AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0080048323.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048323.01.T01 MTR_4g047870 74.286 105 25 2 6 109 104 207 2.26e-47 153
MsG0080048323.01.T01 MTR_5g092060 56.731 104 45 0 6 109 117 220 7.73e-36 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0080048323.01.T01 AT3G21700 54.717 106 45 2 6 109 119 223 1.59e-32 115
MsG0080048323.01.T01 AT3G21700 53.774 106 45 3 6 109 119 222 3.61e-31 111
MsG0080048323.01.T01 AT3G21700 53.774 106 45 3 6 109 119 222 1.02e-30 111
MsG0080048323.01.T01 AT5G54840 51.429 105 49 2 6 109 114 217 2.84e-28 104
MsG0080048323.01.T01 AT5G54840 45.652 92 48 2 6 96 114 204 5.45e-19 79.0
MsG0080048323.01.T01 AT5G54840 40.000 120 63 3 6 124 114 225 6.09e-19 79.3

Find 54 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATGTTTATCTTAAAATA+TGG 0.193855 contig271end:+281261 None:intergenic
TTATGGAATTGAACTCCTTT+TGG 0.234552 contig271end:+281205 None:intergenic
GCTTTACTATAAAGTTAAAT+TGG 0.270408 contig271end:+281109 None:intergenic
CACGTATATCCTATTGTATC+TGG 0.293441 contig271end:-282367 MsG0080048323.01.T01:CDS
CTTTCTAGTTAGTGTATGTT+TGG 0.321872 contig271end:-281665 MsG0080048323.01.T01:three_prime_UTR
ATTGTTGTAGACGGCAATTC+CGG 0.362768 contig271end:-281771 MsG0080048323.01.T01:intron
AGTTGGTTCTGTAAGGTTGT+AGG 0.364672 contig271end:-281290 MsG0080048323.01.T01:three_prime_UTR
GATTCGGCGTTTGTTTGAAT+TGG 0.391960 contig271end:+281430 None:intergenic
TAGGAAGGACAAAACAATAA+AGG 0.401341 contig271end:+281067 None:intergenic
CAATCAATGGACAAAACATT+GGG 0.401724 contig271end:-282400 MsG0080048323.01.T01:CDS
TACATGTAAGACTAATCAAT+TGG 0.431958 contig271end:-281166 MsG0080048323.01.T01:three_prime_UTR
GGTACAAAGAAGCAAGGAAA+TGG 0.432118 contig271end:-281878 MsG0080048323.01.T01:CDS
CCGTCTTGAGGCTGTGGAGG+TGG 0.432294 contig271end:-281572 MsG0080048323.01.T01:three_prime_UTR
CAAGTCGATGCACATTAAAC+AGG 0.439545 contig271end:-282182 MsG0080048323.01.T01:intron
CGTTTGTTTGAATTGGCGTT+AGG 0.443270 contig271end:+281437 None:intergenic
GTATGAATATAAATTATAAG+AGG 0.443761 contig271end:-281332 MsG0080048323.01.T01:three_prime_UTR
AGAAGCAAGGAAATGGAATC+AGG 0.446817 contig271end:-281871 MsG0080048323.01.T01:intron
TGTTTAATAATCATAATCAT+AGG 0.447502 contig271end:+281048 None:intergenic
ATGGTCCATTGCATATCAAT+AGG 0.453073 contig271end:+281711 None:intergenic
TTGTACTTCCCAGATACAAT+AGG 0.464379 contig271end:+282358 None:intergenic
CACTGAGTCCTTACTGCCAT+TGG 0.470504 contig271end:+282231 None:intergenic
GCAGGGAGTGGAACAGAGAA+AGG 0.471396 contig271end:-282430 MsG0080048323.01.T01:CDS
