AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080049078.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080049078.01.T02 MTR_3g035610 96.000 100 4 0 1 100 1 100 4.50e-65 191
MsG0080049078.01.T02 MTR_5g063380 90.566 53 5 0 47 99 41 93 3.94e-28 100
MsG0080049078.01.T02 MTR_8g079770 94.118 51 3 0 1 51 1 51 1.02e-25 90.9
MsG0080049078.01.T01 MTR_3g035610 86.000 100 4 1 1 90 1 100 1.33e-55 167
MsG0080049078.01.T01 MTR_5g063380 90.566 53 5 0 37 89 41 93 5.92e-28 99.4
MsG0080049078.01.T01 MTR_8g079770 74.510 51 3 1 1 41 1 51 1.23e-16 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080049078.01.T02 ATCG00330 85.000 100 15 0 1 100 1 100 3.11e-56 169
MsG0080049078.01.T01 ATCG00330 77.000 100 13 1 1 90 1 100 1.64e-48 149

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 contig65end:-2769 MsG0080049078.01.T02:CDS
AAGTGAGAAATGGGAAATTC+AGG 0.290322 contig65end:-2875 MsG0080049078.01.T02:CDS
AATTTCCCATTTCTCACTTA+AGG 0.310467 contig65end:+2879 None:intergenic
CTCAGTCCTTAAGTGAGAAA+TGG 0.347756 contig65end:-2885 MsG0080049078.01.T02:CDS
ATAATTAGCTCTCGGTCTTC+CGG 0.352637 contig65end:+2789 None:intergenic
AGAGCTAATTATCGAGACTT+TGG 0.411010 contig65end:-2778 MsG0080049078.01.T02:CDS
TGGACACATACTTCGTGAAA+TGG 0.439919 contig65end:-2749 MsG0080049078.01.T02:CDS
TCAGTCCTTAAGTGAGAAAT+GGG 0.440339 contig65end:-2884 MsG0080049078.01.T02:CDS
AGTGAGAAATGGGAAATTCA+GGG 0.463723 contig65end:-2874 MsG0080049078.01.T02:CDS
TGATTGAGAGGGAGAAGAAG+AGG 0.473159 contig65end:-2969 MsG0080049078.01.T02:CDS
CAAAGAAAAGTTTGATTGAG+AGG 0.490515 contig65end:-2981 MsG0080049078.01.T02:CDS
CCAACTCGATCTTGTTGCAC+CGG 0.512828 contig65end:+2708 None:intergenic
AAAGAAAAGTTTGATTGAGA+GGG 0.519434 contig65end:-2980 MsG0080049078.01.T02:CDS
GTTCACGAAGGTTTGTTGCC+CGG 0.536821 contig65end:-2727 MsG0080049078.01.T02:CDS
CAACTCGATCTTGTTGCACC+GGG 0.553300 contig65end:+2709 None:intergenic
AAGTCTCGATAATTAGCTCT+CGG 0.595033 contig65end:+2781 None:intergenic
CAACGTCGACGAAGACGTGT+AGG 0.602876 contig65end:+2820 None:intergenic
CTTCGTGAAATGGTTCACGA+AGG 0.651469 contig65end:-2739 MsG0080049078.01.T02:CDS
CCGGTGCAACAAGATCGAGT+TGG 0.687174 contig65end:-2708 MsG0080049078.01.T02:CDS
CGTGTAGGTGCACTATTACG+CGG 0.722612 contig65end:+2835 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GCTTTTCTTATTTCTTTTTT+TGG + contig65end:2786-2805 None:intergenic 20.0%
! AAAGAAAAGTTTGATTGAGA+GGG - contig65end:2710-2729 MsG0080049078.01.T02:CDS 25.0%
AATTTCCCATTTCTCACTTA+AGG + contig65end:2814-2833 None:intergenic 30.0%
CAAAGAAAAGTTTGATTGAG+AGG - contig65end:2709-2728 MsG0080049078.01.T02:CDS 30.0%
AAGTGAGAAATGGGAAATTC+AGG - contig65end:2815-2834 MsG0080049078.01.T02:CDS 35.0%
AGAGCTAATTATCGAGACTT+TGG - contig65end:2912-2931 MsG0080049078.01.T02:CDS 35.0%
AGTGAGAAATGGGAAATTCA+GGG - contig65end:2816-2835 MsG0080049078.01.T02:CDS 35.0%
TATCGAGACTTTGGATTATC+TGG - contig65end:2921-2940 MsG0080049078.01.T02:CDS 35.0%
TCAGTCCTTAAGTGAGAAAT+GGG - contig65end:2806-2825 MsG0080049078.01.T02:CDS 35.0%
! AAGTCTCGATAATTAGCTCT+CGG + contig65end:2912-2931 None:intergenic 35.0%
CTCAGTCCTTAAGTGAGAAA+TGG - contig65end:2805-2824 MsG0080049078.01.T02:CDS 40.0%
GGAGAAGAAGAGGCAAAAAT+TGG - contig65end:2731-2750 MsG0080049078.01.T02:CDS 40.0%
TGGACACATACTTCGTGAAA+TGG - contig65end:2941-2960 MsG0080049078.01.T02:CDS 40.0%
! ATAATTAGCTCTCGGTCTTC+CGG + contig65end:2904-2923 None:intergenic 40.0%
CTTCGTGAAATGGTTCACGA+AGG - contig65end:2951-2970 MsG0080049078.01.T02:CDS 45.0%
TGATTGAGAGGGAGAAGAAG+AGG - contig65end:2721-2740 MsG0080049078.01.T02:CDS 45.0%
CAACTCGATCTTGTTGCACC+GGG + contig65end:2984-3003 None:intergenic 50.0%
CCAACTCGATCTTGTTGCAC+CGG + contig65end:2985-3004 None:intergenic 50.0%
CGTGTAGGTGCACTATTACG+CGG + contig65end:2858-2877 None:intergenic 50.0%
!! GTTCACGAAGGTTTGTTGCC+CGG - contig65end:2963-2982 MsG0080049078.01.T02:CDS 50.0%
!!! CGTCGACGTTGTTTTTCGAC+CGG - contig65end:2882-2901 MsG0080049078.01.T02:CDS 50.0%
CAACGTCGACGAAGACGTGT+AGG + contig65end:2873-2892 None:intergenic 55.0%
CCGGTGCAACAAGATCGAGT+TGG - contig65end:2982-3001 MsG0080049078.01.T02:CDS 55.0%
Chromosome Type Strat End Strand Name
contig65end gene 2705 3007 2705 ID=MsG0080049078.01;Name=MsG0080049078.01
contig65end mRNA 2705 3007 2705 ID=MsG0080049078.01.T01;Parent=MsG0080049078.01;Name=MsG0080049078.01.T01;_AED=0.49;_eAED=0.50;_QI=0|0|0|1|0|0|2|0|90
contig65end exon 2705 2894 2705 ID=MsG0080049078.01.T01:exon:258;Parent=MsG0080049078.01.T01
contig65end exon 2925 3007 2925 ID=MsG0080049078.01.T01:exon:257;Parent=MsG0080049078.01.T01
contig65end CDS 2925 3007 2925 ID=MsG0080049078.01.T01:cds;Parent=MsG0080049078.01.T01
contig65end CDS 2705 2894 2705 ID=MsG0080049078.01.T01:cds;Parent=MsG0080049078.01.T01
contig65end mRNA 2705 3007 2705 ID=MsG0080049078.01.T02;Parent=MsG0080049078.01;Name=MsG0080049078.01.T02;_AED=0.49;_eAED=0.49;_QI=0|-1|0|1|-1|1|1|0|100
contig65end exon 2705 3007 2705 ID=MsG0080049078.01.T02:exon:259;Parent=MsG0080049078.01.T02
contig65end CDS 2705 3007 2705 ID=MsG0080049078.01.T02:cds;Parent=MsG0080049078.01.T02
contig65end mRNA 2705 2752 2705 ID=MsG0080049078.01.T03;Parent=MsG0080049078.01;Name=MsG0080049078.01.T03;_AED=0.50;_eAED=0.50;_QI=0|-1|0|1|-1|0|1|0|15
contig65end exon 2705 2752 2705 ID=MsG0080049078.01.T03:exon:260;Parent=MsG0080049078.01.T03
contig65end CDS 2705 2752 2705 ID=MsG0080049078.01.T03:cds;Parent=MsG0080049078.01.T03
Gene Sequence

