AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480024028.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480024028.01.T01 MTR_8g099780 99.444 180 1 0 1 180 1 180 2.21e-130 368
MsG0480024028.01.T01 MTR_1g023660 44.920 187 83 9 3 179 2 178 5.18e-32 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480024028.01.T01 AT2G21240 60.684 117 43 2 1 116 1 115 1.64e-39 136
MsG0480024028.01.T01 AT2G21240 60.684 117 43 2 1 116 1 115 1.64e-39 136
MsG0480024028.01.T01 AT4G38910 42.442 172 79 4 1 172 1 152 7.41e-33 119
MsG0480024028.01.T01 AT4G38910 42.553 141 63 3 33 172 4 127 1.86e-22 90.9
MsG0480024028.01.T01 AT5G42520 37.297 185 85 5 1 169 1 170 4.26e-19 83.2
MsG0480024028.01.T01 AT5G42520 37.838 185 80 5 1 169 1 166 4.37e-19 83.2

Find 46 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTGTCATGTTGGATATA+TGG 0.216505 4:-92627962 None:intergenic
TCAGAAGTTATAACAGTAAC+TGG 0.272157 4:-92628026 None:intergenic
TTTGTTCCTTTATTTGATGC+TGG 0.301136 4:-92627659 None:intergenic
TTGTTCCTTTATTTGATGCT+GGG 0.361945 4:-92627658 None:intergenic
CGTTGAATTCCACCATTGAA+TGG 0.413813 4:-92627909 None:intergenic
CAGTACTATTCCGACTTTGA+AGG 0.424329 4:-92627878 None:intergenic
TGCCTGCCTTTCAGCCATAA+TGG 0.435049 4:-92627712 None:intergenic
GGATCCCCAGCATCAAATAA+AGG 0.448615 4:+92627653 MsG0480024028.01.T01:CDS
GGATAATGCTCTACTGGAAC+GGG 0.450868 4:+92627839 MsG0480024028.01.T01:CDS
ACTGGCAACTTTCCATTCAA+TGG 0.459914 4:+92627897 MsG0480024028.01.T01:CDS
ATCTGAAAAGAATGAAGCCC+TGG 0.461756 4:+92627767 MsG0480024028.01.T01:CDS
GTGCTTCATCCCTCTGCCGA+AGG 0.475401 4:-92627806 None:intergenic
GTCCATTATGGCTGAAAGGC+AGG 0.476045 4:+92627710 MsG0480024028.01.T01:CDS
TGGATATATGGTTTGAAGAA+TGG 0.483617 4:-92627950 None:intergenic
TGAAGAATGGTGCATCCGCT+TGG 0.493558 4:-92627937 None:intergenic
TGAAAACGGTAGGCATAAGA+TGG 0.514492 4:+92627501 MsG0480024028.01.T01:CDS
TCAGAGGGATAATGCTCTAC+TGG 0.518249 4:+92627833 MsG0480024028.01.T01:CDS
GGGCTACGTCTCGAGCAGCC+AGG 0.518686 4:-92627785 None:intergenic
CTTCAAAGTCGGAATAGTAC+TGG 0.519466 4:+92627879 MsG0480024028.01.T01:CDS
TGTTCCTTTATTTGATGCTG+GGG 0.520374 4:-92627657 None:intergenic
AGTACTATTCCGACTTTGAA+GGG 0.520694 4:-92627877 None:intergenic
GGATGAAGCACTTGCTCAGA+GGG 0.522036 4:+92627818 MsG0480024028.01.T01:CDS
ATATGCTGCTTCTGTCATGT+TGG 0.532878 4:-92627970 None:intergenic
GAGACGTAGCCCTTCGGCAG+AGG 0.546456 4:+92627796 MsG0480024028.01.T01:CDS
GGCTACGTCTCGAGCAGCCA+GGG 0.552588 4:-92627784 None:intergenic
CAGAAGTTATAACAGTAACT+GGG 0.557616 4:-92628025 None:intergenic
