AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97643

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97643.t1 MTR_1g053530 53.386 251 83 6 21 267 16 236 4.94e-72 223
MS.gene97643.t1 MTR_1g046810 31.884 276 130 10 30 262 30 290 4.07e-25 102
MS.gene97643.t1 MTR_1g052185 28.947 266 143 11 28 286 21 247 1.05e-15 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 62 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATCTGTCAATGCTCTAAA+TGG 0.239919 1.1:-39948787 MS.gene97643:CDS
CACCCTTCTTCGAACCATAT+TGG 0.319665 1.1:+39948746 None:intergenic
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.1:+39948238 None:intergenic
GTTCTCTTCATTATCATCAT+TGG 0.362989 1.1:+39948336 None:intergenic
ATGAAATCGCACAGCCAATA+TGG 0.368027 1.1:-39948760 MS.gene97643:CDS
AGCGGTAACAACTTTCTTCT+AGG 0.371413 1.1:-39948889 MS.gene97643:CDS
TCATCTTCACCAGTGTTGTT+TGG 0.374435 1.1:+39948277 None:intergenic
TGTTATTAATGTTGAATCTC+AGG 0.378670 1.1:-39948629 MS.gene97643:CDS
ATCATTGGAAGCAGATTGAT+TGG 0.381296 1.1:+39948351 None:intergenic
TTCTTTGTCACATACCTCAT+TGG 0.389428 1.1:+39948667 None:intergenic
AAATACTTTCTCAAATCAAT+TGG 0.400225 1.1:+39948694 None:intergenic
TGATTCCCAACAAGGTTGTT+AGG 0.405927 1.1:+39948571 None:intergenic
TCGTCTTCACCAGGGTTGTT+TGG 0.412657 1.1:+39948199 None:intergenic
TGCAGAAATGTGGGTGGGAA+TGG 0.425504 1.1:-39948523 MS.gene97643:CDS
CGATCACCTAACAACCTTGT+TGG 0.429642 1.1:-39948577 MS.gene97643:CDS
TCAGGTTGCTGAAGCAATGC+TGG 0.449143 1.1:-39948611 MS.gene97643:CDS
GATCACCTAACAACCTTGTT+GGG 0.460149 1.1:-39948576 MS.gene97643:CDS
TACCGCTATGGAATGCTTTG+TGG 0.470219 1.1:+39948905 None:intergenic
CAATTGGTGGAAATTGATCT+AGG 0.480999 1.1:+39948710 None:intergenic
TACTTTCTCAAATCAATTGG+TGG 0.486384 1.1:+39948697 None:intergenic
GCAGAAATGTGGGTGGGAAT+GGG 0.488317 1.1:-39948522 MS.gene97643:CDS
CAGCCAATATGGTTCGAAGA+AGG 0.491443 1.1:-39948749 MS.gene97643:CDS
TTTGCTTCATCATCTTCACC+AGG 0.497903 1.1:+39948229 None:intergenic
GAATGCTTTGTGGCCGCCGA+GGG 0.498041 1.1:+39948915 None:intergenic
GGAATCACCGTGTCACGAAA+AGG 0.512728 1.1:-39948555 MS.gene97643:CDS
GAAGAAAGTTGTTACCGCTA+TGG 0.516112 1.1:+39948893 None:intergenic
TTTGTCACATACCTCATTGG+TGG 0.519709 1.1:+39948670 None:intergenic
GATCAAACTTTGCAGAAATG+TGG 0.524856 1.1:-39948533 MS.gene97643:CDS
ATCAAACTTTGCAGAAATGT+GGG 0.554714 1.1:-39948532 MS.gene97643:CDS
TTCACCACTGGTAATGCCCT+CGG 0.560450 1.1:-39948931 MS.gene97643:CDS
