AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045724

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045724.t1 MTR_2g064370 95.506 267 9 1 1 264 1 267 0.0 513
MS.gene045724.t1 MTR_8g046460 71.654 254 66 3 14 264 18 268 2.72e-133 377
MS.gene045724.t1 MTR_8g028425 57.792 154 63 1 75 226 92 245 9.71e-65 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045724.t1 AT1G79510 65.091 275 85 6 1 264 1 275 6.50e-120 343
MS.gene045724.t1 AT1G79510 65.091 275 85 6 1 264 1 275 6.50e-120 343
MS.gene045724.t1 AT1G16320 59.489 274 100 6 1 264 1 273 4.11e-110 319
MS.gene045724.t1 AT2G46220 55.414 157 68 1 72 226 81 237 5.61e-65 203

Find 60 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAAGTACAAATTGATCTTC+TGG 0.216595 2.3:+30571082 MS.gene045724:CDS
GACCCTTTGAACACATTTAC+TGG 0.221962 2.3:+30571054 MS.gene045724:CDS
AGGCACTTCAAAGTATAAAT+TGG 0.231544 2.3:+30571251 MS.gene045724:CDS
TATTAAACCAGTTTCAGTTT+TGG 0.296641 2.3:+30571335 MS.gene045724:CDS
AGAAAATGTGAAGTAGGTTT+TGG 0.326406 2.3:-30570273 None:intergenic
TTCATGGATAACTTTATATA+AGG 0.327641 2.3:+30571428 MS.gene045724:CDS
TTCTGGGCATTGAGGTTTCA+TGG 0.332313 2.3:+30571099 MS.gene045724:CDS
TAACTTTATATAAGGCAGTT+AGG 0.342291 2.3:+30571436 MS.gene045724:CDS
AGGGCGTGCCGCGTGTCCCT+TGG 0.359335 2.3:+30571208 MS.gene045724:CDS
TTGGTGAAGAGGTTTGTCTT+TGG 0.362955 2.3:-30570238 None:intergenic
GAGTTGGGAGATAAGGTTGT+AGG 0.369415 2.3:-30570206 None:intergenic
ACAAAATCCAAAACTGAAAC+TGG 0.373146 2.3:-30571342 None:intergenic
GGGAGATAAGGTTGTAGGTT+TGG 0.374951 2.3:-30570201 None:intergenic
GGGCGTGCCGCGTGTCCCTT+GGG 0.391041 2.3:+30571209 MS.gene045724:CDS
CGAAGAATGTGATATGGATT+AGG 0.391674 2.3:+30571175 MS.gene045724:CDS
TTTGATTGAGTTGGGAGATA+AGG 0.392649 2.3:-30570213 None:intergenic
ATGGATTAGGTGGAAACTTA+AGG 0.394506 2.3:+30571188 MS.gene045724:CDS
TGGAGTTTGAAGGGTGGCTA+AGG 0.408366 2.3:-30570328 None:intergenic
AAAGTACAAATTGATCTTCT+GGG 0.411012 2.3:+30571083 MS.gene045724:CDS
TGGATGTCTACTCTTCTTCA+TGG 0.415651 2.3:+30571412 MS.gene045724:CDS
TTGACATAGAATTCATCCTT+TGG 0.425313 2.3:-30570396 None:intergenic
AATGTAGGGTTTGGACTAGC+AGG 0.427331 2.3:-30571375 None:intergenic
AACTTTATATAAGGCAGTTA+GGG 0.433549 2.3:+30571437 MS.gene045724:CDS
AGGTCTTTGATGAAGATCAT+AGG 0.436047 2.3:-30570456 None:intergenic
TGTTTATCTTGAACACTTGA+CGG 0.437362 2.3:-30570369 None:intergenic
