AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580027407.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580027407.01.T01 MTR_5g056390 98.571 140 2 0 1 140 73 212 8.67e-100 285
MsG0580027407.01.T01 MTR_5g056230 68.571 140 44 0 1 140 73 212 4.13e-65 197
MsG0580027407.01.T01 MTR_5g056390 98.571 70 1 0 1 70 73 142 1.74e-45 145
MsG0580027407.01.T01 MTR_5g056300 69.697 66 17 3 13 76 5 69 2.51e-23 87.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580027407.01.T01 AT1G68260 78.571 140 30 0 1 140 50 189 9.05e-83 241
MsG0580027407.01.T01 AT1G68280 75.714 140 34 0 1 140 52 191 9.06e-78 229
MsG0580027407.01.T01 AT1G35290 70.290 138 41 0 1 138 48 185 6.13e-72 214
MsG0580027407.01.T01 AT1G35250 70.896 134 39 0 1 134 48 181 3.64e-70 209
MsG0580027407.01.T01 AT1G35250 67.241 116 37 1 1 115 48 163 2.67e-53 166
MsG0580027407.01.T01 AT1G35250 74.286 70 18 0 1 70 48 117 2.25e-34 117

Find 25 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCGTAAAGGTTAGAGTTTC+TGG 0.097401 5:+59924244 MsG0580027407.01.T01:CDS
GTGGCCTTGGCTTCCAAAAT+TGG 0.186658 5:-59924408 None:intergenic
ATTTGAATGACAGCCAATTT+TGG 0.285350 5:+59924395 MsG0580027407.01.T01:intron
AAGCCACACTGCTGTGGCCT+TGG 0.320053 5:-59924421 None:intergenic
CTATCGTCCTATTCGAATTC+CGG 0.388058 5:+59924452 MsG0580027407.01.T01:CDS
TGAAAATAGACCTCTTGGTT+TGG 0.456805 5:-59924313 None:intergenic
TAGAGGTGCAAGGAATTTGA+AGG 0.459499 5:-59924071 None:intergenic
GATTATGAGTTGGATCAGTT+TGG 0.461988 5:+59923085 MsG0580027407.01.T01:CDS
CAGGTGTGACTTACTCTTAG+AGG 0.464508 5:-59924088 None:intergenic
ATATCTGCCGGAATTCGAAT+AGG 0.483049 5:-59924459 None:intergenic
GGCTCGCGGTGGTGATGCAT+TGG 0.499513 5:+59924033 MsG0580027407.01.T01:CDS
AATTTAGACTTGATATCTGC+CGG 0.514648 5:-59924471 None:intergenic
TTTGTCAAGCCACACTGCTG+TGG 0.523309 5:-59924427 None:intergenic
AAAAGTTCGCGATTATGAGT+TGG 0.524063 5:+59923075 MsG0580027407.01.T01:CDS
GTCAACAATTCTGTGTATGC+AGG 0.533156 5:+59923112 MsG0580027407.01.T01:CDS
CTCATAATGTCTCACCATGT+TGG 0.533906 5:-59923141 None:intergenic
TGGAGACAGATTTGTCGTAA+AGG 0.565362 5:+59924231 MsG0580027407.01.T01:CDS
TGCATCACCACCGCGAGCCA+CGG 0.601557 5:-59924029 None:intergenic
GACTTACTCTTAGAGGTGCA+AGG 0.604777 5:-59924081 None:intergenic
TGGCATTAATTGTGATGCCG+TGG 0.622604 5:+59924012 MsG0580027407.01.T01:CDS
AATTGTGATGCCGTGGCTCG+CGG 0.636957 5:+59924019 MsG0580027407.01.T01:CDS
