AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015438.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015438.01.T01 MTR_3g070090 64.821 307 41 6 1 240 1 307 1.38e-118 340
MsG0380015438.01.T01 MTR_5g081740 55.215 163 70 2 1 163 1 160 5.70e-53 169
MsG0380015438.01.T01 MTR_5g081740 55.215 163 70 2 1 163 1 160 1.88e-52 170
MsG0380015438.01.T01 MTR_5g081740 55.215 163 70 2 1 163 1 160 5.05e-52 169
MsG0380015438.01.T01 MTR_5g081740 55.215 163 70 2 1 163 1 160 9.42e-52 170
MsG0380015438.01.T01 MTR_5g081740 56.522 69 28 1 166 232 226 294 1.05e-16 77.8
MsG0380015438.01.T01 MTR_7g092870 57.616 151 61 2 1 151 1 148 5.88e-49 158
MsG0380015438.01.T01 MTR_7g092875 62.222 45 17 0 172 216 48 92 7.42e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015438.01.T01 AT2G39920 45.570 158 84 2 1 157 1 157 9.08e-45 152
MsG0380015438.01.T01 AT2G39920 45.570 158 84 2 1 157 1 157 9.08e-45 152
MsG0380015438.01.T01 AT2G39920 45.570 158 84 2 1 157 1 157 9.08e-45 152
MsG0380015438.01.T01 AT2G39920 45.570 158 84 2 1 157 1 157 9.34e-45 151

Find 41 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGCATCATCAAGCCATTA+TGG 0.257908 3:-70220454 MsG0380015438.01.T01:CDS
GCTGAGATCAATAACTTAAA+AGG 0.268132 3:-70220232 MsG0380015438.01.T01:CDS
AAATTCCGTGTTCGAGTATC+TGG 0.273477 3:+70219125 None:intergenic
GCTAGTCTTTCAGATGATTC+TGG 0.303642 3:-70220767 MsG0380015438.01.T01:intron
TTTGCTTCACTTGTCACTCT+TGG 0.322672 3:-70220385 MsG0380015438.01.T01:CDS
TGACGCAATTCGGTAGTATA+AGG 0.391337 3:+70220031 None:intergenic
TGGTTTGGATGTAGTGTTGA+TGG 0.427160 3:-70220080 MsG0380015438.01.T01:CDS
AGTGTTATTAATTACTCTGC+TGG 0.429058 3:-70220362 MsG0380015438.01.T01:CDS
GAATCATGAAACTAATGTTC+AGG 0.431585 3:+70219047 None:intergenic
AATTCGGTAGTATAAGGATT+TGG 0.431804 3:+70220037 None:intergenic
GGAATACCTGTGACGCAATT+CGG 0.434821 3:+70220021 None:intergenic
ATGCATCATCAAGCCATTAT+GGG 0.435331 3:-70220453 MsG0380015438.01.T01:CDS
ACACAGCTATATTCAAGTCT+TGG 0.436907 3:+70220146 None:intergenic
GTCTGCTTATGCGCATCAAA+TGG 0.443393 3:-70220807 MsG0380015438.01.T01:CDS
AGCCATTATGGGATAGAATC+AGG 0.447643 3:-70220442 MsG0380015438.01.T01:CDS
ATCCTGATTCTATCCCATAA+TGG 0.450812 3:+70220440 None:intergenic
CACAGCTATATTCAAGTCTT+GGG 0.455877 3:+70220147 None:intergenic
GAGGCCTTCAGATGATGGTT+TGG 0.461705 3:-70220095 MsG0380015438.01.T01:CDS
GCCAGATCTCTACATATGTT+AGG 0.462986 3:+70220199 None:intergenic
AAGTATTATAGGTAGCCATT+TGG 0.465740 3:-70219162 MsG0380015438.01.T01:CDS
AGTGTGAGGCCTTCAGATGA+TGG 0.472833 3:-70220100 MsG0380015438.01.T01:CDS
AACTTGTCACATACAAGGCC+TGG 0.477255 3:+70219095 None:intergenic
AAGAAGTATGATACAGAAGA+AGG 0.483859 3:-70219198 MsG0380015438.01.T01:CDS
TCCTAACATATGTAGAGATC+TGG 0.491695 3:-70220200 MsG0380015438.01.T01:CDS