AACCTTCGAAGAATGTGATA+TGG 0.437736 2.3:+30571169 MS.gene045724:CDS
TGAACATAAAGTTGATAACT+TGG 0.441163 2.3:+30571293 MS.gene045724:CDS
TGGATTAGGTGGAAACTTAA+GGG 0.463830 2.3:+30571189 MS.gene045724:CDS
ATTCCAGTAAATGTGTTCAA+AGG 0.467787 2.3:-30571057 None:intergenic
AGAAGAAGAATCAGATGAAG+TGG 0.472139 2.3:-30570304 None:intergenic
TTCCAGTAAATGTGTTCAAA+GGG 0.481927 2.3:-30571056 None:intergenic
ACCTCAATTATGATATCTAT+AGG 0.485916 2.3:+30570475 MS.gene045724:CDS
AGGGAGACTTTGAAACAAGA+AGG 0.486403 2.3:+30571456 MS.gene045724:CDS
GATACAAGAAAATGTGAAGT+AGG 0.489505 2.3:-30570279 None:intergenic
GGAGTTTGAAGGGTGGCTAA+GGG 0.505819 2.3:-30570327 None:intergenic
AATTGATCTTCTGGGCATTG+AGG 0.508643 2.3:+30571091 MS.gene045724:CDS
GAAGCTAAAGGAGAATTTCA+AGG 0.512138 2.3:+30571231 MS.gene045724:CDS
AAGTATAAATTGGACAAGAA+TGG 0.514460 2.3:+30571261 MS.gene045724:CDS
ACCTATAGATATCATAATTG+AGG 0.529058 2.3:-30570476 None:intergenic
GATGAATTCTATGTCAACCT+TGG 0.529105 2.3:+30570402 MS.gene045724:CDS
CGTGTCCCTTGGGAAGCTAA+AGG 0.549445 2.3:+30571219 MS.gene045724:CDS
AATTCTCCTTTAGCTTCCCA+AGG 0.554730 2.3:-30571225 None:intergenic
TTGTGAAGTTGGAGTTTGAA+GGG 0.561912 2.3:-30570337 None:intergenic
CTTGTGAAGTTGGAGTTTGA+AGG 0.564715 2.3:-30570338 None:intergenic
ATAGATAATACTTACGAGCA+TGG 0.565339 2.3:-30571507 None:intergenic
ATCCATATCACATTCTTCGA+AGG 0.567194 2.3:-30571171 None:intergenic
GGTGTGTTAACTTGTGAAGT+TGG 0.574807 2.3:-30570348 None:intergenic
AGAATGTGATATGGATTAGG+TGG 0.583307 2.3:+30571178 MS.gene045724:CDS
GAAGAAGAGTAGACATCCAC+AGG 0.583593 2.3:-30571408 None:intergenic
GGGAGACTTTGAAACAAGAA+GGG 0.595464 2.3:+30571457 MS.gene045724:CDS
GAGTTCTAACAGCAAGTCCA+AGG 0.595497 2.3:-30570419 None:intergenic
GATGAAAGAGTTTGGTGAAG+AGG 0.606204 2.3:-30570249 None:intergenic
GGGAGTTTGCTACCACAAGA+TGG 0.611323 2.3:+30571477 MS.gene045724:CDS
ATTCTCCTTTAGCTTCCCAA+GGG 0.617667 2.3:-30571224 None:intergenic
ATGTAGGGTTTGGACTAGCA+GGG 0.639151 2.3:-30571374 None:intergenic
TTAGCTTCCCAAGGGACACG+CGG 0.642123 2.3:-30571216 None:intergenic
CACTTGATGTATATAGAGTG+TGG 0.642892 2.3:+30571145 MS.gene045724:CDS
TCAAGATAAACAGCTTCCAA+AGG 0.645111 2.3:+30570380 MS.gene045724:CDS
CATGGAGCTAGACCATCTTG+TGG 0.685164 2.3:-30571489 None:intergenic
