AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051536


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051536.t1 MTR_1g015000 95.804 143 5 1 1 143 1 142 6.67e-99 280
MS.gene051536.t1 MTR_3g105330 59.732 149 48 4 1 143 1 143 6.85e-56 171
MS.gene051536.t1 MTR_4g019870 31.034 145 71 4 2 138 13 136 5.96e-18 75.1
MS.gene051536.t1 MTR_7g066070 31.618 136 66 3 2 131 22 136 1.15e-15 69.3
MS.gene051536.t1 MTR_0027s0220 29.787 141 77 4 2 140 27 147 1.24e-14 67.0
MS.gene051536.t1 MTR_4g065660 30.645 124 64 3 5 128 35 136 6.89e-14 65.1
MS.gene051536.t1 MTR_4g065123 29.268 123 65 2 1 123 27 127 1.34e-13 63.9
MS.gene051536.t1 MTR_4g064963 31.579 133 66 4 5 133 46 157 2.75e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051536.t1 AT5G20650 55.102 147 61 3 1 143 1 146 1.44e-50 158
MS.gene051536.t1 AT2G26975 35.433 127 60 2 1 126 24 129 6.55e-20 80.5
MS.gene051536.t1 AT5G59040 34.646 127 62 2 1 127 29 134 4.46e-17 73.2
MS.gene051536.t1 AT2G37925 30.469 128 71 2 1 128 29 138 2.46e-13 63.5
MS.gene051536.t1 AT5G59030 27.778 144 80 3 5 142 45 170 3.44e-13 63.5
MS.gene051536.t1 AT3G46900 26.761 142 78 4 7 142 35 156 7.81e-13 62.4

