AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180006006.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180006006.01.T01 MTR_1g111660 58.065 217 23 4 9 158 1353 1568 2.11e-43 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGGCATAAACTTGTTATT+TGG 0.170908 1:-98717693 None:intergenic
GATTATTTCTTCCCAGAAAA+TGG 0.181241 1:+98718073 MsG0180006006.01.T01:CDS
AATATCTTTATAGGCGAAAA+TGG 0.227994 1:+98717554 MsG0180006006.01.T01:intron
TGCCGAGGAAATATTGTTTC+CGG 0.239103 1:-98718098 None:intergenic
AAAAGGAGAAAGATAGAAAA+AGG 0.243572 1:+98716697 MsG0180006006.01.T01:CDS
AAGGGAAATTGAAGAGAAAA+AGG 0.263230 1:+98716680 MsG0180006006.01.T01:CDS
AGTAATATGCAATTCTTCTA+AGG 0.293481 1:-98718489 None:intergenic
TCATCATCATCTGATCTATA+TGG 0.312866 1:-98717654 None:intergenic
GCCGAGGAAATATTGTTTCC+GGG 0.345804 1:-98718097 None:intergenic
AAAGAAGGAGGAAGAAGAAA+TGG 0.360491 1:+98716638 MsG0180006006.01.T01:CDS
TTCTTCCCAGAAAATGGACC+CGG 0.507214 1:+98718079 MsG0180006006.01.T01:CDS
ATAACAAGTTTATGCCATCA+TGG 0.508757 1:+98717697 MsG0180006006.01.T01:CDS
GACATGAAGCTGCAAGAGCA+TGG 0.516786 1:+98716732 MsG0180006006.01.T01:CDS
GGGAAGAAATAATCATTGAC+AGG 0.519799 1:-98718064 None:intergenic
TAACAAGTTTATGCCATCAT+GGG 0.551395 1:+98717698 MsG0180006006.01.T01:CDS
AGTTTATGCCATCATGGGCA+AGG 0.551787 1:+98717703 MsG0180006006.01.T01:CDS
AAGAGAGAAGGAGTTCATGA+TGG 0.556822 1:+98716602 MsG0180006006.01.T01:CDS
ACAACAAACCTTGCCCATGA+TGG 0.570513 1:-98717711 None:intergenic
GATAGCAATGGCAATGGCAA+TGG 0.571981 1:-98718467 None:intergenic
GCGAATGAGCAAAAGAGAGA+AGG 0.572313 1:+98716590 MsG0180006006.01.T01:CDS
ACATGAAGCTGCAAGAGCAT+GGG 0.577354 1:+98716733 MsG0180006006.01.T01:CDS
ACCCGGAAACAATATTTCCT+CGG 0.589237 1:+98718096 MsG0180006006.01.T01:CDS
TCTAAGGATAGCAATGGCAA+TGG 0.633606 1:-98718473 None:intergenic
AATTCTTCTAAGGATAGCAA+TGG 0.648912 1:-98718479 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAATAATAAAGAAATTT+CGG + Chr1:98717991-98718010 MsG0180006006.01.T01:intron 10.0%
!! AAATATTAATTGTGCAAAAT+AGG + Chr1:98717912-98717931 MsG0180006006.01.T01:intron 15.0%
!! TGAGATTTAAATATCTTTAT+AGG + Chr1:98717545-98717564 MsG0180006006.01.T01:intron 15.0%
!!! ATTTTGCACAATTAATATTT+TGG - Chr1:98717912-98717931 None:intergenic 15.0%
!! AAGATATTTAAATCTCACAA+TGG - Chr1:98717542-98717561 None:intergenic 20.0%
!! AGCTAAAGAAAAAAAACAAA+GGG + Chr1:98716662-98716681 MsG0180006006.01.T01:CDS 20.0%
!! TTATCTTTAACAATCATACT+TGG + Chr1:98717113-98717132 MsG0180006006.01.T01:intron 20.0%
!!! AAAGCAACAAAAAAGTTTTT+AGG - Chr1:98718029-98718048 None:intergenic 20.0%
!!! AACAATTTTATTGACAAAAG+AGG - Chr1:98716797-98716816 None:intergenic 20.0%
