AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41101

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41101.t1 AT3G44260 61.232 276 95 4 10 281 11 278 3.80e-114 330
MS.gene41101.t1 AT5G22250 61.993 271 92 5 16 281 12 276 1.35e-113 328
MS.gene41101.t1 AT2G32070 54.478 268 110 5 15 280 9 266 2.34e-96 285
MS.gene41101.t1 AT5G10960 55.431 267 108 5 15 280 9 265 5.93e-96 284
MS.gene41101.t1 AT1G80780 55.056 267 109 5 15 280 9 265 2.14e-93 277
MS.gene41101.t1 AT1G80780 55.056 267 109 5 15 280 9 265 2.14e-93 277
MS.gene41101.t1 AT1G80780 55.056 267 109 5 15 280 9 265 2.94e-93 277
MS.gene41101.t1 AT1G15920 50.000 270 128 5 15 282 13 277 2.52e-85 257
MS.gene41101.t1 AT1G15920 50.000 270 128 5 15 282 13 277 2.52e-85 257
MS.gene41101.t1 AT1G06450 34.082 267 149 8 19 280 10 254 2.10e-40 144
MS.gene41101.t1 AT1G61470 37.860 243 127 8 21 258 5 228 4.29e-38 135
MS.gene41101.t1 AT1G27820 37.052 251 132 9 15 258 3 234 1.50e-35 130
MS.gene41101.t1 AT3G44240 36.245 229 128 6 32 258 3 215 7.79e-32 118
MS.gene41101.t1 AT1G27890 36.929 241 134 6 21 258 4 229 1.72e-31 119

Find 70 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATGAGCTTGCTGAGTTTC+TGG 0.128109 1.3:-42643928 MS.gene41101:CDS
CGGATATGATTTCGGATATT+TGG 0.138980 1.3:-42643979 MS.gene41101:CDS
TTCGAGAAGAATAAGGAATT+TGG 0.145623 1.3:-42644086 MS.gene41101:CDS
TAGAAAAGGAGTTTCTAATT+TGG 0.187567 1.3:-42644193 MS.gene41101:CDS
AGAAAAGGAGTTTCTAATTT+GGG 0.265038 1.3:-42644192 MS.gene41101:CDS
CTGAGTTTCTGGTGCTGGTT+AGG 0.266063 1.3:-42643917 MS.gene41101:CDS
GATTGATTTCGAGAAGAATA+AGG 0.314226 1.3:-42644093 MS.gene41101:CDS
TGAAGGGTTGTATGGTGGTT+TGG 0.322783 1.3:-42643844 MS.gene41101:CDS
TCGAGAAGAATAAGGAATTT+GGG 0.324006 1.3:-42644085 MS.gene41101:CDS
TTTCATAGCGGATATGATTT+CGG 0.332804 1.3:-42643987 MS.gene41101:CDS
GCTGAATTGATGATGAGTTC+TGG 0.333632 1.3:-42644044 MS.gene41101:CDS
CTGAATGTGGATCGTGTTGC+TGG 0.372479 1.3:-42643804 MS.gene41101:CDS
GACGACAACGCCGGGAAATT+CGG 0.381247 1.3:+42644358 None:intergenic
AATTGAATTGCTGAAGAGTC+AGG 0.384892 1.3:-42644117 MS.gene41101:CDS
GATAAGTCGGTGATGCCGTC+AGG 0.408072 1.3:+42644332 None:intergenic
AGAAACTCAGCAAGCTCATC+AGG 0.412221 1.3:+42643930 None:intergenic
AGATTAAGGAAGTTCACTTT+GGG 0.421931 1.3:-42643728 MS.gene41101:CDS
