AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG002031

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002031 MtrunA17_Chr1g0146231 78.488 344 41 8 1 311 1 344 1.29e-178 497
MsaG002031 MtrunA17_Chr3g0140331 50.159 315 117 9 19 311 68 364 5.75e-82 252
MsaG002031 MtrunA17_Chr8g0340401 44.237 321 134 13 23 311 35 342 8.44e-62 199
MsaG002031 MtrunA17_Chr4g0035891 36.014 286 143 9 5 270 15 280 3.87e-41 144
MsaG002031 MtrunA17_Chr8g0372291 42.188 192 90 4 96 271 102 288 5.63e-36 131
MsaG002031 MtrunA17_Chr3g0145121 41.294 201 99 5 87 271 88 285 7.61e-34 125
MsaG002031 MtrunA17_Chr6g0461591 63.953 86 31 0 182 267 173 258 1.11e-33 124
MsaG002031 MtrunA17_Chr1g0169431 76.056 71 17 0 200 270 171 241 4.58e-33 122
MsaG002031 MtrunA17_Chr5g0395391 73.239 71 19 0 200 270 269 339 7.62e-32 121
MsaG002031 MtrunA17_Chr5g0395391 70.833 72 21 0 200 271 167 238 1.35e-28 112
MsaG002031 MtrunA17_Chr5g0404981 61.290 93 28 1 187 271 278 370 1.09e-31 122
MsaG002031 MtrunA17_Chr1g0199671 76.923 65 15 0 201 265 242 306 3.79e-31 119
MsaG002031 MtrunA17_Chr7g0253101 75.385 65 16 0 201 265 188 252 3.82e-31 117
MsaG002031 MtrunA17_Chr1g0213161 55.046 109 44 2 180 287 130 234 5.01e-31 116
MsaG002031 MtrunA17_Chr4g0028961 71.642 67 19 0 201 267 232 298 4.21e-30 116
MsaG002031 MtrunA17_Chr2g0326771 73.846 65 17 0 201 265 216 280 4.59e-30 115
MsaG002031 MtrunA17_Chr7g0232671 62.903 62 23 0 201 262 187 248 1.41e-21 91.7
MsaG002031 MtrunA17_Chr7g0232701 58.065 62 26 0 201 262 73 134 1.10e-19 83.6
MsaG002031 MtrunA17_Chr7g0232681 56.923 65 27 1 198 262 130 193 4.66e-19 83.6
MsaG002031 MtrunA17_Chr7g0271861 67.647 34 11 0 203 236 24 57 6.73e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG002031 AT5G25830.1 49.434 265 88 8 93 311 67 331 7.69e-73 228
MsaG002031 AT4G32890.1 41.693 319 132 13 21 311 16 308 5.62e-65 207
MsaG002031 AT3G60530.1 50.279 179 72 5 93 269 63 226 6.86e-47 158
MsaG002031 AT2G45050.1 43.564 202 101 5 89 281 60 257 2.82e-44 152
MsaG002031 AT4G36240.1 38.521 257 113 10 22 268 10 231 3.04e-35 128
MsaG002031 AT4G34680.1 43.158 190 82 5 90 270 77 249 1.41e-34 127
MsaG002031 AT4G34680.2 43.158 190 82 5 90 270 77 249 1.41e-34 127
MsaG002031 AT3G24050.1 75.000 68 17 0 200 267 193 260 6.35e-33 123
MsaG002031 AT1G08010.2 64.368 87 23 2 195 273 212 298 1.08e-32 123
