AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680030958.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680030958.01.T01 MTR_6g015280 60.345 116 18 3 14 101 1 116 3.03e-27 96.7
MsG0680030958.01.T01 MTR_6g015260 61.739 115 17 4 14 101 1 115 7.69e-27 95.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTCCATTGTTGGAACTTT+TGG 0.191102 6:+12167478 MsG0680030957.01.T01:CDS
TCAGGGTATTTGAATGGTTT+GGG 0.203746 6:+12167349 MsG0680030957.01.T01:intron
TAGATAGATAGATACCTTTC+AGG 0.239960 6:+12167331 MsG0680030957.01.T01:intron
TTCAGGGTATTTGAATGGTT+TGG 0.288724 6:+12167348 MsG0680030957.01.T01:intron
TTATGTGATTCTAATATATA+AGG 0.296326 6:+12167566 MsG0680030957.01.T01:intron
TTAAGATGATCCGGGGTTAC+AGG 0.343133 6:+12167376 MsG0680030957.01.T01:intron
CTAGAAATCAGAAATGAAAA+TGG 0.358654 6:+12167653 MsG0680030957.01.T01:intron
GGTTCCAGAGATGTGCTTGC+AGG 0.409056 6:-12166025 MsG0680030958.01.T01:CDS
TTGCATTGAGATTCCATTGT+TGG 0.417969 6:+12167469 MsG0680030957.01.T01:CDS
TTGGGGAGTTTAAGATGATC+CGG 0.426556 6:+12167367 MsG0680030957.01.T01:intron
AGATCCTGCAAGCACATCTC+TGG 0.429868 6:+12166021 MsG0680030957.01.T01:intron
TACCTTTCAGGGTATTTGAA+TGG 0.436754 6:+12167343 MsG0680030957.01.T01:intron
TTCTACTATACCGTACTACT+TGG 0.450348 6:+12167543 MsG0680030957.01.T01:CDS
AGTGAGTGAGTGTGTCTTTG+AGG 0.464569 6:+12167595 MsG0680030957.01.T01:intron
AACTCCTCCTCTTCCTCCTC+CGG 0.466083 6:-12167437 MsG0680030958.01.T01:CDS
GGTGGTTGATGATGATCAAC+CGG 0.491858 6:+12167418 MsG0680030957.01.T01:CDS
TGATCAACCGGAGGAGGAAG+AGG 0.501763 6:+12167430 MsG0680030957.01.T01:CDS
TGGGGAGTTTAAGATGATCC+GGG 0.508671 6:+12167368 MsG0680030957.01.T01:intron
AGTTTCTCATCAATCAGCAT+TGG 0.509696 6:+12165976 MsG0680030957.01.T01:intron
GGAGGAGGAAGAGGAGGAGT+TGG 0.510057 6:+12167439 MsG0680030957.01.T01:CDS
ATCATATCATATAACTGTGA+TGG 0.521259 6:-12167521 MsG0680030958.01.T01:exon
CAGGGTATTTGAATGGTTTG+GGG 0.526382 6:+12167350 MsG0680030957.01.T01:intron
TAGTTTATGTCAACTACTGC+AGG 0.535207 6:-12166046 MsG0680030958.01.T01:CDS
AGATAGATAGATACCTTTCA+GGG 0.538978 6:+12167332 MsG0680030957.01.T01:intron
AACCATTCAAATACCCTGAA+AGG 0.547136 6:-12167345 MsG0680030958.01.T01:intron
TGATGATGATCAACCGGAGG+AGG 0.560022 6:+12167424 MsG0680030957.01.T01:CDS
TTGAGGAAATATAATTGCAA+CGG 0.579087 6:+12167612 MsG0680030957.01.T01:intron
GAGAAACTCAACTCAACTTG+AGG 0.587059 6:-12165961 None:intergenic
ATTGCGAAAACCTGTAACCC+CGG 0.590078 6:-12167386 MsG0680030958.01.T01:CDS
TTTCGCAATTCATTGGAGGG+TGG 0.613481 6:+12167400 MsG0680030957.01.T01:CDS
AGTGTTGTGGTTTATAACAG+TGG 0.616733 6:-12166069 MsG0680030958.01.T01:CDS
AATCACATAACCAAGTAGTA+CGG 0.620889 6:-12167553 MsG0680030958.01.T01:five_prime_UTR
TCAACCGGAGGAGGAAGAGG+AGG 0.622606 6:+12167433 MsG0680030957.01.T01:CDS
