AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680033115.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680033115.01.T01 MTR_1g047060 55.696 79 30 1 56 134 3 76 4.90e-22 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACTTATGCTTGCAATTA+TGG 0.158474 6:+57297746 MsG0680033115.01.T01:CDS
ATGGATCTAGACTCTGAATT+TGG 0.204240 6:+57296551 MsG0680033115.01.T01:CDS
GGCATTGTAAGACTGGATTT+TGG 0.240614 6:+57296221 MsG0680033115.01.T01:CDS
CCTCCTCGGCTCCTCAGTTT+TGG 0.293397 6:-57296200 None:intergenic
TGGATCTAGACTCTGAATTT+GGG 0.333596 6:+57296552 MsG0680033115.01.T01:CDS
TGTTGGAGCTGATGACGTTT+TGG 0.393392 6:+57296273 MsG0680033115.01.T01:CDS
AAAACACAGCAAACAACAAA+AGG 0.433446 6:-57296512 None:intergenic
GACTAGTTCTAGTGCAGTGC+TGG 0.438305 6:+57296664 MsG0680033115.01.T01:CDS
TGAAGGAACTCAGCAACTTA+AGG 0.444240 6:+57296634 MsG0680033115.01.T01:CDS
TTCTAGTGCAGTGCTGGTGT+TGG 0.478756 6:+57296670 MsG0680033115.01.T01:CDS
CTTGTGTGAGGGGAAGAAAA+AGG 0.480028 6:-57296157 None:intergenic
CCGAGGAGGCATTGTAAGAC+TGG 0.484776 6:+57296214 MsG0680033115.01.T01:CDS
ACTCAGCAACTTAAGGAGGC+TGG 0.487489 6:+57296641 MsG0680033115.01.T01:CDS
CTCAGCAACTTAAGGAGGCT+GGG 0.496847 6:+57296642 MsG0680033115.01.T01:CDS
GAGTCTAGATCCATCCCTCT+AGG 0.505901 6:-57296542 None:intergenic
AGAACGCGATCAAAACTAGT+TGG 0.526855 6:+57296341 MsG0680033115.01.T01:CDS
GCTGTTAGAGACATTACTGT+TGG 0.528259 6:+57296256 MsG0680033115.01.T01:CDS
CACTCTTGTTAACAATCCTC+AGG 0.528444 6:+57296378 MsG0680033115.01.T01:CDS
TCTGATGACAAGGCGAATGA+AGG 0.528665 6:+57296617 MsG0680033115.01.T01:CDS
ACCTTCATCGACATCAGATA+AGG 0.533255 6:-57296576 None:intergenic
CCAGTCTTACAATGCCTCCT+CGG 0.543084 6:-57296214 None:intergenic
CCACATGGAAGCTATGACGC+CGG 0.546830 6:+57297722 MsG0680033115.01.T01:CDS
ATTGCAAGCATAAGTTGCTC+CGG 0.553025 6:-57297741 None:intergenic
AGTAAAACTCCCTTGTGTGA+GGG 0.566795 6:-57296168 None:intergenic
AGTCTAGATCCATCCCTCTA+GGG 0.570873 6:-57296541 None:intergenic
CAGTAAAACTCCCTTGTGTG+AGG 0.584040 6:-57296169 None:intergenic
GCCTTATCTGATGTCGATGA+AGG 0.589295 6:+57296575 MsG0680033115.01.T01:CDS
GTAAAACTCCCTTGTGTGAG+GGG 0.589713 6:-57296167 None:intergenic
GCTGGTGTTGGTGTTGAGCA+AGG 0.596291 6:+57296682 MsG0680033115.01.T01:CDS
CTGCCAAAACTGAGGAGCCG+AGG 0.619650 6:+57296197 MsG0680033115.01.T01:CDS
CCGGCGTCATAGCTTCCATG+TGG 0.629672 6:-57297722 None:intergenic
TGACTATGTTGTGTCCCACA+TGG 0.631632 6:+57297707 MsG0680033115.01.T01:CDS
GGATCTAGACTCTGAATTTG+GGG 0.633562 6:+57296553 MsG0680033115.01.T01:CDS