MsaG002031 AT1G08010.1 64.368 87 23 2 195 273 212 298 1.08e-32 123
MsaG002031 AT1G08010.3 64.368 87 23 2 195 273 212 298 1.08e-32 123
MsaG002031 AT5G66320.2 63.855 83 30 0 201 283 249 331 8.25e-31 119
MsaG002031 AT5G66320.1 63.855 83 30 0 201 283 249 331 8.25e-31 119
MsaG002031 AT1G08000.2 70.833 72 21 0 196 267 213 284 1.17e-30 117
MsaG002031 AT1G08000.1 70.833 72 21 0 196 267 213 284 1.17e-30 117
MsaG002031 AT3G54810.1 61.728 81 31 0 201 281 229 309 3.67e-30 116
MsaG002031 AT3G54810.2 61.728 81 31 0 201 281 229 309 3.67e-30 116
MsaG002031 AT3G51080.1 71.014 69 20 0 201 269 221 289 1.33e-28 112
MsaG002031 AT3G45170.1 62.687 67 25 0 203 269 117 183 2.84e-25 100
MsaG002031 AT2G28340.1 66.667 63 21 0 203 265 193 255 9.45e-25 101

Find 103 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGTCACTGTCCTTTCTTCT+TGG 0.090798 1:+30656770 None:intergenic
AAAATGATTCCTCACCAATA+TGG 0.244883 1:+30657084 None:intergenic
TCAAAAGATGCAACTGATAT+CGG 0.281999 1:-30657048 MsaT002031.1:CDS
GCAGTCTTTGCCTGCTTCCT+TGG 0.291400 1:+30656794 None:intergenic
TACTCTGATGTTGTAAAATC+TGG 0.292416 1:+30656492 None:intergenic
CTCCGGAGACTTGTGTGTTC+CGG 0.327330 1:-30657620 MsaT002031.1:intron
CTAGCTGCAGGCCTGTATTC+AGG 0.333508 1:+30656614 None:intergenic
AAGACGCCACAATGGCGAAC+TGG 0.366662 1:-30656701 MsaT002031.1:CDS
CGACGTCATTGTTGAGGTTA+AGG 0.370723 1:+30657815 None:intergenic
ACGATGCGAGTTGGAGTGTT+TGG 0.387998 1:+30656574 None:intergenic
GTGGAATGGATTTCCCATAT+TGG 0.395528 1:-30657098 MsaT002031.1:CDS
CCTACTGTCGTTCCTGAGAT+TGG 0.402468 1:-30657670 MsaT002031.1:CDS
TTACTTGATTCATCAACATA+TGG 0.411056 1:-30656441 MsaT002031.1:CDS
CACACAAGTCTCCGGAGAAA+TGG 0.416213 1:+30657626 None:intergenic
AATCAAGTAATCATCATTGT+TGG 0.440257 1:+30656454 None:intergenic
GAGGCAGAAGGAAATGTTGC+GGG 0.440995 1:-30656534 MsaT002031.1:CDS
TGTCGGAGGAAAAGGTGGTT+TGG 0.443866 1:+30657872 None:intergenic
CGATGACGCTACCATCATTT+CGG 0.449847 1:-30657791 MsaT002031.1:CDS
TACATCATCTGCCTAAAATC+AGG 0.450652 1:+30656416 None:intergenic
AAATGATTCCTCACCAATAT+GGG 0.451088 1:+30657085 None:intergenic
ATCGATTGGTGCCTGAATAC+AGG 0.462920 1:-30656625 MsaT002031.1:CDS
AGTGTTGTTGTCGGAGGAAA+AGG 0.462952 1:+30657864 None:intergenic
AAGGACAGTGACGGAGGGTC+AGG 0.466229 1:-30656761 MsaT002031.1:CDS
ATGATTTAGCGGACGTGGAA+TGG 0.472347 1:-30657112 MsaT002031.1:CDS