TGAGGTATGTGACAAAGAAA+CGG 0.566626 1.1:-39948663 MS.gene97643:CDS
ATGTGACAAAGAAACGGAGC+TGG 0.572437 1.1:-39948657 MS.gene97643:CDS
GAAGATCAGAGAGCAAGGTA+TGG 0.572806 1.1:-39948494 MS.gene97643:CDS
AATCAATGAGAAGAACAAGT+TGG 0.575910 1.1:-39948425 MS.gene97643:CDS
AGCCAATATGGTTCGAAGAA+GGG 0.577089 1.1:-39948748 MS.gene97643:CDS
AGAAGAACAAGTTGGTGGTG+AGG 0.577583 1.1:-39948417 MS.gene97643:CDS
GGAATGCTTTGTGGCCGCCG+AGG 0.580120 1.1:+39948914 None:intergenic
AACTTTGCAGAAATGTGGGT+GGG 0.585412 1.1:-39948528 MS.gene97643:CDS
GCCGCCGAGGGCATTACCAG+TGG 0.590479 1.1:+39948927 None:intergenic
GCAACGAACACATGAATGGT+TGG 0.590907 1.1:+39948822 None:intergenic
CAATGAGAAGAACAAGTTGG+TGG 0.592690 1.1:-39948422 MS.gene97643:CDS
TGAAGATGATGAAGCAAATG+AGG 0.593094 1.1:-39948224 MS.gene97643:CDS
CGATTTGAATGAGCTGCCAG+TGG 0.597243 1.1:-39948122 MS.gene97643:intron
GATCAGAGAGCAAGGTATGG+TGG 0.597334 1.1:-39948491 MS.gene97643:CDS
AAGATGAAGATCAGAGAGCA+AGG 0.598147 1.1:-39948499 MS.gene97643:CDS
TGTGACAGAGAGTTCACCAC+TGG 0.602656 1.1:-39948943 MS.gene97643:CDS
TTGCTTCATCATCTTCACCA+GGG 0.604583 1.1:+39948230 None:intergenic
TGACACGGTGATTCCCAACA+AGG 0.616814 1.1:+39948563 None:intergenic
AAACTTTGCAGAAATGTGGG+TGG 0.628923 1.1:-39948529 MS.gene97643:CDS
GAAAGTATTTGCCACCAATG+AGG 0.638748 1.1:-39948681 MS.gene97643:CDS
ACCACTGGTAATGCCCTCGG+CGG 0.651139 1.1:-39948928 MS.gene97643:CDS
TGCTGCAACGAACACATGAA+TGG 0.655011 1.1:+39948818 None:intergenic
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.1:-39948263 MS.gene97643:CDS
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.1:-39948302 MS.gene97643:CDS
AATGAAGAGAACAACAACAC+TGG 0.663304 1.1:-39948325 MS.gene97643:CDS
GTGAGGTTAAAGATTCCGAA+TGG 0.667579 1.1:-39948400 MS.gene97643:CDS
GATGAGGAACCAAACAACAC+TGG 0.670709 1.1:-39948286 MS.gene97643:CDS
CAATATGGTTCGAAGAAGGG+TGG 0.676709 1.1:-39948745 MS.gene97643:CDS
AATGAGGAACCAAACAACCC+TGG 0.683544 1.1:-39948208 MS.gene97643:intron
GATGAGGAACCAAACAACCC+TGG 0.684317 1.1:-39948247 MS.gene97643:CDS
GAAAATAAGAAACATCAACA+AGG 0.713766 1.1:-39948991 MS.gene97643:CDS
GGCCACAAAGCATTCCATAG+CGG 0.763914 1.1:-39948907 MS.gene97643:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTTCTCAAATCAAT+TGG + chr1.1:39948505-39948524 None:intergenic 20.0%
!! CTATTCATCATAAACAAAAA+AGG - chr1.1:39948167-39948186 MS.gene97643:intron 20.0%
! AACAAAGAAAAACATGTTGA+TGG - chr1.1:39948337-39948356 MS.gene97643:CDS 25.0%
