AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480022211.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022211.01.T01 MTR_4g083360 59.274 248 30 4 5 208 375 595 2.76e-75 239
MsG0480022211.01.T01 MTR_4g083360 57.258 248 30 4 5 208 375 590 5.18e-71 228
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022211.01.T01 AT5G56360 38.462 234 74 7 13 208 396 597 2.06e-35 132

Find 41 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCCATTCCACCACCCGTTT+GGG 0.243752 4:+69734876 MsG0480022211.01.T01:CDS
ATAACTTACCCTTTACTCTT+TGG 0.276628 4:+69734413 MsG0480022211.01.T01:CDS
CCTCTCAAAACTGAAATAAA+TGG 0.298702 4:-69735157 None:intergenic
GGGCCATTCCACCACCCGTT+TGG 0.326302 4:+69734875 MsG0480022211.01.T01:CDS
TTTCTAATGGTGATCATTGC+TGG 0.357080 4:+69735078 MsG0480022211.01.T01:CDS
TATCAAAGGGTGGTATATAA+TGG 0.377882 4:+69734207 MsG0480022211.01.T01:CDS
TATATCTTCGTCATATTTGC+CGG 0.384323 4:-69734073 None:intergenic
CATACCTTCAAACTCCTATC+AGG 0.404765 4:-69735107 None:intergenic
AAGAGAAGCCAAAGAGTAAA+GGG 0.411845 4:-69734421 None:intergenic
TGGTGGAATGGCCCTCCTCC+TGG 0.417770 4:-69734866 None:intergenic
TACCAAAACCTTACCCCAAA+CGG 0.426842 4:-69734890 None:intergenic
CCCCTATAAACAGGCTAGCC+AGG 0.438029 4:+69734848 MsG0480022211.01.T01:intron
CAGGCGCTGGGACAAATTTG+AGG 0.449184 4:+69735034 MsG0480022211.01.T01:intron
GAGAGTGAACCAGACTTGTC+AGG 0.460654 4:+69734159 MsG0480022211.01.T01:CDS
ATTGCTGGAACGGTCCTGAT+AGG 0.460707 4:+69735093 MsG0480022211.01.T01:CDS
GCTATTAGACAATGAAGATC+AGG 0.465294 4:+69733986 None:intergenic
CTATACAAACCTGACAAGTC+TGG 0.470143 4:-69734168 None:intergenic
ACCAAAACCTTACCCCAAAC+GGG 0.470971 4:-69734889 None:intergenic
TAATTCAAATGTTTATCAAA+GGG 0.473599 4:+69734194 MsG0480022211.01.T01:CDS
AAAGAGAAGCCAAAGAGTAA+AGG 0.479630 4:-69734422 None:intergenic
ACCTTACCCCAAACGGGTGG+TGG 0.480378 4:-69734883 None:intergenic
ACCCCAAACGGGTGGTGGAA+TGG 0.481723 4:-69734878 None:intergenic
TTAATTCAAATGTTTATCAA+AGG 0.484406 4:+69734193 MsG0480022211.01.T01:CDS
CAGATTTGTATGAGGAACTA+AGG 0.503712 4:-69734131 None:intergenic
TGAGGATTCATACAAAGTAA+TGG 0.517215 4:+69735052 MsG0480022211.01.T01:CDS
GCACAACAGATGACCCTTCG+TGG 0.528602 4:+69734268 MsG0480022211.01.T01:CDS
CGGTCCTGATAGGAGTTTGA+AGG 0.533208 4:+69735103 MsG0480022211.01.T01:CDS
ACAAATAATGAAGAGAATGA+AGG 0.542197 4:+69734024 MsG0480022211.01.T01:CDS
CTCTACGTCAGATTTGTATG+AGG 0.542667 4:-69734139 None:intergenic
