AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060723

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060723.t1 MTR_1g049370 96.137 233 9 0 1 233 1 233 2.63e-171 471
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060723.t1 AT2G39020 66.667 222 71 2 12 232 15 234 2.08e-104 301
MS.gene060723.t1 AT2G39030 60.360 222 86 1 7 228 3 222 9.98e-100 290

Find 70 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGACTCACTGGGGAGAATT+TGG 0.144921 1.3:+31852342 MS.gene060723:CDS
TGGCGTGGGAGGGCGGTTTC+TGG 0.146318 1.3:-31851737 None:intergenic
GCGGTTTCTGGCATGGTTGA+TGG 0.245127 1.3:-31851725 None:intergenic
TGTTATAGAAGGAAAGGATT+TGG 0.322014 1.3:+31852175 MS.gene060723:CDS
GTTATAGAAGGAAAGGATTT+GGG 0.325583 1.3:+31852176 MS.gene060723:CDS
GGGGAGAATTTGGAGGCTTA+TGG 0.326367 1.3:+31852352 MS.gene060723:CDS
TGCGAAACAAGCTGTGAAAA+TGG 0.330688 1.3:+31852219 MS.gene060723:CDS
TTGGTGATGGGTTTGTAAAA+TGG 0.335941 1.3:-31851989 None:intergenic
AGACGGATGCGTGTGAAAAC+TGG 0.343289 1.3:-31851761 None:intergenic
TCTTTCTCTGGGTCATCGAT+TGG 0.358639 1.3:-31852031 None:intergenic
CGGTTTCTGGCATGGTTGAT+GGG 0.367929 1.3:-31851724 None:intergenic
GGTTCTGTCGGTGGTGGTGG+CGG 0.375662 1.3:-31851701 None:intergenic
TTGAATGGGTTGTTCTTGAT+TGG 0.376314 1.3:+31852254 MS.gene060723:CDS
AGAGACTTCGAGGATGAGTA+TGG 0.377377 1.3:-31851930 None:intergenic
AAAATGGGTCGTTGTCGAAA+TGG 0.382151 1.3:-31851973 None:intergenic
CTTTCTCTGGGTCATCGATT+GGG 0.385676 1.3:-31852030 None:intergenic
GGTTTCTGGCATGGTTGATG+GGG 0.387609 1.3:-31851723 None:intergenic
TGAAAACTGGGTGGCGTGGG+AGG 0.418820 1.3:-31851748 None:intergenic
TGGAGGCTTTGCAGACTCAC+TGG 0.419524 1.3:+31852331 MS.gene060723:CDS
TGGGAGGGCGGTTTCTGGCA+TGG 0.425483 1.3:-31851732 None:intergenic
GGCGGTGCTGCGGAGGCCAT+TGG 0.427189 1.3:-31851683 None:intergenic
TTGTGAGAGAGTGTTATAGA+AGG 0.433799 1.3:+31852164 MS.gene060723:CDS
CCATTTGATGCATTAGTTTG+TGG 0.444519 1.3:-31851811 None:intergenic
CAAGTTGATAACTTTGGTGA+TGG 0.446222 1.3:-31852002 None:intergenic
GAGTATGGTGGTGGAATGGA+AGG 0.447086 1.3:-31851915 None:intergenic
AAATGGGTCGTTGTCGAAAT+GGG 0.450614 1.3:-31851972 None:intergenic
GGAGAAGAGAGTGGTTGAGT+AGG 0.453969 1.3:-31851879 None:intergenic
AACTGGGTGGCGTGGGAGGG+CGG 0.457571 1.3:-31851744 None:intergenic
