AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76487

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

Find 54 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCACACCCCATTTCTTTA+AGG 0.104108 2.3:-26888721 None:intergenic
TCTGGAAATTCTTCTGATTT+TGG 0.105734 2.3:-26888315 None:intergenic
AATGATGCTACTGAAATTCT+TGG 0.264938 2.3:-26889363 None:intergenic
TCCTGAACCTGAATTAACTA+TGG 0.273538 2.3:+26888781 MS.gene76487:CDS
TTCAAAATGCATGTGAGAAT+TGG 0.274570 2.3:+26888073 MS.gene76487:CDS
ACCATGATCCTGCTGCTAAT+TGG 0.278960 2.3:+26888256 MS.gene76487:CDS
CCCATAGTTAATTCAGGTTC+AGG 0.289025 2.3:-26888782 None:intergenic
CAGATTTCACCTTAAAGAAA+TGG 0.315474 2.3:+26888712 MS.gene76487:CDS
AACATAAACAACTTTCTTGT+TGG 0.326447 2.3:-26888217 None:intergenic
AAGAATTTCCAGAAGTTTGC+AGG 0.326623 2.3:+26888325 MS.gene76487:CDS
GTATTTCCCATAGTTAATTC+AGG 0.327357 2.3:-26888788 None:intergenic
TCAAAATGCATGTGAGAATT+GGG 0.329016 2.3:+26888074 MS.gene76487:CDS
GATGACGAATCAATAGTTTA+TGG 0.337844 2.3:+26889396 MS.gene76487:CDS
TCAGATAATAGTTCCTTGAT+TGG 0.344604 2.3:-26889420 None:intergenic
AATATGATCTTGCAAAAGTA+TGG 0.350855 2.3:-26888837 None:intergenic
GAGCTCTTGTTGTAAACATT+GGG 0.365496 2.3:+26888915 MS.gene76487:CDS
ACATAAACAACTTTCTTGTT+GGG 0.391612 2.3:-26888216 None:intergenic
AGATTTCACCTTAAAGAAAT+GGG 0.397490 2.3:+26888713 MS.gene76487:CDS
ATCCCTACAATTGACTTAAC+AGG 0.400279 2.3:+26888006 MS.gene76487:CDS
ACAACAAGAGCTCCATTGAT+AGG 0.413685 2.3:-26888905 None:intergenic
ATTCCTGTTAAGTCAATTGT+AGG 0.415919 2.3:-26888009 None:intergenic
AAGAAAATCCACCAGTGTAC+AGG 0.418600 2.3:+26889442 MS.gene76487:CDS
TTCTTTCAAGTAATAAATCA+TGG 0.422804 2.3:+26888099 MS.gene76487:CDS
CAATATTATGCAAAGGGCAT+TGG 0.435867 2.3:+26889492 MS.gene76487:CDS
TCCAATTAGCAGCAGGATCA+TGG 0.444471 2.3:-26888257 None:intergenic
GAAGTCATTATCTGTGTGAT+TGG 0.452124 2.3:-26888810 None:intergenic
GAGTTATTGTCAGAAGCTCT+AGG 0.463245 2.3:+26888683 MS.gene76487:CDS
GGAGCTCTTGTTGTAAACAT+TGG 0.484525 2.3:+26888914 MS.gene76487:CDS
TCAAAACAATATTATGCAAA+GGG 0.500438 2.3:+26889486 MS.gene76487:CDS
AAAGAAATGGGGTGTGCTGA+AGG 0.511020 2.3:+26888725 MS.gene76487:CDS
GCTAATTGGAGGGACTCACT+TGG 0.514483 2.3:+26888270 MS.gene76487:CDS
AATAGTTTATGGTCCAATCA+AGG 0.515467 2.3:+26889407 MS.gene76487:CDS