CCAAAACTGAGGAGCCGAGG+AGG 0.634705 6:+57296200 MsG0680033115.01.T01:CDS
CGGCGTCATAGCTTCCATGT+GGG 0.637767 6:-57297721 None:intergenic
CTGCTTCACTGCCAAAACTG+AGG 0.647730 6:+57296189 MsG0680033115.01.T01:CDS
AGGAACTCAGCAACTTAAGG+AGG 0.651240 6:+57296637 MsG0680033115.01.T01:CDS
TGATGACGACTCTGATGACA+AGG 0.678157 6:+57296607 MsG0680033115.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAATATAAATAATT+GGG + Chr6:57296483-57296502 MsG0680033115.01.T01:intron 0.0%
!!! TTTTTTTTAATATAAATAAT+TGG + Chr6:57296482-57296501 MsG0680033115.01.T01:intron 0.0%
!! AAACTTAAAGAAAAATAAAA+AGG - Chr6:57297445-57297464 None:intergenic 10.0%
!!! TTATTTTTCTTTAAGTTTTT+TGG + Chr6:57297447-57297466 MsG0680033115.01.T01:intron 10.0%
!! GTTTGATATTAATGTTTATT+AGG + Chr6:57297665-57297684 MsG0680033115.01.T01:intron 15.0%
!!! TGTTTTTTTTTTTTCCTTTT+TGG + Chr6:57297333-57297352 MsG0680033115.01.T01:intron 15.0%
!! TACATATGATAAACAAAAAC+AGG - Chr6:57296849-57296868 None:intergenic 20.0%
!! TATTCAAAACCTTTATGTAT+TGG + Chr6:57297052-57297071 MsG0680033115.01.T01:intron 20.0%
!! TCGATGATTAATTTATGTAT+TGG + Chr6:57296445-57296464 MsG0680033115.01.T01:intron 20.0%
!! TTTAATATAAATAATTGGGC+AGG + Chr6:57296487-57296506 MsG0680033115.01.T01:intron 20.0%
!!! ATTGAAAATATTTTTACCTG+AGG - Chr6:57296742-57296761 None:intergenic 20.0%
!!! CATCTTTTCATGTAATTTTA+TGG + Chr6:57297605-57297624 MsG0680033115.01.T01:intron 20.0%
!!! GATTAATTTATGTATTGGTA+AGG + Chr6:57296450-57296469 MsG0680033115.01.T01:intron 20.0%
!!! GTTTTGAATAACAACAAATA+TGG - Chr6:57297042-57297061 None:intergenic 20.0%
!!! TTAATTTGTTACATGTTTTG+AGG - Chr6:57297381-57297400 None:intergenic 20.0%
!!! TTTTCATGTAATTTTATGGT+GGG + Chr6:57297609-57297628 MsG0680033115.01.T01:intron 20.0%
!!! TTTTTCTTTAAGTTTTTTGG+TGG + Chr6:57297450-57297469 MsG0680033115.01.T01:intron 20.0%
! ATATGTATTTCACTTTCTGT+TGG + Chr6:57296862-57296881 MsG0680033115.01.T01:intron 25.0%
! CATAAATAATCCAAACACAA+TGG - Chr6:57297113-57297132 None:intergenic 25.0%
! CATGAAAATCATTGATATTG+TGG - Chr6:57297011-57296992 None:intergenic 25.0%
! GAAAAACTACCAATACATAA+AGG - Chr6:57297064-57297083 None:intergenic 25.0%
! TCGATGAAATAAAGAACATA+CGG - Chr6:57296429-57296448 None:intergenic 25.0%
! TTAATTTCTACACACCAAAA+AGG - Chr6:57297350-57297369 None:intergenic 25.0%
!! AATAAAAAGGACATGTTTTG+AGG - Chr6:57297432-57297451 None:intergenic 25.0%
!! CATGATTTTTGATACAATTG+TGG - Chr6:57297167-57297186 None:intergenic 25.0%
!! CTTTTCATGTAATTTTATGG+TGG + Chr6:57297608-57297627 MsG0680033115.01.T01:intron 25.0%