TTCAAATGTTTATCAAAGGG+TGG 0.543853 4:+69734197 MsG0480022211.01.T01:CDS
TAAACAGGCTAGCCAGGAGG+AGG 0.555074 4:+69734854 MsG0480022211.01.T01:intron
AATGGTGATCATTGCTGGAA+CGG 0.578500 4:+69735083 MsG0480022211.01.T01:CDS
AAACGATGAAGAATTTCAAG+AGG 0.591771 4:+69734095 MsG0480022211.01.T01:CDS
GCCATTCCACCACCCGTTTG+GGG 0.596501 4:+69734877 MsG0480022211.01.T01:CDS
AGATGCTGCTCGTATACGCA+AGG 0.627154 4:+69734445 MsG0480022211.01.T01:CDS
TCTGAAACTGACGACGACAC+CGG 0.629370 4:+69734054 MsG0480022211.01.T01:CDS
AAACAGGCTAGCCAGGAGGA+GGG 0.674511 4:+69734855 MsG0480022211.01.T01:intron
AGATCAGGAATATTCTACAC+GGG 0.681933 4:+69734001 MsG0480022211.01.T01:CDS
AAAACCTTACCCCAAACGGG+TGG 0.683329 4:-69734886 None:intergenic
AAGATCAGGAATATTCTACA+CGG 0.684889 4:+69734000 MsG0480022211.01.T01:CDS
CTATAAACAGGCTAGCCAGG+AGG 0.720671 4:+69734851 MsG0480022211.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTCAAATGTTTATCAAA+GGG + Chr4:69734194-69734213 MsG0480022211.01.T01:CDS 15.0%
!! TTAATTCAAATGTTTATCAA+AGG + Chr4:69734193-69734212 MsG0480022211.01.T01:CDS 15.0%
!!! TTTTATATTCTCTGTAAAAG+AGG + Chr4:69734987-69735006 MsG0480022211.01.T01:intron 20.0%
! ACAAATAATGAAGAGAATGA+AGG + Chr4:69734024-69734043 MsG0480022211.01.T01:CDS 25.0%
! ACAAATATTATTTGTCCAGA+TGG + Chr4:69734388-69734407 MsG0480022211.01.T01:intron 25.0%
! AGAAAATACAGAAATCTGTA+TGG + Chr4:69734295-69734314 MsG0480022211.01.T01:intron 25.0%
! ATCTGTATGGAATATTATTC+AGG + Chr4:69734308-69734327 MsG0480022211.01.T01:intron 25.0%
!! AAAGTAATGGTGTTTTCTAA+TGG + Chr4:69735065-69735084 MsG0480022211.01.T01:CDS 25.0%
!! AACAGAAAGTAAACTTTTAG+GGG - Chr4:69734729-69734748 None:intergenic 25.0%
!! ACAAAGCAAAAACTTGATTT+TGG + Chr4:69734526-69734545 MsG0480022211.01.T01:CDS 25.0%
!! ACAACAGAAAGTAAACTTTT+AGG - Chr4:69734731-69734750 None:intergenic 25.0%
!! CAACAGAAAGTAAACTTTTA+GGG - Chr4:69734730-69734749 None:intergenic 25.0%
!! TAATTCAGTTTTCTTTTCAC+AGG + Chr4:69735015-69735034 MsG0480022211.01.T01:intron 25.0%
AAACGATGAAGAATTTCAAG+AGG + Chr4:69734095-69734114 MsG0480022211.01.T01:CDS 30.0%
AAGATCAGGAATATTCTACA+CGG + Chr4:69734000-69734019 MsG0480022211.01.T01:CDS 30.0%
AAGTAAAACTTCAATGCTAC+AGG + Chr4:69734630-69734649 MsG0480022211.01.T01:intron 30.0%
AATGAATAAAACTCCTTTGC+TGG - Chr4:69734657-69734676 None:intergenic 30.0%
ATAACTTACCCTTTACTCTT+TGG + Chr4:69734413-69734432 MsG0480022211.01.T01:CDS 30.0%
TATATCTTCGTCATATTTGC+CGG - Chr4:69734076-69734095 None:intergenic 30.0%