>MsG0080049078.01.T02

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAAATATCATTTGATTCGAAGATCTCCAAAAAAAGAAATAAGAAAAGCTCAGTCCTTAAGTGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0080049078.01.T01

ATGGCAAAGAAAAGTTTGATTGAGAGGGAGAAGAAGAGGCAAAAATTGGAACAAAAATATCATTTGATTCGAAGATCTCCAAATGAGAAATGGGAAATTCAGGGAAAGTTAGAAGCACTACCGCGTAATAGTGCACCTACACGTCTTCGTCGACGTTGTTTTTCGACCGGAAGACCGAGAGCTAATTATCGAGACTTTGGATTATCTGGACACATACTTCGTGAAATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

>MsG0080049078.01.T03

ATGGTTCACGAAGGTTTGTTGCCCGGTGCAACAAGATCGAGTTGGTAA

Protein sequence

>MsG0080049078.01.T02

MAKKSLIEREKKRQKLEQKYHLIRRSPKKEIRKAQSLSEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0080049078.01.T01

MAKKSLIEREKKRQKLEQKYHLIRRSPNEKWEIQGKLEALPRNSAPTRLRRRCFSTGRPRANYRDFGLSGHILREMVHEGLLPGATRSSW*

>MsG0080049078.01.T03

MVHEGLLPGATRSSW*