CTATAAGCTACCAAACCAAG+AGG 0.676363 5:+59924303 MsG0580027407.01.T01:CDS
TGTGATGCCGTGGCTCGCGG+TGG 0.683821 5:+59924022 MsG0580027407.01.T01:CDS
TATGCAGGTTATTGCCAACA+TGG 0.696171 5:+59923127 MsG0580027407.01.T01:CDS
AAGCCAAGGCCACAGCAGTG+TGG 0.715403 5:+59924418 MsG0580027407.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTAACATATTTCAATTA+AGG - Chr5:59923856-59923875 None:intergenic 10.0%
!! AAAAAAAAGAGTAAACTATA+AGG - Chr5:59924341-59924360 None:intergenic 15.0%
!! AAAAAAAGAGTAAACTATAA+GGG - Chr5:59924340-59924359 None:intergenic 15.0%
!! AAATATAAAACCAAGTTAAA+GGG - Chr5:59923760-59923779 None:intergenic 15.0%
!!! AAGAAATTATAGCTTTTAAT+TGG - Chr5:59923921-59923940 None:intergenic 15.0%
!!! TTTTAATTGGTACAAAATTT+AGG - Chr5:59923908-59923927 None:intergenic 15.0%
!! AAGATTAAAGTAACAATCAA+TGG - Chr5:59923190-59923209 None:intergenic 20.0%
!! AATATAAAACCAAGTTAAAG+GGG - Chr5:59923759-59923778 None:intergenic 20.0%
!! ATACAATGTAGTAATGTTAA+AGG + Chr5:59924151-59924170 MsG0580027407.01.T01:intron 20.0%
!! GAAATATAAAACCAAGTTAA+AGG - Chr5:59923761-59923780 None:intergenic 20.0%
!! GTTTAATCATGATAAAATGA+AGG - Chr5:59923518-59923537 None:intergenic 20.0%
!! TTATGATATTTCTCATATCT+TGG + Chr5:59923715-59923734 MsG0580027407.01.T01:intron 20.0%
!! TTTAATCTTCATATCACTTT+AGG + Chr5:59923201-59923220 MsG0580027407.01.T01:intron 20.0%
!!! AATACAGGTAATTTGTAATA+TGG - Chr5:59923403-59923422 None:intergenic 20.0%
!!! TTCTTTATTGTTTTTGATCT+GGG + Chr5:59923797-59923816 MsG0580027407.01.T01:intron 20.0%
!!! TTTAAAATCAGAACAAACAT+TGG - Chr5:59924195-59924214 None:intergenic 20.0%
! AATCATGTCATATCAAACAT+TGG - Chr5:59923241-59923260 None:intergenic 25.0%
! ATAAACAATCAGTTTATGTG+TGG - Chr5:59923948-59923967 None:intergenic 25.0%
! ATGTTTGATATGACATGATT+AGG + Chr5:59923241-59923260 MsG0580027407.01.T01:intron 25.0%
! CAGATCAAAAACAATAAAGA+AGG - Chr5:59923798-59923817 None:intergenic 25.0%
! CGAAAATGTTTCTTGATATT+TGG + Chr5:59924369-59924388 MsG0580027407.01.T01:intron 25.0%
! TAACATTACTACATTGTATC+AGG - Chr5:59924150-59924169 None:intergenic 25.0%
! TATATGCAAATACCTTCATA+AGG + Chr5:59923965-59923984 MsG0580027407.01.T01:intron 25.0%
! TTCAATTAAGGATCCTTTAT+GGG - Chr5:59923844-59923863 None:intergenic 25.0%
! TTTCAATTAAGGATCCTTTA+TGG - Chr5:59923845-59923864 None:intergenic 25.0%
!! TAAATGGATTCTCTTAATAC+AGG - Chr5:59923418-59923437 None:intergenic 25.0%
