AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1116520

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1116520 MtrunA17_Chr7g0258981 94.410 161 9 0 1 161 1 161 3.20e-104 295
Msa1116520 MtrunA17_Chr3g0080591 48.352 91 23 2 72 138 32 122 6.13e-18 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATAATATCGATGGATCTT+TGG 0.212883 7_3:-64205170 Msa1116520:CDS
AATAATATCGATGGATCTTT+GGG 0.246908 7_3:-64205169 Msa1116520:CDS
GAACTGCACGAGATCTTTCT+TGG 0.257265 7_3:-64205399 Msa1116520:CDS
ACACAATTTGCAACATAAAT+CGG 0.291650 7_3:-64205363 Msa1116520:CDS
CAAATCAAGGTTGATGTCAT+TGG 0.397831 7_3:+64205057 None:intergenic
GTGCAGTTCTGAAGGTTTCA+TGG 0.407889 7_3:+64205413 None:intergenic
TGCAAATTGTGTATGTGCTT+TGG 0.408651 7_3:+64205374 None:intergenic
CACAATTTGCAACATAAATC+GGG 0.419218 7_3:-64205362 Msa1116520:CDS
ACAATTGGAACCTCTGGTAT+AGG 0.430649 7_3:+64205214 None:intergenic
TGGCAATGGTTGCATGGAAT+AGG 0.448209 7_3:+64205433 None:intergenic
CGATCAGTACGAGTGACAAT+TGG 0.450600 7_3:+64205199 None:intergenic
TTCTGAAGGTTTCATGGCAA+TGG 0.457643 7_3:+64205419 None:intergenic
TCAGATGATGAGAGCAGTAC+TGG 0.465223 7_3:-64205481 Msa1116520:CDS
TCAGTTGGAGCTGAATCAAT+CGG 0.471657 7_3:+64205112 None:intergenic
CAACCTAGAGCTTCAAATCA+AGG 0.475468 7_3:+64205044 None:intergenic
CGAGTGACAATTGGAACCTC+TGG 0.493144 7_3:+64205208 None:intergenic
TCTCATCATCTGATTCAGAT+AGG 0.499444 7_3:+64205491 None:intergenic
CTTCCATCCCGCCACACCAC+TGG 0.504811 7_3:+64205082 None:intergenic
TCTGGTATAGGCCTCATGTA+TGG 0.510085 7_3:+64205226 None:intergenic
ACCACTGGTAATTCTTCAGT+TGG 0.510267 7_3:+64205097 None:intergenic
CAACCTTGATTTGAAGCTCT+AGG 0.512638 7_3:-64205047 None:intergenic
TGTGATGAAGGTGGTGGAGA+TGG 0.521845 7_3:+64205301 None:intergenic
TAATTACCGCTTCCATGCAT+AGG 0.528205 7_3:+64205265 None:intergenic
ACTATGTTGTTTCCTATGCA+TGG 0.528781 7_3:-64205277 Msa1116520:CDS
TTACCAGTGGTGTGGCGGGA+TGG 0.529438 7_3:-64205085 Msa1116520:CDS
CGTGATTACAATAATATCGA+TGG 0.538614 7_3:-64205178 Msa1116520:CDS
GTTTCATGGCAATGGTTGCA+TGG 0.544580 7_3:+64205427 None:intergenic
AAGAATTACCAGTGGTGTGG+CGG 0.548905 7_3:-64205090 Msa1116520:CDS
GCCTCATGTATGGATGAAAA+CGG 0.550640 7_3:+64205236 None:intergenic
AAGATCTCGTGCAGTTCTGA+AGG 0.551614 7_3:+64205405 None:intergenic
TTGTTTCCTATGCATGGAAG+CGG 0.563807 7_3:-64205271 Msa1116520:CDS
TGGATCTTTGGGGAGAACAA+TGG 0.585871 7_3:-64205158 Msa1116520:CDS
AACAACATAGTGTGTGATGA+AGG 0.595436 7_3:+64205289 None:intergenic
AGAATTACCAGTGGTGTGGC+GGG 0.597554 7_3:-64205089 Msa1116520:CDS
GATGAAGGTGGTGGAGATGG+TGG 0.599841 7_3:+64205304 None:intergenic
GTGGAGATGGTGGTCCAATG+TGG 0.619599 7_3:+64205314 None:intergenic
CTAAACAACACACACCACAT+TGG 0.630539 7_3:-64205328 Msa1116520:CDS
CTGAAGAATTACCAGTGGTG+TGG 0.651724 7_3:-64205093 Msa1116520:CDS
ATACATGAGGCCTATACCAG+AGG 0.686494 7_3:-64205224 Msa1116520:CDS
TCCAACTGAAGAATTACCAG+TGG 0.699300 7_3:-64205098 Msa1116520:CDS
ATAGTGTGTGATGAAGGTGG+TGG 0.699659 7_3:+64205295 None:intergenic
ATAATATCGATGGATCTTTG+GGG 0.708326 7_3:-64205168 Msa1116520:CDS
AACATAGTGTGTGATGAAGG+TGG 0.727614 7_3:+64205292 None:intergenic
TCATGTATGGATGAAAACGG+CGG 0.744847 7_3:+64205239 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACACAATTTGCAACATAAAT+CGG - chr7_3:64205196-64205215 Msa1116520:CDS 25.0%
! AATAATATCGATGGATCTTT+GGG - chr7_3:64205390-64205409 Msa1116520:CDS 25.0%
CACAATTTGCAACATAAATC+GGG - chr7_3:64205197-64205216 Msa1116520:CDS 30.0%
