AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCACGCCTCCGTTACCTTT+TGG 0.196515 6_2:+9518017 Msa0908280:CDS
TCTCAGGTAGACAGTTTCTA+TGG 0.287253 6_2:-9518052 None:intergenic
CTTCCCGGTCCTCTCGTACT+AGG 0.332779 6_2:+9517634 Msa0908280:CDS
TTTACCGTTGGCACGATAAC+TGG 0.336021 6_2:+9517594 Msa0908280:CDS
CACCAGAGGTGCGTCCTTCC+CGG 0.345036 6_2:+9517619 Msa0908280:CDS
TCCTCGGGCCAGACGGAGAT+TGG 0.349112 6_2:-9517988 None:intergenic
AAAGTTACTCTAGGGATAAC+AGG 0.383241 6_2:-9517851 None:intergenic
CCCTTCTGCCTTTGCACTCG+AGG 0.411231 6_2:+9517964 Msa0908280:CDS
TTCCCGTCGATGTGAGCTCT+TGG 0.415639 6_2:+9517819 Msa0908280:CDS
CTCACATCGACGGGAAGGTT+TGG 0.420533 6_2:-9517812 None:intergenic
TTCCCGGTCCTCTCGTACTA+GGG 0.424464 6_2:+9517635 Msa0908280:CDS
TGTAGTATGTTCCAAGGGTT+GGG 0.424624 6_2:-9517757 None:intergenic
GACCGGGAAGGACGCACCTC+TGG 0.443036 6_2:-9517621 None:intergenic
CTGTAGTATGTTCCAAGGGT+TGG 0.452990 6_2:-9517758 None:intergenic
ACAGACCAAGGGACAGTCTC+AGG 0.456050 6_2:-9518068 None:intergenic
CCTTCTGCCTTTGCACTCGA+GGG 0.461384 6_2:+9517965 Msa0908280:CDS
GCAGTTATCCGCTCCGCACT+TGG 0.463896 6_2:+9517561 Msa0908280:CDS
GACTGTCCCTTGGTCTGTAC+TGG 0.464231 6_2:+9518073 Msa0908280:CDS
TCCCGTCGATGTGAGCTCTT+GGG 0.466297 6_2:+9517820 Msa0908280:CDS
TCCCAAGAGCTCACATCGAC+GGG 0.478923 6_2:-9517821 None:intergenic
CTCGAGGGCCAATCTCCGTC+TGG 0.480699 6_2:+9517980 Msa0908280:CDS
GATGTCGGCTCTTCGCCACC+TGG 0.508239 6_2:-9517783 None:intergenic
CTCAGGTAGACAGTTTCTAT+GGG 0.510655 6_2:-9518051 None:intergenic
CCCTCGAGTGCAAAGGCAGA+AGG 0.511073 6_2:-9517965 None:intergenic
GAGGCGTGCAAAGGTTTCCT+CGG 0.526013 6_2:-9518004 None:intergenic
TTTCCCTAGTACGAGAGGAC+CGG 0.526023 6_2:-9517638 None:intergenic
GGCTACCCAGCGTTTACCGT+TGG 0.526912 6_2:+9517582 Msa0908280:CDS
AGGCGTGCAAAGGTTTCCTC+GGG 0.527025 6_2:-9518003 None:intergenic
CCTTGGTCTGTACTGGCACA+AGG 0.538614 6_2:+9518080 Msa0908280:CDS
AAGGTTTGGCACCTCGATGT+CGG 0.545826 6_2:-9517798 None:intergenic
TGGGCGAACAGCCCAACCCT+TGG 0.548090 6_2:+9517746 Msa0908280:intron
TTCCCTAGTACGAGAGGACC+GGG 0.554934 6_2:-9517637 None:intergenic
TTCCCAAGAGCTCACATCGA+CGG 0.555494 6_2:-9517822 None:intergenic
GCCAATCTCCGTCTGGCCCG+AGG 0.562208 6_2:+9517987 Msa0908280:CDS
TGGAGCTGTAGTATGTTCCA+AGG 0.564153 6_2:-9517763 None:intergenic
TTGGAACATACTACAGCTCC+AGG 0.579135 6_2:+9517765 Msa0908280:CDS
GTCTACCTGAGACTGTCCCT+TGG 0.586612 6_2:+9518063 Msa0908280:CDS