TGAAGTTGGAGTTTGAAGGG+TGG 0.695576 2.3:-30570334 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAGATGTTATAAGAAA+TGG - chr2.3:30570529-30570548 None:intergenic 15.0%
!! TATCAATAGTTTAATACTAT+TGG - chr2.3:30570871-30570890 None:intergenic 15.0%
!! TATTTAATTGTACTATATAC+AGG + chr2.3:30570648-30570667 MS.gene045724:intron 15.0%
!! GTTTATAAAATGAGCTTATT+AGG + chr2.3:30570963-30570982 MS.gene045724:intron 20.0%
!! TGTTAAATAGGCTTATAATA+GGG - chr2.3:30570599-30570618 None:intergenic 20.0%
!! TTACACATTAAGTGTTAAAT+AGG - chr2.3:30570611-30570630 None:intergenic 20.0%
!! TTCATGGATAACTTTATATA+AGG + chr2.3:30571428-30571447 MS.gene045724:CDS 20.0%
!!! GAAACTGGTTTAATATTTTT+GGG - chr2.3:30571330-30571349 None:intergenic 20.0%
!!! TGAAACTGGTTTAATATTTT+TGG - chr2.3:30571331-30571350 None:intergenic 20.0%
!!! TGAAATTTGATCAATTTTCA+GGG + chr2.3:30571014-30571033 MS.gene045724:intron 20.0%
!!! TTATTAGGTTGTGAATTTTA+AGG + chr2.3:30570978-30570997 MS.gene045724:intron 20.0%
!!! TTGAAATTTGATCAATTTTC+AGG + chr2.3:30571013-30571032 MS.gene045724:intron 20.0%
! AAAGTACAAATTGATCTTCT+GGG + chr2.3:30571083-30571102 MS.gene045724:CDS 25.0%
! AACTTTATATAAGGCAGTTA+GGG + chr2.3:30571437-30571456 MS.gene045724:CDS 25.0%
! AAGTATAAATTGGACAAGAA+TGG + chr2.3:30571261-30571280 MS.gene045724:CDS 25.0%
! ACCTATAGATATCATAATTG+AGG - chr2.3:30570479-30570498 None:intergenic 25.0%
! ACCTCAATTATGATATCTAT+AGG + chr2.3:30570475-30570494 MS.gene045724:CDS 25.0%
! GTGTTAAATAGGCTTATAAT+AGG - chr2.3:30570600-30570619 None:intergenic 25.0%
! TAACTTTATATAAGGCAGTT+AGG + chr2.3:30571436-30571455 MS.gene045724:CDS 25.0%
! TTATAAGAAATGGTGAAATG+AGG - chr2.3:30570519-30570538 None:intergenic 25.0%
!! AAAAGTACAAATTGATCTTC+TGG + chr2.3:30571082-30571101 MS.gene045724:CDS 25.0%
!! TATTAAACCAGTTTCAGTTT+TGG + chr2.3:30571335-30571354 MS.gene045724:CDS 25.0%
!!! AGACAAGTTTTTTTATGCTT+AGG + chr2.3:30570754-30570773 MS.gene045724:intron 25.0%
!!! TGAACATAAAGTTGATAACT+TGG + chr2.3:30571293-30571312 MS.gene045724:CDS 25.0%
AATTGTACTATATACAGGAC+CGG + chr2.3:30570653-30570672 MS.gene045724:intron 30.0%
ACAAAATCCAAAACTGAAAC+TGG - chr2.3:30571345-30571364 None:intergenic 30.0%
AGGCACTTCAAAGTATAAAT+TGG + chr2.3:30571251-30571270 MS.gene045724:CDS 30.0%
ATTCCAGTAAATGTGTTCAA+AGG - chr2.3:30571060-30571079 None:intergenic 30.0%
GATACAAGAAAATGTGAAGT+AGG - chr2.3:30570282-30570301 None:intergenic 30.0%
