AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280006569.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006569.01.T01 MTR_2g010890 59.494 158 10 2 43 146 165 322 7.79e-49 164
MsG0280006569.01.T01 MTR_2g010890 53.571 84 28 3 102 184 356 429 8.43e-16 74.7
MsG0280006569.01.T01 MTR_4g045767 55.556 54 24 0 92 145 338 391 1.86e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006569.01.T01 AT3G22104 58.182 55 23 0 92 146 331 385 6.04e-16 75.5
MsG0280006569.01.T01 AT3G22104 58.182 55 23 0 92 146 256 310 7.51e-16 75.1
MsG0280006569.01.T01 AT3G22104 58.182 55 23 0 92 146 256 310 7.51e-16 75.1
MsG0280006569.01.T01 AT3G22104 58.182 55 23 0 92 146 256 310 7.51e-16 75.1

Find 40 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTCTCATTGCTTGATAT+TGG 0.269406 2:+3548841 MsG0280006569.01.T01:CDS
TAAGAGAGTTACTAAATTGA+TGG 0.270336 2:+3549105 MsG0280006569.01.T01:CDS
TTAACTTGATCAGTTGTGTT+GGG 0.301874 2:+3548773 MsG0280006569.01.T01:intron
GATAAAGAGGTATGGAGAAT+TGG 0.308656 2:+3550082 MsG0280006569.01.T01:CDS
TGTGATTCCCTCGCAGCATC+TGG 0.320998 2:-3549202 None:intergenic
TGTTAAGATTGAGACGATTA+AGG 0.322350 2:+3548807 MsG0280006569.01.T01:CDS
AATCTTAATCGAATTGCTAT+TGG 0.350422 2:+3548889 MsG0280006569.01.T01:CDS
TGTATCTAAAGGCAAGTTAC+TGG 0.393418 2:+3549251 MsG0280006569.01.T01:CDS
CTGGCTTGTGTAAAGAAGTC+AGG 0.412840 2:+3550128 MsG0280006569.01.T01:CDS
GAAGGCTGGAGATGAGGATC+AGG 0.415316 2:-3549151 None:intergenic
CTTAACTTGATCAGTTGTGT+TGG 0.425064 2:+3548772 MsG0280006569.01.T01:intron
TCCATATGAGGCTTCAAACT+TGG 0.429267 2:-3548388 None:intergenic
AATGGAATGTGGGACCCATC+TGG 0.457405 2:+3550109 MsG0280006569.01.T01:CDS
GTTGAAGAGATAAAGAGGTA+TGG 0.458167 2:+3550074 MsG0280006569.01.T01:CDS
ATTTAGTAACTCTCTTAACT+TGG 0.462016 2:-3549099 None:intergenic
ACCAAGTTTGAAGCCTCATA+TGG 0.471749 2:+3548387 MsG0280006569.01.T01:CDS
GTATGGAGAATTGGAAGGAA+TGG 0.482357 2:+3550091 MsG0280006569.01.T01:CDS
AGGATGTTGAAGAGATAAAG+AGG 0.487290 2:+3550069 MsG0280006569.01.T01:CDS
ATGCTTCAAATTCAGAAGGC+TGG 0.488106 2:-3549165 None:intergenic
TATTGGATCAATTTCTTGCA+AGG 0.490862 2:+3548858 MsG0280006569.01.T01:CDS
CAAGAACATAGATGTGAAAG+AGG 0.507528 2:+3550049 MsG0280006569.01.T01:CDS
CTTCTTTACACAAGCCAGAT+GGG 0.520558 2:-3550123 None:intergenic
TAACTTGATCAGTTGTGTTG+GGG 0.536130 2:+3548774 MsG0280006569.01.T01:intron
AGCCATGGACATGTATCTAA+AGG 0.542092 2:+3549240 MsG0280006569.01.T01:CDS
GAATTGGAAGGAATGGAATG+TGG 0.550446 2:+3550098 MsG0280006569.01.T01:CDS
ACTTCTTTACACAAGCCAGA+TGG 0.554159 2:-3550124 None:intergenic
ATCAATGCTTCAAATTCAGA+AGG 0.564510 2:-3549169 None:intergenic
GTGATTCCCTCGCAGCATCT+GGG 0.573530 2:-3549201 None:intergenic
