AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480022807.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480022807.01.T01 MTR_4g094680 57.282 103 9 3 1 68 1 103 3.66e-30 106
MsG0480022807.01.T01 MTR_2g036170 41.176 85 15 3 21 70 36 120 7.02e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 148 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCCCTTTGCTTCTGATGA+TGG 0.298330 4:+76931402 None:intergenic
ACCTTCTCACCTGCACAATA+TGG 0.353912 4:+76929131 None:intergenic
TATTTGTTTGACCTGAATAT+AGG 0.411844 4:+76929054 None:intergenic
CATCGATTGCTCCTATATTC+AGG 0.420826 4:-76929065 MsG0480022807.01.T01:CDS
CTCCCTTTGCTTCTGATGAT+GGG 0.428222 4:+76931403 None:intergenic
TGCATGGTTAGAGAGGTTAA+TGG 0.448349 4:-76931358 MsG0480022807.01.T01:CDS
TTACCATGACGTGGTTCAAT+TGG 0.448712 4:-76929104 MsG0480022807.01.T01:CDS
GGGTGAGACATGAGAGGAAG+TGG 0.470262 4:-76931432 None:intergenic
GCATGGTTAGAGAGGTTAAT+GGG 0.474331 4:-76931357 MsG0480022807.01.T01:intron
CTATTGCTGCCATATTGTGC+AGG 0.484249 4:-76929140 MsG0480022807.01.T01:CDS
TACCATGACGTGGTTCAATT+GGG 0.505968 4:-76929103 MsG0480022807.01.T01:CDS
TGACCCATCATCAGAAGCAA+AGG 0.564164 4:-76931406 MsG0480022807.01.T01:CDS
GACCCATCATCAGAAGCAAA+GGG 0.572363 4:-76931405 MsG0480022807.01.T01:CDS
GCCATATTGTGCAGGTGAGA+AGG 0.589373 4:-76929132 MsG0480022807.01.T01:CDS
ATTAACCTCTCTAACCATGC+AGG 0.589991 4:+76931360 None:intergenic
AGAAACCTGCATGGTTAGAG+AGG 0.605580 4:-76931365 MsG0480022807.01.T01:CDS
CACCCAATTGAACCACGTCA+TGG 0.626928 4:+76929101 None:intergenic
AAGTGAATCAGAAACCTGCA+TGG 0.669083 4:-76931374 MsG0480022807.01.T01:CDS
AAGGTATGTTTACCATGACG+TGG 0.686416 4:-76929113 MsG0480022807.01.T01:CDS
GTTGTGGGGTGAGACATGAG+AGG 0.704900 4:-76931438 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATTATTATTATTAT+AGG - Chr4:76929929-76929948 MsG0480022807.01.T01:intron 0.0%
!!! TTAATTTAATTTTTATTTTT+TGG - Chr4:76929975-76929994 MsG0480022807.01.T01:intron 0.0%
!! TGTAATAAAGAATAATTTAA+TGG - Chr4:76930550-76930569 MsG0480022807.01.T01:intron 10.0%
!!! AATTAAGTTTAATTTTGTAA+AGG - Chr4:76929696-76929715 MsG0480022807.01.T01:intron 10.0%
!!! CAAAATAAATATTTTTGTTA+AGG - Chr4:76930867-76930886 MsG0480022807.01.T01:intron 10.0%
!!! CTTAACAAAAATATTTATTT+TGG + Chr4:76930869-76930888 None:intergenic 10.0%
!!! GATTTTATTTTATTTTCTTA+AGG + Chr4:76930977-76930996 None:intergenic 10.0%
!!! TCTTTATTTATTTTTTTTTC+GGG - Chr4:76930471-76930490 MsG0480022807.01.T01:intron 10.0%
