AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01892

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01892.t1 MTR_2g023100 89.610 77 8 0 1 77 1 77 1.10e-47 145
MS.gene01892.t1 MTR_4g046737 50.667 75 34 2 1 74 1 73 4.78e-21 78.6
MS.gene01892.t1 MTR_2g088730 56.863 51 22 0 25 75 30 80 7.15e-18 70.9
MS.gene01892.t1 MTR_5g009460 58.537 41 17 0 27 67 37 77 1.77e-14 62.4
MS.gene01892.t1 MTR_3g083540 51.111 45 22 0 28 72 98 142 4.62e-12 59.7
MS.gene01892.t1 MTR_4g100720 51.163 43 21 0 29 71 71 113 9.42e-12 57.4
MS.gene01892.t1 MTR_7g117730 51.163 43 21 0 30 72 71 113 2.20e-11 57.4
MS.gene01892.t1 MTR_0197s0010 47.727 44 23 0 29 72 59 102 2.23e-11 57.0
MS.gene01892.t1 MTR_0247s0040 45.455 44 24 0 28 71 64 107 2.79e-11 56.2
MS.gene01892.t1 MTR_8g060940 47.727 44 23 0 29 72 65 108 4.73e-11 56.2
MS.gene01892.t1 MTR_5g079670 48.837 43 22 0 29 71 69 111 4.75e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01892.t1 AT2G46410 63.636 44 16 0 27 70 36 79 1.13e-17 70.9
MS.gene01892.t1 AT5G53200 44.000 75 33 2 5 76 12 80 7.02e-16 66.6
MS.gene01892.t1 AT1G01380 56.818 44 19 0 27 70 32 75 2.15e-15 64.7
MS.gene01892.t1 AT4G01060 59.091 44 18 0 27 70 30 73 1.01e-14 62.8
MS.gene01892.t1 AT4G01060 59.091 44 18 0 27 70 33 76 1.02e-14 62.8
MS.gene01892.t1 AT4G01060 59.091 44 18 0 27 70 31 74 1.33e-14 62.4
MS.gene01892.t1 AT2G30420 47.826 46 24 0 27 72 38 83 1.29e-12 58.2
MS.gene01892.t1 AT2G30424 50.000 44 22 0 27 70 34 77 5.18e-12 56.6
MS.gene01892.t1 AT5G52600 45.455 44 24 0 29 72 70 113 1.07e-11 57.8
MS.gene01892.t1 AT5G14750 43.182 44 25 0 29 72 13 56 2.13e-11 55.8
MS.gene01892.t1 AT5G14750 43.182 44 25 0 29 72 13 56 2.13e-11 55.8
MS.gene01892.t1 AT2G30432 45.455 44 24 0 27 70 33 76 5.13e-11 53.5
MS.gene01892.t1 AT2G47460 50.000 44 22 0 29 72 70 113 6.39e-11 56.6
MS.gene01892.t1 AT3G13540 52.500 40 19 0 30 69 82 121 9.73e-11 55.5