TCCTTACTGCCATTGGAAGC+TGG 0.471765 contig271end:+282238 None:intergenic
ACGGCAATTCCGGTGTTGAT+AGG 0.475548 contig271end:-281761 MsG0080048323.01.T01:CDS
GAAAATCCGTCTTGAGGCTG+TGG 0.511067 contig271end:-281578 MsG0080048323.01.T01:three_prime_UTR
GAAAGGAAAGGACCAATCAA+TGG 0.511358 contig271end:-282413 MsG0080048323.01.T01:CDS
ACCAGCTTCCAATGGCAGTA+AGG 0.514453 contig271end:-282239 MsG0080048323.01.T01:CDS
TTTATTTCAGTGTTCTGGGA+TGG 0.514652 contig271end:-281899 MsG0080048323.01.T01:intron
AGCTTCCTATTGATATGCAA+TGG 0.521296 contig271end:-281716 MsG0080048323.01.T01:CDS
CCAATCAATGGACAAAACAT+TGG 0.522028 contig271end:-282401 MsG0080048323.01.T01:CDS
TATGAATATAAATTATAAGA+GGG 0.530653 contig271end:-281331 MsG0080048323.01.T01:three_prime_UTR
GCTGAATGAATCATCAAACT+TGG 0.531948 contig271end:+281736 None:intergenic
CGTCTTGAGGCTGTGGAGGT+GGG 0.533625 contig271end:-281571 MsG0080048323.01.T01:three_prime_UTR
GGACAAAACATTGGGGTGAG+TGG 0.539391 contig271end:-282392 MsG0080048323.01.T01:CDS
GTCTCACATTGAATGAGATA+AGG 0.540019 contig271end:-281354 MsG0080048323.01.T01:three_prime_UTR
ACGTATATCCTATTGTATCT+GGG 0.564779 contig271end:-282366 MsG0080048323.01.T01:CDS
TGTGTTGCAGGTGAAATATG+TGG 0.564840 contig271end:-282465 MsG0080048323.01.T01:CDS
TATTGTATCTGGGAAGTACA+AGG 0.574671 contig271end:-282356 MsG0080048323.01.T01:intron
TTAGTGTATGTTTGGTTGAG+CGG 0.589107 contig271end:-281657 MsG0080048323.01.T01:three_prime_UTR
AGAAGTGAAAATCCGTCTTG+AGG 0.589834 contig271end:-281584 MsG0080048323.01.T01:three_prime_UTR
ATCAGAAGACCAGCTTCCAA+TGG 0.601240 contig271end:-282247 MsG0080048323.01.T01:CDS
GAGTGGAACAGAGAAAGGAA+AGG 0.606061 contig271end:-282425 MsG0080048323.01.T01:CDS
GCAATGGACCATCGCTAGTG+AGG 0.615352 contig271end:-281700 MsG0080048323.01.T01:CDS
TAATAATCATAATCATAGGA+AGG 0.618613 contig271end:+281052 None:intergenic
AATCCGTCTTGAGGCTGTGG+AGG 0.624523 contig271end:-281575 MsG0080048323.01.T01:three_prime_UTR
AGCGATTACCTCACTAGCGA+TGG 0.627900 contig271end:+281692 None:intergenic
GTGTTGCAGGTGAAATATGT+GGG 0.632141 contig271end:-282464 MsG0080048323.01.T01:CDS
TCCTGATTTCACTGAAAACG+CGG 0.634035 contig271end:+281515 None:intergenic
TGGGATGGTACAAAGAAGCA+AGG 0.641092 contig271end:-281884 MsG0080048323.01.T01:CDS
AACTTGGTTCCTATCAACAC+CGG 0.647380 contig271end:+281752 None:intergenic
CCACCTCCACAGCCTCAAGA+CGG 0.653250 contig271end:+281572 None:intergenic
TCTCTATGCAAATTTGAACG+TGG 0.661048 contig271end:+281475 None:intergenic
GGAGGTGGGAATTCCACGTG+AGG 0.707752 contig271end:-281557 MsG0080048323.01.T01:three_prime_UTR
