AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680030299.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCTGATGATGTGGCTTC+TGG 0.245844 6:-280795 None:intergenic
TCCAGTTGATATTCAGCTTC+TGG 0.302244 6:-280909 None:intergenic
CTTCTGGACCTCTTGTCTTC+AGG 0.312293 6:-280779 None:intergenic
TCAATGCAAAAGCTGTCTAT+TGG 0.318241 6:+280954 MsG0680030299.01.T01:CDS
ATGCAGGCGAAACCGTATTC+TGG 0.346013 6:-281151 None:intergenic
ATTTCAAATTTGTTCTTCAT+AGG 0.360877 6:+281199 MsG0680030299.01.T01:CDS
ATATTCAGCTTCTGGTGAAA+TGG 0.385392 6:-280901 None:intergenic
CATAGATGTTCCTTTGGATA+AGG 0.386892 6:+281171 MsG0680030299.01.T01:CDS
AACATGACTACTCCTCCTTC+TGG 0.389248 6:+282017 MsG0680030299.01.T01:CDS
CGCCTGCATAGATGTTCCTT+TGG 0.398386 6:+281165 MsG0680030299.01.T01:CDS
ACCAGAAGCTGAATATCAAC+TGG 0.409160 6:+280908 MsG0680030299.01.T01:CDS
TCAGCATCTCCATTGAACTT+TGG 0.415028 6:-282112 None:intergenic
GGAAAAGTTCCAAAGTTCAA+TGG 0.457730 6:+282103 MsG0680030299.01.T01:CDS
CATAGGACAACAACCAAATC+AGG 0.467136 6:+281216 MsG0680030299.01.T01:CDS
AAACACAAACAAAGGATTAG+TGG 0.468328 6:+280983 MsG0680030299.01.T01:CDS
CAAATCAGGCAAAAGATCAT+TGG 0.472983 6:+281230 MsG0680030299.01.T01:CDS
ATGTTCCTTTGGATAAGGAA+TGG 0.497106 6:+281176 MsG0680030299.01.T01:CDS
AAGAAAACAGCTCCAGAATA+CGG 0.512774 6:+281139 MsG0680030299.01.T01:CDS
GAAATCCATTCCTTATCCAA+AGG 0.527815 6:-281181 None:intergenic
CATGATGTAACTGTAAAAGT+TGG 0.536668 6:-282155 None:intergenic
GTTTGCAACGGTCATTTCAA+AGG 0.538528 6:+281007 MsG0680030299.01.T01:CDS
GATAGTAAGAAAACCAGTGT+TGG 0.541975 6:+282082 MsG0680030299.01.T01:CDS
GAGATGCTGAAGAGTTCTCT+TGG 0.543033 6:+282125 MsG0680030299.01.T01:CDS
ATCCAAAGGAACATCTATGC+AGG 0.557914 6:-281167 None:intergenic
TGGTGAAATGGCTTCTGATG+AGG 0.574708 6:-280889 None:intergenic
TGATGCAGCTTCTGATGATG+TGG 0.586400 6:-280802 None:intergenic
GGATTCGAAAACACAAACAA+AGG 0.597975 6:+280975 MsG0680030299.01.T01:CDS
ATGCTGAAGAGTTCTCTTGG+TGG 0.602563 6:+282128 MsG0680030299.01.T01:CDS
ATAGTGCTCCTGAAGACAAG+AGG 0.620594 6:+280771 None:intergenic
AGGATTAGTGGAGTTTGCAA+CGG 0.620872 6:+280995 MsG0680030299.01.T01:CDS
CTAGTATCACTAGAACCAGA+AGG 0.636453 6:-282032 None:intergenic
GTATCACTAGAACCAGAAGG+AGG 0.679152 6:-282029 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTACACAGAAAATTGTTTA+AGG - Chr6:281538-281557 None:intergenic 20.0%
!!! ATTTCAAATTTGTTCTTCAT+AGG + Chr6:281199-281218 MsG0680030299.01.T01:CDS 20.0%
