AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG004033

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG004033 MtrunA17_Chr5g0435401 53.814 236 84 1 25 235 44 279 3.07e-78 243
MsaG004033 MtrunA17_Chr5g0435401 51.299 154 62 6 145 291 265 412 1.05e-34 129
MsaG004033 MtrunA17_Chr1g0192841 60.804 199 35 4 135 291 46 243 2.03e-68 213
MsaG004033 MtrunA17_Chr5g0445971 55.484 155 44 2 2 133 11 163 2.57e-48 159
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 59 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACAACACAACTGTGAAAT+TGG 0.165362 1:+64981080 MsaT004033.1:CDS
TGTTCATTATATATGCTAAA+TGG 0.187259 1:+64981165 MsaT004033.1:CDS
AATTTATAATACCTGTTTAT+CGG 0.282746 1:-64980827 None:intergenic
TTCTTGCTTTCCTCCATATA+TGG 0.290634 1:-64980943 None:intergenic
CTCCTCTTCTGGTGACTTCC+AGG 0.296417 1:-64979442 None:intergenic
ACAAAAGAGTAATTTGTTAG+AGG 0.335421 1:-64981057 None:intergenic
TTGTTTCCCATTGGTGAGTT+TGG 0.349267 1:-64978980 None:intergenic
AGTTGTCTCTGCACTAAAAC+TGG 0.350191 1:+64979745 MsaT004033.1:CDS
ACACTTGGTGTATAGTCATT+TGG 0.363252 1:-64981193 None:intergenic
AATTCTTATAACTTGTCATT+TGG 0.372266 1:-64980304 None:intergenic
TTTGAGAAATTGTACTTCTC+TGG 0.396109 1:+64979830 MsaT004033.1:CDS
GGAGGAAAGCAAGAAGATAA+AGG 0.402572 1:+64980951 MsaT004033.1:CDS
GTTCATTATATATGCTAAAT+GGG 0.404440 1:+64981166 MsaT004033.1:CDS
ATCAAAATCAACTGGTAAGA+AGG 0.411049 1:-64981136 None:intergenic
GATGTCTGTCACCGATAAAC+AGG 0.415647 1:+64980816 MsaT004033.1:CDS
GTAAAGCAGATACAAGTCTA+AGG 0.420658 1:-64979420 None:intergenic
GCTCATGATCAGGACATAGA+TGG 0.434442 1:+64980754 MsaT004033.1:CDS
CTGGTGAAAACCTCCTCTTC+TGG 0.440306 1:-64979453 None:intergenic
AAACAACGAGGTTCTCCAAC+TGG 0.449981 1:+64980682 MsaT004033.1:CDS
TACGCATGGCTGTTGATGCT+TGG 0.488165 1:+64980788 MsaT004033.1:CDS
CAGTAGGTATCAAAATCAAC+TGG 0.503013 1:-64981144 None:intergenic
CTTGAGGAATATTTGATACC+CGG 0.504489 1:-64980710 None:intergenic
ACTCAAGTGTTGGATTCCAC+CGG 0.509294 1:+64979045 MsaT004033.1:CDS
CAGATACCAAACTCACCAAT+GGG 0.515202 1:+64978974 MsaT004033.1:CDS
TCGATTAAAAGCTCATGATC+AGG 0.520471 1:+64980744 MsaT004033.1:CDS
TGTATAGAAGTATTGCATAG+AGG 0.522591 1:-64979805 None:intergenic
ATCGAGCACATTCCTGCTTG+AGG 0.522606 1:-64980726 None:intergenic
TACTTCTCTGGCAGCCCCAA+AGG 0.522716 1:+64979842 MsaT004033.1:CDS
CAGGAGTCACCGCACACACT+AGG 0.532678 1:-64981021 None:intergenic
AGAAGGGTATTGTTTCCCAT+TGG 0.538605 1:-64978989 None:intergenic
ACAAGTCTAAGGATGTTTCT+CGG 0.546217 1:-64979409 None:intergenic
CTCAAGTGTTGGATTCCACC+GGG 0.546841 1:+64979046 MsaT004033.1:CDS
TGTCAAACTCACTCAAGTGT+TGG 0.553345 1:+64979035 MsaT004033.1:CDS
TCAAAATCAACTGGTAAGAA+GGG 0.553575 1:-64981135 None:intergenic
AGGTTGCTCTACAAAACCGA+TGG 0.556726 1:+64979717 MsaT004033.1:intron
AGACTTGTATCTGCTTTACC+TGG 0.567418 1:+64979424 MsaT004033.1:CDS
TTTCTAAGTCATCAGGAGAA+GGG 0.578999 1:-64979005 None:intergenic
TAGCATATATAATGAACAGT+AGG 0.579522 1:-64981160 None:intergenic
AACTGACATGAGATTGAACC+CGG 0.583220 1:-64979064 None:intergenic
TCAGATACCAAACTCACCAA+TGG 0.586380 1:+64978973 MsaT004033.1:CDS
TACCTGGAAGTCACCAGAAG+AGG 0.586600 1:+64979440 MsaT004033.1:CDS
CTGGAAGTCACCAGAAGAGG+AGG 0.587472 1:+64979443 MsaT004033.1:CDS
GTATCAAATATTCCTCAAGC+AGG 0.590617 1:+64980714 MsaT004033.1:CDS
TAGAGGTTGCGAAGTTACGC+AGG 0.591832 1:-64981040 None:intergenic
TGGTCTCTTAGATACCTTTG+GGG 0.598172 1:-64979856 None:intergenic
TTGGTGAGTTTGGTATCTGA+TGG 0.598278 1:-64978970 None:intergenic
GTCTCTGCACTAAAACTGGA+AGG 0.599079 1:+64979749 MsaT004033.1:CDS
GAAGGTGGCAAAGATGTCAA+AGG 0.612132 1:+64980271 MsaT004033.1:CDS
GGTGCTTCTAGAAGCACTTG+AGG 0.614692 1:-64980637 None:intergenic
TTTCATGTAGCCATATATGG+AGG 0.617104 1:+64980933 MsaT004033.1:intron
CAGAGACAACTTCAACCCAT+CGG 0.637039 1:-64979733 None:intergenic
AAGCATCAACAGCCATGCGT+AGG 0.637247 1:-64980786 None:intergenic
GGCTGATGAAGATAATCTGA+AGG 0.641633 1:+64980253 MsaT004033.1:intron
GGTTGCTCTACAAAACCGAT+GGG 0.647381 1:+64979718 MsaT004033.1:intron
GAAGATAAAGGAAACAAACA+AGG 0.647918 1:+64980963 MsaT004033.1:CDS
CAGAACAGACCTAGTGTGTG+CGG 0.664594 1:+64981012 MsaT004033.1:CDS
TGATGAAGATAATCTGAAGG+TGG 0.711410 1:+64980256 MsaT004033.1:intron
TGACATGAGATTGAACCCGG+TGG 0.732137 1:-64979061 None:intergenic
AAAGAAAAGAAGAAACAACG+AGG 0.850112 1:+64980670 MsaT004033.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 64978952 64981200 64978952 ID=MsaG004033
Chr1 mRNA 64978952 64981200 64978952 ID=MsaT004033.1;Parent=MsaG004033
Chr1 exon 64978952 64979079 64978952 ID=MsaT004033.1.exon1;Parent=MsaT004033.1
Chr1 CDS 64978952 64979079 64978952 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Chr1 exon 64979400 64979475 64979400 ID=MsaT004033.1.exon2;Parent=MsaT004033.1
Chr1 CDS 64979400 64979475 64979400 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Chr1 exon 64979719 64979863 64979719 ID=MsaT004033.1.exon3;Parent=MsaT004033.1
Chr1 CDS 64979719 64979863 64979719 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Chr1 exon 64980264 64980314 64980264 ID=MsaT004033.1.exon4;Parent=MsaT004033.1
Chr1 CDS 64980264 64980314 64980264 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Chr1 exon 64980620 64980837 64980620 ID=MsaT004033.1.exon5;Parent=MsaT004033.1
Chr1 CDS 64980620 64980837 64980620 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Chr1 exon 64980943 64981200 64980943 ID=MsaT004033.1.exon6;Parent=MsaT004033.1
Chr1 CDS 64980943 64981200 64980943 ID=cds.MsaT004033.1;Parent=MsaT004033.1
Gene Sequence

