AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180004278.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180004278.01.T01 MTR_1g076330 94.891 137 7 0 22 158 39 175 5.21e-88 270
MsG0180004278.01.T01 MTR_1g076330 94.891 137 7 0 22 158 60 196 1.31e-87 270
MsG0180004278.01.T01 MTR_1g076330 94.891 137 7 0 22 158 39 175 1.76e-87 271
MsG0180004278.01.T01 MTR_1g076330 94.891 137 7 0 22 158 60 196 4.27e-87 271
MsG0180004278.01.T01 MTR_1g076330 94.891 137 7 0 22 158 60 196 7.58e-87 271
MsG0180004278.01.T01 MTR_1g076330 85.401 137 4 1 22 158 60 180 8.61e-74 236
MsG0180004278.01.T01 MTR_1g076330 97.938 97 2 0 62 158 6 102 9.03e-60 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180004278.01.T01 AT5G43745 47.826 92 37 3 67 158 84 164 3.15e-18 80.9

Find 26 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCTCTGTCCAAATGAAAT+TGG 0.236075 1:+75937000 None:intergenic
ATGTTCACTATGTTCTGAAT+TGG 0.356478 1:+75937042 None:intergenic
ATGTGAGCACCAATTTCATT+TGG 0.382678 1:-75937009 MsG0180004278.01.T01:CDS
CTGACACATACAAAGTTTGT+TGG 0.400547 1:-75936696 MsG0180004278.01.T01:CDS
AAGTGGCTTAGGTGTATTCA+AGG 0.445370 1:+75936584 None:intergenic
TCAACCTGCCATCTCCCTAC+AGG 0.446031 1:+75937088 None:intergenic
ACGTCTAATTTAAGTGGCTT+AGG 0.446496 1:+75936573 None:intergenic
GGAAAATAATAGTAGCTCTC+AGG 0.460845 1:-75936981 MsG0180004278.01.T01:intron
GACTCTTGACGGAACAAGCT+TGG 0.493689 1:-75936628 MsG0180004278.01.T01:CDS
TTAATTAATGTAAACCCTGT+AGG 0.499479 1:-75937103 MsG0180004278.01.T01:CDS
TCTGAATTGGAATTAAAAGC+TGG 0.502397 1:+75937055 None:intergenic
TATGTGCCTCAGACTCTTGA+CGG 0.505688 1:-75936639 MsG0180004278.01.T01:CDS
CATCTAATATCATGAAAAGA+AGG 0.511608 1:+75936543 None:intergenic
AAGGAGACGTCTAATTTAAG+TGG 0.517014 1:+75936567 None:intergenic
GCATGTGCTACAGGGTCGAC+AGG 0.519355 1:-75936763 MsG0180004278.01.T01:intron
GCACATATCGAACTATTGCT+TGG 0.525302 1:+75936655 None:intergenic
GTACGAATGAACAATCAAAT+CGG 0.529247 1:+75937140 None:intergenic
ATGTAAACCCTGTAGGGAGA+TGG 0.559911 1:-75937096 MsG0180004278.01.T01:CDS
TAATTAATGTAAACCCTGTA+GGG 0.560680 1:-75937102 MsG0180004278.01.T01:CDS
CACCAATTTCATTTGGACAG+AGG 0.569663 1:-75937002 MsG0180004278.01.T01:CDS
CAACCTGCCATCTCCCTACA+GGG 0.574963 1:+75937089 None:intergenic
AATATCATGAAAAGAAGGCA+AGG 0.592571 1:+75936548 None:intergenic
CTTGTTCCGTCAAGAGTCTG+AGG 0.618450 1:+75936633 None:intergenic
AAACCCTGTAGGGAGATGGC+AGG 0.622638 1:-75937092 MsG0180004278.01.T01:CDS
ATATTAGATGGAGCTTAGCG+CGG 0.663174 1:-75936530 MsG0180004278.01.T01:CDS
AATGAAGTGATTAACTTACG+TGG 0.695797 1:+75936467 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTCAAAATTCAAATATTT+TGG - Chr1:75936780-75936799 MsG0180004278.01.T01:intron 15.0%
!!! TTTTGAACATAAAACATTAA+AGG + Chr1:75936769-75936788 None:intergenic 15.0%
!!! AAAATGTACAAAAGTATTGA+TGG - Chr1:75936695-75936714 MsG0180004278.01.T01:CDS 20.0%
! CATCTAATATCATGAAAAGA+AGG + Chr1:75937087-75937106 None:intergenic 25.0%
! TAATTAATGTAAACCCTGTA+GGG - Chr1:75936525-75936544 MsG0180004278.01.T01:CDS 25.0%
! TTAATTAATGTAAACCCTGT+AGG - Chr1:75936524-75936543 MsG0180004278.01.T01:CDS 25.0%
!! CTTCTTTTCATGATATTAGA+TGG - Chr1:75937085-75937104 MsG0180004278.01.T01:CDS 25.0%
!!! ATTCAAATATTTTGGAGCAA+TGG - Chr1:75936788-75936807 MsG0180004278.01.T01:intron 25.0%
AATATCATGAAAAGAAGGCA+AGG + Chr1:75937082-75937101 None:intergenic 30.0%
GCACTGAATACAAAGAAAAT+AGG + Chr1:75936734-75936753 None:intergenic 30.0%
GTACGAATGAACAATCAAAT+CGG + Chr1:75936490-75936509 None:intergenic 30.0%
TCTGAATTGGAATTAAAAGC+TGG + Chr1:75936575-75936594 None:intergenic 30.0%
! ATGTTCACTATGTTCTGAAT+TGG + Chr1:75936588-75936607 None:intergenic 30.0%
AAGAAATGCGTGGAAAAGTT+TGG - Chr1:75936670-75936689 MsG0180004278.01.T01:CDS 35.0%
AAGGAGACGTCTAATTTAAG+TGG + Chr1:75937063-75937082 None:intergenic 35.0%
ACGTCTAATTTAAGTGGCTT+AGG + Chr1:75937057-75937076 None:intergenic 35.0%
ATGTGAGCACCAATTTCATT+TGG - Chr1:75936618-75936637 MsG0180004278.01.T01:CDS 35.0%
CTGACACATACAAAGTTTGT+TGG - Chr1:75936931-75936950 MsG0180004278.01.T01:intron 35.0%
GGAAAATAATAGTAGCTCTC+AGG - Chr1:75936646-75936665 MsG0180004278.01.T01:CDS 35.0%
TTCCTCTGTCCAAATGAAAT+TGG + Chr1:75936630-75936649 None:intergenic 35.0%
!! AAATTGGTGCTCACATTTTC+TGG + Chr1:75936614-75936633 None:intergenic 35.0%
AAGTGGCTTAGGTGTATTCA+AGG + Chr1:75937046-75937065 None:intergenic 40.0%
ATATTAGATGGAGCTTAGCG+CGG - Chr1:75937097-75937116 MsG0180004278.01.T01:CDS 40.0%
CACCAATTTCATTTGGACAG+AGG - Chr1:75936625-75936644 MsG0180004278.01.T01:CDS 40.0%
GCACATATCGAACTATTGCT+TGG + Chr1:75936975-75936994 None:intergenic 40.0%
!!! GATGGCAGGTTGATTTTCAA+AGG - Chr1:75936549-75936568 MsG0180004278.01.T01:CDS 40.0%
ATGTAAACCCTGTAGGGAGA+TGG - Chr1:75936531-75936550 MsG0180004278.01.T01:CDS 45.0%
TATGTGCCTCAGACTCTTGA+CGG - Chr1:75936988-75937007 MsG0180004278.01.T01:CDS 45.0%
CTTGTTCCGTCAAGAGTCTG+AGG + Chr1:75936997-75937016 None:intergenic 50.0%
GAAATGCCGCATGTGCTACA+GGG - Chr1:75936856-75936875 MsG0180004278.01.T01:intron 50.0%
GACTCTTGACGGAACAAGCT+TGG - Chr1:75936999-75937018 MsG0180004278.01.T01:CDS 50.0%
GCTCTCAGGTAAGAAATGCG+TGG - Chr1:75936660-75936679 MsG0180004278.01.T01:CDS 50.0%
AAACCCTGTAGGGAGATGGC+AGG - Chr1:75936535-75936554 MsG0180004278.01.T01:CDS 55.0%
CAACCTGCCATCTCCCTACA+GGG + Chr1:75936541-75936560 None:intergenic 55.0%
CGAAATGCCGCATGTGCTAC+AGG - Chr1:75936855-75936874 MsG0180004278.01.T01:intron 55.0%
TCAACCTGCCATCTCCCTAC+AGG + Chr1:75936542-75936561 None:intergenic 55.0%
TGTCGACCCTGTAGCACATG+CGG + Chr1:75936865-75936884 None:intergenic 55.0%
GCATGTGCTACAGGGTCGAC+AGG - Chr1:75936864-75936883 MsG0180004278.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 75936482 75937167 75936482 ID=MsG0180004278.01;Name=MsG0180004278.01
Chr1 mRNA 75936482 75937167 75936482 ID=MsG0180004278.01.T01;Parent=MsG0180004278.01;Name=MsG0180004278.01.T01;_AED=0.47;_eAED=0.51;_QI=0|1|0|1|1|1|2|0|158
Chr1 exon 75936982 75937167 75936982 ID=MsG0180004278.01.T01:exon:5590;Parent=MsG0180004278.01.T01
Chr1 exon 75936482 75936772 75936482 ID=MsG0180004278.01.T01:exon:5589;Parent=MsG0180004278.01.T01
Chr1 CDS 75936982 75937167 75936982 ID=MsG0180004278.01.T01:cds;Parent=MsG0180004278.01.T01
Chr1 CDS 75936482 75936772 75936482 ID=MsG0180004278.01.T01:cds;Parent=MsG0180004278.01.T01
Gene Sequence