TCATGTCAAAGTAAAAGTAC+TGG 0.493627 3:-70220316 MsG0380015438.01.T01:CDS
AGAAAAGTACTCATCCCCTT+TGG 0.500648 3:+70219226 None:intergenic
AAGAATCGGACTCTGCCAAA+GGG 0.509917 3:-70219241 MsG0380015438.01.T01:CDS
GAGTGCTCAATTCATCCAAA+TGG 0.532212 3:+70219147 None:intergenic
TCGGTAGTATAAGGATTTGG+AGG 0.540719 3:+70220040 None:intergenic
ATACTACCGAATTGCGTCAC+AGG 0.546143 3:-70220027 MsG0380015438.01.T01:intron
CTGGCTATACATTATGTCAA+AGG 0.560936 3:-70220181 MsG0380015438.01.T01:CDS
GAAGAATCGGACTCTGCCAA+AGG 0.574512 3:-70219242 MsG0380015438.01.T01:CDS
GTTCAAACTTGTCACATACA+AGG 0.614224 3:+70219090 None:intergenic
AGAAGTATGATACAGAAGAA+GGG 0.619155 3:-70219197 MsG0380015438.01.T01:CDS
ACATCCAAACCATCATCTGA+AGG 0.625982 3:+70220091 None:intergenic
GCTATACATTATGTCAAAGG+AGG 0.630795 3:-70220178 MsG0380015438.01.T01:CDS
ATGATTATCACAAGAGTGTG+AGG 0.631778 3:-70220114 MsG0380015438.01.T01:CDS
TGATTGCAGCATAATCGTCA+AGG 0.644438 3:+70220336 None:intergenic
AGAATCGGACTCTGCCAAAG+GGG 0.681596 3:-70219240 MsG0380015438.01.T01:CDS
GCACTCCAGATACTCGAACA+CGG 0.714450 3:-70219130 MsG0380015438.01.T01:CDS
AATGCACACTGCAATAACTG+TGG 0.734913 3:+70220263 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACCTATAATACTTTTTATA+TGG + Chr3:70220699-70220718 None:intergenic 15.0%
!!! TTCCATATAAAAAGTATTAT+AGG - Chr3:70220694-70220713 MsG0380015438.01.T01:intron 15.0%
!! ATTTAACAGATTTATAGTTC+TGG - Chr3:70220155-70220174 MsG0380015438.01.T01:CDS 20.0%
!! TGATTACAATTTCCATTATA+TGG - Chr3:70220214-70220233 MsG0380015438.01.T01:CDS 20.0%
!! TTGTTATCAAAACCATATAA+TGG + Chr3:70220229-70220248 None:intergenic 20.0%
! AATGGAAATTGTAATCAAGT+TGG + Chr3:70220211-70220230 None:intergenic 25.0%
! CAAAAGTTTGATATGATAAC+CGG - Chr3:70220565-70220584 MsG0380015438.01.T01:intron 25.0%
! CAAATAGTATTGTCAAATCA+TGG - Chr3:70219927-70219946 MsG0380015438.01.T01:intron 25.0%
! CGAACAAACTAATATATTCT+GGG - Chr3:70220064-70220083 MsG0380015438.01.T01:CDS 25.0%
! TCGAACAAACTAATATATTC+TGG - Chr3:70220063-70220082 MsG0380015438.01.T01:CDS 25.0%
!! TTTGTAAAAAAGCATAGTTG+AGG + Chr3:70220528-70220547 None:intergenic 25.0%
!!! CAGTTTTTTAAAAAGCAAAC+CGG + Chr3:70219352-70219371 None:intergenic 25.0%
AAATCATGGTTATAGCTAGA+TGG - Chr3:70219941-70219960 MsG0380015438.01.T01:intron 30.0%
AACATTGACAGTTAAAGATC+CGG + Chr3:70220587-70220606 None:intergenic 30.0%
AAGTATTATAGGTAGCCATT+TGG - Chr3:70220705-70220724 MsG0380015438.01.T01:intron 30.0%
AATTCGGTAGTATAAGGATT+TGG + Chr3:70219833-70219852 None:intergenic 30.0%
ACATTATCTTGGAGATACAA+AGG + Chr3:70220494-70220513 None:intergenic 30.0%
ATCTGTTAAATGTTGCAAGT+TGG + Chr3:70220146-70220165 None:intergenic 30.0%
ATTTACACCATCCTATATCA+AGG + Chr3:70219887-70219906 None:intergenic 30.0%
CATTATCTTGGAGATACAAA+GGG + Chr3:70220493-70220512 None:intergenic 30.0%
