AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98409

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98409.t1 MTR_2g045670 91.045 201 18 0 1 201 81 281 5.48e-128 362
MS.gene98409.t1 MTR_2g045700 81.592 201 37 0 1 201 71 271 1.46e-110 317
MS.gene98409.t1 MTR_1g034500 77.670 206 39 4 1 201 104 307 1.66e-101 295
MS.gene98409.t1 MTR_2g045630 72.897 214 41 2 1 201 69 278 3.01e-100 291
MS.gene98409.t1 MTR_8g077950 44.318 88 49 0 108 195 250 337 6.81e-18 80.5
MS.gene98409.t1 MTR_8g077950 44.318 88 49 0 108 195 252 339 7.73e-18 80.5
MS.gene98409.t1 MTR_8g077950 44.318 88 49 0 108 195 192 279 7.85e-18 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98409.t1 AT4G36730 37.383 107 57 2 91 195 201 299 3.05e-14 70.1
MS.gene98409.t1 AT4G36730 37.383 107 57 2 91 195 203 301 3.55e-14 70.1
MS.gene98409.t1 AT2G35530 39.437 71 43 0 113 183 302 372 9.23e-11 60.5

Find 32 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTGGACTGGCACAGAATT+TGG 0.131374 2.4:+45031336 MS.gene98409:CDS
GCAAATAATTTGTTGAAATC+AGG 0.241071 2.4:-45030790 None:intergenic
CGGAAATCTAACATGATTAC+TGG 0.322511 2.4:+45031191 MS.gene98409:CDS
TCTGGACTGGCACAGAATTT+GGG 0.326766 2.4:+45031337 MS.gene98409:CDS
GATTTCAACAAATTATTTGC+TGG 0.331658 2.4:+45030793 MS.gene98409:CDS
ACTGGCGAATCAAGAGAATA+TGG 0.350738 2.4:+45030844 MS.gene98409:CDS
CACTCTTAAGGATGAAAATT+CGG 0.352734 2.4:+45032262 MS.gene98409:CDS
GCTCAGTGAGCATTTGTGTT+AGG 0.359601 2.4:-45032286 None:intergenic
AAAGTTTCAAGTAGGCTTCA+TGG 0.384295 2.4:-45032634 None:intergenic
TGGAACAGGAAGAGCTAGTT+AGG 0.389858 2.4:+45032577 MS.gene98409:intron
TCAAAAGATAAACACTCTTA+AGG 0.422261 2.4:+45032250 MS.gene98409:CDS
AATAGATCTGCAATTGATTC+TGG 0.425545 2.4:-45032609 None:intergenic
AAGATCAAAGATAAAGAAAC+AGG 0.437513 2.4:+45032013 MS.gene98409:CDS
CCAGTCATTAAACTTACATC+AGG 0.439376 2.4:-45030826 None:intergenic
CAAATAATTTGTTGAAATCA+GGG 0.443190 2.4:-45030789 None:intergenic
TTTGTTGCAGAAAATCCATC+TGG 0.471248 2.4:+45031319 MS.gene98409:intron
GAAGAGCTAGTTAGGATGTA+TGG 0.483100 2.4:+45032585 MS.gene98409:CDS
AAGTTTCAAGTAGGCTTCAT+GGG 0.491094 2.4:-45032633 None:intergenic
AAATTCTGTGCCAGTCCAGA+TGG 0.539538 2.4:-45031334 None:intergenic
GGAAATCTAACATGATTACT+GGG 0.546159 2.4:+45031192 MS.gene98409:CDS
CAATGAAAACGATTCTATTG+AGG 0.546332 2.4:+45032334 MS.gene98409:CDS
TCTAACATGATTACTGGGGA+TGG 0.558549 2.4:+45031197 MS.gene98409:CDS
CCTGATGTAAGTTTAATGAC+TGG 0.574077 2.4:+45030826 MS.gene98409:CDS
TGCAGAAAATCCATCTGGAC+TGG 0.574891 2.4:+45031324 MS.gene98409:intron
TACATCTGCAGTGCAGCAAG+TGG 0.589547 2.4:+45030990 MS.gene98409:intron