TTTAAATGTGCAGTGGAATG+TGG 0.558628 4:+92627632 MsG0480024028.01.T01:intron
CTGCTCGAGACGTAGCCCTT+CGG 0.563490 4:+92627790 MsG0480024028.01.T01:CDS
CTACAGAGGAGCACATTCCC+TGG 0.565304 4:+92627528 MsG0480024028.01.T01:CDS
AGACGTAGCCCTTCGGCAGA+GGG 0.565616 4:+92627797 MsG0480024028.01.T01:CDS
CTCTTGCAGCCCTTCAAAGT+CGG 0.574408 4:+92627868 MsG0480024028.01.T01:CDS
TGCTTCATCCCTCTGCCGAA+GGG 0.577861 4:-92627805 None:intergenic
GGGATAATGCTCTACTGGAA+CGG 0.583003 4:+92627838 MsG0480024028.01.T01:CDS
TCTTCTTGAACTTGAACTAG+AGG 0.590105 4:+92627737 MsG0480024028.01.T01:CDS
TTAGGTCCATTATGGCTGAA+AGG 0.590519 4:+92627706 MsG0480024028.01.T01:CDS
GATGACCGCCAATATGAAAA+CGG 0.592001 4:+92627487 MsG0480024028.01.T01:CDS
GGCAACTTTCCATTCAATGG+TGG 0.607937 4:+92627900 MsG0480024028.01.T01:CDS
CATAAGATGGACTACTACAG+AGG 0.628336 4:+92627514 MsG0480024028.01.T01:CDS
TCATCTAACTAAGAGAACAA+AGG 0.650253 4:+92628061 MsG0480024028.01.T01:CDS
ACCGCCAATATGAAAACGGT+AGG 0.665966 4:+92627491 MsG0480024028.01.T01:CDS
GGGATGAAGCACTTGCTCAG+AGG 0.669930 4:+92627817 MsG0480024028.01.T01:CDS
AGTTATAACAGTAACTGGGG+AGG 0.670600 4:-92628021 None:intergenic
AGAAGTTATAACAGTAACTG+GGG 0.682187 4:-92628024 None:intergenic
GAATTCAACGTGGATCCAAG+CGG 0.708406 4:+92627922 MsG0480024028.01.T01:CDS
TTCAATGGTGGAATTCAACG+TGG 0.712678 4:+92627912 MsG0480024028.01.T01:CDS
AGAAGCAGCATATAGCACGA+CGG 0.752304 4:+92627980 MsG0480024028.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGTTATGAATAAAAAAATT+AGG + Chr4:92627688-92627707 MsG0480024028.01.T01:CDS 10.0%
!!! AATTTTTTTATTCATAACTA+GGG - Chr4:92627688-92627707 None:intergenic 10.0%
!!! TAATTTTTTTATTCATAACT+AGG - Chr4:92627689-92627708 None:intergenic 10.0%
!! TAAAAAAATTAGGTCCATTA+TGG + Chr4:92627698-92627717 MsG0480024028.01.T01:CDS 20.0%
AGAAGTTATAACAGTAACTG+GGG - Chr4:92628027-92628046 None:intergenic 30.0%
CAGAAGTTATAACAGTAACT+GGG - Chr4:92628028-92628047 None:intergenic 30.0%
TCAGAAGTTATAACAGTAAC+TGG - Chr4:92628029-92628048 None:intergenic 30.0%
TCATCTAACTAAGAGAACAA+AGG + Chr4:92628061-92628080 MsG0480024028.01.T01:CDS 30.0%
TGGATATATGGTTTGAAGAA+TGG - Chr4:92627953-92627972 None:intergenic 30.0%
! ATTGGATTTTAAATGTGCAG+TGG + Chr4:92627625-92627644 MsG0480024028.01.T01:intron 30.0%
! TTGTTCCTTTATTTGATGCT+GGG - Chr4:92627661-92627680 None:intergenic 30.0%
! TTTGTTCCTTTATTTGATGC+TGG - Chr4:92627662-92627681 None:intergenic 30.0%
!! ATTGGGTTGATTTATTGGAT+TGG + Chr4:92627607-92627626 MsG0480024028.01.T01:intron 30.0%
AGTACTATTCCGACTTTGAA+GGG - Chr4:92627880-92627899 None:intergenic 35.0%