!!! TTATTTTTGATAAATTTGAT+AGG - Chr4:76929539-76929558 MsG0480022807.01.T01:intron 10.0%
!! AATATATAGTTAATCTTACA+CGG + Chr4:76930814-76930833 None:intergenic 15.0%
!! ATTAACAAACTCTATTTAAT+GGG + Chr4:76930390-76930409 None:intergenic 15.0%
!! CAATCTTAATAATATTTCAT+TGG - Chr4:76931017-76931036 MsG0480022807.01.T01:intron 15.0%
!! CAATGAAATATTATTAAGAT+TGG + Chr4:76931019-76931038 None:intergenic 15.0%
!! TAAAAATAAAAACTAGAGTT+GGG + Chr4:76930322-76930341 None:intergenic 15.0%
!!! AAATATTATTAAGATTGGTT+CGG + Chr4:76931014-76931033 None:intergenic 15.0%
!!! AATTTTGTAAAACAACTTAT+AGG - Chr4:76930785-76930804 MsG0480022807.01.T01:intron 15.0%
!!! GAATTTTTTGTTTAAACATT+TGG - Chr4:76929732-76929751 MsG0480022807.01.T01:intron 15.0%
!!! TAATTTCTACTTTTATGTTT+TGG - Chr4:76930166-76930185 MsG0480022807.01.T01:intron 15.0%
!!! TTATTTTATTTTCTTAAGGA+AGG + Chr4:76930973-76930992 None:intergenic 15.0%
!!! TTTGTTTGAATTTTATAAGA+AGG + Chr4:76929819-76929838 None:intergenic 15.0%
!! AAGTTTGGTTAATGTTATAT+TGG + Chr4:76930359-76930378 None:intergenic 20.0%
!! ACAAAATTATAGTACAAATG+AGG + Chr4:76931235-76931254 None:intergenic 20.0%
!! CAAAAAATAAATAGAGTGAT+AGG + Chr4:76930679-76930698 None:intergenic 20.0%
!! CAAAATTATAGTACAAATGA+GGG + Chr4:76931234-76931253 None:intergenic 20.0%
!! CATTAACAAACTCTATTTAA+TGG + Chr4:76930391-76930410 None:intergenic 20.0%
!! CTAAAAATAAAAACTAGAGT+TGG + Chr4:76930323-76930342 None:intergenic 20.0%
!! TAGAAATAGAATACTATGTT+AGG - Chr4:76931148-76931167 MsG0480022807.01.T01:intron 20.0%
!! TATTTGCAAATTAATTCATG+TGG - Chr4:76929310-76929329 MsG0480022807.01.T01:intron 20.0%
!! TTTGTGATGATATGTAAATA+TGG - Chr4:76931179-76931198 MsG0480022807.01.T01:intron 20.0%
!!! CAACTCTAGTTTTTATTTTT+AGG - Chr4:76930321-76930340 MsG0480022807.01.T01:intron 20.0%
!!! TCACTCTATTTATTTTTTGA+AGG - Chr4:76930680-76930699 MsG0480022807.01.T01:intron 20.0%
! AAAACCAATCATAGACAATT+TGG + Chr4:76929577-76929596 None:intergenic 25.0%
! AATTGGAAGACCATATATAT+AGG + Chr4:76929439-76929458 None:intergenic 25.0%
! ACAGAAAAATAAAGGAAATC+TGG + Chr4:76929847-76929866 None:intergenic 25.0%
! AGAATAAAGTAATGATCCAA+AGG + Chr4:76929390-76929409 None:intergenic 25.0%
! ATAATGTGTGACAATAATTG+AGG - Chr4:76931287-76931306 MsG0480022807.01.T01:intron 25.0%
! CAATTATTGTCACACATTAT+TGG + Chr4:76931287-76931306 None:intergenic 25.0%
! GAAATTAATCATACAAGACA+TGG + Chr4:76930153-76930172 None:intergenic 25.0%