!!! ATTCTTTAATATGTGTCATT+TGG + Chr1:98717505-98717524 MsG0180006006.01.T01:intron 20.0%
!!! CAAAAAAGTTTTTAGGTAAA+TGG - Chr1:98718022-98718041 None:intergenic 20.0%
!!! TTGTATTTCCTTTTAATTCT+TGG + Chr1:98718369-98718388 MsG0180006006.01.T01:intron 20.0%
!!! TTGTTTTAATATTCTCAGTT+TGG + Chr1:98718422-98718441 MsG0180006006.01.T01:intron 20.0%
!!! TTTTAATTCAAACTGTAACA+AGG + Chr1:98717842-98717861 MsG0180006006.01.T01:intron 20.0%
! AAAAGGAGAAAGATAGAAAA+AGG + Chr1:98716697-98716716 MsG0180006006.01.T01:CDS 25.0%
! AAATCTCACAATGGTTATAA+AGG - Chr1:98717533-98717552 None:intergenic 25.0%
! AATATCTTTATAGGCGAAAA+TGG + Chr1:98717554-98717573 MsG0180006006.01.T01:intron 25.0%
! AATGCTTACCAAGAATTAAA+AGG - Chr1:98718380-98718399 None:intergenic 25.0%
! AGAACTATAAAAGAATGCAT+TGG - Chr1:98718209-98718228 None:intergenic 25.0%
! AGTAATATGCAATTCTTCTA+AGG - Chr1:98718492-98718511 None:intergenic 25.0%
! ATATCCTTCAAAAACAAAAG+TGG - Chr1:98717355-98717374 None:intergenic 25.0%
! CAGCTAAAGAAAAAAAACAA+AGG + Chr1:98716661-98716680 MsG0180006006.01.T01:CDS 25.0%
! TAAGCATTTGGTTATTCTAA+GGG + Chr1:98718392-98718411 MsG0180006006.01.T01:intron 25.0%
! TATAAATACTAGGAAACAGT+TGG - Chr1:98717296-98717315 None:intergenic 25.0%
! TATTCTTTACAATGATCTTC+TGG + Chr1:98717474-98717493 MsG0180006006.01.T01:intron 25.0%
! TTTAATTCTTGGTAAGCATT+TGG + Chr1:98718380-98718399 MsG0180006006.01.T01:intron 25.0%
!! AGCAATTAAACAAAAAGCAT+TGG - Chr1:98717252-98717271 None:intergenic 25.0%
!! AGGCTAATATATAGATTTTC+TGG + Chr1:98716848-98716867 MsG0180006006.01.T01:intron 25.0%
!! TCATTTTACCTTTCCTTTAT+TGG - Chr1:98717071-98717090 None:intergenic 25.0%
!!! AAAGCTTTAAAAGCAATATG+TGG + Chr1:98717880-98717899 MsG0180006006.01.T01:intron 25.0%
!!! ATATATAGATTTTCTGGTCT+AGG + Chr1:98716854-98716873 MsG0180006006.01.T01:intron 25.0%
!!! TATATAGATTTTCTGGTCTA+GGG + Chr1:98716855-98716874 MsG0180006006.01.T01:intron 25.0%
!!! TTATCCACTTTTGTTTTTGA+AGG + Chr1:98717348-98717367 MsG0180006006.01.T01:intron 25.0%
!!! TTCTCTTTTGATTTGTGAAA+AGG + Chr1:98716828-98716847 MsG0180006006.01.T01:intron 25.0%
AAGAACTTCTTGTATAGAAC+TGG - Chr1:98717182-98717201 None:intergenic 30.0%
AAGGATATGATTTATCCACT+TGG + Chr1:98717367-98717386 MsG0180006006.01.T01:intron 30.0%
AAGGGAAATTGAAGAGAAAA+AGG + Chr1:98716680-98716699 MsG0180006006.01.T01:CDS 30.0%
AGGCACCATAACATTATTAA+TGG - Chr1:98717762-98717781 None:intergenic 30.0%
AGTGCTCAACAATTATTTGA+AGG + Chr1:98717315-98717334 MsG0180006006.01.T01:intron 30.0%
ATAACAAGTTTATGCCATCA+TGG + Chr1:98717697-98717716 MsG0180006006.01.T01:CDS 30.0%
CAAGCAATAGTAAATCTATC+TGG - Chr1:98717968-98717987 None:intergenic 30.0%
