AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380013970.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013970.01.T01 MTR_3g035610 86.000 100 4 1 1 90 1 100 1.33e-55 167
MsG0380013970.01.T01 MTR_5g063380 90.566 53 5 0 37 89 41 93 5.92e-28 99.4
MsG0380013970.01.T01 MTR_8g079770 74.510 51 3 1 1 41 1 51 1.23e-16 67.4
MsG0380013970.01.T02 MTR_3g035610 96.000 100 4 0 1 100 1 100 4.50e-65 191
MsG0380013970.01.T02 MTR_5g063380 90.566 53 5 0 47 99 41 93 3.94e-28 100
MsG0380013970.01.T02 MTR_8g079770 94.118 51 3 0 1 51 1 51 1.02e-25 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380013970.01.T01 ATCG00330 77.000 100 13 1 1 90 1 100 1.64e-48 149
MsG0380013970.01.T02 ATCG00330 85.000 100 15 0 1 100 1 100 3.11e-56 169

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:-48535622 MsG0380013970.01.T02:CDS
AAGTGAGAAATGGGAAATTC+AGG 0.290322 3:-48535728 MsG0380013970.01.T02:CDS
AATTTCCCATTTCTCACTTA+AGG 0.310467 3:+48535732 None:intergenic
CTCAGTCCTTAAGTGAGAAA+TGG 0.347756 3:-48535738 MsG0380013970.01.T02:CDS
ATAATTAGCTCTCGGTCTTC+CGG 0.352637 3:+48535642 None:intergenic
AGAGCTAATTATCGAGACTT+TGG 0.411010 3:-48535631 MsG0380013970.01.T02:CDS
TGGACACATACTTCGTGAAA+TGG 0.439919 3:-48535602 MsG0380013970.01.T02:CDS
TCAGTCCTTAAGTGAGAAAT+GGG 0.440339 3:-48535737 MsG0380013970.01.T02:CDS
AGTGAGAAATGGGAAATTCA+GGG 0.463723 3:-48535727 MsG0380013970.01.T02:CDS
TGATTGAGAGGGAGAAGAAG+AGG 0.473159 3:-48535822 MsG0380013970.01.T02:CDS
CAAAGAAAAGTTTGATTGAG+AGG 0.490515 3:-48535834 MsG0380013970.01.T02:CDS
CCAACTCGATCTTGTTGCAC+CGG 0.512828 3:+48535561 None:intergenic
AAAGAAAAGTTTGATTGAGA+GGG 0.519434 3:-48535833 MsG0380013970.01.T02:CDS
GTTCACGAAGGTTTGTTGCC+CGG 0.536821 3:-48535580 MsG0380013970.01.T02:CDS
CAACTCGATCTTGTTGCACC+GGG 0.553300 3:+48535562 None:intergenic
AAGTCTCGATAATTAGCTCT+CGG 0.595033 3:+48535634 None:intergenic
CAACGTCGACGAAGACGTGT+AGG 0.602876 3:+48535673 None:intergenic
CTTCGTGAAATGGTTCACGA+AGG 0.651469 3:-48535592 MsG0380013970.01.T02:CDS
CCGGTGCAACAAGATCGAGT+TGG 0.687174 3:-48535561 MsG0380013970.01.T02:CDS
CGTGTAGGTGCACTATTACG+CGG 0.722612 3:+48535688 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GCTTTTCTTATTTCTTTTTT+TGG + Chr3:48535639-48535658 None:intergenic 20.0%
! AAAGAAAAGTTTGATTGAGA+GGG - Chr3:48535563-48535582 MsG0380013970.01.T02:CDS 25.0%
AATTTCCCATTTCTCACTTA+AGG + Chr3:48535667-48535686 None:intergenic 30.0%
CAAAGAAAAGTTTGATTGAG+AGG - Chr3:48535562-48535581 MsG0380013970.01.T02:CDS 30.0%
AAGTGAGAAATGGGAAATTC+AGG - Chr3:48535668-48535687 MsG0380013970.01.T02:CDS 35.0%
AGAGCTAATTATCGAGACTT+TGG - Chr3:48535765-48535784 MsG0380013970.01.T02:CDS 35.0%
AGTGAGAAATGGGAAATTCA+GGG - Chr3:48535669-48535688 MsG0380013970.01.T02:CDS 35.0%
TATCGAGACTTTGGATTATC+TGG - Chr3:48535774-48535793 MsG0380013970.01.T02:CDS 35.0%
TCAGTCCTTAAGTGAGAAAT+GGG - Chr3:48535659-48535678 MsG0380013970.01.T02:CDS 35.0%
! AAGTCTCGATAATTAGCTCT+CGG + Chr3:48535765-48535784 None:intergenic 35.0%
CTCAGTCCTTAAGTGAGAAA+TGG - Chr3:48535658-48535677 MsG0380013970.01.T02:CDS 40.0%