! TAATGGGATAAATCAAAGTT+TGG + Chr4:76930374-76930393 None:intergenic 25.0%
! TACTAACTTAACTTCTGTTA+TGG - Chr4:76929259-76929278 MsG0480022807.01.T01:intron 25.0%
! TATTTGTTTGACCTGAATAT+AGG + Chr4:76931405-76931424 None:intergenic 25.0%
! TTTCATTTGGAGATGATTAA+AGG + Chr4:76930507-76930526 None:intergenic 25.0%
! TTTCGAGAAAAAGAATTTGA+AGG + Chr4:76929645-76929664 None:intergenic 25.0%
!!! AGATTTCCTTTATTTTTCTG+TGG - Chr4:76929846-76929865 MsG0480022807.01.T01:intron 25.0%
!!! GATTTCCTTTATTTTTCTGT+GGG - Chr4:76929847-76929866 MsG0480022807.01.T01:intron 25.0%
!!! TGAAGGAAGTATTTAGAAAT+AGG + Chr4:76929628-76929647 None:intergenic 25.0%
AAAAAGGGATCTTCCATTAA+TGG + Chr4:76930200-76930219 None:intergenic 30.0%
AAAAGGGATCTTCCATTAAT+GGG + Chr4:76930199-76930218 None:intergenic 30.0%
AAAGGAAAAGAAACATCCAA+AGG + Chr4:76929372-76929391 None:intergenic 30.0%
AATGAAATGTGACAGTTTCT+GGG + Chr4:76931059-76931078 None:intergenic 30.0%
AGAAAGACAGAAGAAGAATT+TGG + Chr4:76930274-76930293 None:intergenic 30.0%
AGGGGAAATTGGATAAAAAA+AGG + Chr4:76930216-76930235 None:intergenic 30.0%
ATATGGTCTTCCAATTAATG+AGG - Chr4:76929443-76929462 MsG0480022807.01.T01:intron 30.0%
CAAACACAATGAGACAAAAT+TGG + Chr4:76930062-76930081 None:intergenic 30.0%
GAAAGACAGAAGAAGAATTT+GGG + Chr4:76930273-76930292 None:intergenic 30.0%
GGGGAAATTGGATAAAAAAA+GGG + Chr4:76930215-76930234 None:intergenic 30.0%
GTTCAAAAGACCTCATTAAT+TGG + Chr4:76929456-76929475 None:intergenic 30.0%
GTTTGTCTCAAATTAGAAGT+CGG - Chr4:76930608-76930627 MsG0480022807.01.T01:intron 30.0%
TTCAGATGCACCTATATATA+TGG - Chr4:76929426-76929445 MsG0480022807.01.T01:intron 30.0%
TTCTCGAAATCTTTCTACTA+CGG - Chr4:76929656-76929675 MsG0480022807.01.T01:intron 30.0%
TTTGCCAAATTGTCTATGAT+TGG - Chr4:76929570-76929589 MsG0480022807.01.T01:intron 30.0%
! AAACTTTTATAACCTGGTAC+AGG + Chr4:76930592-76930611 None:intergenic 30.0%
! ACATGGATTTATGCTTTGTT+TGG - Chr4:76929600-76929619 MsG0480022807.01.T01:intron 30.0%
! ATCGACTCCAAAATTTCAAA+GGG - Chr4:76929287-76929306 MsG0480022807.01.T01:intron 30.0%
! TGAGACAAACTTTTATAACC+TGG + Chr4:76930598-76930617 None:intergenic 30.0%
! TTTGGATGTTTCTTTTCCTT+TGG - Chr4:76929371-76929390 MsG0480022807.01.T01:intron 30.0%
! TTTGGTTTCTTTCCCATTAA+TGG - Chr4:76930184-76930203 MsG0480022807.01.T01:intron 30.0%
!! TATCGACTCCAAAATTTCAA+AGG - Chr4:76929286-76929305 MsG0480022807.01.T01:intron 30.0%
!! TATTATTAAGATTGGTTCGG+TGG + Chr4:76931011-76931030 None:intergenic 30.0%
