AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65442

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65442.t1 MTR_1g041455 91.617 167 12 1 1 165 1 167 1.34e-113 319
MS.gene65442.t1 MTR_1g048880 58.788 165 56 3 1 165 1 153 3.90e-59 181
MS.gene65442.t1 MTR_5g056450 58.721 172 50 4 1 165 1 158 3.33e-53 166
MS.gene65442.t1 MTR_1g075780 35.802 162 77 6 11 165 4 145 7.89e-16 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATTGATTTCATTGATT+TGG 0.219457 1.1:+25554376 MS.gene65442:CDS
TAGAACCAACATTTAGAAAA+TGG 0.241260 1.1:-25554235 None:intergenic
TTTAGAAAATGGTTTCTTCT+TGG 0.277705 1.1:-25554224 None:intergenic
ATTGCACTTGAGGGTTGATA+TGG 0.307074 1.1:-25554118 None:intergenic
CAACTCGGGTGCTCAATCAT+TGG 0.434933 1.1:+25554415 MS.gene65442:CDS
AAATGGTTTCTTCTTGGTTG+TGG 0.446475 1.1:-25554218 None:intergenic
ATTGATTTCATTGATTTGGT+TGG 0.453682 1.1:+25554380 MS.gene65442:CDS
TCCTTCTCATTGTATCCCAC+CGG 0.457479 1.1:+25554142 MS.gene65442:CDS
CGAGAAGAATCTTCAAATGA+TGG 0.494040 1.1:+25554314 MS.gene65442:CDS
ATCTTCAAATGATGGTACTA+AGG 0.499653 1.1:+25554322 MS.gene65442:CDS
CTTCTCGTAGATGCTTCCAT+TGG 0.515514 1.1:-25554298 None:intergenic
GAGAAGGAAATTGCACTTGA+GGG 0.519458 1.1:-25554127 None:intergenic
GACACTCAAAACATCAATGA+TGG 0.521574 1.1:+25554182 MS.gene65442:CDS
GGTTTCTTCTTGGTTGTGGT+TGG 0.536103 1.1:-25554214 None:intergenic
CCTTCTCATTGTATCCCACC+GGG 0.540543 1.1:+25554143 MS.gene65442:CDS
TGAGAAGGAAATTGCACTTG+AGG 0.543034 1.1:-25554128 None:intergenic
CCTCGTGTTACTAAAGCCAT+TGG 0.551040 1.1:-25553964 None:intergenic
GTTACTAAAGCCATTGGTCA+TGG 0.570356 1.1:-25553958 None:intergenic
AGTCTCACATGGAGAACGAA+GGG 0.570612 1.1:+25554066 MS.gene65442:CDS
CTTGAGTGTTTATGAAAACT+CGG 0.571989 1.1:-25554025 None:intergenic
AACTCACCTCGAGTCTCACA+TGG 0.572212 1.1:+25554055 MS.gene65442:CDS
TCTATGCAACTTACACAACA+TGG 0.577004 1.1:+25554254 MS.gene65442:CDS
TTCACCACCACCATGACCAA+TGG 0.588746 1.1:+25553948 None:intergenic
CTCAAAACATCAATGATGGT+AGG 0.621185 1.1:+25554186 MS.gene65442:CDS
CCCGGTGGGATACAATGAGA+AGG 0.621815 1.1:-25554143 None:intergenic
CGTTCTCCATGTGAGACTCG+AGG 0.634567 1.1:-25554061 None:intergenic
TCAATTGGAACATGAAAACC+CGG 0.639654 1.1:-25554161 None:intergenic
TTGGAACATGAAAACCCGGT+GGG 0.650710 1.1:-25554157 None:intergenic
TGGTAATGATGATGACAACT+CGG 0.654905 1.1:+25554400 MS.gene65442:CDS
GATAAGAAGACTCTATTCGA+CGG 0.664525 1.1:+25554094 MS.gene65442:CDS
GAGTCTCACATGGAGAACGA+AGG 0.673296 1.1:+25554065 MS.gene65442:CDS
GAGGCATGATGTGTTAAACT+CGG 0.676388 1.1:+25553983 MS.gene65442:CDS
CCAATGGCTTTAGTAACACG+AGG 0.678872 1.1:+25553964 MS.gene65442:CDS
GTCTCACATGGAGAACGAAG+GGG 0.692736 1.1:+25554067 MS.gene65442:CDS
ATTGGAACATGAAAACCCGG+TGG 0.715311 1.1:-25554158 None:intergenic
GGTAATGATGATGACAACTC+GGG 0.729679 1.1:+25554401 MS.gene65442:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAATCAATTTTCTTGAT+AGG - chr1.1:25554371-25554390 None:intergenic 20.0%
!!! GAAAATTGATTTCATTGATT+TGG + chr1.1:25554376-25554395 MS.gene65442:CDS 20.0%
! TAGAACCAACATTTAGAAAA+TGG - chr1.1:25554238-25554257 None:intergenic 25.0%
