AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0933220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0933220 MtrunA17_Chr6g0450121 96.133 181 6 1 1 180 1 181 7.37e-120 336
Msa0933220 MtrunA17_Chr8g0372561 31.928 166 92 3 35 179 29 194 5.29e-16 72.4
Msa0933220 MtrunA17_Chr7g0234831 34.351 131 76 2 59 179 86 216 7.27e-15 69.7
Msa0933220 MtrunA17_Chr2g0293431 33.333 141 84 3 47 177 12 152 4.28e-14 67.4
Msa0933220 MtrunA17_Chr2g0293341 49.254 67 34 0 109 175 119 185 2.07e-13 65.5
Msa0933220 MtrunA17_Chr2g0310131 33.333 132 76 2 59 179 85 215 4.82e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0933220 AT3G27850.1 58.696 184 70 3 1 180 6 187 1.01e-51 164
Msa0933220 AT3G27830.2 68.531 143 41 2 42 180 49 191 3.68e-50 160
Msa0933220 AT3G27830.1 68.531 143 41 2 42 180 49 191 3.68e-50 160
Msa0933220 AT3G27840.1 50.299 167 65 3 31 179 26 192 3.30e-43 142
Msa0933220 AT4G36420.1 36.301 146 79 3 48 179 33 178 1.69e-17 76.3
Msa0933220 AT1G70190.2 34.074 135 75 2 59 179 73 207 5.04e-13 65.1
Msa0933220 AT1G70190.1 34.074 135 75 2 59 179 73 207 5.04e-13 65.1
Msa0933220 AT3G06040.3 46.667 75 40 0 101 175 107 181 5.28e-13 64.3
Msa0933220 AT3G06040.2 46.667 75 40 0 101 175 107 181 5.28e-13 64.3
Msa0933220 AT3G06040.1 46.667 75 40 0 101 175 107 181 5.28e-13 64.3
Msa0933220 AT4G37660.1 32.258 155 92 3 38 179 12 166 1.07e-12 63.2

Find 53 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTAGAGCTTTAACGAGTT+TGG 0.267140 6_3:-1702568 Msa0933220:CDS
GTGGGAGATGGAGAGGGGTT+TGG 0.285418 6_3:+1702860 None:intergenic
GAGGTAGTTGACGAGGTCTT+TGG 0.302408 6_3:+1702746 None:intergenic
TTCAATTACCACATCGAATT+CGG 0.338695 6_3:+1702629 None:intergenic
TTCTTCGACTACTGCGACTT+CGG 0.340678 6_3:+1702656 None:intergenic
GGAGATGGAGAGGGGTTTGG+AGG 0.359975 6_3:+1702863 None:intergenic
GTTAGAGCTTTAACGAGTTT+GGG 0.364862 6_3:-1702567 Msa0933220:CDS
GGGAGATTGAGAGTGGAGAT+TGG 0.375739 6_3:+1702885 None:intergenic
AGATGGAGAGGGGTTTGGAG+GGG 0.389473 6_3:+1702865 None:intergenic
ACACCTTCTTTAAATTTCTT+CGG 0.390394 6_3:+1702510 None:intergenic
GGAGACGAGTGCGGTGGTGG+TGG 0.390691 6_3:+1702841 None:intergenic
GGTGGTGGTGGGAGATGGAG+AGG 0.392248 6_3:+1702853 None:intergenic
TGGTGGTGGGAGATGGAGAG+GGG 0.394112 6_3:+1702855 None:intergenic
AGTTGACGAGGTCTTTGGCC+TGG 0.400262 6_3:+1702751 None:intergenic
AGCGGCGACAGTGGCGGCGG+CGG 0.407686 6_3:+1702686 None:intergenic
GCCGCAATTCTCGCGTTACT+AGG 0.408930 6_3:+1702600 None:intergenic
TTCAGTGGCCACGGCGGAGA+TGG 0.416551 6_3:+1702815 None:intergenic
GCGGCGACAGTGGCGGCGGC+GGG 0.421106 6_3:+1702687 None:intergenic
GGCGGCGGGAGCGAAGGAAG+CGG 0.431011 6_3:+1702701 None:intergenic
AGTGCGGTGGTGGTGGGAGA+TGG 0.438739 6_3:+1702848 None:intergenic