GCTTGCTGAGTTTCTGGTGC+TGG 0.433612 1.3:-42643922 MS.gene41101:CDS
AAGATTAAGGAAGTTCACTT+TGG 0.442516 1.3:-42643729 MS.gene41101:CDS
TGAGTTTCTGGTGCTGGTTA+GGG 0.447849 1.3:-42643916 MS.gene41101:CDS
AAGTATGCTGGTGTGTTGTA+TGG 0.453388 1.3:-42643684 MS.gene41101:CDS
TGTGTAATGAGGAGGTTAGC+TGG 0.455691 1.3:-42644016 MS.gene41101:CDS
GGCGTTGTCGTCCGCCCTGA+CGG 0.458271 1.3:-42644347 MS.gene41101:CDS
ACCGGTCGGATTGAGATTGA+TGG 0.470117 1.3:+42644458 None:intergenic
AGGAATTTGGGATTGACTCA+TGG 0.472026 1.3:-42644073 MS.gene41101:CDS
ATGGTGGTTTGGATAGAGTT+GGG 0.481050 1.3:-42643833 MS.gene41101:CDS
TCAGGGCGGACGACAACGCC+GGG 0.482357 1.3:+42644350 None:intergenic
TCAATGGACACCGAATTTCC+CGG 0.485725 1.3:-42644368 MS.gene41101:CDS
TGTTTATGATGTGAAGCATT+TGG 0.488890 1.3:-42643877 MS.gene41101:CDS
CTGGGAAGAGTCATCAGGCT+GGG 0.498125 1.3:-42643785 MS.gene41101:CDS
CTGATAAAGTGAGACCAACT+TGG 0.500178 1.3:+42644240 None:intergenic
AGTAATGAGTGGCAGGTGTT+CGG 0.504156 1.3:+42644300 None:intergenic
TAACCTTCCGAAATTAGAAA+AGG 0.506679 1.3:-42644207 MS.gene41101:CDS
GCTGGGAAGAGTCATCAGGC+TGG 0.512555 1.3:-42643786 MS.gene41101:CDS
GTCCTCAAGGCGAATGTCGA+CGG 0.520336 1.3:-42644275 MS.gene41101:CDS
TGTTGCTGGGAAGAGTCATC+AGG 0.533863 1.3:-42643790 MS.gene41101:CDS
ATTGAGATTGATGGAGCGTA+GGG 0.534551 1.3:+42644467 None:intergenic
GACCGTCGACATTCGCCTTG+AGG 0.535332 1.3:+42644273 None:intergenic
TTCACATCCGATCATCTCAA+TGG 0.540047 1.3:-42644384 MS.gene41101:CDS
TATGGTGGTTTGGATAGAGT+TGG 0.541004 1.3:-42643834 MS.gene41101:CDS
AGGACGGAGTAATGAGTGGC+AGG 0.543146 1.3:+42644293 None:intergenic
GTCAGGGCGGACGACAACGC+CGG 0.547017 1.3:+42644349 None:intergenic
GATTGAGATTGATGGAGCGT+AGG 0.549476 1.3:+42644466 None:intergenic
GTGTAATGAGGAGGTTAGCT+GGG 0.552375 1.3:-42644015 MS.gene41101:CDS
TAATTTCGGAAGGTTACCCT+CGG 0.571733 1.3:+42644214 None:intergenic
GTTGTATGGATTAGAAAATG+TGG 0.574852 1.3:-42643670 MS.gene41101:CDS
CACTCATTACTCCGTCCTCA+AGG 0.577080 1.3:-42644288 MS.gene41101:CDS
ATTGAATTGCTGAAGAGTCA+GGG 0.581241 1.3:-42644116 MS.gene41101:CDS
AGTTGGGAAGACGCTGAATG+TGG 0.590046 1.3:-42643817 MS.gene41101:CDS
TCCATCAATCTCAATCCGAC+CGG 0.592312 1.3:-42644459 MS.gene41101:CDS
GTCGACATTCGCCTTGAGGA+CGG 0.603932 1.3:+42644277 None:intergenic