GCTGAGATCAATAACTTAAA+AGG - Chr3:70219635-70219654 MsG0380015438.01.T01:intron 30.0%
TACACAAAAGAAACTCTGTT+AGG + Chr3:70220252-70220271 None:intergenic 30.0%
TATTTGCTTGGACATTATCT+TGG + Chr3:70220505-70220524 None:intergenic 30.0%
TGCAGAAACAAGATGATTAA+TGG + Chr3:70220422-70220441 None:intergenic 30.0%
TGCTATGCTATAAGTTATAG+CGG + Chr3:70220039-70220058 None:intergenic 30.0%
TGTTGTCAAATAACAGCTAT+AGG - Chr3:70220012-70220031 MsG0380015438.01.T01:intron 30.0%
! AAGAAGTATGATACAGAAGA+AGG - Chr3:70220669-70220688 MsG0380015438.01.T01:intron 30.0%
! AGAAGTATGATACAGAAGAA+GGG - Chr3:70220670-70220689 MsG0380015438.01.T01:intron 30.0%
! AGTGTTATTAATTACTCTGC+TGG - Chr3:70219505-70219524 MsG0380015438.01.T01:intron 30.0%
! CGGTTATCATATCAAACTTT+TGG + Chr3:70220567-70220586 None:intergenic 30.0%
! GATGATTAATGGTGACATTT+TGG + Chr3:70220411-70220430 None:intergenic 30.0%
! TAACAGAGTTTCTTTTGTGT+AGG - Chr3:70220251-70220270 MsG0380015438.01.T01:CDS 30.0%
! TCATGTCAAAGTAAAAGTAC+TGG - Chr3:70219551-70219570 MsG0380015438.01.T01:intron 30.0%
!! ATTAATCATCTTGTTTCTGC+AGG - Chr3:70220421-70220440 MsG0380015438.01.T01:CDS 30.0%
!!! TTTTTTCAGAGCTGAAGAAT+CGG - Chr3:70220612-70220631 MsG0380015438.01.T01:intron 30.0%
ACACAGCTATATTCAAGTCT+TGG + Chr3:70219724-70219743 None:intergenic 35.0%
ACATGAACCTTCAAACTGAT+GGG - Chr3:70220347-70220366 MsG0380015438.01.T01:CDS 35.0%
ATCCTGATTCTATCCCATAA+TGG + Chr3:70219430-70219449 None:intergenic 35.0%
ATGCATCATCAAGCCATTAT+GGG - Chr3:70219414-70219433 MsG0380015438.01.T01:intron 35.0%
CAACTAATGCTCCTTGATAT+AGG - Chr3:70219873-70219892 MsG0380015438.01.T01:intron 35.0%
CACAGCTATATTCAAGTCTT+GGG + Chr3:70219723-70219742 None:intergenic 35.0%
CTGGCTATACATTATGTCAA+AGG - Chr3:70219686-70219705 MsG0380015438.01.T01:intron 35.0%
GCTATACATTATGTCAAAGG+AGG - Chr3:70219689-70219708 MsG0380015438.01.T01:intron 35.0%
GTTCAAACTTGTCACATACA+AGG + Chr3:70220780-70220799 None:intergenic 35.0%
TAATGCTCCTTGATATAGGA+TGG - Chr3:70219877-70219896 MsG0380015438.01.T01:intron 35.0%
TACATGAACCTTCAAACTGA+TGG - Chr3:70220346-70220365 MsG0380015438.01.T01:CDS 35.0%
TCCTAACATATGTAGAGATC+TGG - Chr3:70219667-70219686 MsG0380015438.01.T01:intron 35.0%
TCTATAACCAGAACAAACTG+CGG - Chr3:70219263-70219282 MsG0380015438.01.T01:intron 35.0%
TTTCTGCAGGATTTAGTAGT+TGG - Chr3:70220434-70220453 MsG0380015438.01.T01:CDS 35.0%
! ATGATTATCACAAGAGTGTG+AGG - Chr3:70219753-70219772 MsG0380015438.01.T01:intron 35.0%
AAATTCCGTGTTCGAGTATC+TGG + Chr3:70220745-70220764 None:intergenic 40.0%
AACTGAATTGTAGACCGTGT+TGG - Chr3:70219301-70219320 MsG0380015438.01.T01:intron 40.0%
AATGCACACTGCAATAACTG+TGG + Chr3:70219607-70219626 None:intergenic 40.0%
ACATCCAAACCATCATCTGA+AGG + Chr3:70219779-70219798 None:intergenic 40.0%