GTTAATTCAGGTTCAGGACA+TGG 0.521966 2.3:-26888776 None:intergenic
ATTGATGTAACTCCTATCAA+TGG 0.530271 2.3:+26888893 MS.gene76487:CDS
CCTGAACCTGAATTAACTAT+GGG 0.530329 2.3:+26888782 MS.gene76487:CDS
AAGTTCTTCATGACAATCAG+TGG 0.532579 2.3:+26888870 MS.gene76487:CDS
ATGATCCTGCTGCTAATTGG+AGG 0.534155 2.3:+26888259 MS.gene76487:CDS
CTCTCAAAACAAGATCATCA+TGG 0.540096 2.3:-26888032 None:intergenic
CTCAAAACAATATTATGCAA+AGG 0.543006 2.3:+26889485 MS.gene76487:CDS
AGTTATTGTCAGAAGCTCTA+GGG 0.549571 2.3:+26888684 MS.gene76487:CDS
GAGTCCCTCCAATTAGCAGC+AGG 0.553194 2.3:-26888264 None:intergenic
TTCCTGTTAAGTCAATTGTA+GGG 0.572686 2.3:-26888008 None:intergenic
CAAAATGCATGTGAGAATTG+GGG 0.577869 2.3:+26888075 MS.gene76487:CDS
TGTTCACAATAGAACATATG+TGG 0.578199 2.3:-26887934 None:intergenic
AGAAAATCCACCAGTGTACA+GGG 0.586210 2.3:+26889443 MS.gene76487:CDS
AAGAAATGGGGTGTGCTGAA+GGG 0.599939 2.3:+26888726 MS.gene76487:CDS
AAAGAAACATCCCTGTACAC+TGG 0.604288 2.3:-26889453 None:intergenic
ATTTCATCAACAAGATGCCA+AGG 0.607497 2.3:+26888167 MS.gene76487:CDS
GAAACATCCCTGTACACTGG+TGG 0.619504 2.3:-26889450 None:intergenic
ATTCAGGTTCAGGACATGGA+GGG 0.623067 2.3:-26888772 None:intergenic
TGATCCTGCTGCTAATTGGA+GGG 0.625454 2.3:+26888260 MS.gene76487:CDS
AGCTCTTGTTGTAAACATTG+GGG 0.655058 2.3:+26888916 MS.gene76487:CDS
GATTTCACCTTAAAGAAATG+GGG 0.657216 2.3:+26888714 MS.gene76487:CDS
AATTCAGGTTCAGGACATGG+AGG 0.676379 2.3:-26888773 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATAGACTAAATTGA+CGG - chr2.3:26888493-26888512 None:intergenic 15.0%
!! TTTAAGTATATAAAGTCTAT+AGG + chr2.3:26888445-26888464 MS.gene76487:intron 15.0%
!!! ACTTTTTAATTTATTCTAGA+AGG + chr2.3:26888398-26888417 MS.gene76487:intron 15.0%
!!! CTTTTTAATTTATTCTAGAA+GGG + chr2.3:26888399-26888418 MS.gene76487:intron 15.0%
!! ATTCTTCAAAAATTCTTGTT+TGG + chr2.3:26888546-26888565 MS.gene76487:intron 20.0%
!! TCAAAACAATATTATGCAAA+GGG + chr2.3:26889486-26889505 MS.gene76487:CDS 20.0%
!! TGCACAAAATACAATTAAAT+TGG - chr2.3:26889282-26889301 None:intergenic 20.0%
!! TTTACAGGTAAATAATCATT+TGG + chr2.3:26888943-26888962 MS.gene76487:intron 20.0%
!!! ATAACATCTGAAATAAGAAT+TGG + chr2.3:26889248-26889267 MS.gene76487:intron 20.0%
!!! TCAATATTTTCTTAACCTTA+AGG - chr2.3:26888379-26888398 None:intergenic 20.0%