GGAGAAGAAGAGGCAAAAAT+TGG - Chr3:48535584-48535603 MsG0380013970.01.T02:CDS 40.0%
TGGACACATACTTCGTGAAA+TGG - Chr3:48535794-48535813 MsG0380013970.01.T02:CDS 40.0%
! ATAATTAGCTCTCGGTCTTC+CGG + Chr3:48535757-48535776 None:intergenic 40.0%
CTTCGTGAAATGGTTCACGA+AGG - Chr3:48535804-48535823 MsG0380013970.01.T02:CDS 45.0%
TGATTGAGAGGGAGAAGAAG+AGG - Chr3:48535574-48535593 MsG0380013970.01.T02:CDS 45.0%
CAACTCGATCTTGTTGCACC+GGG + Chr3:48535837-48535856 None:intergenic 50.0%
CCAACTCGATCTTGTTGCAC+CGG + Chr3:48535838-48535857 None:intergenic 50.0%
CGTGTAGGTGCACTATTACG+CGG + Chr3:48535711-48535730 None:intergenic 50.0%
!! GTTCACGAAGGTTTGTTGCC+CGG - Chr3:48535816-48535835 MsG0380013970.01.T02:CDS 50.0%
!!! CGTCGACGTTGTTTTTCGAC+CGG - Chr3:48535735-48535754 MsG0380013970.01.T02:CDS 50.0%
CAACGTCGACGAAGACGTGT+AGG + Chr3:48535726-48535745 None:intergenic 55.0%
CCGGTGCAACAAGATCGAGT+TGG - Chr3:48535835-48535854 MsG0380013970.01.T02:CDS 55.0%
Chromosome Type Strat End Strand Name
Chr3 gene 48535558 48535860 48535558 ID=MsG0380013970.01;Name=MsG0380013970.01
Chr3 mRNA 48535558 48535860 48535558 ID=MsG0380013970.01.T01;Parent=MsG0380013970.01;Name=MsG0380013970.01.T01;_AED=0.50;_eAED=0.51;_QI=0|0|0|1|0|0|2|0|90
Chr3 exon 48535558 48535747 48535558 ID=MsG0380013970.01.T01:exon:11291;Parent=MsG0380013970.01.T01
Chr3 exon 48535778 48535860 48535778 ID=MsG0380013970.01.T01:exon:11290;Parent=MsG0380013970.01.T01
Chr3 CDS 48535778 48535860 48535778 ID=MsG0380013970.01.T01:cds;Parent=MsG0380013970.01.T01
Chr3 CDS 48535558 48535747 48535558 ID=MsG0380013970.01.T01:cds;Parent=MsG0380013970.01.T01
Chr3 mRNA 48535558 48535860 48535558 ID=MsG0380013970.01.T02;Parent=MsG0380013970.01;Name=MsG0380013970.01.T02;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|100
Chr3 exon 48535558 48535860 48535558 ID=MsG0380013970.01.T02:exon:11292;Parent=MsG0380013970.01.T02
Chr3 CDS 48535558 48535860 48535558 ID=MsG0380013970.01.T02:cds;Parent=MsG0380013970.01.T02
Chr3 mRNA 48535558 48535605 48535558 ID=MsG0380013970.01.T03;Parent=MsG0380013970.01;Name=MsG0380013970.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|15
Chr3 exon 48535558 48535605 48535558 ID=MsG0380013970.01.T03:exon:11293;Parent=MsG0380013970.01.T03
Chr3 CDS 48535558 48535605 48535558 ID=MsG0380013970.01.T03:cds;Parent=MsG0380013970.01.T03
Gene Sequence

>MsG0380013970.01.T01

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAAATATCATTTGATTCGAAGATCTCCAAATGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013970.01.T03

ATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0380013970.01.T02

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAAATATCATTTGATTCGAAGATCTCCAAAAAAAGAAATAAGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

Protein sequence

>MsG0380013970.01.T01

MAKKSLIEREKKRQKLEQKYHLIRRSPNEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0380013970.01.T03

MVHEGLLPGATRSSW*

>MsG0380013970.01.T02

MAKKSLIEREKKRQKLEQKYHLIRRSPKKEIRKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*