AGAACATAGCATGGACACAT+TGG 0.577656 2:-3548322 None:intergenic
TGCCTTTAGATACATGTCCA+TGG 0.578884 2:-3549242 None:intergenic
AGTTCTCCCAGATGCTGCGA+GGG 0.592260 2:+3549195 MsG0280006569.01.T01:CDS
AATTCAGAAGGCTGGAGATG+AGG 0.594161 2:-3549157 None:intergenic
TGATCAATTATACATAGCCA+TGG 0.599608 2:+3549225 MsG0280006569.01.T01:CDS
TTGAGCAGCAGAACATAGCA+TGG 0.601035 2:-3548331 None:intergenic
AAGAGGTATGGAGAATTGGA+AGG 0.605606 2:+3550086 MsG0280006569.01.T01:CDS
AATTGGAAGGAATGGAATGT+GGG 0.609226 2:+3550099 MsG0280006569.01.T01:CDS
ATTGATGGATTTGTTCCTTG+TGG 0.613773 2:+3549120 MsG0280006569.01.T01:CDS
TGGCTTGTGTAAAGAAGTCA+GGG 0.614803 2:+3550129 MsG0280006569.01.T01:CDS
CAGTTCTCCCAGATGCTGCG+AGG 0.652508 2:+3549194 MsG0280006569.01.T01:CDS
GATCAGGAGCAACTTCCACA+AGG 0.673647 2:-3549135 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATATTAAGAATCATAA+AGG - Chr2:3549344-3549363 None:intergenic 10.0%
!! ATAATATTAAGAATCATAAA+GGG - Chr2:3549343-3549362 None:intergenic 10.0%
!!! AACAATATAGAAAGTCTTAT+AGG + Chr2:3548937-3548956 MsG0280006569.01.T01:intron 20.0%
!!! ATATGGAAAATTTTCTTGAA+GGG + Chr2:3548404-3548423 MsG0280006569.01.T01:CDS 20.0%
!!! ATTGTACAAGATTTTAAGTT+AGG + Chr2:3549309-3549328 MsG0280006569.01.T01:intron 20.0%
! AAAATCGTTATTTGTGATCT+AGG - Chr2:3549423-3549442 None:intergenic 25.0%
! AACCTATGAAAATTTATCAG+TGG - Chr2:3549816-3549835 None:intergenic 25.0%
! AAGAATTTCTAAGTAACCTT+TGG - Chr2:3548493-3548512 None:intergenic 25.0%
! AATCTTAATCGAATTGCTAT+TGG + Chr2:3548889-3548908 MsG0280006569.01.T01:CDS 25.0%
! ATTTAGTAACTCTCTTAACT+TGG - Chr2:3549102-3549121 None:intergenic 25.0%
! CAGCATAATTTATGATGAAA+TGG - Chr2:3549454-3549473 None:intergenic 25.0%
! TAAGAGAGTTACTAAATTGA+TGG + Chr2:3549105-3549124 MsG0280006569.01.T01:CDS 25.0%
! TGTGTTTAAAGACTATTGTT+CGG - Chr2:3549601-3549620 None:intergenic 25.0%
!! ATTTGTTAGACAATGTCATA+AGG + Chr2:3548696-3548715 MsG0280006569.01.T01:intron 25.0%
!! CATATGGAAAATTTTCTTGA+AGG + Chr2:3548403-3548422 MsG0280006569.01.T01:CDS 25.0%
!! TCAAGAAAATTTTCCATATG+AGG - Chr2:3548403-3548422 None:intergenic 25.0%
!! TTCCACTGATAAATTTTCAT+AGG + Chr2:3549811-3549830 MsG0280006569.01.T01:intron 25.0%
!!! TATGTGTTGATTTTGTCATA+AGG + Chr2:3549027-3549046 MsG0280006569.01.T01:intron 25.0%
!!! TTGTGTGCTATTTAAGTTTT+TGG + Chr2:3549720-3549739 MsG0280006569.01.T01:intron 25.0%
AAGACATCTTACAAGAAACT+TGG + Chr2:3549909-3549928 MsG0280006569.01.T01:intron 30.0%
AGAAATTCTTGACAGAATCA+TGG + Chr2:3548503-3548522 MsG0280006569.01.T01:intron 30.0%
ATCAATGCTTCAAATTCAGA+AGG - Chr2:3549172-3549191 None:intergenic 30.0%
ATTATCTTGAAACCATACCA+CGG - Chr2:3549570-3549589 None:intergenic 30.0%
