AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0327250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0327250 MtrunA17_Chr2g0281511 84.167 120 19 0 1 120 1 120 1.24e-72 212
Msa0327250 MtrunA17_Chr2g0309121 80.000 120 23 1 1 120 1 119 7.22e-67 197
Msa0327250 MtrunA17_Chr3g0081891 82.278 79 14 0 1 79 1 79 8.58e-44 137
Msa0327250 MtrunA17_Chr7g0276661 34.351 131 66 4 7 119 38 166 1.51e-20 81.6
Msa0327250 MtrunA17_Chr0c01g0489371 40.659 91 52 1 22 110 224 314 6.74e-17 74.7
Msa0327250 MtrunA17_Chr8g0356961 39.326 89 52 1 24 110 77 165 2.77e-16 70.9
Msa0327250 MtrunA17_Chr8g0372431 28.866 97 69 0 24 120 6 102 5.92e-16 68.2
Msa0327250 MtrunA17_Chr8g0356951 38.462 91 52 2 24 110 217 307 2.71e-13 64.7
Msa0327250 MtrunA17_Chr6g0485871 32.558 86 57 1 24 108 214 299 3.11e-12 61.6
Msa0327250 MtrunA17_Chr5g0434641 32.967 91 59 1 22 110 208 298 5.97e-12 60.8
Msa0327250 MtrunA17_Chr5g0430431 46.296 54 29 0 63 116 201 254 1.45e-11 59.3
Msa0327250 MtrunA17_Chr7g0228081 30.000 80 56 0 41 120 13 92 2.18e-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 21 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGTTACTGCTTCTATTT+TGG 0.123735 2_4:-38944625 Msa0327250:CDS
TACCAGTTTCTTCATTAAAA+AGG 0.194631 2_4:+38944431 None:intergenic
AAAATTCCGATGTTCATTAT+TGG 0.199581 2_4:-38944653 Msa0327250:CDS
GAAGTCAATGGTGCTGAATT+AGG 0.200131 2_4:-38944684 Msa0327250:CDS
CCTCGACGTGTTGCCGAGAA+TGG 0.307864 2_4:-38944481 Msa0327250:CDS
CGGTCAATAATCCTCCTAAT+AGG 0.355854 2_4:-38944288 Msa0327250:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 2_4:-38944607 Msa0327250:intron
AAGTCAATGGTGCTGAATTA+GGG 0.416476 2_4:-38944683 Msa0327250:CDS
ACGGTAGCATACATCCTATT+AGG 0.440754 2_4:+38944274 None:intergenic
ATTGGTATACAAACCATTCT+CGG 0.470714 2_4:+38944468 None:intergenic
GCATGGATCAGAAATACATA+GGG 0.559318 2_4:-38944372 Msa0327250:CDS
AGCATGGATCAGAAATACAT+AGG 0.564126 2_4:-38944373 Msa0327250:CDS
AGAAATACATAGGGAGAGGA+TGG 0.566622 2_4:-38944363 Msa0327250:CDS
CTTGAAAAGTGCCTAAAAGT+TGG 0.570138 2_4:-38944328 Msa0327250:CDS
GATCAGAAATACATAGGGAG+AGG 0.587262 2_4:-38944367 Msa0327250:CDS
TCACACTGCGTCAAGAAGCA+TGG 0.587686 2_4:-38944389 Msa0327250:CDS
CCATTCTCGGCAACACGTCG+AGG 0.599354 2_4:+38944481 None:intergenic
GAGATTGGAGTTGAAGTCAA+TGG 0.619642 2_4:-38944696 Msa0327250:CDS
GTAGCATACATCCTATTAGG+AGG 0.633251 2_4:+38944277 None:intergenic
ATACTTCCAATAATGAACAT+CGG 0.646998 2_4:+38944647 None:intergenic
TAATCAGTCTCAGTTAACGA+CGG 0.726011 2_4:+38944255 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGGAAAATTTTAGATTGAT+TGG + chr2_4:38944519-38944538 None:intergenic 20.0%
! AAAATTCCGATGTTCATTAT+TGG - chr2_4:38944313-38944332 Msa0327250:CDS 25.0%
! ATACTTCCAATAATGAACAT+CGG + chr2_4:38944322-38944341 None:intergenic 25.0%
!! TAATGTTACTGCTTCTATTT+TGG - chr2_4:38944341-38944360 Msa0327250:CDS 25.0%