GTCGAAATGGGTATCGGTGA+AGG 0.459643 1.3:-31851960 None:intergenic
TGGTGATGGGTTTGTAAAAT+GGG 0.465138 1.3:-31851988 None:intergenic
GCGAAACAAGCTGTGAAAAT+GGG 0.467825 1.3:+31852220 MS.gene060723:CDS
TGGTGGTGGCGGTGCTGCGG+AGG 0.474664 1.3:-31851690 None:intergenic
CCACAAACTAATGCATCAAA+TGG 0.477989 1.3:+31851811 MS.gene060723:CDS
AGAGAGTGTTATAGAAGGAA+AGG 0.484459 1.3:+31852169 MS.gene060723:CDS
TGGATGTAGGGAACGTCGGA+AGG 0.497082 1.3:-31851791 None:intergenic
GAGATCCAAGTTGATAACTT+TGG 0.497094 1.3:-31852008 None:intergenic
TGGGGTATGGAAGAGTTGAA+TGG 0.498138 1.3:+31852239 MS.gene060723:CDS
CGTCGGAAGGGGTGGCTAGA+CGG 0.500858 1.3:-31851778 None:intergenic
GAAAACTGGGTGGCGTGGGA+GGG 0.501040 1.3:-31851747 None:intergenic
GGAGGCTTTGCAGACTCACT+GGG 0.510969 1.3:+31852332 MS.gene060723:CDS
GGGGTATGGAAGAGTTGAAT+GGG 0.513899 1.3:+31852240 MS.gene060723:CDS
ACTCACTGGGGAGAATTTGG+AGG 0.518312 1.3:+31852345 MS.gene060723:CDS
CGGTGGTGGTGGCGGTGCTG+CGG 0.522277 1.3:-31851693 None:intergenic
TGCATTAGTTTGTGGATGTA+GGG 0.523176 1.3:-31851803 None:intergenic
CATCACCAAAGTTATCAACT+TGG 0.525135 1.3:+31852003 MS.gene060723:CDS
AAGTTGATAACTTTGGTGAT+GGG 0.527173 1.3:-31852001 None:intergenic
GATGTAGGGAACGTCGGAAG+GGG 0.527743 1.3:-31851789 None:intergenic
ATGCATTAGTTTGTGGATGT+AGG 0.527995 1.3:-31851804 None:intergenic
GTAGGGAACGTCGGAAGGGG+TGG 0.529853 1.3:-31851786 None:intergenic
CAAGCTGTGAAAATGGGGTA+TGG 0.543716 1.3:+31852226 MS.gene060723:CDS
TTCGAGGATGAGTATGGTGG+TGG 0.544978 1.3:-31851924 None:intergenic
GGATGAGTATGGTGGTGGAA+TGG 0.551232 1.3:-31851919 None:intergenic
ATGTGTGAGTTGTTCGAAAA+CGG 0.552949 1.3:-31851834 None:intergenic
TCGAAATGGGTATCGGTGAA+GGG 0.559274 1.3:-31851959 None:intergenic
GTGTGAAAACTGGGTGGCGT+GGG 0.564107 1.3:-31851751 None:intergenic
GTCGTTGTCGAAATGGGTAT+CGG 0.570206 1.3:-31851966 None:intergenic
GTTTCTGGCATGGTTGATGG+GGG 0.577631 1.3:-31851722 None:intergenic
GGATGTAGGGAACGTCGGAA+GGG 0.582464 1.3:-31851790 None:intergenic
GACGGATGCGTGTGAAAACT+GGG 0.582552 1.3:-31851760 None:intergenic
CGAAATGGGTATCGGTGAAG+GGG 0.588125 1.3:-31851958 None:intergenic
CGTGTGAAAACTGGGTGGCG+TGG 0.593886 1.3:-31851752 None:intergenic
CGAAACAAGCTGTGAAAATG+GGG 0.605125 1.3:+31852221 MS.gene060723:CDS
TTTGTGGATGTAGGGAACGT+CGG 0.617809 1.3:-31851795 None:intergenic