Find 33 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAACATTCTACCAATATT+TGG 0.138215 1.3:-7144951 MS.gene051536:CDS
GAGATTCGGACTCCTCTTCT+TGG 0.249119 1.3:-7144866 MS.gene051536:CDS
ACCAATATTTGGAAAATATT+CGG 0.254322 1.3:-7144940 MS.gene051536:CDS
TCCTCTTCTTGGGTTGAATA+AGG 0.262656 1.3:-7144855 MS.gene051536:CDS
TGACACTCTTATTTGATTCA+TGG 0.286816 1.3:-7145027 MS.gene051536:CDS
CGTTTGGTTACTTCTTGTTT+AGG 0.336421 1.3:-7144709 MS.gene051536:CDS
TGATGCACATGACACTATAT+TGG 0.342150 1.3:-7145060 MS.gene051536:CDS
ATTCATGGAAAACCAATTCA+TGG 0.342364 1.3:-7145012 MS.gene051536:CDS
TTGGCTATAATGTCGTTTAA+TGG 0.343696 1.3:-7144764 MS.gene051536:CDS
TTTGGTGTGAATTCTGCTAT+TGG 0.364233 1.3:-7144800 MS.gene051536:CDS
GATGCACATGACACTATATT+GGG 0.370954 1.3:-7145059 MS.gene051536:CDS
ATTGTGGTTGGTTTAACGTT+TGG 0.388729 1.3:-7144725 MS.gene051536:CDS
TAGATAACTCGTCCATGAAT+TGG 0.393378 1.3:+7145000 None:intergenic
AGATTCGGACTCCTCTTCTT+GGG 0.397569 1.3:-7144865 MS.gene051536:CDS
TTGGTGTGAATTCTGCTATT+GGG 0.404245 1.3:-7144799 MS.gene051536:CDS
ATTTGGAAAATATTCGGATT+CGG 0.414816 1.3:-7144934 MS.gene051536:CDS
AGTCGCCGGTGCCGGAGATT+CGG 0.431491 1.3:-7144880 MS.gene051536:CDS
TATTGGGTATTTGTTGATGT+TGG 0.437573 1.3:-7144783 MS.gene051536:CDS
GAGGAACAAGGTTGTTGAAT+CGG 0.457237 1.3:-7144828 MS.gene051536:CDS
TACTTCTTGTTTAGGAGTCA+AGG 0.469886 1.3:-7144701 MS.gene051536:CDS
TTGGGTTGAATAAGGTTTCG+AGG 0.486516 1.3:-7144847 MS.gene051536:CDS
AGAAGAGGAGTCCGAATCTC+CGG 0.488903 1.3:+7144869 None:intergenic
TAGGAGTCAAGGTGAGGAAG+AGG 0.504862 1.3:-7144690 MS.gene051536:CDS
GAGGACGCAGTCGCCGGTGC+CGG 0.509370 1.3:-7144888 MS.gene051536:CDS
TGAGGGGAGGACGCAGTCGC+CGG 0.519658 1.3:-7144894 MS.gene051536:CDS
ACCTTATTCAACCCAAGAAG+AGG 0.545808 1.3:+7144854 None:intergenic
GGAGTCCGAATCTCCGGCAC+CGG 0.550760 1.3:+7144875 None:intergenic
TCAAGGTGAGGAAGAGGCTG+CGG 0.577917 1.3:-7144684 MS.gene051536:CDS
GAATAAGGTTTCGAGGAACA+AGG 0.583225 1.3:-7144840 MS.gene051536:CDS
GCTATAATGTCGTTTAATGG+TGG 0.610087 1.3:-7144761 MS.gene051536:CDS
CTTGTTTAGGAGTCAAGGTG+AGG 0.615505 1.3:-7144696 MS.gene051536:CDS
ATGCACATGACACTATATTG+GGG 0.639974 1.3:-7145058 MS.gene051536:CDS
TGCACATGACACTATATTGG+GGG 0.689179 1.3:-7145057 MS.gene051536:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACCAATATTTGGAAAATATT+CGG - chr1.3:7144773-7144792 MS.gene051536:CDS 20.0%
! ATTTGGAAAATATTCGGATT+CGG - chr1.3:7144779-7144798 MS.gene051536:CDS 25.0%
!! TCCGAATATTTTCCAAATAT+TGG + chr1.3:7144777-7144796 None:intergenic 25.0%
ATTCATGGAAAACCAATTCA+TGG - chr1.3:7144701-7144720 MS.gene051536:CDS 30.0%
TGCAACATTCTACCAATATT+TGG - chr1.3:7144762-7144781 MS.gene051536:CDS 30.0%
! TATTGGGTATTTGTTGATGT+TGG - chr1.3:7144930-7144949 MS.gene051536:CDS 30.0%
! TGACACTCTTATTTGATTCA+TGG - chr1.3:7144686-7144705 MS.gene051536:CDS 30.0%
! TTGGCTATAATGTCGTTTAA+TGG - chr1.3:7144949-7144968 MS.gene051536:CDS 30.0%
!!! GTTGTTGAATCGGTTTTATT+TGG - chr1.3:7144895-7144914 MS.gene051536:CDS 30.0%
ATGCACATGACACTATATTG+GGG - chr1.3:7144655-7144674 MS.gene051536:CDS 35.0%
GATGCACATGACACTATATT+GGG - chr1.3:7144654-7144673 MS.gene051536:CDS 35.0%
TAGATAACTCGTCCATGAAT+TGG + chr1.3:7144716-7144735 None:intergenic 35.0%
TGATGCACATGACACTATAT+TGG - chr1.3:7144653-7144672 MS.gene051536:CDS 35.0%
TTGGTGTGAATTCTGCTATT+GGG - chr1.3:7144914-7144933 MS.gene051536:CDS 35.0%
! ATTCGGTTGAAGTTTTTCTC+TGG - chr1.3:7144796-7144815 MS.gene051536:CDS 35.0%
! CGTTTGGTTACTTCTTGTTT+AGG - chr1.3:7145004-7145023 MS.gene051536:CDS 35.0%
! GCTATAATGTCGTTTAATGG+TGG - chr1.3:7144952-7144971 MS.gene051536:CDS 35.0%
! TACTTCTTGTTTAGGAGTCA+AGG - chr1.3:7145012-7145031 MS.gene051536:CDS 35.0%
! TTGAAGTTTTTCTCTGGTGA+GGG - chr1.3:7144802-7144821 MS.gene051536:CDS 35.0%
! TTTGGTGTGAATTCTGCTAT+TGG - chr1.3:7144913-7144932 MS.gene051536:CDS 35.0%
!! ATTGTGGTTGGTTTAACGTT+TGG - chr1.3:7144988-7145007 MS.gene051536:CDS 35.0%
!! GTTTAATGGTGGTGTTTTTG+TGG - chr1.3:7144963-7144982 MS.gene051536:CDS 35.0%
ACCTTATTCAACCCAAGAAG+AGG + chr1.3:7144862-7144881 None:intergenic 40.0%
GAATAAGGTTTCGAGGAACA+AGG - chr1.3:7144873-7144892 MS.gene051536:CDS 40.0%
GAGGAACAAGGTTGTTGAAT+CGG - chr1.3:7144885-7144904 MS.gene051536:CDS 40.0%
TGCACATGACACTATATTGG+GGG - chr1.3:7144656-7144675 MS.gene051536:CDS 40.0%
! GTTGAAGTTTTTCTCTGGTG+AGG - chr1.3:7144801-7144820 MS.gene051536:CDS 40.0%
! GTTTTTGTGGCTATTGTGGT+TGG - chr1.3:7144976-7144995 MS.gene051536:CDS 40.0%
! TGAAGTTTTTCTCTGGTGAG+GGG - chr1.3:7144803-7144822 MS.gene051536:CDS 40.0%
!! TCCTCTTCTTGGGTTGAATA+AGG - chr1.3:7144858-7144877 MS.gene051536:CDS 40.0%
!! TGGTGTTTTTGTGGCTATTG+TGG - chr1.3:7144972-7144991 MS.gene051536:CDS 40.0%
!! TTGGGTTGAATAAGGTTTCG+AGG - chr1.3:7144866-7144885 MS.gene051536:CDS 40.0%
AGATTCGGACTCCTCTTCTT+GGG - chr1.3:7144848-7144867 MS.gene051536:CDS 45.0%
CTTGTTTAGGAGTCAAGGTG+AGG - chr1.3:7145017-7145036 MS.gene051536:CDS 45.0%
AGAAGAGGAGTCCGAATCTC+CGG + chr1.3:7144847-7144866 None:intergenic 50.0%
GAGATTCGGACTCCTCTTCT+TGG - chr1.3:7144847-7144866 MS.gene051536:CDS 50.0%
TAGGAGTCAAGGTGAGGAAG+AGG - chr1.3:7145023-7145042 MS.gene051536:CDS 50.0%
! AGTTTTTCTCTGGTGAGGGG+AGG - chr1.3:7144806-7144825 MS.gene051536:CDS 50.0%
TCAAGGTGAGGAAGAGGCTG+CGG - chr1.3:7145029-7145048 MS.gene051536:CDS 55.0%
GGAGTCCGAATCTCCGGCAC+CGG + chr1.3:7144841-7144860 None:intergenic 65.0%
! AGTCGCCGGTGCCGGAGATT+CGG - chr1.3:7144833-7144852 MS.gene051536:CDS 65.0%
TGAGGGGAGGACGCAGTCGC+CGG - chr1.3:7144819-7144838 MS.gene051536:CDS 70.0%
GAGGACGCAGTCGCCGGTGC+CGG - chr1.3:7144825-7144844 MS.gene051536:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 7144652 7145083 7144652 ID=MS.gene051536
chr1.3 mRNA 7144652 7145083 7144652 ID=MS.gene051536.t1;Parent=MS.gene051536
chr1.3 exon 7144652 7145083 7144652 ID=MS.gene051536.t1.exon1;Parent=MS.gene051536.t1
chr1.3 CDS 7144652 7145083 7144652 ID=cds.MS.gene051536.t1;Parent=MS.gene051536.t1
Gene Sequence