!!! CTGTGTAATTTTGTTTAGTT+AGG + Chr6:281549-281568 MsG0680030299.01.T01:intron 25.0%
AAACACAAACAAAGGATTAG+TGG + Chr6:280983-281002 MsG0680030299.01.T01:CDS 30.0%
AACACTTGATATACAATCAG+AGG - Chr6:281512-281531 None:intergenic 30.0%
CATGATGTAACTGTAAAAGT+TGG - Chr6:282158-282177 None:intergenic 30.0%
TAATCAGAATCTAAATGCAG+CGG - Chr6:281817-281836 None:intergenic 30.0%
TCTTTCACACCTCTATATAA+AGG + Chr6:281308-281327 MsG0680030299.01.T01:intron 30.0%
AAGAAAACAGCTCCAGAATA+CGG + Chr6:281139-281158 MsG0680030299.01.T01:CDS 35.0%
AAGGTGAGAAAAACACAAGA+AGG - Chr6:281930-281949 None:intergenic 35.0%
ACGACACAAAGCAATTATAC+TGG - Chr6:281769-281788 None:intergenic 35.0%
AGGTGAGAAAAACACAAGAA+GGG - Chr6:281929-281948 None:intergenic 35.0%
ATATTCAGCTTCTGGTGAAA+TGG - Chr6:280904-280923 None:intergenic 35.0%
ATGTTCCTTTGGATAAGGAA+TGG + Chr6:281176-281195 MsG0680030299.01.T01:CDS 35.0%
CAAATCAGATACAGACTCAA+TGG - Chr6:281478-281497 None:intergenic 35.0%
CAAATCAGGCAAAAGATCAT+TGG + Chr6:281230-281249 MsG0680030299.01.T01:CDS 35.0%
CATAGATGTTCCTTTGGATA+AGG + Chr6:281171-281190 MsG0680030299.01.T01:CDS 35.0%
GAAATCCATTCCTTATCCAA+AGG - Chr6:281184-281203 None:intergenic 35.0%
GATAGTAAGAAAACCAGTGT+TGG + Chr6:282082-282101 MsG0680030299.01.T01:CDS 35.0%
GGAAAAGTTCCAAAGTTCAA+TGG + Chr6:282103-282122 MsG0680030299.01.T01:CDS 35.0%
GGATTCGAAAACACAAACAA+AGG + Chr6:280975-280994 MsG0680030299.01.T01:CDS 35.0%
GTCTTCACTCCTTTATATAG+AGG - Chr6:281320-281339 None:intergenic 35.0%
TAAGTGTTACACAACAGACA+AGG - Chr6:281969-281988 None:intergenic 35.0%
TACTCATAGTGAAATCTCCT+TGG + Chr6:281701-281720 MsG0680030299.01.T01:intron 35.0%
TCAATGCAAAAGCTGTCTAT+TGG + Chr6:280954-280973 MsG0680030299.01.T01:CDS 35.0%
TCTTGCATTACCAATTCTCT+AGG - Chr6:281342-281361 None:intergenic 35.0%
TTGATTGTGTTCTTGAGCAA+AGG + Chr6:281607-281626 MsG0680030299.01.T01:intron 35.0%
! CAATGATCTTTTGCCTGATT+TGG - Chr6:281232-281251 None:intergenic 35.0%
! GATCAGTGTGTTCAGTTTTT+AGG + Chr6:281867-281886 MsG0680030299.01.T01:intron 35.0%
! GTGTTTTTCTCACCTTCAAT+TGG + Chr6:281934-281953 MsG0680030299.01.T01:intron 35.0%
!! GTCATTTCAAAGGTGTTTGA+AGG + Chr6:281017-281036 MsG0680030299.01.T01:intron 35.0%
AAGCTTCAACAACGACTCTT+TGG + Chr6:281262-281281 MsG0680030299.01.T01:intron 40.0%
ACCAGAAGCTGAATATCAAC+TGG + Chr6:280908-280927 MsG0680030299.01.T01:CDS 40.0%
ATCCAAAGGAACATCTATGC+AGG - Chr6:281170-281189 None:intergenic 40.0%