AATCAATGGACAAAACATTG+GGG 0.720287 contig271end:-282399 MsG0080048323.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGAATATAAATTATAAGA+GGG - contig271end:282200-282219 MsG0080048323.01.T01:CDS 10.0%
!! TGATCAAATTATATTTATAA+GGG + contig271end:281232-281251 None:intergenic 10.0%
!! TTGATCAAATTATATTTATA+AGG + contig271end:281233-281252 None:intergenic 10.0%
!!! AATTTTAATTTGATGATTTT+AGG - contig271end:281204-281223 MsG0080048323.01.T01:three_prime_UTR 10.0%
!! ACTGAAATAAAACAAAAAAT+AGG + contig271end:281623-281642 None:intergenic 15.0%
!! ATCATGTTTATCTTAAAATA+TGG + contig271end:282273-282292 None:intergenic 15.0%
!! ATGTTTAATATTATACTTGA+AGG - contig271end:281252-281271 MsG0080048323.01.T01:three_prime_UTR 15.0%
!! GTATGAATATAAATTATAAG+AGG - contig271end:282199-282218 MsG0080048323.01.T01:CDS 15.0%
!! TGTTTAATAATCATAATCAT+AGG + contig271end:282486-282505 None:intergenic 15.0%
!! AATCAGGTAACATATTTATT+TGG - contig271end:281676-281695 MsG0080048323.01.T01:three_prime_UTR 20.0%
!! GCTTTACTATAAAGTTAAAT+TGG + contig271end:282425-282444 None:intergenic 20.0%
!! GTTAAGAATGAAAAATGATT+CGG + contig271end:282120-282139 None:intergenic 20.0%
!! TAATAATCATAATCATAGGA+AGG + contig271end:282482-282501 None:intergenic 20.0%
!! TTTCTGATGTCAATTATATT+TGG - contig271end:281557-281576 MsG0080048323.01.T01:three_prime_UTR 20.0%
!!! TTAATCTTCATCTTTTAAGT+TGG - contig271end:282224-282243 MsG0080048323.01.T01:CDS 20.0%
!!! TTTCACTTCTAAAAATAAGA+TGG + contig271end:281937-281956 None:intergenic 20.0%
! AATATTATACTTGAAGGTGA+TGG - contig271end:281258-281277 MsG0080048323.01.T01:three_prime_UTR 25.0%
! AATTTCTGCTGAAAATTGAT+TGG - contig271end:281704-281723 MsG0080048323.01.T01:CDS 25.0%
! TAAACAGGTAATTCTCAATT+CGG - contig271end:281364-281383 MsG0080048323.01.T01:three_prime_UTR 25.0%
! TACATGTAAGACTAATCAAT+TGG - contig271end:282365-282384 MsG0080048323.01.T01:CDS 25.0%
!! TATTCAGCTTTTCTCAATAA+AGG + contig271end:282398-282417 None:intergenic 25.0%
!! TCTTACATGTAGATTTTGTT+TGG + contig271end:282356-282375 None:intergenic 25.0%
!!! TAACAACGTTTTATTCCAAA+AGG - contig271end:282311-282330 MsG0080048323.01.T01:intron 25.0%
!!! TTGTTTTATTTCAGTGTTCT+GGG - contig271end:281628-281647 MsG0080048323.01.T01:three_prime_UTR 25.0%
!!! TTTGTTTTATTTCAGTGTTC+TGG - contig271end:281627-281646 MsG0080048323.01.T01:three_prime_UTR 25.0%
AATCAATGGACAAAACATTG+GGG - contig271end:281132-281151 MsG0080048323.01.T01:three_prime_UTR 30.0%
ACGTATATCCTATTGTATCT+GGG - contig271end:281165-281184 MsG0080048323.01.T01:three_prime_UTR 30.0%