GGTCTTAATCTCATCCAAGT+TGG 0.608054 1.3:-42644254 MS.gene41101:CDS
TCTCACTTTATCAGATGCCG+AGG 0.613235 1.3:-42644231 MS.gene41101:CDS
TGAATGTGGATCGTGTTGCT+GGG 0.618716 1.3:-42643803 MS.gene41101:CDS
AATGAGTGGCAGGTGTTCGG+TGG 0.620595 1.3:+42644303 None:intergenic
GATTGAATGACCACACCGGT+CGG 0.621202 1.3:+42644444 None:intergenic
TTCTGGACTTGTGTGTAATG+AGG 0.621770 1.3:-42644027 MS.gene41101:CDS
GATCGATTGATGAAGTATGC+TGG 0.628077 1.3:-42643696 MS.gene41101:CDS
ATAAGTCGGTGATGCCGTCA+GGG 0.629413 1.3:+42644333 None:intergenic
TTGAATTGCTGAAGAGTCAG+GGG 0.634045 1.3:-42644115 MS.gene41101:CDS
TGGACTTGTGTGTAATGAGG+AGG 0.634444 1.3:-42644024 MS.gene41101:CDS
TCGGTGTCCATTGAGATGAT+CGG 0.640764 1.3:+42644377 None:intergenic
CTTGAGGACGGAGTAATGAG+TGG 0.656338 1.3:+42644289 None:intergenic
CAATCTCAATCCGACCGGTG+TGG 0.685580 1.3:-42644454 MS.gene41101:CDS
CTCACTTTATCAGATGCCGA+GGG 0.688262 1.3:-42644230 MS.gene41101:CDS
TCGGTGGTAAGATGATAAGT+CGG 0.692107 1.3:+42644319 None:intergenic
GATGTGAATCAACGAAAGAG+CGG 0.694715 1.3:+42644399 None:intergenic
AGTCGGTGATGCCGTCAGGG+CGG 0.706791 1.3:+42644336 None:intergenic
AGCTGGGTGACATTTCATAG+CGG 0.756943 1.3:-42643999 MS.gene41101:CDS
TCGAGATTGAATGACCACAC+CGG 0.757455 1.3:+42644440 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAAAGGAGTTTCTAATTT+GGG - chr1.3:42643970-42643989 MS.gene41101:CDS 25.0%
! TAGAAAAGGAGTTTCTAATT+TGG - chr1.3:42643969-42643988 MS.gene41101:CDS 25.0%
!! AGAAACTCCTTTTCTAATTT+CGG + chr1.3:42643965-42643984 None:intergenic 25.0%
AAGATTAAGGAAGTTCACTT+TGG - chr1.3:42644433-42644452 MS.gene41101:CDS 30.0%
AGATTAAGGAAGTTCACTTT+GGG - chr1.3:42644434-42644453 MS.gene41101:CDS 30.0%
TAACCTTCCGAAATTAGAAA+AGG - chr1.3:42643955-42643974 MS.gene41101:CDS 30.0%
TCGAGAAGAATAAGGAATTT+GGG - chr1.3:42644077-42644096 MS.gene41101:CDS 30.0%
TTCGAGAAGAATAAGGAATT+TGG - chr1.3:42644076-42644095 MS.gene41101:CDS 30.0%
! GATTGATTTCGAGAAGAATA+AGG - chr1.3:42644069-42644088 MS.gene41101:CDS 30.0%
! TGTTTATGATGTGAAGCATT+TGG - chr1.3:42644285-42644304 MS.gene41101:CDS 30.0%
!! ATTTGGTGAAGTTTTGTGAA+GGG - chr1.3:42644302-42644321 MS.gene41101:CDS 30.0%
!! GTTGTATGGATTAGAAAATG+TGG - chr1.3:42644492-42644511 MS.gene41101:CDS 30.0%
!! TCATGCTTTTAGGAAGATTA+AGG - chr1.3:42644420-42644439 MS.gene41101:CDS 30.0%