CTGGACTGGCACAGAATTTG+GGG 0.608435 2.4:+45031338 MS.gene98409:CDS
GAATTTGGGGACAGTCGTCA+AGG 0.619324 2.4:+45031351 MS.gene98409:CDS
GAACAATCTATACCTCATTG+AGG 0.632955 2.4:-45030905 None:intergenic
GGAAGCAAGAGATTGACAGA+TGG 0.638909 2.4:+45031011 MS.gene98409:CDS
GAAATCTAACATGATTACTG+GGG 0.696860 2.4:+45031193 MS.gene98409:CDS
ATTCTCACTTAAGCACGAAG+CGG 0.709549 2.4:+45031171 MS.gene98409:CDS
ATAGGGATGGAACCTCAATG+AGG 0.736670 2.4:+45030893 MS.gene98409:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTACTATTAATTACAAAAA+AGG + chr2.4:45032448-45032467 MS.gene98409:intron 10.0%
!!! TTAGTTTTTATATAAATATG+TGG + chr2.4:45031069-45031088 MS.gene98409:intron 10.0%
!! ATAAAATTGAACAAATAAGA+AGG - chr2.4:45032377-45032396 None:intergenic 15.0%
!! TAAAATTGAACAAATAAGAA+GGG - chr2.4:45032376-45032395 None:intergenic 15.0%
!! TGTTAAAAAGAAAAAGATAT+TGG + chr2.4:45032053-45032072 MS.gene98409:intron 15.0%
!! AAAATTGAACAAATAAGAAG+GGG - chr2.4:45032375-45032394 None:intergenic 20.0%
!! AGTAGAAAAGAAAAACAATT+TGG - chr2.4:45032091-45032110 None:intergenic 20.0%
!! ATAAATACTAGAAAACAAGA+TGG - chr2.4:45032474-45032493 None:intergenic 20.0%
!! CTACTAATTTAAGTATGATT+TGG + chr2.4:45032551-45032570 MS.gene98409:intron 20.0%
!! GAATATGATTATAACTATAG+TGG - chr2.4:45031706-45031725 None:intergenic 20.0%
!! GTAGAAAAGAAAAACAATTT+GGG - chr2.4:45032090-45032109 None:intergenic 20.0%
!! TTTGTTCAAAAATTCTACTA+CGG - chr2.4:45031593-45031612 None:intergenic 20.0%
!!! CAAATAATTTGTTGAAATCA+GGG - chr2.4:45030792-45030811 None:intergenic 20.0%
!!! TGGTAACATTTTAACATAAA+AGG - chr2.4:45031841-45031860 None:intergenic 20.0%
! AAAAATTCTACTACGGTATA+GGG - chr2.4:45031586-45031605 None:intergenic 25.0%
! AAGAAAGTTGGATTGATAAA+TGG - chr2.4:45031864-45031883 None:intergenic 25.0%
! AAGATCAAAGATAAAGAAAC+AGG + chr2.4:45032013-45032032 MS.gene98409:CDS 25.0%
! ACTTAAATTAGTAGCAATCT+TGG - chr2.4:45032545-45032564 None:intergenic 25.0%
! ATGTGGACATCATAATAAAA+GGG - chr2.4:45031526-45031545 None:intergenic 25.0%
! CAAAAGAAATGCAACTAAAT+AGG - chr2.4:45031933-45031952 None:intergenic 25.0%
! CAGTAACAAAGTATGTTTAT+CGG + chr2.4:45031046-45031065 MS.gene98409:intron 25.0%
! GATTTCAACAAATTATTTGC+TGG + chr2.4:45030793-45030812 MS.gene98409:CDS 25.0%
! GCAATCTTGGATAATATTAA+AGG - chr2.4:45032532-45032551 None:intergenic 25.0%
! TATGTGGACATCATAATAAA+AGG - chr2.4:45031527-45031546 None:intergenic 25.0%
! TCAAAAGATAAACACTCTTA+AGG + chr2.4:45032250-45032269 MS.gene98409:CDS 25.0%
! TGATGCTCAACTAAAAAATA+TGG + chr2.4:45031396-45031415 MS.gene98409:CDS 25.0%
! TTCTTCACCAAAAAATGATA+GGG + chr2.4:45030876-45030895 MS.gene98409:CDS 25.0%