GGTTGAGTAGGAAGCTTCTG+TGG 0.642533 1.3:-31851867 None:intergenic
TGAGTAGGAAGCTTCTGTGG+CGG 0.687951 1.3:-31851864 None:intergenic
GAAAACTTCAAAACTCAACA+TGG 0.690199 1.3:+31852052 MS.gene060723:CDS
AGTATGGTGGTGGAATGGAA+GGG 0.693293 1.3:-31851914 None:intergenic
GACTTCGAGGATGAGTATGG+TGG 0.694705 1.3:-31851927 None:intergenic
GAGGCTTTGCAGACTCACTG+GGG 0.729456 1.3:+31852333 MS.gene060723:CDS
GGATGCGTGTGAAAACTGGG+TGG 0.835632 1.3:-31851757 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAAGTTTTATGAAGATAT+GGG + chr1.3:31852289-31852308 MS.gene060723:CDS 15.0%
!!! TATAAAGTTTTATGAAGATA+TGG + chr1.3:31852288-31852307 MS.gene060723:CDS 15.0%
!!! TTTTGAAGTTTTCTTTCTCT+GGG - chr1.3:31852045-31852064 None:intergenic 25.0%
GAAAACTTCAAAACTCAACA+TGG + chr1.3:31852052-31852071 MS.gene060723:CDS 30.0%
GTTATAGAAGGAAAGGATTT+GGG + chr1.3:31852176-31852195 MS.gene060723:CDS 30.0%
TGTTATAGAAGGAAAGGATT+TGG + chr1.3:31852175-31852194 MS.gene060723:CDS 30.0%
! GTAATGAAGTTTTTGTTGCT+GGG + chr1.3:31852074-31852093 MS.gene060723:CDS 30.0%
!! AAGTTGATAACTTTGGTGAT+GGG - chr1.3:31852004-31852023 None:intergenic 30.0%
!!! CCTAACTACTCAACTTTTTT+GGG + chr1.3:31852112-31852131 MS.gene060723:CDS 30.0%
!!! CTAACTACTCAACTTTTTTG+GGG + chr1.3:31852113-31852132 MS.gene060723:CDS 30.0%
!!! GTTTTGAAGTTTTCTTTCTC+TGG - chr1.3:31852046-31852065 None:intergenic 30.0%
!!! TCCTAACTACTCAACTTTTT+TGG + chr1.3:31852111-31852130 MS.gene060723:CDS 30.0%
ATGTGTGAGTTGTTCGAAAA+CGG - chr1.3:31851837-31851856 None:intergenic 35.0%
CATCACCAAAGTTATCAACT+TGG + chr1.3:31852003-31852022 MS.gene060723:CDS 35.0%
CCACAAACTAATGCATCAAA+TGG + chr1.3:31851811-31851830 MS.gene060723:CDS 35.0%
CCCAAAAAAGTTGAGTAGTT+AGG - chr1.3:31852115-31852134 None:intergenic 35.0%
! CCATTTGATGCATTAGTTTG+TGG - chr1.3:31851814-31851833 None:intergenic 35.0%
! GGTAATGAAGTTTTTGTTGC+TGG + chr1.3:31852073-31852092 MS.gene060723:CDS 35.0%
!! AATGGAAGGGTTTGTTTTCA+GGG - chr1.3:31851904-31851923 None:intergenic 35.0%
!! AGAGAGTGTTATAGAAGGAA+AGG + chr1.3:31852169-31852188 MS.gene060723:CDS 35.0%
!! ATGCATTAGTTTGTGGATGT+AGG - chr1.3:31851807-31851826 None:intergenic 35.0%
!! CAAGTTGATAACTTTGGTGA+TGG - chr1.3:31852005-31852024 None:intergenic 35.0%
