AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015977.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015977.01.T01 MTR_3g080910 95.333 150 7 0 49 198 15 164 1.65e-89 259
MsG0380015977.01.T01 MTR_1g009780 67.213 183 42 3 15 197 35 199 1.90e-69 210
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015977.01.T01 AT1G71430 68.966 58 14 1 49 106 59 112 2.17e-19 81.3

Find 34 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGCAGCTGCCACAGCCT+CGG 0.349576 3:+77423201 None:intergenic
TGCATAAATAACACAAAGTA+TGG 0.364597 3:+77423615 None:intergenic
TTCTGGCAGGATTTGATGCT+TGG 0.389672 3:-77423244 MsG0380015977.01.T01:intron
ACTAAGAGACTCCCCATTGA+TGG 0.410116 3:-77424961 MsG0380015977.01.T01:CDS
TCTTCAAAATCATATTTCTC+TGG 0.421371 3:+77423415 None:intergenic
TCTGCAGCTGCCACAGCCTC+GGG 0.423318 3:+77423202 None:intergenic
TGAAATCACAGGCTGACAAC+TGG 0.430242 3:+77423168 None:intergenic
TGAATCCGAAGTTATTGAAA+TGG 0.431704 3:-77423380 MsG0380015977.01.T01:intron
AGGAGGAAGTGGAGCAGTGA+AGG 0.457109 3:+77424933 None:intergenic
AATGTTGATGGATGTGATTA+TGG 0.457598 3:-77423064 MsG0380015977.01.T01:CDS
GAAATTGATAGCAATGTTGA+TGG 0.467712 3:-77423076 MsG0380015977.01.T01:CDS
TTGTCAGCCTGTGATTTCAT+TGG 0.468422 3:-77423164 MsG0380015977.01.T01:CDS
GGGAAGGTTAAAGACTTCCT+AGG 0.469316 3:-77423586 MsG0380015977.01.T01:CDS
GTACGTTGGCTAGGAGGAAG+TGG 0.487451 3:+77424922 None:intergenic
ACTGACCATTTCAATAACTT+CGG 0.515230 3:+77423375 None:intergenic
GTGATTTCATTGGCAGCTGA+TGG 0.517345 3:-77423154 MsG0380015977.01.T01:CDS
GGAGGAAGTGGAGCAGTGAA+GGG 0.517770 3:+77424934 None:intergenic
GCGATAGTTGAGCTATCATA+AGG 0.519781 3:-77422938 None:intergenic
TCTTCATACACCCGAGGCTG+TGG 0.530064 3:-77423212 MsG0380015977.01.T01:CDS
TTGCTTCTGACATCACTCCT+AGG 0.532335 3:+77423569 None:intergenic
GTCAGAAGCAAATAAGCGGT+TGG 0.557918 3:-77423557 MsG0380015977.01.T01:CDS
TTAGAAAGAGTACGTTGGCT+AGG 0.562603 3:+77424913 None:intergenic
GAAAGAGTACGTTGGCTAGG+AGG 0.570426 3:+77424916 None:intergenic
ATAGATTCAGAAGAAGAAAG+TGG 0.571807 3:-77423124 MsG0380015977.01.T01:CDS
GCGGTTGGAGCATGATGCAA+AGG 0.584323 3:-77423542 MsG0380015977.01.T01:intron
GAGGAAGTGGAGCAGTGAAG+GGG 0.586631 3:+77424935 None:intergenic
TCAGCTGCCAATGAAATCAC+AGG 0.597271 3:+77423157 None:intergenic
AGGAAGTGGAGCAGTGAAGG+GGG 0.601530 3:+77424936 None:intergenic
GGATGTGATTATGGAAATGA+CGG 0.606116 3:-77423055 MsG0380015977.01.T01:CDS
GTTATCGCATACAAGAAGAG+TGG 0.618295 3:+77425005 None:intergenic
TATGATAGCTCAACTATCGC+CGG 0.637257 3:+77422941 None:intergenic
TGCTGATCTTCATACACCCG+AGG 0.644796 3:-77423218 MsG0380015977.01.T01:CDS
TGATGTCAGAAGCAAATAAG+CGG 0.692081 3:-77423561 MsG0380015977.01.T01:CDS