ATGCAGAACAATTTCAGCAG+AGG - Chr6:281406-281425 None:intergenic 40.0%
CATAGGACAACAACCAAATC+AGG + Chr6:281216-281235 MsG0680030299.01.T01:CDS 40.0%
CTAGTATCACTAGAACCAGA+AGG - Chr6:282035-282054 None:intergenic 40.0%
GAACAATTTCAGCAGAGGTT+TGG - Chr6:281401-281420 None:intergenic 40.0%
GGTGAGAAAAACACAAGAAG+GGG - Chr6:281928-281947 None:intergenic 40.0%
GTGAGAAAAACACAAGAAGG+GGG - Chr6:281927-281946 None:intergenic 40.0%
GTTTGCAACGGTCATTTCAA+AGG + Chr6:281007-281026 MsG0680030299.01.T01:CDS 40.0%
TCAGATCTTTGACTGTTGCA+CGG - Chr6:281993-282012 None:intergenic 40.0%
TCAGCATCTCCATTGAACTT+TGG - Chr6:282115-282134 None:intergenic 40.0%
TGAGAAAAACACAAGAAGGG+GGG - Chr6:281926-281945 None:intergenic 40.0%
! AAATCTCCTTGGAAGTGCAA+GGG + Chr6:281712-281731 MsG0680030299.01.T01:intron 40.0%
! AGGATTAGTGGAGTTTGCAA+CGG + Chr6:280995-281014 MsG0680030299.01.T01:CDS 40.0%
! TCCAGTTGATATTCAGCTTC+TGG - Chr6:280912-280931 None:intergenic 40.0%
!! AGGCTCTAGATACCAATTGA+AGG - Chr6:281949-281968 None:intergenic 40.0%
!!! CTTTGGAACTTTTCCAACAC+TGG - Chr6:282098-282117 None:intergenic 40.0%
AACATGACTACTCCTCCTTC+TGG + Chr6:282017-282036 MsG0680030299.01.T01:CDS 45.0%
ATGCTGAAGAGTTCTCTTGG+TGG + Chr6:282128-282147 MsG0680030299.01.T01:CDS 45.0%
GAGATGCTGAAGAGTTCTCT+TGG + Chr6:282125-282144 MsG0680030299.01.T01:CDS 45.0%
GCGGAATAAAACAGAGAGAG+AGG - Chr6:281798-281817 None:intergenic 45.0%
GGAGTGAAGACCTAGAGAAT+TGG + Chr6:281329-281348 MsG0680030299.01.T01:intron 45.0%
GTATCACTAGAACCAGAAGG+AGG - Chr6:282032-282051 None:intergenic 45.0%
TGGTGAAATGGCTTCTGATG+AGG - Chr6:280892-280911 None:intergenic 45.0%
TTGCTTGTGTGCTTGAGCAT+TGG + Chr6:281637-281656 MsG0680030299.01.T01:intron 45.0%
! AAACAGAGTAGTGGAGAACG+TGG - Chr6:281100-281119 None:intergenic 45.0%
! AATCTCCTTGGAAGTGCAAG+GGG + Chr6:281713-281732 MsG0680030299.01.T01:intron 45.0%
! GAAATCTCCTTGGAAGTGCA+AGG + Chr6:281711-281730 MsG0680030299.01.T01:intron 45.0%
! GAAGGCGTGTGTTTGCAATT+TGG + Chr6:281035-281054 MsG0680030299.01.T01:intron 45.0%
! TGATGCAGCTTCTGATGATG+TGG - Chr6:280805-280824 None:intergenic 45.0%
! TGTTTTCTTGTCCTGTAGCG+CGG - Chr6:281128-281147 None:intergenic 45.0%
!! TACTGGTTCCTTCCACAATC+CGG - Chr6:281752-281771 None:intergenic 45.0%
ACTGGACTACTTCCGGATTG+TGG + Chr6:281737-281756 MsG0680030299.01.T01:intron 50.0%
ATGCAGGCGAAACCGTATTC+TGG - Chr6:281154-281173 None:intergenic 50.0%
CGCCTGCATAGATGTTCCTT+TGG + Chr6:281165-281184 MsG0680030299.01.T01:CDS 50.0%