GGTCCTCTCGTACTAGGGAA+AGG 0.589950 6_2:+9517640 Msa0908280:CDS
AAGGTAACGGAGGCGTGCAA+AGG 0.595805 6_2:-9518013 None:intergenic
CCTCGAGTGCAAAGGCAGAA+GGG 0.595841 6_2:-9517964 None:intergenic
AAAGGTTTCCTCGGGCCAGA+CGG 0.597813 6_2:-9517995 None:intergenic
TGGGGCGTAGGCCTCCCAAA+AGG 0.606913 6_2:-9518032 None:intergenic
ATCGTGCCAACGGTAAACGC+TGG 0.607055 6_2:-9517588 None:intergenic
TCGTGCCAACGGTAAACGCT+GGG 0.607071 6_2:-9517587 None:intergenic
AAGAGCTCACATCGACGGGA+AGG 0.613365 6_2:-9517817 None:intergenic
CACGATAACTGGCACACCAG+AGG 0.619554 6_2:+9517605 Msa0908280:CDS
AGACAGTTTCTATGGGGCGT+AGG 0.622986 6_2:-9518044 None:intergenic
GTAGGCCTCCCAAAAGGTAA+CGG 0.632223 6_2:-9518026 None:intergenic
GGAGCTGTAGTATGTTCCAA+GGG 0.640199 6_2:-9517762 None:intergenic
AAACGCTGGGTAGCCAAGTG+CGG 0.642570 6_2:-9517574 None:intergenic
CCTTGTGCCAGTACAGACCA+AGG 0.645647 6_2:-9518080 None:intergenic
TGTGCCAGTTATCGTGCCAA+CGG 0.646438 6_2:-9517598 None:intergenic
GGACCTTTCCCTAGTACGAG+AGG 0.658731 6_2:-9517643 None:intergenic
AGATTGGCCCTCGAGTGCAA+AGG 0.670375 6_2:-9517972 None:intergenic
CTGGGTAGCCAAGTGCGGAG+CGG 0.679241 6_2:-9517569 None:intergenic
GGCCTCCCAAAAGGTAACGG+AGG 0.683463 6_2:-9518023 None:intergenic
CTAGTACGAGAGGACCGGGA+AGG 0.687441 6_2:-9517633 None:intergenic
CTTGTGCCAGTACAGACCAA+GGG 0.693537 6_2:-9518079 None:intergenic
GTGGCGAAGAGCCGACATCG+AGG 0.704477 6_2:+9517787 Msa0908280:CDS
TCAGGTAGACAGTTTCTATG+GGG 0.720720 6_2:-9518050 None:intergenic
GAACATACTACAGCTCCAGG+TGG 0.771466 6_2:+9517768 Msa0908280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGGATAAAAGTTACTCTA+GGG - chr6_2:9517862-9517881 None:intergenic 30.0%
! AAAGTTACTCTAGGGATAAC+AGG - chr6_2:9517854-9517873 None:intergenic 35.0%
CAACGGATAAAAGTTACTCT+AGG - chr6_2:9517863-9517882 None:intergenic 35.0%
TGTAGTATGTTCCAAGGGTT+GGG - chr6_2:9517760-9517779 None:intergenic 40.0%
TCAGGTAGACAGTTTCTATG+GGG - chr6_2:9518053-9518072 None:intergenic 40.0%
CTCAGGTAGACAGTTTCTAT+GGG - chr6_2:9518054-9518073 None:intergenic 40.0%
TCTCAGGTAGACAGTTTCTA+TGG - chr6_2:9518055-9518074 None:intergenic 40.0%
TTTACCGTTGGCACGATAAC+TGG + chr6_2:9517594-9517613 Msa0908280:CDS 45.0%
ATTAAAGCGGTACGTGAGCT+GGG - chr6_2:9517727-9517746 None:intergenic 45.0%
AGCTCACGTACCGCTTTAAT+GGG + chr6_2:9517727-9517746 Msa0908280:intron 45.0%
CTGTAGTATGTTCCAAGGGT+TGG - chr6_2:9517761-9517780 None:intergenic 45.0%
GGAGCTGTAGTATGTTCCAA+GGG - chr6_2:9517765-9517784 None:intergenic 45.0%