GCCCACGAGTCCTCTTGCTA+CGG 0.473059 1:+30656925 None:intergenic
TACTTGATTCATCAACATAT+GGG 0.478713 1:-30656440 MsaT002031.1:CDS
AGACGCCACAATGGCGAACT+GGG 0.479058 1:-30656700 MsaT002031.1:CDS
ACAATGACGGTGGGTAAGGT+AGG 0.479672 1:+30656818 None:intergenic
GACACGAGCTCTGGTCGCAA+GGG 0.486620 1:+30656901 None:intergenic
GTTAGCTCGTCATCATTGTC+CGG 0.486841 1:-30657700 MsaT002031.1:CDS
TGGAACAATGACGGTGGGTA+AGG 0.491771 1:+30656814 None:intergenic
AAATTCTGACAGCCAATCTC+AGG 0.491898 1:+30657658 None:intergenic
CAAAAGATGCAACTGATATC+GGG 0.494290 1:-30657047 MsaT002031.1:CDS
CAATGACGGTGGGTAAGGTA+GGG 0.498486 1:+30656819 None:intergenic
ATGACGGTGGGTAAGGTAGG+GGG 0.502940 1:+30656821 None:intergenic
TGTTTGGTCAGCACAAATGT+AGG 0.504596 1:+30656590 None:intergenic
ATCGTAAAGTGTTGGAGCTA+CGG 0.505579 1:-30656556 MsaT002031.1:CDS
AAGATATAAGTCGGATCGAT+TGG 0.506690 1:-30656639 MsaT002031.1:CDS
AAGGTTGGTGTCCGAAATGA+TGG 0.507635 1:+30657780 None:intergenic
GGTGGTTTGGAAAATGTTGT+TGG 0.508256 1:+30657885 None:intergenic
GAAATAAGAGGATGATTTAG+CGG 0.515604 1:-30657123 MsaT002031.1:intron
ACCAACCTTGACTCGGCCAC+AGG 0.517123 1:-30657766 MsaT002031.1:CDS
TACCGACAATTTCATTGTTG+AGG 0.524862 1:-30657842 MsaT002031.1:CDS
TACCGGAACACACAAGTCTC+CGG 0.526624 1:+30657618 None:intergenic
CCAATCTCAGGAACGACAGT+AGG 0.529252 1:+30657670 None:intergenic
CGTCATTGTTCCAAGGAAGC+AGG 0.532509 1:-30656804 MsaT002031.1:CDS
GCCCGTAGCAAGAGGACTCG+TGG 0.533598 1:-30656927 MsaT002031.1:CDS
CCCACGAGTCCTCTTGCTAC+GGG 0.537511 1:+30656926 None:intergenic
GACGGAGGGTCAGGTGGAGA+TGG 0.539597 1:-30656752 MsaT002031.1:CDS
GTTGTTGTCGGAGGAAAAGG+TGG 0.541025 1:+30657867 None:intergenic
TTCGGACACCAACCTTGACT+CGG 0.544203 1:-30657773 MsaT002031.1:CDS
GAGGGTCAGGTGGAGATGGT+CGG 0.544742 1:-30656748 MsaT002031.1:CDS
GGTAACAATGGAGGAGGAGG+CGG 0.546438 1:+30657735 None:intergenic
CTAGGCCCAGTTCGCCATTG+TGG 0.547627 1:+30656695 None:intergenic
AAACAAGAAGACACGAGCTC+TGG 0.547703 1:+30656892 None:intergenic
CAACACTTTACGATGCGAGT+TGG 0.550252 1:+30656565 None:intergenic
GCTATTGACGACGGTAACAA+TGG 0.551418 1:+30657723 None:intergenic
AGACACGAGCTCTGGTCGCA+AGG 0.553521 1:+30656900 None:intergenic
AATGACGGTGGGTAAGGTAG+GGG 0.553618 1:+30656820 None:intergenic
AAAGACTGCTCCAAGAAGAA+AGG 0.555772 1:-30656780 MsaT002031.1:CDS
AGAGGATGATTTAGCGGACG+TGG 0.556862 1:-30657117 MsaT002031.1:intron