!! TCTCTCTTCATTTTCTATAT+AGG + Chr6:57296307-57296326 MsG0680033115.01.T01:CDS 25.0%
!!! TTATGTATTGGTAGTTTTTC+TGG + Chr6:57297064-57297083 MsG0680033115.01.T01:intron 25.0%
AAAACACAGCAAACAACAAA+AGG - Chr6:57296515-57296534 None:intergenic 30.0%
AACTCAATTCATTCATGTGA+TGG + Chr6:57297257-57297276 MsG0680033115.01.T01:intron 30.0%
AAGAGGATCAAAACATTAAC+AGG - Chr6:57297221-57297240 None:intergenic 30.0%
ACAATTGTGGATGTAGAATT+CGG - Chr6:57297154-57297173 None:intergenic 30.0%
TGTAAAATTCAGTTGCAAAG+AGG - Chr6:57297238-57297257 None:intergenic 30.0%
! AAGCATTGTAAAATTGTTGC+CGG - Chr6:57296791-57296810 None:intergenic 30.0%
!! AAATATTTTTACCTGAGGAG+TGG - Chr6:57296737-57296756 None:intergenic 30.0%
!!! CTCGATATTTATTTTGTCAC+CGG + Chr6:57296769-57296788 MsG0680033115.01.T01:intron 30.0%
AATCATGGTCACACTAATTG+TGG + Chr6:57296963-57296982 MsG0680033115.01.T01:intron 35.0%
ATATTGTGGCTGACATATGA+TGG - Chr6:57296911-57296930 None:intergenic 35.0%
ATGGATCTAGACTCTGAATT+TGG + Chr6:57296551-57296570 MsG0680033115.01.T01:CDS 35.0%
GCAACTTATGCTTGCAATTA+TGG + Chr6:57297746-57297765 MsG0680033115.01.T01:CDS 35.0%
GTGTGACCATGATTAAAAGT+TGG - Chr6:57296957-57296976 None:intergenic 35.0%
TGGATCTAGACTCTGAATTT+GGG + Chr6:57296552-57296571 MsG0680033115.01.T01:CDS 35.0%
TGGATGTAGAATTCGGTAAT+TGG - Chr6:57297147-57297166 None:intergenic 35.0%
! AATCCTCAGGTATGTCATTT+GGG + Chr6:57296391-57296410 MsG0680033115.01.T01:intron 35.0%
! GCATGACCAACTTTTAATCA+TGG + Chr6:57296948-57296967 MsG0680033115.01.T01:intron 35.0%
ACCTTCATCGACATCAGATA+AGG - Chr6:57296579-57296598 None:intergenic 40.0%
AGAACGCGATCAAAACTAGT+TGG + Chr6:57296341-57296360 MsG0680033115.01.T01:CDS 40.0%
AGTAAAACTCCCTTGTGTGA+GGG - Chr6:57296171-57296190 None:intergenic 40.0%
ATTGCAAGCATAAGTTGCTC+CGG - Chr6:57297744-57297763 None:intergenic 40.0%
CAATCCTCAGGTATGTCATT+TGG + Chr6:57296390-57296409 MsG0680033115.01.T01:intron 40.0%
CACTCTTGTTAACAATCCTC+AGG + Chr6:57296378-57296397 MsG0680033115.01.T01:CDS 40.0%
CCAAACACAATGGAGCTATT+TGG - Chr6:57297103-57297122 None:intergenic 40.0%
CCAAATAGCTCCATTGTGTT+TGG + Chr6:57297100-57297119 MsG0680033115.01.T01:intron 40.0%
GCTGTTAGAGACATTACTGT+TGG + Chr6:57296256-57296275 MsG0680033115.01.T01:CDS 40.0%
GGATCTAGACTCTGAATTTG+GGG + Chr6:57296553-57296572 MsG0680033115.01.T01:CDS 40.0%
TGAAGGAACTCAGCAACTTA+AGG + Chr6:57296634-57296653 MsG0680033115.01.T01:CDS 40.0%
TTTCCCAAATGACATACCTG+AGG - Chr6:57296397-57296416 None:intergenic 40.0%
! ACTGGATTTTGGATGCAGAA+GGG + Chr6:57296232-57296251 MsG0680033115.01.T01:CDS 40.0%