!!! CTATGATTGGTTTTATGACA+TGG - Chr4:76929583-76929602 MsG0480022807.01.T01:intron 30.0%
!!! GCAAATACCCTTTGAAATTT+TGG + Chr4:76929297-76929316 None:intergenic 30.0%
!!! TAGCACTTCTTTTTTTCCTT+TGG - Chr4:76929353-76929372 MsG0480022807.01.T01:intron 30.0%
!!! TGGTTTTCTAGAATTGACAA+GGG - Chr4:76929995-76930014 MsG0480022807.01.T01:intron 30.0%
!!! TTGAAATTTTGGAGTCGATA+AGG + Chr4:76929286-76929305 None:intergenic 30.0%
!!! TTGGTTTTCTAGAATTGACA+AGG - Chr4:76929994-76930013 MsG0480022807.01.T01:intron 30.0%
!!! TTTTCCACTTTTTGTTTTCC+AGG - Chr4:76930119-76930138 MsG0480022807.01.T01:intron 30.0%
AAAAACTAGAGTTGGGAAGT+AGG + Chr4:76930315-76930334 None:intergenic 35.0%
AAAACTAGAGTTGGGAAGTA+GGG + Chr4:76930314-76930333 None:intergenic 35.0%
AAGCATCAACAGTGATATCT+GGG + Chr4:76930091-76930110 None:intergenic 35.0%
AAGCTTTCGCTTTCAATGAA+AGG + Chr4:76930247-76930266 None:intergenic 35.0%
CATTTGGAGATGATTAAAGG+TGG + Chr4:76930504-76930523 None:intergenic 35.0%
CGAATCCCACAGAAAAATAA+AGG + Chr4:76929855-76929874 None:intergenic 35.0%
GAATGAAATGTGACAGTTTC+TGG + Chr4:76931060-76931079 None:intergenic 35.0%
GTTAAGTTAGTAGTACCTGA+AGG + Chr4:76929251-76929270 None:intergenic 35.0%
TAAGCATCAACAGTGATATC+TGG + Chr4:76930092-76930111 None:intergenic 35.0%
! CTGTCTTTCTACTTCAAGTT+TGG - Chr4:76930284-76930303 MsG0480022807.01.T01:intron 35.0%
! TAATGGGTGAGACATTCTTT+GGG - Chr4:76929115-76929134 MsG0480022807.01.T01:CDS 35.0%
! TGTTCTTTTCGTTCTTCCTT+TGG + Chr4:76929161-76929180 None:intergenic 35.0%
! TTAATGGGTGAGACATTCTT+TGG - Chr4:76929114-76929133 MsG0480022807.01.T01:CDS 35.0%
AAGGTATGTTTACCATGACG+TGG - Chr4:76931343-76931362 MsG0480022807.01.T01:intron 40.0%
AAGTGAATCAGAAACCTGCA+TGG - Chr4:76929082-76929101 MsG0480022807.01.T01:CDS 40.0%
AAGTTAGTAGTACCTGAAGG+AGG + Chr4:76929248-76929267 None:intergenic 40.0%
AATGGGTGAGACATTCTTTG+GGG - Chr4:76929116-76929135 MsG0480022807.01.T01:CDS 40.0%
AATTGGTCACTAGTGTCTAG+TGG + Chr4:76930045-76930064 None:intergenic 40.0%
AGTTAGTAGTACCTGAAGGA+GGG + Chr4:76929247-76929266 None:intergenic 40.0%
ATTAACCTCTCTAACCATGC+AGG + Chr4:76929099-76929118 None:intergenic 40.0%
GCATGGTTAGAGAGGTTAAT+GGG - Chr4:76929099-76929118 MsG0480022807.01.T01:CDS 40.0%
TACCATGACGTGGTTCAATT+GGG - Chr4:76931353-76931372 MsG0480022807.01.T01:intron 40.0%
TCAATGAAAGGAACGTTGCA+GGG + Chr4:76930235-76930254 None:intergenic 40.0%