GACAGTGACGGAGGGTCAGG+TGG 0.558691 1:-30656758 MsaT002031.1:CDS
ACAAATGTAGGGCTAGCTGC+AGG 0.560737 1:+30656602 None:intergenic
GACGGTAACAATGGAGGAGG+AGG 0.565457 1:+30657732 None:intergenic
GTCCTCAACAATGAAATTGT+CGG 0.566137 1:+30657840 None:intergenic
GCAACTGATATCGGGCATGA+AGG 0.569194 1:-30657039 MsaT002031.1:intron
GTTTGGTCAGCACAAATGTA+GGG 0.574012 1:+30656591 None:intergenic
CCCGTAGCAAGAGGACTCGT+GGG 0.574146 1:-30656926 MsaT002031.1:CDS
AGTTGCCTGTGGCCGAGTCA+AGG 0.576465 1:+30657761 None:intergenic
CTGCTTCCTTGGAACAATGA+CGG 0.577447 1:+30656805 None:intergenic
CAGCTAAGGCCCGTAGCAAG+AGG 0.579929 1:-30656935 MsaT002031.1:CDS
TTAGCTCGTCATCATTGTCC+GGG 0.587117 1:-30657699 MsaT002031.1:CDS
ATTCCCTACGTAGGAATGGA+AGG 0.590186 1:-30657913 None:intergenic
ATTGTCGGTAGTGTTGTTGT+CGG 0.590207 1:+30657855 None:intergenic
GGTCAGGTGGAGATGGTCGG+AGG 0.590443 1:-30656745 MsaT002031.1:CDS
GTCGGTAGTGTTGTTGTCGG+AGG 0.590547 1:+30657858 None:intergenic
AACGACAGTAGGGTCGCACC+CGG 0.593053 1:+30657681 None:intergenic
CAATCTCAGGAACGACAGTA+GGG 0.595868 1:+30657671 None:intergenic
CATCGTCGACGTCATTGTTG+AGG 0.596242 1:+30657809 None:intergenic
ACACGAGCTCTGGTCGCAAG+GGG 0.601565 1:+30656902 None:intergenic
GCCTGTGGCCGAGTCAAGGT+TGG 0.601677 1:+30657765 None:intergenic
CAACTCGCATCGTAAAGTGT+TGG 0.604228 1:-30656564 MsaT002031.1:CDS
TACCCACCGTCATTGTTCCA+AGG 0.605444 1:-30656811 MsaT002031.1:CDS
GTTGGAGCTACGGAGGCAGA+AGG 0.611025 1:-30656546 MsaT002031.1:CDS
CGTCATTGTTGAGGTTAAGG+AGG 0.612987 1:+30657818 None:intergenic
TTCCTTGGAACAATGACGGT+GGG 0.619946 1:+30656809 None:intergenic
GACGACGGTAACAATGGAGG+AGG 0.621230 1:+30657729 None:intergenic
CAATGGCGAACTGGGCCTAG+TGG 0.623266 1:-30656692 MsaT002031.1:CDS
ATGGATTTCCCATATTGGTG+AGG 0.624760 1:-30657093 MsaT002031.1:CDS
AAAACATTATGCAATGCTTG+TGG 0.626014 1:-30656665 MsaT002031.1:CDS
TTGTGGCGTAAGATATAAGT+CGG 0.628177 1:-30656648 MsaT002031.1:CDS
GAAGAAAGGACAGTGACGGA+GGG 0.637953 1:-30656766 MsaT002031.1:CDS
CCAAGAAGAAAGGACAGTGA+CGG 0.640630 1:-30656770 MsaT002031.1:CDS
AGAAGAAAGGACAGTGACGG+AGG 0.643844 1:-30656767 MsaT002031.1:CDS
GTAAAGTGTTGGAGCTACGG+AGG 0.667005 1:-30656553 MsaT002031.1:CDS
CTTCCTTGGAACAATGACGG+TGG 0.667737 1:+30656808 None:intergenic
GGAGGCGGTTGAGTTGCCTG+TGG 0.675099 1:+30657750 None:intergenic