CGTACCCATTAATAATGTTA+TGG + Chr1:98717754-98717773 MsG0180006006.01.T01:intron 30.0%
CTTTAACAATCATACTTGGA+AGG + Chr1:98717117-98717136 MsG0180006006.01.T01:intron 30.0%
GAAAGCAGGAAAATTATAGA+AGG + Chr1:98716891-98716910 MsG0180006006.01.T01:intron 30.0%
GGCACCATAACATTATTAAT+GGG - Chr1:98717761-98717780 None:intergenic 30.0%
GTAAGCATTTGGTTATTCTA+AGG + Chr1:98718391-98718410 MsG0180006006.01.T01:intron 30.0%
GTGCTCAACAATTATTTGAA+GGG + Chr1:98717316-98717335 MsG0180006006.01.T01:intron 30.0%
TAACAAGTTTATGCCATCAT+GGG + Chr1:98717698-98717717 MsG0180006006.01.T01:CDS 30.0%
TCATCATCATCTGATCTATA+TGG - Chr1:98717657-98717676 None:intergenic 30.0%
TGTTGAGCACTATAAATACT+AGG - Chr1:98717306-98717325 None:intergenic 30.0%
TTAAACAGTTTAACACCAAG+TGG - Chr1:98717385-98717404 None:intergenic 30.0%
TTACACGAGAGAATTATGTT+TGG - Chr1:98717408-98717427 None:intergenic 30.0%
TTCCATGCATTTCACAATAA+GGG + Chr1:98718285-98718304 MsG0180006006.01.T01:intron 30.0%
! AATTCTTCTAAGGATAGCAA+TGG - Chr1:98718482-98718501 None:intergenic 30.0%
! AGTTTTTGCGATATTGCAAA+AGG + Chr1:98718122-98718141 MsG0180006006.01.T01:CDS 30.0%
! CAATAAGGGATTTTGTGTTA+AGG + Chr1:98718299-98718318 MsG0180006006.01.T01:intron 30.0%
! CTATAATTTTCCTGCTTTCA+TGG - Chr1:98716890-98716909 None:intergenic 30.0%
! CTTCTCTCAATGTGATTTTT+GGG + Chr1:98717780-98717799 MsG0180006006.01.T01:intron 30.0%
! CTTTAAAAGCAATATGTGGT+TGG + Chr1:98717884-98717903 MsG0180006006.01.T01:intron 30.0%
! GATTATTTCTTCCCAGAAAA+TGG + Chr1:98718073-98718092 MsG0180006006.01.T01:CDS 30.0%
! TTCTTTTCTTCTAACAATGC+AGG + Chr1:98717197-98717216 MsG0180006006.01.T01:intron 30.0%
!! GATGGCATAAACTTGTTATT+TGG - Chr1:98717696-98717715 None:intergenic 30.0%
AAAGAAGGAGGAAGAAGAAA+TGG + Chr1:98716638-98716657 MsG0180006006.01.T01:CDS 35.0%
ATCCCTTATTGTGAAATGCA+TGG - Chr1:98718290-98718309 None:intergenic 35.0%
ATTATTTCCAGAACCCAAAC+AGG - Chr1:98717942-98717961 None:intergenic 35.0%
CCAAAAATCACATTGAGAGA+AGG - Chr1:98717782-98717801 None:intergenic 35.0%
CTTATCATAACAGCTTTCCT+TGG - Chr1:98717026-98717045 None:intergenic 35.0%
CTTCCATGCATTTCACAATA+AGG + Chr1:98718284-98718303 MsG0180006006.01.T01:intron 35.0%
GCTTTCCTTGGTTATGTTAT+TGG - Chr1:98717014-98717033 None:intergenic 35.0%
GGAGAAAGATAGAAAAAGGA+AGG + Chr1:98716701-98716720 MsG0180006006.01.T01:CDS 35.0%
GGGAAGAAATAATCATTGAC+AGG - Chr1:98718067-98718086 None:intergenic 35.0%
TTATTTCCAGAACCCAAACA+GGG - Chr1:98717941-98717960 None:intergenic 35.0%
TTCAGCCAATAACATAACCA+AGG + Chr1:98717006-98717025 MsG0180006006.01.T01:intron 35.0%
TTCTGTTATAGTACCAACTC+AGG + Chr1:98718243-98718262 MsG0180006006.01.T01:intron 35.0%
! CATCTTATACCTTGTTTGCA+TGG + Chr1:98718337-98718356 MsG0180006006.01.T01:intron 35.0%
