AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067155

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067155.t1 MTR_1g019850 86.857 175 23 0 1 175 28 202 1.03e-106 305
MS.gene067155.t1 MTR_0853s0010 56.204 137 53 1 40 169 22 158 1.72e-47 152
MS.gene067155.t1 MTR_2g024230 77.000 100 22 1 1 99 47 146 5.44e-47 151
MS.gene067155.t1 MTR_1g033820 59.184 49 20 0 39 87 23 71 5.67e-16 69.7
MS.gene067155.t1 MTR_6g048540 37.500 112 59 2 38 138 23 134 9.52e-14 67.4
MS.gene067155.t1 MTR_7g113010 29.012 162 103 4 5 162 416 569 4.79e-12 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067155.t1 AT4G38180 30.247 162 102 3 24 175 54 214 3.91e-15 72.8

Find 29 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCCAAAACCTTCTTTCT+TGG 0.194532 2.2:+27979411 None:intergenic
TATTTGTCCTATTGTTGATA+TGG 0.229024 2.2:-27979479 MS.gene067155:CDS
AAGCAGGGAAGAGAAGTAAA+TGG 0.304863 2.2:-27979246 MS.gene067155:CDS
CACATATTGGCCACACTCTT+AGG 0.328854 2.2:+27979178 None:intergenic
TTTGCCAAGAAAGAAGGTTT+TGG 0.354079 2.2:-27979415 MS.gene067155:CDS
TTTCTTATGAGAACACATAT+TGG 0.382977 2.2:+27979165 None:intergenic
TCAAATTCCATATCAACAAT+AGG 0.427064 2.2:+27979472 None:intergenic
GAAGGTACACATATAGTAAA+GGG 0.439216 2.2:-27979340 MS.gene067155:CDS
ATTGAGAAGTTTGATGAAGA+AGG 0.450541 2.2:-27979118 MS.gene067155:CDS
TCACTTACTGTTTCAAAAGC+AGG 0.452498 2.2:-27979262 MS.gene067155:CDS
ACATCGTTTGCCAAGAAAGA+AGG 0.462978 2.2:-27979421 MS.gene067155:CDS
ATAGGACAAATATTAGCTTC+AGG 0.478911 2.2:+27979490 None:intergenic
AAAGTTGCTACGATGTTTCA+AGG 0.482139 2.2:-27979083 None:intergenic
AGCAGGGAAGAGAAGTAAAT+GGG 0.489503 2.2:-27979245 MS.gene067155:CDS
TGAAGGTACACATATAGTAA+AGG 0.494494 2.2:-27979341 MS.gene067155:CDS
GTAAAGGGTGAAAATGAAGA+AGG 0.507431 2.2:-27979325 MS.gene067155:CDS
TGCTTTACAATCAGTTCTTG+AGG 0.537334 2.2:+27979285 None:intergenic
CACTTACTGTTTCAAAAGCA+GGG 0.542698 2.2:-27979261 MS.gene067155:CDS
ATAAACAATGATCACAATCA+TGG 0.544230 2.2:-27979211 MS.gene067155:CDS
GTACATGGATAATGAGTATG+TGG 0.550566 2.2:-27979602 None:intergenic
GATGAAGAAGGAGTACCTAC+AGG 0.552486 2.2:-27979106 MS.gene067155:CDS
TAAAGGGTGAAAATGAAGAA+GGG 0.554329 2.2:-27979324 MS.gene067155:CDS
CTTCATCAAACTTCTCAATG+AGG 0.566857 2.2:+27979122 None:intergenic
CAATGATCACAATCATGGAA+TGG 0.570975 2.2:-27979206 MS.gene067155:CDS
ACACATCATCAACTATCTCA+TGG 0.582009 2.2:+27979551 None:intergenic
CATCGTAGCAACTTTCCTGT+AGG 0.608916 2.2:+27979091 None:intergenic
TATGGAATTTGACTCCATTG+TGG 0.618496 2.2:-27979461 MS.gene067155:CDS
ATGCTTGTATGCGCTAATGA+AGG 0.648792 2.2:-27979358 MS.gene067155:CDS
AATGGTTAGTCCTAAGAGTG+TGG 0.676645 2.2:-27979188 MS.gene067155:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GACTTGAAATTTTCTAAATT+TGG + chr2.2:27979171-27979190 None:intergenic 20.0%
! ATAAACAATGATCACAATCA+TGG - chr2.2:27979471-27979490 MS.gene067155:CDS 25.0%
! TATTTGTCCTATTGTTGATA+TGG - chr2.2:27979203-27979222 MS.gene067155:CDS 25.0%
! TCAAATTCCATATCAACAAT+AGG + chr2.2:27979213-27979232 None:intergenic 25.0%
! TTTCTTATGAGAACACATAT+TGG + chr2.2:27979520-27979539 None:intergenic 25.0%
ATTGAGAAGTTTGATGAAGA+AGG - chr2.2:27979564-27979583 MS.gene067155:CDS 30.0%
TAAAGGGTGAAAATGAAGAA+GGG - chr2.2:27979358-27979377 MS.gene067155:CDS 30.0%
! ATAGGACAAATATTAGCTTC+AGG + chr2.2:27979195-27979214 None:intergenic 30.0%
! GAAGGTACACATATAGTAAA+GGG - chr2.2:27979342-27979361 MS.gene067155:CDS 30.0%
! GAATTCTTTTACATCCACAA+TGG + chr2.2:27979238-27979257 None:intergenic 30.0%
! TGAAGGTACACATATAGTAA+AGG - chr2.2:27979341-27979360 MS.gene067155:CDS 30.0%
AACTCCAAAACCTTCTTTCT+TGG + chr2.2:27979274-27979293 None:intergenic 35.0%
ACACATCATCAACTATCTCA+TGG + chr2.2:27979134-27979153 None:intergenic 35.0%
CAATGATCACAATCATGGAA+TGG - chr2.2:27979476-27979495 MS.gene067155:CDS 35.0%
CACTTACTGTTTCAAAAGCA+GGG - chr2.2:27979421-27979440 MS.gene067155:CDS 35.0%
CTTCATCAAACTTCTCAATG+AGG + chr2.2:27979563-27979582 None:intergenic 35.0%
GTAAAGGGTGAAAATGAAGA+AGG - chr2.2:27979357-27979376 MS.gene067155:CDS 35.0%
TATGGAATTTGACTCCATTG+TGG - chr2.2:27979221-27979240 MS.gene067155:CDS 35.0%
TCACTTACTGTTTCAAAAGC+AGG - chr2.2:27979420-27979439 MS.gene067155:CDS 35.0%
TGCTTTACAATCAGTTCTTG+AGG + chr2.2:27979400-27979419 None:intergenic 35.0%
! TTTGCCAAGAAAGAAGGTTT+TGG - chr2.2:27979267-27979286 MS.gene067155:CDS 35.0%
!!! AAGGTTTTGGAGTTTGTGTT+CGG - chr2.2:27979280-27979299 MS.gene067155:CDS 35.0%
AAGCAGGGAAGAGAAGTAAA+TGG - chr2.2:27979436-27979455 MS.gene067155:CDS 40.0%
ACATCGTTTGCCAAGAAAGA+AGG - chr2.2:27979261-27979280 MS.gene067155:CDS 40.0%
AGCAGGGAAGAGAAGTAAAT+GGG - chr2.2:27979437-27979456 MS.gene067155:CDS 40.0%
ATGCTTGTATGCGCTAATGA+AGG - chr2.2:27979324-27979343 MS.gene067155:CDS 40.0%
! AATGGTTAGTCCTAAGAGTG+TGG - chr2.2:27979494-27979513 MS.gene067155:CDS 40.0%
CACATATTGGCCACACTCTT+AGG + chr2.2:27979507-27979526 None:intergenic 45.0%
CATCGTAGCAACTTTCCTGT+AGG + chr2.2:27979594-27979613 None:intergenic 45.0%
!! GATGAAGAAGGAGTACCTAC+AGG - chr2.2:27979576-27979595 MS.gene067155:CDS 45.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 27979084 27979620 27979084 ID=MS.gene067155
chr2.2 mRNA 27979084 27979620 27979084 ID=MS.gene067155.t1;Parent=MS.gene067155
chr2.2 exon 27979084 27979620 27979084 ID=MS.gene067155.t1.exon1;Parent=MS.gene067155.t1
chr2.2 CDS 27979084 27979620 27979084 ID=cds.MS.gene067155.t1;Parent=MS.gene067155.t1
Gene Sequence