! GAAAATAAGAAACATCAACA+AGG - chr1.1:39948205-39948224 MS.gene97643:intron 25.0%
! TGTTATTAATGTTGAATCTC+AGG - chr1.1:39948567-39948586 MS.gene97643:CDS 25.0%
AATCAATGAGAAGAACAAGT+TGG - chr1.1:39948771-39948790 MS.gene97643:CDS 30.0%
ATCAAACTTTGCAGAAATGT+GGG - chr1.1:39948664-39948683 MS.gene97643:CDS 30.0%
GTTCTCTTCATTATCATCAT+TGG + chr1.1:39948863-39948882 None:intergenic 30.0%
TACTTTCTCAAATCAATTGG+TGG + chr1.1:39948502-39948521 None:intergenic 30.0%
! CTTGTGATTTTTGAATGACA+AGG + chr1.1:39948822-39948841 None:intergenic 30.0%
AATGAAGAGAACAACAACAC+TGG - chr1.1:39948871-39948890 MS.gene97643:CDS 35.0%
ATCATTGGAAGCAGATTGAT+TGG + chr1.1:39948848-39948867 None:intergenic 35.0%
CAATTGGTGGAAATTGATCT+AGG + chr1.1:39948489-39948508 None:intergenic 35.0%
GATCAAACTTTGCAGAAATG+TGG - chr1.1:39948663-39948682 MS.gene97643:CDS 35.0%
TGAAGATGATGAAGCAAATG+AGG - chr1.1:39948972-39948991 MS.gene97643:CDS 35.0%
TGAGGTATGTGACAAAGAAA+CGG - chr1.1:39948533-39948552 MS.gene97643:CDS 35.0%
TTCTTTGTCACATACCTCAT+TGG + chr1.1:39948532-39948551 None:intergenic 35.0%
TTTAACCCCAATTCATGAGT+TGG + chr1.1:39949039-39949058 None:intergenic 35.0%
! TCATCTGTCAATGCTCTAAA+TGG - chr1.1:39948409-39948428 MS.gene97643:CDS 35.0%
! TTTTGAATGACAAGGCCATT+CGG + chr1.1:39948814-39948833 None:intergenic 35.0%
AAACTTTGCAGAAATGTGGG+TGG - chr1.1:39948667-39948686 MS.gene97643:CDS 40.0%
AACTTTGCAGAAATGTGGGT+GGG - chr1.1:39948668-39948687 MS.gene97643:CDS 40.0%
AAGATGAAGATCAGAGAGCA+AGG - chr1.1:39948697-39948716 MS.gene97643:CDS 40.0%
AGCCAATATGGTTCGAAGAA+GGG - chr1.1:39948448-39948467 MS.gene97643:CDS 40.0%
AGCGGTAACAACTTTCTTCT+AGG - chr1.1:39948307-39948326 MS.gene97643:CDS 40.0%
AGGAACCAACTCATGAATTG+GGG - chr1.1:39949031-39949050 MS.gene97643:CDS 40.0%
ATGAAATCGCACAGCCAATA+TGG - chr1.1:39948436-39948455 MS.gene97643:CDS 40.0%
GAAGAAAGTTGTTACCGCTA+TGG + chr1.1:39948306-39948325 None:intergenic 40.0%
GAGGAACCAACTCATGAATT+GGG - chr1.1:39949030-39949049 MS.gene97643:CDS 40.0%
GATCACCTAACAACCTTGTT+GGG - chr1.1:39948620-39948639 MS.gene97643:CDS 40.0%
GTGAGGTTAAAGATTCCGAA+TGG - chr1.1:39948796-39948815 MS.gene97643:CDS 40.0%
TGAAGACGATGAAGCAAATG+AGG - chr1.1:39949011-39949030 MS.gene97643:CDS 40.0%
TGAAGATGATGAAGCAGATG+AGG - chr1.1:39948894-39948913 MS.gene97643:CDS 40.0%
TGAGGAACCAACTCATGAAT+TGG - chr1.1:39949029-39949048 MS.gene97643:CDS 40.0%