Find 13 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATCTTCTGGGGTTCTTCC+TGG 0.250868 2.2:-62608289 None:intergenic
TGTTTAGATTGGTTGGAAAA+AGG 0.291636 2.2:+62608084 MS.gene01892:CDS
GCAACGATATCTTCCTCTTC+TGG 0.298430 2.2:-62608056 None:intergenic
CTCATTGCTGGAAGAATTCC+AGG 0.344017 2.2:+62608271 MS.gene01892:CDS
GATGAAACGTGAGGCTGAAT+TGG 0.367460 2.2:+62608025 MS.gene01892:CDS
TGTAGATGGCATCTCATTGC+TGG 0.394303 2.2:+62608259 MS.gene01892:intron
CGTTGCGAAAATGTTTAGAT+TGG 0.408347 2.2:+62608073 MS.gene01892:CDS
GCGAAAATGTTTAGATTGGT+TGG 0.408611 2.2:+62608077 MS.gene01892:CDS
CAGAAGATATTGAAAAGTAT+TGG 0.446559 2.2:+62608302 MS.gene01892:CDS
AACGACCAGTGTGTATCTGC+AGG 0.565195 2.2:+62607870 MS.gene01892:CDS
ACACTGGTCGTTGTTTGCAG+CGG 0.624404 2.2:-62607859 None:intergenic
TTCAGATCAGATGAAACGTG+AGG 0.676121 2.2:+62608016 MS.gene01892:intron
GGGTACCTGCAGATACACAC+TGG 0.694181 2.2:-62607875 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATACTTTTCAATATCTTCT+GGG - chr2.2:62608303-62608322 None:intergenic 20.0%
!!! GTTCATTCTTTTTAAATGAA+AGG + chr2.2:62607973-62607992 MS.gene01892:intron 20.0%
!! ATACTTTTCAATATCTTCTG+GGG - chr2.2:62608302-62608321 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG - chr2.2:62608304-62608323 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG + chr2.2:62608302-62608321 MS.gene01892:CDS 25.0%
CGTACATTGTTAATTGTAGA+TGG + chr2.2:62608245-62608264 MS.gene01892:intron 30.0%
! TGTTTAGATTGGTTGGAAAA+AGG + chr2.2:62608084-62608103 MS.gene01892:CDS 30.0%
CGTTGCGAAAATGTTTAGAT+TGG + chr2.2:62608073-62608092 MS.gene01892:CDS 35.0%
GCGAAAATGTTTAGATTGGT+TGG + chr2.2:62608077-62608096 MS.gene01892:CDS 35.0%
! ATTGGAATTTTCACCAGAAG+AGG + chr2.2:62608043-62608062 MS.gene01892:CDS 35.0%
AAGATCAACTTGAAGTGCAG+GGG - chr2.2:62607898-62607917 None:intergenic 40.0%
ATCAAGTGTGTGCATATGCA+AGG - chr2.2:62608177-62608196 None:intergenic 40.0%
GAAGATCAACTTGAAGTGCA+GGG - chr2.2:62607899-62607918 None:intergenic 40.0%
TGAAGATCAACTTGAAGTGC+AGG - chr2.2:62607900-62607919 None:intergenic 40.0%
TTCAGATCAGATGAAACGTG+AGG + chr2.2:62608016-62608035 MS.gene01892:intron 40.0%
AGGCAATTAGCATCATGTGC+TGG + chr2.2:62608198-62608217 MS.gene01892:intron 45.0%
CTCATTGCTGGAAGAATTCC+AGG + chr2.2:62608271-62608290 MS.gene01892:CDS 45.0%
GATGAAACGTGAGGCTGAAT+TGG + chr2.2:62608025-62608044 MS.gene01892:CDS 45.0%
GCAACGATATCTTCCTCTTC+TGG - chr2.2:62608059-62608078 None:intergenic 45.0%
GCATATGCACACACTTGATG+AGG + chr2.2:62608178-62608197 MS.gene01892:intron 45.0%
TGTAGATGGCATCTCATTGC+TGG + chr2.2:62608259-62608278 MS.gene01892:intron 45.0%
!! ATATCTTCTGGGGTTCTTCC+TGG - chr2.2:62608292-62608311 None:intergenic 45.0%
AACGACCAGTGTGTATCTGC+AGG + chr2.2:62607870-62607889 MS.gene01892:CDS 50.0%
ACACTGGTCGTTGTTTGCAG+CGG - chr2.2:62607862-62607881 None:intergenic 50.0%
GGGTACCTGCAGATACACAC+TGG - chr2.2:62607878-62607897 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 62607837 62608357 62607837 ID=MS.gene01892
chr2.2 mRNA 62607837 62608357 62607837 ID=MS.gene01892.t1;Parent=MS.gene01892
chr2.2 exon 62607837 62607891 62607837 ID=MS.gene01892.t1.exon1;Parent=MS.gene01892.t1
chr2.2 CDS 62607837 62607891 62607837 ID=cds.MS.gene01892.t1;Parent=MS.gene01892.t1
chr2.2 exon 62608021 62608105 62608021 ID=MS.gene01892.t1.exon2;Parent=MS.gene01892.t1
chr2.2 CDS 62608021 62608105 62608021 ID=cds.MS.gene01892.t1;Parent=MS.gene01892.t1
chr2.2 exon 62608264 62608357 62608264 ID=MS.gene01892.t1.exon3;Parent=MS.gene01892.t1
chr2.2 CDS 62608264 62608357 62608264 ID=cds.MS.gene01892.t1;Parent=MS.gene01892.t1
Gene Sequence

>MS.gene01892

ATGAGTGATTCAAAGCATGCAACCGCTGCAAACAACGACCAGTGTGTATCTGCAGGTACCCCTGCACTTCAAGTTGATCTTCATATTCATGCATGCGTCAAGTTTTTGACTAATCTTTATATTTTTCAATCAAATTGTTCATTCTTTTTAAATGAAAGGCTGTATTTGTTACTTGTTGTTTCAGATCAGATGAAACGTGAGGCTGAATTGGAATTTTCACCAGAAGAGGAAGATATCGTTGCGAAAATGTTTAGATTGGTTGGAAAAAGGTTAACTGTCATATATATATAAATATATATGTGTGTGTGTGTGTGTTAATTAACTTTGTATGTATCTTCCTTGCATATGCACACACTTGATGAGGCAATTAGCATCATGTGCTGGTCTAATTAATGAAAGTATGTTTGACGTACATTGTTAATTGTAGATGGCATCTCATTGCTGGAAGAATTCCAGGAAGAACCCCAGAAGATATTGAAAAGTATTGGACATCAAAATTCTCTTCATCAACTGCATGTTAA
Protein sequence

>MS.gene01892.t1

MSDSKHATAANNDQCVSADQMKREAELEFSPEEEDIVAKMFRLVGKRWHLIAGRIPGRTPEDIEKYWTSKFSSSTAC