TGGAGCTGTAGTATGTTCCA+AGG - chr6_2:9517766-9517785 None:intergenic 45.0%
TTGGAACATACTACAGCTCC+AGG + chr6_2:9517765-9517784 Msa0908280:CDS 45.0%
TGTGCCAGTTATCGTGCCAA+CGG - chr6_2:9517601-9517620 None:intergenic 50.0%
TTTCCCTAGTACGAGAGGAC+CGG - chr6_2:9517641-9517660 None:intergenic 50.0%
GAGACAGTTCGGTCCATATC+CGG - chr6_2:9517691-9517710 None:intergenic 50.0%
CAGAACGTCGTGAGACAGTT+CGG - chr6_2:9517702-9517721 None:intergenic 50.0%
CATTAAAGCGGTACGTGAGC+TGG - chr6_2:9517728-9517747 None:intergenic 50.0%
CAGCTCACGTACCGCTTTAA+TGG + chr6_2:9517726-9517745 Msa0908280:intron 50.0%
GAACATACTACAGCTCCAGG+TGG + chr6_2:9517768-9517787 Msa0908280:CDS 50.0%
AAGGTTTGGCACCTCGATGT+CGG - chr6_2:9517801-9517820 None:intergenic 50.0%
TTCCCAAGAGCTCACATCGA+CGG - chr6_2:9517825-9517844 None:intergenic 50.0%
GTAGGCCTCCCAAAAGGTAA+CGG - chr6_2:9518029-9518048 None:intergenic 50.0%
AGACAGTTTCTATGGGGCGT+AGG - chr6_2:9518047-9518066 None:intergenic 50.0%
CTTGTGCCAGTACAGACCAA+GGG - chr6_2:9518082-9518101 None:intergenic 50.0%
AAACGCTGGGTAGCCAAGTG+CGG - chr6_2:9517577-9517596 None:intergenic 55.0%
TCGTGCCAACGGTAAACGCT+GGG - chr6_2:9517590-9517609 None:intergenic 55.0%
ATCGTGCCAACGGTAAACGC+TGG - chr6_2:9517591-9517610 None:intergenic 55.0%
CACGATAACTGGCACACCAG+AGG + chr6_2:9517605-9517624 Msa0908280:CDS 55.0%
TTCCCGGTCCTCTCGTACTA+GGG + chr6_2:9517635-9517654 Msa0908280:CDS 55.0%
TTCCCTAGTACGAGAGGACC+GGG - chr6_2:9517640-9517659 None:intergenic 55.0%
GGTCCTCTCGTACTAGGGAA+AGG + chr6_2:9517640-9517659 Msa0908280:CDS 55.0%
GGACCTTTCCCTAGTACGAG+AGG - chr6_2:9517646-9517665 None:intergenic 55.0%
!! GTGGGCGTTAGAGCATTGAG+AGG - chr6_2:9517667-9517686 None:intergenic 55.0%
CAATGCTCTAACGCCCACAC+CGG + chr6_2:9517669-9517688 Msa0908280:intron 55.0%
TCTAACGCCCACACCGGATA+TGG + chr6_2:9517675-9517694 Msa0908280:intron 55.0%
GTTCGGTCCATATCCGGTGT+GGG - chr6_2:9517685-9517704 None:intergenic 55.0%
AGTTCGGTCCATATCCGGTG+TGG - chr6_2:9517686-9517705 None:intergenic 55.0%
GGGCTGTTCGCCCATTAAAG+CGG - chr6_2:9517740-9517759 None:intergenic 55.0%
CTCACATCGACGGGAAGGTT+TGG - chr6_2:9517815-9517834 None:intergenic 55.0%
AAGAGCTCACATCGACGGGA+AGG - chr6_2:9517820-9517839 None:intergenic 55.0%
TTCCCGTCGATGTGAGCTCT+TGG + chr6_2:9517819-9517838 Msa0908280:CDS 55.0%
TCCCGTCGATGTGAGCTCTT+GGG + chr6_2:9517820-9517839 Msa0908280:CDS 55.0%
TCCCAAGAGCTCACATCGAC+GGG - chr6_2:9517824-9517843 None:intergenic 55.0%
