AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG027278

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG027278 MtrunA17_Chr5g0420701 98.209 335 6 0 1 335 1 335 0.0 687
MsaG027278 MtrunA17_Chr4g0061791 47.531 324 131 11 35 332 256 566 5.56e-78 249
MsaG027278 MtrunA17_Chr7g0220371 41.613 310 150 7 41 332 47 343 3.24e-59 194
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG027278 AT1G69010.1 52.695 334 133 5 1 333 1 310 1.09e-112 330
MsaG027278 AT5G08130.3 39.313 262 118 7 46 303 158 382 4.88e-49 169
MsaG027278 AT5G08130.1 38.931 262 120 7 46 303 158 383 3.18e-48 167
MsaG027278 AT5G08130.7 39.382 259 122 6 46 303 278 502 1.31e-47 168
MsaG027278 AT5G08130.5 39.382 259 122 6 46 303 282 506 1.36e-47 168
MsaG027278 AT5G38860.1 36.656 311 163 6 27 332 16 297 6.09e-47 161
MsaG027278 AT5G08130.2 38.996 259 124 6 46 303 278 503 9.33e-47 166
MsaG027278 AT5G08130.4 38.996 259 124 6 46 303 278 503 9.33e-47 166
MsaG027278 AT5G08130.6 38.636 264 128 6 41 303 273 503 9.83e-47 166
MsaG027278 AT5G08130.8 38.996 259 124 6 46 303 282 507 1.17e-46 166
MsaG027278 AT5G38860.2 45.963 161 75 2 27 185 16 166 2.00e-35 128

