AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene018784

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018784.t1 MTR_1g053530 54.251 247 82 9 20 261 16 236 1.39e-67 212
MS.gene018784.t1 MTR_1g046810 31.498 327 135 12 29 314 37 315 5.04e-29 113
MS.gene018784.t1 MTR_1g052185 30.818 318 163 15 5 312 8 278 1.03e-21 93.2
MS.gene018784.t1 MTR_4g073310 28.053 303 125 9 13 313 16 227 1.34e-12 66.6
MS.gene018784.t1 MTR_5g098470 38.095 126 64 5 7 121 35 157 4.91e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 53 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAATTCCAGCTCCGTTTCT+TGG 0.269877 1.2:+39492161 None:intergenic
AAAGAAAGTTGTTGCCTCTA+TGG 0.288255 1.2:+39492409 None:intergenic
TCATCTTCACCAGGGTTGTT+TGG 0.341135 1.2:+39491748 None:intergenic
TGAGGAACCAACTCATGAAT+TGG 0.350528 1.2:-39491716 MS.gene018784:CDS
ACTCTCATCACAAACCAAAA+AGG 0.357704 1.2:-39492524 MS.gene018784:CDS
GTTCTCTTCATTATCATCAT+TGG 0.362989 1.2:+39491846 None:intergenic
TCTTCGAAGTCGAACCATAT+TGG 0.367921 1.2:+39492262 None:intergenic
ATGAAATCGCACAGCCAATA+TGG 0.368027 1.2:-39492276 MS.gene018784:CDS
TCATCTTCACCAGTGTTGTT+TGG 0.374435 1.2:+39491787 None:intergenic
ATCATTGGAAGCAGATTGAT+TGG 0.381296 1.2:+39491861 None:intergenic
GAGGAACCAACTCATGAATT+GGG 0.382420 1.2:-39491715 MS.gene018784:CDS
AAATACTTTCTCAAATCAAT+TGG 0.400225 1.2:+39492204 None:intergenic
TGATTCACATCATGGTTGTT+AGG 0.402276 1.2:+39492081 None:intergenic
TGCCTCTATGGAATGCTTTG+TGG 0.438332 1.2:+39492421 None:intergenic
TCATGTTGCTGAAGCAATGC+TGG 0.444801 1.2:-39492121 MS.gene018784:CDS
TTCTTGGTCACATAACTCAT+TGG 0.463818 1.2:+39492177 None:intergenic
TGTGACAGAGAATTCTCAAC+TGG 0.474765 1.2:-39492459 MS.gene018784:CDS
CAATTGGTGGAAATTGATCT+AGG 0.480999 1.2:+39492220 None:intergenic
TACTTTCTCAAATCAATTGG+TGG 0.486384 1.2:+39492207 None:intergenic
TTTGCTTCATCATCTTCACC+AGG 0.497903 1.2:+39491739 None:intergenic
GATCAAACTTTGCAGAAATG+TGG 0.502317 1.2:-39492043 MS.gene018784:CDS
TTTAACCCCAATTCATGAGT+TGG 0.505846 1.2:+39491709 None:intergenic
TGAATCACCGTGTCACGAAA+AGG 0.510288 1.2:-39492065 MS.gene018784:CDS
TTCTCAACTGGTAATGCTCT+CGG 0.517217 1.2:-39492447 MS.gene018784:CDS
TGAAGATGATGAAGCAGATA+AGG 0.520831 1.2:-39491812 MS.gene018784:CDS
TTGGTCACATAACTCATTGG+TGG 0.531076 1.2:+39492180 None:intergenic
GATCAGAGAGCAAGGTATTG+TGG 0.542266 1.2:-39492001 MS.gene018784:CDS
TGACACGGTGATTCACATCA+TGG 0.544582 1.2:+39492073 None:intergenic
ATCAAACTTTGCAGAAATGT+GGG 0.546245 1.2:-39492042 MS.gene018784:CDS
TGAGTTATGTGACCAAGAAA+CGG 0.560971 1.2:-39492173 MS.gene018784:CDS