TGTTTATCTTGAACACTTGA+CGG - chr2.3:30570372-30570391 None:intergenic 30.0%
TTCCAGTAAATGTGTTCAAA+GGG - chr2.3:30571059-30571078 None:intergenic 30.0%
TTGACATAGAATTCATCCTT+TGG - chr2.3:30570399-30570418 None:intergenic 30.0%
! AGAAAATGTGAAGTAGGTTT+TGG - chr2.3:30570276-30570295 None:intergenic 30.0%
! CAGGGATGATATAACATTTT+TGG + chr2.3:30571032-30571051 MS.gene045724:intron 30.0%
!!! CTTTGGATTTTGATTGAGTT+GGG - chr2.3:30570224-30570243 None:intergenic 30.0%
!!! TCTTTGGATTTTGATTGAGT+TGG - chr2.3:30570225-30570244 None:intergenic 30.0%
AACCTTCGAAGAATGTGATA+TGG + chr2.3:30571169-30571188 MS.gene045724:CDS 35.0%
AGAAGAAGAATCAGATGAAG+TGG - chr2.3:30570307-30570326 None:intergenic 35.0%
AGGTCTTTGATGAAGATCAT+AGG - chr2.3:30570459-30570478 None:intergenic 35.0%
ATCCATATCACATTCTTCGA+AGG - chr2.3:30571174-30571193 None:intergenic 35.0%
CACTTGATGTATATAGAGTG+TGG + chr2.3:30571145-30571164 MS.gene045724:CDS 35.0%
CGAAGAATGTGATATGGATT+AGG + chr2.3:30571175-30571194 MS.gene045724:CDS 35.0%
GAAGCTAAAGGAGAATTTCA+AGG + chr2.3:30571231-30571250 MS.gene045724:CDS 35.0%
GATGAATTCTATGTCAACCT+TGG + chr2.3:30570402-30570421 MS.gene045724:CDS 35.0%
TCAAGATAAACAGCTTCCAA+AGG + chr2.3:30570380-30570399 MS.gene045724:CDS 35.0%
TTATGCTTAGGAGTTGAACT+TGG + chr2.3:30570766-30570785 MS.gene045724:intron 35.0%
TTGTGAAGTTGGAGTTTGAA+GGG - chr2.3:30570340-30570359 None:intergenic 35.0%
! TCCAAACCCTACATTTTTGT+GGG + chr2.3:30571383-30571402 MS.gene045724:CDS 35.0%
! TGGATTAGGTGGAAACTTAA+GGG + chr2.3:30571189-30571208 MS.gene045724:CDS 35.0%
!! AGAATGTGATATGGATTAGG+TGG + chr2.3:30571178-30571197 MS.gene045724:CDS 35.0%
!! ATGGATTAGGTGGAAACTTA+AGG + chr2.3:30571188-30571207 MS.gene045724:CDS 35.0%
!! TTTGATTGAGTTGGGAGATA+AGG - chr2.3:30570216-30570235 None:intergenic 35.0%
!!! GTTTTGGTGATGAAAGAGTT+TGG - chr2.3:30570260-30570279 None:intergenic 35.0%
!!! TGTTTTGAAAACTCGATGTC+CGG - chr2.3:30570675-30570694 None:intergenic 35.0%
CTTGTGAAGTTGGAGTTTGA+AGG - chr2.3:30570341-30570360 None:intergenic 40.0%
GACCCTTTGAACACATTTAC+TGG + chr2.3:30571054-30571073 MS.gene045724:CDS 40.0%
TGGATGTCTACTCTTCTTCA+TGG + chr2.3:30571412-30571431 MS.gene045724:CDS 40.0%
TTGGTGAAGAGGTTTGTCTT+TGG - chr2.3:30570241-30570260 None:intergenic 40.0%
! AATTCTCCTTTAGCTTCCCA+AGG - chr2.3:30571228-30571247 None:intergenic 40.0%