GACTACTTCCGGATTGTGGA+AGG + Chr6:281741-281760 MsG0680030299.01.T01:intron 50.0%
GCGGACACAAAACAGAGTAG+TGG - Chr6:281109-281128 None:intergenic 50.0%
TCTTGCAGTTGTGCTTGAGC+AGG + Chr6:281577-281596 MsG0680030299.01.T01:intron 50.0%
! ACAACGACTCTTTGGTGTGC+TGG + Chr6:281270-281289 MsG0680030299.01.T01:intron 50.0%
! ATCTCCTTGGAAGTGCAAGG+GGG + Chr6:281714-281733 MsG0680030299.01.T01:intron 50.0%
! GCTTCTGATGATGTGGCTTC+TGG - Chr6:280798-280817 None:intergenic 50.0%
AAGGGGGACTGGACTACTTC+CGG + Chr6:281730-281749 MsG0680030299.01.T01:intron 55.0%
! CTGTTTTGTGTCCGCGCTAC+AGG + Chr6:281114-281133 MsG0680030299.01.T01:intron 55.0%
CAGTCCCCCTTGCACTTCCA+AGG - Chr6:281721-281740 None:intergenic 60.0%
! CTTGGAAGTGCAAGGGGGAC+TGG + Chr6:281719-281738 MsG0680030299.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr6 gene 280780 282178 280780 ID=MsG0680030299.01;Name=MsG0680030299.01
Chr6 mRNA 280780 282178 280780 ID=MsG0680030299.01.T01;Parent=MsG0680030299.01;Name=MsG0680030299.01.T01;_AED=0.67;_eAED=1.00;_QI=0|0|0|1|1|1|3|0|180
Chr6 exon 280780 281028 280780 ID=MsG0680030299.01.T01:exon:1987;Parent=MsG0680030299.01.T01
Chr6 exon 281136 281251 281136 ID=MsG0680030299.01.T01:exon:1988;Parent=MsG0680030299.01.T01
Chr6 exon 282001 282178 282001 ID=MsG0680030299.01.T01:exon:1989;Parent=MsG0680030299.01.T01
Chr6 CDS 280780 281028 280780 ID=MsG0680030299.01.T01:cds;Parent=MsG0680030299.01.T01
Chr6 CDS 281136 281251 281136 ID=MsG0680030299.01.T01:cds;Parent=MsG0680030299.01.T01
Chr6 CDS 282001 282178 282001 ID=MsG0680030299.01.T01:cds;Parent=MsG0680030299.01.T01
Gene Sequence

>MsG0680030299.01.T01

CTGAAGACAAGAGGTCCAGAAGCCACATCATCAGAAGCTGCATCATCAGAAGCTGCAGAAGTCATCTCATCAGAAGCTGCATCATCAGAAGCTGCATCATCAGAAGCTGCCTCATCAGAAGCCATTTCACCAGAAGCTGAATATCAACTGGATTTGCAAAGAATAGAAGAATTATCAATGCAAAAGCTGTCTATTGGATTCGAAAACACAAACAAAGGATTAGTGGAGTTTGCAACGGTCATTTCAAAGGACAAGAAAACAGCTCCAGAATACGGTTTCGCCTGCATAGATGTTCCTTTGGATAAGGAATGGATTTCAAATTTGTTCTTCATAGGACAACAACCAAATCAGGCAAAAGATCATTGTCAAAGATCTGAGAAAAACATGACTACTCCTCCTTCTGGTTCTAGTGATACTAGCTATAAAATGTCTCACATGATTATAGTGATAGTAAGAAAACCAGTGTTGGAAAAGTTCCAAAGTTCAATGGAGATGCTGAAGAGTTCTCTTGGTGGAAGACCAACTTTTACAGTTACATCATGA
Protein sequence

>MsG0680030299.01.T01

LKTRGPEATSSEAASSEAAEVISSEAASSEAASSEAASSEAISPEAEYQLDLQRIEELSMQKLSIGFENTNKGLVEFATVISKDKKTAPEYGFACIDVPLDKEWISNLFFIGQQPNQAKDHCQRSEKNMTTPPSGSSDTSYKMSHMIIVIVRKPVLEKFQSSMEMLKSSLGGRPTFTVTS*