AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380013955.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013955.01.T02 MTR_3g035610 97.260 73 2 0 5 77 28 100 5.91e-48 147
MsG0380013955.01.T02 MTR_5g063380 90.566 53 5 0 24 76 41 93 3.27e-28 99.4
MsG0380013955.01.T01 MTR_3g035610 97.260 73 2 0 9 81 28 100 5.92e-48 147
MsG0380013955.01.T01 MTR_5g063380 90.566 53 5 0 28 80 41 93 3.26e-28 99.8
MsG0380013955.01.T03 MTR_3g035610 98.529 68 1 0 2 69 33 100 2.45e-45 140
MsG0380013955.01.T03 MTR_5g063380 90.566 53 5 0 16 68 41 93 6.42e-28 98.2
MsG0380013955.01.T04 MTR_3g035610 98.462 65 1 0 1 65 36 100 3.76e-43 134
MsG0380013955.01.T04 MTR_5g063380 90.566 53 5 0 12 64 41 93 7.62e-28 97.8
MsG0380013955.01.T05 MTR_8g079770 93.103 29 2 0 1 29 1 29 4.16e-11 50.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013955.01.T02 ATCG00330 83.784 74 12 0 4 77 27 100 3.21e-40 127
MsG0380013955.01.T01 ATCG00330 83.784 74 12 0 8 81 27 100 3.39e-40 128
MsG0380013955.01.T03 ATCG00330 83.824 68 11 0 2 69 33 100 5.03e-37 119
MsG0380013955.01.T04 ATCG00330 86.154 65 9 0 1 65 36 100 1.06e-36 118

