AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene032094

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032094.t1 MTR_2g081580 100.000 102 0 0 1 102 17 118 4.61e-69 202
MS.gene032094.t1 MTR_8g466250 81.443 97 18 0 1 97 18 114 4.69e-52 159
MS.gene032094.t1 MTR_1g052885 70.408 98 29 0 1 98 13 110 3.27e-43 137
MS.gene032094.t1 MTR_2g089210 68.687 99 31 0 1 99 17 115 3.74e-42 134
MS.gene032094.t1 MTR_2g011400 64.894 94 33 0 1 94 21 114 5.86e-37 121
MS.gene032094.t1 MTR_2g081300 67.045 88 28 1 1 88 12 98 5.41e-35 116
MS.gene032094.t1 MTR_2g081350 65.169 89 30 1 1 89 16 103 2.91e-34 114
MS.gene032094.t1 MTR_2g081440 62.500 88 32 1 1 88 16 102 1.69e-31 107
MS.gene032094.t1 MTR_8g027180 47.000 100 53 0 1 100 26 125 2.27e-31 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032094.t1 AT5G54490 66.327 98 32 1 1 97 26 123 3.71e-41 132
MS.gene032094.t1 AT4G27280 66.327 98 32 1 1 97 26 123 4.78e-41 132
MS.gene032094.t1 AT2G46600 52.041 98 47 0 1 98 29 126 2.89e-33 112