GTGGTGGTGGGAGATGGAGA+GGG 0.450215 6_3:+1702854 None:intergenic
TGGAGCGGCGACAGTGGCGG+CGG 0.453386 6_3:+1702683 None:intergenic
GTTGACGAGGTCTTTGGCCT+GGG 0.463645 6_3:+1702752 None:intergenic
GAAGCGAAGGAATTGATTGA+AGG 0.470442 6_3:-1702537 Msa0933220:CDS
GGCTGGAGCGGCGACAGTGG+CGG 0.474590 6_3:+1702680 None:intergenic
TTTGGAGGGGAGATTGAGAG+TGG 0.477307 6_3:+1702878 None:intergenic
ACTACTGCGACTTCGGCGGC+TGG 0.482100 6_3:+1702663 None:intergenic
GAGATGGAGAGGGGTTTGGA+GGG 0.482993 6_3:+1702864 None:intergenic
GACGGAGACGAGTGCGGTGG+TGG 0.484373 6_3:+1702838 None:intergenic
TGCGACTTCGGCGGCTGGAG+CGG 0.489099 6_3:+1702668 None:intergenic
AGTGGCGGCGGCGGGAGCGA+AGG 0.497332 6_3:+1702695 None:intergenic
TTGCCGAAGAAATTTAAAGA+AGG 0.505106 6_3:-1702513 Msa0933220:CDS
CTCTGACCTCACTCTCTCCC+AGG 0.540588 6_3:-1702769 Msa0933220:CDS
TCAGTGGCCACGGCGGAGAT+GGG 0.542642 6_3:+1702816 None:intergenic
TCCTAGTAACGCGAGAATTG+CGG 0.544335 6_3:-1702601 Msa0933220:CDS
GAGACGAGTGCGGTGGTGGT+GGG 0.552373 6_3:+1702842 None:intergenic
GTGGTGAGAAAGTGTGAGGG+TGG 0.553869 6_3:+1702926 None:intergenic
GGCGGCTGGAGCGGCGACAG+TGG 0.556006 6_3:+1702677 None:intergenic
AAGAAACAACTTGAAGCTGC+AGG 0.564071 6_3:-1702462 Msa0933220:CDS
TGGCCACGGCGGAGATGGGA+CGG 0.564429 6_3:+1702820 None:intergenic
GGCGGGAGCGAAGGAAGCGG+CGG 0.574913 6_3:+1702704 None:intergenic
CTTTGGCCTGGGAGAGAGTG+AGG 0.585614 6_3:+1702763 None:intergenic
GGTGTGGTGAGAAAGTGTGA+GGG 0.597396 6_3:+1702923 None:intergenic
GGGTGTGGTGAGAAAGTGTG+AGG 0.603340 6_3:+1702922 None:intergenic
TTTGGGATTGAAAGAAGCGA+AGG 0.613094 6_3:-1702550 Msa0933220:CDS
TTCGACTACTGCGACTTCGG+CGG 0.637460 6_3:+1702659 None:intergenic
GAGAATTGCGGCGATTAAAG+CGG 0.638455 6_3:-1702589 Msa0933220:CDS
TTCTATTTCAGTGGCCACGG+CGG 0.638885 6_3:+1702809 None:intergenic
GGTGGAGATAGTTGTGAAAG+CGG 0.640687 6_3:+1702944 None:intergenic
TTTCTTGGAGGTAGTTGACG+AGG 0.645375 6_3:+1702739 None:intergenic
TCTCCGTCCCATCTCCGCCG+TGG 0.646628 6_3:-1702823 Msa0933220:CDS
AGATGGGACGGAGACGAGTG+CGG 0.648615 6_3:+1702832 None:intergenic
TGGGACGGAGACGAGTGCGG+TGG 0.682439 6_3:+1702835 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACACCTTCTTTAAATTTCTT+CGG + chr6_3:1702893-1702912 None:intergenic 25.0%
TTCAATTACCACATCGAATT+CGG + chr6_3:1702774-1702793 None:intergenic 30.0%
TTGCCGAAGAAATTTAAAGA+AGG - chr6_3:1702887-1702906 Msa0933220:CDS 30.0%
!!! AGATTGGTTTTTTTGAGAGG+GGG + chr6_3:1702502-1702521 None:intergenic 35.0%
!!! GAGATTGGTTTTTTTGAGAG+GGG + chr6_3:1702503-1702522 None:intergenic 35.0%
!!! GGAGATTGGTTTTTTTGAGA+GGG + chr6_3:1702504-1702523 None:intergenic 35.0%
!!! TGGAGATTGGTTTTTTTGAG+AGG + chr6_3:1702505-1702524 None:intergenic 35.0%
! TTTTTCTATTTCAGTGGCCA+CGG + chr6_3:1702597-1702616 None:intergenic 35.0%