CCCTCCAAAAGTTCCAACAA+TGG 0.630400 6:-12167482 MsG0680030958.01.T01:CDS
GGGGAGTTTAAGATGATCCG+GGG 0.666058 6:+12167369 MsG0680030957.01.T01:intron
GGTTGATGATGATCAACCGG+AGG 0.700628 6:+12167421 MsG0680030957.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATTTAACAATAAATTTG+AGG + Chr6:12166510-12166529 MsG0680030957.01.T01:intron 10.0%
!! CAATAAAAAGAAATAGAAAT+AGG + Chr6:12167014-12167033 MsG0680030957.01.T01:intron 15.0%
!! TTATGTGATTCTAATATATA+AGG + Chr6:12166074-12166093 MsG0680030957.01.T01:intron 15.0%
!! AATCATTTGCATAAATTCTA+TGG - Chr6:12167123-12167142 MsG0680030958.01.T01:intron 20.0%
!! TATATTTGAATACATTGAGT+CGG + Chr6:12166660-12166679 MsG0680030957.01.T01:intron 20.0%
!! TGATATTTATCATTATGTGT+TGG - Chr6:12167187-12167206 MsG0680030958.01.T01:intron 20.0%
!!! CTTTTTTACTTCATTTTGTA+AGG - Chr6:12167219-12167238 MsG0680030958.01.T01:intron 20.0%
!!! TATTGACTTAAGATTTTAGA+CGG - Chr6:12167029-12167048 MsG0680030958.01.T01:intron 20.0%
! AATTAAGGAACTTCAACTAT+TGG + Chr6:12166801-12166820 MsG0680030957.01.T01:intron 25.0%
! ACTATACTTTCACACAATTA+AGG + Chr6:12166816-12166835 MsG0680030957.01.T01:intron 25.0%
! ATCATATCATATAACTGTGA+TGG - Chr6:12166116-12166135 MsG0680030958.01.T01:intron 25.0%
! CTAGAAATCAGAAATGAAAA+TGG + Chr6:12165987-12166006 MsG0680030957.01.T01:intron 25.0%
! CTGATATAACATATATAGCA+CGG - Chr6:12167376-12167395 MsG0680030958.01.T01:CDS 25.0%
! CTTCAACTATTGGATATAAA+TGG + Chr6:12166791-12166810 MsG0680030957.01.T01:intron 25.0%
! TCAAGACAAAAAGTCAATTA+TGG + Chr6:12166628-12166647 MsG0680030957.01.T01:intron 25.0%
! TGCAAATGAGTTTAATAGTT+GGG - Chr6:12167155-12167174 MsG0680030958.01.T01:intron 25.0%
! TTGAGGAAATATAATTGCAA+CGG + Chr6:12166028-12166047 MsG0680030957.01.T01:intron 25.0%
!! AATGTACTACTATTTGTTGA+AGG + Chr6:12167094-12167113 MsG0680030957.01.T01:intron 25.0%
!!! GTGTGAAAGTATAGTTTTTT+GGG - Chr6:12166821-12166840 MsG0680030958.01.T01:intron 25.0%
!!! TGTGTGAAAGTATAGTTTTT+TGG - Chr6:12166820-12166839 MsG0680030958.01.T01:intron 25.0%
AATCACATAACCAAGTAGTA+CGG - Chr6:12166084-12166103 MsG0680030958.01.T01:intron 30.0%
AGACAAAAAGTCAATTATGG+AGG + Chr6:12166625-12166644 MsG0680030957.01.T01:intron 30.0%
AGATAGATAGATACCTTTCA+GGG + Chr6:12166308-12166327 MsG0680030957.01.T01:intron 30.0%
AGGCAGCTATTGTATAAAAA+TGG + Chr6:12166605-12166624 MsG0680030957.01.T01:intron 30.0%
ATTTGTGTGTTTGATTATGC+GGG + Chr6:12166758-12166777 MsG0680030957.01.T01:intron 30.0%
CATTTGTGTGTTTGATTATG+CGG + Chr6:12166759-12166778 MsG0680030957.01.T01:intron 30.0%
GCATAATCAAACACACAAAT+GGG - Chr6:12166758-12166777 MsG0680030958.01.T01:intron 30.0%
GGCAGCTATTGTATAAAAAT+GGG + Chr6:12166604-12166623 MsG0680030957.01.T01:intron 30.0%