AGCCATTATGGGATAGAATC+AGG - Chr3:70219425-70219444 MsG0380015438.01.T01:intron 40.0%
GAGTGCTCAATTCATCCAAA+TGG + Chr3:70220723-70220742 None:intergenic 40.0%
GATGCATCATCAAGCCATTA+TGG - Chr3:70219413-70219432 MsG0380015438.01.T01:intron 40.0%
GCCAGATCTCTACATATGTT+AGG + Chr3:70219671-70219690 None:intergenic 40.0%
GTCATCATACCTCATCATCA+AGG + Chr3:70220464-70220483 None:intergenic 40.0%
TCAGATGATTCTGGTATGTC+AGG - Chr3:70219109-70219128 MsG0380015438.01.T01:CDS 40.0%
TCGGTAGTATAAGGATTTGG+AGG + Chr3:70219830-70219849 None:intergenic 40.0%
TGACAGCATTAGCAACTGTA+CGG - Chr3:70220282-70220301 MsG0380015438.01.T01:CDS 40.0%
TGACGCAATTCGGTAGTATA+AGG + Chr3:70219839-70219858 None:intergenic 40.0%
TGATTGCAGCATAATCGTCA+AGG + Chr3:70219534-70219553 None:intergenic 40.0%
TTTGCTTCACTTGTCACTCT+TGG - Chr3:70219482-70219501 MsG0380015438.01.T01:intron 40.0%
! AAGGGGATGAGTACTTTTCT+AGG - Chr3:70220644-70220663 MsG0380015438.01.T01:intron 40.0%
! GCATAGTTGAGGTATTTGCT+TGG + Chr3:70220517-70220536 None:intergenic 40.0%
! TGGTTTGGATGTAGTGTTGA+TGG - Chr3:70219787-70219806 MsG0380015438.01.T01:intron 40.0%
!! AGAAAAGTACTCATCCCCTT+TGG + Chr3:70220644-70220663 None:intergenic 40.0%
!! ATCAAGGAGCATTAGTTGCA+AGG + Chr3:70219871-70219890 None:intergenic 40.0%
!! CGTTGGTTCAATGTCTAGTT+CGG + Chr3:70219209-70219228 None:intergenic 40.0%
!! GCTAGTCTTTCAGATGATTC+TGG - Chr3:70219100-70219119 MsG0380015438.01.T01:CDS 40.0%
!! TCAAGGAGCATTAGTTGCAA+GGG + Chr3:70219870-70219889 None:intergenic 40.0%
AACTTGTCACATACAAGGCC+TGG + Chr3:70220775-70220794 None:intergenic 45.0%
AAGAATCGGACTCTGCCAAA+GGG - Chr3:70220626-70220645 MsG0380015438.01.T01:intron 45.0%
AGCAAACCGGACAGTTCAAT+CGG + Chr3:70219339-70219358 None:intergenic 45.0%
ATACTACCGAATTGCGTCAC+AGG - Chr3:70219840-70219859 MsG0380015438.01.T01:intron 45.0%
CATTAGCAACTGTACGGAAG+AGG - Chr3:70220288-70220307 MsG0380015438.01.T01:CDS 45.0%
CCAGTTGAAGCATAATCCAG+AGG + Chr3:70219235-70219254 None:intergenic 45.0%
CCTCTGGATTATGCTTCAAC+TGG - Chr3:70219232-70219251 MsG0380015438.01.T01:CDS 45.0%
GGAATACCTGTGACGCAATT+CGG + Chr3:70219849-70219868 None:intergenic 45.0%
GGATTGACGATTGACAACAC+TGG - Chr3:70220085-70220104 MsG0380015438.01.T01:CDS 45.0%
GTCTGCTTATGCGCATCAAA+TGG - Chr3:70219060-70219079 MsG0380015438.01.T01:CDS 45.0%
GTTCAACCGATTGAACTGTC+CGG - Chr3:70219330-70219349 MsG0380015438.01.T01:intron 45.0%
TAGACCACCCATCAGTTTGA+AGG + Chr3:70220357-70220376 None:intergenic 45.0%
TGAACCTTCAAACTGATGGG+TGG - Chr3:70220350-70220369 MsG0380015438.01.T01:CDS 45.0%
TTGACGATTGACAACACTGG+TGG - Chr3:70220088-70220107 MsG0380015438.01.T01:CDS 45.0%
! ACACGGAATTTTCTGCTTCC+AGG - Chr3:70220754-70220773 MsG0380015438.01.T01:intron 45.0%
!! GTTGGTCTTCCTTGATGATG+AGG - Chr3:70220452-70220471 MsG0380015438.01.T01:CDS 45.0%