!! TTCCTTTTTAATGAAGAAAC+TGG - chr2_4:38944533-38944552 Msa0327250:intron 25.0%
! TACCAGTTTCTTCATTAAAA+AGG + chr2_4:38944538-38944557 None:intergenic 25.0%
! TTTGGATGGAAACAATGTTT+TGG - chr2_4:38944359-38944378 Msa0327250:CDS 30.0%
ATTGGTATACAAACCATTCT+CGG + chr2_4:38944501-38944520 None:intergenic 30.0%
! AAACAACATCACCAACTTTT+AGG + chr2_4:38944652-38944671 None:intergenic 30.0%
! AAGTCAATGGTGCTGAATTA+GGG - chr2_4:38944283-38944302 Msa0327250:CDS 35.0%
!! GTTACTGCTTCTATTTTGGA+TGG - chr2_4:38944345-38944364 Msa0327250:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG - chr2_4:38944366-38944385 Msa0327250:CDS 35.0%
AGCATGGATCAGAAATACAT+AGG - chr2_4:38944593-38944612 Msa0327250:intron 35.0%
GCATGGATCAGAAATACATA+GGG - chr2_4:38944594-38944613 Msa0327250:intron 35.0%
!! CTTGAAAAGTGCCTAAAAGT+TGG - chr2_4:38944638-38944657 Msa0327250:CDS 35.0%
!!! TGGTGATGTTGTTTTGTTCA+CGG - chr2_4:38944658-38944677 Msa0327250:CDS 35.0%
GAGATTGGAGTTGAAGTCAA+TGG - chr2_4:38944270-38944289 Msa0327250:CDS 40.0%
! GAAGTCAATGGTGCTGAATT+AGG - chr2_4:38944282-38944301 Msa0327250:CDS 40.0%
GATCAGAAATACATAGGGAG+AGG - chr2_4:38944599-38944618 Msa0327250:intron 40.0%
AGAAATACATAGGGAGAGGA+TGG - chr2_4:38944603-38944622 Msa0327250:intron 40.0%
CGGTCAATAATCCTCCTAAT+AGG - chr2_4:38944678-38944697 Msa0327250:CDS 40.0%
GTAGCATACATCCTATTAGG+AGG + chr2_4:38944692-38944711 None:intergenic 40.0%
ACGGTAGCATACATCCTATT+AGG + chr2_4:38944695-38944714 None:intergenic 40.0%
TCACACTGCGTCAAGAAGCA+TGG - chr2_4:38944577-38944596 Msa0327250:intron 50.0%
CCATTCTCGGCAACACGTCG+AGG + chr2_4:38944488-38944507 None:intergenic 60.0%
CCTCGACGTGTTGCCGAGAA+TGG - chr2_4:38944485-38944504 Msa0327250:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 38944264 38944724 38944264 ID=Msa0327250;Name=Msa0327250
chr2_4 mRNA 38944264 38944724 38944264 ID=Msa0327250-mRNA-1;Parent=Msa0327250;Name=Msa0327250-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|120
chr2_4 exon 38944608 38944724 38944608 ID=Msa0327250-mRNA-1:exon:11646;Parent=Msa0327250-mRNA-1
chr2_4 exon 38944264 38944509 38944264 ID=Msa0327250-mRNA-1:exon:11645;Parent=Msa0327250-mRNA-1
chr2_4 CDS 38944608 38944724 38944608 ID=Msa0327250-mRNA-1:cds;Parent=Msa0327250-mRNA-1
chr2_4 CDS 38944264 38944509 38944264 ID=Msa0327250-mRNA-1:cds;Parent=Msa0327250-mRNA-1
Gene Sequence

>Msa0327250

ATGAATGAGATTGGAGTTGAAGTCAATGGTGCTGAATTAGGGAATCTTCAAAATTCCGATGTTCATTATTGGAAGTATAATGTTACTGCTTCTATTTTGGATGGAAACAATGTTTTGAATTTTCCTCGACGTGTTGCCGAGAATGGTTTGTATACCAATCAATCTAAAATTTTCCTTTTTAATGAAGAAACTGGTAAATCTTATGACTGTGATGTTCACACTGCGTCAAGAAGCATGGATCAGAAATACATAGGGAGAGGATGGTATGACTTTGTTCTTGAAAAGTGCCTAAAAGTTGGTGATGTTGTTTTGTTCACGGTCAATAATCCTCCTAATAGGATGTATGCTACCGTCGTTAACTGA
Protein sequence

>Msa0327250

MNEIGVEVNGAELGNLQNSDVHYWKYNVTASILDGNNVLNFPRRVAENGLYTNQSKIFLFNEETGKSYDCDVHTASRSMDQKYIGRGWYDFVLEKCLKVGDVVLFTVNNPPNRMYATVVN*