!!! TCTATTTTATTACGATGTTA+GGG + chr2.3:26888502-26888521 MS.gene76487:intron 20.0%
!!! TTCTTTCAAGTAATAAATCA+TGG + chr2.3:26888099-26888118 MS.gene76487:CDS 20.0%
! AACATAAACAACTTTCTTGT+TGG - chr2.3:26888220-26888239 None:intergenic 25.0%
! AATATGATCTTGCAAAAGTA+TGG - chr2.3:26888840-26888859 None:intergenic 25.0%
! ACATAAACAACTTTCTTGTT+GGG - chr2.3:26888219-26888238 None:intergenic 25.0%
! AGAGATTAAATTAGACTGAA+AGG - chr2.3:26888426-26888445 None:intergenic 25.0%
! AGATTTCACCTTAAAGAAAT+GGG + chr2.3:26888713-26888732 MS.gene76487:CDS 25.0%
! CTCAAAACAATATTATGCAA+AGG + chr2.3:26889485-26889504 MS.gene76487:CDS 25.0%
! TATACATTATCAATGCATCA+AGG - chr2.3:26888603-26888622 None:intergenic 25.0%
! TGAATACTCAGAAAAAGTAA+TGG + chr2.3:26888640-26888659 MS.gene76487:CDS 25.0%
! TGGTAACACAATTATTGTTT+AGG + chr2.3:26888566-26888585 MS.gene76487:intron 25.0%
!! ATACTTTTGCAAGATCATAT+TGG + chr2.3:26888839-26888858 MS.gene76487:CDS 25.0%
!! GTCTATTTTATTACGATGTT+AGG + chr2.3:26888501-26888520 MS.gene76487:intron 25.0%
!! TTTTTCCTTCTTAATGTTGT+GGG + chr2.3:26888351-26888370 MS.gene76487:intron 25.0%
!!! TGGAATTTTAACTCATGTTT+TGG + chr2.3:26888119-26888138 MS.gene76487:CDS 25.0%
!!! TTTTTTCCTTCTTAATGTTG+TGG + chr2.3:26888350-26888369 MS.gene76487:intron 25.0%
AAAAAAAACCTGCAAACTTC+TGG - chr2.3:26888336-26888355 None:intergenic 30.0%
AATAGTTTATGGTCCAATCA+AGG + chr2.3:26889407-26889426 MS.gene76487:CDS 30.0%
AATGATGCTACTGAAATTCT+TGG - chr2.3:26889366-26889385 None:intergenic 30.0%
ACATTATAGACATGTAGCAA+AGG + chr2.3:26889223-26889242 MS.gene76487:intron 30.0%
ATTCCTGTTAAGTCAATTGT+AGG - chr2.3:26888012-26888031 None:intergenic 30.0%
ATTGATGTAACTCCTATCAA+TGG + chr2.3:26888893-26888912 MS.gene76487:CDS 30.0%
CAGATTTCACCTTAAAGAAA+TGG + chr2.3:26888712-26888731 MS.gene76487:CDS 30.0%
GATGACGAATCAATAGTTTA+TGG + chr2.3:26889396-26889415 MS.gene76487:CDS 30.0%
GATTTCACCTTAAAGAAATG+GGG + chr2.3:26888714-26888733 MS.gene76487:CDS 30.0%
GTATTTCCCATAGTTAATTC+AGG - chr2.3:26888791-26888810 None:intergenic 30.0%
TCAAAATGCATGTGAGAATT+GGG + chr2.3:26888074-26888093 MS.gene76487:CDS 30.0%
TCAGATAATAGTTCCTTGAT+TGG - chr2.3:26889423-26889442 None:intergenic 30.0%
TGTTCACAATAGAACATATG+TGG - chr2.3:26887937-26887956 None:intergenic 30.0%