ATATGTGCATTCTACTTACC+AGG - Chr4:92627549-92627568 None:intergenic 35.0%
CTTCTGTCATGTTGGATATA+TGG - Chr4:92627965-92627984 None:intergenic 35.0%
TATGTGCATTCTACTTACCA+GGG - Chr4:92627548-92627567 None:intergenic 35.0%
TCTTCTTGAACTTGAACTAG+AGG + Chr4:92627737-92627756 MsG0480024028.01.T01:CDS 35.0%
TTTAAATGTGCAGTGGAATG+TGG + Chr4:92627632-92627651 MsG0480024028.01.T01:intron 35.0%
! TAACTTGCAGTTGCACTATT+GGG + Chr4:92627590-92627609 MsG0480024028.01.T01:intron 35.0%
! TATGCCTACCGTTTTCATAT+TGG - Chr4:92627498-92627517 None:intergenic 35.0%
! TGTTCCTTTATTTGATGCTG+GGG - Chr4:92627660-92627679 None:intergenic 35.0%
!! GCACTATTGGGTTGATTTAT+TGG + Chr4:92627602-92627621 MsG0480024028.01.T01:intron 35.0%
!! TTAACTTGCAGTTGCACTAT+TGG + Chr4:92627589-92627608 MsG0480024028.01.T01:intron 35.0%
ACTGGCAACTTTCCATTCAA+TGG + Chr4:92627897-92627916 MsG0480024028.01.T01:CDS 40.0%
AGTTATAACAGTAACTGGGG+AGG - Chr4:92628024-92628043 None:intergenic 40.0%
ATCTGAAAAGAATGAAGCCC+TGG + Chr4:92627767-92627786 MsG0480024028.01.T01:CDS 40.0%
CAGTACTATTCCGACTTTGA+AGG - Chr4:92627881-92627900 None:intergenic 40.0%
CGTTGAATTCCACCATTGAA+TGG - Chr4:92627912-92627931 None:intergenic 40.0%
CTTCAAAGTCGGAATAGTAC+TGG + Chr4:92627879-92627898 MsG0480024028.01.T01:CDS 40.0%
GATGACCGCCAATATGAAAA+CGG + Chr4:92627487-92627506 MsG0480024028.01.T01:CDS 40.0%
TGAAAACGGTAGGCATAAGA+TGG + Chr4:92627501-92627520 MsG0480024028.01.T01:CDS 40.0%
TTAGGTCCATTATGGCTGAA+AGG + Chr4:92627706-92627725 MsG0480024028.01.T01:CDS 40.0%
! ATATGCTGCTTCTGTCATGT+TGG - Chr4:92627973-92627992 None:intergenic 40.0%
! TTCAATGGTGGAATTCAACG+TGG + Chr4:92627912-92627931 MsG0480024028.01.T01:CDS 40.0%
!! CATAAGATGGACTACTACAG+AGG + Chr4:92627514-92627533 MsG0480024028.01.T01:CDS 40.0%
ACCGCCAATATGAAAACGGT+AGG + Chr4:92627491-92627510 MsG0480024028.01.T01:CDS 45.0%
AGAAGCAGCATATAGCACGA+CGG + Chr4:92627980-92627999 MsG0480024028.01.T01:CDS 45.0%
GAATTCAACGTGGATCCAAG+CGG + Chr4:92627922-92627941 MsG0480024028.01.T01:CDS 45.0%
GGATAATGCTCTACTGGAAC+GGG + Chr4:92627839-92627858 MsG0480024028.01.T01:CDS 45.0%
GGATCCCCAGCATCAAATAA+AGG + Chr4:92627653-92627672 MsG0480024028.01.T01:CDS 45.0%
GGCAACTTTCCATTCAATGG+TGG + Chr4:92627900-92627919 MsG0480024028.01.T01:CDS 45.0%
GGGATAATGCTCTACTGGAA+CGG + Chr4:92627838-92627857 MsG0480024028.01.T01:CDS 45.0%
TCAGAGGGATAATGCTCTAC+TGG + Chr4:92627833-92627852 MsG0480024028.01.T01:CDS 45.0%
! GCCTACCGTTTTCATATTGG+CGG - Chr4:92627495-92627514 None:intergenic 45.0%