Find 19 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGACTTAGTCCTGAACTTA+TGG 0.262199 2.3:-16686653 MS.gene032094:CDS
AAAATCACCTTCAACAATCA+TGG 0.442153 2.3:+16686723 None:intergenic
AAAAGAATTCAGCTTTGCTT+GGG 0.443368 2.3:-16686777 MS.gene032094:CDS
CTTCAATCCATGATTGTTGA+AGG 0.479434 2.3:-16686730 MS.gene032094:CDS
TTAGACCCATCCATAAGTTC+AGG 0.481132 2.3:+16686643 None:intergenic
GCAAACAAGCTTGGTGGGGA+TGG 0.482564 2.3:-16686877 MS.gene032094:CDS
CCCCTCATGGCAAACAAGCT+TGG 0.492739 2.3:-16686886 None:intergenic
CTCATGGCAAACAAGCTTGG+TGG 0.508830 2.3:-16686883 MS.gene032094:CDS
TCATGGCAAACAAGCTTGGT+GGG 0.509220 2.3:-16686882 MS.gene032094:CDS
CTTAGTCCTGAACTTATGGA+TGG 0.521531 2.3:-16686649 MS.gene032094:CDS
TGATGGTGCTCTTAATCAAA+TGG 0.521789 2.3:-16686695 MS.gene032094:CDS
TTAATAGATGAATTATGCAA+TGG 0.547432 2.3:-16686853 MS.gene032094:CDS
TTTGATGGATTCTACTAAAG+GGG 0.572126 2.3:-16686821 MS.gene032094:CDS
GGATGGGTCTAAGATGTGGT+TGG 0.605170 2.3:-16686632 MS.gene032094:CDS
GTTACAAGATTTGACCGATG+TGG 0.613980 2.3:-16686755 MS.gene032094:CDS
TTAGTCCTGAACTTATGGAT+GGG 0.620182 2.3:-16686648 MS.gene032094:CDS
CATGGCAAACAAGCTTGGTG+GGG 0.632642 2.3:-16686881 MS.gene032094:CDS
TTATGGATGGGTCTAAGATG+TGG 0.687819 2.3:-16686636 MS.gene032094:CDS
CATGGATTGAAGTTCCACAT+CGG 0.713256 2.3:+16686741 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATAGATGAATTATGCAA+TGG - chr2.3:16686621-16686640 MS.gene032094:CDS 20.0%
!!! ATTCTTTTTAAGGCTTTCAA+AGG + chr2.3:16686685-16686704 None:intergenic 25.0%
!!! TTTTGATGGATTCTACTAAA+GGG - chr2.3:16686652-16686671 MS.gene032094:CDS 25.0%
AAAAAGAATTCAGCTTTGCT+TGG - chr2.3:16686696-16686715 MS.gene032094:CDS 30.0%
AAAAGAATTCAGCTTTGCTT+GGG - chr2.3:16686697-16686716 MS.gene032094:CDS 30.0%
AAAATCACCTTCAACAATCA+TGG + chr2.3:16686754-16686773 None:intergenic 30.0%
! ATTGTTGAAGGTGATTTTGA+TGG - chr2.3:16686756-16686775 MS.gene032094:CDS 30.0%
! CAATGGTTTCAATCTTTTGA+TGG - chr2.3:16686638-16686657 MS.gene032094:CDS 30.0%
! GCAAAGCTGAATTCTTTTTA+AGG + chr2.3:16686695-16686714 None:intergenic 30.0%
!! TTTGATGGATTCTACTAAAG+GGG - chr2.3:16686653-16686672 MS.gene032094:CDS 30.0%
!!! CTTTTGATGGATTCTACTAA+AGG - chr2.3:16686651-16686670 MS.gene032094:CDS 30.0%
CTTCAATCCATGATTGTTGA+AGG - chr2.3:16686744-16686763 MS.gene032094:CDS 35.0%
TAGACTTAGTCCTGAACTTA+TGG - chr2.3:16686821-16686840 MS.gene032094:CDS 35.0%
TTAGTCCTGAACTTATGGAT+GGG - chr2.3:16686826-16686845 MS.gene032094:CDS 35.0%
! TGATGGTGCTCTTAATCAAA+TGG - chr2.3:16686779-16686798 MS.gene032094:CDS 35.0%
CTTAGTCCTGAACTTATGGA+TGG - chr2.3:16686825-16686844 MS.gene032094:CDS 40.0%
GTTACAAGATTTGACCGATG+TGG - chr2.3:16686719-16686738 MS.gene032094:CDS 40.0%
TTAGACCCATCCATAAGTTC+AGG + chr2.3:16686834-16686853 None:intergenic 40.0%
! CATGGATTGAAGTTCCACAT+CGG + chr2.3:16686736-16686755 None:intergenic 40.0%
! TTATGGATGGGTCTAAGATG+TGG - chr2.3:16686838-16686857 MS.gene032094:CDS 40.0%
!!! GAAGGTGATTTTGATGGTGA+TGG - chr2.3:16686762-16686781 MS.gene032094:CDS 40.0%
! GGATGGGTCTAAGATGTGGT+TGG - chr2.3:16686842-16686861 MS.gene032094:CDS 50.0%
! GCAAACAAGCTTGGTGGGGA+TGG - chr2.3:16686597-16686616 MS.gene032094:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 16686594 16686902 16686594 ID=MS.gene032094
chr2.3 mRNA 16686594 16686902 16686594 ID=MS.gene032094.t1;Parent=MS.gene032094
chr2.3 exon 16686594 16686902 16686594 ID=MS.gene032094.t1.exon1;Parent=MS.gene032094.t1
chr2.3 CDS 16686594 16686902 16686594 ID=cds.MS.gene032094.t1;Parent=MS.gene032094.t1
Gene Sequence

>MS.gene032094

ATGGCAAACAAGCTTGGTGGGGATGGATTAATAGATGAATTATGCAATGGTTTCAATCTTTTGATGGATTCTACTAAAGGGGTTATTACCTTTGAAAGCCTTAAAAAGAATTCAGCTTTGCTTGGGTTACAAGATTTGACCGATGTGGAACTTCAATCCATGATTGTTGAAGGTGATTTTGATGGTGATGGTGCTCTTAATCAAATGGAGTTTTGTGTTTTGATGTTTAGACTTAGTCCTGAACTTATGGATGGGTCTAAGATGTGGTTGGAACAAATGCTTCAACAAGAAGTCCAAGATTCTTTCTAA
Protein sequence

>MS.gene032094.t1

MANKLGGDGLIDELCNGFNLLMDSTKGVITFESLKKNSALLGLQDLTDVELQSMIVEGDFDGDGALNQMEFCVLMFRLSPELMDGSKMWLEQMLQQEVQDSF