!!! CTTCTTTATTGTTTTTGATC+TGG + Chr5:59923796-59923815 MsG0580027407.01.T01:intron 25.0%
!!! CTTTTTTGAACAAGACTAAA+TGG - Chr5:59923434-59923453 None:intergenic 25.0%
!!! TAACTTGGTTTTATATTTCC+TGG + Chr5:59923762-59923781 MsG0580027407.01.T01:intron 25.0%
!!! TCTTTATTGTTTTTGATCTG+GGG + Chr5:59923798-59923817 MsG0580027407.01.T01:intron 25.0%
!!! TTATTATGGTTTTGTGCTTT+GGG + Chr5:59923587-59923606 MsG0580027407.01.T01:intron 25.0%
AAAGAAGGATCAAATATACC+AGG - Chr5:59923783-59923802 None:intergenic 30.0%
AATTTAGACTTGATATCTGC+CGG - Chr5:59924474-59924493 None:intergenic 30.0%
! ATAAGGTCGTCATGAATTTT+TGG + Chr5:59923982-59924001 MsG0580027407.01.T01:intron 30.0%
! ATCTTATGATTGTGTTGTTC+TGG - Chr5:59923482-59923501 None:intergenic 30.0%
! ATTTGAATGACAGCCAATTT+TGG + Chr5:59924395-59924414 MsG0580027407.01.T01:intron 30.0%
! TCAAGAAACATTTTCGAAGA+TGG - Chr5:59924365-59924384 None:intergenic 30.0%
! TGTGGTAATTTGATGACTTT+AGG + Chr5:59923274-59923293 MsG0580027407.01.T01:intron 30.0%
!! CATGAATTTTTGGAAAGCAT+TGG + Chr5:59923992-59924011 MsG0580027407.01.T01:CDS 30.0%
!!! CTTATTATGGTTTTGTGCTT+TGG + Chr5:59923586-59923605 MsG0580027407.01.T01:intron 30.0%
!!! CTTTATTGTTTTTGATCTGG+GGG + Chr5:59923799-59923818 MsG0580027407.01.T01:intron 30.0%
!!! TAAGTCACACCTGATTTTTT+CGG + Chr5:59924098-59924117 MsG0580027407.01.T01:intron 30.0%
!!! TGGTTTTGTTGCTTACTAAA+TGG - Chr5:59923462-59923481 None:intergenic 30.0%
!!! TTTATTGTTTTTGATCTGGG+GGG + Chr5:59923800-59923819 MsG0580027407.01.T01:intron 30.0%
AAAAGTTCGCGATTATGAGT+TGG + Chr5:59923075-59923094 MsG0580027407.01.T01:CDS 35.0%
AATTCATGACGACCTTATGA+AGG - Chr5:59923980-59923999 None:intergenic 35.0%
CACAAATGACCGAAAAAATC+AGG - Chr5:59924110-59924129 None:intergenic 35.0%
TAAAAAACTTGCAACCAGAG+TGG + Chr5:59924211-59924230 MsG0580027407.01.T01:intron 35.0%
TAAATGTTGCCCCTTTAACT+TGG + Chr5:59923747-59923766 MsG0580027407.01.T01:intron 35.0%
TGAAAATAGACCTCTTGGTT+TGG - Chr5:59924316-59924335 None:intergenic 35.0%
TTCGGTCATTTGTGTTTGTT+AGG + Chr5:59924116-59924135 MsG0580027407.01.T01:intron 35.0%
! GATTATGAGTTGGATCAGTT+TGG + Chr5:59923085-59923104 MsG0580027407.01.T01:CDS 35.0%
!!! TTATTGTTTTTGATCTGGGG+GGG + Chr5:59923801-59923820 MsG0580027407.01.T01:intron 35.0%
ACGTGATGCATGGCTTATTA+TGG + Chr5:59923573-59923592 MsG0580027407.01.T01:intron 40.0%
AGGGATGAAAATAGACCTCT+TGG - Chr5:59924321-59924340 None:intergenic 40.0%
