AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043809

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043809.t1 MTR_1g019850 83.099 213 25 1 1 213 28 229 3.62e-114 327
MS.gene043809.t1 MTR_0853s0010 56.204 137 53 1 40 169 22 158 9.19e-47 153
MS.gene043809.t1 MTR_2g024230 77.000 100 22 1 1 99 47 146 1.56e-46 152
MS.gene043809.t1 MTR_1g033820 58.000 50 21 0 38 87 22 71 1.50e-15 70.1
MS.gene043809.t1 MTR_6g048540 49.351 77 33 2 26 96 5 81 5.01e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043809.t1 AT4G38180 28.910 211 120 7 12 201 31 232 3.27e-15 74.7

Find 34 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCCAAAACCTTCTTTCT+TGG 0.194532 2.2:+27920496 None:intergenic
TATTTGTCCTATTGTTGATA+TGG 0.229024 2.2:-27920564 MS.gene043809:CDS
AAGCAGGGAAGAGAAGTAAA+TGG 0.304863 2.2:-27920331 MS.gene043809:CDS
CACATATTGGCCACACTCTT+AGG 0.328854 2.2:+27920263 None:intergenic
TTTGCCAAGAAAGAAGGTTT+TGG 0.354079 2.2:-27920500 MS.gene043809:CDS
CCTTGTCTAGTCAGGATTGC+TGG 0.382474 2.2:-27920134 MS.gene043809:CDS
TTTCTTATGAGAACACATAT+TGG 0.382977 2.2:+27920250 None:intergenic
TCAAATTCCATATCAACAAT+AGG 0.427064 2.2:+27920557 None:intergenic
GAAGGTACACATATAGTAAA+GGG 0.439216 2.2:-27920425 MS.gene043809:CDS
ATTGAGAAGTTTGATGAAGA+AGG 0.450541 2.2:-27920203 MS.gene043809:CDS
TCACTTACTGTTTCAAAAGC+AGG 0.452498 2.2:-27920347 MS.gene043809:CDS
ACATCGTTTGCCAAGAAAGA+AGG 0.462978 2.2:-27920506 MS.gene043809:CDS
ATAGGACAAATATTAGCTTC+AGG 0.478911 2.2:+27920575 None:intergenic
AAAGTTGCTACGATGTTTCA+AGG 0.482139 2.2:-27920168 MS.gene043809:CDS
AGATAATGCCTTGTCTAGTC+AGG 0.485015 2.2:-27920142 MS.gene043809:CDS
AGCAGGGAAGAGAAGTAAAT+GGG 0.489503 2.2:-27920330 MS.gene043809:CDS
TGAAGGTACACATATAGTAA+AGG 0.494494 2.2:-27920426 MS.gene043809:CDS
GTAAAGGGTGAAAATGAAGA+AGG 0.507431 2.2:-27920410 MS.gene043809:CDS
TGCTTTACAATCAGTTCTTG+AGG 0.537334 2.2:+27920370 None:intergenic
CACTTACTGTTTCAAAAGCA+GGG 0.542698 2.2:-27920346 MS.gene043809:CDS
ATAAACAATGATCACAATCA+TGG 0.544230 2.2:-27920296 MS.gene043809:CDS
GTACATGGATAATGAGTATG+TGG 0.550566 2.2:-27920687 None:intergenic
GATGAAGAAGGAGTACCTAC+AGG 0.552486 2.2:-27920191 MS.gene043809:CDS
TAAAGGGTGAAAATGAAGAA+GGG 0.554329 2.2:-27920409 MS.gene043809:CDS
CAAAAGAAGAAATCTTGATG+TGG 0.555631 2.2:-27920094 MS.gene043809:CDS
AAAAGAAGAAATCTTGATGT+GGG 0.562793 2.2:-27920093 MS.gene043809:CDS
CTTCATCAAACTTCTCAATG+AGG 0.566857 2.2:+27920207 None:intergenic
CAATGATCACAATCATGGAA+TGG 0.570975 2.2:-27920291 MS.gene043809:CDS
ACACATCATCAACTATCTCA+TGG 0.582009 2.2:+27920636 None:intergenic
CCAGCAATCCTGACTAGACA+AGG 0.599935 2.2:+27920134 None:intergenic
CATCGTAGCAACTTTCCTGT+AGG 0.608916 2.2:+27920176 None:intergenic
TATGGAATTTGACTCCATTG+TGG 0.618496 2.2:-27920546 MS.gene043809:CDS
ATGCTTGTATGCGCTAATGA+AGG 0.648792 2.2:-27920443 MS.gene043809:CDS
AATGGTTAGTCCTAAGAGTG+TGG 0.676645 2.2:-27920273 MS.gene043809:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTATTGCATAAAAAAAATT+GGG + chr2.2:27920663-27920682 None:intergenic 15.0%
!! TTGTATTGCATAAAAAAAAT+TGG + chr2.2:27920664-27920683 None:intergenic 15.0%
