AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0528870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0528870 MtrunA17_Chr3g0087871 96.311 244 7 2 1 244 1 242 4.52e-171 471
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0528870 AT3G63540.1 78.261 138 30 0 106 243 3 140 4.30e-82 242

Find 48 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATATCTAACTTTCCTTTC+TGG 0.121727 4_1:-1847788 Msa0528870:CDS
TCTTTCTCTGTTCTCTTCTT+TGG 0.152693 4_1:+1847809 None:intergenic
GGTGGAGGAGGAGGAGAAAA+TGG 0.215436 4_1:+1848174 None:intergenic
GGTGGTGGTGCTGGTGGAGG+AGG 0.233443 4_1:+1848162 None:intergenic
AAACGTTCCTTCCAACCTTC+TGG 0.272048 4_1:+1847884 None:intergenic
AATATCTAACTTTCCTTTCT+GGG 0.289515 4_1:-1847787 Msa0528870:CDS
TTAATATCAAAAGTTGAAAA+AGG 0.291067 4_1:-1847863 Msa0528870:CDS
TTCTGCTGAGTCTTTCTTGT+TGG 0.307382 4_1:+1847922 None:intergenic
GGTGGTGCTGGTGGAGGAGG+AGG 0.318310 4_1:+1848165 None:intergenic
GGTGGTGGTGGTGCTGGTGG+AGG 0.347609 4_1:+1848159 None:intergenic
TGTGGTGGTTGTTGTGGTGG+TGG 0.368516 4_1:+1848144 None:intergenic
TGAAGAAGTGAAAGATGATA+AGG 0.401018 4_1:-1847666 Msa0528870:CDS
GTTAAGGTGGTGGTTATTAG+AGG 0.416358 4_1:+1848076 None:intergenic
GGTTGTGGTGGTTGTTGTGG+TGG 0.423034 4_1:+1848141 None:intergenic
GGTGGTTGTTGTGGTGGTGG+TGG 0.425792 4_1:+1848147 None:intergenic
TTGTTCAAAACAGCATCTTT+TGG 0.430262 4_1:+1847749 None:intergenic
GGTGGTTGTGGTGGTTGTTG+TGG 0.449989 4_1:+1848138 None:intergenic
TATTATGTTTATGAGATTGA+TGG 0.453881 4_1:-1847635 Msa0528870:CDS
GTGGAGGAGGAGGAGAAAAT+GGG 0.454320 4_1:+1848175 None:intergenic
TGTGCCGTAGTAGAGATTGT+AGG 0.481893 4_1:+1847985 None:intergenic
GGGAGATGATTCTGCTGCTA+TGG 0.482398 4_1:+1848006 None:intergenic
TCTTTATTCCACTCAGGAGT+AGG 0.485770 4_1:+1847542 None:intergenic
GAAGAAGTGAAAGATGATAA+GGG 0.493393 4_1:-1847665 Msa0528870:CDS
GCAGCAAACTACGGCGGCTA+CGG 0.501712 4_1:-1847953 Msa0528870:CDS
TGATATTGTGGTGGTTGTGG+TGG 0.513282 4_1:+1848129 None:intergenic
AATTTGCAAGATATTATTAG+TGG 0.515902 4_1:-1847707 Msa0528870:CDS
TCCTTATCTTTATTCCACTC+AGG 0.519893 4_1:+1847536 None:intergenic
TTGTGTTTGAATGAGATAAG+AGG 0.520933 4_1:+1848103 None:intergenic
AGGAGGTGATGTTGTGAGAA+TGG 0.523239 4_1:+1848030 None:intergenic