TTCAAAATGCATGTGAGAAT+TGG + chr2.3:26888073-26888092 MS.gene76487:CDS 30.0%
TTCCTGTTAAGTCAATTGTA+GGG - chr2.3:26888011-26888030 None:intergenic 30.0%
! ATAATACTCTTTTCTCACCT+TGG - chr2.3:26888187-26888206 None:intergenic 30.0%
! TCTGGAAATTCTTCTGATTT+TGG - chr2.3:26888318-26888337 None:intergenic 30.0%
!! AGAGTTTTAGCAAAGCATAT+TGG + chr2.3:26889339-26889358 MS.gene76487:CDS 30.0%
!! GTTCTCTCAAGATTTTTCAA+TGG - chr2.3:26889152-26889171 None:intergenic 30.0%
AAGAATTTCCAGAAGTTTGC+AGG + chr2.3:26888325-26888344 MS.gene76487:CDS 35.0%
AAGTTCTTCATGACAATCAG+TGG + chr2.3:26888870-26888889 MS.gene76487:CDS 35.0%
AGATGTTGCCAAAATCACAA+TGG - chr2.3:26889027-26889046 None:intergenic 35.0%
AGTTATTGTCAGAAGCTCTA+GGG + chr2.3:26888684-26888703 MS.gene76487:CDS 35.0%
ATCAATGCATCAAGGTTAGT+AGG - chr2.3:26888595-26888614 None:intergenic 35.0%
ATTTCATCAACAAGATGCCA+AGG + chr2.3:26888167-26888186 MS.gene76487:CDS 35.0%
CAAAATGCATGTGAGAATTG+GGG + chr2.3:26888075-26888094 MS.gene76487:CDS 35.0%
CCTGAACCTGAATTAACTAT+GGG + chr2.3:26888782-26888801 MS.gene76487:CDS 35.0%
CTCTCAAAACAAGATCATCA+TGG - chr2.3:26888035-26888054 None:intergenic 35.0%
GAAGTCATTATCTGTGTGAT+TGG - chr2.3:26888813-26888832 None:intergenic 35.0%
TAGATGTTCATGAAACCATG+CGG - chr2.3:26889081-26889100 None:intergenic 35.0%
TCCTGAACCTGAATTAACTA+TGG + chr2.3:26888781-26888800 MS.gene76487:CDS 35.0%
TTAATGTTGTGGGATCCTTA+AGG + chr2.3:26888361-26888380 MS.gene76487:intron 35.0%
! AAACATTGGGGATCTTTTAC+AGG + chr2.3:26888928-26888947 MS.gene76487:CDS 35.0%
! AGCTCTTGTTGTAAACATTG+GGG + chr2.3:26888916-26888935 MS.gene76487:CDS 35.0%
! ATCCCTACAATTGACTTAAC+AGG + chr2.3:26888006-26888025 MS.gene76487:CDS 35.0%
! CAATATTATGCAAAGGGCAT+TGG + chr2.3:26889492-26889511 MS.gene76487:CDS 35.0%
! CTTTTGCAAGATCATATTGG+TGG + chr2.3:26888842-26888861 MS.gene76487:CDS 35.0%
! GAGCTCTTGTTGTAAACATT+GGG + chr2.3:26888915-26888934 MS.gene76487:CDS 35.0%
! GGAAATTCTTCTGATTTTGG+TGG - chr2.3:26888315-26888334 None:intergenic 35.0%
!! GTTTTGGATGAGATGATCAA+AGG + chr2.3:26888135-26888154 MS.gene76487:CDS 35.0%
!!! TCTTCTGATTTTGGTGGATT+TGG - chr2.3:26888309-26888328 None:intergenic 35.0%
AAAGAAACATCCCTGTACAC+TGG - chr2.3:26889456-26889475 None:intergenic 40.0%
AAGAAAATCCACCAGTGTAC+AGG + chr2.3:26889442-26889461 MS.gene76487:CDS 40.0%
