AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene91912

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91912.t1 MTR_5g039180 98.925 93 1 0 1 93 1 93 9.70e-61 180
MS.gene91912.t1 MTR_7g010120 72.826 92 24 1 1 92 1 91 1.01e-40 129
MS.gene91912.t1 MTR_6g011670 69.737 76 23 0 17 92 15 90 4.66e-34 112
MS.gene91912.t1 MTR_3g438070 74.026 77 18 1 17 93 17 91 4.82e-34 112
MS.gene91912.t1 MTR_7g059260 45.946 74 40 0 8 81 3 76 1.26e-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
MS.gene91912.t1 AT1G26945 83.784 74 12 0 19 92 19 92 3.13e-39 125
MS.gene91912.t1 AT3G28857 64.894 94 30 2 1 93 1 92 3.72e-36 118
MS.gene91912.t1 AT3G47710 69.149 94 25 3 1 93 1 91 3.48e-35 115
MS.gene91912.t1 AT5G15160 73.333 75 19 1 19 92 18 92 3.25e-32 108
MS.gene91912.t1 AT1G74500 72.727 77 18 2 17 92 17 91 2.96e-31 105
MS.gene91912.t1 AT5G39860 65.385 78 26 1 17 93 15 92 1.73e-30 103

Find 16 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACCGATTGTCACAACTTT+TGG 0.275530 5.3:-27464994 MS.gene91912:CDS
GAGCGGCTAGCGCGAAGTTC+GGG 0.276939 5.3:+27465511 None:intergenic
GTGCTCAAGCAGCTATTATT+AGG 0.330670 5.3:-27464953 MS.gene91912:CDS
GGAGCGGCTAGCGCGAAGTT+CGG 0.362273 5.3:+27465510 None:intergenic
CTTATAGGTTTCAGCTACTA+AGG 0.382941 5.3:-27465075 MS.gene91912:intron
AGAGGAACCACCGGATTGTC+TGG 0.389390 5.3:+27465588 None:intergenic
GGGGATAAGTTGTTGTAACT+TGG 0.418381 5.3:+27465531 None:intergenic
AATAGCTGCTTGAGCACTGT+TGG 0.496664 5.3:+27464959 None:intergenic
AAGCCAAAAGTTGTGACAAT+CGG 0.524888 5.3:+27464991 None:intergenic
AGATCTCGTTCCAGACAATC+CGG 0.532260 5.3:-27465598 MS.gene91912:CDS
AAATAAATACCTTGTTGGAG+CGG 0.605762 5.3:+27465494 None:intergenic
TCGCGCTAGCCGCTCCAACA+AGG 0.613710 5.3:-27465503 MS.gene91912:intron
AGTGATCTCAGAGGAACCAC+CGG 0.628272 5.3:+27465579 None:intergenic
AGCGGCTAGCGCGAAGTTCG+GGG 0.650397 5.3:+27465512 None:intergenic
TCTCGTTCCAGACAATCCGG+TGG 0.728257 5.3:-27465595 MS.gene91912:CDS
TTGAGCATCAGTGATCTCAG+AGG 0.728981 5.3:+27465570 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTTTTATGGTCTTAT+AGG - chr5.3:27465458-27465477 MS.gene91912:intron 15.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5.3:27465062-27465081 None:intergenic 20.0%
AAATAAATACCTTGTTGGAG+CGG + chr5.3:27465057-27465076 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5.3:27465319-27465338 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5.3:27465518-27465537 MS.gene91912:CDS 30.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5.3:27465560-27465579 None:intergenic 35.0%
ATGCATGTGAATGATGACTT+GGG + chr5.3:27465205-27465224 None:intergenic 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5.3:27465473-27465492 MS.gene91912:intron 35.0%
GATACAATGCACATATTGTG+TGG - chr5.3:27465236-27465255 MS.gene91912:intron 35.0%
TATGCATGTGAATGATGACT+TGG + chr5.3:27465206-27465225 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5.3:27465181-27465200 None:intergenic 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5.3:27465252-27465271 MS.gene91912:intron 35.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5.3:27465306-27465325 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5.3:27465020-27465039 None:intergenic 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5.3:27465595-27465614 MS.gene91912:CDS 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5.3:27465554-27465573 MS.gene91912:CDS 40.0%
AGATCTCGTTCCAGACAATC+CGG - chr5.3:27464950-27464969 MS.gene91912:CDS 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5.3:27465380-27465399 MS.gene91912:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5.3:27465381-27465400 MS.gene91912:intron 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5.3:27464981-27465000 None:intergenic 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5.3:27465592-27465611 None:intergenic 45.0%
!!! GTAATATTTTTTATTTTTTA+TGG - chr5.3:27465449-27465468 MS.gene91912:intron 5.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5.3:27464972-27464991 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5.3:27465384-27465403 MS.gene91912:intron 50.0%
AGAGGAACCACCGGATTGTC+TGG + chr5.3:27464963-27464982 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5.3:27464953-27464972 MS.gene91912:CDS 55.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5.3:27465039-27465058 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5.3:27465040-27465059 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5.3:27465041-27465060 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5.3:27465045-27465064 MS.gene91912:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 27464938 27465632 27464938 ID=MS.gene91912
chr5.3 mRNA 27464938 27465632 27464938 ID=MS.gene91912.t1;Parent=MS.gene91912
chr5.3 exon 27465504 27465632 27465504 ID=MS.gene91912.t1.exon1;Parent=MS.gene91912.t1
chr5.3 CDS 27465504 27465632 27465504 ID=cds.MS.gene91912.t1;Parent=MS.gene91912.t1
chr5.3 exon 27464938 27465090 27464938 ID=MS.gene91912.t1.exon2;Parent=MS.gene91912.t1
chr5.3 CDS 27464938 27465090 27464938 ID=cds.MS.gene91912.t1;Parent=MS.gene91912.t1
Gene Sequence

>MS.gene91912

ATGTCTAGCAGAAGATCTCGTTCCAGACAATCCGGTGGTTCCTCTGAGATCACTGATGCTCAAATCACTGATCTCATTTCCAAGTTACAACAACTTATCCCCGAACTTCGCGCTAGCCGCTCCAACAAGGTATTTATTTTTCTAAATATCGCTGTCTTCGTTCTTTAAACTGTCTGCAATTGTACGCAAATGATACTTAATTTATAAAAAATAAAATTATATTTTACTTATAAAACTTTTCCTTCATACACACTCTCACAAATTCCCAAGTCATCATTCACATGCATAATATAAGAATGATACAATGCACATATTGTGTGGACATTGTTAGTTTTGGTAGATAAACAATGTTTATTATGACTCTTCCTCAATTCTTTGCCACAACTTGTGTATTGTATTGTATTGTACTCATTTACTAATCATGCATTAATTACTAGCTTGTAGCTAGTTGCAACATGCAAGTGGGTGGTGTATAAAACTAAAAAAGAAACTCTTTAAAATTTATTAATTTGTAATATTTTTTATTTTTTATGGTCTTATAGGTTTCAGCTACTAAGGTATTGCAAGAGACTTGCAACTACATAAAAAACTTGCATAGAGAGGTTGATGATTTAAGTGACCGATTGTCACAACTTTTGGCTTCTACAGATTCCAACAGTGCTCAAGCAGCTATTATTAGGAGCTTACTTATGTAA
Protein sequence

>MS.gene91912.t1

MSSRRSRSRQSGGSSEITDAQITDLISKLQQLIPELRASRSNKVSATKVLQETCNYIKNLHREVDDLSDRLSQLLASTDSNSAQAAIIRSLLM