AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0552550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0552550 MtrunA17_Chr7g0236851 69.022 184 23 1 4 153 274 457 1.62e-75 237
Msa0552550 MtrunA17_Chr4g0037781 78.378 148 31 1 3 150 35 181 8.02e-74 219
Msa0552550 MtrunA17_Chr4g0037771 87.379 103 13 0 26 128 1 103 1.58e-62 187
Msa0552550 MtrunA17_Chr6g0468561 49.242 132 66 1 21 151 292 423 1.15e-31 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0552550 AT5G52510.1 53.535 99 41 1 21 119 265 358 3.96e-23 95.1

Find 26 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTCAAGCTCTCTTTCA+TGG 0.207322 4_1:+49223381 Msa0552550:CDS
GAAAACCATCGGAGAACTTT+TGG 0.233386 4_1:+49223498 Msa0552550:CDS
AGCTTCGAGGATTGCAATAT+TGG 0.276706 4_1:-49223407 None:intergenic
CGCGATTTCTGAAGGCAAAA+TGG 0.282354 4_1:+49223165 Msa0552550:CDS
TGGATCGAGAAGCTGAGTTT+AGG 0.401971 4_1:+49223518 Msa0552550:CDS
TTGCTGAACAATTCCACTAC+TGG 0.420472 4_1:-49223316 None:intergenic
AGAAGCTGAGTTTAGGAATC+GGG 0.442246 4_1:+49223525 Msa0552550:CDS
TCATTGGTTATTGGATTGCA+TGG 0.453909 4_1:+49223249 Msa0552550:CDS
TGAAGCAAAGAGAGTGATCA+AGG 0.468963 4_1:-49223366 None:intergenic
TATCTTCGAATGCAGCTTCG+AGG 0.471918 4_1:-49223420 None:intergenic
ATTCTCGTCATCGACGTTCA+CGG 0.490344 4_1:-49223473 None:intergenic
GTGTTTGAGAGAAACGAGAA+AGG 0.509883 4_1:-49223204 None:intergenic
AACAATTCCACTACTGGAGG+TGG 0.519425 4_1:-49223310 None:intergenic
GAGAAGCTGAGTTTAGGAAT+CGG 0.520002 4_1:+49223524 Msa0552550:CDS
TGTTTAGAAAACTCAGAAGC+AGG 0.526933 4_1:-49223121 None:intergenic
GCAGGTGAAACAATAAATGA+AGG 0.537435 4_1:-49223103 None:intergenic
TCGATCCAAAAGTTCTCCGA+TGG 0.537749 4_1:-49223503 None:intergenic
TTGTCAACACCAATGATGAA+TGG 0.543873 4_1:+49222982 None:intergenic
AGAAAATCCACCTCCAGTAG+TGG 0.576106 4_1:+49223303 Msa0552550:CDS
AAAGAGAGTGATCAAGGAGA+AGG 0.593121 4_1:-49223360 None:intergenic
GCAGCCACCGCGATTTCTGA+AGG 0.593218 4_1:+49223157 Msa0552550:CDS
GACGAGAATCTGAAAACCAT+CGG 0.602879 4_1:+49223487 Msa0552550:CDS
CTGAACAATTCCACTACTGG+AGG 0.606255 4_1:-49223313 None:intergenic
AGGCAAAATGGAATATGCGA+AGG 0.666561 4_1:+49223177 Msa0552550:CDS
AGGAGATGAATTTAGCGATG+TGG 0.715095 4_1:-49223083 None:intergenic
TTTGCCTTCAGAAATCGCGG+TGG 0.730189 4_1:-49223161 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATGATAAAAATTCAGTTTT+GGG - chr4_1:49223234-49223253 None:intergenic 15.0%
!!! CAATGATAAAAATTCAGTTT+TGG - chr4_1:49223235-49223254 None:intergenic 20.0%
!!! CAAAACTGAATTTTTATCAT+TGG + chr4_1:49223233-49223252 Msa0552550:CDS 20.0%
!!! GAATTTTTATCATTGGTTAT+TGG + chr4_1:49223240-49223259 Msa0552550:CDS 20.0%
! TGCTCAAACTATTCAAATTA+CGG - chr4_1:49223019-49223038 None:intergenic 25.0%
ATGAAACAGGTTTATGGATA+GGG - chr4_1:49223045-49223064 None:intergenic 30.0%
AATGAAACAGGTTTATGGAT+AGG - chr4_1:49223046-49223065 None:intergenic 30.0%
AAAGTATGTGAGAATGAAAC+AGG - chr4_1:49223058-49223077 None:intergenic 30.0%
GTGAGAATGAAACAGGTTTA+TGG - chr4_1:49223051-49223070 None:intergenic 35.0%
GCAGGTGAAACAATAAATGA+AGG - chr4_1:49223106-49223125 None:intergenic 35.0%
TGTTTAGAAAACTCAGAAGC+AGG - chr4_1:49223124-49223143 None:intergenic 35.0%
! TCATTGGTTATTGGATTGCA+TGG + chr4_1:49223249-49223268 Msa0552550:CDS 35.0%
AGGAGATGAATTTAGCGATG+TGG - chr4_1:49223086-49223105 None:intergenic 40.0%
! CATTTTGCCTTCAGAAATCG+CGG - chr4_1:49223167-49223186 None:intergenic 40.0%
AGGCAAAATGGAATATGCGA+AGG + chr4_1:49223177-49223196 Msa0552550:CDS 40.0%
GTGTTTGAGAGAAACGAGAA+AGG - chr4_1:49223207-49223226 None:intergenic 40.0%
TTGCTGAACAATTCCACTAC+TGG - chr4_1:49223319-49223338 None:intergenic 40.0%
AAAGAGAGTGATCAAGGAGA+AGG - chr4_1:49223363-49223382 None:intergenic 40.0%
TGAAGCAAAGAGAGTGATCA+AGG - chr4_1:49223369-49223388 None:intergenic 40.0%
TTGCTTCAAGCTCTCTTTCA+TGG + chr4_1:49223381-49223400 Msa0552550:CDS 40.0%
AGCTTCGAGGATTGCAATAT+TGG - chr4_1:49223410-49223429 None:intergenic 40.0%
GACGAGAATCTGAAAACCAT+CGG + chr4_1:49223487-49223506 Msa0552550:CDS 40.0%
! GAAAACCATCGGAGAACTTT+TGG + chr4_1:49223498-49223517 Msa0552550:CDS 40.0%
GAGAAGCTGAGTTTAGGAAT+CGG + chr4_1:49223524-49223543 Msa0552550:CDS 40.0%
AGAAGCTGAGTTTAGGAATC+GGG + chr4_1:49223525-49223544 Msa0552550:CDS 40.0%
GATGAATTTAGCGATGTGGC+TGG - chr4_1:49223082-49223101 None:intergenic 45.0%
! CGCGATTTCTGAAGGCAAAA+TGG + chr4_1:49223165-49223184 Msa0552550:CDS 45.0%
AGAAAATCCACCTCCAGTAG+TGG + chr4_1:49223303-49223322 Msa0552550:CDS 45.0%
AACAATTCCACTACTGGAGG+TGG - chr4_1:49223313-49223332 None:intergenic 45.0%
CTGAACAATTCCACTACTGG+AGG - chr4_1:49223316-49223335 None:intergenic 45.0%
TATCTTCGAATGCAGCTTCG+AGG - chr4_1:49223423-49223442 None:intergenic 45.0%
ATTCTCGTCATCGACGTTCA+CGG - chr4_1:49223476-49223495 None:intergenic 45.0%
TCGATCCAAAAGTTCTCCGA+TGG - chr4_1:49223506-49223525 None:intergenic 45.0%
TGGATCGAGAAGCTGAGTTT+AGG + chr4_1:49223518-49223537 Msa0552550:CDS 45.0%
TTTGCCTTCAGAAATCGCGG+TGG - chr4_1:49223164-49223183 None:intergenic 50.0%
GCAGCCACCGCGATTTCTGA+AGG + chr4_1:49223157-49223176 Msa0552550:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 49222997 49223552 49222997 ID=Msa0552550;Name=Msa0552550
chr4_1 mRNA 49222997 49223552 49222997 ID=Msa0552550-mRNA-1;Parent=Msa0552550;Name=Msa0552550-mRNA-1;_AED=0.20;_eAED=0.21;_QI=0|0|0|1|1|1|2|0|158
chr4_1 exon 49222997 49223003 49222997 ID=Msa0552550-mRNA-1:exon:13733;Parent=Msa0552550-mRNA-1
chr4_1 exon 49223083 49223552 49223083 ID=Msa0552550-mRNA-1:exon:13734;Parent=Msa0552550-mRNA-1
chr4_1 CDS 49222997 49223003 49222997 ID=Msa0552550-mRNA-1:cds;Parent=Msa0552550-mRNA-1
chr4_1 CDS 49223083 49223552 49223083 ID=Msa0552550-mRNA-1:cds;Parent=Msa0552550-mRNA-1
Gene Sequence