AGTCGGCCTTAGTGATCCGA+CGG - chr6_2:9517906-9517925 None:intergenic 55.0%
CCTCGAGTGCAAAGGCAGAA+GGG - chr6_2:9517967-9517986 None:intergenic 55.0%
CCTTCTGCCTTTGCACTCGA+GGG + chr6_2:9517965-9517984 Msa0908280:CDS 55.0%
! AGATTGGCCCTCGAGTGCAA+AGG - chr6_2:9517975-9517994 None:intergenic 55.0%
AAAGGTTTCCTCGGGCCAGA+CGG - chr6_2:9517998-9518017 None:intergenic 55.0%
AGGCGTGCAAAGGTTTCCTC+GGG - chr6_2:9518006-9518025 None:intergenic 55.0%
GAGGCGTGCAAAGGTTTCCT+CGG - chr6_2:9518007-9518026 None:intergenic 55.0%
!! AAGGTAACGGAGGCGTGCAA+AGG - chr6_2:9518016-9518035 None:intergenic 55.0%
! TGCACGCCTCCGTTACCTTT+TGG + chr6_2:9518017-9518036 Msa0908280:CDS 55.0%
! GCACGCCTCCGTTACCTTTT+GGG + chr6_2:9518018-9518037 Msa0908280:CDS 55.0%
GTCTACCTGAGACTGTCCCT+TGG + chr6_2:9518063-9518082 Msa0908280:CDS 55.0%
ACAGACCAAGGGACAGTCTC+AGG - chr6_2:9518071-9518090 None:intergenic 55.0%
GACTGTCCCTTGGTCTGTAC+TGG + chr6_2:9518073-9518092 Msa0908280:CDS 55.0%
CCTTGTGCCAGTACAGACCA+AGG - chr6_2:9518083-9518102 None:intergenic 55.0%
! CCTTGGTCTGTACTGGCACA+AGG + chr6_2:9518080-9518099 Msa0908280:CDS 55.0%
GCAGTTATCCGCTCCGCACT+TGG + chr6_2:9517561-9517580 Msa0908280:CDS 60.0%
GGCTACCCAGCGTTTACCGT+TGG + chr6_2:9517582-9517601 Msa0908280:CDS 60.0%
CTAGTACGAGAGGACCGGGA+AGG - chr6_2:9517636-9517655 None:intergenic 60.0%
CTTCCCGGTCCTCTCGTACT+AGG + chr6_2:9517634-9517653 Msa0908280:CDS 60.0%
CGAGTGGAAGGGTCGCTCAA+CGG - chr6_2:9517880-9517899 None:intergenic 60.0%
CGTTGAGCGACCCTTCCACT+CGG + chr6_2:9517878-9517897 Msa0908280:intron 60.0%
TCGGCACCGTCGGATCACTA+AGG + chr6_2:9517897-9517916 Msa0908280:intron 60.0%
CGTCGAGCAGGGACGAAAGT+CGG - chr6_2:9517923-9517942 None:intergenic 60.0%
CGACTTTCGTCCCTGCTCGA+CGG + chr6_2:9517921-9517940 Msa0908280:intron 60.0%
GACTTTCGTCCCTGCTCGAC+GGG + chr6_2:9517922-9517941 Msa0908280:intron 60.0%
CCCTTCTGCCTTTGCACTCG+AGG + chr6_2:9517964-9517983 Msa0908280:CDS 60.0%
CCCTCGAGTGCAAAGGCAGA+AGG - chr6_2:9517968-9517987 None:intergenic 60.0%
! CGCCTCCGTTACCTTTTGGG+AGG + chr6_2:9518021-9518040 Msa0908280:CDS 60.0%
! GGCCTCCCAAAAGGTAACGG+AGG - chr6_2:9518026-9518045 None:intergenic 60.0%
CTGGGTAGCCAAGTGCGGAG+CGG - chr6_2:9517572-9517591 None:intergenic 65.0%
! CACCAGAGGTGCGTCCTTCC+CGG + chr6_2:9517619-9517638 Msa0908280:CDS 65.0%
TGGGCGAACAGCCCAACCCT+TGG + chr6_2:9517746-9517765 Msa0908280:intron 65.0%
!! GATGTCGGCTCTTCGCCACC+TGG - chr6_2:9517786-9517805 None:intergenic 65.0%
