AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47914

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47914.t1 MTR_8g089170 88.462 156 18 0 1 156 1 156 3.79e-95 272
MS.gene47914.t1 MTR_8g089130 81.646 158 27 2 1 156 1 158 1.71e-87 253
MS.gene47914.t1 MTR_8g089145 86.301 73 10 0 1 73 1 73 1.78e-41 133
MS.gene47914.t1 MTR_1g089830 39.456 147 60 5 4 150 3 120 1.51e-21 85.1
MS.gene47914.t1 MTR_4g028990 53.425 73 32 1 81 151 20 92 1.02e-17 73.9
MS.gene47914.t1 MTR_1g045040 38.621 145 63 5 7 150 6 125 1.56e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATACCTTCAAATGAAAT+TGG 0.206576 4.1:-11576230 MS.gene47914:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.1:+11577241 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.1:+11577197 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.1:+11577268 None:intergenic
ATCCTCAAACAACGTCTCTT+TGG 0.317203 4.1:+11576377 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.1:-11577082 MS.gene47914:intron
CTGTTAGTAACAAGTTCTTT+TGG 0.373720 4.1:+11577151 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.1:+11577259 None:intergenic
CTCCAAAGAGACGTTGTTTG+AGG 0.374170 4.1:-11576379 MS.gene47914:CDS
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.1:+11577173 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.396727 4.1:-11576224 MS.gene47914:CDS
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.1:-11577210 MS.gene47914:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.1:+11577229 None:intergenic
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.1:+11576224 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.1:-11577266 MS.gene47914:CDS
TCCCTTCTACATAGAAGAAC+CGG 0.461538 4.1:+11576181 None:intergenic
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.1:+11577182 None:intergenic
TCTTCTGAGGATGACTCATC+TGG 0.485391 4.1:+11576281 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.1:+11577087 None:intergenic
GCAGTTCTTCTTAAACCAGC+CGG 0.561335 4.1:-11576200 MS.gene47914:CDS
GAACAATAAGGCCTCTTCTG+AGG 0.569819 4.1:+11576268 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.1:-11577265 MS.gene47914:CDS
AGATGAGTCATCCTCAGAAG+AGG 0.600054 4.1:-11576279 MS.gene47914:CDS
CAATCAAAAGATGACACCGA+TGG 0.604219 4.1:-11576351 MS.gene47914:CDS
AAAGAACTTGTTACTAACAG+TGG 0.608058 4.1:-11577148 MS.gene47914:CDS
TTCTACATAGAAGAACCGGC+TGG 0.612139 4.1:+11576185 None:intergenic
TGGACTAAGATACCAAAACT+GGG 0.618651 4.1:-11577209 MS.gene47914:CDS
GTTTAAGAAGAACTGCTCCA+AGG 0.642127 4.1:+11576207 None:intergenic
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.1:-11577273 MS.gene47914:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.1:-11577208 MS.gene47914:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAAAATTAACTTTAAAATA+AGG - chr4.1:11576878-11576897 MS.gene47914:intron 10.0%
!!! TTATTAACAGTTTAAAATAA+GGG + chr4.1:11577012-11577031 None:intergenic 10.0%
!!! TTTATTAACAGTTTAAAATA+AGG + chr4.1:11577013-11577032 None:intergenic 10.0%
!! TATAAATGAGTTTACTTTAA+AGG + chr4.1:11576627-11576646 None:intergenic 15.0%
!!! ATGAATTTTCATATTTTTGA+CGG - chr4.1:11576746-11576765 MS.gene47914:intron 15.0%
!!! GAAAAGTTGATATATTTATA+GGG - chr4.1:11576969-11576988 MS.gene47914:intron 15.0%