>Msa0552550

ATGAATGCCACATCGCTAAATTCATCTCCTTCATTTATTGTTTCACCTGCTTCTGAGTTTTCTAAACAATCGTTAATGAAAGCAGCCACCGCGATTTCTGAAGGCAAAATGGAATATGCGAAGGAAATCCTTTCTCGTTTCTCTCAAACACAAAACCCAAAACTGAATTTTTATCATTGGTTATTGGATTGCATGGCTTTAGCGTTGAAATCGCGTGTGAATAACATAGAAAATCCACCTCCAGTAGTGGAATTGTTCAGCAAAGAACATGTTGAGTCGACTCACCTTCTCCTTGATCACTCTCTTTGCTTCAAGCTCTCTTTCATGGCTGCCAATATTGCAATCCTCGAAGCTGCATTCGAAGATACAACAAAGAGCGTGAAGATTATGACTTTGACCGTGAACGTCGATGACGAGAATCTGAAAACCATCGGAGAACTTTTGGATCGAGAAGCTGAGTTTAGGAATCGGGTTTGA
Protein sequence

>Msa0552550

MNATSLNSSPSFIVSPASEFSKQSLMKAATAISEGKMEYAKEILSRFSQTQNPKLNFYHWLLDCMALALKSRVNNIENPPPVVELFSKEHVESTHLLLDHSLCFKLSFMAANIAILEAAFEDTTKSVKIMTLTVNVDDENLKTIGELLDREAEFRNRV*