GTGGCGAAGAGCCGACATCG+AGG + chr6_2:9517787-9517806 Msa0908280:CDS 65.0%
ACCCTTCCACTCGGCACCGT+CGG + chr6_2:9517887-9517906 Msa0908280:intron 65.0%
! TCCGACGGTGCCGAGTGGAA+GGG - chr6_2:9517891-9517910 None:intergenic 65.0%
! ATCCGACGGTGCCGAGTGGA+AGG - chr6_2:9517892-9517911 None:intergenic 65.0%
! AGTGATCCGACGGTGCCGAG+TGG - chr6_2:9517896-9517915 None:intergenic 65.0%
TTTCGTCCCTGCTCGACGGG+TGG + chr6_2:9517925-9517944 Msa0908280:intron 65.0%
TTCGTCCCTGCTCGACGGGT+GGG + chr6_2:9517926-9517945 Msa0908280:intron 65.0%
CAAGACCCACCCGTCGAGCA+GGG - chr6_2:9517934-9517953 None:intergenic 65.0%
CTCGAGGGCCAATCTCCGTC+TGG + chr6_2:9517980-9517999 Msa0908280:CDS 65.0%
TCCTCGGGCCAGACGGAGAT+TGG - chr6_2:9517991-9518010 None:intergenic 65.0%
TGGGGCGTAGGCCTCCCAAA+AGG - chr6_2:9518035-9518054 None:intergenic 65.0%
GACCGGGAAGGACGCACCTC+TGG - chr6_2:9517624-9517643 None:intergenic 70.0%
GCAAGACCCACCCGTCGAGC+AGG - chr6_2:9517935-9517954 None:intergenic 70.0%
GCCAATCTCCGTCTGGCCCG+AGG + chr6_2:9517987-9518006 Msa0908280:CDS 70.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9517552 9518106 9517552 ID=Msa0908280;Name=Msa0908280
chr6_2 mRNA 9517552 9518106 9517552 ID=Msa0908280-mRNA-1;Parent=Msa0908280;Name=Msa0908280-mRNA-1;_AED=0.57;_eAED=1.00;_QI=0|0|0|0.66|1|1|3|0|122
chr6_2 exon 9517552 9517661 9517552 ID=Msa0908280-mRNA-1:exon:2289;Parent=Msa0908280-mRNA-1
chr6_2 exon 9517757 9517865 9517757 ID=Msa0908280-mRNA-1:exon:2290;Parent=Msa0908280-mRNA-1
chr6_2 exon 9517957 9518106 9517957 ID=Msa0908280-mRNA-1:exon:2291;Parent=Msa0908280-mRNA-1
chr6_2 CDS 9517552 9517661 9517552 ID=Msa0908280-mRNA-1:cds;Parent=Msa0908280-mRNA-1
chr6_2 CDS 9517757 9517865 9517757 ID=Msa0908280-mRNA-1:cds;Parent=Msa0908280-mRNA-1
chr6_2 CDS 9517957 9518106 9517957 ID=Msa0908280-mRNA-1:cds;Parent=Msa0908280-mRNA-1
Gene Sequence

>Msa0908280

ATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTACCCAGCGTTTACCGTTGGCACGATAACTGGCACACCAGAGGTGCGTCCTTCCCGGTCCTCTCGTACTAGGGAAAGCCCAACCCTTGGAACATACTACAGCTCCAGGTGGCGAAGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAGCTCTTGGGAAGATCAGCCTGTTATCCCTAGATCAAGCTCCCTTCTGCCTTTGCACTCGAGGGCCAATCTCCGTCTGGCCCGAGGAAACCTTTGCACGCCTCCGTTACCTTTTGGGAGGCCTACGCCCCATAGAAACTGTCTACCTGAGACTGTCCCTTGGTCTGTACTGGCACAAGGTTAG

Protein sequence

>Msa0908280

MLSAVIRSALGYPAFTVGTITGTPEVRPSRSSRTRESPTLGTYYSSRWRRADIEVPNLPVDVSSWEDQPVIPRSSSLLPLHSRANLRLARGNLCTPPLPFGRPTPHRNCLPETVPWSVLAQG*