GCCACTGAAATAGAAAAACT+CGG - chr6_3:1702599-1702618 Msa0933220:CDS 35.0%
AACTACCTCCAAGAAAAACT+CGG - chr6_3:1702668-1702687 Msa0933220:CDS 35.0%
AGAAAAAACCGAATTCGATG+TGG - chr6_3:1702763-1702782 Msa0933220:CDS 35.0%
! GTTAGAGCTTTAACGAGTTT+GGG - chr6_3:1702833-1702852 Msa0933220:CDS 35.0%
!!! GATTGGTTTTTTTGAGAGGG+GGG + chr6_3:1702501-1702520 None:intergenic 40.0%
! GCCGAGTTTTTCTATTTCAG+TGG + chr6_3:1702603-1702622 None:intergenic 40.0%
! GGTTAGAGCTTTAACGAGTT+TGG - chr6_3:1702832-1702851 Msa0933220:CDS 40.0%
! TTTGGGATTGAAAGAAGCGA+AGG - chr6_3:1702850-1702869 Msa0933220:CDS 40.0%
GAAGCGAAGGAATTGATTGA+AGG - chr6_3:1702863-1702882 Msa0933220:CDS 40.0%
AAGAAACAACTTGAAGCTGC+AGG - chr6_3:1702938-1702957 Msa0933220:CDS 40.0%
GGTGGAGATAGTTGTGAAAG+CGG + chr6_3:1702459-1702478 None:intergenic 45.0%
TTTCTTGGAGGTAGTTGACG+AGG + chr6_3:1702664-1702683 None:intergenic 45.0%
TTCTTCGACTACTGCGACTT+CGG + chr6_3:1702747-1702766 None:intergenic 45.0%
TCCTAGTAACGCGAGAATTG+CGG - chr6_3:1702799-1702818 Msa0933220:CDS 45.0%
GAGAATTGCGGCGATTAAAG+CGG - chr6_3:1702811-1702830 Msa0933220:CDS 45.0%
! GGTGTGGTGAGAAAGTGTGA+GGG + chr6_3:1702480-1702499 None:intergenic 50.0%
!!! GTTTTTTTGAGAGGGGGGTG+TGG + chr6_3:1702496-1702515 None:intergenic 50.0%
GGGAGATTGAGAGTGGAGAT+TGG + chr6_3:1702518-1702537 None:intergenic 50.0%
TTTGGAGGGGAGATTGAGAG+TGG + chr6_3:1702525-1702544 None:intergenic 50.0%
TTCTATTTCAGTGGCCACGG+CGG + chr6_3:1702594-1702613 None:intergenic 50.0%
GAGGTAGTTGACGAGGTCTT+TGG + chr6_3:1702657-1702676 None:intergenic 50.0%
! TGACGCCGAGTTTTTCTTGG+AGG + chr6_3:1702676-1702695 None:intergenic 50.0%
! GTGGTGAGAAAGTGTGAGGG+TGG + chr6_3:1702477-1702496 None:intergenic 55.0%
! GGGTGTGGTGAGAAAGTGTG+AGG + chr6_3:1702481-1702500 None:intergenic 55.0%
AGATGGAGAGGGGTTTGGAG+GGG + chr6_3:1702538-1702557 None:intergenic 55.0%
GAGATGGAGAGGGGTTTGGA+GGG + chr6_3:1702539-1702558 None:intergenic 55.0%
GTTGACGAGGTCTTTGGCCT+GGG + chr6_3:1702651-1702670 None:intergenic 55.0%
AGTTGACGAGGTCTTTGGCC+TGG + chr6_3:1702652-1702671 None:intergenic 55.0%
! CGGTGACGCCGAGTTTTTCT+TGG + chr6_3:1702679-1702698 None:intergenic 55.0%
TTCGACTACTGCGACTTCGG+CGG + chr6_3:1702744-1702763 None:intergenic 55.0%
GCCGCAATTCTCGCGTTACT+AGG + chr6_3:1702803-1702822 None:intergenic 55.0%
GGAGATGGAGAGGGGTTTGG+AGG + chr6_3:1702540-1702559 None:intergenic 60.0%
GTGGGAGATGGAGAGGGGTT+TGG + chr6_3:1702543-1702562 None:intergenic 60.0%
!! TGGTGGTGGGAGATGGAGAG+GGG + chr6_3:1702548-1702567 None:intergenic 60.0%
!! GTGGTGGTGGGAGATGGAGA+GGG + chr6_3:1702549-1702568 None:intergenic 60.0%
AGATGGGACGGAGACGAGTG+CGG + chr6_3:1702571-1702590 None:intergenic 60.0%
CTCTGACCTCACTCTCTCCC+AGG - chr6_3:1702631-1702650 Msa0933220:CDS 60.0%