AAAAGGAGTGTTGTTGATCA+TGG 0.562216 1.2:-39492507 MS.gene018784:CDS
AAAAGAACAGCTTGGTGGTG+AGG 0.570897 1.2:-39491927 MS.gene018784:CDS
TCATCTGTCAATGCTCTCAA+CGG 0.575258 1.2:-39492303 MS.gene018784:CDS
TCATCTGCATCATCATCCAC+TGG 0.575486 1.2:+39491655 None:intergenic
AAACAATGAAAAGAACAGCT+TGG 0.582230 1.2:-39491935 MS.gene018784:CDS
CAATGAAAAGAACAGCTTGG+TGG 0.584869 1.2:-39491932 MS.gene018784:CDS
AAGATGAAGATCAGAGAGCA+AGG 0.587874 1.2:-39492009 MS.gene018784:CDS
AACTTTGCAGAAATGTGGGA+GGG 0.590470 1.2:-39492038 MS.gene018784:CDS
GCAACGAACACATGAATGGT+TGG 0.590907 1.2:+39492338 None:intergenic
TGAAGATGATGAAGCAAATG+AGG 0.593094 1.2:-39491734 MS.gene018784:CDS
CGATTTGAATGAGCTGCCAG+TGG 0.597243 1.2:-39491671 MS.gene018784:CDS
ATGTGACCAAGAAACGGAGC+TGG 0.597485 1.2:-39492167 MS.gene018784:CDS
TTGCTTCATCATCTTCACCA+GGG 0.604583 1.2:+39491740 None:intergenic
AGGAACCAACTCATGAATTG+GGG 0.629510 1.2:-39491714 MS.gene018784:CDS
AAACTTTGCAGAAATGTGGG+AGG 0.645217 1.2:-39492039 MS.gene018784:CDS
GGCCACAAAGCATTCCATAG+AGG 0.645608 1.2:-39492423 MS.gene018784:CDS
TGCTGCAACGAACACATGAA+TGG 0.655011 1.2:+39492334 None:intergenic
TGAAGATGATGAAGCAGATG+AGG 0.659995 1.2:-39491773 MS.gene018784:CDS
AATGAAGAGAACAACAACAC+TGG 0.663304 1.2:-39491835 MS.gene018784:CDS
GATAAGGAACCAAACAACAC+TGG 0.664805 1.2:-39491796 MS.gene018784:CDS
GTGAGGTTAAAGATTCCGAA+TGG 0.667579 1.2:-39491910 MS.gene018784:CDS
GATGAGGAACCAAACAACCC+TGG 0.684317 1.2:-39491757 MS.gene018784:CDS
TCAACTGGTAATGCTCTCGG+CGG 0.775161 1.2:-39492444 MS.gene018784:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACTTTCTCAAATCAAT+TGG + chr1.2:39492011-39492030 None:intergenic 20.0%
AAACAATGAAAAGAACAGCT+TGG - chr1.2:39492277-39492296 MS.gene018784:CDS 30.0%
AACAAAGAAAAACAAGCTGA+TGG - chr1.2:39491837-39491856 MS.gene018784:CDS 30.0%
ATCAAACTTTGCAGAAATGT+GGG - chr1.2:39492170-39492189 MS.gene018784:CDS 30.0%
GTTCTCTTCATTATCATCAT+TGG + chr1.2:39492369-39492388 None:intergenic 30.0%
TACTTTCTCAAATCAATTGG+TGG + chr1.2:39492008-39492027 None:intergenic 30.0%
! CTTCTGATTTTTGAATGACA+AGG + chr1.2:39492328-39492347 None:intergenic 30.0%
AAAGAAAGTTGTTGCCTCTA+TGG + chr1.2:39491806-39491825 None:intergenic 35.0%
AATGAAGAGAACAACAACAC+TGG - chr1.2:39492377-39492396 MS.gene018784:CDS 35.0%
ACTCTCATCACAAACCAAAA+AGG - chr1.2:39491688-39491707 MS.gene018784:CDS 35.0%
ATCATTGGAAGCAGATTGAT+TGG + chr1.2:39492354-39492373 None:intergenic 35.0%
CAATTGGTGGAAATTGATCT+AGG + chr1.2:39491995-39492014 None:intergenic 35.0%
GATCAAACTTTGCAGAAATG+TGG - chr1.2:39492169-39492188 MS.gene018784:CDS 35.0%
TGAAGATGATGAAGCAAATG+AGG - chr1.2:39492478-39492497 MS.gene018784:CDS 35.0%