!! TTTCATAGCGGATATGATTT+CGG - chr1.3:42644175-42644194 MS.gene41101:CDS 30.0%
AATTGAATTGCTGAAGAGTC+AGG - chr1.3:42644045-42644064 MS.gene41101:CDS 35.0%
ATTGAATTGCTGAAGAGTCA+GGG - chr1.3:42644046-42644065 MS.gene41101:CDS 35.0%
CGGATATGATTTCGGATATT+TGG - chr1.3:42644183-42644202 MS.gene41101:CDS 35.0%
! ACTCCTTTTCTAATTTCGGA+AGG + chr1.3:42643961-42643980 None:intergenic 35.0%
!! AAGTTTTGTGAAGGGTTGTA+TGG - chr1.3:42644310-42644329 MS.gene41101:CDS 35.0%
!! CATTTGGTGAAGTTTTGTGA+AGG - chr1.3:42644301-42644320 MS.gene41101:CDS 35.0%
AAGTATGCTGGTGTGTTGTA+TGG - chr1.3:42644478-42644497 MS.gene41101:CDS 40.0%
ATTGAGATTGATGGAGCGTA+GGG + chr1.3:42643698-42643717 None:intergenic 40.0%
CTGATAAAGTGAGACCAACT+TGG + chr1.3:42643925-42643944 None:intergenic 40.0%
GATCGATTGATGAAGTATGC+TGG - chr1.3:42644466-42644485 MS.gene41101:CDS 40.0%
GATGTGAATCAACGAAAGAG+CGG + chr1.3:42643766-42643785 None:intergenic 40.0%
GGTCTTAATCTCATCCAAGT+TGG - chr1.3:42643908-42643927 MS.gene41101:CDS 40.0%
TAATTTCGGAAGGTTACCCT+CGG + chr1.3:42643951-42643970 None:intergenic 40.0%
TCGGTGGTAAGATGATAAGT+CGG + chr1.3:42643846-42643865 None:intergenic 40.0%
TTCACATCCGATCATCTCAA+TGG - chr1.3:42643778-42643797 MS.gene41101:CDS 40.0%
TTCTGGACTTGTGTGTAATG+AGG - chr1.3:42644135-42644154 MS.gene41101:CDS 40.0%
TTGAATTGCTGAAGAGTCAG+GGG - chr1.3:42644047-42644066 MS.gene41101:CDS 40.0%
! AGGAATTTGGGATTGACTCA+TGG - chr1.3:42644089-42644108 MS.gene41101:CDS 40.0%
! ATGGTGGTTTGGATAGAGTT+GGG - chr1.3:42644329-42644348 MS.gene41101:CDS 40.0%
! TATGGTGGTTTGGATAGAGT+TGG - chr1.3:42644328-42644347 MS.gene41101:CDS 40.0%
! TTTTGTGAAGGGTTGTATGG+TGG - chr1.3:42644313-42644332 MS.gene41101:CDS 40.0%
!! GCTGAATTGATGATGAGTTC+TGG - chr1.3:42644118-42644137 MS.gene41101:CDS 40.0%
!! TGCTGGTTAGGGTTTTCTTT+GGG - chr1.3:42644257-42644276 MS.gene41101:CDS 40.0%
!!! TGCTGACTCTTCATGCTTTT+AGG - chr1.3:42644410-42644429 MS.gene41101:CDS 40.0%
AGAAACTCAGCAAGCTCATC+AGG + chr1.3:42644235-42644254 None:intergenic 45.0%
AGCTGGGTGACATTTCATAG+CGG - chr1.3:42644163-42644182 MS.gene41101:CDS 45.0%
AGTAATGAGTGGCAGGTGTT+CGG + chr1.3:42643865-42643884 None:intergenic 45.0%
CTCACTTTATCAGATGCCGA+GGG - chr1.3:42643932-42643951 MS.gene41101:CDS 45.0%