TATCAAAGGGTGGTATATAA+TGG + Chr4:69734207-69734226 MsG0480022211.01.T01:CDS 30.0%
TGAGGATTCATACAAAGTAA+TGG + Chr4:69735052-69735071 MsG0480022211.01.T01:CDS 30.0%
TTCAAATGTTTATCAAAGGG+TGG + Chr4:69734197-69734216 MsG0480022211.01.T01:CDS 30.0%
!! AGACTGTATTTTAGACAACT+TGG - Chr4:69734489-69734508 None:intergenic 30.0%
!!! ACTTTCTGGGATGAAAATTT+TGG + Chr4:69734802-69734821 MsG0480022211.01.T01:intron 30.0%
AAAGAGAAGCCAAAGAGTAA+AGG - Chr4:69734425-69734444 None:intergenic 35.0%
AAGAGAAGCCAAAGAGTAAA+GGG - Chr4:69734424-69734443 None:intergenic 35.0%
AAGGGTAAGTTATATCCATC+TGG - Chr4:69734406-69734425 None:intergenic 35.0%
AGATCAGGAATATTCTACAC+GGG + Chr4:69734001-69734020 MsG0480022211.01.T01:CDS 35.0%
CAGATTTGTATGAGGAACTA+AGG - Chr4:69734134-69734153 None:intergenic 35.0%
TTAATCAGACTGTGTTTCTC+CGG + Chr4:69734927-69734946 MsG0480022211.01.T01:intron 35.0%
TTTCTAATGGTGATCATTGC+TGG + Chr4:69735078-69735097 MsG0480022211.01.T01:CDS 35.0%
! CACAATACAAATGCTTTGAG+TGG - Chr4:69734576-69734595 None:intergenic 35.0%
! CACTCAAAGCATTTGTATTG+TGG + Chr4:69734574-69734593 MsG0480022211.01.T01:intron 35.0%
! GTATTTTCTCTAACCACGAA+GGG - Chr4:69734284-69734303 None:intergenic 35.0%
! TCAAAGCATTTGTATTGTGG+AGG + Chr4:69734577-69734596 MsG0480022211.01.T01:intron 35.0%
! TCAAGTTTTTGCTTTGTGTC+AGG - Chr4:69734523-69734542 None:intergenic 35.0%
! TGTATTTTCTCTAACCACGA+AGG - Chr4:69734285-69734304 None:intergenic 35.0%
!!! GATTTTGGTTAGTATCATGC+TGG + Chr4:69734541-69734560 MsG0480022211.01.T01:CDS 35.0%
!!! TGGGATGAAAATTTTGGTTC+AGG + Chr4:69734808-69734827 MsG0480022211.01.T01:intron 35.0%
AATGGTGATCATTGCTGGAA+CGG + Chr4:69735083-69735102 MsG0480022211.01.T01:CDS 40.0%
AGAAAGTGAGATGACGAGAT+AGG - Chr4:69734789-69734808 None:intergenic 40.0%
ATCTCGTCATCTCACTTTCT+GGG + Chr4:69734789-69734808 MsG0480022211.01.T01:intron 40.0%
CATACCTTCAAACTCCTATC+AGG - Chr4:69735110-69735129 None:intergenic 40.0%
CTATACAAACCTGACAAGTC+TGG - Chr4:69734171-69734190 None:intergenic 40.0%
CTCTACGTCAGATTTGTATG+AGG - Chr4:69734142-69734161 None:intergenic 40.0%
GTATTGTGGAGGTTTAGTTG+TGG + Chr4:69734588-69734607 MsG0480022211.01.T01:intron 40.0%
TACCAAAACCTTACCCCAAA+CGG - Chr4:69734893-69734912 None:intergenic 40.0%
TATCTCGTCATCTCACTTTC+TGG + Chr4:69734788-69734807 MsG0480022211.01.T01:intron 40.0%
TCAAAAACTCGAGCATCAGT+TGG + Chr4:69734951-69734970 MsG0480022211.01.T01:intron 40.0%