TGGCGCTGATGATGACAATG+AGG 0.716466 3:-77423104 MsG0380015977.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTAAACTTTTAAAATTA+TGG - Chr3:77424134-77424153 MsG0380015977.01.T01:intron 10.0%
!! AAGTATTAGTATACATGTAT+GGG + Chr3:77423646-77423665 None:intergenic 20.0%
!! AATATAGATCTACTTATAGT+GGG - Chr3:77423573-77423592 MsG0380015977.01.T01:CDS 20.0%
!! ATTACAGAAGAAAAAGAAAA+AGG + Chr3:77423082-77423101 None:intergenic 20.0%
!!! CGATTTGATAATAATTTGTA+TGG + Chr3:77423673-77423692 None:intergenic 20.0%
!!! TTATTTTCTGTTTTGATTTC+TGG - Chr3:77424702-77424721 MsG0380015977.01.T01:intron 20.0%
!!! TTCAAGATTTTGTATCATAT+TGG - Chr3:77423976-77423995 MsG0380015977.01.T01:intron 20.0%
!!! TTTTTTGAATTGGATGTATA+AGG + Chr3:77424513-77424532 None:intergenic 20.0%
! AATATCTGGTTATATGATAG+TGG - Chr3:77424246-77424265 MsG0380015977.01.T01:intron 25.0%
! AATTGGATGTATAAGGAAAT+AGG + Chr3:77424506-77424525 None:intergenic 25.0%
! AGTATTAGTATACATGTATG+GGG + Chr3:77423645-77423664 None:intergenic 25.0%
! ATGAATATAGACTGATATGA+AGG + Chr3:77424647-77424666 None:intergenic 25.0%
! ATTGGATGTATAAGGAAATA+GGG + Chr3:77424505-77424524 None:intergenic 25.0%
! CAAGTATTAGTATACATGTA+TGG + Chr3:77423647-77423666 None:intergenic 25.0%
! CAATATAGATCTACTTATAG+TGG - Chr3:77423572-77423591 MsG0380015977.01.T01:CDS 25.0%
! CCAATTCAAAAAACAAATGT+AGG - Chr3:77424520-77424539 MsG0380015977.01.T01:intron 25.0%
! TATATCCATGAAAAACAGAA+AGG - Chr3:77424977-77424996 MsG0380015977.01.T01:CDS 25.0%
! TCTTCAAAATCATATTTCTC+TGG + Chr3:77424551-77424570 None:intergenic 25.0%
! TGAATATAGACTGATATGAA+GGG + Chr3:77424646-77424665 None:intergenic 25.0%
! TGCATAAATAACACAAAGTA+TGG + Chr3:77424351-77424370 None:intergenic 25.0%
!! GACTTGTTCAAATTTCAATA+CGG + Chr3:77423262-77423281 None:intergenic 25.0%
!!! AGGTTTTGTATCATATTGAT+TGG - Chr3:77424048-77424067 MsG0380015977.01.T01:intron 25.0%
!!! CCTACATTTGTTTTTTGAAT+TGG + Chr3:77424523-77424542 None:intergenic 25.0%
!!! GTGTTATTTATGCAGTTTTA+GGG - Chr3:77424357-77424376 MsG0380015977.01.T01:intron 25.0%
!!! TATAAGCTTGTTAGAAATGA+TGG - Chr3:77423455-77423474 MsG0380015977.01.T01:intron 25.0%
!!! TATGATTTTGAAGAGTTAAC+AGG - Chr3:77424557-77424576 MsG0380015977.01.T01:intron 25.0%
!!! TGTGTTATTTATGCAGTTTT+AGG - Chr3:77424356-77424375 MsG0380015977.01.T01:intron 25.0%
!!! TTAAGTGTTTTTGTCAAGTA+TGG + Chr3:77423179-77423198 None:intergenic 25.0%
ACTGACCATTTCAATAACTT+CGG + Chr3:77424591-77424610 None:intergenic 30.0%
ATAGATTCAGAAGAAGAAAG+TGG - Chr3:77424839-77424858 MsG0380015977.01.T01:intron 30.0%
ATATTCAACACTGGAATCTT+AGG + Chr3:77424225-77424244 None:intergenic 30.0%
ATGTGACTAAAAGAAACGTT+TGG + Chr3:77423484-77423503 None:intergenic 30.0%
