AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene038902

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene038902.t1 MTR_2g012700 85.246 122 18 0 1 122 1 122 2.11e-75 219
MS.gene038902.t1 MTR_2g062330 81.667 120 21 1 3 122 23 141 2.55e-68 202
MS.gene038902.t1 MTR_7g117590 35.385 130 65 5 7 119 44 171 3.01e-20 81.3
MS.gene038902.t1 MTR_7g117585 34.653 101 64 1 18 116 42 142 3.25e-17 72.8
MS.gene038902.t1 MTR_0010s0310 41.758 91 51 1 22 110 150 240 3.35e-16 72.0
MS.gene038902.t1 MTR_5g071410 35.644 101 63 1 18 116 165 265 6.13e-16 71.6
MS.gene038902.t1 MTR_3g008190 27.835 97 70 0 24 120 6 102 8.22e-15 65.5
MS.gene038902.t1 MTR_6g087720 32.979 94 62 1 16 108 206 299 1.33e-12 62.8
MS.gene038902.t1 MTR_0010s0320 39.560 91 51 3 24 110 192 282 5.38e-12 61.2
MS.gene038902.t1 MTR_0010s0290 39.560 91 51 3 24 110 223 313 8.05e-12 60.8
MS.gene038902.t1 MTR_6g477950 33.333 81 54 0 39 119 64 144 2.26e-11 59.7
MS.gene038902.t1 MTR_5g078270 34.066 91 58 1 22 110 208 298 3.06e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGTTACTGCTTCTATTT+TGG 0.123735 2.1:+38155283 MS.gene038902:CDS
GAAGTTAATGGTGCTGAATT+AGG 0.163350 2.1:+38155224 MS.gene038902:CDS
AAAATTCCAATGTTCATTAT+TGG 0.164838 2.1:+38155255 MS.gene038902:CDS
TGTATGCTACCGTCGTTAAC+TGG 0.297739 2.1:+38155644 MS.gene038902:CDS
GAGATTGGAGTTGAAGTTAA+TGG 0.344431 2.1:+38155212 MS.gene038902:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 2.1:+38155301 MS.gene038902:CDS
AAGTTAATGGTGCTGAATTA+GGG 0.367629 2.1:+38155225 MS.gene038902:CDS
CAGTCAATAATCCTCCTAAT+AGG 0.398760 2.1:+38155620 MS.gene038902:CDS
TTACCAGTTTCTTCATCAAA+AGG 0.404700 2.1:-38155478 None:intergenic
CCTCGACGTATTGCTGAGAA+TGG 0.434646 2.1:+38155427 MS.gene038902:CDS
ACGGTAGCATACATCCTATT+AGG 0.440754 2.1:-38155634 None:intergenic
TACCAGTTTCTTCATCAAAA+GGG 0.488019 2.1:-38155477 None:intergenic
GTATGCTACCGTCGTTAACT+GGG 0.522932 2.1:+38155645 MS.gene038902:CDS
ATACTTCCAATAATGAACAT+TGG 0.558425 2.1:-38155261 None:intergenic
AGCATGCATCAGAAATACAT+AGG 0.564126 2.1:+38155535 MS.gene038902:CDS
CTTGAAAAGTGCCTAAAAGT+TGG 0.570138 2.1:+38155580 MS.gene038902:CDS
AGAAATACATAGGGAGAGGA+TGG 0.573439 2.1:+38155545 MS.gene038902:CDS
CATCAGAAATACATAGGGAG+AGG 0.580360 2.1:+38155541 MS.gene038902:CDS
GCATGCATCAGAAATACATA+GGG 0.596673 2.1:+38155536 MS.gene038902:CDS
GTAGCATACATCCTATTAGG+AGG 0.633251 2.1:-38155631 None:intergenic
CCATTCTCAGCAATACGTCG+AGG 0.710417 2.1:-38155427 None:intergenic
GAATCAGTCCCAGTTAACGA+CGG 0.733495 2.1:-38155653 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTCCAATGTTCATTAT+TGG + chr2.1:38155255-38155274 MS.gene038902:CDS 20.0%
! ATACTTCCAATAATGAACAT+TGG - chr2.1:38155264-38155283 None:intergenic 25.0%
!! TAATGTTACTGCTTCTATTT+TGG + chr2.1:38155283-38155302 MS.gene038902:CDS 25.0%
TACCAGTTTCTTCATCAAAA+GGG - chr2.1:38155480-38155499 None:intergenic 30.0%
TTACCAGTTTCTTCATCAAA+AGG - chr2.1:38155481-38155500 None:intergenic 30.0%
! AAATAACGTCACCAACTTTT+AGG - chr2.1:38155594-38155613 None:intergenic 30.0%
! AAGTTAATGGTGCTGAATTA+GGG + chr2.1:38155225-38155244 MS.gene038902:CDS 30.0%
! TTTGGATGGAAACAATGTTT+TGG + chr2.1:38155301-38155320 MS.gene038902:CDS 30.0%
AGCATGCATCAGAAATACAT+AGG + chr2.1:38155535-38155554 MS.gene038902:CDS 35.0%
CAGTCAATAATCCTCCTAAT+AGG + chr2.1:38155620-38155639 MS.gene038902:CDS 35.0%
GAGATTGGAGTTGAAGTTAA+TGG + chr2.1:38155212-38155231 MS.gene038902:CDS 35.0%
GCATGCATCAGAAATACATA+GGG + chr2.1:38155536-38155555 MS.gene038902:CDS 35.0%
! GAAGTTAATGGTGCTGAATT+AGG + chr2.1:38155224-38155243 MS.gene038902:CDS 35.0%
!! CTTGAAAAGTGCCTAAAAGT+TGG + chr2.1:38155580-38155599 MS.gene038902:CDS 35.0%
!! GTTACTGCTTCTATTTTGGA+TGG + chr2.1:38155287-38155306 MS.gene038902:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG + chr2.1:38155308-38155327 MS.gene038902:intron 35.0%
ACGGTAGCATACATCCTATT+AGG - chr2.1:38155637-38155656 None:intergenic 40.0%
AGAAATACATAGGGAGAGGA+TGG + chr2.1:38155545-38155564 MS.gene038902:CDS 40.0%
CATCAGAAATACATAGGGAG+AGG + chr2.1:38155541-38155560 MS.gene038902:CDS 40.0%
GTAGCATACATCCTATTAGG+AGG - chr2.1:38155634-38155653 None:intergenic 40.0%
! CTCCCTTTTGATGAAGAAAC+TGG + chr2.1:38155475-38155494 MS.gene038902:CDS 40.0%
GTATGCTACCGTCGTTAACT+GGG + chr2.1:38155645-38155664 MS.gene038902:CDS 45.0%
TGTATGCTACCGTCGTTAAC+TGG + chr2.1:38155644-38155663 MS.gene038902:CDS 45.0%
CCATTCTCAGCAATACGTCG+AGG - chr2.1:38155430-38155449 None:intergenic 50.0%
CCTCGACGTATTGCTGAGAA+TGG + chr2.1:38155427-38155446 MS.gene038902:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 38155206 38155672 38155206 ID=MS.gene038902
chr2.1 mRNA 38155206 38155672 38155206 ID=MS.gene038902.t1;Parent=MS.gene038902
chr2.1 exon 38155206 38155322 38155206 ID=MS.gene038902.t1.exon1;Parent=MS.gene038902.t1
chr2.1 CDS 38155206 38155322 38155206 ID=cds.MS.gene038902.t1;Parent=MS.gene038902.t1
chr2.1 exon 38155421 38155672 38155421 ID=MS.gene038902.t1.exon2;Parent=MS.gene038902.t1
chr2.1 CDS 38155421 38155672 38155421 ID=cds.MS.gene038902.t1;Parent=MS.gene038902.t1
Gene Sequence

