AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068236

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068236.t1 MTR_1g048880 82.353 153 12 1 1 138 1 153 2.35e-88 254
MS.gene068236.t1 MTR_1g041455 54.491 167 47 4 1 138 1 167 2.40e-48 153
MS.gene068236.t1 MTR_5g056450 44.118 170 51 7 1 138 1 158 6.72e-28 100
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 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAAACATGTGACGGAATT+TGG 0.152253 1.1:+33374607 None:intergenic
ACCCTCAAGGACAATTTCTT+TGG 0.288680 1.1:-33374740 MS.gene068236:CDS
CGAGAAACCTATCAAGAAAA+AGG 0.292133 1.1:-33374550 MS.gene068236:CDS
TTCTCGAGTTGCATGATATA+TGG 0.301047 1.1:+33374567 None:intergenic
CATGATTACTTCTGAAAACT+TGG 0.381949 1.1:+33374829 None:intergenic
TATGGCTTGGTGCCATCATT+TGG 0.403211 1.1:+33374585 None:intergenic
GTTGGCTGAAACATCATCAT+AGG 0.427829 1.1:+33374636 None:intergenic
ACCAAAGAAATTGTCCTTGA+GGG 0.436733 1.1:+33374739 None:intergenic
GACGGAATTTGGTTTCTTGT+TGG 0.441716 1.1:+33374618 None:intergenic
AATTGTCCTTGAGGGTTGAC+AGG 0.443467 1.1:+33374747 None:intergenic
TGCAATACTCGGTCGCATGC+AGG 0.453126 1.1:-33374860 MS.gene068236:CDS
TGAATAGAATCTTCTAATTG+AGG 0.475140 1.1:+33374773 None:intergenic
CTTTGGTATAGTTCCCCACC+AGG 0.476657 1.1:-33374723 MS.gene068236:CDS
CAACTCAGCTGTTCCTACAT+TGG 0.498861 1.1:-33374520 MS.gene068236:CDS
GTTACTAAAGTCGTTGGCCA+TGG 0.504250 1.1:+33374896 None:intergenic
TTGAGTGTTAAATCCAATGT+AGG 0.524429 1.1:+33374507 None:intergenic
GATACTCAAAACATGAATGA+TGG 0.528985 1.1:-33374684 MS.gene068236:CDS
ATCATCATAGGATGTGGTTG+AGG 0.539731 1.1:+33374648 None:intergenic
CCTCTTGTTACTAAAGTCGT+TGG 0.543235 1.1:+33374890 None:intergenic
TACCAAAGAAATTGTCCTTG+AGG 0.579677 1.1:+33374738 None:intergenic
GCAATACTCGGTCGCATGCA+GGG 0.585277 1.1:-33374859 MS.gene068236:CDS
TCAGAACCTGTCAACCCTCA+AGG 0.588149 1.1:-33374753 MS.gene068236:CDS
GAGGCATGATGTGCAATACT+CGG 0.590219 1.1:-33374871 MS.gene068236:CDS
TTGGAACATGAAAACCTGGT+GGG 0.591198 1.1:+33374709 None:intergenic
TCATTTGGCAAAACATGTGA+CGG 0.602209 1.1:+33374600 None:intergenic
TCATTTGGAACATGAAAACC+TGG 0.608295 1.1:+33374705 None:intergenic
CTCAAAACATGAATGATGGT+AGG 0.612081 1.1:-33374680 MS.gene068236:CDS
CTCACATGGAGTCTCACGAA+GGG 0.634625 1.1:-33374797 MS.gene068236:CDS
TGGAACATGAAAACCTGGTG+GGG 0.648382 1.1:+33374710 None:intergenic
TGAAACATCATCATAGGATG+TGG 0.653978 1.1:+33374642 None:intergenic
TCATGCATTAGTAACTCACA+TGG 0.657144 1.1:-33374811 MS.gene068236:CDS
CCAACGACTTTAGTAACAAG+AGG 0.660073 1.1:-33374890 MS.gene068236:CDS
GAGTTGCATGATATATGGCT+TGG 0.666515 1.1:+33374572 None:intergenic
TCACATGGAGTCTCACGAAG+GGG 0.674235 1.1:-33374796 MS.gene068236:CDS
ACTCACATGGAGTCTCACGA+AGG 0.681368 1.1:-33374798 MS.gene068236:CDS
TTTGGAACATGAAAACCTGG+TGG 0.685806 1.1:+33374708 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATAGAATCTTCTAATTG+AGG + chr1.1:33374624-33374643 None:intergenic 25.0%
!!! TTCATGTTTTGAGTATCATT+TGG + chr1.1:33374707-33374726 None:intergenic 25.0%
GATACTCAAAACATGAATGA+TGG - chr1.1:33374710-33374729 MS.gene068236:CDS 30.0%
TTGAGTGTTAAATCCAATGT+AGG + chr1.1:33374890-33374909 None:intergenic 30.0%
! CATGATTACTTCTGAAAACT+TGG + chr1.1:33374568-33374587 None:intergenic 30.0%
! TCATCATCCTTTTTCTTGAT+AGG + chr1.1:33374854-33374873 None:intergenic 30.0%
ACCAAAGAAATTGTCCTTGA+GGG + chr1.1:33374658-33374677 None:intergenic 35.0%
CGAGAAACCTATCAAGAAAA+AGG - chr1.1:33374844-33374863 MS.gene068236:CDS 35.0%
CTCAAAACATGAATGATGGT+AGG - chr1.1:33374714-33374733 MS.gene068236:CDS 35.0%
TACCAAAGAAATTGTCCTTG+AGG + chr1.1:33374659-33374678 None:intergenic 35.0%
TCATGCATTAGTAACTCACA+TGG - chr1.1:33374583-33374602 MS.gene068236:CDS 35.0%
TCATTTGGCAAAACATGTGA+CGG + chr1.1:33374797-33374816 None:intergenic 35.0%
TGAAACATCATCATAGGATG+TGG + chr1.1:33374755-33374774 None:intergenic 35.0%
! TCACATGTTTTGCCAAATGA+TGG - chr1.1:33374797-33374816 MS.gene068236:CDS 35.0%
! TCATTTGGAACATGAAAACC+TGG + chr1.1:33374692-33374711 None:intergenic 35.0%
! TTCTCGAGTTGCATGATATA+TGG + chr1.1:33374830-33374849 None:intergenic 35.0%
ACCCTCAAGGACAATTTCTT+TGG - chr1.1:33374654-33374673 MS.gene068236:CDS 40.0%
ATCATCATAGGATGTGGTTG+AGG + chr1.1:33374749-33374768 None:intergenic 40.0%
CCAACGACTTTAGTAACAAG+AGG - chr1.1:33374504-33374523 MS.gene068236:CDS 40.0%
CCTCTTGTTACTAAAGTCGT+TGG + chr1.1:33374507-33374526 None:intergenic 40.0%
GAGTTGCATGATATATGGCT+TGG + chr1.1:33374825-33374844 None:intergenic 40.0%
GTTGGCTGAAACATCATCAT+AGG + chr1.1:33374761-33374780 None:intergenic 40.0%
TTGGAACATGAAAACCTGGT+GGG + chr1.1:33374688-33374707 None:intergenic 40.0%
! GACGGAATTTGGTTTCTTGT+TGG + chr1.1:33374779-33374798 None:intergenic 40.0%
! GCAAAACATGTGACGGAATT+TGG + chr1.1:33374790-33374809 None:intergenic 40.0%
! TTTGGAACATGAAAACCTGG+TGG + chr1.1:33374689-33374708 None:intergenic 40.0%
AATTGTCCTTGAGGGTTGAC+AGG + chr1.1:33374650-33374669 None:intergenic 45.0%
CAACTCAGCTGTTCCTACAT+TGG - chr1.1:33374874-33374893 MS.gene068236:CDS 45.0%
GAGGCATGATGTGCAATACT+CGG - chr1.1:33374523-33374542 MS.gene068236:CDS 45.0%
TGGAACATGAAAACCTGGTG+GGG + chr1.1:33374687-33374706 None:intergenic 45.0%
!! TATGGCTTGGTGCCATCATT+TGG + chr1.1:33374812-33374831 None:intergenic 45.0%
ACTCACATGGAGTCTCACGA+AGG - chr1.1:33374596-33374615 MS.gene068236:CDS 50.0%
CTCACATGGAGTCTCACGAA+GGG - chr1.1:33374597-33374616 MS.gene068236:CDS 50.0%
CTTTGGTATAGTTCCCCACC+AGG - chr1.1:33374671-33374690 MS.gene068236:CDS 50.0%
TCACATGGAGTCTCACGAAG+GGG - chr1.1:33374598-33374617 MS.gene068236:CDS 50.0%
TCAGAACCTGTCAACCCTCA+AGG - chr1.1:33374641-33374660 MS.gene068236:CDS 50.0%
GCAATACTCGGTCGCATGCA+GGG - chr1.1:33374535-33374554 MS.gene068236:CDS 55.0%
TGCAATACTCGGTCGCATGC+AGG - chr1.1:33374534-33374553 MS.gene068236:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 33374500 33374916 33374500 ID=MS.gene068236
chr1.1 mRNA 33374500 33374916 33374500 ID=MS.gene068236.t1;Parent=MS.gene068236
chr1.1 exon 33374500 33374916 33374500 ID=MS.gene068236.t1.exon1;Parent=MS.gene068236.t1
chr1.1 CDS 33374500 33374916 33374500 ID=cds.MS.gene068236.t1;Parent=MS.gene068236.t1
Gene Sequence