TGGAGGTTTAGTTGTGGAAT+TGG + Chr4:69734594-69734613 MsG0480022211.01.T01:intron 40.0%
! ATGTCTACCTGACTGATTCA+CGG - Chr4:69734355-69734374 None:intergenic 40.0%
! GGGTGTCTGGAATATATTGA+CGG - Chr4:69734334-69734353 None:intergenic 40.0%
! TGATGCTCGAGTTTTTGAAC+CGG - Chr4:69734949-69734968 None:intergenic 40.0%
ACCAAAACCTTACCCCAAAC+GGG - Chr4:69734892-69734911 None:intergenic 45.0%
CAAAGTCTGCCCCTATAAAC+AGG + Chr4:69734839-69734858 MsG0480022211.01.T01:intron 45.0%
! AGTTTTCTTTTCACAGGCGC+TGG + Chr4:69735021-69735040 MsG0480022211.01.T01:intron 45.0%
! GTTTTCTTTTCACAGGCGCT+GGG + Chr4:69735022-69735041 MsG0480022211.01.T01:intron 45.0%
! TGTCTACCTGACTGATTCAC+GGG - Chr4:69734354-69734373 None:intergenic 45.0%
!! TCCTGGCTAGCCTGTTTATA+GGG - Chr4:69734852-69734871 None:intergenic 45.0%
AAAACCTTACCCCAAACGGG+TGG - Chr4:69734889-69734908 None:intergenic 50.0%
AGATGCTGCTCGTATACGCA+AGG + Chr4:69734445-69734464 MsG0480022211.01.T01:CDS 50.0%
ATTGCTGGAACGGTCCTGAT+AGG + Chr4:69735093-69735112 MsG0480022211.01.T01:CDS 50.0%
CAATGCTACAGGTCCAGCAA+AGG + Chr4:69734641-69734660 MsG0480022211.01.T01:intron 50.0%
CGGTCCTGATAGGAGTTTGA+AGG + Chr4:69735103-69735122 MsG0480022211.01.T01:CDS 50.0%
GAGAGTGAACCAGACTTGTC+AGG + Chr4:69734159-69734178 MsG0480022211.01.T01:CDS 50.0%
! CTATAAACAGGCTAGCCAGG+AGG + Chr4:69734851-69734870 MsG0480022211.01.T01:intron 50.0%
! TCTGAAACTGACGACGACAC+CGG + Chr4:69734054-69734073 MsG0480022211.01.T01:CDS 50.0%
!! ACCCGTTTGGGGTAAGGTTT+TGG + Chr4:69734888-69734907 MsG0480022211.01.T01:intron 50.0%
!! CCTGGCTAGCCTGTTTATAG+GGG - Chr4:69734851-69734870 None:intergenic 50.0%
!! CTCCTGGCTAGCCTGTTTAT+AGG - Chr4:69734853-69734872 None:intergenic 50.0%
CAGACACCCGTGAATCAGTC+AGG + Chr4:69734345-69734364 MsG0480022211.01.T01:intron 55.0%
GCACAACAGATGACCCTTCG+TGG + Chr4:69734268-69734287 MsG0480022211.01.T01:CDS 55.0%
! AAACAGGCTAGCCAGGAGGA+GGG + Chr4:69734855-69734874 MsG0480022211.01.T01:intron 55.0%
! CCCCTATAAACAGGCTAGCC+AGG + Chr4:69734848-69734867 MsG0480022211.01.T01:intron 55.0%
! CTGACTGATTCACGGGTGTC+TGG - Chr4:69734347-69734366 None:intergenic 55.0%
! TAAACAGGCTAGCCAGGAGG+AGG + Chr4:69734854-69734873 MsG0480022211.01.T01:intron 55.0%
!! CAGGCGCTGGGACAAATTTG+AGG + Chr4:69735034-69735053 MsG0480022211.01.T01:intron 55.0%
ACCTTACCCCAAACGGGTGG+TGG - Chr4:69734886-69734905 None:intergenic 60.0%
GCCATTCCACCACCCGTTTG+GGG + Chr4:69734877-69734896 MsG0480022211.01.T01:CDS 60.0%