!!! GACTTGAAATTTTCTAAATT+TGG + chr2.2:27920085-27920104 None:intergenic 20.0%
! AAAAGAAGAAATCTTGATGT+GGG - chr2.2:27920588-27920607 MS.gene043809:CDS 25.0%
! ATAAACAATGATCACAATCA+TGG - chr2.2:27920385-27920404 MS.gene043809:CDS 25.0%
! TATTTGTCCTATTGTTGATA+TGG - chr2.2:27920117-27920136 MS.gene043809:CDS 25.0%
! TCAAATTCCATATCAACAAT+AGG + chr2.2:27920127-27920146 None:intergenic 25.0%
! TTTCTTATGAGAACACATAT+TGG + chr2.2:27920434-27920453 None:intergenic 25.0%
ATTGAGAAGTTTGATGAAGA+AGG - chr2.2:27920478-27920497 MS.gene043809:CDS 30.0%
CAAAAGAAGAAATCTTGATG+TGG - chr2.2:27920587-27920606 MS.gene043809:CDS 30.0%
TAAAGGGTGAAAATGAAGAA+GGG - chr2.2:27920272-27920291 MS.gene043809:CDS 30.0%
! ATAGGACAAATATTAGCTTC+AGG + chr2.2:27920109-27920128 None:intergenic 30.0%
! GAAGGTACACATATAGTAAA+GGG - chr2.2:27920256-27920275 MS.gene043809:CDS 30.0%
! GAATTCTTTTACATCCACAA+TGG + chr2.2:27920152-27920171 None:intergenic 30.0%
! TGAAGGTACACATATAGTAA+AGG - chr2.2:27920255-27920274 MS.gene043809:CDS 30.0%
AAAGTTGCTACGATGTTTCA+AGG - chr2.2:27920513-27920532 MS.gene043809:CDS 35.0%
AACTCCAAAACCTTCTTTCT+TGG + chr2.2:27920188-27920207 None:intergenic 35.0%
ACACATCATCAACTATCTCA+TGG + chr2.2:27920048-27920067 None:intergenic 35.0%
CAATGATCACAATCATGGAA+TGG - chr2.2:27920390-27920409 MS.gene043809:CDS 35.0%
CACTTACTGTTTCAAAAGCA+GGG - chr2.2:27920335-27920354 MS.gene043809:CDS 35.0%
CTTCATCAAACTTCTCAATG+AGG + chr2.2:27920477-27920496 None:intergenic 35.0%
GTAAAGGGTGAAAATGAAGA+AGG - chr2.2:27920271-27920290 MS.gene043809:CDS 35.0%
TATGGAATTTGACTCCATTG+TGG - chr2.2:27920135-27920154 MS.gene043809:CDS 35.0%
TCACTTACTGTTTCAAAAGC+AGG - chr2.2:27920334-27920353 MS.gene043809:CDS 35.0%
TGCTTTACAATCAGTTCTTG+AGG + chr2.2:27920314-27920333 None:intergenic 35.0%
! TTTGCCAAGAAAGAAGGTTT+TGG - chr2.2:27920181-27920200 MS.gene043809:CDS 35.0%
!!! AAGGTTTTGGAGTTTGTGTT+CGG - chr2.2:27920194-27920213 MS.gene043809:CDS 35.0%
AAGCAGGGAAGAGAAGTAAA+TGG - chr2.2:27920350-27920369 MS.gene043809:CDS 40.0%
ACATCGTTTGCCAAGAAAGA+AGG - chr2.2:27920175-27920194 MS.gene043809:CDS 40.0%
AGATAATGCCTTGTCTAGTC+AGG - chr2.2:27920539-27920558 MS.gene043809:CDS 40.0%
AGCAGGGAAGAGAAGTAAAT+GGG - chr2.2:27920351-27920370 MS.gene043809:CDS 40.0%
ATGCTTGTATGCGCTAATGA+AGG - chr2.2:27920238-27920257 MS.gene043809:CDS 40.0%
! AATGGTTAGTCCTAAGAGTG+TGG - chr2.2:27920408-27920427 MS.gene043809:CDS 40.0%
CACATATTGGCCACACTCTT+AGG + chr2.2:27920421-27920440 None:intergenic 45.0%
CATCGTAGCAACTTTCCTGT+AGG + chr2.2:27920508-27920527 None:intergenic 45.0%
!! GATGAAGAAGGAGTACCTAC+AGG - chr2.2:27920490-27920509 MS.gene043809:CDS 45.0%
CCAGCAATCCTGACTAGACA+AGG + chr2.2:27920550-27920569 None:intergenic 50.0%
CCTTGTCTAGTCAGGATTGC+TGG - chr2.2:27920547-27920566 MS.gene043809:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 27919998 27920705 27919998 ID=MS.gene043809
chr2.2 mRNA 27919998 27920705 27919998 ID=MS.gene043809.t1;Parent=MS.gene043809
chr2.2 exon 27919998 27920705 27919998 ID=MS.gene043809.t1.exon1;Parent=MS.gene043809.t1
chr2.2 CDS 27919998 27920705 27919998 ID=cds.MS.gene043809.t1;Parent=MS.gene043809.t1
Gene Sequence