CGTGATTACAATAATATCGA+TGG - chr7_3:64205381-64205400 Msa1116520:CDS 30.0%
CAATAATATCGATGGATCTT+TGG - chr7_3:64205389-64205408 Msa1116520:CDS 30.0%
ATAATATCGATGGATCTTTG+GGG - chr7_3:64205391-64205410 Msa1116520:CDS 30.0%
TCTCATCATCTGATTCAGAT+AGG + chr7_3:64205071-64205090 None:intergenic 35.0%
TGCAAATTGTGTATGTGCTT+TGG + chr7_3:64205188-64205207 None:intergenic 35.0%
AACAACATAGTGTGTGATGA+AGG + chr7_3:64205273-64205292 None:intergenic 35.0%
!! ACTATGTTGTTTCCTATGCA+TGG - chr7_3:64205282-64205301 Msa1116520:CDS 35.0%
!! CAAATCAAGGTTGATGTCAT+TGG + chr7_3:64205505-64205524 None:intergenic 35.0%
! TTCTGAAGGTTTCATGGCAA+TGG + chr7_3:64205143-64205162 None:intergenic 40.0%
CTAAACAACACACACCACAT+TGG - chr7_3:64205231-64205250 Msa1116520:CDS 40.0%
AACATAGTGTGTGATGAAGG+TGG + chr7_3:64205270-64205289 None:intergenic 40.0%
TTGTTTCCTATGCATGGAAG+CGG - chr7_3:64205288-64205307 Msa1116520:CDS 40.0%
TAATTACCGCTTCCATGCAT+AGG + chr7_3:64205297-64205316 None:intergenic 40.0%
TCATGTATGGATGAAAACGG+CGG + chr7_3:64205323-64205342 None:intergenic 40.0%
GCCTCATGTATGGATGAAAA+CGG + chr7_3:64205326-64205345 None:intergenic 40.0%
ACAATTGGAACCTCTGGTAT+AGG + chr7_3:64205348-64205367 None:intergenic 40.0%
TCAGTTGGAGCTGAATCAAT+CGG + chr7_3:64205450-64205469 None:intergenic 40.0%
TCCAACTGAAGAATTACCAG+TGG - chr7_3:64205461-64205480 Msa1116520:CDS 40.0%
ACCACTGGTAATTCTTCAGT+TGG + chr7_3:64205465-64205484 None:intergenic 40.0%
TCAGATGATGAGAGCAGTAC+TGG - chr7_3:64205078-64205097 Msa1116520:CDS 45.0%
TGGCAATGGTTGCATGGAAT+AGG + chr7_3:64205129-64205148 None:intergenic 45.0%
GTTTCATGGCAATGGTTGCA+TGG + chr7_3:64205135-64205154 None:intergenic 45.0%
!! GTGCAGTTCTGAAGGTTTCA+TGG + chr7_3:64205149-64205168 None:intergenic 45.0%
! AAGATCTCGTGCAGTTCTGA+AGG + chr7_3:64205157-64205176 None:intergenic 45.0%
GAACTGCACGAGATCTTTCT+TGG - chr7_3:64205160-64205179 Msa1116520:CDS 45.0%
ATAGTGTGTGATGAAGGTGG+TGG + chr7_3:64205267-64205286 None:intergenic 45.0%
!! GCCGTTTTCATCCATACATG+AGG - chr7_3:64205322-64205341 Msa1116520:CDS 45.0%
TCTGGTATAGGCCTCATGTA+TGG + chr7_3:64205336-64205355 None:intergenic 45.0%
ATACATGAGGCCTATACCAG+AGG - chr7_3:64205335-64205354 Msa1116520:CDS 45.0%
CGATCAGTACGAGTGACAAT+TGG + chr7_3:64205363-64205382 None:intergenic 45.0%
! TGGATCTTTGGGGAGAACAA+TGG - chr7_3:64205401-64205420 Msa1116520:CDS 45.0%
CTGAAGAATTACCAGTGGTG+TGG - chr7_3:64205466-64205485 Msa1116520:CDS 45.0%
AAGAATTACCAGTGGTGTGG+CGG - chr7_3:64205469-64205488 Msa1116520:CDS 45.0%
!! TGTGATGAAGGTGGTGGAGA+TGG + chr7_3:64205261-64205280 None:intergenic 50.0%
CGAGTGACAATTGGAACCTC+TGG + chr7_3:64205354-64205373 None:intergenic 50.0%
AGAATTACCAGTGGTGTGGC+GGG - chr7_3:64205470-64205489 Msa1116520:CDS 50.0%
! GTGGAGATGGTGGTCCAATG+TGG + chr7_3:64205248-64205267 None:intergenic 55.0%
!! GATGAAGGTGGTGGAGATGG+TGG + chr7_3:64205258-64205277 None:intergenic 55.0%
! TTACCAGTGGTGTGGCGGGA+TGG - chr7_3:64205474-64205493 Msa1116520:CDS 60.0%
CTTCCATCCCGCCACACCAC+TGG + chr7_3:64205480-64205499 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 64205048 64205533 64205048 ID=Msa1116520;Name=Msa1116520
chr7_3 mRNA 64205048 64205533 64205048 ID=Msa1116520-mRNA-1;Parent=Msa1116520;Name=Msa1116520-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|161
chr7_3 exon 64205048 64205533 64205048 ID=Msa1116520-mRNA-1:exon:15234;Parent=Msa1116520-mRNA-1
chr7_3 CDS 64205048 64205533 64205048 ID=Msa1116520-mRNA-1:cds;Parent=Msa1116520-mRNA-1
Gene Sequence