CAATCAATGGACAAAACATT+GGG - contig271end:281131-281150 MsG0080048323.01.T01:three_prime_UTR 30.0%
TAGGAAGGACAAAACAATAA+AGG + contig271end:282467-282486 None:intergenic 30.0%
TTTGTTGAAAAATGTGTTGC+AGG - contig271end:281054-281073 MsG0080048323.01.T01:three_prime_UTR 30.0%
! ATATTTTCCCACAATTACTC+GGG + contig271end:281511-281530 None:intergenic 30.0%
! GATATTTTCCCACAATTACT+CGG + contig271end:281512-281531 None:intergenic 30.0%
! TTATGGAATTGAACTCCTTT+TGG + contig271end:282329-282348 None:intergenic 30.0%
!! AGATTTTGTTTGGCTTCTTA+TGG + contig271end:282346-282365 None:intergenic 30.0%
!! CTTTCTAGTTAGTGTATGTT+TGG - contig271end:281866-281885 MsG0080048323.01.T01:intron 30.0%
!!! TCTTTTAAGTTGGTTCTGTA+AGG - contig271end:282234-282253 MsG0080048323.01.T01:CDS 30.0%
AGCTTCCTATTGATATGCAA+TGG - contig271end:281815-281834 MsG0080048323.01.T01:intron 35.0%
ATGGTCCATTGCATATCAAT+AGG + contig271end:281823-281842 None:intergenic 35.0%
CACGTATATCCTATTGTATC+TGG - contig271end:281164-281183 MsG0080048323.01.T01:three_prime_UTR 35.0%
CCAATCAATGGACAAAACAT+TGG - contig271end:281130-281149 MsG0080048323.01.T01:three_prime_UTR 35.0%
GCTGAATGAATCATCAAACT+TGG + contig271end:281798-281817 None:intergenic 35.0%
GTCTCACATTGAATGAGATA+AGG - contig271end:282177-282196 MsG0080048323.01.T01:intron 35.0%
GTGTGATTGATTGTTGTAGA+CGG - contig271end:281751-281770 MsG0080048323.01.T01:CDS 35.0%
TAACTACATTAGTCCGATCT+CGG + contig271end:281425-281444 None:intergenic 35.0%
TCTCTATGCAAATTTGAACG+TGG + contig271end:282059-282078 None:intergenic 35.0%
TTAGTGTATGTTTGGTTGAG+CGG - contig271end:281874-281893 MsG0080048323.01.T01:CDS 35.0%
TTGTACTTCCCAGATACAAT+AGG + contig271end:281176-281195 None:intergenic 35.0%
! CCAATGTTTTGTCCATTGAT+TGG + contig271end:281133-281152 None:intergenic 35.0%
! TATTGTATCTGGGAAGTACA+AGG - contig271end:281175-281194 MsG0080048323.01.T01:three_prime_UTR 35.0%
! TATTTTCCCACAATTACTCG+GGG + contig271end:281510-281529 None:intergenic 35.0%
!! ACTGTTTGATTTTGATCCAC+CGG - contig271end:281473-281492 MsG0080048323.01.T01:three_prime_UTR 35.0%
!! TTTATTTCAGTGTTCTGGGA+TGG - contig271end:281632-281651 MsG0080048323.01.T01:three_prime_UTR 35.0%
AACTTGGTTCCTATCAACAC+CGG + contig271end:281782-281801 None:intergenic 40.0%
AGAAGCAAGGAAATGGAATC+AGG - contig271end:281660-281679 MsG0080048323.01.T01:three_prime_UTR 40.0%
AGAAGTGAAAATCCGTCTTG+AGG - contig271end:281947-281966 MsG0080048323.01.T01:intron 40.0%
ATGTGGGAATGAAAAAGAGC+AGG - contig271end:281083-281102 MsG0080048323.01.T01:three_prime_UTR 40.0%
ATTGTTGTAGACGGCAATTC+CGG - contig271end:281760-281779 MsG0080048323.01.T01:CDS 40.0%