>MS.gene067155

ATGGATAATGAGTATGTGGAAAATTTTACTGTTGAGTGTTTAGAAGACCATGAGATAGTTGATGATGTGTCTAATGATTTAGAACCAAATTTAGAAAATTTCAAGTCACCTGAAGCTAATATTTGTCCTATTGTTGATATGGAATTTGACTCCATTGTGGATGTAAAAGAATTCTACACATCGTTTGCCAAGAAAGAAGGTTTTGGAGTTTGTGTTCGGTCTACTAAGCAAAAATTTTGCATGCTTGTATGCGCTAATGAAGGTACACATATAGTAAAGGGTGAAAATGAAGAAGGGAAGAGAAAGCGTTCAACCTCAAGAACTGATTGTAAAGCATCACTTACTGTTTCAAAAGCAGGGAAGAGAAGTAAATGGGTTATAAAAAGCATAAACAATGATCACAATCATGGAATGGTTAGTCCTAAGAGTGTGGCCAATATGTGTTCTCATAAGAAAATGACTGCAGCAACTAAGAGCCTCATTGAGAAGTTTGATGAAGAAGGAGTACCTACAGGAAAGTTGCTACGATGTTTCAAG
Protein sequence

>MS.gene067155.t1

MDNEYVENFTVECLEDHEIVDDVSNDLEPNLENFKSPEANICPIVDMEFDSIVDVKEFYTSFAKKEGFGVCVRSTKQKFCMLVCANEGTHIVKGENEEGKRKRSTSRTDCKASLTVSKAGKRSKWVIKSINNDHNHGMVSPKSVANMCSHKKMTAATKSLIEKFDEEGVPTGKLLRCFK