ATATCTGCCGGAATTCGAAT+AGG - Chr5:59924462-59924481 None:intergenic 40.0%
CAAGAAGAAAACGTGATGCA+TGG + Chr5:59923563-59923582 MsG0580027407.01.T01:intron 40.0%
CTATAAGCTACCAAACCAAG+AGG + Chr5:59924303-59924322 MsG0580027407.01.T01:CDS 40.0%
CTATCGTCCTATTCGAATTC+CGG + Chr5:59924452-59924471 MsG0580027407.01.T01:CDS 40.0%
CTCATAATGTCTCACCATGT+TGG - Chr5:59923144-59923163 None:intergenic 40.0%
GTCAACAATTCTGTGTATGC+AGG + Chr5:59923112-59923131 MsG0580027407.01.T01:CDS 40.0%
GTCGTAAAGGTTAGAGTTTC+TGG + Chr5:59924244-59924263 MsG0580027407.01.T01:CDS 40.0%
TATGCAGGTTATTGCCAACA+TGG + Chr5:59923127-59923146 MsG0580027407.01.T01:CDS 40.0%
TGGAGACAGATTTGTCGTAA+AGG + Chr5:59924231-59924250 MsG0580027407.01.T01:CDS 40.0%
! CTAGCATCTTTTTGCTCTGT+AGG + Chr5:59923684-59923703 MsG0580027407.01.T01:intron 40.0%
! TAGAGGTGCAAGGAATTTGA+AGG - Chr5:59924074-59924093 None:intergenic 40.0%
!! TTTTGTGCTTTGGGTTTTGG+AGG + Chr5:59923596-59923615 MsG0580027407.01.T01:intron 40.0%
!!! TGGTTTTGTGCTTTGGGTTT+TGG + Chr5:59923593-59923612 MsG0580027407.01.T01:intron 40.0%
!!! TTTGTGCTTTGGGTTTTGGA+GGG + Chr5:59923597-59923616 MsG0580027407.01.T01:intron 40.0%
CAGGTGTGACTTACTCTTAG+AGG - Chr5:59924091-59924110 None:intergenic 45.0%
TGGCATTAATTGTGATGCCG+TGG + Chr5:59924012-59924031 MsG0580027407.01.T01:CDS 45.0%
! GACTTACTCTTAGAGGTGCA+AGG - Chr5:59924084-59924103 None:intergenic 45.0%
!! ACAGCCAATTTTGGAAGCCA+AGG + Chr5:59924404-59924423 MsG0580027407.01.T01:intron 45.0%
!! TGATTAGGACAGAAGTGCTG+TGG + Chr5:59923256-59923275 MsG0580027407.01.T01:intron 45.0%
CGACAAATCTGTCTCCACTC+TGG - Chr5:59924228-59924247 None:intergenic 50.0%
TTTGTCAAGCCACACTGCTG+TGG - Chr5:59924430-59924449 None:intergenic 50.0%
! GTGGCCTTGGCTTCCAAAAT+TGG - Chr5:59924411-59924430 None:intergenic 50.0%
!! TGTTTTTGATCTGGGGGGGA+GGG + Chr5:59923805-59923824 MsG0580027407.01.T01:intron 50.0%
!!! TTGTTTTTGATCTGGGGGGG+AGG + Chr5:59923804-59923823 MsG0580027407.01.T01:intron 50.0%
AATTGTGATGCCGTGGCTCG+CGG + Chr5:59924019-59924038 MsG0580027407.01.T01:CDS 55.0%
AGGGGGAGGGTAACCCATAA+AGG + Chr5:59923828-59923847 MsG0580027407.01.T01:intron 55.0%
AAGCCAAGGCCACAGCAGTG+TGG + Chr5:59924418-59924437 MsG0580027407.01.T01:CDS 60.0%
AAGCCACACTGCTGTGGCCT+TGG - Chr5:59924424-59924443 None:intergenic 60.0%
TTTGATCTGGGGGGGAGGGA+GGG + Chr5:59923809-59923828 MsG0580027407.01.T01:intron 60.0%