GTGCAAATGAGTTTAATAGT+TGG - Chr6:12167154-12167173 MsG0680030958.01.T01:intron 30.0%
TAGATAGATAGATACCTTTC+AGG + Chr6:12166309-12166328 MsG0680030957.01.T01:intron 30.0%
! AGAAATAGGTATGATAACGT+GGG + Chr6:12167000-12167019 MsG0680030957.01.T01:intron 30.0%
! TAGAAATAGGTATGATAACG+TGG + Chr6:12167001-12167020 MsG0680030957.01.T01:intron 30.0%
! TTGTGTAATTTTCAGTGTTG+TGG - Chr6:12167555-12167574 MsG0680030958.01.T01:five_prime_UTR 30.0%
AACCATTCAAATACCCTGAA+AGG - Chr6:12166292-12166311 MsG0680030958.01.T01:intron 35.0%
AGCTGGTAAATATCAACCAA+AGG - Chr6:12167331-12167350 MsG0680030958.01.T01:intron 35.0%
AGTGTTGTGGTTTATAACAG+TGG - Chr6:12167568-12167587 MsG0680030958.01.T01:five_prime_UTR 35.0%
AGTTTCTCATCAATCAGCAT+TGG + Chr6:12167664-12167683 MsG0680030957.01.T01:intron 35.0%
CGCATAATCAAACACACAAA+TGG - Chr6:12166757-12166776 MsG0680030958.01.T01:intron 35.0%
CTTCTTGCCAGAAACAAAAA+GGG - Chr6:12167287-12167306 MsG0680030958.01.T01:intron 35.0%
GAAGCTGTTATTGATACCTT+TGG + Chr6:12167350-12167369 MsG0680030957.01.T01:intron 35.0%
TAGTTTATGTCAACTACTGC+AGG - Chr6:12167591-12167610 MsG0680030958.01.T01:five_prime_UTR 35.0%
TTCGCATGTGTTTGTTTGTA+CGG + Chr6:12166962-12166981 MsG0680030957.01.T01:intron 35.0%
TTCTACTATACCGTACTACT+TGG + Chr6:12166097-12166116 MsG0680030957.01.T01:intron 35.0%
TTGCATTGAGATTCCATTGT+TGG + Chr6:12166171-12166190 MsG0680030957.01.T01:intron 35.0%
! GATTCCATTGTTGGAACTTT+TGG + Chr6:12166162-12166181 MsG0680030957.01.T01:intron 35.0%
! TACAGGTTTTCGCAATTCAT+TGG + Chr6:12166247-12166266 MsG0680030957.01.T01:intron 35.0%
! TACCTTTCAGGGTATTTGAA+TGG + Chr6:12166297-12166316 MsG0680030957.01.T01:intron 35.0%
! TCAGGGTATTTGAATGGTTT+GGG + Chr6:12166291-12166310 MsG0680030957.01.T01:intron 35.0%
! TTCAGGGTATTTGAATGGTT+TGG + Chr6:12166292-12166311 MsG0680030957.01.T01:intron 35.0%
!!! ATTGGAAGCTTGTTTTGAAG+AGG + Chr6:12167646-12167665 MsG0680030957.01.T01:intron 35.0%
ACACATGCGAAACACGAATT+TGG - Chr6:12166971-12166990 MsG0680030958.01.T01:intron 40.0%
CCTTCTTGCCAGAAACAAAA+AGG - Chr6:12167286-12167305 MsG0680030958.01.T01:intron 40.0%
CTTCGTATTGTAGACGTGTT+TGG - Chr6:12167402-12167421 MsG0680030958.01.T01:CDS 40.0%
GGAGATGTGATGTGATATTG+AGG - Chr6:12167050-12167069 MsG0680030958.01.T01:intron 40.0%
GGGACATCATCATATCAGTT+GGG + Chr6:12167253-12167272 MsG0680030957.01.T01:intron 40.0%
! AGGTTTTCGCAATTCATTGG+AGG + Chr6:12166244-12166263 MsG0680030957.01.T01:intron 40.0%
! CAGGGTATTTGAATGGTTTG+GGG + Chr6:12166290-12166309 MsG0680030957.01.T01:intron 40.0%
! CCATTGTTGGAACTTTTGGA+GGG + Chr6:12166158-12166177 MsG0680030957.01.T01:intron 40.0%
! GAAGCTACAACTGTTAGCTT+CGG - Chr6:12166910-12166929 MsG0680030958.01.T01:intron 40.0%
! GGTTTTCGCAATTCATTGGA+GGG + Chr6:12166243-12166262 MsG0680030957.01.T01:intron 40.0%