!!! TAGTGATTGAAAATTTTATA+GGG - chr4.1:11576909-11576928 MS.gene47914:intron 15.0%
!! TTTATACCTTCAAATGAAAT+TGG - chr4.1:11577237-11577256 MS.gene47914:CDS 20.0%
!!! AAAATTTTCATCTTCACTTT+TGG - chr4.1:11576596-11576615 MS.gene47914:intron 20.0%
!!! AAATTTTCAATCACTACTTT+TGG + chr4.1:11576905-11576924 None:intergenic 20.0%
!!! ATAAGGGTTAAATATGTTTT+TGG + chr4.1:11576996-11577015 None:intergenic 20.0%
!!! ATACTACTTTAATTTTGTGA+GGG - chr4.1:11576460-11576479 MS.gene47914:intron 20.0%
!!! CGAAAAGTTGATATATTTAT+AGG - chr4.1:11576968-11576987 MS.gene47914:intron 20.0%
!!! GTAGTGATTGAAAATTTTAT+AGG - chr4.1:11576908-11576927 MS.gene47914:intron 20.0%
!!! TATACTACTTTAATTTTGTG+AGG - chr4.1:11576459-11576478 MS.gene47914:intron 20.0%
!!! TGAAGATGAAAATTTTTTGA+TGG + chr4.1:11576592-11576611 None:intergenic 20.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.1:11576433-11576452 None:intergenic 25.0%
!! AAATGAGTTTACTTTAAAGG+AGG + chr4.1:11576624-11576643 None:intergenic 25.0%
!! AAGTTGAAGGAAAATTTTAG+AGG - chr4.1:11576937-11576956 MS.gene47914:intron 25.0%
!! AATGAGTTTACTTTAAAGGA+GGG + chr4.1:11576623-11576642 None:intergenic 25.0%
!! AGTTGAAGGAAAATTTTAGA+GGG - chr4.1:11576938-11576957 MS.gene47914:intron 25.0%
!! GTTCACATTTTTGAACAATA+AGG + chr4.1:11577214-11577233 None:intergenic 25.0%
!! TTAGGGGTTAAATATGTTTT+TGG - chr4.1:11576505-11576524 MS.gene47914:intron 25.0%
!!! AAGTTGAAGAAATTTTTTCG+AGG + chr4.1:11576564-11576583 None:intergenic 25.0%
!!! AGTTGAAGAAATTTTTTCGA+GGG + chr4.1:11576563-11576582 None:intergenic 25.0%
!!! GTGCGTGAATATTTATTTTA+GGG - chr4.1:11576488-11576507 MS.gene47914:intron 25.0%
!!! TGCGTGAATATTTATTTTAG+GGG - chr4.1:11576489-11576508 MS.gene47914:intron 25.0%
!!! TGTGCGTGAATATTTATTTT+AGG - chr4.1:11576487-11576506 MS.gene47914:intron 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.1:11576383-11576402 None:intergenic 30.0%
TTATAGGGACTAAAAGTTGA+AGG - chr4.1:11576924-11576943 MS.gene47914:intron 30.0%
! CTGTTAGTAACAAGTTCTTT+TGG + chr4.1:11576319-11576338 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.1:11576385-11576404 MS.gene47914:CDS 30.0%
! TCTTGTTGAAACTTTTCCAT+CGG + chr4.1:11577135-11577154 None:intergenic 30.0%
!! AAAGAACTTGTTACTAACAG+TGG - chr4.1:11576319-11576338 MS.gene47914:CDS 30.0%
!! TACTTTAATTTTGTGAGGGT+GGG - chr4.1:11576464-11576483 MS.gene47914:intron 30.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.1:11576297-11576316 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.1:11576258-11576277 MS.gene47914:CDS 35.0%
!! CTACTTTAATTTTGTGAGGG+TGG - chr4.1:11576463-11576482 MS.gene47914:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.1:11576229-11576248 None:intergenic 35.0%
ATCCTCAAACAACGTCTCTT+TGG + chr4.1:11577093-11577112 None:intergenic 40.0%
CAATCAAAAGATGACACCGA+TGG - chr4.1:11577116-11577135 MS.gene47914:CDS 40.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.1:11577246-11577265 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.1:11576241-11576260 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.1:11576259-11576278 MS.gene47914:CDS 40.0%