TGAGACAACAGTGCAAACAA+AGG + Chr4:76929185-76929204 None:intergenic 40.0%
TGCATGGTTAGAGAGGTTAA+TGG - Chr4:76929098-76929117 MsG0480022807.01.T01:CDS 40.0%
TTACCATGACGTGGTTCAAT+TGG - Chr4:76931352-76931371 MsG0480022807.01.T01:intron 40.0%
TTCAATGAAAGGAACGTTGC+AGG + Chr4:76930236-76930255 None:intergenic 40.0%
TTGGAGATGATTAAAGGTGG+AGG + Chr4:76930501-76930520 None:intergenic 40.0%
! AAATGAGGGTATGAGTAAGC+AGG + Chr4:76931220-76931239 None:intergenic 40.0%
! AAGGAGTGTGAGAGTTAAAG+AGG + Chr4:76930954-76930973 None:intergenic 40.0%
! AGGAGTGTGAGAGTTAAAGA+GGG + Chr4:76930953-76930972 None:intergenic 40.0%
! CATCGATTGCTCCTATATTC+AGG - Chr4:76931391-76931410 MsG0480022807.01.T01:CDS 40.0%
! CTTTTATAACCTGGTACAGG+AGG + Chr4:76930589-76930608 None:intergenic 40.0%
!! TTCTAGAATTGACAAGGGCT+TGG - Chr4:76930000-76930019 MsG0480022807.01.T01:intron 40.0%
!!! CCACTTTTTGTTTTCCAGGA+GGG - Chr4:76930123-76930142 MsG0480022807.01.T01:intron 40.0%
!!! CGTTCTTCCTTTGGTTTTTG+TGG + Chr4:76929152-76929171 None:intergenic 40.0%
!!! TCCACTTTTTGTTTTCCAGG+AGG - Chr4:76930122-76930141 MsG0480022807.01.T01:intron 40.0%
ACCTTCTCACCTGCACAATA+TGG + Chr4:76931328-76931347 None:intergenic 45.0%
AGAAACCTGCATGGTTAGAG+AGG - Chr4:76929091-76929110 MsG0480022807.01.T01:CDS 45.0%
ATGGGTGAGACATTCTTTGG+GGG - Chr4:76929117-76929136 MsG0480022807.01.T01:CDS 45.0%
CAATGAAAGGAACGTTGCAG+GGG + Chr4:76930234-76930253 None:intergenic 45.0%
CCCTCCTGGAAAACAAAAAG+TGG + Chr4:76930126-76930145 None:intergenic 45.0%
CTATTGCTGCCATATTGTGC+AGG - Chr4:76931316-76931335 MsG0480022807.01.T01:intron 45.0%
CTCCCTTTGCTTCTGATGAT+GGG + Chr4:76929056-76929075 None:intergenic 45.0%
GACCCATCATCAGAAGCAAA+GGG - Chr4:76929051-76929070 MsG0480022807.01.T01:CDS 45.0%
GTTAGTAGTACCTGAAGGAG+GGG + Chr4:76929246-76929265 None:intergenic 45.0%
TCTCCCTTTGCTTCTGATGA+TGG + Chr4:76929057-76929076 None:intergenic 45.0%
TGACCCATCATCAGAAGCAA+AGG - Chr4:76929050-76929069 MsG0480022807.01.T01:CDS 45.0%
! AGACATTCTTTGGGGGTTGT+GGG - Chr4:76929124-76929143 MsG0480022807.01.T01:CDS 45.0%
!! TTTATAATATTACATAAATA+TGG + Chr4:76930426-76930445 None:intergenic 5.0%
!!! AAAATAAATATTTTTGTTAA+GGG - Chr4:76930868-76930887 MsG0480022807.01.T01:intron 5.0%
!!! AATTAATTTAAATTTTCATT+TGG + Chr4:76930520-76930539 None:intergenic 5.0%
!!! ATCTTTATTTATTTTTTTTT+CGG - Chr4:76930470-76930489 MsG0480022807.01.T01:intron 5.0%
AGGAACGTTGCAGGGGAAAT+TGG + Chr4:76930227-76930246 None:intergenic 50.0%