! TTTAGAAAATGGTTTCTTCT+TGG - chr1.1:25554227-25554246 None:intergenic 25.0%
!! AGAAACCATTTTCTAAATGT+TGG + chr1.1:25554230-25554249 MS.gene65442:CDS 25.0%
!! CAAATCAACATTTTTACCAA+TGG + chr1.1:25554282-25554301 MS.gene65442:CDS 25.0%
!! CATTGGTAAAAATGTTGATT+TGG - chr1.1:25554284-25554303 None:intergenic 25.0%
!!! ATTGATTTCATTGATTTGGT+TGG + chr1.1:25554380-25554399 MS.gene65442:CDS 25.0%
ATCTTCAAATGATGGTACTA+AGG + chr1.1:25554322-25554341 MS.gene65442:CDS 30.0%
CTTGAGTGTTTATGAAAACT+CGG - chr1.1:25554028-25554047 None:intergenic 30.0%
!! TTGATGTTTTGAGTGTCAAT+TGG - chr1.1:25554179-25554198 None:intergenic 30.0%
AAATGGTTTCTTCTTGGTTG+TGG - chr1.1:25554221-25554240 None:intergenic 35.0%
CGAGAAGAATCTTCAAATGA+TGG + chr1.1:25554314-25554333 MS.gene65442:CDS 35.0%
CTCAAAACATCAATGATGGT+AGG + chr1.1:25554186-25554205 MS.gene65442:CDS 35.0%
GACACTCAAAACATCAATGA+TGG + chr1.1:25554182-25554201 MS.gene65442:CDS 35.0%
GATAAGAAGACTCTATTCGA+CGG + chr1.1:25554094-25554113 MS.gene65442:CDS 35.0%
TCAATTGGAACATGAAAACC+CGG - chr1.1:25554164-25554183 None:intergenic 35.0%
TCTATGCAACTTACACAACA+TGG + chr1.1:25554254-25554273 MS.gene65442:CDS 35.0%
! TGGTAATGATGATGACAACT+CGG + chr1.1:25554400-25554419 MS.gene65442:CDS 35.0%
GAGAAGGAAATTGCACTTGA+GGG - chr1.1:25554130-25554149 None:intergenic 40.0%
GAGGCATGATGTGTTAAACT+CGG + chr1.1:25553983-25554002 MS.gene65442:CDS 40.0%
TGAGAAGGAAATTGCACTTG+AGG - chr1.1:25554131-25554150 None:intergenic 40.0%
! GGTAATGATGATGACAACTC+GGG + chr1.1:25554401-25554420 MS.gene65442:CDS 40.0%
!! ATTGCACTTGAGGGTTGATA+TGG - chr1.1:25554121-25554140 None:intergenic 40.0%
AGTCTCACATGGAGAACGAA+GGG + chr1.1:25554066-25554085 MS.gene65442:CDS 45.0%
ATTGGAACATGAAAACCCGG+TGG - chr1.1:25554161-25554180 None:intergenic 45.0%
CTTCTCGTAGATGCTTCCAT+TGG - chr1.1:25554301-25554320 None:intergenic 45.0%
GGTTTCTTCTTGGTTGTGGT+TGG - chr1.1:25554217-25554236 None:intergenic 45.0%
TCCTTCTCATTGTATCCCAC+CGG + chr1.1:25554142-25554161 MS.gene65442:CDS 45.0%
TTGGAACATGAAAACCCGGT+GGG - chr1.1:25554160-25554179 None:intergenic 45.0%
! CCTCGTGTTACTAAAGCCAT+TGG - chr1.1:25553967-25553986 None:intergenic 45.0%
!! CCAATGGCTTTAGTAACACG+AGG + chr1.1:25553964-25553983 MS.gene65442:CDS 45.0%
AACTCACCTCGAGTCTCACA+TGG + chr1.1:25554055-25554074 MS.gene65442:CDS 50.0%
CAACTCGGGTGCTCAATCAT+TGG + chr1.1:25554415-25554434 MS.gene65442:CDS 50.0%
CCTTCTCATTGTATCCCACC+GGG + chr1.1:25554143-25554162 MS.gene65442:CDS 50.0%
GAGTCTCACATGGAGAACGA+AGG + chr1.1:25554065-25554084 MS.gene65442:CDS 50.0%
GTCTCACATGGAGAACGAAG+GGG + chr1.1:25554067-25554086 MS.gene65442:CDS 50.0%
CCCGGTGGGATACAATGAGA+AGG - chr1.1:25554146-25554165 None:intergenic 55.0%
CGTTCTCCATGTGAGACTCG+AGG - chr1.1:25554064-25554083 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 25553960 25554457 25553960 ID=MS.gene65442
chr1.1 mRNA 25553960 25554457 25553960 ID=MS.gene65442.t1;Parent=MS.gene65442
chr1.1 exon 25553960 25554457 25553960 ID=MS.gene65442.t1.exon1;Parent=MS.gene65442.t1
chr1.1 CDS 25553960 25554457 25553960 ID=cds.MS.gene65442.t1;Parent=MS.gene65442.t1
Gene Sequence

