AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380014007.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014007.01.T02 MTR_3g035610 98.462 65 1 0 1 65 36 100 3.76e-43 134
MsG0380014007.01.T02 MTR_5g063380 90.566 53 5 0 12 64 41 93 7.62e-28 97.8
MsG0380014007.01.T01 MTR_3g035610 96.296 81 3 0 1 81 20 100 9.49e-53 159
MsG0380014007.01.T01 MTR_5g063380 90.566 53 5 0 28 80 41 93 9.37e-28 98.6
MsG0380014007.01.T01 MTR_8g079770 93.750 32 2 0 1 32 20 51 2.54e-14 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380014007.01.T02 ATCG00330 86.154 65 9 0 1 65 36 100 1.06e-36 118
MsG0380014007.01.T01 ATCG00330 83.951 81 13 0 1 81 20 100 1.64e-44 139

Find 20 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCGAGACTTTGGATTATC+TGG 0.188027 3:-48637965 MsG0380014007.01.T01:CDS
AAGTGAGAAATGGGAAATTC+AGG 0.290322 3:-48638071 MsG0380014007.01.T01:CDS
AATTTCCCATTTCTCACTTA+AGG 0.310467 3:+48638075 None:intergenic
CTCAGTCCTTAAGTGAGAAA+TGG 0.347756 3:-48638081 MsG0380014007.01.T01:CDS
ATAATTAGCTCTCGGTCTTC+CGG 0.352637 3:+48637985 None:intergenic
AGAGCTAATTATCGAGACTT+TGG 0.411010 3:-48637974 MsG0380014007.01.T01:CDS
TGGACACATACTTCGTGAAA+TGG 0.439919 3:-48637945 MsG0380014007.01.T01:CDS
TCAGTCCTTAAGTGAGAAAT+GGG 0.440339 3:-48638080 MsG0380014007.01.T01:CDS
AGTGAGAAATGGGAAATTCA+GGG 0.463723 3:-48638070 MsG0380014007.01.T01:CDS
TGATTGAGAGGGAGAAGAAG+AGG 0.473159 3:-48638164 MsG0380014007.01.T03:CDS
CAAAGAAAAGTTTGATTGAG+AGG 0.490515 3:-48638176 MsG0380014007.01.T03:CDS
CCAACTCGATCTTGTTGCAC+CGG 0.512828 3:+48637904 None:intergenic
AAAGAAAAGTTTGATTGAGA+GGG 0.519434 3:-48638175 MsG0380014007.01.T03:CDS
GTTCACGAAGGTTTGTTGCC+CGG 0.536821 3:-48637923 MsG0380014007.01.T01:CDS
CAACTCGATCTTGTTGCACC+GGG 0.553300 3:+48637905 None:intergenic
AAGTCTCGATAATTAGCTCT+CGG 0.595033 3:+48637977 None:intergenic
CAACGTCGACGAAGACGTGT+AGG 0.602876 3:+48638016 None:intergenic
CTTCGTGAAATGGTTCACGA+AGG 0.651469 3:-48637935 MsG0380014007.01.T01:CDS
CCGGTGCAACAAGATCGAGT+TGG 0.687174 3:-48637904 MsG0380014007.01.T01:CDS
CGTGTAGGTGCACTATTACG+CGG 0.722612 3:+48638031 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GCTTTTCTTATTTCTTTTTT+TGG + Chr3:48637981-48638000 None:intergenic 20.0%
! AAAGAAAAGTTTGATTGAGA+GGG - Chr3:48637906-48637925 MsG0380014007.01.T01:CDS 25.0%
AATTTCCCATTTCTCACTTA+AGG + Chr3:48638009-48638028 None:intergenic 30.0%
CAAAGAAAAGTTTGATTGAG+AGG - Chr3:48637905-48637924 MsG0380014007.01.T01:CDS 30.0%
AAGTGAGAAATGGGAAATTC+AGG - Chr3:48638010-48638029 MsG0380014007.01.T01:CDS 35.0%
AGAGCTAATTATCGAGACTT+TGG - Chr3:48638107-48638126 MsG0380014007.01.T01:CDS 35.0%
AGTGAGAAATGGGAAATTCA+GGG - Chr3:48638011-48638030 MsG0380014007.01.T01:CDS 35.0%
TATCGAGACTTTGGATTATC+TGG - Chr3:48638116-48638135 MsG0380014007.01.T01:CDS 35.0%
TCAGTCCTTAAGTGAGAAAT+GGG - Chr3:48638001-48638020 MsG0380014007.01.T01:CDS 35.0%
! AAGTCTCGATAATTAGCTCT+CGG + Chr3:48638107-48638126 None:intergenic 35.0%
CTCAGTCCTTAAGTGAGAAA+TGG - Chr3:48638000-48638019 MsG0380014007.01.T01:CDS 40.0%
GGAGAAGAAGAGGCAAAAAT+TGG - Chr3:48637927-48637946 MsG0380014007.01.T01:CDS 40.0%