CAGATATTGATATTCAACAC+TGG + Chr3:77424234-77424253 None:intergenic 30.0%
CCAAACACTACAAATTCAAT+CGG + Chr3:77423342-77423361 None:intergenic 30.0%
GAATATAGACTGATATGAAG+GGG + Chr3:77424645-77424664 None:intergenic 30.0%
GTTTCAACTATGATGTTAAC+TGG - Chr3:77423132-77423151 MsG0380015977.01.T01:CDS 30.0%
TATTCAACACTGGAATCTTA+GGG + Chr3:77424224-77424243 None:intergenic 30.0%
TCTCTAACAAACAGACAATT+GGG + Chr3:77423912-77423931 None:intergenic 30.0%
TGAATCCGAAGTTATTGAAA+TGG - Chr3:77424583-77424602 MsG0380015977.01.T01:intron 30.0%
TGATGTTAACTGGTATTTGT+TGG - Chr3:77423142-77423161 MsG0380015977.01.T01:CDS 30.0%
TGTGTAGAAAATGTTCAGAT+TGG + Chr3:77423789-77423808 None:intergenic 30.0%
TTCTCTAACAAACAGACAAT+TGG + Chr3:77423913-77423932 None:intergenic 30.0%
! AAAGCACTTTGGTCAAATAT+TGG + Chr3:77423718-77423737 None:intergenic 30.0%
! AAATTGACAGTAAAGCACTT+TGG + Chr3:77423729-77423748 None:intergenic 30.0%
! AATCCTTTTTGACGACTTAA+TGG + Chr3:77423813-77423832 None:intergenic 30.0%
! AATGTTGATGGATGTGATTA+TGG - Chr3:77424899-77424918 MsG0380015977.01.T01:intron 30.0%
! AATTGTCTGTTTGTTAGAGA+AGG - Chr3:77423912-77423931 MsG0380015977.01.T01:intron 30.0%
! ATGAATTAGAAAGAGTACGT+TGG + Chr3:77423058-77423077 None:intergenic 30.0%
! ATTGACAACATTTTGTACCA+AGG + Chr3:77423556-77423575 None:intergenic 30.0%
! CAGTGTTGAATATCAATATC+TGG - Chr3:77424232-77424251 MsG0380015977.01.T01:intron 30.0%
! GAAATTGATAGCAATGTTGA+TGG - Chr3:77424887-77424906 MsG0380015977.01.T01:intron 30.0%
! TATAGCAGGTTCTTTAAAGA+AGG - Chr3:77424296-77424315 MsG0380015977.01.T01:intron 30.0%
! TGTGTGTGATGATTTTTGTA+AGG - Chr3:77424028-77424047 MsG0380015977.01.T01:intron 30.0%
! TTGACAACATTTTGTACCAA+GGG + Chr3:77423555-77423574 None:intergenic 30.0%
!! CTAAACCAGAAGTATGTTTT+TGG + Chr3:77424955-77424974 None:intergenic 30.0%
!! GATTTCCTTTCTGTTTTTCA+TGG + Chr3:77424985-77425004 None:intergenic 30.0%
!!! AGAAGTATGTTTTTGGTCAA+GGG + Chr3:77424948-77424967 None:intergenic 30.0%
!!! TATTTATGCAGTTTTAGGGA+AGG - Chr3:77424361-77424380 MsG0380015977.01.T01:intron 30.0%
AGCATTATGTGAATCAAACC+AGG + Chr3:77423855-77423874 None:intergenic 35.0%
CAGATTGGAATCTGAATTCA+AGG + Chr3:77423774-77423793 None:intergenic 35.0%
CCGATTGAATTTGTAGTGTT+TGG - Chr3:77423339-77423358 MsG0380015977.01.T01:intron 35.0%
CTTGACCAAAAACATACTTC+TGG - Chr3:77424947-77424966 MsG0380015977.01.T01:CDS 35.0%
GGATGTGATTATGGAAATGA+CGG - Chr3:77424908-77424927 MsG0380015977.01.T01:intron 35.0%
GTTTGATTCACATAATGCTG+TGG - Chr3:77423856-77423875 MsG0380015977.01.T01:intron 35.0%
TGATGTCAGAAGCAAATAAG+CGG - Chr3:77424402-77424421 MsG0380015977.01.T01:intron 35.0%
TGTACGGCTATATATGTATG+CGG - Chr3:77424112-77424131 MsG0380015977.01.T01:intron 35.0%