>Msa1116520

ATGGAGTCAGATATTGAACTCCTATCTGAATCAGATGATGAGAGCAGTACTGGCAGCAGCATCATTACTAACGTTGCTCCTATTCCATGCAACCATTGCCATGAAACCTTCAGAACTGCACGAGATCTTTCTTGGCACCAAAGCACATACACAATTTGCAACATAAATCGGGCTTTATTGAGACTAAACAACACACACCACATTGGACCACCATCTCCACCACCTTCATCACACACTATGTTGTTTCCTATGCATGGAAGCGGTAATTATAACCGCCGTTTTCATCCATACATGAGGCCTATACCAGAGGTTCCAATTGTCACTCGTACTGATCGTGATTACAATAATATCGATGGATCTTTGGGGAGAACAATGGATCTTATTTCTCTGATCGACAAGCCGATTGATTCAGCTCCAACTGAAGAATTACCAGTGGTGTGGCGGGATGGAAGCACCAATGACATCAACCTTGATTTGAAGCTCTAG
Protein sequence

>Msa1116520

MESDIELLSESDDESSTGSSIITNVAPIPCNHCHETFRTARDLSWHQSTYTICNINRALLRLNNTHHIGPPSPPPSSHTMLFPMHGSGNYNRRFHPYMRPIPEVPIVTRTDRDYNNIDGSLGRTMDLISLIDKPIDSAPTEELPVVWRDGSTNDINLDLKL*