AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21828

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21828.t1 MTR_5g006510 88.083 193 21 1 1 193 1 191 4.99e-123 346
MS.gene21828.t1 MTR_5g006460 80.829 193 29 3 9 193 1 193 2.14e-108 309
MS.gene21828.t1 MTR_5g006470 72.626 179 44 3 17 193 13 188 1.36e-89 261
MS.gene21828.t1 MTR_5g006450 70.681 191 49 3 9 193 1 190 4.70e-89 260
MS.gene21828.t1 MTR_5g006520 68.508 181 54 2 15 193 1729 1908 3.99e-77 251
MS.gene21828.t1 MTR_1g103110 61.538 182 63 4 16 193 12 190 3.15e-74 222
MS.gene21828.t1 MTR_1g103150 59.659 176 66 3 20 193 18 190 1.43e-71 216
MS.gene21828.t1 MTR_7g114410 44.186 172 90 3 21 190 4 171 4.63e-43 142
MS.gene21828.t1 MTR_7g024760 47.024 168 83 4 24 190 7 169 2.29e-42 141
MS.gene21828.t1 MTR_7g024780 45.349 172 89 3 20 190 3 170 3.07e-42 140
MS.gene21828.t1 MTR_3g463610 42.105 171 98 1 21 190 3 173 4.10e-41 139
MS.gene21828.t1 MTR_7g024765 44.970 169 85 4 24 190 7 169 4.84e-39 132
MS.gene21828.t1 MTR_7g114410 43.312 157 83 3 21 175 4 156 2.17e-37 127
MS.gene21828.t1 MTR_1g103320 50.000 82 39 1 53 134 10 89 1.33e-17 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21828.t1 AT2G32030 48.705 193 86 6 1 190 3 185 3.04e-54 171
MS.gene21828.t1 AT2G32020 51.765 170 72 5 24 190 18 180 3.77e-52 166
MS.gene21828.t1 AT3G22560 38.857 175 99 4 20 190 2 172 5.48e-34 119