GATTGAGATTGATGGAGCGT+AGG + chr1.3:42643699-42643718 None:intergenic 45.0%
TCAATGGACACCGAATTTCC+CGG - chr1.3:42643794-42643813 MS.gene41101:CDS 45.0%
TCCATCAATCTCAATCCGAC+CGG - chr1.3:42643703-42643722 MS.gene41101:CDS 45.0%
TCGAGATTGAATGACCACAC+CGG + chr1.3:42643725-42643744 None:intergenic 45.0%
TCTCACTTTATCAGATGCCG+AGG - chr1.3:42643931-42643950 MS.gene41101:CDS 45.0%
TGAAGGGTTGTATGGTGGTT+TGG - chr1.3:42644318-42644337 MS.gene41101:CDS 45.0%
TGGACTTGTGTGTAATGAGG+AGG - chr1.3:42644138-42644157 MS.gene41101:CDS 45.0%
TGTGTAATGAGGAGGTTAGC+TGG - chr1.3:42644146-42644165 MS.gene41101:CDS 45.0%
! GCTGGTTAGGGTTTTCTTTG+GGG - chr1.3:42644258-42644277 MS.gene41101:CDS 45.0%
! GTGTAATGAGGAGGTTAGCT+GGG - chr1.3:42644147-42644166 MS.gene41101:CDS 45.0%
! TCGGTGTCCATTGAGATGAT+CGG + chr1.3:42643788-42643807 None:intergenic 45.0%
! TGAATGTGGATCGTGTTGCT+GGG - chr1.3:42644359-42644378 MS.gene41101:CDS 45.0%
!! TGAGTTTCTGGTGCTGGTTA+GGG - chr1.3:42644246-42644265 MS.gene41101:CDS 45.0%
!! TGATGAGCTTGCTGAGTTTC+TGG - chr1.3:42644234-42644253 MS.gene41101:CDS 45.0%
!!! GTGCTGGTTAGGGTTTTCTT+TGG - chr1.3:42644256-42644275 MS.gene41101:CDS 45.0%
ACCGGTCGGATTGAGATTGA+TGG + chr1.3:42643707-42643726 None:intergenic 50.0%
AGTTGGGAAGACGCTGAATG+TGG - chr1.3:42644345-42644364 MS.gene41101:CDS 50.0%
ATAAGTCGGTGATGCCGTCA+GGG + chr1.3:42643832-42643851 None:intergenic 50.0%
CACTCATTACTCCGTCCTCA+AGG - chr1.3:42643874-42643893 MS.gene41101:CDS 50.0%
CTGAATGTGGATCGTGTTGC+TGG - chr1.3:42644358-42644377 MS.gene41101:CDS 50.0%
CTTGAGGACGGAGTAATGAG+TGG + chr1.3:42643876-42643895 None:intergenic 50.0%
GATTGAATGACCACACCGGT+CGG + chr1.3:42643721-42643740 None:intergenic 50.0%
TGTTGCTGGGAAGAGTCATC+AGG - chr1.3:42644372-42644391 MS.gene41101:CDS 50.0%
!! CTGAGTTTCTGGTGCTGGTT+AGG - chr1.3:42644245-42644264 MS.gene41101:CDS 50.0%
AATGAGTGGCAGGTGTTCGG+TGG + chr1.3:42643862-42643881 None:intergenic 55.0%
AGGACGGAGTAATGAGTGGC+AGG + chr1.3:42643872-42643891 None:intergenic 55.0%
CAATCTCAATCCGACCGGTG+TGG - chr1.3:42643708-42643727 MS.gene41101:CDS 55.0%
CTGGGAAGAGTCATCAGGCT+GGG - chr1.3:42644377-42644396 MS.gene41101:CDS 55.0%
GACGACAACGCCGGGAAATT+CGG + chr1.3:42643807-42643826 None:intergenic 55.0%
GATAAGTCGGTGATGCCGTC+AGG + chr1.3:42643833-42643852 None:intergenic 55.0%