TGATTCCCAACAAGGTTGTT+AGG + chr1.1:39948628-39948647 None:intergenic 40.0%
TTGCTTCATCATCTTCACCA+GGG + chr1.1:39948969-39948988 None:intergenic 40.0%
TTTGCTTCATCATCTTCACC+AGG + chr1.1:39948970-39948989 None:intergenic 40.0%
TTTGTCACATACCTCATTGG+TGG + chr1.1:39948529-39948548 None:intergenic 40.0%
! CAATGAGAAGAACAAGTTGG+TGG - chr1.1:39948774-39948793 MS.gene97643:CDS 40.0%
! GTTTGATCCTTTTCGTGACA+CGG + chr1.1:39948651-39948670 None:intergenic 40.0%
! TCATCTTCACCAGTGTTGTT+TGG + chr1.1:39948883-39948902 None:intergenic 40.0%
!! GAAAGTATTTGCCACCAATG+AGG - chr1.1:39948515-39948534 MS.gene97643:CDS 40.0%
AATGAGGAACCAAACAACCC+TGG - chr1.1:39948988-39949007 MS.gene97643:CDS 45.0%
ATGTGACAAAGAAACGGAGC+TGG - chr1.1:39948539-39948558 MS.gene97643:CDS 45.0%
CAATATGGTTCGAAGAAGGG+TGG - chr1.1:39948451-39948470 MS.gene97643:CDS 45.0%
CACCCTTCTTCGAACCATAT+TGG + chr1.1:39948453-39948472 None:intergenic 45.0%
CAGCCAATATGGTTCGAAGA+AGG - chr1.1:39948447-39948466 MS.gene97643:CDS 45.0%
CGATCACCTAACAACCTTGT+TGG - chr1.1:39948619-39948638 MS.gene97643:CDS 45.0%
GAAGATCAGAGAGCAAGGTA+TGG - chr1.1:39948702-39948721 MS.gene97643:CDS 45.0%
GATGAGGAACCAAACAACAC+TGG - chr1.1:39948910-39948929 MS.gene97643:CDS 45.0%
GCAACGAACACATGAATGGT+TGG + chr1.1:39948377-39948396 None:intergenic 45.0%
TACCGCTATGGAATGCTTTG+TGG + chr1.1:39948294-39948313 None:intergenic 45.0%
TCATCTTCACCAGGGTTGTT+TGG + chr1.1:39948961-39948980 None:intergenic 45.0%
TGCTGCAACGAACACATGAA+TGG + chr1.1:39948381-39948400 None:intergenic 45.0%
TTGCTTCATCGTCTTCACCA+GGG + chr1.1:39949008-39949027 None:intergenic 45.0%
TTTGCTTCATCGTCTTCACC+AGG + chr1.1:39949009-39949028 None:intergenic 45.0%
!! AGAAGAACAAGTTGGTGGTG+AGG - chr1.1:39948779-39948798 MS.gene97643:CDS 45.0%
CGATTTGAATGAGCTGCCAG+TGG - chr1.1:39949074-39949093 MS.gene97643:CDS 50.0%
GATCAGAGAGCAAGGTATGG+TGG - chr1.1:39948705-39948724 MS.gene97643:CDS 50.0%
GATGAGGAACCAAACAACCC+TGG - chr1.1:39948949-39948968 MS.gene97643:CDS 50.0%
GCAGAAATGTGGGTGGGAAT+GGG - chr1.1:39948674-39948693 MS.gene97643:CDS 50.0%
GGAATCACCGTGTCACGAAA+AGG - chr1.1:39948641-39948660 MS.gene97643:CDS 50.0%
TCGTCTTCACCAGGGTTGTT+TGG + chr1.1:39949000-39949019 None:intergenic 50.0%
TGACACGGTGATTCCCAACA+AGG + chr1.1:39948636-39948655 None:intergenic 50.0%
TGCAGAAATGTGGGTGGGAA+TGG - chr1.1:39948673-39948692 MS.gene97643:CDS 50.0%
TGTGACAGAGAGTTCACCAC+TGG - chr1.1:39948253-39948272 MS.gene97643:CDS 50.0%