Find 36 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAAGTATGTATTCTTTAA+AGG 0.161729 5.2:-1246031 MS.gene21828:CDS
TTGTTGATGTGGATAATTTA+AGG 0.203228 5.2:-1246102 MS.gene21828:CDS
CAAATCAATGATCTCTTCTT+TGG 0.204931 5.2:+1246489 None:intergenic
GTTGATGCCTTGGTCTTTGC+TGG 0.262298 5.2:+1246366 None:intergenic
GCTTGAAGCCTTTCCAAGTA+TGG 0.276638 5.2:+1246127 None:intergenic
TGCCATAACGATCATGCTAT+TGG 0.288303 5.2:-1246298 MS.gene21828:CDS
GCAGAACTTGGGTATGTTCT+AGG 0.307665 5.2:-1246223 MS.gene21828:CDS
ATGTTCTAGGCTCTAAATAC+TGG 0.313478 5.2:-1246210 MS.gene21828:CDS
CCTTGGTCTTTGCTGGTGTA+AGG 0.327596 5.2:+1246373 None:intergenic
GAAAAGATCGGAGTGTGATT+TGG 0.386444 5.2:+1246464 None:intergenic
ACCTCGATGATCTCATGGTT+TGG 0.401354 5.2:-1246432 MS.gene21828:CDS
GGCTCTAAATACTGGGGTAA+AGG 0.409375 5.2:-1246202 MS.gene21828:CDS
ATTCAGTGAATTTCCATACT+TGG 0.413337 5.2:-1246140 MS.gene21828:CDS
GCCATAACGATCATGCTATT+GGG 0.423146 5.2:-1246297 MS.gene21828:CDS
AGGATCACATGTGCAGAACT+TGG 0.424567 5.2:-1246235 MS.gene21828:CDS
TTCTGACCTCGATGATCTCA+TGG 0.433346 5.2:-1246437 MS.gene21828:CDS
GCTCTAAATACTGGGGTAAA+GGG 0.442106 5.2:-1246201 MS.gene21828:CDS
TGAGTTCACTTGATGATAAG+AGG 0.442621 5.2:-1246258 MS.gene21828:CDS
CAAAGAGTAGTTGAGAAAGT+TGG 0.450786 5.2:-1246076 MS.gene21828:CDS
ACCCAATAGCATGATCGTTA+TGG 0.457877 5.2:+1246296 None:intergenic
CTACTGATCTTAAACTAATG+AGG 0.474389 5.2:-1245973 MS.gene21828:CDS
GTAAGGTTCACCCCAGAACT+TGG 0.480302 5.2:+1246390 None:intergenic
TAAACTAATGAGGATGTTCA+AGG 0.483858 5.2:-1245963 MS.gene21828:CDS
GTGAATTTCCATACTTGGAA+AGG 0.490341 5.2:-1246135 MS.gene21828:CDS
TGCTGTGAAACAAATGGTTA+AGG 0.500098 5.2:-1246167 MS.gene21828:CDS
TGTTCTAGGCTCTAAATACT+GGG 0.526941 5.2:-1246209 MS.gene21828:CDS
CTTATCATCAAGTGAACTCA+AGG 0.556721 5.2:+1246261 None:intergenic
GCTTCAAGCTCTTGTTGATG+TGG 0.560091 5.2:-1246113 MS.gene21828:CDS
GGATCACATGTGCAGAACTT+GGG 0.577727 5.2:-1246234 MS.gene21828:CDS
GGTCAGAAAGATGAAAAGAT+CGG 0.592412 5.2:+1246452 None:intergenic
CATTTGTTTCACAGCACATG+TGG 0.625218 5.2:+1246174 None:intergenic
CACATGTGCTGTGAAACAAA+TGG 0.647600 5.2:-1246173 MS.gene21828:CDS
GTTCACTTGATGATAAGAGG+AGG 0.664638 5.2:-1246255 MS.gene21828:CDS
CCTTACACCAGCAAAGACCA+AGG 0.673207 5.2:-1246373 MS.gene21828:CDS
GTTCTAGGCTCTAAATACTG+GGG 0.712321 5.2:-1246208 MS.gene21828:CDS
GCCAAACCATGAGATCATCG+AGG 0.781144 5.2:+1246431 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATCAACTTCATTAAAAATA+TGG - chr5.2:1246119-1246138 MS.gene21828:CDS 20.0%
! TTGTTGATGTGGATAATTTA+AGG - chr5.2:1246367-1246386 MS.gene21828:CDS 25.0%
!! AGGAAGTATGTATTCTTTAA+AGG - chr5.2:1246438-1246457 MS.gene21828:CDS 25.0%
!!! AAAGTTGGTTTTCAAAAAGA+GGG - chr5.2:1246408-1246427 MS.gene21828:CDS 25.0%
ATTCAGTGAATTTCCATACT+TGG - chr5.2:1246329-1246348 MS.gene21828:CDS 30.0%
CAAATCAATGATCTCTTCTT+TGG + chr5.2:1245983-1246002 None:intergenic 30.0%
CTACTGATCTTAAACTAATG+AGG - chr5.2:1246496-1246515 MS.gene21828:CDS 30.0%
TAAACTAATGAGGATGTTCA+AGG - chr5.2:1246506-1246525 MS.gene21828:CDS 30.0%
TCATTAAAAATATGGCAAGC+AGG - chr5.2:1246127-1246146 MS.gene21828:CDS 30.0%
!!! GAAAGTTGGTTTTCAAAAAG+AGG - chr5.2:1246407-1246426 MS.gene21828:CDS 30.0%
!!! TTTTAATGAAGTTGATGCCT+TGG + chr5.2:1246116-1246135 None:intergenic 30.0%
CAAAGAGTAGTTGAGAAAGT+TGG - chr5.2:1246393-1246412 MS.gene21828:CDS 35.0%
CTTATCATCAAGTGAACTCA+AGG + chr5.2:1246211-1246230 None:intergenic 35.0%
GGTCAGAAAGATGAAAAGAT+CGG + chr5.2:1246020-1246039 None:intergenic 35.0%
GTGAATTTCCATACTTGGAA+AGG - chr5.2:1246334-1246353 MS.gene21828:CDS 35.0%
TGCTGTGAAACAAATGGTTA+AGG - chr5.2:1246302-1246321 MS.gene21828:CDS 35.0%
TTCAAAAAGAGGGAGTTCTT+AGG - chr5.2:1246418-1246437 MS.gene21828:CDS 35.0%
TTGGCATACTGATGAAAAAG+TGG - chr5.2:1246056-1246075 MS.gene21828:CDS 35.0%
! TGAGTTCACTTGATGATAAG+AGG - chr5.2:1246211-1246230 MS.gene21828:CDS 35.0%
!! ATGTTCTAGGCTCTAAATAC+TGG - chr5.2:1246259-1246278 MS.gene21828:CDS 35.0%
!! TGTTCTAGGCTCTAAATACT+GGG - chr5.2:1246260-1246279 MS.gene21828:CDS 35.0%
ACCCAATAGCATGATCGTTA+TGG + chr5.2:1246176-1246195 None:intergenic 40.0%
ATGAAAAAGTGGCCAAGTTC+TGG - chr5.2:1246067-1246086 MS.gene21828:CDS 40.0%
CACATGTGCTGTGAAACAAA+TGG - chr5.2:1246296-1246315 MS.gene21828:CDS 40.0%
CATTTGTTTCACAGCACATG+TGG + chr5.2:1246298-1246317 None:intergenic 40.0%
GAAAAGATCGGAGTGTGATT+TGG + chr5.2:1246008-1246027 None:intergenic 40.0%
GCCATAACGATCATGCTATT+GGG - chr5.2:1246172-1246191 MS.gene21828:CDS 40.0%
TGAAAAAGTGGCCAAGTTCT+GGG - chr5.2:1246068-1246087 MS.gene21828:CDS 40.0%
TGCCATAACGATCATGCTAT+TGG - chr5.2:1246171-1246190 MS.gene21828:CDS 40.0%
! GCTCTAAATACTGGGGTAAA+GGG - chr5.2:1246268-1246287 MS.gene21828:CDS 40.0%
! GTTCACTTGATGATAAGAGG+AGG - chr5.2:1246214-1246233 MS.gene21828:CDS 40.0%
!! GTTCTAGGCTCTAAATACTG+GGG - chr5.2:1246261-1246280 MS.gene21828:CDS 40.0%
ACCTCGATGATCTCATGGTT+TGG - chr5.2:1246037-1246056 MS.gene21828:CDS 45.0%
AGGATCACATGTGCAGAACT+TGG - chr5.2:1246234-1246253 MS.gene21828:CDS 45.0%
GAAAAAGTGGCCAAGTTCTG+GGG - chr5.2:1246069-1246088 MS.gene21828:CDS 45.0%
GCAGAACTTGGGTATGTTCT+AGG - chr5.2:1246246-1246265 MS.gene21828:CDS 45.0%
GCTTCAAGCTCTTGTTGATG+TGG - chr5.2:1246356-1246375 MS.gene21828:CDS 45.0%
GCTTGAAGCCTTTCCAAGTA+TGG + chr5.2:1246345-1246364 None:intergenic 45.0%
GGATCACATGTGCAGAACTT+GGG - chr5.2:1246235-1246254 MS.gene21828:CDS 45.0%
TTCTGACCTCGATGATCTCA+TGG - chr5.2:1246032-1246051 MS.gene21828:CDS 45.0%
!! GGCTCTAAATACTGGGGTAA+AGG - chr5.2:1246267-1246286 MS.gene21828:CDS 45.0%
CCTTACACCAGCAAAGACCA+AGG - chr5.2:1246096-1246115 MS.gene21828:CDS 50.0%
GCCAAACCATGAGATCATCG+AGG + chr5.2:1246041-1246060 None:intergenic 50.0%
GTAAGGTTCACCCCAGAACT+TGG + chr5.2:1246082-1246101 None:intergenic 50.0%
! CCTTGGTCTTTGCTGGTGTA+AGG + chr5.2:1246099-1246118 None:intergenic 50.0%
! GTTGATGCCTTGGTCTTTGC+TGG + chr5.2:1246106-1246125 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 1245934 1246557 1245934 ID=MS.gene21828
chr5.2 mRNA 1245934 1246557 1245934 ID=MS.gene21828.t1;Parent=MS.gene21828
chr5.2 exon 1245934 1246557 1245934 ID=MS.gene21828.t1.exon1;Parent=MS.gene21828.t1
chr5.2 CDS 1245934 1246557 1245934 ID=cds.MS.gene21828.t1;Parent=MS.gene21828.t1
Gene Sequence