! CCTTCTCTCAATGTGATTTT+TGG + Chr1:98717779-98717798 MsG0180006006.01.T01:intron 35.0%
! CTGGAAAAGATTTTTCCTAG+CGG - Chr1:98717163-98717182 None:intergenic 35.0%
! CTTTTATAGTTCTCCTACCT+CGG + Chr1:98718216-98718235 MsG0180006006.01.T01:intron 35.0%
! TGGAAAAGATTTTTCCTAGC+GGG - Chr1:98717162-98717181 None:intergenic 35.0%
!! TTTGGGTTTTCAACCTTTCA+TGG + Chr1:98717797-98717816 MsG0180006006.01.T01:intron 35.0%
!!! TGTTGTTTTCCATGCAAACA+AGG - Chr1:98718349-98718368 None:intergenic 35.0%
AAGAGAGAAGGAGTTCATGA+TGG + Chr1:98716602-98716621 MsG0180006006.01.T01:CDS 40.0%
ACCCGGAAACAATATTTCCT+CGG + Chr1:98718096-98718115 MsG0180006006.01.T01:CDS 40.0%
ATAGTACCAACTCAGGAATC+AGG + Chr1:98718250-98718269 MsG0180006006.01.T01:intron 40.0%
ATATCGCAAAAACTTTGCCG+AGG - Chr1:98718116-98718135 None:intergenic 40.0%
CAAAATAGGTACCCCTGTTT+GGG + Chr1:98717926-98717945 MsG0180006006.01.T01:intron 40.0%
CGAATGTGCCAATAAAGGAA+AGG + Chr1:98717060-98717079 MsG0180006006.01.T01:intron 40.0%
TATTTCCAGAACCCAAACAG+GGG - Chr1:98717940-98717959 None:intergenic 40.0%
TCTAAGGATAGCAATGGCAA+TGG - Chr1:98718476-98718495 None:intergenic 40.0%
TGCCGAGGAAATATTGTTTC+CGG - Chr1:98718101-98718120 None:intergenic 40.0%
! CTGCAAGAGCATAATAGACA+AGG + Chr1:98716939-98716958 MsG0180006006.01.T01:intron 40.0%
ACAACAAACCTTGCCCATGA+TGG - Chr1:98717714-98717733 None:intergenic 45.0%
AGTTTATGCCATCATGGGCA+AGG + Chr1:98717703-98717722 MsG0180006006.01.T01:CDS 45.0%
GATAGCAATGGCAATGGCAA+TGG - Chr1:98718470-98718489 None:intergenic 45.0%
GCAAAATAGGTACCCCTGTT+TGG + Chr1:98717925-98717944 MsG0180006006.01.T01:intron 45.0%
GCAGCAGAAGAAAAAGAAGG+AGG + Chr1:98716626-98716645 MsG0180006006.01.T01:CDS 45.0%
GCCGAGGAAATATTGTTTCC+GGG - Chr1:98718100-98718119 None:intergenic 45.0%
GCGAATGAGCAAAAGAGAGA+AGG + Chr1:98716590-98716609 MsG0180006006.01.T01:CDS 45.0%
GGAGCAGCAGAAGAAAAAGA+AGG + Chr1:98716623-98716642 MsG0180006006.01.T01:CDS 45.0%
GTGAAGAAGTCCATGAAAGC+AGG + Chr1:98716877-98716896 MsG0180006006.01.T01:intron 45.0%
GTGAGCGAATGTGCCAATAA+AGG + Chr1:98717055-98717074 MsG0180006006.01.T01:intron 45.0%
TACTATAACAGAAGCCTCCG+AGG - Chr1:98718236-98718255 None:intergenic 45.0%
TTATAGTTCTCCTACCTCGG+AGG + Chr1:98718219-98718238 MsG0180006006.01.T01:intron 45.0%
TTCTTCCCAGAAAATGGACC+CGG + Chr1:98718079-98718098 MsG0180006006.01.T01:CDS 45.0%
! AAAAGCACATGCGCCATGAA+AGG - Chr1:98717813-98717832 None:intergenic 45.0%
! ACATGAAGCTGCAAGAGCAT+GGG + Chr1:98716733-98716752 MsG0180006006.01.T01:CDS 45.0%
! GTTATTGGCTGAATCGCTGA+TGG - Chr1:98716999-98717018 None:intergenic 45.0%
! TGTTTCCGGGTCCATTTTCT+GGG - Chr1:98718087-98718106 None:intergenic 45.0%