TGGACACATACTTCGTGAAA+TGG - Chr3:48638136-48638155 None:intergenic 40.0%
! ATAATTAGCTCTCGGTCTTC+CGG + Chr3:48638099-48638118 None:intergenic 40.0%
CTTCGTGAAATGGTTCACGA+AGG - Chr3:48638146-48638165 MsG0380014007.01.T03:CDS 45.0%
TGATTGAGAGGGAGAAGAAG+AGG - Chr3:48637917-48637936 MsG0380014007.01.T01:CDS 45.0%
CAACTCGATCTTGTTGCACC+GGG + Chr3:48638179-48638198 None:intergenic 50.0%
CCAACTCGATCTTGTTGCAC+CGG + Chr3:48638180-48638199 None:intergenic 50.0%
CGTGTAGGTGCACTATTACG+CGG + Chr3:48638053-48638072 None:intergenic 50.0%
!! GTTCACGAAGGTTTGTTGCC+CGG - Chr3:48638158-48638177 MsG0380014007.01.T03:CDS 50.0%
!!! CGTCGACGTTGTTTTTCGAC+CGG - Chr3:48638077-48638096 MsG0380014007.01.T01:CDS 50.0%
CAACGTCGACGAAGACGTGT+AGG + Chr3:48638068-48638087 None:intergenic 55.0%
CCGGTGCAACAAGATCGAGT+TGG - Chr3:48638177-48638196 MsG0380014007.01.T03:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48637901 48638202 48637901 ID=MsG0380014007.01;Name=MsG0380014007.01
Chr3 mRNA 48637901 48638146 48637901 ID=MsG0380014007.01.T01;Parent=MsG0380014007.01;Name=MsG0380014007.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|81
Chr3 exon 48637901 48638146 48637901 ID=MsG0380014007.01.T01:exon:9420;Parent=MsG0380014007.01.T01
Chr3 CDS 48637901 48638146 48637901 ID=MsG0380014007.01.T01:cds;Parent=MsG0380014007.01.T01
Chr3 mRNA 48637901 48638098 48637901 ID=MsG0380014007.01.T02;Parent=MsG0380014007.01;Name=MsG0380014007.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|65
Chr3 exon 48637901 48638098 48637901 ID=MsG0380014007.01.T02:exon:9421;Parent=MsG0380014007.01.T02
Chr3 CDS 48637901 48638098 48637901 ID=MsG0380014007.01.T02:cds;Parent=MsG0380014007.01.T02
Chr3 mRNA 48638137 48638202 48638137 ID=MsG0380014007.01.T03;Parent=MsG0380014007.01;Name=MsG0380014007.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|21
Chr3 exon 48638137 48638202 48638137 ID=MsG0380014007.01.T03:exon:9422;Parent=MsG0380014007.01.T03
Chr3 CDS 48638137 48638202 48638137 ID=MsG0380014007.01.T03:cds;Parent=MsG0380014007.01.T03
Chr3 mRNA 48637901 48637948 48637901 ID=MsG0380014007.01.T04;Parent=MsG0380014007.01;Name=MsG0380014007.01.T04;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|15
Chr3 exon 48637901 48637948 48637901 ID=MsG0380014007.01.T04:exon:9423;Parent=MsG0380014007.01.T04
Chr3 CDS 48637901 48637948 48637901 ID=MsG0380014007.01.T04:cds;Parent=MsG0380014007.01.T04
Gene Sequence

>MsG0380014007.01.T02

TCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380014007.01.T03

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAATATCATTTGA

>MsG0380014007.01.T04

ATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380014007.01.T01

TATCATTTGATTCGAAGATCTCCAAAAAAAGAAATAAGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

Protein sequence

>MsG0380014007.01.T02

SLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380014007.01.T03

MAKKSLIEREKKRQKLEQNII*

>MsG0380014007.01.T04

MVHEGLLPGATRSSW*

>MsG0380014007.01.T01

YHLIRRSPKKEIRKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*