ACAACAAGAGCTCCATTGAT+AGG - chr2.3:26888908-26888927 None:intergenic 40.0%
AGAAAATCCACCAGTGTACA+GGG + chr2.3:26889443-26889462 MS.gene76487:CDS 40.0%
AGGATCCCACAACATTAAGA+AGG - chr2.3:26888359-26888378 None:intergenic 40.0%
GAGTTATTGTCAGAAGCTCT+AGG + chr2.3:26888683-26888702 MS.gene76487:CDS 40.0%
! CCCATAGTTAATTCAGGTTC+AGG - chr2.3:26888785-26888804 None:intergenic 40.0%
! GGAGCTCTTGTTGTAAACAT+TGG + chr2.3:26888914-26888933 MS.gene76487:CDS 40.0%
! GTTAATTCAGGTTCAGGACA+TGG - chr2.3:26888779-26888798 None:intergenic 40.0%
!! GGACTCACTTGGTTTTTCTA+TGG + chr2.3:26888281-26888300 MS.gene76487:CDS 40.0%
!! GTTGTGTGCCATTGTGATTT+TGG + chr2.3:26889016-26889035 MS.gene76487:intron 40.0%
AAAGAAATGGGGTGTGCTGA+AGG + chr2.3:26888725-26888744 MS.gene76487:CDS 45.0%
AAGAAATGGGGTGTGCTGAA+GGG + chr2.3:26888726-26888745 MS.gene76487:CDS 45.0%
ACAAAATCACAGTGTCCGCA+TGG + chr2.3:26889063-26889082 MS.gene76487:intron 45.0%
ACCATGATCCTGCTGCTAAT+TGG + chr2.3:26888256-26888275 MS.gene76487:CDS 45.0%
ACGAGAAGTCAGAGGATCAA+TGG + chr2.3:26889170-26889189 MS.gene76487:intron 45.0%
ATGATCCTGCTGCTAATTGG+AGG + chr2.3:26888259-26888278 MS.gene76487:CDS 45.0%
CAGCACACCCCATTTCTTTA+AGG - chr2.3:26888724-26888743 None:intergenic 45.0%
TCCAATTAGCAGCAGGATCA+TGG - chr2.3:26888260-26888279 None:intergenic 45.0%
TGATCCTGCTGCTAATTGGA+GGG + chr2.3:26888260-26888279 MS.gene76487:CDS 45.0%
TTGAGAGAACGAGAAGTCAG+AGG + chr2.3:26889162-26889181 MS.gene76487:intron 45.0%
! AATTCAGGTTCAGGACATGG+AGG - chr2.3:26888776-26888795 None:intergenic 45.0%
! ATTCAGGTTCAGGACATGGA+GGG - chr2.3:26888775-26888794 None:intergenic 45.0%
GAAACATCCCTGTACACTGG+TGG - chr2.3:26889453-26889472 None:intergenic 50.0%
GCTAATTGGAGGGACTCACT+TGG + chr2.3:26888270-26888289 MS.gene76487:CDS 50.0%
GAGTCCCTCCAATTAGCAGC+AGG - chr2.3:26888267-26888286 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 26887932 26889545 26887932 ID=MS.gene76487
chr2.3 mRNA 26887932 26889545 26887932 ID=MS.gene76487.t1;Parent=MS.gene76487
chr2.3 exon 26887932 26888346 26887932 ID=MS.gene76487.t1.exon1;Parent=MS.gene76487.t1
chr2.3 CDS 26887932 26888346 26887932 ID=cds.MS.gene76487.t1;Parent=MS.gene76487.t1
chr2.3 exon 26888628 26888949 26888628 ID=MS.gene76487.t1.exon2;Parent=MS.gene76487.t1