CAAGTCGATGCACATTAAAC+AGG - contig271end:281349-281368 MsG0080048323.01.T01:three_prime_UTR 40.0%
CGTTTGTTTGAATTGGCGTT+AGG + contig271end:282097-282116 None:intergenic 40.0%
GAAAGGAAAGGACCAATCAA+TGG - contig271end:281118-281137 MsG0080048323.01.T01:three_prime_UTR 40.0%
GATTCGGCGTTTGTTTGAAT+TGG + contig271end:282104-282123 None:intergenic 40.0%
GGTACAAAGAAGCAAGGAAA+TGG - contig271end:281653-281672 MsG0080048323.01.T01:three_prime_UTR 40.0%
GTGTTGCAGGTGAAATATGT+GGG - contig271end:281067-281086 MsG0080048323.01.T01:three_prime_UTR 40.0%
GTTGGATATTAGACCGAGAT+CGG - contig271end:281409-281428 MsG0080048323.01.T01:three_prime_UTR 40.0%
TATGTACCCCGAGTAATTGT+GGG - contig271end:281501-281520 MsG0080048323.01.T01:three_prime_UTR 40.0%
TCCTGATTTCACTGAAAACG+CGG + contig271end:282019-282038 None:intergenic 40.0%
TGTGGGAATGAAAAAGAGCA+GGG - contig271end:281084-281103 MsG0080048323.01.T01:three_prime_UTR 40.0%
TGTGTTGCAGGTGAAATATG+TGG - contig271end:281066-281085 MsG0080048323.01.T01:three_prime_UTR 40.0%
TTATGTACCCCGAGTAATTG+TGG - contig271end:281500-281519 MsG0080048323.01.T01:three_prime_UTR 40.0%
!! AGTTGGTTCTGTAAGGTTGT+AGG - contig271end:282241-282260 MsG0080048323.01.T01:CDS 40.0%
ATCAGAAGACCAGCTTCCAA+TGG - contig271end:281284-281303 MsG0080048323.01.T01:three_prime_UTR 45.0%
GAATGAAAAAGAGCAGGGAG+TGG - contig271end:281089-281108 MsG0080048323.01.T01:three_prime_UTR 45.0%
GAGTGGAACAGAGAAAGGAA+AGG - contig271end:281106-281125 MsG0080048323.01.T01:three_prime_UTR 45.0%
TGGGATGGTACAAAGAAGCA+AGG - contig271end:281647-281666 MsG0080048323.01.T01:three_prime_UTR 45.0%
! TCCGCGTTTTCAGTGAAATC+AGG - contig271end:282015-282034 MsG0080048323.01.T01:intron 45.0%
!! TGTGTAGCGTTGATGGTAGT+TGG - contig271end:281391-281410 MsG0080048323.01.T01:three_prime_UTR 45.0%
ACCAGCTTCCAATGGCAGTA+AGG - contig271end:281292-281311 MsG0080048323.01.T01:three_prime_UTR 50.0%
ACTCGGGGTACATAAGTGAC+CGG + contig271end:281495-281514 None:intergenic 50.0%
AGCGATTACCTCACTAGCGA+TGG + contig271end:281842-281861 None:intergenic 50.0%
CACTGAGTCCTTACTGCCAT+TGG + contig271end:281303-281322 None:intergenic 50.0%
GAAAATCCGTCTTGAGGCTG+TGG - contig271end:281953-281972 MsG0080048323.01.T01:intron 50.0%
GGACAAAACATTGGGGTGAG+TGG - contig271end:281139-281158 MsG0080048323.01.T01:three_prime_UTR 50.0%
TCCTTACTGCCATTGGAAGC+TGG + contig271end:281296-281315 None:intergenic 50.0%
! CGGAATGTGTGTAGCGTTGA+TGG - contig271end:281384-281403 MsG0080048323.01.T01:three_prime_UTR 50.0%
!! ACGGCAATTCCGGTGTTGAT+AGG - contig271end:281770-281789 MsG0080048323.01.T01:intron 50.0%