TATTGGATCAATTTCTTGCA+AGG + Chr2:3548858-3548877 MsG0280006569.01.T01:CDS 30.0%
TGATCAATTATACATAGCCA+TGG + Chr2:3549225-3549244 MsG0280006569.01.T01:CDS 30.0%
TGTTAAGATTGAGACGATTA+AGG + Chr2:3548807-3548826 MsG0280006569.01.T01:CDS 30.0%
! AAATTTTCATAGGTTCATGC+AGG + Chr2:3549821-3549840 MsG0280006569.01.T01:intron 30.0%
! TATCTGTTTTCTTTCGAATG+AGG + Chr2:3549743-3549762 MsG0280006569.01.T01:intron 30.0%
! TTAACTTGATCAGTTGTGTT+GGG + Chr2:3548773-3548792 MsG0280006569.01.T01:intron 30.0%
AATTGGAAGGAATGGAATGT+GGG + Chr2:3550099-3550118 MsG0280006569.01.T01:CDS 35.0%
AGGATGTTGAAGAGATAAAG+AGG + Chr2:3550069-3550088 MsG0280006569.01.T01:CDS 35.0%
CAAGAACATAGATGTGAAAG+AGG + Chr2:3550049-3550068 MsG0280006569.01.T01:CDS 35.0%
CCAAGAATCATTTCTTCCAA+AGG + Chr2:3548474-3548493 MsG0280006569.01.T01:intron 35.0%
CTGTTTGAAGAACATGTGTA+TGG - Chr2:3548573-3548592 None:intergenic 35.0%
CTTCTCTCATTGCTTGATAT+TGG + Chr2:3548841-3548860 MsG0280006569.01.T01:CDS 35.0%
CTTGAGAAATAACTTCTCTG+AGG + Chr2:3548635-3548654 MsG0280006569.01.T01:intron 35.0%
GTTGAAGAGATAAAGAGGTA+TGG + Chr2:3550074-3550093 MsG0280006569.01.T01:CDS 35.0%
TAACTTGATCAGTTGTGTTG+GGG + Chr2:3548774-3548793 MsG0280006569.01.T01:intron 35.0%
TACTTCTTCCATCTCCAAAT+GGG + Chr2:3548992-3549011 MsG0280006569.01.T01:intron 35.0%
TATGCATGATCTTTCCCATT+TGG - Chr2:3549009-3549028 None:intergenic 35.0%
TATGGACTTGTAACAAGACA+TGG - Chr2:3548555-3548574 None:intergenic 35.0%
TGTATCTAAAGGCAAGTTAC+TGG + Chr2:3549251-3549270 MsG0280006569.01.T01:CDS 35.0%
TTATCTTGAAACCATACCAC+GGG - Chr2:3549569-3549588 None:intergenic 35.0%
! ATGTTCTGCTGCTCAATTTT+TGG + Chr2:3548338-3548357 MsG0280006569.01.T01:CDS 35.0%
! CCTTTGGAAGAAATGATTCT+TGG - Chr2:3548477-3548496 None:intergenic 35.0%
! CTTAACTTGATCAGTTGTGT+TGG + Chr2:3548772-3548791 MsG0280006569.01.T01:intron 35.0%
! GATAAAGAGGTATGGAGAAT+TGG + Chr2:3550082-3550101 MsG0280006569.01.T01:CDS 35.0%
! TTCTTGAAGGGATTCGTTTT+TGG + Chr2:3548416-3548435 MsG0280006569.01.T01:CDS 35.0%
!! ATTGATGGATTTGTTCCTTG+TGG + Chr2:3549120-3549139 MsG0280006569.01.T01:CDS 35.0%
!!! CGTGAAGATTTTTTGTTAGG+AGG + Chr2:3549052-3549071 MsG0280006569.01.T01:intron 35.0%
!!! GAAGATTTTTTGTTAGGAGG+AGG + Chr2:3549055-3549074 MsG0280006569.01.T01:intron 35.0%
!!! GCTCGTGAAGATTTTTTGTT+AGG + Chr2:3549049-3549068 MsG0280006569.01.T01:intron 35.0%
ACTTCTTTACACAAGCCAGA+TGG - Chr2:3550127-3550146 None:intergenic 40.0%
AGCCATGGACATGTATCTAA+AGG + Chr2:3549240-3549259 MsG0280006569.01.T01:CDS 40.0%
ATGCTTCAAATTCAGAAGGC+TGG - Chr2:3549168-3549187 None:intergenic 40.0%
CAATATGTAGTCAGAGACGT+AGG + Chr2:3549669-3549688 MsG0280006569.01.T01:intron 40.0%
CTACGTCTCTGACTACATAT+TGG - Chr2:3549671-3549690 None:intergenic 40.0%