! GGCATTGTAAGACTGGATTT+TGG + Chr6:57296221-57296240 MsG0680033115.01.T01:CDS 40.0%
! TTTTTCTTCCCCTCACACAA+GGG + Chr6:57296159-57296178 MsG0680033115.01.T01:CDS 40.0%
!!! AGGACATGTTTTGAGGAATC+TGG - Chr6:57297425-57297444 None:intergenic 40.0%
!!! TAGTTTTGATCGCGTTCTGA+GGG - Chr6:57296339-57296358 None:intergenic 40.0%
AGGAACTCAGCAACTTAAGG+AGG + Chr6:57296637-57296656 MsG0680033115.01.T01:CDS 45.0%
AGTCTAGATCCATCCCTCTA+GGG - Chr6:57296544-57296563 None:intergenic 45.0%
CAGTAAAACTCCCTTGTGTG+AGG - Chr6:57296172-57296191 None:intergenic 45.0%
CTTGTGTGAGGGGAAGAAAA+AGG - Chr6:57296160-57296179 None:intergenic 45.0%
GCCTTATCTGATGTCGATGA+AGG + Chr6:57296575-57296594 MsG0680033115.01.T01:CDS 45.0%
GTAAAACTCCCTTGTGTGAG+GGG - Chr6:57296170-57296189 None:intergenic 45.0%
TCTGATGACAAGGCGAATGA+AGG + Chr6:57296617-57296636 MsG0680033115.01.T01:CDS 45.0%
TGACTATGTTGTGTCCCACA+TGG + Chr6:57297707-57297726 MsG0680033115.01.T01:CDS 45.0%
TTGTGGCTGACATATGATGG+AGG - Chr6:57296908-57296927 None:intergenic 45.0%
! CTTTTTCTTCCCCTCACACA+AGG + Chr6:57296158-57296177 MsG0680033115.01.T01:CDS 45.0%
! GACTGGATTTTGGATGCAGA+AGG + Chr6:57296231-57296250 MsG0680033115.01.T01:CDS 45.0%
! TGATGACGACTCTGATGACA+AGG + Chr6:57296607-57296626 MsG0680033115.01.T01:CDS 45.0%
!! AGTTTTGATCGCGTTCTGAG+GGG - Chr6:57296338-57296357 None:intergenic 45.0%
!! GTGTTTTTGACTGCCCTAGA+GGG + Chr6:57296528-57296547 MsG0680033115.01.T01:CDS 45.0%
!! TGTGTTTTTGACTGCCCTAG+AGG + Chr6:57296527-57296546 MsG0680033115.01.T01:CDS 45.0%
!! TGTTGGAGCTGATGACGTTT+TGG + Chr6:57296273-57296292 MsG0680033115.01.T01:CDS 45.0%
!!! CTAGTTTTGATCGCGTTCTG+AGG - Chr6:57296340-57296359 None:intergenic 45.0%
ACTCAGCAACTTAAGGAGGC+TGG + Chr6:57296641-57296660 MsG0680033115.01.T01:CDS 50.0%
AGGTGATGCATCGCATTCCA+TGG + Chr6:57296702-57296721 MsG0680033115.01.T01:intron 50.0%
CCAGTCTTACAATGCCTCCT+CGG - Chr6:57296217-57296236 None:intergenic 50.0%
CTCAGCAACTTAAGGAGGCT+GGG + Chr6:57296642-57296661 MsG0680033115.01.T01:CDS 50.0%
CTGCTTCACTGCCAAAACTG+AGG + Chr6:57296189-57296208 MsG0680033115.01.T01:CDS 50.0%
GAGTCTAGATCCATCCCTCT+AGG - Chr6:57296545-57296564 None:intergenic 50.0%
!! GACTAGTTCTAGTGCAGTGC+TGG + Chr6:57296664-57296683 MsG0680033115.01.T01:CDS 50.0%
!! GGAGCTGATGACGTTTTGGT+GGG + Chr6:57296277-57296296 MsG0680033115.01.T01:CDS 50.0%
!! TGGAGCTGATGACGTTTTGG+TGG + Chr6:57296276-57296295 MsG0680033115.01.T01:CDS 50.0%
!! TTCTAGTGCAGTGCTGGTGT+TGG + Chr6:57296670-57296689 MsG0680033115.01.T01:CDS 50.0%