! GGCCACAAAGCATTCCATAG+CGG - chr1.1:39948289-39948308 MS.gene97643:CDS 50.0%
! TCAGGTTGCTGAAGCAATGC+TGG - chr1.1:39948585-39948604 MS.gene97643:CDS 50.0%
! TTCACCACTGGTAATGCCCT+CGG - chr1.1:39948265-39948284 MS.gene97643:CDS 50.0%
GAATGCTTTGTGGCCGCCGA+GGG + chr1.1:39948284-39948303 None:intergenic 60.0%
! ACCACTGGTAATGCCCTCGG+CGG - chr1.1:39948268-39948287 MS.gene97643:CDS 60.0%
GGAATGCTTTGTGGCCGCCG+AGG + chr1.1:39948285-39948304 None:intergenic 65.0%
!! GCCGCCGAGGGCATTACCAG+TGG + chr1.1:39948272-39948291 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 39948118 39949100 39948118 ID=MS.gene97643
chr1.1 mRNA 39948118 39949100 39948118 ID=MS.gene97643.t1;Parent=MS.gene97643
chr1.1 exon 39948209 39949100 39948209 ID=MS.gene97643.t1.exon1;Parent=MS.gene97643.t1
chr1.1 CDS 39948209 39949100 39948209 ID=cds.MS.gene97643.t1;Parent=MS.gene97643.t1
chr1.1 exon 39948118 39948131 39948118 ID=MS.gene97643.t1.exon2;Parent=MS.gene97643.t1
chr1.1 CDS 39948118 39948131 39948118 ID=cds.MS.gene97643.t1;Parent=MS.gene97643.t1
Gene Sequence

>MS.gene97643

ATGAAACATTTTTTTTCTTCAGCTTCTTCTTCATCTCACTCTCATCATTCTATTCATCATAAACAAAAAAGGAGTGTTGTTTATCATGAAAATAAGAAACATCAACAAGGTGCAAAACTTCACAAATGTGATTTGTGTGACAGAGAGTTCACCACTGGTAATGCCCTCGGCGGCCACAAAGCATTCCATAGCGGTAACAACTTTCTTCTAGGCAAAATCAACAAAGAAAAACATGTTGATGGTATTAAGATCGAAACCAACCATTCATGTGTTCGTTGCAGCAAGACTTTTTCATCTGTCAATGCTCTAAATGGACACATGAAATCGCACAGCCAATATGGTTCGAAGAAGGGTGGTAAAATTTATGACCTAGATCAATTTCCACCAATTGATTTGAGAAAGTATTTGCCACCAATGAGGTATGTGACAAAGAAACGGAGCTGGAATTATGTTATTAATGTTGAATCTCAGGTTGCTGAAGCAATGCTGGATATGTCACAGCGATCACCTAACAACCTTGTTGGGAATCACCGTGTCACGAAAAGGATCAAACTTTGCAGAAATGTGGGTGGGAATGGGAAGATGAAGATCAGAGAGCAAGGTATGGTGGTAAAACATTGTGTTGATGAAACAATTGTGAGAGAGACTGATCGAATCAATGAGAAGAACAAGTTGGTGGTGAGGTTAAAGATTCCGAATGGCCTTGTCATTCAAAAATCACAAGCTTCCAATCAATCTGCTTCCAATGATGATAATGAAGAGAACAACAACACTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACACTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAAATGAGGAACCAAACAACCCTGGTGAAGACGATGAAGCAAATGAGGAACCAACTCATGAATTGGGGTTAAATGTTGTTCGAGATTTCGATTTGAATGAGCTGCCAGTGGATGA
Protein sequence

>MS.gene97643.t1

MKHFFSSASSSSHSHHSIHHKQKRSVVYHENKKHQQGAKLHKCDLCDREFTTGNALGGHKAFHSGNNFLLGKINKEKHVDGIKIETNHSCVRCSKTFSSVNALNGHMKSHSQYGSKKGGKIYDLDQFPPIDLRKYLPPMRYVTKKRSWNYVINVESQVAEAMLDMSQRSPNNLVGNHRVTKRIKLCRNVGGNGKMKIREQGMVVKHCVDETIVRETDRINEKNKLVVRLKIPNGLVIQKSQASNQSASNDDNEENNNTGEDDEADEEPNNTGEDDEADEEPNNPGEDDEANEEPNNPAASG