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:-48503961 MsG0380013955.01.T01:CDS
AAGTGAGAAATGGGAAATTC+AGG 0.290322 3:-48504067 MsG0380013955.01.T01:CDS
AATTTCCCATTTCTCACTTA+AGG 0.310467 3:+48504071 None:intergenic
CTCAGTCCTTAAGTGAGAAA+TGG 0.347756 3:-48504077 MsG0380013955.01.T01:CDS
ATAATTAGCTCTCGGTCTTC+CGG 0.352637 3:+48503981 None:intergenic
AGAGCTAATTATCGAGACTT+TGG 0.411010 3:-48503970 MsG0380013955.01.T01:CDS
TGGACACATACTTCGTGAAA+TGG 0.439919 3:-48503941 MsG0380013955.01.T01:CDS
TCAGTCCTTAAGTGAGAAAT+GGG 0.440339 3:-48504076 MsG0380013955.01.T01:CDS
AGTGAGAAATGGGAAATTCA+GGG 0.463723 3:-48504066 MsG0380013955.01.T01:CDS
TGATTGAGAGGGAGAAGAAG+AGG 0.473159 3:-48504160 MsG0380013955.01.T05:CDS
CAAAGAAAAGTTTGATTGAG+AGG 0.490515 3:-48504172 MsG0380013955.01.T05:CDS
CCAACTCGATCTTGTTGCAC+CGG 0.512828 3:+48503900 None:intergenic
AAAGAAAAGTTTGATTGAGA+GGG 0.519434 3:-48504171 MsG0380013955.01.T05:CDS
GTTCACGAAGGTTTGTTGCC+CGG 0.536821 3:-48503919 MsG0380013955.01.T01:CDS
CAACTCGATCTTGTTGCACC+GGG 0.553300 3:+48503901 None:intergenic
AAGTCTCGATAATTAGCTCT+CGG 0.595033 3:+48503973 None:intergenic
CAACGTCGACGAAGACGTGT+AGG 0.602876 3:+48504012 None:intergenic
CTTCGTGAAATGGTTCACGA+AGG 0.651469 3:-48503931 MsG0380013955.01.T01:CDS
CCGGTGCAACAAGATCGAGT+TGG 0.687174 3:-48503900 MsG0380013955.01.T01:CDS
CGTGTAGGTGCACTATTACG+CGG 0.722612 3:+48504027 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGCTTTTCTTATTTCTTTTT+TGG + Chr3:48503978-48503997 None:intergenic 20.0%
! AAAGAAAAGTTTGATTGAGA+GGG - Chr3:48503902-48503921 MsG0380013955.01.T01:CDS 25.0%
AATTTCCCATTTCTCACTTA+AGG + Chr3:48504005-48504024 None:intergenic 30.0%
CAAAGAAAAGTTTGATTGAG+AGG - Chr3:48503901-48503920 MsG0380013955.01.T01:CDS 30.0%
AAGTGAGAAATGGGAAATTC+AGG - Chr3:48504006-48504025 MsG0380013955.01.T01:CDS 35.0%
AGAGCTAATTATCGAGACTT+TGG - Chr3:48504103-48504122 MsG0380013955.01.T01:CDS 35.0%
AGTGAGAAATGGGAAATTCA+GGG - Chr3:48504007-48504026 MsG0380013955.01.T01:CDS 35.0%
TATCGAGACTTTGGATTATC+TGG - Chr3:48504112-48504131 MsG0380013955.01.T01:CDS 35.0%
TCAGTCCTTAAGTGAGAAAT+GGG - Chr3:48503997-48504016 MsG0380013955.01.T01:CDS 35.0%
! AAGTCTCGATAATTAGCTCT+CGG + Chr3:48504103-48504122 None:intergenic 35.0%
CTCAGTCCTTAAGTGAGAAA+TGG - Chr3:48503996-48504015 MsG0380013955.01.T01:CDS 40.0%
GGAGAAGAAGAGGCAAAAAT+TGG - Chr3:48503923-48503942 MsG0380013955.01.T01:CDS 40.0%
TGGACACATACTTCGTGAAA+TGG - Chr3:48504132-48504151 MsG0380013955.01.T05:CDS 40.0%
! ATAATTAGCTCTCGGTCTTC+CGG + Chr3:48504095-48504114 None:intergenic 40.0%
CTTCGTGAAATGGTTCACGA+AGG - Chr3:48504142-48504161 MsG0380013955.01.T05:CDS 45.0%
TGATTGAGAGGGAGAAGAAG+AGG - Chr3:48503913-48503932 MsG0380013955.01.T01:CDS 45.0%
CAACTCGATCTTGTTGCACC+GGG + Chr3:48504175-48504194 None:intergenic 50.0%
CCAACTCGATCTTGTTGCAC+CGG + Chr3:48504176-48504195 None:intergenic 50.0%
CGTGTAGGTGCACTATTACG+CGG + Chr3:48504049-48504068 None:intergenic 50.0%
!! GTTCACGAAGGTTTGTTGCC+CGG - Chr3:48504154-48504173 MsG0380013955.01.T05:CDS 50.0%
!!! CGTCGACGTTGTTTTTCGAC+CGG - Chr3:48504073-48504092 MsG0380013955.01.T01:CDS 50.0%
CAACGTCGACGAAGACGTGT+AGG + Chr3:48504064-48504083 None:intergenic 55.0%
CCGGTGCAACAAGATCGAGT+TGG - Chr3:48504173-48504192 MsG0380013955.01.T05:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48503897 48504198 48503897 ID=MsG0380013955.01;Name=MsG0380013955.01
Chr3 mRNA 48503897 48504142 48503897 ID=MsG0380013955.01.T01;Parent=MsG0380013955.01;Name=MsG0380013955.01.T01;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|81
Chr3 exon 48503897 48504142 48503897 ID=MsG0380013955.01.T01:exon:5402;Parent=MsG0380013955.01.T01
Chr3 CDS 48503897 48504142 48503897 ID=MsG0380013955.01.T01:cds;Parent=MsG0380013955.01.T01
Chr3 mRNA 48503897 48504130 48503897 ID=MsG0380013955.01.T02;Parent=MsG0380013955.01;Name=MsG0380013955.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|77
Chr3 exon 48503897 48504130 48503897 ID=MsG0380013955.01.T02:exon:5403;Parent=MsG0380013955.01.T02
Chr3 CDS 48503897 48504130 48503897 ID=MsG0380013955.01.T02:cds;Parent=MsG0380013955.01.T02
Chr3 mRNA 48503897 48504106 48503897 ID=MsG0380013955.01.T03;Parent=MsG0380013955.01;Name=MsG0380013955.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|69
Chr3 exon 48503897 48504106 48503897 ID=MsG0380013955.01.T03:exon:5404;Parent=MsG0380013955.01.T03
Chr3 CDS 48503897 48504106 48503897 ID=MsG0380013955.01.T03:cds;Parent=MsG0380013955.01.T03
Chr3 mRNA 48503897 48504094 48503897 ID=MsG0380013955.01.T04;Parent=MsG0380013955.01;Name=MsG0380013955.01.T04;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|65
Chr3 exon 48503897 48504094 48503897 ID=MsG0380013955.01.T04:exon:5405;Parent=MsG0380013955.01.T04
Chr3 CDS 48503897 48504094 48503897 ID=MsG0380013955.01.T04:cds;Parent=MsG0380013955.01.T04
Chr3 mRNA 48504106 48504198 48504106 ID=MsG0380013955.01.T05;Parent=MsG0380013955.01;Name=MsG0380013955.01.T05;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|30
Chr3 exon 48504106 48504198 48504106 ID=MsG0380013955.01.T05:exon:5406;Parent=MsG0380013955.01.T05
Chr3 CDS 48504106 48504198 48504106 ID=MsG0380013955.01.T05:cds;Parent=MsG0380013955.01.T05
Chr3 mRNA 48503897 48503944 48503897 ID=MsG0380013955.01.T06;Parent=MsG0380013955.01;Name=MsG0380013955.01.T06;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|15
Chr3 exon 48503897 48503944 48503897 ID=MsG0380013955.01.T06:exon:5407;Parent=MsG0380013955.01.T06
Chr3 CDS 48503897 48503944 48503897 ID=MsG0380013955.01.T06:cds;Parent=MsG0380013955.01.T06
Gene Sequence

>MsG0380013955.01.T02

TCGAAGATCTCCAAAAAAGAAATAAGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013955.01.T01

ATATCATTTGATTCGAAGATCTCCAAAAAAGAAATAAGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013955.01.T06

ATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013955.01.T03

AGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013955.01.T04

TCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013955.01.T05

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAAATATCATTTGATTCGAAGATCTCCAAAAAAGAAATAA

Protein sequence

>MsG0380013955.01.T02

SKISKKEIRKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380013955.01.T01

ISFDSKISKKEIRKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380013955.01.T06

MVHEGLLPGATRSSW*

>MsG0380013955.01.T03

RKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380013955.01.T04

SLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380013955.01.T05

MAKKSLIEREKKRQKLEQKYHLIRRSPKKK*