! AATTGATCTTCTGGGCATTG+AGG + chr2.3:30571091-30571110 MS.gene045724:CDS 40.0%
! ATTCTCCTTTAGCTTCCCAA+GGG - chr2.3:30571227-30571246 None:intergenic 40.0%
! CCAAACCCTACATTTTTGTG+GGG + chr2.3:30571384-30571403 MS.gene045724:CDS 40.0%
! GATGAAAGAGTTTGGTGAAG+AGG - chr2.3:30570252-30570271 None:intergenic 40.0%
! GTCCAAACCCTACATTTTTG+TGG + chr2.3:30571382-30571401 MS.gene045724:CDS 40.0%
!! AGGGAGACTTTGAAACAAGA+AGG + chr2.3:30571456-30571475 MS.gene045724:CDS 40.0%
!! GGGAGACTTTGAAACAAGAA+GGG + chr2.3:30571457-30571476 MS.gene045724:CDS 40.0%
!! GGTGTGTTAACTTGTGAAGT+TGG - chr2.3:30570351-30570370 None:intergenic 40.0%
ACAGGACCCCACAAAAATGT+AGG - chr2.3:30571393-30571412 None:intergenic 45.0%
CAGGACCCCACAAAAATGTA+GGG - chr2.3:30571392-30571411 None:intergenic 45.0%
CCCCACAAAAATGTAGGGTT+TGG - chr2.3:30571387-30571406 None:intergenic 45.0%
GAAGAAGAGTAGACATCCAC+AGG - chr2.3:30571411-30571430 None:intergenic 45.0%
GAGTTGGGAGATAAGGTTGT+AGG - chr2.3:30570209-30570228 None:intergenic 45.0%
GGGAGATAAGGTTGTAGGTT+TGG - chr2.3:30570204-30570223 None:intergenic 45.0%
TGAAGTTGGAGTTTGAAGGG+TGG - chr2.3:30570337-30570356 None:intergenic 45.0%
! GAGTTCTAACAGCAAGTCCA+AGG - chr2.3:30570422-30570441 None:intergenic 45.0%
! TACATTTTTGTGGGGTCCTG+TGG + chr2.3:30571392-30571411 MS.gene045724:CDS 45.0%
!! AATGTAGGGTTTGGACTAGC+AGG - chr2.3:30571378-30571397 None:intergenic 45.0%
!! ATGTAGGGTTTGGACTAGCA+GGG - chr2.3:30571377-30571396 None:intergenic 45.0%
!! TTCTGGGCATTGAGGTTTCA+TGG + chr2.3:30571099-30571118 MS.gene045724:CDS 45.0%
CATGGAGCTAGACCATCTTG+TGG - chr2.3:30571492-30571511 None:intergenic 50.0%
CTATTGGAGTCTAGCGCAAG+TGG - chr2.3:30570855-30570874 None:intergenic 50.0%
GGAGTTTGAAGGGTGGCTAA+GGG - chr2.3:30570330-30570349 None:intergenic 50.0%
TGGAGTTTGAAGGGTGGCTA+AGG - chr2.3:30570331-30570350 None:intergenic 50.0%
!! GGGAGTTTGCTACCACAAGA+TGG + chr2.3:30571477-30571496 MS.gene045724:CDS 50.0%
CGTGTCCCTTGGGAAGCTAA+AGG + chr2.3:30571219-30571238 MS.gene045724:CDS 55.0%
TGGAGTCTAGCGCAAGTGGT+TGG - chr2.3:30570851-30570870 None:intergenic 55.0%
TTAGCTTCCCAAGGGACACG+CGG - chr2.3:30571219-30571238 None:intergenic 55.0%
! GGTTGGTGCATGTGGTGTGT+CGG - chr2.3:30570834-30570853 None:intergenic 55.0%
! GCGCAAGTGGTTGGTGCATG+TGG - chr2.3:30570842-30570861 None:intergenic 60.0%
AGGGCGTGCCGCGTGTCCCT+TGG + chr2.3:30571208-30571227 MS.gene045724:CDS 75.0%