GTTTAAGAAGAACTGCTCCA+AGG + chr4.1:11577263-11577282 None:intergenic 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.1:11576288-11576307 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.1:11577243-11577262 MS.gene47914:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.1:11576257-11576276 MS.gene47914:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.1:11576238-11576257 MS.gene47914:CDS 40.0%
AGATGAGTCATCCTCAGAAG+AGG - chr4.1:11577188-11577207 MS.gene47914:CDS 45.0%
CTCCAAAGAGACGTTGTTTG+AGG - chr4.1:11577088-11577107 MS.gene47914:CDS 45.0%
GAACAATAAGGCCTCTTCTG+AGG + chr4.1:11577202-11577221 None:intergenic 45.0%
GCAGTTCTTCTTAAACCAGC+CGG - chr4.1:11577267-11577286 MS.gene47914:CDS 45.0%
! TCTTCTGAGGATGACTCATC+TGG + chr4.1:11577189-11577208 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.1:11576273-11576292 None:intergenic 45.0%
!!! AAAAAAATTCTAATTTTTTT+TGG - chr4.1:11576800-11576819 MS.gene47914:intron 5.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.1:11576194-11576213 MS.gene47914:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.1:11576222-11576241 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.1:11576201-11576220 MS.gene47914:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.1:11576202-11576221 MS.gene47914:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.1:11576202-11576221 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.1:11576211-11576230 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 11576187 11577302 11576187 ID=MS.gene47914
chr4.1 mRNA 11576187 11577302 11576187 ID=MS.gene47914.t1;Parent=MS.gene47914
chr4.1 exon 11577083 11577302 11577083 ID=MS.gene47914.t1.exon1;Parent=MS.gene47914.t1
chr4.1 CDS 11577083 11577302 11577083 ID=cds.MS.gene47914.t1;Parent=MS.gene47914.t1
chr4.1 exon 11576187 11576437 11576187 ID=MS.gene47914.t1.exon2;Parent=MS.gene47914.t1
chr4.1 CDS 11576187 11576437 11576187 ID=cds.MS.gene47914.t1;Parent=MS.gene47914.t1
Gene Sequence

>MS.gene47914

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACTAACAGTGGCAACAGTAGCAACAAGAGTCTCAACGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTCATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGCTATATACTACTTTAATTTTGTGAGGGTGGGTGTGCGTGAATATTTATTTTAGGGGTTAAATATGTTTTTGGTCTCTATAAATATGTCAACTTTTCGTTTTAGTCCCTCGAAAAAATTTCTTCAACTTTTAGTCCATCAAAAAATTTTCATCTTCACTTTTGGTCCCTCCTTTAAAGTAAACTCATTTATAAAACTCATATTTTTGAATAAAATTTTGCAGAAAAATTCATAATATTATAAGAATCTCTTCAAAAAAAATTAAATTTTTTTAACAAAACATGAATTTAATATGAATTTTCATATTTTTGACGGTTAAAAATTCATATTTGATCTGTGTTTTGCTAAAAAAATTCTAATTTTTTTTGGTATTTTTTTACAATATTCTACACAATTCTGCACAATTTCATTATAAAAAAAAATACAAAAATTAACTTTAAAATAAGGACCAAAAGTAGTGATTGAAAATTTTATAGGGACTAAAAGTTGAAGGAAAATTTTAGAGGGACTAAAACGAAAAGTTGATATATTTATAGGGACCAAAAACATATTTAACCCTTATTTTAAACTGTTAATAAATTAGAGAATTTTTACTTAGATGAAAAAGATTCAGATTCTTGCAAGTCTGCAGTCTCTCCAAAGAGACGTTGTTTGAGGATTATCAATCAAAAGATGACACCGATGGAAAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCCTCAGAAGAGGCCTTATTGTTCAAAAATGTGAACAACTTTATACCTTCAAATGAAATTGGCCTTGGAGCAGTTCTTCTTAAACCAGCCGGTTCTTCTATGTAG
Protein sequence

>MS.gene47914.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNKSLNESSSTIDVSDSDNDEKDSDSCKSAVSPKRRCLRIINQKMTPMEKFQQELLDELKNHEIPDESSSEEALLFKNVNNFIPSNEIGLGAVLLKPAGSSM