TGACAGACAAGACGCCACAA+TGG 0.677162 1:-30656709 MsaT002031.1:CDS
ATTGACGACGGTAACAATGG+AGG 0.678642 1:+30657726 None:intergenic
AGTTCTGACTCAGAAGAAGA+CGG 0.679246 1:+30656855 None:intergenic
GGAGGCAGAAGGAAATGTTG+CGG 0.688988 1:-30656535 MsaT002031.1:CDS
CACGAGCTCTGGTCGCAAGG+GGG 0.707033 1:+30656903 None:intergenic
CGAGCTAACGCTATTGACGA+CGG 0.724527 1:+30657714 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 30656415 30657920 30656415 ID=MsaG002031
Chr1 mRNA 30656415 30657920 30656415 ID=MsaT002031.1;Parent=MsaG002031
Chr1 exon 30656415 30656954 30656415 ID=MsaT002031.1.exon3;Parent=MsaT002031.1
Chr1 CDS 30656415 30656954 30656415 ID=cds.MsaT002031.1;Parent=MsaT002031.1
Chr1 exon 30657040 30657135 30657040 ID=MsaT002031.1.exon2;Parent=MsaT002031.1
Chr1 CDS 30657040 30657135 30657040 ID=cds.MsaT002031.1;Parent=MsaT002031.1
Chr1 exon 30657621 30657920 30657621 ID=MsaT002031.1.exon1;Parent=MsaT002031.1
Chr1 CDS 30657621 30657920 30657621 ID=cds.MsaT002031.1;Parent=MsaT002031.1
Gene Sequence

>MsaT002031.1

ATGGAAGGCACAACCAACAACATTTTCCAAACCACCTTTTCCTCCGACAACAACACTACCGACAATTTCATTGTTGAGGACCTCCTTAACCTCAACAATGACGTCGACGATGACGCTACCATCATTTCGGACACCAACCTTGACTCGGCCACAGGCAACTCAACCGCCTCCTCCTCCATTGTTACCGTCGTCAATAGCGTTAGCTCGTCATCATTGTCCGGGTGCGACCCTACTGTCGTTCCTGAGATTGGCTGTCAGAATTTTTCTGACAGCCATTTCTCCGGAGACTTGTGTGTTCCGGATGATTTAGCGGACGTGGAATGGATTTCCCATATTGGTGAGGAATCATTTTCAAGCGAGGATCTTCAAAAGATGCAACTGATATCGGGCATGAAGCTAAGGCCCGTAGCAAGAGGACTCGTGGGCCCCCTTGCGACCAGAGCTCGTGTCTTCTTGTTTTGTCTCAAACAACACCGTCTTCTTCTGAGTCAGAACTCCTTATTCCCACCCCCTACCTTACCCACCGTCATTGTTCCAAGGAAGCAGGCAAAGACTGCTCCAAGAAGAAAGGACAGTGACGGAGGGTCAGGTGGAGATGGTCGGAGGTGTCTGCATTGCATGACAGACAAGACGCCACAATGGCGAACTGGGCCTAGTGGCCCAAAAACATTATGCAATGCTTGTGGCGTAAGATATAAGTCGGATCGATTGGTGCCTGAATACAGGCCTGCAGCTAGCCCTACATTTGTGCTGACCAAACACTCCAACTCGCATCGTAAAGTGTTGGAGCTACGGAGGCAGAAGGAAATGTTGCGGGCGCACCAACACCAACAAAACCAGATTTTACAACATCAGAGTATGATGTTTGATATGTCCAACAATGATGATTACTTGATTCATCAACATATGGGACCTGATTTTAGGCAGATGATGTAG
Protein sequence

>MsaT002031.1

MEGTTNNIFQTTFSSDNNTTDNFIVEDLLNLNNDVDDDATIISDTNLDSATGNSTASSSIVTVVNSVSSSSLSGCDPTVVPEIGCQNFSDSHFSGDLCVPDDLADVEWISHIGEESFSSEDLQKMQLISGMKLRPVARGLVGPLATRARVFLFCLKQHRLLLSQNSLFPPPTLPTVIVPRKQAKTAPRRKDSDGGSGGDGRRCLHCMTDKTPQWRTGPSGPKTLCNACGVRYKSDRLVPEYRPAASPTFVLTKHSNSHRKVLELRRQKEMLRAHQHQQNQILQHQSMMFDMSNNDDYLIHQHMGPDFRQMM*