TGCTGCTGCTGTTAAGGTGG+TGG 0.525546 4_1:+1848066 None:intergenic
TCCTGAGTGGAATAAAGATA+AGG 0.526998 4_1:-1847537 Msa0528870:CDS
GTGCCGTAGTAGAGATTGTA+GGG 0.548540 4_1:+1847986 None:intergenic
TGCTGCTGCTGCTGTTAAGG+TGG 0.548707 4_1:+1848063 None:intergenic
GAGGAGGAGGAGAAAATGGG+TGG 0.548714 4_1:+1848178 None:intergenic
GCAGCAAGTGCAGCAAACTA+CGG 0.563093 4_1:-1847962 Msa0528870:CDS
GATGATTCTGCTGCTATGGA+AGG 0.565590 4_1:+1848010 None:intergenic
TCTACGACGTTCCAGAAGGT+TGG 0.565732 4_1:-1847895 Msa0528870:CDS
GAGGAGGAGAAAATGGGTGG+TGG 0.570174 4_1:+1848181 None:intergenic
GCAAACTACGGCGGCTACGG+CGG 0.573351 4_1:-1847950 Msa0528870:CDS
CGACGTTCCAGAAGGTTGGA+AGG 0.585452 4_1:-1847891 Msa0528870:CDS
TCTCCCTACAATCTCTACTA+CGG 0.599583 4_1:-1847989 Msa0528870:CDS
GCAAGTGCAGCAAACTACGG+CGG 0.619443 4_1:-1847959 Msa0528870:CDS
TACATCTACGACGTTCCAGA+AGG 0.628307 4_1:-1847899 Msa0528870:CDS
CTAACTGACGAAACCCAGAA+AGG 0.634618 4_1:+1847774 None:intergenic
TTAATGCTCCTACTCCTGAG+TGG 0.644053 4_1:-1847550 Msa0528870:CDS
GATTCTGCTGCTATGGAAGG+AGG 0.660500 4_1:+1848013 None:intergenic
AGGTGATGTTGTGAGAATGG+TGG 0.683595 4_1:+1848033 None:intergenic
TGGTGATGATGAGAAAATTG+TGG 0.687506 4_1:+1848201 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATCAAAAGTTGAAAA+AGG - chr4_1:1847835-1847854 Msa0528870:CDS 15.0%
!! AATTTGCAAGATATTATTAG+TGG - chr4_1:1847991-1848010 Msa0528870:CDS 20.0%
!! TATTATGTTTATGAGATTGA+TGG - chr4_1:1848063-1848082 Msa0528870:CDS 20.0%
!! AAAGTTGAAAAAGGTACAAA+TGG - chr4_1:1847844-1847863 Msa0528870:CDS 25.0%
! AATATCTAACTTTCCTTTCT+GGG - chr4_1:1847911-1847930 Msa0528870:CDS 25.0%
!! GATAAGAGGTTTTGATATTG+TGG + chr4_1:1847584-1847603 None:intergenic 30.0%
TTGTGTTTGAATGAGATAAG+AGG + chr4_1:1847598-1847617 None:intergenic 30.0%
GAATATCTAACTTTCCTTTC+TGG - chr4_1:1847910-1847929 Msa0528870:CDS 30.0%
! TTGTTCAAAACAGCATCTTT+TGG + chr4_1:1847952-1847971 None:intergenic 30.0%
TGAAGAAGTGAAAGATGATA+AGG - chr4_1:1848032-1848051 Msa0528870:CDS 30.0%
GAAGAAGTGAAAGATGATAA+GGG - chr4_1:1848033-1848052 Msa0528870:CDS 30.0%
! TGGTGATGATGAGAAAATTG+TGG + chr4_1:1847500-1847519 None:intergenic 35.0%
! TTTTGATATTGTGGTGGTTG+TGG + chr4_1:1847575-1847594 None:intergenic 35.0%
!! AAGAGGTTTTGATATTGTGG+TGG + chr4_1:1847581-1847600 None:intergenic 35.0%