TGAAGATGATGAAGCAGATA+AGG - chr1.2:39492400-39492419 MS.gene018784:CDS 35.0%
TGAGTTATGTGACCAAGAAA+CGG - chr1.2:39492039-39492058 MS.gene018784:CDS 35.0%
TGATTCACATCATGGTTGTT+AGG + chr1.2:39492134-39492153 None:intergenic 35.0%
TTCTTGGTCACATAACTCAT+TGG + chr1.2:39492038-39492057 None:intergenic 35.0%
TTTAACCCCAATTCATGAGT+TGG + chr1.2:39492506-39492525 None:intergenic 35.0%
! AGAGGCAACAACTTTCTTTT+AGG - chr1.2:39491807-39491826 MS.gene018784:CDS 35.0%
! TGATCAACAACACTCCTTTT+TGG + chr1.2:39491705-39491724 None:intergenic 35.0%
! TTTTGAATGACAAGGCCATT+CGG + chr1.2:39492320-39492339 None:intergenic 35.0%
!! AAAAGGAGTGTTGTTGATCA+TGG - chr1.2:39491705-39491724 MS.gene018784:CDS 35.0%
AAACTTTGCAGAAATGTGGG+AGG - chr1.2:39492173-39492192 MS.gene018784:CDS 40.0%
AACTTTGCAGAAATGTGGGA+GGG - chr1.2:39492174-39492193 MS.gene018784:CDS 40.0%
AAGATGAAGATCAGAGAGCA+AGG - chr1.2:39492203-39492222 MS.gene018784:CDS 40.0%
AGGAACCAACTCATGAATTG+GGG - chr1.2:39492498-39492517 MS.gene018784:CDS 40.0%
ATAATTCCAGCTCCGTTTCT+TGG + chr1.2:39492054-39492073 None:intergenic 40.0%
ATGAAATCGCACAGCCAATA+TGG - chr1.2:39491936-39491955 MS.gene018784:CDS 40.0%
CAATGAAAAGAACAGCTTGG+TGG - chr1.2:39492280-39492299 MS.gene018784:CDS 40.0%
GAGGAACCAACTCATGAATT+GGG - chr1.2:39492497-39492516 MS.gene018784:CDS 40.0%
GATAAGGAACCAAACAACAC+TGG - chr1.2:39492416-39492435 MS.gene018784:CDS 40.0%
GTGAGGTTAAAGATTCCGAA+TGG - chr1.2:39492302-39492321 MS.gene018784:CDS 40.0%
TCATCTGTCAATGCTCTCAA+CGG - chr1.2:39491909-39491928 MS.gene018784:CDS 40.0%
TCTTCGAAGTCGAACCATAT+TGG + chr1.2:39491953-39491972 None:intergenic 40.0%
TGAAGATGATGAAGCAGATG+AGG - chr1.2:39492439-39492458 MS.gene018784:CDS 40.0%
TGAGGAACCAACTCATGAAT+TGG - chr1.2:39492496-39492515 MS.gene018784:CDS 40.0%
TGTGACAGAGAATTCTCAAC+TGG - chr1.2:39491753-39491772 MS.gene018784:CDS 40.0%
TTGCTTCATCATCTTCACCA+GGG + chr1.2:39492475-39492494 None:intergenic 40.0%
TTGGTCACATAACTCATTGG+TGG + chr1.2:39492035-39492054 None:intergenic 40.0%
TTTGCTTCATCATCTTCACC+AGG + chr1.2:39492476-39492495 None:intergenic 40.0%
! GTTTGATCCTTTTCGTGACA+CGG + chr1.2:39492157-39492176 None:intergenic 40.0%
! TCATCTTCACCAGTGTTGTT+TGG + chr1.2:39492389-39492408 None:intergenic 40.0%
! TTCTCAACTGGTAATGCTCT+CGG - chr1.2:39491765-39491784 MS.gene018784:CDS 40.0%
GCAACGAACACATGAATGGT+TGG + chr1.2:39491877-39491896 None:intergenic 45.0%
TCATCTGCATCATCATCCAC+TGG + chr1.2:39492560-39492579 None:intergenic 45.0%
TCATCTTCACCAGGGTTGTT+TGG + chr1.2:39492467-39492486 None:intergenic 45.0%
TCATGTTGCTGAAGCAATGC+TGG - chr1.2:39492091-39492110 MS.gene018784:CDS 45.0%