! TGTGGTCTTAAACTTATTCC+TGG - Chr3:77423834-77423853 MsG0380015977.01.T01:intron 35.0%
!!! CAGAAGTATGTTTTTGGTCA+AGG + Chr3:77424949-77424968 None:intergenic 35.0%
!!! TTTCTGTTTTGATTTCTGGC+AGG - Chr3:77424706-77424725 MsG0380015977.01.T01:intron 35.0%
AGTCGTCAAAAAGGATTCTG+TGG - Chr3:77423816-77423835 MsG0380015977.01.T01:intron 40.0%
AGTCGTCGTTTGAATATAGC+AGG - Chr3:77424282-77424301 MsG0380015977.01.T01:intron 40.0%
CACAGATTGCGGAAAAAAAG+AGG + Chr3:77423609-77423628 None:intergenic 40.0%
CAGCCATTAAGTCGTCAAAA+AGG - Chr3:77423807-77423826 MsG0380015977.01.T01:intron 40.0%
GCATTGTCATACACAGATTG+CGG + Chr3:77423620-77423639 None:intergenic 40.0%
GTTATCGCATACAAGAAGAG+TGG + Chr3:77422961-77422980 None:intergenic 40.0%
TATGATAGCTCAACTATCGC+CGG + Chr3:77425025-77425044 None:intergenic 40.0%
TTGTCAGCCTGTGATTTCAT+TGG - Chr3:77424799-77424818 MsG0380015977.01.T01:intron 40.0%
! GCACTGTTTTCGTTCTTGTA+CGG - Chr3:77424096-77424115 MsG0380015977.01.T01:intron 40.0%
! TATTGGTCTCTTACACTAGC+AGG + Chr3:77423701-77423720 None:intergenic 40.0%
! TTAGAAAGAGTACGTTGGCT+AGG + Chr3:77423053-77423072 None:intergenic 40.0%
! TTTTGTACCAAGGGTCTGTA+TGG + Chr3:77423546-77423565 None:intergenic 40.0%
ACTAAGAGACTCCCCATTGA+TGG - Chr3:77423002-77423021 MsG0380015977.01.T01:CDS 45.0%
CACTGGAATCTTAGGGCAAA+AGG + Chr3:77424217-77424236 None:intergenic 45.0%
GGGAAGGTTAAAGACTTCCT+AGG - Chr3:77424377-77424396 MsG0380015977.01.T01:intron 45.0%
GTCAGAAGCAAATAAGCGGT+TGG - Chr3:77424406-77424425 MsG0380015977.01.T01:intron 45.0%
GTGATTTCATTGGCAGCTGA+TGG - Chr3:77424809-77424828 MsG0380015977.01.T01:intron 45.0%
TCAGCTGCCAATGAAATCAC+AGG + Chr3:77424809-77424828 None:intergenic 45.0%
TGAAATCACAGGCTGACAAC+TGG + Chr3:77424798-77424817 None:intergenic 45.0%
TTCTGGCAGGATTTGATGCT+TGG - Chr3:77424719-77424738 MsG0380015977.01.T01:intron 45.0%
TTGCTTCTGACATCACTCCT+AGG + Chr3:77424397-77424416 None:intergenic 45.0%
TTGGGACAACATGCAAGACA+AGG + Chr3:77423894-77423913 None:intergenic 45.0%
!!! TGTTTTTGGTCAAGGGACGA+AGG + Chr3:77424941-77424960 None:intergenic 45.0%
AGTGAAGGGGGTTCCATCAA+TGG + Chr3:77423018-77423037 None:intergenic 50.0%
GTGAAGGGGGTTCCATCAAT+GGG + Chr3:77423017-77423036 None:intergenic 50.0%
TGAAGGGGGTTCCATCAATG+GGG + Chr3:77423016-77423035 None:intergenic 50.0%
TGCTGATCTTCATACACCCG+AGG - Chr3:77424745-77424764 MsG0380015977.01.T01:intron 50.0%
! GAAAGAGTACGTTGGCTAGG+AGG + Chr3:77423050-77423069 None:intergenic 50.0%
!! TCGTCCTTCGAAAAAGCGTC+CGG - Chr3:77425003-77425022 MsG0380015977.01.T01:CDS 50.0%
!! TGGCGCTGATGATGACAATG+AGG - Chr3:77424859-77424878 MsG0380015977.01.T01:intron 50.0%
AGGAAGTGGAGCAGTGAAGG+GGG + Chr3:77423030-77423049 None:intergenic 55.0%