CTACTTCTTCCATCTCCAAA+TGG + Chr2:3548991-3549010 MsG0280006569.01.T01:intron 40.0%
CTTCTTTACACAAGCCAGAT+GGG - Chr2:3550126-3550145 None:intergenic 40.0%
GAATTGGAAGGAATGGAATG+TGG + Chr2:3550098-3550117 MsG0280006569.01.T01:CDS 40.0%
GTATGGAGAATTGGAAGGAA+TGG + Chr2:3550091-3550110 MsG0280006569.01.T01:CDS 40.0%
TATCTTGAAACCATACCACG+GGG - Chr2:3549568-3549587 None:intergenic 40.0%
TCCATATGAGGCTTCAAACT+TGG - Chr2:3548391-3548410 None:intergenic 40.0%
TCTACTTCTAGCCTGATAAG+CGG + Chr2:3549519-3549538 MsG0280006569.01.T01:intron 40.0%
TGATCTTTCCCATTTGGAGA+TGG - Chr2:3549003-3549022 None:intergenic 40.0%
TGCCTTTAGATACATGTCCA+TGG - Chr2:3549245-3549264 None:intergenic 40.0%
TGCTTGTGTCACAAGAAAAC+TGG - Chr2:3548605-3548624 None:intergenic 40.0%
TTTCTTGTGACATCTTCTCG+TGG - Chr2:3549885-3549904 None:intergenic 40.0%
! AAGAGGTATGGAGAATTGGA+AGG + Chr2:3550086-3550105 MsG0280006569.01.T01:CDS 40.0%
! AAGTCTTATAGGTCCTCTGT+TGG + Chr2:3548948-3548967 MsG0280006569.01.T01:intron 40.0%
! ACCAAGTTTGAAGCCTCATA+TGG + Chr2:3548387-3548406 MsG0280006569.01.T01:CDS 40.0%
! ATTGTTGCTTGATCCAACAG+AGG - Chr2:3548964-3548983 None:intergenic 40.0%
! GTGATCTAGGCCATAGTTTT+AGG - Chr2:3549410-3549429 None:intergenic 40.0%
! TGGCTTGTGTAAAGAAGTCA+GGG + Chr2:3550129-3550148 MsG0280006569.01.T01:CDS 40.0%
! TTGGACTTGGTTTGAACTCA+TGG + Chr2:3548435-3548454 MsG0280006569.01.T01:intron 40.0%
!! AAGGGATTCGTTTTTGGACT+TGG + Chr2:3548422-3548441 MsG0280006569.01.T01:CDS 40.0%
!! ATAACTTCTCTGAGGCTACA+TGG + Chr2:3548643-3548662 MsG0280006569.01.T01:intron 40.0%
!! TGCTGCTCAATTTTTGGAGA+TGG + Chr2:3548344-3548363 MsG0280006569.01.T01:CDS 40.0%
!!! GCTCTTGGTTTTGTTTCTGA+AGG - Chr2:3549940-3549959 None:intergenic 40.0%
AATTCAGAAGGCTGGAGATG+AGG - Chr2:3549160-3549179 None:intergenic 45.0%
ATCTTGAAACCATACCACGG+GGG - Chr2:3549567-3549586 None:intergenic 45.0%
CGCAGACACACCTAAAACTA+TGG + Chr2:3549397-3549416 MsG0280006569.01.T01:intron 45.0%
CTACTTCTAGCCTGATAAGC+GGG + Chr2:3549520-3549539 MsG0280006569.01.T01:intron 45.0%
GTCACAAGAAAACTGGAAGC+TGG - Chr2:3548598-3548617 None:intergenic 45.0%
TCATAGGTTCATGCAGGCAT+AGG + Chr2:3549827-3549846 MsG0280006569.01.T01:intron 45.0%
TCATGCAGGCATAGGTGAAA+AGG + Chr2:3549835-3549854 MsG0280006569.01.T01:intron 45.0%
TGTCTAGTGACATGAGCTCT+TGG - Chr2:3549955-3549974 None:intergenic 45.0%
TTGAGCAGCAGAACATAGCA+TGG - Chr2:3548334-3548353 None:intergenic 45.0%
! CTGGCTTGTGTAAAGAAGTC+AGG + Chr2:3550128-3550147 MsG0280006569.01.T01:CDS 45.0%
AATGGAATGTGGGACCCATC+TGG + Chr2:3550109-3550128 MsG0280006569.01.T01:CDS 50.0%
AGTCAGAGACGTAGGCACAT+TGG + Chr2:3549677-3549696 MsG0280006569.01.T01:intron 50.0%