!! CAACTGTCACATAAAATTTT+CGG + chr2.4:45031114-45031133 MS.gene98409:intron 25.0%
!! CTAATTTAAGTATGATTTGG+TGG + chr2.4:45032554-45032573 MS.gene98409:intron 25.0%
!! TCTTCAATTTCTTTCTGAAA+AGG - chr2.4:45032224-45032243 None:intergenic 25.0%
!! TTTTCGTAGCATAAATGAAA+CGG + chr2.4:45031438-45031457 MS.gene98409:intron 25.0%
!!! GCAAATAATTTGTTGAAATC+AGG - chr2.4:45030793-45030812 None:intergenic 25.0%
AAAGTTGGATTGATAAATGG+TGG - chr2.4:45031861-45031880 None:intergenic 30.0%
ATAAAAGGCTCATATATGAC+AGG - chr2.4:45031826-45031845 None:intergenic 30.0%
CAAAAATTCTACTACGGTAT+AGG - chr2.4:45031587-45031606 None:intergenic 30.0%
CAATGAAAACGATTCTATTG+AGG + chr2.4:45032334-45032353 MS.gene98409:CDS 30.0%
CACTCTTAAGGATGAAAATT+CGG + chr2.4:45032262-45032281 MS.gene98409:CDS 30.0%
CTTAGCAACATTAAGAAAGT+TGG - chr2.4:45031876-45031895 None:intergenic 30.0%
CTTCTTCACCAAAAAATGAT+AGG + chr2.4:45030875-45030894 MS.gene98409:CDS 30.0%
GAAATCTAACATGATTACTG+GGG + chr2.4:45031193-45031212 MS.gene98409:CDS 30.0%
GAAATGCAACTAAATAGGTT+AGG - chr2.4:45031928-45031947 None:intergenic 30.0%
GGAAATCTAACATGATTACT+GGG + chr2.4:45031192-45031211 MS.gene98409:CDS 30.0%
! AATAGATCTGCAATTGATTC+TGG - chr2.4:45032612-45032631 None:intergenic 30.0%
! ACAAGTTGAAAAACTAACAC+AGG - chr2.4:45031728-45031747 None:intergenic 30.0%
! AGAATAACAGTCTTGCATTT+TGG + chr2.4:45031296-45031315 MS.gene98409:intron 30.0%
! CTCAATAGAATCGTTTTCAT+TGG - chr2.4:45032336-45032355 None:intergenic 30.0%
! TTAGTTGCATTTCTTTTGAC+AGG + chr2.4:45031935-45031954 MS.gene98409:intron 30.0%
!! ATTTAAGTATGATTTGGTGG+TGG + chr2.4:45032557-45032576 MS.gene98409:intron 30.0%
AAAGAAAAAGACTGTCGAAC+AGG + chr2.4:45031979-45031998 MS.gene98409:CDS 35.0%
AATTAAATCCTTTCTGTCGC+AGG + chr2.4:45031148-45031167 MS.gene98409:intron 35.0%
ATGATGTCCACATATGTGAT+AGG + chr2.4:45031533-45031552 MS.gene98409:intron 35.0%
CCAGTCATTAAACTTACATC+AGG - chr2.4:45030829-45030848 None:intergenic 35.0%
CCTGATGTAAGTTTAATGAC+TGG + chr2.4:45030826-45030845 MS.gene98409:CDS 35.0%
CGGAAATCTAACATGATTAC+TGG + chr2.4:45031191-45031210 MS.gene98409:CDS 35.0%
GAACAATCTATACCTCATTG+AGG - chr2.4:45030908-45030927 None:intergenic 35.0%
TAGGCAGTGTAGTTAAATAG+AGG + chr2.4:45031552-45031571 MS.gene98409:intron 35.0%
TCACCAAAAAATGATAGGGA+TGG + chr2.4:45030880-45030899 MS.gene98409:CDS 35.0%
TGTTCTTGTTCTTGTTCTTC+TGG + chr2.4:45030923-45030942 MS.gene98409:intron 35.0%
TTTGTTGCAGAAAATCCATC+TGG + chr2.4:45031319-45031338 MS.gene98409:intron 35.0%
!! CAAGATATGCTTAGCTTTGT+TGG + chr2.4:45031680-45031699 MS.gene98409:intron 35.0%