!! TTGTAGACCGTGTTGGTTCA+CGG - Chr3:70219308-70219327 MsG0380015438.01.T01:intron 45.0%
AGAATCGGACTCTGCCAAAG+GGG - Chr3:70220627-70220646 MsG0380015438.01.T01:intron 50.0%
AGTGTGAGGCCTTCAGATGA+TGG - Chr3:70219767-70219786 MsG0380015438.01.T01:intron 50.0%
CATTGAACCAACGAGACCTC+TGG - Chr3:70219216-70219235 MsG0380015438.01.T01:CDS 50.0%
GAAGAATCGGACTCTGCCAA+AGG - Chr3:70220625-70220644 MsG0380015438.01.T01:intron 50.0%
GCACTCCAGATACTCGAACA+CGG - Chr3:70220737-70220756 MsG0380015438.01.T01:intron 50.0%
GCATAATCCAGAGGTCTCGT+TGG + Chr3:70219226-70219245 None:intergenic 50.0%
GGTTGAACCGTGAACCAACA+CGG + Chr3:70219318-70219337 None:intergenic 50.0%
! AGTTCGACCGCAGTTTGTTC+TGG + Chr3:70219273-70219292 None:intergenic 50.0%
! GAGGCCTTCAGATGATGGTT+TGG - Chr3:70219772-70219791 MsG0380015438.01.T01:intron 50.0%
Chromosome Type Strat End Strand Name
Chr3 gene 70219058 70220831 70219058 ID=MsG0380015438.01;Name=MsG0380015438.01
Chr3 mRNA 70219058 70220831 70219058 ID=MsG0380015438.01.T01;Parent=MsG0380015438.01;Name=MsG0380015438.01.T01;_AED=0.49;_eAED=0.50;_QI=0|0|0|1|1|1|3|0|240
Chr3 exon 70220768 70220831 70220768 ID=MsG0380015438.01.T01:exon:375;Parent=MsG0380015438.01.T01
Chr3 exon 70220028 70220475 70220028 ID=MsG0380015438.01.T01:exon:374;Parent=MsG0380015438.01.T01
Chr3 exon 70219058 70219268 70219058 ID=MsG0380015438.01.T01:exon:373;Parent=MsG0380015438.01.T01
Chr3 CDS 70220768 70220831 70220768 ID=MsG0380015438.01.T01:cds;Parent=MsG0380015438.01.T01
Chr3 CDS 70220028 70220475 70220028 ID=MsG0380015438.01.T01:cds;Parent=MsG0380015438.01.T01
Chr3 CDS 70219058 70219268 70219058 ID=MsG0380015438.01.T01:cds;Parent=MsG0380015438.01.T01
Gene Sequence

>MsG0380015438.01.T01

ATGTCTGCTTATGCGCATCAAATGGAGCAGCAGTATGCTGCAGCTAGTCTTTCAGATGATTCTGATGCATCATCAAGCCATTATGGGATAGAATCAGGATTCTACATGACATCTCTTACAGCAACGATCTTTTTTGCTTCACTTGTCACTCTTGGAGTGTTATTAATTACTCTGCTGGTTTCCTTGACGATTATGCTGCAATCATGTCAAAGTAAAAGTACTGGAGTTATTGAACTTGTGAATATGAATGATTACCACAGTTATTGCAGTGTGCATTCTCTGCATGCTGAGATCAATAACTTAAAAGGATATGATCTTCCTAACATATGTAGAGATCTGGCTATACATTATGTCAAAGGAGGTCATTATGCCCAAGACTTGAATATAGCTGTGTCTATGATTGATGATTATCACAAGAGTGTGAGGCCTTCAGATGATGGTTTGGATGTAGTGTTGATGGACATAGATGACATTGTTCCTCCAAATCCTTATACTACCGAATTGCGTCACAGAGCTGAAGAATCGGACTCTGCCAAAGGGGATGAGTACTTTTCTAGGCAAAGAAGTATGATACAGAAGAAGGGTTTCCATATAAAAAGTATTATAGGTAGCCATTTGGATGAATTGAGCACTCCAGATACTCGAACACGGAATTTTCTGCTTCCAGGCCTTGTATGTGACAAGTTTGAACATCAGATAGAGAGTAAAGATCCTGAACATTAG

Protein sequence

>MsG0380015438.01.T01

MSAYAHQMEQQYAAASLSDDSDASSSHYGIESGFYMTSLTATIFFASLVTLGVLLITLLVSLTIMLQSCQSKSTGVIELVNMNDYHSYCSVHSLHAEINNLKGYDLPNICRDLAIHYVKGGHYAQDLNIAVSMIDDYHKSVRPSDDGLDVVLMDIDDIVPPNPYTTELRHRAEESDSAKGDEYFSRQRSMIQKKGFHIKSIIGSHLDELSTPDTRTRNFLLPGLVCDKFEHQIESKDPEH*