>MS.gene038902

ATGAATGAGATTGGAGTTGAAGTTAATGGTGCTGAATTAGGGAATCTTCAAAATTCCAATGTTCATTATTGGAAGTATAATGTTACTGCTTCTATTTTGGATGGAAACAATGTTTTGGTTAGTGGCATTTACGAAACATTTTTTTTTGTTTTCATGTTGTTAAGTTGTTGTTGATTAATTATAATTTGTATGATTTCATGACAAATCTATTGTAGAATTTTCCTCGACGTATTGCTGAGAATGGTTTGTATATCAATCAATCTAAAATTCTCCCTTTTGATGAAGAAACTGGTAAATCTTATGACTGTGATGTTCACACTGCGTCAAGAAGCATGCATCAGAAATACATAGGGAGAGGATGGTACGACTTTGTTCTTGAAAAGTGCCTAAAAGTTGGTGACGTTATTTTGTTCACAGTCAATAATCCTCCTAATAGGATGTATGCTACCGTCGTTAACTGGGACTGA
Protein sequence

>MS.gene038902.t1

MNEIGVEVNGAELGNLQNSNVHYWKYNVTASILDGNNVLNFPRRIAENGLYINQSKILPFDEETGKSYDCDVHTASRSMHQKYIGRGWYDFVLEKCLKVGDVILFTVNNPPNRMYATVVNWD