chr2.3 CDS 26888628 26888949 26888628 ID=cds.MS.gene76487.t1;Parent=MS.gene76487.t1
chr2.3 exon 26889303 26889545 26889303 ID=MS.gene76487.t1.exon3;Parent=MS.gene76487.t1
chr2.3 CDS 26889303 26889545 26889303 ID=cds.MS.gene76487.t1;Parent=MS.gene76487.t1
Gene Sequence

>MS.gene76487

TTCCACATATGTTCTATTGTGAACAATCTAGTATCAATGATGTTTCAGTCAATGATTCAAATTCAAAGCTAAGTATCCCTACAATTGACTTAACAGGAATCCATGATGATCTTGTTTTGAGAGATGAAGTTGTGAGAAAAGTTCAAAATGCATGTGAGAATTGGGGATTCTTTCAAGTAATAAATCATGGAATTTTAACTCATGTTTTGGATGAGATGATCAAAGGAACTTGTAGATTTCATCAACAAGATGCCAAGGTGAGAAAAGAGTATTATACACGCGATCCCAACAAGAAAGTTGTTTATGTTTCTAATTATAGTCTTTACCATGATCCTGCTGCTAATTGGAGGGACTCACTTGGTTTTTCTATGGCACCAAATCCACCAAAATCAGAAGAATTTCCAGAAGTTTGCAGGTTTTTTTTCCTTCTTAATGTTGTGGGATCCTTAAGGTTAAGAAAATATTGACTTTTTAATTTATTCTAGAAGGGACCTTTCAGTCTAATTTAATCTCTTTAAGTATATAAAGTCTATAGGCAGTCTCTATAATCTATGAAATCCGTCAATTTAGTCTATTTTATTACGATGTTAGGGACTAACGTAACAGATTTTTATATTCTTCAAAAATTCTTGTTTGGTAACACAATTATTGTTTAGGTATCCTACTAACCTTGATGCATTGATAATGTATATGCAGAGATATTGTGATTGAATACTCAGAAAAAGTAATGGTGTTTGCTTCTACATTACTTGAGTTATTGTCAGAAGCTCTAGGGCTAAACAGATTTCACCTTAAAGAAATGGGGTGTGCTGAAGGGTCTATTGTTCTATGTCACTATTACCCTCCATGTCCTGAACCTGAATTAACTATGGGAAATACCAATCACACAGATAATGACTTCATAACCATACTTTTGCAAGATCATATTGGTGGCTTACAAGTTCTTCATGACAATCAGTGGATTGATGTAACTCCTATCAATGGAGCTCTTGTTGTAAACATTGGGGATCTTTTACAGGTAAATAATCATTTGGATCTGCGTAGTTGAAACTTAAAATTGATTTTGATTGAGTTTCATAGAATCGTTGTGTGCCATTGTGATTTTGGCAACATCTACAATTCGAAACTTCTACAAAATCACAGTGTCCGCATGGTTTCATGAACATCTATAATTTTGTTTATATTTTTCATGAACTAAATAAAATTTTCATATGTTTCCATTGAAAAATCTTGAGAGAACGAGAAGTCAGAGGATCAATGGATTTGTTCTTATTATTTTACTTCTCTGTGAACATTATAGACATGTAGCAAAGGTTATAACATCTGAAATAAGAATTGGATTGATTACCAATTTAATTGTATTTTGTGCAGCTTGTTACTAATGACAAGTTCATTAGCGTTCAACACAGAGTTTTAGCAAAGCATATTGGTCCAAGAATTTCAGTAGCATCATTGTTTAGAACAGATGACGAATCAATAGTTTATGGTCCAATCAAGGAACTATTATCTGAAGAAAATCCACCAGTGTACAGGGATGTTTCTTTAAAAGACTACTCAAAACAATATTATGCAAAGGGCATTGGAATTTCTGCATTATCACATTTCAAATTGTGA
Protein sequence

>MS.gene76487.t1

FHICSIVNNLVSMMFQSMIQIQSUVSLQLTUQESMMILFUEMKLUEKFKMHVRIGDSFKUUIMEFULMFWMRUSKELVDFINKMPRUEKSIIHAIPTRKLFMFLIIVFTMILLLIGGTHLVFLWHQIHQNQKNFQKFAEILULNTQKKUWCLLLHYLSYCQKLUGUTDFTLKKWGVLKGLLFYVTITLHVLNLNULWEIPITQIMTSUPYFCKIILVAYKFFMTISGLMULLSMELLLUTLGIFYSLLLMTSSLAFNTEFUQSILVQEFQUHHCLEQMTNQUFMVQSRNYYLKKIHQCTGMFLUKTTQNNIMQRALEFLHYHISNC