GGGCGTGCCGCGTGTCCCTT+GGG + chr2.3:30571209-30571228 MS.gene045724:CDS 75.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 30570186 30571518 30570186 ID=MS.gene045724
chr2.3 mRNA 30570186 30571518 30570186 ID=MS.gene045724.t1;Parent=MS.gene045724
chr2.3 exon 30570186 30570496 30570186 ID=MS.gene045724.t1.exon1;Parent=MS.gene045724.t1
chr2.3 CDS 30570186 30570496 30570186 ID=cds.MS.gene045724.t1;Parent=MS.gene045724.t1
chr2.3 exon 30571035 30571518 30571035 ID=MS.gene045724.t1.exon2;Parent=MS.gene045724.t1
chr2.3 CDS 30571035 30571518 30571035 ID=cds.MS.gene045724.t1;Parent=MS.gene045724.t1
Gene Sequence

>MS.gene045724

ATGGCTTTTCTTCTACCAAACCTACAACCTTATCTCCCAACTCAATCAAAATCCAAAGACAAACCTCTTCACCAAACTCTTTCATCACCAAAACCTACTTCACATTTTCTTGTATCTTCCACTTCATCTGATTCTTCTTCTCCCTTAGCCACCCTTCAAACTCCAACTTCACAAGTTAACACACCGTCAAGTGTTCAAGATAAACAGCTTCCAAAGGATGAATTCTATGTCAACCTTGGACTTGCTGTTAGAACTCTTCGTGAAGACATGCCTATGATCTTCATCAAAGACCTCAATTATGATATCTATAGGTTATTTGACTATTTCTCACCTCATTTCACCATTTCTTATAACATCTTTTTTTGATTATTTTTGATATATAATTATTCTAACTTTTATTATGTCATCATCCCTATTATAAGCCTATTTAACACTTAATGTGTAAATTTTGTATATGAATATTATTTAATTGTACTATATACAGGACCGGACATCGAGTTTTCAAAACAAAAAAAAAAATTGCACTATATACAAAGATATGTTCAATATTTATTTTTCTTTTCTTCTAAGACAAGTTTTTTTATGCTTAGGAGTTGAACTTGGCATCTCGATATTTACAACACTAGCACACGCAAGAGTGTAACACCGACACACCACATGCACCAACCACTTGCGCTAGACTCCAATAGTATTAAACTATTGATAAATGATGTAATTTTTTTTATAAAAAGATAGCTAGTAATTTGAAATGATGTTTATATTTTTTATTTTTCGTTTGTTTATAAAATGAGCTTATTAGGTTGTGAATTTTAAGGAGCTTATTTTCATTGAAATTTGATCAATTTTCAGGGATGATATAACATTTTTGGACCCTTTGAACACATTTACTGGAATTGAAAAGTACAAATTGATCTTCTGGGCATTGAGGTTTCATGGTAAGCTCTTGTTTCATGATATAGCACTTGATGTATATAGAGTGTGGCAACCTTCGAAGAATGTGATATGGATTAGGTGGAAACTTAAGGGCGTGCCGCGTGTCCCTTGGGAAGCTAAAGGAGAATTTCAAGGCACTTCAAAGTATAAATTGGACAAGAATGGCAAAATTTATGAACATAAAGTTGATAACTTGGCATTCAATTTTCCCAAAAATATTAAACCAGTTTCAGTTTTGGATTTTGTTACTTCATGCCCTGCTAGTCCAAACCCTACATTTTTGTGGGGTCCTGTGGATGTCTACTCTTCTTCATGGATAACTTTATATAAGGCAGTTAGGGAGACTTTGAAACAAGAAGGGAGTTTGCTACCACAAGATGGTCTAGCTCCATGCTCGTAA
Protein sequence

>MS.gene045724.t1

MAFLLPNLQPYLPTQSKSKDKPLHQTLSSPKPTSHFLVSSTSSDSSSPLATLQTPTSQVNTPSSVQDKQLPKDEFYVNLGLAVRTLREDMPMIFIKDLNYDIYRDDITFLDPLNTFTGIEKYKLIFWALRFHGKLLFHDIALDVYRVWQPSKNVIWIRWKLKGVPRVPWEAKGEFQGTSKYKLDKNGKIYEHKVDNLAFNFPKNIKPVSVLDFVTSCPASPNPTFLWGPVDVYSSSWITLYKAVRETLKQEGSLLPQDGLAPCS