GGCCATTCCACCACCCGTTT+GGG + Chr4:69734876-69734895 MsG0480022211.01.T01:CDS 60.0%
! TCCACCACCCGTTTGGGGTA+AGG + Chr4:69734882-69734901 MsG0480022211.01.T01:intron 60.0%
!! ACCCCAAACGGGTGGTGGAA+TGG - Chr4:69734881-69734900 None:intergenic 60.0%
GGGCCATTCCACCACCCGTT+TGG + Chr4:69734875-69734894 MsG0480022211.01.T01:CDS 65.0%
TGGTGGAATGGCCCTCCTCC+TGG - Chr4:69734869-69734888 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 69733997 69735175 69733997 ID=MsG0480022211.01;Name=MsG0480022211.01
Chr4 mRNA 69733997 69735175 69733997 ID=MsG0480022211.01.T01;Parent=MsG0480022211.01;Name=MsG0480022211.01.T01;_AED=0.49;_eAED=0.61;_QI=0|0.33|0|1|0.66|0.5|4|0|215
Chr4 exon 69733997 69734311 69733997 ID=MsG0480022211.01.T01:exon:59560;Parent=MsG0480022211.01.T01
Chr4 exon 69734407 69734562 69734407 ID=MsG0480022211.01.T01:exon:59561;Parent=MsG0480022211.01.T01
Chr4 exon 69734861 69734898 69734861 ID=MsG0480022211.01.T01:exon:59562;Parent=MsG0480022211.01.T01
Chr4 exon 69735037 69735175 69735037 ID=MsG0480022211.01.T01:exon:59563;Parent=MsG0480022211.01.T01
Chr4 CDS 69733997 69734311 69733997 ID=MsG0480022211.01.T01:cds;Parent=MsG0480022211.01.T01
Chr4 CDS 69734407 69734562 69734407 ID=MsG0480022211.01.T01:cds;Parent=MsG0480022211.01.T01
Chr4 CDS 69734861 69734898 69734861 ID=MsG0480022211.01.T01:cds;Parent=MsG0480022211.01.T01
Chr4 CDS 69735037 69735175 69735037 ID=MsG0480022211.01.T01:cds;Parent=MsG0480022211.01.T01
Gene Sequence

>MsG0480022211.01.T01

ATGAAGATCAGGAATATTCTACACGGGACAAATAATGAAGAGAATGAAGGATATGCTTCTGAAACTGACGACGACACCGGCAAATATGACGAAGATATAAACGATGAAGAATTTCAAGAGGATGAGCACGAAGACCTTAGTTCCTCATACAAATCTGACGTAGAGAGTGAACCAGACTTGTCAGGTTTGTATAGTATTAATTCAAATGTTTATCAAAGGGTGGTATATAATGGACTTGTGATTATGATAATTCAAATTAACTCAGATGTTAGCACAACAGATGACCCTTCGTGGTTAGAGAAAATACAGAAATCTATGGATATAACTTACCCTTTACTCTTTGGCTTCTCTTTAGATGCTGCTCGTATACGCAAGGAATATGACGAATCAAGTGCCAAGTTGTCTAAAATACAGTCTAGAATATCGAGCCTGACACAAAGCAAAAACTTGATTTTGGTTAGTATCATGCTGGCTAGCCAGGAGGAGGGCCATTCCACCACCCGTTTGGGGCGCTGGGACAAATTTGAGGATTCATACAAAGTAATGGTGTTTTCTAATGGTGATCATTGCTGGAACGGTCCTGATAGGAGTTTGAAGGTATGTATGTTTCTTAATTTTAAAAATTATTGCCATTTATTTCAGTTTTGA
Protein sequence

>MsG0480022211.01.T01

MKIRNILHGTNNEENEGYASETDDDTGKYDEDINDEEFQEDEHEDLSSSYKSDVESEPDLSGLYSINSNVYQRVVYNGLVIMIIQINSDVSTTDDPSWLEKIQKSMDITYPLLFGFSLDAARIRKEYDESSAKLSKIQSRISSLTQSKNLILVSIMLASQEEGHSTTRLGRWDKFEDSYKVMVFSNGDHCWNGPDRSLKVCMFLNFKNYCHLFQF*