! TTTTGATCTGGGGGGGAGGG+AGG + Chr5:59923808-59923827 MsG0580027407.01.T01:intron 60.0%
TGCATCACCACCGCGAGCCA+CGG - Chr5:59924032-59924051 None:intergenic 65.0%
TTGATCTGGGGGGGAGGGAG+GGG + Chr5:59923810-59923829 MsG0580027407.01.T01:intron 65.0%
! GGCTCGCGGTGGTGATGCAT+TGG + Chr5:59924033-59924052 MsG0580027407.01.T01:CDS 65.0%
TGATCTGGGGGGGAGGGAGG+GGG + Chr5:59923811-59923830 MsG0580027407.01.T01:intron 70.0%
TGTGATGCCGTGGCTCGCGG+TGG + Chr5:59924022-59924041 MsG0580027407.01.T01:CDS 70.0%
! CTGGGGGGGAGGGAGGGGGA+GGG + Chr5:59923815-59923834 MsG0580027407.01.T01:intron 80.0%
! TCTGGGGGGGAGGGAGGGGG+AGG + Chr5:59923814-59923833 MsG0580027407.01.T01:intron 80.0%
Chromosome Type Strat End Strand Name
Chr5 gene 59923049 59924524 59923049 ID=MsG0580027407.01;Name=MsG0580027407.01
Chr5 mRNA 59923049 59924524 59923049 ID=MsG0580027407.01.T01;Parent=MsG0580027407.01;Name=MsG0580027407.01.T01;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|1|0.75|4|0|140
Chr5 exon 59923049 59923148 59923049 ID=MsG0580027407.01.T01:exon:42830;Parent=MsG0580027407.01.T01
Chr5 exon 59923987 59924096 59923987 ID=MsG0580027407.01.T01:exon:42831;Parent=MsG0580027407.01.T01
Chr5 exon 59924229 59924324 59924229 ID=MsG0580027407.01.T01:exon:42832;Parent=MsG0580027407.01.T01
Chr5 exon 59924408 59924524 59924408 ID=MsG0580027407.01.T01:exon:42833;Parent=MsG0580027407.01.T01
Chr5 CDS 59923049 59923148 59923049 ID=MsG0580027407.01.T01:cds;Parent=MsG0580027407.01.T01
Chr5 CDS 59923987 59924096 59923987 ID=MsG0580027407.01.T01:cds;Parent=MsG0580027407.01.T01
Chr5 CDS 59924229 59924324 59924229 ID=MsG0580027407.01.T01:cds;Parent=MsG0580027407.01.T01
Chr5 CDS 59924408 59924524 59924408 ID=MsG0580027407.01.T01:cds;Parent=MsG0580027407.01.T01
Gene Sequence

>MsG0580027407.01.T01

ATGAGTGGGTTCTGTGACGTCGAACTAAAAGTTCGCGATTATGAGTTGGATCAGTTTGGTGTTGTCAACAATTCTGTGTATGCAGGTTATTGCCAACATGGTCGTCATGAATTTTTGGAAAGCATTGGCATTAATTGTGATGCCGTGGCTCGCGGTGGTGATGCATTGGCACTGTCAGAACTATCCTTCAAATTCCTTGCACCTCTAAGAAGTGGAGACAGATTTGTCGTAAAGGTTAGAGTTTCTGGCTCTTCAGCTGCACGTATATACTTTGATCACTTTATCTATAAGCTACCAAACCAAGAGCCAATTTTGGAAGCCAAGGCCACAGCAGTGTGGCTTGACAAAAACTATCGTCCTATTCGAATTCCGGCAGATATCAAGTCTAAATTTGTTAAATTTATTCGCAGTGAAGACTCATGA
Protein sequence

>MsG0580027407.01.T01

MSGFCDVELKVRDYELDQFGVVNNSVYAGYCQHGRHEFLESIGINCDAVARGGDALALSELSFKFLAPLRSGDRFVVKVRVSGSSAARIYFDHFIYKLPNQEPILEAKATAVWLDKNYRPIRIPADIKSKFVKFIRSEDS*