>MS.gene043809

ATGGATAATGAGTATGTGGAAAATTTTACTGTTGAGTGTTTAGAAGACCATGAGATAGTTGATGATGTGTCTAATGATTTAGAACCAAATTTAGAAAATTTCAAGTCACCTGAAGCTAATATTTGTCCTATTGTTGATATGGAATTTGACTCCATTGTGGATGTAAAAGAATTCTACACATCGTTTGCCAAGAAAGAAGGTTTTGGAGTTTGTGTTCGGTCTACTAAGCAAAAATTTTGCATGCTTGTATGCGCTAATGAAGGTACACATATAGTAAAGGGTGAAAATGAAGAAGGGAAGAGAAAGCGTTCAACCTCAAGAACTGATTGTAAAGCATCACTTACTGTTTCAAAAGCAGGGAAGAGAAGTAAATGGGTTATAAAAAGCATAAACAATGATCACAATCATGGAATGGTTAGTCCTAAGAGTGTGGCCAATATGTGTTCTCATAAGAAAATGACTGCAGCAACTAAGAGCCTCATTGAGAAGTTTGATGAAGAAGGAGTACCTACAGGAAAGTTGCTACGATGTTTCAAGGTGAAGATAATGCCTTGTCTAGTCAGGATTGCTGGAATCATCTTAGAAATCTCAAAAGAAGAAATCTTGATGTGGGAGATGCTCAAGCTGTCTTTAAATTTTGCAAGAAAAAACAAGTTGAGAATCCCAATTTTTTTTATGCAATACAATGTGATGATGAAGATAGAATGA
Protein sequence

>MS.gene043809.t1

MDNEYVENFTVECLEDHEIVDDVSNDLEPNLENFKSPEANICPIVDMEFDSIVDVKEFYTSFAKKEGFGVCVRSTKQKFCMLVCANEGTHIVKGENEEGKRKRSTSRTDCKASLTVSKAGKRSKWVIKSINNDHNHGMVSPKSVANMCSHKKMTAATKSLIEKFDEEGVPTGKLLRCFKVKIMPCLVRIAGIILEISKEEILMWEMLKLSLNFARKNKLRIPIFFMQYNVMMKIE