Find 82 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCGTGATCTATCATATTA+TGG 0.225408 5:-41119986 None:intergenic
GAGGTTGACCGACAAAATTT+TGG 0.267640 5:-41119869 None:intergenic
TGTACTTTCCCATCCTCTTC+AGG 0.272008 5:+41120124 MsaT027278.1:CDS
GTATGAGATCCCTCAATATT+TGG 0.276214 5:-41118865 None:intergenic
AGGGTACCTTTGTTGGTGTT+AGG 0.276576 5:-41116978 None:intergenic
CACAGCTTCATTCTTATTAG+AGG 0.312925 5:+41118910 MsaT027278.1:CDS
GGGTACCTTTGTTGGTGTTA+GGG 0.323081 5:-41116977 None:intergenic
GGCGGAGAGGCAACCTGATT+TGG 0.323743 5:+41120034 MsaT027278.1:CDS
ATTTCAGTTCAAATTGATCT+TGG 0.329165 5:+41122438 MsaT027278.1:CDS
CCTGAACCATTCTTTACAAT+TGG 0.334279 5:-41119891 None:intergenic
TTTCCGGGAAACGGTGATAC+TGG 0.349733 5:-41119915 None:intergenic
ATTCCCTTGCTCGCCAAATC+AGG 0.384265 5:-41120047 None:intergenic
TTAAGGAAGGGTACCTTTGT+TGG 0.391183 5:-41116985 None:intergenic
TGAGTATGTTCAGTACTTAC+AGG 0.412725 5:+41119034 MsaT027278.1:CDS
GGTGTTAGGGGCAGAGGAAG+TGG 0.420329 5:-41116964 None:intergenic
TGGGAGCCACTAAGCATTGT+TGG 0.420920 5:-41119966 None:intergenic
ATCTCTCCAACAATGCTTAG+TGG 0.434167 5:+41119960 MsaT027278.1:CDS
ATCGTGATCTATCATATTAT+GGG 0.435013 5:-41119985 None:intergenic
GTACTTTCCCATCCTCTTCA+GGG 0.437126 5:+41120125 MsaT027278.1:CDS
TTTCAGTTCAAATTGATCTT+GGG 0.437219 5:+41122439 MsaT027278.1:CDS
CCAATTGTAAAGAATGGTTC+AGG 0.442919 5:+41119891 MsaT027278.1:CDS
CCTTCAGATTCCAAATATTG+AGG 0.448909 5:+41118855 MsaT027278.1:intron
CTTCAGATTCCAAATATTGA+GGG 0.451155 5:+41118856 MsaT027278.1:intron
TCATCAAACTTTCCGGGAAA+CGG 0.451349 5:-41119924 None:intergenic
GAACCATTCTTTACAATTGG+AGG 0.459728 5:-41119888 None:intergenic
CAGGATGAACTTACAGTTGA+AGG 0.460627 5:+41120206 MsaT027278.1:CDS
GGAGATGAGGCTGTGCCACT+TGG 0.463787 5:-41122480 None:intergenic
CAACTGTAAGTTCATCCTGC+TGG 0.473427 5:-41120202 None:intergenic
ACTCAAGCGCTACAGAGTGC+TGG 0.475738 5:+41122393 MsaT027278.1:CDS
GGTCCAGTATCACCGTTTCC+CGG 0.476824 5:+41119912 MsaT027278.1:CDS
CAACCTCCAATTGTAAAGAA+TGG 0.480239 5:+41119885 MsaT027278.1:CDS
TTTGTTGGTGTTAGGGGCAG+AGG 0.484917 5:-41116970 None:intergenic
AAATATGAAGGCTCGTATCA+AGG 0.490493 5:+41119068 MsaT027278.1:CDS
GCAACCTGATTTGGCGAGCA+AGG 0.490959 5:+41120043 MsaT027278.1:CDS
TGATAGATCACGATCCGACT+CGG 0.499986 5:+41119994 MsaT027278.1:CDS
CAAGGGAATTCCTCTGCCTA+TGG 0.504233 5:+41120061 MsaT027278.1:CDS
TCTTGGGAAGCGTGCAAAGA+AGG 0.509091 5:+41122455 MsaT027278.1:CDS
TTGAGTTGTTCACTCGTTGT+GGG 0.512133 5:-41120179 None:intergenic
ATGAAGGCTCGTATCAAGGC+TGG 0.517535 5:+41119072 MsaT027278.1:CDS
GGTACCTTTGTTGGTGTTAG+GGG 0.522122 5:-41116976 None:intergenic
CTCAAGCGCTACAGAGTGCT+GGG 0.524190 5:+41122394 MsaT027278.1:CDS
TACCTCAATGCGATCAAAAG+AGG 0.538263 5:+41118885 MsaT027278.1:CDS
TTGCCTACAACAATGAAAGC+AGG 0.539094 5:+41116879 None:intergenic
GATAGATCACGATCCGACTC+GGG 0.540435 5:+41119995 MsaT027278.1:CDS
AGATGGGAAAGCTACTGATA+AGG 0.542435 5:+41118111 MsaT027278.1:intron
AAACAGTTCCCTGAAGAGGA+TGG 0.542486 5:-41120133 None:intergenic
GTTGAGTTGTTCACTCGTTG+TGG 0.544799 5:-41120180 None:intergenic
AACCGTCGAAGTTGATGCCA+TGG 0.544835 5:+41119102 MsaT027278.1:CDS
TCTGTTCCTGTCAGAAGTGA+TGG 0.550958 5:+41120101 MsaT027278.1:CDS
AATGATTGATTGCTACAAAG+AGG 0.557171 5:-41123674 None:intergenic
ACCCATGGCATCAACTTCGA+CGG 0.559522 5:-41119104 None:intergenic
TCTGTATACCTTGGGAGATG+AGG 0.560824 5:-41122493 None:intergenic
AACAGTTCCCTGAAGAGGAT+GGG 0.561389 5:-41120132 None:intergenic
ATCTCGAGTGTATACTCCCA+AGG 0.571871 5:+41120242 MsaT027278.1:CDS
ATGATTGATTGCTACAAAGA+GGG 0.583430 5:-41123673 None:intergenic
ACATTCAGTTGATTGTGCAT+CGG 0.585244 5:-41120156 None:intergenic
ATGTTTGCATGCATAGCCAT+AGG 0.589737 5:-41120077 None:intergenic
GATCCGACTCGGGATATTGT+CGG 0.590573 5:+41120005 MsaT027278.1:CDS
CAACCTGATTTGGCGAGCAA+GGG 0.591521 5:+41120044 MsaT027278.1:CDS
GAAGAAGCAAGATAAATGAG+AGG 0.595996 5:+41118176 MsaT027278.1:CDS
TCGGAAACAGTTCCCTGAAG+AGG 0.597102 5:-41120137 None:intergenic
TGCCTACAACAATGAAAGCA+GGG 0.600473 5:+41116880 None:intergenic
GAGTGAACAACTCAACCAGC+AGG 0.605106 5:+41120187 MsaT027278.1:CDS
GCATGCATAGCCATAGGCAG+AGG 0.609045 5:-41120071 None:intergenic
AGTACACCATCACTTCTGAC+AGG 0.614723 5:-41120107 None:intergenic
ACCTCAATGCGATCAAAAGA+GGG 0.615266 5:+41118886 MsaT027278.1:CDS
TCGGGATATTGTCGGCAAGA+CGG 0.618174 5:+41120013 MsaT027278.1:CDS
AACATTCTGTAACGGAGCAG+CGG 0.620536 5:+41118152 MsaT027278.1:CDS
TGGCACAGCCTCATCTCCCA+AGG 0.623367 5:+41122485 MsaT027278.1:CDS
ACCGTCGAAGTTGATGCCAT+GGG 0.624180 5:+41119103 MsaT027278.1:CDS
AAGATCGAAACATTCTGTAA+CGG 0.625212 5:+41118144 MsaT027278.1:CDS
ATGTTCAGTACTTACAGGAG+AGG 0.638295 5:+41119039 MsaT027278.1:CDS
TGCTGGGTTAGATCTGTCAA+AGG 0.641347 5:+41122410 MsaT027278.1:CDS
GATGAACTTACAGTTGAAGG+AGG 0.651861 5:+41120209 MsaT027278.1:CDS
TGTTCAGTACTTACAGGAGA+GGG 0.653015 5:+41119040 MsaT027278.1:CDS
TCTCGAGTGTATACTCCCAA+GGG 0.653032 5:+41120243 MsaT027278.1:CDS
GGATATTGTCGGCAAGACGG+CGG 0.664149 5:+41120016 MsaT027278.1:CDS
ATGAACTTACAGTTGAAGGA+GGG 0.671653 5:+41120210 MsaT027278.1:CDS
TTGCCGACAATATCCCGAGT+CGG 0.672673 5:-41120008 None:intergenic
TTGTCGGCAAGACGGCGGAG+AGG 0.684251 5:+41120021 MsaT027278.1:CDS
TCTGCCCCTAACACCAACAA+AGG 0.684939 5:+41116972 MsaT027278.1:CDS
CGTGCAAAGAAGGATCCAAG+TGG 0.732676 5:+41122465 MsaT027278.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 41116891 41123769 41116891 ID=MsaG027278
Chr5 mRNA 41116891 41123769 41116891 ID=MsaT027278.1;Parent=MsaG027278
Chr5 exon 41116891 41116993 41116891 ID=MsaT027278.1.exon1;Parent=MsaT027278.1
Chr5 CDS 41116891 41116993 41116891 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41118113 41118197 41118113 ID=MsaT027278.1.exon2;Parent=MsaT027278.1
Chr5 CDS 41118113 41118197 41118113 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41118862 41118931 41118862 ID=MsaT027278.1.exon3;Parent=MsaT027278.1
Chr5 CDS 41118862 41118931 41118862 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41119029 41119124 41119029 ID=MsaT027278.1.exon4;Parent=MsaT027278.1
Chr5 CDS 41119029 41119124 41119029 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41119849 41120264 41119849 ID=MsaT027278.1.exon5;Parent=MsaT027278.1
Chr5 CDS 41119849 41120264 41119849 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41122377 41122506 41122377 ID=MsaT027278.1.exon6;Parent=MsaT027278.1
Chr5 CDS 41122377 41122506 41122377 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Chr5 exon 41123662 41123769 41123662 ID=MsaT027278.1.exon7;Parent=MsaT027278.1
Chr5 CDS 41123662 41123769 41123662 ID=cds.MsaT027278.1;Parent=MsaT027278.1
Gene Sequence