!! GAGATCCAAGTTGATAACTT+TGG - chr1.3:31852011-31852030 None:intergenic 35.0%
!! TGCATTAGTTTGTGGATGTA+GGG - chr1.3:31851806-31851825 None:intergenic 35.0%
!! TGGTGATGGGTTTGTAAAAT+GGG - chr1.3:31851991-31852010 None:intergenic 35.0%
!! TTGAATGGGTTGTTCTTGAT+TGG + chr1.3:31852254-31852273 MS.gene060723:CDS 35.0%
!! TTGGTGATGGGTTTGTAAAA+TGG - chr1.3:31851992-31852011 None:intergenic 35.0%
!! TTGTGAGAGAGTGTTATAGA+AGG + chr1.3:31852164-31852183 MS.gene060723:CDS 35.0%
!!! CAACTTTTTTGGGGAAACAT+GGG + chr1.3:31852122-31852141 MS.gene060723:CDS 35.0%
!!! TCAACTTTTTTGGGGAAACA+TGG + chr1.3:31852121-31852140 MS.gene060723:CDS 35.0%
AAAATGGGTCGTTGTCGAAA+TGG - chr1.3:31851976-31851995 None:intergenic 40.0%
AAATGGGTCGTTGTCGAAAT+GGG - chr1.3:31851975-31851994 None:intergenic 40.0%
CGAAACAAGCTGTGAAAATG+GGG + chr1.3:31852221-31852240 MS.gene060723:CDS 40.0%
GCGAAACAAGCTGTGAAAAT+GGG + chr1.3:31852220-31852239 MS.gene060723:CDS 40.0%
TGCGAAACAAGCTGTGAAAA+TGG + chr1.3:31852219-31852238 MS.gene060723:CDS 40.0%
! CTAAGATTTTGCAGGAATGG+AGG + chr1.3:31852314-31852333 MS.gene060723:CDS 40.0%
! GTGCTAAGATTTTGCAGGAA+TGG + chr1.3:31852311-31852330 MS.gene060723:CDS 40.0%
! TATGGGTGCTAAGATTTTGC+AGG + chr1.3:31852306-31852325 MS.gene060723:CDS 40.0%
!! ATGGAAGGGTTTGTTTTCAG+GGG - chr1.3:31851903-31851922 None:intergenic 40.0%
!! GAATGGAAGGGTTTGTTTTC+AGG - chr1.3:31851905-31851924 None:intergenic 40.0%
AGAGACTTCGAGGATGAGTA+TGG - chr1.3:31851933-31851952 None:intergenic 45.0%
CAAGCTGTGAAAATGGGGTA+TGG + chr1.3:31852226-31852245 MS.gene060723:CDS 45.0%
GGGGTATGGAAGAGTTGAAT+GGG + chr1.3:31852240-31852259 MS.gene060723:CDS 45.0%
GTCGTTGTCGAAATGGGTAT+CGG - chr1.3:31851969-31851988 None:intergenic 45.0%
TCTTTCTCTGGGTCATCGAT+TGG - chr1.3:31852034-31852053 None:intergenic 45.0%
TGGGGTATGGAAGAGTTGAA+TGG + chr1.3:31852239-31852258 MS.gene060723:CDS 45.0%
TTTGTGGATGTAGGGAACGT+CGG - chr1.3:31851798-31851817 None:intergenic 45.0%
! CTTTCTCTGGGTCATCGATT+GGG - chr1.3:31852033-31852052 None:intergenic 45.0%
!! AGTATGGTGGTGGAATGGAA+GGG - chr1.3:31851917-31851936 None:intergenic 45.0%
!! TCGAAATGGGTATCGGTGAA+GGG - chr1.3:31851962-31851981 None:intergenic 45.0%
ACTCACTGGGGAGAATTTGG+AGG + chr1.3:31852345-31852364 MS.gene060723:CDS 50.0%