TCTTTCTCTGTTCTCTTCTT+TGG + chr4_1:1847892-1847911 None:intergenic 35.0%
TCCTGAGTGGAATAAAGATA+AGG - chr4_1:1848161-1848180 Msa0528870:CDS 35.0%
TCCTTATCTTTATTCCACTC+AGG + chr4_1:1848165-1848184 None:intergenic 35.0%
! GTTAAGGTGGTGGTTATTAG+AGG + chr4_1:1847625-1847644 None:intergenic 40.0%
TCTCCCTACAATCTCTACTA+CGG - chr4_1:1847709-1847728 Msa0528870:CDS 40.0%
TTCTGCTGAGTCTTTCTTGT+TGG + chr4_1:1847779-1847798 None:intergenic 40.0%
TCTTTATTCCACTCAGGAGT+AGG + chr4_1:1848159-1848178 None:intergenic 40.0%
TGATATTGTGGTGGTTGTGG+TGG + chr4_1:1847572-1847591 None:intergenic 45.0%
AGGTGATGTTGTGAGAATGG+TGG + chr4_1:1847668-1847687 None:intergenic 45.0%
AGGAGGTGATGTTGTGAGAA+TGG + chr4_1:1847671-1847690 None:intergenic 45.0%
GATGATTCTGCTGCTATGGA+AGG + chr4_1:1847691-1847710 None:intergenic 45.0%
GTGCCGTAGTAGAGATTGTA+GGG + chr4_1:1847715-1847734 None:intergenic 45.0%
TGTGCCGTAGTAGAGATTGT+AGG + chr4_1:1847716-1847735 None:intergenic 45.0%
TACATCTACGACGTTCCAGA+AGG - chr4_1:1847799-1847818 Msa0528870:CDS 45.0%
AAACGTTCCTTCCAACCTTC+TGG + chr4_1:1847817-1847836 None:intergenic 45.0%
CTAACTGACGAAACCCAGAA+AGG + chr4_1:1847927-1847946 None:intergenic 45.0%
TTAATGCTCCTACTCCTGAG+TGG - chr4_1:1848148-1848167 Msa0528870:CDS 45.0%
GTGGAGGAGGAGGAGAAAAT+GGG + chr4_1:1847526-1847545 None:intergenic 50.0%
GATTCTGCTGCTATGGAAGG+AGG + chr4_1:1847688-1847707 None:intergenic 50.0%
GGGAGATGATTCTGCTGCTA+TGG + chr4_1:1847695-1847714 None:intergenic 50.0%
GCAGCAAGTGCAGCAAACTA+CGG - chr4_1:1847736-1847755 Msa0528870:CDS 50.0%
TCTACGACGTTCCAGAAGGT+TGG - chr4_1:1847803-1847822 Msa0528870:CDS 50.0%
GAGGAGGAGAAAATGGGTGG+TGG + chr4_1:1847520-1847539 None:intergenic 55.0%
GAGGAGGAGGAGAAAATGGG+TGG + chr4_1:1847523-1847542 None:intergenic 55.0%
GGTGGAGGAGGAGGAGAAAA+TGG + chr4_1:1847527-1847546 None:intergenic 55.0%
TGTGGTGGTTGTTGTGGTGG+TGG + chr4_1:1847557-1847576 None:intergenic 55.0%
GGTTGTGGTGGTTGTTGTGG+TGG + chr4_1:1847560-1847579 None:intergenic 55.0%
GGTGGTTGTGGTGGTTGTTG+TGG + chr4_1:1847563-1847582 None:intergenic 55.0%
TGCTGCTGCTGTTAAGGTGG+TGG + chr4_1:1847635-1847654 None:intergenic 55.0%
TGCTGCTGCTGCTGTTAAGG+TGG + chr4_1:1847638-1847657 None:intergenic 55.0%
AGCTGCTGCTGCTGCTGTTA+AGG + chr4_1:1847641-1847660 None:intergenic 55.0%