GTCCTCAAGGCGAATGTCGA+CGG - chr1.3:42643887-42643906 MS.gene41101:CDS 55.0%
GTCGACATTCGCCTTGAGGA+CGG + chr1.3:42643888-42643907 None:intergenic 55.0%
!! GCTTGCTGAGTTTCTGGTGC+TGG - chr1.3:42644240-42644259 MS.gene41101:CDS 55.0%
GACCGTCGACATTCGCCTTG+AGG + chr1.3:42643892-42643911 None:intergenic 60.0%
GCTGGGAAGAGTCATCAGGC+TGG - chr1.3:42644376-42644395 MS.gene41101:CDS 60.0%
AGTCGGTGATGCCGTCAGGG+CGG + chr1.3:42643829-42643848 None:intergenic 65.0%
GGCGTTGTCGTCCGCCCTGA+CGG - chr1.3:42643815-42643834 MS.gene41101:CDS 70.0%
GTCAGGGCGGACGACAACGC+CGG + chr1.3:42643816-42643835 None:intergenic 70.0%
TCAGGGCGGACGACAACGCC+GGG + chr1.3:42643815-42643834 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 42643665 42644519 42643665 ID=MS.gene41101
chr1.3 mRNA 42643665 42644519 42643665 ID=MS.gene41101.t1;Parent=MS.gene41101
chr1.3 exon 42643665 42644519 42643665 ID=MS.gene41101.t1.exon1;Parent=MS.gene41101.t1
chr1.3 CDS 42643665 42644519 42643665 ID=cds.MS.gene41101.t1;Parent=MS.gene41101.t1
Gene Sequence

>MS.gene41101

ATGTTCACACAAAGCATGTTCATCGCAAAACCCTACGCTCCATCAATCTCAATCCGACCGGTGTGGTCATTCAATCTCGAATCAGAGTTCAAACTCATCCGCTCTTTCGTTGATTCACATCCGATCATCTCAATGGACACCGAATTTCCCGGCGTTGTCGTCCGCCCTGACGGCATCACCGACTTATCATCTTACCACCGAACACCTGCCACTCATTACTCCGTCCTCAAGGCGAATGTCGACGGTCTTAATCTCATCCAAGTTGGTCTCACTTTATCAGATGCCGAGGGTAACCTTCCGAAATTAGAAAAGGAGTTTCTAATTTGGGAATTTAATTTCAGTGATTTTGATGTTGCACGTGATAATCACGCGCACGAGTCAATTGAATTGCTGAAGAGTCAGGGGATTGATTTCGAGAAGAATAAGGAATTTGGGATTGACTCATGGAAATTTGCTGAATTGATGATGAGTTCTGGACTTGTGTGTAATGAGGAGGTTAGCTGGGTGACATTTCATAGCGGATATGATTTCGGATATTTGGTGAAAGCGTTGACGCAGAGAGCTTTGCCTGATGAGCTTGCTGAGTTTCTGGTGCTGGTTAGGGTTTTCTTTGGGGAGAGTGTTTATGATGTGAAGCATTTGGTGAAGTTTTGTGAAGGGTTGTATGGTGGTTTGGATAGAGTTGGGAAGACGCTGAATGTGGATCGTGTTGCTGGGAAGAGTCATCAGGCTGGGTCTGATAGTTTGCTGACTCTTCATGCTTTTAGGAAGATTAAGGAAGTTCACTTTGGGAATGATGTTGATCGATTGATGAAGTATGCTGGTGTGTTGTATGGATTAGAAAATGTGGTTTAA
Protein sequence

>MS.gene41101.t1

MFTQSMFIAKPYAPSISIRPVWSFNLESEFKLIRSFVDSHPIISMDTEFPGVVVRPDGITDLSSYHRTPATHYSVLKANVDGLNLIQVGLTLSDAEGNLPKLEKEFLIWEFNFSDFDVARDNHAHESIELLKSQGIDFEKNKEFGIDSWKFAELMMSSGLVCNEEVSWVTFHSGYDFGYLVKALTQRALPDELAEFLVLVRVFFGESVYDVKHLVKFCEGLYGGLDRVGKTLNVDRVAGKSHQAGSDSLLTLHAFRKIKEVHFGNDVDRLMKYAGVLYGLENVV