AGACGGATGCGTGTGAAAAC+TGG - chr1.3:31851764-31851783 None:intergenic 50.0%
CAGACTCACTGGGGAGAATT+TGG + chr1.3:31852342-31852361 MS.gene060723:CDS 50.0%
GACGGATGCGTGTGAAAACT+GGG - chr1.3:31851763-31851782 None:intergenic 50.0%
GACTTCGAGGATGAGTATGG+TGG - chr1.3:31851930-31851949 None:intergenic 50.0%
GGAGAAGAGAGTGGTTGAGT+AGG - chr1.3:31851882-31851901 None:intergenic 50.0%
GGGGAGAATTTGGAGGCTTA+TGG + chr1.3:31852352-31852371 MS.gene060723:CDS 50.0%
GGTTGAGTAGGAAGCTTCTG+TGG - chr1.3:31851870-31851889 None:intergenic 50.0%
TGAGTAGGAAGCTTCTGTGG+CGG - chr1.3:31851867-31851886 None:intergenic 50.0%
TTCGAGGATGAGTATGGTGG+TGG - chr1.3:31851927-31851946 None:intergenic 50.0%
!! ATGGTTGATGGGGGTTCTGT+CGG - chr1.3:31851716-31851735 None:intergenic 50.0%
!! CGAAATGGGTATCGGTGAAG+GGG - chr1.3:31851961-31851980 None:intergenic 50.0%
!! CGGTTTCTGGCATGGTTGAT+GGG - chr1.3:31851727-31851746 None:intergenic 50.0%
!! GAGTATGGTGGTGGAATGGA+AGG - chr1.3:31851918-31851937 None:intergenic 50.0%
!! GGATGAGTATGGTGGTGGAA+TGG - chr1.3:31851922-31851941 None:intergenic 50.0%
!! GGTTTCTGGCATGGTTGATG+GGG - chr1.3:31851726-31851745 None:intergenic 50.0%
!! GTCGAAATGGGTATCGGTGA+AGG - chr1.3:31851963-31851982 None:intergenic 50.0%
!! GTTTCTGGCATGGTTGATGG+GGG - chr1.3:31851725-31851744 None:intergenic 50.0%
!! GTTTTCAGGGGAGAAGAGAG+TGG - chr1.3:31851891-31851910 None:intergenic 50.0%
!!! AGGGGTTTTGAGAGACTTCG+AGG - chr1.3:31851943-31851962 None:intergenic 50.0%
GAGGCTTTGCAGACTCACTG+GGG + chr1.3:31852333-31852352 MS.gene060723:CDS 55.0%
GATGTAGGGAACGTCGGAAG+GGG - chr1.3:31851792-31851811 None:intergenic 55.0%
GGAGGCTTTGCAGACTCACT+GGG + chr1.3:31852332-31852351 MS.gene060723:CDS 55.0%
GGATGCGTGTGAAAACTGGG+TGG - chr1.3:31851760-31851779 None:intergenic 55.0%
GGATGTAGGGAACGTCGGAA+GGG - chr1.3:31851793-31851812 None:intergenic 55.0%
GTGTGAAAACTGGGTGGCGT+GGG - chr1.3:31851754-31851773 None:intergenic 55.0%
TGGAGGCTTTGCAGACTCAC+TGG + chr1.3:31852331-31852350 MS.gene060723:CDS 55.0%
TGGATGTAGGGAACGTCGGA+AGG - chr1.3:31851794-31851813 None:intergenic 55.0%
!! GCGGTTTCTGGCATGGTTGA+TGG - chr1.3:31851728-31851747 None:intergenic 55.0%
CGTGTGAAAACTGGGTGGCG+TGG - chr1.3:31851755-31851774 None:intergenic 60.0%
GAAAACTGGGTGGCGTGGGA+GGG - chr1.3:31851750-31851769 None:intergenic 60.0%