! TCCATTGTTGGAACTTTTGG+AGG + Chr6:12166159-12166178 MsG0680030957.01.T01:intron 40.0%
! TGGTTGATATTTACCAGCTC+CGG + Chr6:12167330-12167349 MsG0680030957.01.T01:intron 40.0%
! TTGGGGAGTTTAAGATGATC+CGG + Chr6:12166273-12166292 MsG0680030957.01.T01:intron 40.0%
!! CATTGTTGGAACTTTTGGAG+GGG + Chr6:12166157-12166176 MsG0680030957.01.T01:intron 40.0%
!!! CCTTTTTGTTTCTGGCAAGA+AGG + Chr6:12167289-12167308 MsG0680030957.01.T01:intron 40.0%
AAGAAGGCCTTTGGTTACTG+GGG + Chr6:12167273-12167292 MsG0680030957.01.T01:intron 45.0%
AGTGAGTGAGTGTGTCTTTG+AGG + Chr6:12166045-12166064 MsG0680030957.01.T01:intron 45.0%
ATGATGTCCCCAGTAACCAA+AGG - Chr6:12167263-12167282 MsG0680030958.01.T01:intron 45.0%
ATTGCGAAAACCTGTAACCC+CGG - Chr6:12166251-12166270 MsG0680030958.01.T01:intron 45.0%
CAAGAAGGCCTTTGGTTACT+GGG + Chr6:12167274-12167293 MsG0680030957.01.T01:intron 45.0%
CCCTCCAAAAGTTCCAACAA+TGG - Chr6:12166155-12166174 MsG0680030958.01.T01:intron 45.0%
CTTGCCAGAAACAAAAAGGG+CGG - Chr6:12167290-12167309 MsG0680030958.01.T01:intron 45.0%
GGGGACATCATCATATCAGT+TGG + Chr6:12167254-12167273 MsG0680030957.01.T01:intron 45.0%
TTAAGATGATCCGGGGTTAC+AGG + Chr6:12166264-12166283 MsG0680030957.01.T01:intron 45.0%
TTGAGGTGTGAAGTCTCGTT+AGG - Chr6:12167067-12167086 MsG0680030958.01.T01:intron 45.0%
TTTCGCAATTCATTGGAGGG+TGG + Chr6:12166240-12166259 MsG0680030957.01.T01:intron 45.0%
! GGTTGATATTTACCAGCTCC+GGG + Chr6:12167329-12167348 MsG0680030957.01.T01:intron 45.0%
! TGGGGAGTTTAAGATGATCC+GGG + Chr6:12166272-12166291 MsG0680030957.01.T01:intron 45.0%
!! GGTGGTTGATGATGATCAAC+CGG + Chr6:12166222-12166241 MsG0680030957.01.T01:intron 45.0%
ACCTCGAATTCCGTGTTGGA+CGG + Chr6:12166851-12166870 MsG0680030957.01.T01:intron 50.0%
AGATCCTGCAAGCACATCTC+TGG + Chr6:12167619-12167638 MsG0680030957.01.T01:intron 50.0%
AGCTACCTCGAATTCCGTGT+TGG + Chr6:12166855-12166874 MsG0680030957.01.T01:intron 50.0%
GCAAGAAGGCCTTTGGTTAC+TGG + Chr6:12167275-12167294 MsG0680030957.01.T01:intron 50.0%
GCTTCGGATTCAACACACTG+TGG - Chr6:12166926-12166945 MsG0680030958.01.T01:intron 50.0%
TGATATTTACCAGCTCCGGG+TGG + Chr6:12167326-12167345 MsG0680030957.01.T01:intron 50.0%
TTTGGGAATCCCGTCCAACA+CGG - Chr6:12166838-12166857 MsG0680030958.01.T01:intron 50.0%
! GGGGAGTTTAAGATGATCCG+GGG + Chr6:12166271-12166290 MsG0680030957.01.T01:intron 50.0%
! TGATGATGATCAACCGGAGG+AGG + Chr6:12166216-12166235 MsG0680030957.01.T01:intron 50.0%
! TTCAACACACTGTGGTGCTG+CGG - Chr6:12166934-12166953 MsG0680030958.01.T01:intron 50.0%
!! ACTCATTTTTCCACGCCTCG+AGG - Chr6:12166875-12166894 MsG0680030958.01.T01:intron 50.0%
!! GGAACTTTTGGAGGGGTTTG+CGG + Chr6:12166150-12166169 MsG0680030957.01.T01:intron 50.0%