GCAAGTGCAGCAAACTACGG+CGG - chr4_1:1847739-1847758 Msa0528870:CDS 55.0%
CGACGTTCCAGAAGGTTGGA+AGG - chr4_1:1847807-1847826 Msa0528870:CDS 55.0%
!! TGTTGTGGTGGTGGTGGTGC+TGG + chr4_1:1847548-1847567 None:intergenic 60.0%
!! GGTGGTTGTTGTGGTGGTGG+TGG + chr4_1:1847554-1847573 None:intergenic 60.0%
GCAGCAAACTACGGCGGCTA+CGG - chr4_1:1847745-1847764 Msa0528870:CDS 60.0%
!! TGTGGTGGTGGTGGTGCTGG+TGG + chr4_1:1847545-1847564 None:intergenic 65.0%
GCAAACTACGGCGGCTACGG+CGG - chr4_1:1847748-1847767 Msa0528870:CDS 65.0%
!! GGTGGTGCTGGTGGAGGAGG+AGG + chr4_1:1847536-1847555 None:intergenic 70.0%
!! GGTGGTGGTGCTGGTGGAGG+AGG + chr4_1:1847539-1847558 None:intergenic 70.0%
!! GGTGGTGGTGGTGCTGGTGG+AGG + chr4_1:1847542-1847561 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 1847493 1848227 1847493 ID=Msa0528870;Name=Msa0528870
chr4_1 mRNA 1847493 1848227 1847493 ID=Msa0528870-mRNA-1;Parent=Msa0528870;Name=Msa0528870-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|244
chr4_1 exon 1847493 1848227 1847493 ID=Msa0528870-mRNA-1:exon:569;Parent=Msa0528870-mRNA-1
chr4_1 CDS 1847493 1848227 1847493 ID=Msa0528870-mRNA-1:cds;Parent=Msa0528870-mRNA-1
Gene Sequence

>Msa0528870

ATGGCCACAATTTTCTCATCATCACCACCACCCATTTTCTCCTCCTCCTCCACCAGCACCACCACCACCACAACAACCACCACAACCACCACAATATCAAAACCTCTTATCTCATTCAAACACAAACAACCTCTAATAACCACCACCTTAACAGCAGCAGCAGCAGCTATAGCCACCATTCTCACAACATCACCTCCTTCCATAGCAGCAGAATCATCTCCCTACAATCTCTACTACGGCACAGCAGCAAGTGCAGCAAACTACGGCGGCTACGGCGGAAACTCCAACAAGAAAGACTCAGCAGAATACATCTACGACGTTCCAGAAGGTTGGAAGGAACGTTTAATATCAAAAGTTGAAAAAGGTACAAATGGAACAGACAGTGAATTCTACAATCCAAAGAAGAGAACAGAGAAAGAATATCTAACTTTCCTTTCTGGGTTTCGTCAGTTAGCACCAAAAGATGCTGTTTTGAACAACTTAGCACTTTCTGATGTGAATTTGCAAGATATTATTAGTGGTGCTGATAATGTGAGTTCTGAAGAAGTGAAAGATGATAAGGGTCAAGTTTATTATGTTTATGAGATTGATGGTGTTGCTTATCATAGCTTGATTTCTGTTACTTGTGCTAATAATAAGCTTTATGCTCATTTTGTTAATGCTCCTACTCCTGAGTGGAATAAAGATAAGGATCTTCTCACTCATGTTCATAAGTCTTTTAAGACTATTGTATAA

Protein sequence

>Msa0528870

MATIFSSSPPPIFSSSSTSTTTTTTTTTTTTISKPLISFKHKQPLITTTLTAAAAAIATILTTSPPSIAAESSPYNLYYGTAASAANYGGYGGNSNKKDSAEYIYDVPEGWKERLISKVEKGTNGTDSEFYNPKKRTEKEYLTFLSGFRQLAPKDAVLNNLALSDVNLQDIISGADNVSSEEVKDDKGQVYYVYEIDGVAYHSLISVTCANNKLYAHFVNAPTPEWNKDKDLLTHVHKSFKTIV*