>MsaT004033.1

ATGGTTTCATCAACATCACCATCAGATACCAAACTCACCAATGGGAAACAATACCCTTCTCCTGATGACTTAGAAAACTTCTATGTCAAACTCACTCAAGTGTTGGATTCCACCGGGTTCAATCTCATGTTCAATGTCCGAGAAACATCCTTAGACTTGTATCTGCTTTACCTGGAAGTCACCAGAAGAGGAGGTTTTCACCAGGTTGCTCTACAAAACCGATGGGTTGAAGTTGTCTCTGCACTAAAACTGGAAGGCAACAATGCAATCTTATCTATTCAAGTTGAAAGCCTCTATGCAATACTTCTATACAAATTTGAGAAATTGTACTTCTCTGGCAGCCCCAAAGATAATCTGAAGGTGGCAAAGATGTCAAAGGACTACTCTAGCCAAATGACAAGAGCTGACAGTCAAGAACCTCAAGTGCTTCTAGAAGCACCTTCAAATAACAAAGAAAAGAAGAAACAACGAGGTTCTCCAACTGGAAAAACCGGGTATCAAATATTCCTCAAGCAGGAATGTGCTCGATTAAAAGCTCATGATCAGGACATAGATGGCAAAAAAGTCCTACGCATGGCTGTTGATGCTTGGCAGAAGATGTCTGTCACCGATAAACAGCCATATATGGAGGAAAGCAAGAAGATAAAGGAAACAAACAAGGAAGCGATGATCGTTAATGACAATAAACAGAACAGACCTAGTGTGTGCGGTGACTCCTGCGTAACTTCGCAACCTCTAACAAATTACTCTTTTGTCAACAACACAACTGTGAAATTGGCTTTTGAAATGACTGAAGAAGCACTCAAGAATCCCTTCTTACCAGTTGATTTTGATACCTACTGTTCATTATATATGCTAAATGGGAAATCCAAATGA
Protein sequence

>MsaT004033.1

MVSSTSPSDTKLTNGKQYPSPDDLENFYVKLTQVLDSTGFNLMFNVRETSLDLYLLYLEVTRRGGFHQVALQNRWVEVVSALKLEGNNAILSIQVESLYAILLYKFEKLYFSGSPKDNLKVAKMSKDYSSQMTRADSQEPQVLLEAPSNNKEKKKQRGSPTGKTGYQIFLKQECARLKAHDQDIDGKKVLRMAVDAWQKMSVTDKQPYMEESKKIKETNKEAMIVNDNKQNRPSVCGDSCVTSQPLTNYSFVNNTTVKLAFEMTEEALKNPFLPVDFDTYCSLYMLNGKSK*