>MS.gene65442

ATGACCAATGGCTTTAGTAACACGAGGCATGATGTGTTAAACTCGGTTGCATGTAGATTATGCAACCGAGTTTTCATAAACACTCAAGCACTCATAACTCACCTCGAGTCTCACATGGAGAACGAAGGGGCTGCGATAAGAAGACTCTATTCGACGGACCATATCAACCCTCAAGTGCAATTTCCTTCTCATTGTATCCCACCGGGTTTTCATGTTCCAATTGACACTCAAAACATCAATGATGGTAGGATTTTCCAACCACAACCAAGAAGAAACCATTTTCTAAATGTTGGTTCTATGCAACTTACACAACATGGTTTGCCAAATCAACATTTTTACCAATGGAAGCATCTACGAGAAGAATCTTCAAATGATGGTACTAAGGCATATATCATGCAGCTTGAGAAACCTATCAAGAAAATTGATTTCATTGATTTGGTTGGTAATGATGATGACAACTCGGGTGCTCAATCATTGGATTTAGCACTTAAGCTCTAG
Protein sequence

>MS.gene65442.t1

MTNGFSNTRHDVLNSVACRLCNRVFINTQALITHLESHMENEGAAIRRLYSTDHINPQVQFPSHCIPPGFHVPIDTQNINDGRIFQPQPRRNHFLNVGSMQLTQHGLPNQHFYQWKHLREESSNDGTKAYIMQLEKPIKKIDFIDLVGNDDDNSGAQSLDLALKL