>MsG0180004278.01.T01

ATGAACCGATTTGATTGTTCATTCGTACATGAAACTATACGCTTAATTAATGTAAACCCTGTAGGGAGATGGCAGGTTGATTTTCAAAGGCCAGCTTTTAATTCCAATTCAGAACATAGTGAACATGTTCCAGAAAATGTGAGCACCAATTTCATTTGGACAGAGGAAAATAATAGTAGCTCTCAGGGTCGACAGGCTAAAAACATGATAGAGTACTTATCGTTGTACTTTGTACTGAAACTGACACATACAAAGTTTGTTGGTCTGATGATAAATGTTGTCCAAGCAATAGTTCGATATGTGCCTCAGACTCTTGACGGAACAAGCTTGGCACTTGCTTGTGTTTCTAATGCCTTGAATACACCTAAGCCACTTAAATTAGACGTCTCCTTGCCTTCTTTTCATGATATTAGATGGAGCTTAGCGCGGTTGTTGTACTTATTTAACATACAACTCGAGAGAAATGTTGCCACGTAA
Protein sequence

>MsG0180004278.01.T01

MNRFDCSFVHETIRLINVNPVGRWQVDFQRPAFNSNSEHSEHVPENVSTNFIWTEENNSSSQGRQAKNMIEYLSLYFVLKLTHTKFVGLMINVVQAIVRYVPQTLDGTSLALACVSNALNTPKPLKLDVSLPSFHDIRWSLARLLYLFNIQLERNVAT*