!! GTCGTGATTTTGACCTCACG+TGG + contig271end:281990-282009 None:intergenic 50.0%
AATCCGTCTTGAGGCTGTGG+AGG - contig271end:281956-281975 MsG0080048323.01.T01:intron 55.0%
GCAATGGACCATCGCTAGTG+AGG - contig271end:281831-281850 MsG0080048323.01.T01:intron 55.0%
GCAGGGAGTGGAACAGAGAA+AGG - contig271end:281101-281120 MsG0080048323.01.T01:three_prime_UTR 55.0%
CCACCTCCACAGCCTCAAGA+CGG + contig271end:281962-281981 None:intergenic 60.0%
CGGGGTACATAAGTGACCGG+TGG + contig271end:281492-281511 None:intergenic 60.0%
CGTCTTGAGGCTGTGGAGGT+GGG - contig271end:281960-281979 MsG0080048323.01.T01:intron 60.0%
GGAGGTGGGAATTCCACGTG+AGG - contig271end:281974-281993 MsG0080048323.01.T01:intron 60.0%
CCGTCTTGAGGCTGTGGAGG+TGG - contig271end:281959-281978 MsG0080048323.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
contig271end gene 281046 282507 281046 ID=MsG0080048323.01;Name=MsG0080048323.01
contig271end mRNA 281046 282507 281046 ID=MsG0080048323.01.T01;Parent=MsG0080048323.01;Name=MsG0080048323.01.T01;_AED=0.32;_eAED=0.33;_QI=0|1|0.75|1|1|1|4|651|124
contig271end exon 282357 282507 282357 ID=MsG0080048323.01.T01:exon:19218;Parent=MsG0080048323.01.T01
contig271end exon 282183 282279 282183 ID=MsG0080048323.01.T01:exon:19219;Parent=MsG0080048323.01.T01
contig271end exon 281872 281911 281872 ID=MsG0080048323.01.T01:exon:19220;Parent=MsG0080048323.01.T01
contig271end exon 281046 281783 281046 ID=MsG0080048323.01.T01:exon:19221;Parent=MsG0080048323.01.T01
contig271end CDS 282357 282507 282357 ID=MsG0080048323.01.T01:cds;Parent=MsG0080048323.01.T01
contig271end CDS 282183 282279 282183 ID=MsG0080048323.01.T01:cds;Parent=MsG0080048323.01.T01
contig271end CDS 281872 281911 281872 ID=MsG0080048323.01.T01:cds;Parent=MsG0080048323.01.T01
contig271end CDS 281697 281783 281697 ID=MsG0080048323.01.T01:cds;Parent=MsG0080048323.01.T01
contig271end three_prime_UTR 281046 281696 281046 ID=MsG0080048323.01.T01:three_prime_utr;Parent=MsG0080048323.01.T01
Gene Sequence

>MsG0080048323.01.T01

ATTTTTGTTTTGTTGAAAAATGTGTTGCAGGTGAAATATGTGGGAATGAAAAAGAGCAGGGAGTGGAACAGAGAAAGGAAAGGACCAATCAATGGACAAAACATTGGGGTGAGTGGAGCACGTATATCCTATTGTATCTGGGAAGTACAAGGTGATGGAAAATCAGAAGACCAGCTTCCAATGGCAGTAAGGACTCAGTGTGCAATTTTGATCATGTTTGATCGTACAAGTCGATGCACATTAAACAGTGTTCTGGGATGGTACAAAGAAGCAAGGAAATGGAATCAGACGGCAATTCCGGTGTTGATAGGAACCAAGTTTGATGATTCATTCAGCTTCCTATTGATATGCAATGGACCATCGCTAGTGAGGTAA
Protein sequence

>MsG0080048323.01.T01

IFVLLKNVLQVKYVGMKKSREWNRERKGPINGQNIGVSGARISYCIWEVQGDGKSEDQLPMAVRTQCAILIMFDRTSRCTLNSVLGWYKEARKWNQTAIPVLIGTKFDDSFSFLLICNGPSLVR*