TGAATCACCGTGTCACGAAA+AGG - chr1.2:39492147-39492166 MS.gene018784:CDS 45.0%
TGACACGGTGATTCACATCA+TGG + chr1.2:39492142-39492161 None:intergenic 45.0%
TGCCTCTATGGAATGCTTTG+TGG + chr1.2:39491794-39491813 None:intergenic 45.0%
TGCTGCAACGAACACATGAA+TGG + chr1.2:39491881-39491900 None:intergenic 45.0%
!! AAAAGAACAGCTTGGTGGTG+AGG - chr1.2:39492285-39492304 MS.gene018784:CDS 45.0%
!! GATCAGAGAGCAAGGTATTG+TGG - chr1.2:39492211-39492230 MS.gene018784:CDS 45.0%
ATGTGACCAAGAAACGGAGC+TGG - chr1.2:39492045-39492064 MS.gene018784:CDS 50.0%
CGATTTGAATGAGCTGCCAG+TGG - chr1.2:39492541-39492560 MS.gene018784:CDS 50.0%
GATGAGGAACCAAACAACCC+TGG - chr1.2:39492455-39492474 MS.gene018784:CDS 50.0%
! GGCCACAAAGCATTCCATAG+AGG - chr1.2:39491789-39491808 MS.gene018784:CDS 50.0%
! TCAACTGGTAATGCTCTCGG+CGG - chr1.2:39491768-39491787 MS.gene018784:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 39491642 39492592 39491642 ID=MS.gene018784
chr1.2 mRNA 39491642 39492592 39491642 ID=MS.gene018784.t1;Parent=MS.gene018784
chr1.2 exon 39491642 39492592 39491642 ID=MS.gene018784.t1.exon1;Parent=MS.gene018784.t1
chr1.2 CDS 39491642 39492592 39491642 ID=cds.MS.gene018784.t1;Parent=MS.gene018784.t1
Gene Sequence

>MS.gene018784

ATGAAGCATTTTTTTTCTTCTGCTTCTTCTTCTTCTTCTTCATCTCACTCTCATCACAAACCAAAAAGGAGTGTTGTTGATCATGGTGCAAAACTTCACAAATGTGATTTGTGTGACAGAGAATTCTCAACTGGTAATGCTCTCGGCGGCCACAAAGCATTCCATAGAGGCAACAACTTTCTTTTAGGAAAAATCAACAAAGAAAAACAAGCTGATGGTATTAAGATCGAAACCAACCATTCATGTGTTCGTTGCAGCAAGACTTTTTCATCTGTCAATGCTCTCAACGGACACATGAAATCGCACAGCCAATATGGTTCGACTTCGAAGAAGAGTAGTAAGATTTATGACCTAGATCAATTTCCACCAATTGATTTGAGAAAGTATTTGCCACCAATGAGTTATGTGACCAAGAAACGGAGCTGGAATTATGTTATTAATGTTGAATCTCATGTTGCTGAAGCAATGCTGGATATGTCACAGCGATCACCTAACAACCATGATGTGAATCACCGTGTCACGAAAAGGATCAAACTTTGCAGAAATGTGGGAGGGATTGAGAAGATGAAGATCAGAGAGCAAGGTATTGTGGTAAAACATTGTGTTGATGAAACAATTGTGAGAGAGAATGATAAAAACAATGAAAAGAACAGCTTGGTGGTGAGGTTAAAGATTCCGAATGGCCTTGTCATTCAAAAATCAGAAGCTTCCAATCAATCTGCTTCCAATGATGATAATGAAGAGAACAACAACACTGGTGAAGATGATGAAGCAGATAAGGAACCAAACAACACTGGTGAAGATGATGAAGCAGATGAGGAACCAAACAACCCTGGTGAAGATGATGAAGCAAATGAGGAACCAACTCATGAATTGGGGTTAAATGTTGTTCGAGATTTCGATTTGAATGAGCTGCCAGTGGATGATGATGCAGATGAAACCGCCCATTAG
Protein sequence

>MS.gene018784.t1

MKHFFSSASSSSSSSHSHHKPKRSVVDHGAKLHKCDLCDREFSTGNALGGHKAFHRGNNFLLGKINKEKQADGIKIETNHSCVRCSKTFSSVNALNGHMKSHSQYGSTSKKSSKIYDLDQFPPIDLRKYLPPMSYVTKKRSWNYVINVESHVAEAMLDMSQRSPNNHDVNHRVTKRIKLCRNVGGIEKMKIREQGIVVKHCVDETIVRENDKNNEKNSLVVRLKIPNGLVIQKSEASNQSASNDDNEENNNTGEDDEADKEPNNTGEDDEADEEPNNPGEDDEANEEPTHELGLNVVRDFDLNELPVDDDADETAH