATTATGCATGGTGCTTCCTATGCCGCCACTACCACCAGATGAAAAAGCATACTATGATAAGTTTTTTTATGCAAAAGAAACTCAGCTGTTTACTGATGAGGATTTGAAAATGTGGTTATCAACGATTCGAGGTATGAACATGCCAGTAATATATCATTGTGCGTGCGCTCGGGCCGCGAGCACGAGCAATGTGAATGCTTTTGCTTGA

Protein sequence

>MsaT042264.1

MESDEFQSAAKLRRYHGPVAGVKVLVVDASSACRTIVSKMLLSLGYEVMTASLASDALSIICEKKNEVNLVLVEVQLPDMEIYDLIGKMGESSNLPSFIMTAYDDDTPSISRALGFGAKWCFRKPVQISDLHDLWRFAVWNRYETTVIEAVPDFVWHLSDVIMATKGPKCQPSMNTGEWFRQNAIGLEGQPSLNAGEKTFRSANGKEQEFPEKDNSVLLNRKRKSWTDDLHMKFLEAVEIAGIDAGPKTIFQIMNVEGFTKESASNYLQRYRQSMNLRATAMEQHVNEYVSRTNKSQGKRPLEKQVLINDPDADPKDLSNFVPVHILDTSATFLPLESSSCPESPFRQNQLSLPLEQQRKQLNFSTPLSFDMCEPLCMVLPMPPLPPDEKAYYDKFFYAKETQLFTDEDLKMWLSTIRGMNMPVIYHCACARAASTSNVNAFA*