>MS.gene21828

ATGGAGCAAAACACAAGTATTATGATAGAGCGACTTTCTATTTCTTCCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGATCTTTTCATCTTTCTGACCTCGATGATCTCATGGTTTGGCATACTGATGAAAAAGTGGCCAAGTTCTGGGGTGAACCTTACACCAGCAAAGACCAAGGCATCAACTTCATTAAAAATATGGCAAGCAGGTATCTAAGTTGCAAAGCAATATGCCATAACGATCATGCTATTGGGTGTATTAAGTTGTCCTTGAGTTCACTTGATGATAAGAGGAGGATCACATGTGCAGAACTTGGGTATGTTCTAGGCTCTAAATACTGGGGTAAAGGGATTGCCACATGTGCTGTGAAACAAATGGTTAAGGTTGCATTCAGTGAATTTCCATACTTGGAAAGGCTTCAAGCTCTTGTTGATGTGGATAATTTAAGGTCGCAAAGAGTAGTTGAGAAAGTTGGTTTTCAAAAAGAGGGAGTTCTTAGGAAGTATGTATTCTTTAAAGGAAAAAGCAGAGATATGATCATGTTTAGTCTTCTTTCTACTGATCTTAAACTAATGAGGATGTTCAAGGTGAAGAACTTATATATTGCTGCATTTTAA
Protein sequence

>MS.gene21828.t1

MEQNTSIMIERLSISSKEEIIDLNQITLRSFHLSDLDDLMVWHTDEKVAKFWGEPYTSKDQGINFIKNMASRYLSCKAICHNDHAIGCIKLSLSSLDDKRRITCAELGYVLGSKYWGKGIATCAVKQMVKVAFSEFPYLERLQALVDVDNLRSQRVVEKVGFQKEGVLRKYVFFKGKSRDMIMFSLLSTDLKLMRMFKVKNLYIAAF