!!! CATTTTTTGGTGAAGAAGAC+TGG - chr2.4:45030873-45030892 None:intergenic 35.0%
!!! GTTCCATCCCTATCATTTTT+TGG - chr2.4:45030886-45030905 None:intergenic 35.0%
ACTGGCGAATCAAGAGAATA+TGG + chr2.4:45030844-45030863 MS.gene98409:CDS 40.0%
ATTCTCACTTAAGCACGAAG+CGG + chr2.4:45031171-45031190 MS.gene98409:CDS 40.0%
GAAGAGCTAGTTAGGATGTA+TGG + chr2.4:45032585-45032604 MS.gene98409:CDS 40.0%
TACACTGCCTATCACATATG+TGG - chr2.4:45031543-45031562 None:intergenic 40.0%
TACTGGGGATGGTAAGATTA+TGG + chr2.4:45031208-45031227 MS.gene98409:intron 40.0%
TCTAACATGATTACTGGGGA+TGG + chr2.4:45031197-45031216 MS.gene98409:CDS 40.0%
AAATTCTGTGCCAGTCCAGA+TGG - chr2.4:45031337-45031356 None:intergenic 45.0%
ATAGGGATGGAACCTCAATG+AGG + chr2.4:45030893-45030912 MS.gene98409:CDS 45.0%
GCTCAGTGAGCATTTGTGTT+AGG - chr2.4:45032289-45032308 None:intergenic 45.0%
GGAAGCAAGAGATTGACAGA+TGG + chr2.4:45031011-45031030 MS.gene98409:CDS 45.0%
TGCAGAAAATCCATCTGGAC+TGG + chr2.4:45031324-45031343 MS.gene98409:intron 45.0%
TGGAACAGGAAGAGCTAGTT+AGG + chr2.4:45032577-45032596 MS.gene98409:intron 45.0%
!! ATCTGGACTGGCACAGAATT+TGG + chr2.4:45031336-45031355 MS.gene98409:CDS 45.0%
!! GTATGATTTGGTGGTGGAAC+AGG + chr2.4:45032563-45032582 MS.gene98409:intron 45.0%
!! TCTGGACTGGCACAGAATTT+GGG + chr2.4:45031337-45031356 MS.gene98409:CDS 45.0%
GAATTTGGGGACAGTCGTCA+AGG + chr2.4:45031351-45031370 MS.gene98409:CDS 50.0%
GTGAGAATCCTGCGACAGAA+AGG - chr2.4:45031159-45031178 None:intergenic 50.0%
TACATCTGCAGTGCAGCAAG+TGG + chr2.4:45030990-45031009 MS.gene98409:intron 50.0%
TTGCTACAGCGCAGCTATTG+CGG - chr2.4:45031640-45031659 None:intergenic 50.0%
!! CTGGACTGGCACAGAATTTG+GGG + chr2.4:45031338-45031357 MS.gene98409:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 45030772 45032650 45030772 ID=MS.gene98409
chr2.4 mRNA 45030772 45032650 45030772 ID=MS.gene98409.t1;Parent=MS.gene98409
chr2.4 exon 45030772 45030914 45030772 ID=MS.gene98409.t1.exon1;Parent=MS.gene98409.t1
chr2.4 CDS 45030772 45030914 45030772 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45031001 45031055 45031001 ID=MS.gene98409.t1.exon2;Parent=MS.gene98409.t1
chr2.4 CDS 45031001 45031055 45031001 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45031170 45031218 45031170 ID=MS.gene98409.t1.exon3;Parent=MS.gene98409.t1
chr2.4 CDS 45031170 45031218 45031170 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45031329 45031417 45031329 ID=MS.gene98409.t1.exon4;Parent=MS.gene98409.t1
chr2.4 CDS 45031329 45031417 45031329 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45031957 45032034 45031957 ID=MS.gene98409.t1.exon5;Parent=MS.gene98409.t1