CTCTTGCAGCCCTTCAAAGT+CGG + Chr4:92627868-92627887 MsG0480024028.01.T01:CDS 50.0%
GTCCATTATGGCTGAAAGGC+AGG + Chr4:92627710-92627729 MsG0480024028.01.T01:CDS 50.0%
TGAAGAATGGTGCATCCGCT+TGG - Chr4:92627940-92627959 None:intergenic 50.0%
TGCCTGCCTTTCAGCCATAA+TGG - Chr4:92627715-92627734 None:intergenic 50.0%
! GGATGAAGCACTTGCTCAGA+GGG + Chr4:92627818-92627837 MsG0480024028.01.T01:CDS 50.0%
TGCTTCATCCCTCTGCCGAA+GGG - Chr4:92627808-92627827 None:intergenic 55.0%
! CTACAGAGGAGCACATTCCC+TGG + Chr4:92627528-92627547 MsG0480024028.01.T01:CDS 55.0%
! GGGATGAAGCACTTGCTCAG+AGG + Chr4:92627817-92627836 MsG0480024028.01.T01:CDS 55.0%
AGACGTAGCCCTTCGGCAGA+GGG + Chr4:92627797-92627816 MsG0480024028.01.T01:CDS 60.0%
CTGCTCGAGACGTAGCCCTT+CGG + Chr4:92627790-92627809 MsG0480024028.01.T01:CDS 60.0%
GTGCTTCATCCCTCTGCCGA+AGG - Chr4:92627809-92627828 None:intergenic 60.0%
GAGACGTAGCCCTTCGGCAG+AGG + Chr4:92627796-92627815 MsG0480024028.01.T01:CDS 65.0%
GGCTACGTCTCGAGCAGCCA+GGG - Chr4:92627787-92627806 None:intergenic 65.0%
GGGCTACGTCTCGAGCAGCC+AGG - Chr4:92627788-92627807 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr4 gene 92627481 92628118 92627481 ID=MsG0480024028.01;Name=MsG0480024028.01
Chr4 mRNA 92627481 92628118 92627481 ID=MsG0480024028.01.T01;Parent=MsG0480024028.01;Name=MsG0480024028.01.T01;_AED=0.43;_eAED=0.43;_QI=0|0|0|1|1|1|2|0|180
Chr4 exon 92627481 92627549 92627481 ID=MsG0480024028.01.T01:exon:1319;Parent=MsG0480024028.01.T01
Chr4 exon 92627645 92628118 92627645 ID=MsG0480024028.01.T01:exon:1318;Parent=MsG0480024028.01.T01
Chr4 CDS 92627481 92627549 92627481 ID=MsG0480024028.01.T01:cds;Parent=MsG0480024028.01.T01
Chr4 CDS 92627645 92628118 92627645 ID=MsG0480024028.01.T01:cds;Parent=MsG0480024028.01.T01
Gene Sequence

>MsG0480024028.01.T01

ATGGACGATGACCGCCAATATGAAAACGGTAGGCATAAGATGGACTACTACAGAGGAGCACATTCCCTGTGGAATGTGGATCCCCAGCATCAAATAAAGGAACAAAATGCCCTAGTTATGAATAAAAAAATTAGGTCCATTATGGCTGAAAGGCAGGCAGCTCTTCTTGAACTTGAACTAGAGGCTGCTATATCTGAAAAGAATGAAGCCCTGGCTGCTCGAGACGTAGCCCTTCGGCAGAGGGATGAAGCACTTGCTCAGAGGGATAATGCTCTACTGGAACGGGACAATGCTCTTGCAGCCCTTCAAAGTCGGAATAGTACTGGCAACTTTCCATTCAATGGTGGAATTCAACGTGGATCCAAGCGGATGCACCATTCTTCAAACCATATATCCAACATGACAGAAGCAGCATATAGCACGACGGATATAATAATAAGAGATGCCTCCCCAGTTACTGTTATAACTTCTGAAGATGTCAAATCTCATCTAACTAAGAGAACAAAGGAGAACAAAGCATCACAGACACCTACCAAAATATGA
Protein sequence

>MsG0480024028.01.T01

MDDDRQYENGRHKMDYYRGAHSLWNVDPQHQIKEQNALVMNKKIRSIMAERQAALLELELEAAISEKNEALAARDVALRQRDEALAQRDNALLERDNALAALQSRNSTGNFPFNGGIQRGSKRMHHSSNHISNMTEAAYSTTDIIIRDASPVTVITSEDVKSHLTKRTKENKASQTPTKI*