>MS.gene051536

ATGATGCACATGACACTATATTGGGGGAAAAACGTGACACTCTTATTTGATTCATGGAAAACCAATTCATGGACGAGTTATCTACTGAGTTTAATTGCATGTTTCATGATTGCAACATTCTACCAATATTTGGAAAATATTCGGATTCGGTTGAAGTTTTTCTCTGGTGAGGGGAGGACGCAGTCGCCGGTGCCGGAGATTCGGACTCCTCTTCTTGGGTTGAATAAGGTTTCGAGGAACAAGGTTGTTGAATCGGTTTTATTTGGTGTGAATTCTGCTATTGGGTATTTGTTGATGTTGGCTATAATGTCGTTTAATGGTGGTGTTTTTGTGGCTATTGTGGTTGGTTTAACGTTTGGTTACTTCTTGTTTAGGAGTCAAGGTGAGGAAGAGGCTGCGGTTGTTGTTGATAATTCTTGTGCATGTGCTTAG

Protein sequence

>MS.gene051536.t1

MMHMTLYWGKNVTLLFDSWKTNSWTSYLLSLIACFMIATFYQYLENIRIRLKFFSGEGRTQSPVPEIRTPLLGLNKVSRNKVVESVLFGVNSAIGYLLMLAIMSFNGGVFVAIVVGLTFGYFLFRSQGEEEAAVVVDNSCACA