!! GGTTGATGATGATCAACCGG+AGG + Chr6:12166219-12166238 MsG0680030957.01.T01:intron 50.0%
!! GTTTCTGGCAAGAAGGCCTT+TGG + Chr6:12167282-12167301 MsG0680030957.01.T01:intron 50.0%
AACTCCTCCTCTTCCTCCTC+CGG - Chr6:12166200-12166219 MsG0680030958.01.T01:intron 55.0%
CCTCGAATTCCGTGTTGGAC+GGG + Chr6:12166850-12166869 MsG0680030957.01.T01:intron 55.0%
GGTTCCAGAGATGTGCTTGC+AGG - Chr6:12167612-12167631 MsG0680030958.01.T01:five_prime_UTR 55.0%
TGATCAACCGGAGGAGGAAG+AGG + Chr6:12166210-12166229 MsG0680030957.01.T01:intron 55.0%
!! TCAACACACTGTGGTGCTGC+GGG - Chr6:12166935-12166954 MsG0680030958.01.T01:intron 55.0%
!! TGCGCCGCCCTTTTTGTTTC+TGG + Chr6:12167297-12167316 MsG0680030957.01.T01:intron 55.0%
CCAGACACGACACTCACACG+AGG + Chr6:12167502-12167521 MsG0680030957.01.T01:CDS 60.0%
CCCGTCCAACACGGAATTCG+AGG - Chr6:12166847-12166866 MsG0680030958.01.T01:intron 60.0%
GCACTATTACCACCCGGAGC+TGG - Chr6:12167314-12167333 MsG0680030958.01.T01:intron 60.0%
GGAGGAGGAAGAGGAGGAGT+TGG + Chr6:12166201-12166220 MsG0680030957.01.T01:intron 60.0%
TCAACCGGAGGAGGAAGAGG+AGG + Chr6:12166207-12166226 MsG0680030957.01.T01:intron 60.0%
TTCTCACTTGTCGCGCCTCG+AGG + Chr6:12166893-12166912 MsG0680030957.01.T01:intron 60.0%
! CCTCGTGTGAGTGTCGTGTC+TGG - Chr6:12167499-12167518 MsG0680030958.01.T01:CDS 60.0%
GGCGGCGCACTATTACCACC+CGG - Chr6:12167308-12167327 MsG0680030958.01.T01:intron 65.0%
ACTTGTCGCGCCTCGAGGCG+TGG + Chr6:12166888-12166907 MsG0680030957.01.T01:intron 70.0%
Chromosome Type Strat End Strand Name
Chr6 gene 12165963 12167696 12165963 ID=MsG0680030958.01;Name=MsG0680030958.01
Chr6 mRNA 12165963 12167696 12165963 ID=MsG0680030958.01.T01;Parent=MsG0680030958.01;Name=MsG0680030958.01.T01;_AED=0.49;_eAED=0.53;_QI=172|0|0.5|1|0|0|2|0|101
Chr6 exon 12165963 12166089 12165963 ID=MsG0680030958.01.T01:exon:8757;Parent=MsG0680030958.01.T01
Chr6 exon 12167346 12167696 12167346 ID=MsG0680030958.01.T01:exon:8756;Parent=MsG0680030958.01.T01
Chr6 five_prime_UTR 12167525 12167696 12167525 ID=MsG0680030958.01.T01:five_prime_utr;Parent=MsG0680030958.01.T01
Chr6 CDS 12167346 12167524 12167346 ID=MsG0680030958.01.T01:cds;Parent=MsG0680030958.01.T01
Chr6 CDS 12165963 12166089 12165963 ID=MsG0680030958.01.T01:cds;Parent=MsG0680030958.01.T01
Gene Sequence

>MsG0680030958.01.T01

ATGGAAAATATGCCGCAAACCCCTCCAAAAGTTCCAACAATGGAATCTCAATGCAAAACAACACCAACTCCTCCTCTTCCTCCTCCGGTTGATCATCATCAACCACCCTCCAATGAATTGCGAAAACCTGTAACCCCGGATCATCTTAAACTCCCCAAACCATTCAAATACCCTGAAAGTGTTGTGGTTTATAACAGTGGTAGTTTATGTCAACTACTGCAGGTTCCAGAGATGTGCTTGCAGGATCTGAGTCCTCTTCAAAACAAGCTTCCAATGCTGATTGATGAGAAACTCAACTCAACTTGA
Protein sequence

>MsG0680030958.01.T01

MENMPQTPPKVPTMESQCKTTPTPPLPPPVDHHQPPSNELRKPVTPDHLKLPKPFKYPESVVVYNSGSLCQLLQVPEMCLQDLSPLQNKLPMLIDEKLNST*