AGGAGGAAGTGGAGCAGTGA+AGG + Chr3:77423033-77423052 None:intergenic 55.0%
GAGGAAGTGGAGCAGTGAAG+GGG + Chr3:77423031-77423050 None:intergenic 55.0%
GCGGTTGGAGCATGATGCAA+AGG - Chr3:77424421-77424440 MsG0380015977.01.T01:intron 55.0%
GGAGGAAGTGGAGCAGTGAA+GGG + Chr3:77423032-77423051 None:intergenic 55.0%
GTGCTTGCCATACAGACCCT+TGG - Chr3:77423536-77423555 MsG0380015977.01.T01:intron 55.0%
TCTTCATACACCCGAGGCTG+TGG - Chr3:77424751-77424770 MsG0380015977.01.T01:intron 55.0%
! GTACGTTGGCTAGGAGGAAG+TGG + Chr3:77423044-77423063 None:intergenic 55.0%
!!! ATCGCCGGACGCTTTTTCGA+AGG + Chr3:77425010-77425029 None:intergenic 55.0%
CTCTGCAGCTGCCACAGCCT+CGG + Chr3:77424765-77424784 None:intergenic 65.0%
TCTGCAGCTGCCACAGCCTC+GGG + Chr3:77424764-77424783 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 77422940 77425045 77422940 ID=MsG0380015977.01;Name=MsG0380015977.01
Chr3 mRNA 77422940 77425045 77422940 ID=MsG0380015977.01.T01;Parent=MsG0380015977.01;Name=MsG0380015977.01.T01;_AED=0.47;_eAED=0.55;_QI=0|0|0|1|0.66|0.75|4|0|198
Chr3 exon 77424926 77425045 77424926 ID=MsG0380015977.01.T01:exon:25088;Parent=MsG0380015977.01.T01
Chr3 exon 77423543 77423638 77423543 ID=MsG0380015977.01.T01:exon:25087;Parent=MsG0380015977.01.T01
Chr3 exon 77423381 77423443 77423381 ID=MsG0380015977.01.T01:exon:25086;Parent=MsG0380015977.01.T01
Chr3 exon 77422940 77423257 77422940 ID=MsG0380015977.01.T01:exon:25085;Parent=MsG0380015977.01.T01
Chr3 CDS 77424926 77425045 77424926 ID=MsG0380015977.01.T01:cds;Parent=MsG0380015977.01.T01
Chr3 CDS 77423543 77423638 77423543 ID=MsG0380015977.01.T01:cds;Parent=MsG0380015977.01.T01
Chr3 CDS 77423381 77423443 77423381 ID=MsG0380015977.01.T01:cds;Parent=MsG0380015977.01.T01
Chr3 CDS 77422940 77423257 77422940 ID=MsG0380015977.01.T01:cds;Parent=MsG0380015977.01.T01
Gene Sequence

>MsG0380015977.01.T01

ATGAAACTTTTGCAGAAACCACTCTTCTTGTATGCGATAACAACAAAGAATCAAACACTCAGACTAAGAGACTCCCCATTGATGGAACCCCCTTCACTGCTCCACTTCCTCCTAGCCAACACCATACTTTGTGTTATTTATGCAGTTTTAGGGAAGGTTAAAGACTTCCTAGGAGTGATGTCAGAAGCAAATAAGCGGTTGGAGCATGATGCAAAGGATCATCCAGAGAAATATGATTTTGAAGAGTTAACAGGAAATGAATCCGAAGTTATTGAAATGGATTTGATGCTTGGTGTTGCTGATCTTCATACACCCGAGGCTGTGGCAGCTGCAGAGTCAGCTGTTTCCAGTTGTCAGCCTGTGATTTCATTGGCAGCTGATGGTAGTGAAATAGATTCAGAAGAAGAAAGTGGCGCTGATGATGACAATGAGGATGCTGAAATTGATAGCAATGTTGATGGATGTGATTATGGAAATGACGGTAAAAAGCCTTCGTCCCTTGACCAAAAACATACTTCTGGTTTAGATTATATCCATGAAAAACAGAAAGGAAATCGTCCTTCGAAAAAGCGTCCGGCGATAGTTGAGCTATCATAA
Protein sequence

>MsG0380015977.01.T01

MKLLQKPLFLYAITTKNQTLRLRDSPLMEPPSLLHFLLANTILCVIYAVLGKVKDFLGVMSEANKRLEHDAKDHPEKYDFEELTGNESEVIEMDLMLGVADLHTPEAVAAAESAVSSCQPVISLAADGSEIDSEEESGADDDNEDAEIDSNVDGCDYGNDGKKPSSLDQKHTSGLDYIHEKQKGNRPSKKRPAIVELS*