!! TTTTGACTGCCCTAGAGGGA+TGG + Chr6:57296532-57296551 MsG0680033115.01.T01:CDS 50.0%
AGGAGTGGCTTGAGTAGCCA+TGG - Chr6:57296722-57296741 None:intergenic 55.0%
CCACATGGAAGCTATGACGC+CGG + Chr6:57297722-57297741 MsG0680033115.01.T01:CDS 55.0%
CGGCGTCATAGCTTCCATGT+GGG - Chr6:57297724-57297743 None:intergenic 55.0%
!! CCGAGGAGGCATTGTAAGAC+TGG + Chr6:57296214-57296233 MsG0680033115.01.T01:CDS 55.0%
!! GCTGGTGTTGGTGTTGAGCA+AGG + Chr6:57296682-57296701 MsG0680033115.01.T01:CDS 55.0%
CCAAAACTGAGGAGCCGAGG+AGG + Chr6:57296200-57296219 MsG0680033115.01.T01:CDS 60.0%
CCGGCGTCATAGCTTCCATG+TGG - Chr6:57297725-57297744 None:intergenic 60.0%
CTGCCAAAACTGAGGAGCCG+AGG + Chr6:57296197-57296216 MsG0680033115.01.T01:CDS 60.0%
GGCTACTCAAGCCACTCCTC+AGG + Chr6:57296723-57296742 MsG0680033115.01.T01:intron 60.0%
! CCTCCTCGGCTCCTCAGTTT+TGG - Chr6:57296203-57296222 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr6 gene 57296157 57297788 57296157 ID=MsG0680033115.01;Name=MsG0680033115.01
Chr6 mRNA 57296157 57297788 57296157 ID=MsG0680033115.01.T01;Parent=MsG0680033115.01;Name=MsG0680033115.01.T01;_AED=0.52;_eAED=0.53;_QI=0|0|0|0.33|1|0.66|3|0|179
Chr6 exon 57296157 57296399 57296157 ID=MsG0680033115.01.T01:exon:4439;Parent=MsG0680033115.01.T01
Chr6 exon 57296509 57296703 57296509 ID=MsG0680033115.01.T01:exon:4440;Parent=MsG0680033115.01.T01
Chr6 exon 57297687 57297788 57297687 ID=MsG0680033115.01.T01:exon:4441;Parent=MsG0680033115.01.T01
Chr6 CDS 57296157 57296399 57296157 ID=MsG0680033115.01.T01:cds;Parent=MsG0680033115.01.T01
Chr6 CDS 57296509 57296703 57296509 ID=MsG0680033115.01.T01:cds;Parent=MsG0680033115.01.T01
Chr6 CDS 57297687 57297788 57297687 ID=MsG0680033115.01.T01:cds;Parent=MsG0680033115.01.T01
Gene Sequence

>MsG0680033115.01.T01

CCTTTTTCTTCCCCTCACACAAGGGAGTTTTACTGCTTCACTGCCAAAACTGAGGAGCCGAGGAGGCATTGTAAGACTGGATTTTGGATGCAGAAGGGAGCTGTTAGAGACATTACTGTTGGAGCTGATGACGTTTTGGTGGGAAAGAAGTCTCTCTTCATTTTCTATATAGGAAATTCCCCTCAGAACGCGATCAAAACTAGTTGGACTATGTACGAGTACACTCTTGTTAACAATCCTCAGGCTCCTTTTGTTGTTTGCTGTGTTTTTGACTGCCCTAGAGGGATGGATCTAGACTCTGAATTTGGGGCCTTATCTGATGTCGATGAAGGTGATGTTGCTGATGACGACTCTGATGACAAGGCGAATGAAGGAACTCAGCAACTTAAGGAGGCTGGGACTAGTTCTAGTGCAGTGCTGGTGTTGGTGTTGAGCAAGGAGAGTTATACTGCATTTCTTGACTATGTTGTGTCCCACATGGAAGCTATGACGCCGGAGCAACTTATGCTTGCAATTATGGATGAGAAAGATTTTATTTAA
Protein sequence

>MsG0680033115.01.T01

PFSSPHTREFYCFTAKTEEPRRHCKTGFWMQKGAVRDITVGADDVLVGKKSLFIFYIGNSPQNAIKTSWTMYEYTLVNNPQAPFVVCCVFDCPRGMDLDSEFGALSDVDEGDVADDDSDDKANEGTQQLKEAGTSSSAVLVLVLSKESYTAFLDYVVSHMEAMTPEQLMLAIMDEKDFI*