! TTGTTTCCGGGTCCATTTTC+TGG - Chr1:98718088-98718107 None:intergenic 45.0%
AGCTTGTACGTGTGCTTAGC+AGG + Chr1:98717435-98717454 MsG0180006006.01.T01:intron 50.0%
ATAACAGAAGCCTCCGAGGT+AGG - Chr1:98718232-98718251 None:intergenic 50.0%
ATAGCAGTTTGTGTCCCGCT+AGG + Chr1:98717145-98717164 MsG0180006006.01.T01:intron 50.0%
CTACGTCCTGATTCCTGAGT+TGG - Chr1:98718259-98718278 None:intergenic 50.0%
GACATGAAGCTGCAAGAGCA+TGG + Chr1:98716732-98716751 MsG0180006006.01.T01:CDS 50.0%
GCTTGTACGTGTGCTTAGCA+GGG + Chr1:98717436-98717455 MsG0180006006.01.T01:intron 50.0%
! TCATGGCGCATGTGCTTTTG+TGG + Chr1:98717814-98717833 MsG0180006006.01.T01:intron 50.0%
GGCTGAATCGCTGATGGTCA+AGG - Chr1:98716993-98717012 None:intergenic 55.0%
! AGGTACCCCTGTTTGGGTTC+TGG + Chr1:98717932-98717951 MsG0180006006.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr1 gene 98716576 98718513 98716576 ID=MsG0180006006.01;Name=MsG0180006006.01
Chr1 mRNA 98716576 98718513 98716576 ID=MsG0180006006.01.T01;Parent=MsG0180006006.01;Name=MsG0180006006.01.T01;_AED=0.26;_eAED=0.27;_QI=0|0.6|0.83|1|0.8|0.66|6|0|176
Chr1 exon 98716576 98716785 98716576 ID=MsG0180006006.01.T01:exon:50921;Parent=MsG0180006006.01.T01
Chr1 exon 98717567 98717724 98717567 ID=MsG0180006006.01.T01:exon:50922;Parent=MsG0180006006.01.T01
Chr1 exon 98718055 98718143 98718055 ID=MsG0180006006.01.T01:exon:50923;Parent=MsG0180006006.01.T01
Chr1 exon 98718440 98718513 98718440 ID=MsG0180006006.01.T01:exon:50924;Parent=MsG0180006006.01.T01
Chr1 CDS 98716576 98716785 98716576 ID=MsG0180006006.01.T01:cds;Parent=MsG0180006006.01.T01
Chr1 CDS 98717567 98717724 98717567 ID=MsG0180006006.01.T01:cds;Parent=MsG0180006006.01.T01
Chr1 CDS 98718055 98718143 98718055 ID=MsG0180006006.01.T01:cds;Parent=MsG0180006006.01.T01
Chr1 CDS 98718440 98718513 98718440 ID=MsG0180006006.01.T01:cds;Parent=MsG0180006006.01.T01
Gene Sequence

>MsG0180006006.01.T01

ATGCTGACATTAAAGCGAATGAGCAAAAGAGAGAAGGAGTTCATGATGGAGCAGCAGAAGAAAAAGAAGGAGGAAGAAGAAATGGCAGCTAAAGAAAAAAAACAAAGGGAAATTGAAGAGAAAAAGGAGAAAGATAGAAAAAGGAAGGCTGTTAATGACATGAAGCTGCAAGAGCATGGGAAGATACATGCGAAGAAAGCTAGAGCTGCAGCGAAAATGGTTGATTTGATCAAAGCTGTTGAAGACAATGACTCTATCATCAAAAACTCACTTCAAGAGCAATCATACGAGATGTCTCCATATAGATCAGATGATGATGAAGATGATGATGATGTACCAAATAACAAGTTTATGCCATCATGGGCAAGTAAGCATAGCCTGTCAATGATTATTTCTTCCCAGAAAATGGACCCGGAAACAATATTTCCTCGGCAAAGTTTTTGCGATATTGCAAAAGTTTGGAGACTACTTGTAAATAATACTGCCATTGCCATTGCCATTGCTATCCTTAGAAGAATTGCATATTACTAA
Protein sequence

>MsG0180006006.01.T01

MLTLKRMSKREKEFMMEQQKKKKEEEEMAAKEKKQREIEEKKEKDRKRKAVNDMKLQEHGKIHAKKARAAAKMVDLIKAVEDNDSIIKNSLQEQSYEMSPYRSDDDEDDDDVPNNKFMPSWASKHSLSMIISSQKMDPETIFPRQSFCDIAKVWRLLVNNTAIAIAIAILRRIAYY*