ATTGGAAATCCCCCGTGGTA+TGG + Chr2:3549555-3549574 MsG0280006569.01.T01:intron 50.0%
GATCAGGAGCAACTTCCACA+AGG - Chr2:3549138-3549157 None:intergenic 50.0%
!! ACTTCTCTGAGGCTACATGG+TGG + Chr2:3548646-3548665 MsG0280006569.01.T01:intron 50.0%
AGTTCTCCCAGATGCTGCGA+GGG + Chr2:3549195-3549214 MsG0280006569.01.T01:CDS 55.0%
GAAGGCTGGAGATGAGGATC+AGG - Chr2:3549154-3549173 None:intergenic 55.0%
GTGATTCCCTCGCAGCATCT+GGG - Chr2:3549204-3549223 None:intergenic 55.0%
TGTGATTCCCTCGCAGCATC+TGG - Chr2:3549205-3549224 None:intergenic 55.0%
CAGTTCTCCCAGATGCTGCG+AGG + Chr2:3549194-3549213 MsG0280006569.01.T01:CDS 60.0%
CGCGAATTGGAAATCCCCCG+TGG + Chr2:3549550-3549569 MsG0280006569.01.T01:intron 60.0%
GCGTGACAAGCCCGCTTATC+AGG - Chr2:3549533-3549552 None:intergenic 60.0%
! AGCGGGCTTGTCACGCGAAT+TGG + Chr2:3549537-3549556 MsG0280006569.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 3548325 3550163 3548325 ID=MsG0280006569.01;Name=MsG0280006569.01
Chr2 mRNA 3548325 3550163 3548325 ID=MsG0280006569.01.T01;Parent=MsG0280006569.01;Name=MsG0280006569.01.T01;_AED=0.49;_eAED=0.52;_QI=0|0|0|1|1|1|4|0|187
Chr2 exon 3548325 3548443 3548325 ID=MsG0280006569.01.T01:exon:759;Parent=MsG0280006569.01.T01
Chr2 exon 3548786 3548910 3548786 ID=MsG0280006569.01.T01:exon:760;Parent=MsG0280006569.01.T01
Chr2 exon 3549071 3549272 3549071 ID=MsG0280006569.01.T01:exon:761;Parent=MsG0280006569.01.T01
Chr2 exon 3550046 3550163 3550046 ID=MsG0280006569.01.T01:exon:762;Parent=MsG0280006569.01.T01
Chr2 CDS 3548325 3548443 3548325 ID=MsG0280006569.01.T01:cds;Parent=MsG0280006569.01.T01
Chr2 CDS 3548786 3548910 3548786 ID=MsG0280006569.01.T01:cds;Parent=MsG0280006569.01.T01
Chr2 CDS 3549071 3549272 3549071 ID=MsG0280006569.01.T01:cds;Parent=MsG0280006569.01.T01
Chr2 CDS 3550046 3550163 3550046 ID=MsG0280006569.01.T01:cds;Parent=MsG0280006569.01.T01
Gene Sequence

>MsG0280006569.01.T01

ATGTGTCCATGCTATGTTCTGCTGCTCAATTTTTGGAGATGGAAGAGTGATAGTCTTGAAGCACCAAGTTTGAAGCCTCATATGGAAAATTTTCTTGAAGGGATTCGTTTTTGGACTTGTTGTGTTGGGGCTGAACAAGATGTTAAGATTGAGACGATTAAGGTTCTAATCGATCTTCTCTCATTGCTTGATATTGGATCAATTTCTTGCAAGGATTTGTTCAATCTTAATCGAATTGCTATTGGAGGAGGTAGTTTTGAGTTAGATTTGAACCAAGTTAAGAGAGTTACTAAATTGATGGATTTGTTCCTTGTGGAAGTTGCTCCTGATCCTCATCTCCAGCCTTCTGAATTTGAAGCATTGATTACAGTTCTCCCAGATGCTGCGAGGGAATCACATGATCAATTATACATAGCCATGGACATGTATCTAAAGGCAAGTTACTGCTTCAAGAACATAGATGTGAAAGAGGATGTTGAAGAGATAAAGAGGTATGGAGAATTGGAAGGAATGGAATGTGGGACCCATCTGGCTTGTGTAAAGAAGTCAGGGTTCATACTTTGA
Protein sequence

>MsG0280006569.01.T01

MCPCYVLLLNFWRWKSDSLEAPSLKPHMENFLEGIRFWTCCVGAEQDVKIETIKVLIDLLSLLDIGSISCKDLFNLNRIAIGGGSFELDLNQVKRVTKLMDLFLVEVAPDPHLQPSEFEALITVLPDAARESHDQLYIAMDMYLKASYCFKNIDVKEDVEEIKRYGELEGMECGTHLACVKKSGFIL*