chr2.4 CDS 45031957 45032034 45031957 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45032230 45032355 45032230 ID=MS.gene98409.t1.exon6;Parent=MS.gene98409.t1
chr2.4 CDS 45032230 45032355 45032230 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
chr2.4 exon 45032585 45032650 45032585 ID=MS.gene98409.t1.exon7;Parent=MS.gene98409.t1
chr2.4 CDS 45032585 45032650 45032585 ID=cds.MS.gene98409.t1;Parent=MS.gene98409.t1
Gene Sequence

>MS.gene98409

ATGGTACACAGAAGAAACCCTGATTTCAACAAATTATTTGCTGGAAACTCAAAGCCTGATGTAAGTTTAATGACTGGCGAATCAAGAGAATATGGAAACCAGTCTTCTTCACCAAAAAATGATAGGGATGGAACCTCAATGAGGTATAGATTGTTCTTGTTCTTGTTCTTCTGGTAAACTTTTTAATAGCATTTTCGCAAAGACTGAACAAAAAACTTTACATCTGCAGTGCAGCAAGTGGAAGCAAGAGATTGACAGATGGTGATCAAGATGACAGTAACAAAGTATGTTTATCGGTTAGTTTTTATATAAATATGTGGTTGATGAATGTAATGTGTTCTTCAACTGTCACATAAAATTTTCGGCAAAAAAGTCTAATTAAATCCTTTCTGTCGCAGGATTCTCACTTAAGCACGAAGCGGAAATCTAACATGATTACTGGGGATGGTAAGATTATGGATTTTTCTTTTGACTATCTTATAATAAAATGTCATGTTTTATTATGATTTATCATTTGAATGTTAAGAATAACAGTCTTGCATTTTGGTTTGTTGCAGAAAATCCATCTGGACTGGCACAGAATTTGGGGACAGTCGTCAAGGAATCTGACACTGACGTTGATGTTGATGCTCAACTAAAAAATATGGTATTATAAAGCTTTATGTGTTTTCGTAGCATAAATGAAACGGTTTTTTTTAGATTAGCTAAATTAGAAGAACAATCAGTCTTTTATTAAGATAACTTGTAAAATCCCTTTTATTATGATGTCCACATATGTGATAGGCAGTGTAGTTAAATAGAGGCGCTGTAGCCCTATACCGTAGTAGAATTTTTGAACAAATCGCTATTGTTTGTGATATGCTAGCCGCAATAGCTGCGCTGTAGCAATGATGCGTAGCACTTATTGACAAGATATGCTTAGCTTTGTTGGCCACTATAGTTATAATCATATTCCTGTGTTAGTTTTTCAACTTGTAAGAACATAAATTTTCAACTTGTCTAAATTATTTCTTTTGTTTTAGTTTGCATAATTTTCTTTCTACGCTTCATTCCTGTCATATATGAGCCTTTTATGTTAAAATGTTACCACCATTTATCAATCCAACTTTCTTAATGTTGCTAAGTTTAGTTGCATTTCTTGCATAATGTCTAGCCTAACCTATTTAGTTGCATTTCTTTTGACAGGAAGATGATGAAAGAAGAAAAGAAAGAAAAAGACTGTCGAACAGGAAATCAGCTAAAAGATCAAAGATAAAGAAACAGGTACATACGAAAATGCTTTGTTAAAAAGAAAAAGATATTGGTTTTCTTCTGTCCCAAATTGTTTTTCTTTTCTACTCTGATTTTTTAAATTATTAAATGTTAAGATGATCTGATTATCTAATTTTTGATGTGTTTGTTTGATGATCTATTTAACTTGTATTTCATTTGATGTTATCATTATTTGTGCCTTTTCAGAAAGAAATTGAAGAGCAATGTCAAAAGATAAACACTCTTAAGGATGAAAATTCGGTCCTAACACAAATGCTCACTGAGCTTTCAGAGAAATGTCTCGAGCTCACCAATGAAAACGATTCTATTGAGGTCAATCATTTTAACTCCCCTTCTTATTTGTTCAATTTTATATCATTCATTAAACTAAGATACTTGTTTGATTTGAGAAACTAGTTTCTGTTTTTACTATTAATTACAAAAAAGGCCATCTTGTTTTCTAGTATTTATATGAAAAACAGTTAAATAAACTAAGATACTTATATCCTTTAATATTATCCAAGATTGCTACTAATTTAAGTATGATTTGGTGGTGGAACAGGAAGAGCTAGTTAGGATGTATGGACCAGAATCAATTGCAGATCTATTGCCCATGAAGCCTACTTGA
Protein sequence

>MS.gene98409.t1

MVHRRNPDFNKLFAGNSKPDVSLMTGESREYGNQSSSPKNDRDGTSMSAASGSKRLTDGDQDDSNKDSHLSTKRKSNMITGDENPSGLAQNLGTVVKESDTDVDVDAQLKNMEDDERRKERKRLSNRKSAKRSKIKKQKEIEEQCQKINTLKDENSVLTQMLTELSEKCLELTNENDSIEEELVRMYGPESIADLLPMKPT