CACCCAATTGAACCACGTCA+TGG + Chr4:76931358-76931377 None:intergenic 50.0%
GCCATATTGTGCAGGTGAGA+AGG - Chr4:76931324-76931343 MsG0480022807.01.T01:intron 50.0%
GTGGGGTCCACAAAAACCAA+AGG - Chr4:76929142-76929161 MsG0480022807.01.T01:CDS 50.0%
TCACTAGTGTCTAGTGGTGG+TGG + Chr4:76930039-76930058 None:intergenic 50.0%
TGGTCACTAGTGTCTAGTGG+TGG + Chr4:76930042-76930061 None:intergenic 50.0%
! GACATTCTTTGGGGGTTGTG+GGG - Chr4:76929125-76929144 MsG0480022807.01.T01:CDS 50.0%
! GAGACATTCTTTGGGGGTTG+TGG - Chr4:76929123-76929142 MsG0480022807.01.T01:CDS 50.0%
ACCTGAAGGAGGGGATGAGA+GGG + Chr4:76929237-76929256 None:intergenic 55.0%
CAAGACATGGTGAACCCTCC+TGG + Chr4:76930140-76930159 None:intergenic 55.0%
GGTGAGAAGGGAGACAGTGA+GGG + Chr4:76929215-76929234 None:intergenic 55.0%
TACCTGAAGGAGGGGATGAG+AGG + Chr4:76929238-76929257 None:intergenic 55.0%
TCTTGCACTCCTCCTGTACC+AGG - Chr4:76930577-76930596 MsG0480022807.01.T01:intron 55.0%
AGGGAGACAGTGAGGGCAGA+TGG + Chr4:76929208-76929227 None:intergenic 60.0%
AGGGGATGAGAGGGGTGAGA+AGG + Chr4:76929228-76929247 None:intergenic 60.0%
CCTGAAGGAGGGGATGAGAG+GGG + Chr4:76929236-76929255 None:intergenic 60.0%
GGGGATGAGAGGGGTGAGAA+GGG + Chr4:76929227-76929246 None:intergenic 60.0%
GGGTGAGAAGGGAGACAGTG+AGG + Chr4:76929216-76929235 None:intergenic 60.0%
CCCCTCTCATCCCCTCCTTC+AGG - Chr4:76929233-76929252 MsG0480022807.01.T01:intron 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 76929033 76931445 76929033 ID=MsG0480022807.01;Name=MsG0480022807.01
Chr4 mRNA 76929033 76931445 76929033 ID=MsG0480022807.01.T01;Parent=MsG0480022807.01;Name=MsG0480022807.01.T01;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0|0|2|0|74
Chr4 exon 76931358 76931445 76931358 ID=MsG0480022807.01.T01:exon:8670;Parent=MsG0480022807.01.T01
Chr4 exon 76929033 76929169 76929033 ID=MsG0480022807.01.T01:exon:8669;Parent=MsG0480022807.01.T01
Chr4 CDS 76931358 76931445 76931358 ID=MsG0480022807.01.T01:cds;Parent=MsG0480022807.01.T01
Chr4 CDS 76929033 76929169 76929033 ID=MsG0480022807.01.T01:cds;Parent=MsG0480022807.01.T01
Gene Sequence

>MsG0480022807.01.T01

ATGAGAGGAAGTGGAAGTGACCCATCATCAGAAGCAAAGGGAGACATGAAAGTGAATCAGAAACCTGCATGGTTAGAGAGGTTAATGGGTGTTTGCTATTGCTGCCATATTGTGCAGGTGAGAAGGTATGTTTACCATGACGTGGTTCAATTGGGTGATCTTGAAAAGCTCATCGATTGCTCCTATATTCAGGTCAAACAAATACTACTACTACTACTACTCTAA
Protein sequence

>MsG0480022807.01.T01

MRGSGSDPSSEAKGDMKVNQKPAWLERLMGVCYCCHIVQVRRYVYHDVVQLGDLEKLIDCSYIQVKQILLLLLL*