>MS.gene068236

ATGGCCAACGACTTTAGTAACAAGAGGCATGATGTGCAATACTCGGTCGCATGCAGGGTTTGCAACCAAGTTTTCAGAAGTAATCATGCATTAGTAACTCACATGGAGTCTCACGAAGGGGCCTCAATTAGAAGATTCTATTCAGAACCTGTCAACCCTCAAGGACAATTTCTTTGGTATAGTTCCCCACCAGGTTTTCATGTTCCAAATGATACTCAAAACATGAATGATGGTAGGATTTTTCAACCTCAACCACATCCTATGATGATGTTTCAGCCAACAAGAAACCAAATTCCGTCACATGTTTTGCCAAATGATGGCACCAAGCCATATATCATGCAACTCGAGAAACCTATCAAGAAAAAGGATGATGACAACTCAGCTGTTCCTACATTGGATTTAACACTCAAGCTTTAG
Protein sequence

>MS.gene068236.t1

MANDFSNKRHDVQYSVACRVCNQVFRSNHALVTHMESHEGASIRRFYSEPVNPQGQFLWYSSPPGFHVPNDTQNMNDGRIFQPQPHPMMMFQPTRNQIPSHVLPNDGTKPYIMQLEKPIKKKDDDNSAVPTLDLTLKL