>MsaT027278.1

ATGAAAGCAGGGAAAGTTAATCATGAAGAAGACGAGTACGATGATGATGAGTTTAATTCCAACAAAAAACAAGCCACTTCCTCTGCCCCTAACACCAACAAAGATGGGAAAGCTACTGATAAGGCTAGTGTGATAAGATCGAAACATTCTGTAACGGAGCAGCGGAGAAGAAGCAAGATAAATGAGAGATTCCAAATATTGAGGGATCTCATACCTCAATGCGATCAAAAGAGGGACACAGCTTCATTCTTATTAGAGGTGATTGAGTATGTTCAGTACTTACAGGAGAGGGTACAAAAATATGAAGGCTCGTATCAAGGCTGGAGTCAAGAACCGTCGAAGTTGATGCCATGGAGAAATAGCCATTGGCGTGCCCAAAATTTTGTCGGTCAACCTCCAATTGTAAAGAATGGTTCAGGTCCAGTATCACCGTTTCCCGGAAAGTTTGATGAAAACAGCGTTAGTATCTCTCCAACAATGCTTAGTGGCTCCCATAATATGATAGATCACGATCCGACTCGGGATATTGTCGGCAAGACGGCGGAGAGGCAACCTGATTTGGCGAGCAAGGGAATTCCTCTGCCTATGGCTATGCATGCAAACATGTCTGTTCCTGTCAGAAGTGATGGTGTACTTTCCCATCCTCTTCAGGGAACTGTTTCCGATGCACAATCAACTGAATGTCCCACAACGAGTGAACAACTCAACCAGCAGGATGAACTTACAGTTGAAGGAGGGACAATTAGCATCTCGAGTGTATACTCCCAAGGGCTGTTGAACAATCTGACTCAAGCGCTACAGAGTGCTGGGTTAGATCTGTCAAAGGCTAACATTTCAGTTCAAATTGATCTTGGGAAGCGTGCAAAGAAGGATCCAAGTGGCACAGCCTCATCTCCCAAGAATCATGATAACCCTCTTTGTAGCAATCAATCATTTGCACATTTTAGAGATGGTGGCAATAGAGAAGACTCAGATCAAGCTCAAAAAAGAATGAAAACATACAAGTGA
Protein sequence

>MsaT027278.1

MKAGKVNHEEDEYDDDEFNSNKKQATSSAPNTNKDGKATDKASVIRSKHSVTEQRRRSKINERFQILRDLIPQCDQKRDTASFLLEVIEYVQYLQERVQKYEGSYQGWSQEPSKLMPWRNSHWRAQNFVGQPPIVKNGSGPVSPFPGKFDENSVSISPTMLSGSHNMIDHDPTRDIVGKTAERQPDLASKGIPLPMAMHANMSVPVRSDGVLSHPLQGTVSDAQSTECPTTSEQLNQQDELTVEGGTISISSVYSQGLLNNLTQALQSAGLDLSKANISVQIDLGKRAKKDPSGTASSPKNHDNPLCSNQSFAHFRDGGNREDSDQAQKRMKTYK*