CTTTGGCCTGGGAGAGAGTG+AGG + chr6_3:1702640-1702659 None:intergenic 60.0%
!! GGTGGTGGTGGGAGATGGAG+AGG + chr6_3:1702550-1702569 None:intergenic 65.0%
!! AGTGCGGTGGTGGTGGGAGA+TGG + chr6_3:1702555-1702574 None:intergenic 65.0%
! GAGACGAGTGCGGTGGTGGT+GGG + chr6_3:1702561-1702580 None:intergenic 65.0%
TCAGTGGCCACGGCGGAGAT+GGG + chr6_3:1702587-1702606 None:intergenic 65.0%
TTCAGTGGCCACGGCGGAGA+TGG + chr6_3:1702588-1702607 None:intergenic 65.0%
ACTACTGCGACTTCGGCGGC+TGG + chr6_3:1702740-1702759 None:intergenic 65.0%
! GGAGACGAGTGCGGTGGTGG+TGG + chr6_3:1702562-1702581 None:intergenic 70.0%
GACGGAGACGAGTGCGGTGG+TGG + chr6_3:1702565-1702584 None:intergenic 70.0%
TGGGACGGAGACGAGTGCGG+TGG + chr6_3:1702568-1702587 None:intergenic 70.0%
TCTCCGTCCCATCTCCGCCG+TGG - chr6_3:1702577-1702596 Msa0933220:CDS 70.0%
TGGCCACGGCGGAGATGGGA+CGG + chr6_3:1702583-1702602 None:intergenic 70.0%
TGCGACTTCGGCGGCTGGAG+CGG + chr6_3:1702735-1702754 None:intergenic 70.0%
GGCGGGAGCGAAGGAAGCGG+CGG + chr6_3:1702699-1702718 None:intergenic 75.0%
GGCGGCGGGAGCGAAGGAAG+CGG + chr6_3:1702702-1702721 None:intergenic 75.0%
TGGAGCGGCGACAGTGGCGG+CGG + chr6_3:1702720-1702739 None:intergenic 75.0%
GGCTGGAGCGGCGACAGTGG+CGG + chr6_3:1702723-1702742 None:intergenic 75.0%
! AGTGGCGGCGGCGGGAGCGA+AGG + chr6_3:1702708-1702727 None:intergenic 80.0%
! AGCGGCGACAGTGGCGGCGG+CGG + chr6_3:1702717-1702736 None:intergenic 80.0%
! GGCGGCTGGAGCGGCGACAG+TGG + chr6_3:1702726-1702745 None:intergenic 80.0%
! GCGGCGACAGTGGCGGCGGC+GGG + chr6_3:1702716-1702735 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 1702440 1702982 1702440 ID=Msa0933220;Name=Msa0933220
chr6_3 mRNA 1702440 1702982 1702440 ID=Msa0933220-mRNA-1;Parent=Msa0933220;Name=Msa0933220-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|180
chr6_3 exon 1702440 1702982 1702440 ID=Msa0933220-mRNA-1:exon:685;Parent=Msa0933220-mRNA-1
chr6_3 CDS 1702440 1702982 1702440 ID=Msa0933220-mRNA-1:cds;Parent=Msa0933220-mRNA-1
Gene Sequence

>Msa0933220

ATGGCATTATCAACAACCGCTTTCACAACTATCTCCACCCTCACACTTTCTCACCACACCCCCCTCTCAAAAAAACCAATCTCCACTCTCAATCTCCCCTCCAAACCCCTCTCCATCTCCCACCACCACCGCACTCGTCTCCGTCCCATCTCCGCCGTGGCCACTGAAATAGAAAAACTCGGCAACGACATCTCTGACCTCACTCTCTCCCAGGCCAAAGACCTCGTCAACTACCTCCAAGAAAAACTCGGCGTCACCGCCGCTTCCTTCGCTCCCGCCGCCGCCACTGTCGCCGCTCCAGCCGCCGAAGTCGCAGTAGTCGAAGAAAAAACCGAATTCGATGTGGTAATTGAAGATGTTCCTAGTAACGCGAGAATTGCGGCGATTAAAGCGGTTAGAGCTTTAACGAGTTTGGGATTGAAAGAAGCGAAGGAATTGATTGAAGGTTTGCCGAAGAAATTTAAAGAAGGTGTGAGTAAAGATGAAGCTGATGATGCTAAGAAACAACTTGAAGCTGCAGGTGCTAAAGTTACTATTGCTTAA
Protein sequence

>Msa0933220

MALSTTAFTTISTLTLSHHTPLSKKPISTLNLPSKPLSISHHHRTRLRPISAVATEIEKLGNDISDLTLSQAKDLVNYLQEKLGVTAASFAPAAATVAAPAAEVAVVEEKTEFDVVIEDVPSNARIAAIKAVRALTSLGLKEAKELIEGLPKKFKEGVSKDEADDAKKQLEAAGAKVTIA*