TGAAAACTGGGTGGCGTGGG+AGG - chr1.3:31851751-31851770 None:intergenic 60.0%
! GTTGATGGGGGTTCTGTCGG+TGG - chr1.3:31851713-31851732 None:intergenic 60.0%
CGTCGGAAGGGGTGGCTAGA+CGG - chr1.3:31851781-31851800 None:intergenic 65.0%
GATGGGGGTTCTGTCGGTGG+TGG - chr1.3:31851710-31851729 None:intergenic 65.0%
GTAGGGAACGTCGGAAGGGG+TGG - chr1.3:31851789-31851808 None:intergenic 65.0%
!! GGTTCTGTCGGTGGTGGTGG+CGG - chr1.3:31851704-31851723 None:intergenic 65.0%
!! TGGGAGGGCGGTTTCTGGCA+TGG - chr1.3:31851735-31851754 None:intergenic 65.0%
AACTGGGTGGCGTGGGAGGG+CGG - chr1.3:31851747-31851766 None:intergenic 70.0%
TGGCGTGGGAGGGCGGTTTC+TGG - chr1.3:31851740-31851759 None:intergenic 70.0%
! GGGGGTTCTGTCGGTGGTGG+TGG - chr1.3:31851707-31851726 None:intergenic 70.0%
!! CGGTGGTGGTGGCGGTGCTG+CGG - chr1.3:31851696-31851715 None:intergenic 75.0%
!! TGGTGGTGGCGGTGCTGCGG+AGG - chr1.3:31851693-31851712 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 31851686 31852387 31851686 ID=MS.gene060723
chr1.3 mRNA 31851686 31852387 31851686 ID=MS.gene060723.t1;Parent=MS.gene060723
chr1.3 exon 31851686 31852387 31851686 ID=MS.gene060723.t1.exon1;Parent=MS.gene060723.t1
chr1.3 CDS 31851686 31852387 31851686 ID=cds.MS.gene060723.t1;Parent=MS.gene060723.t1
Gene Sequence

>MS.gene060723

ATGGCCTCCGCAGCACCGCCACCACCACCGACAGAACCCCCATCAACCATGCCAGAAACCGCCCTCCCACGCCACCCAGTTTTCACACGCATCCGTCTAGCCACCCCTTCCGACGTTCCCTACATCCACAAACTAATGCATCAAATGGCCGTTTTCGAACAACTCACACATCTCATGACCGCCACAGAAGCTTCCTACTCAACCACTCTCTTCTCCCCTGAAAACAAACCCTTCCATTCCACCACCATACTCATCCTCGAAGTCTCTCAAAACCCCTTCACCGATACCCATTTCGACAACGACCCATTTTACAAACCCATCACCAAAGTTATCAACTTGGATCTCCCAATCGATGACCCAGAGAAAGAAAACTTCAAAACTCAACATGGTAATGAAGTTTTTGTTGCTGGGTTTGTTTTGTTTTTTCCTAACTACTCAACTTTTTTGGGGAAACATGGGTTTTATGTTGAAGATCTGTTTGTGAGAGAGTGTTATAGAAGGAAAGGATTTGGGAAGATGTTGCTTACTGCTGTTGCGAAACAAGCTGTGAAAATGGGGTATGGAAGAGTTGAATGGGTTGTTCTTGATTGGAATGTTAATGCTATAAAGTTTTATGAAGATATGGGTGCTAAGATTTTGCAGGAATGGAGGCTTTGCAGACTCACTGGGGAGAATTTGGAGGCTTATGGAGCTATTGAGTAA
Protein sequence

>MS.gene060723.t1

MASAAPPPPPTEPPSTMPETALPRHPVFTRIRLATPSDVPYIHKLMHQMAVFEQLTHLMTATEASYSTTLFSPENKPFHSTTILILEVSQNPFTDTHFDNDPFYKPITKVINLDLPIDDPEKENFKTQHGNEVFVAGFVLFFPNYSTFLGKHGFYVEDLFVRECYRRKGFGKMLLTAVAKQAVKMGYGRVEWVVLDWNVNAIKFYEDMGAKILQEWRLCRLTGENLEAYGAIE