AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene067489

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene067489.t1 MTR_2g105340 74.815 135 17 3 1 133 1 120 9.17e-39 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCCATTTCTTTCAGTTTCC+CGG 0.179440 2.4:+355894 None:intergenic
TTAACTGTGCCAGCAACTTC+TGG 0.273818 2.4:-355716 MS.gene067489:CDS
AAGAGAGTAGAAAGACATAT+TGG 0.339499 2.4:+356555 None:intergenic
GAGTTGGCCCAGGATTATAT+TGG 0.353506 2.4:+355747 None:intergenic
TCCCGGGAAACTGAAAGAAA+TGG 0.360508 2.4:-355896 MS.gene067489:CDS
AGTTGGCCCAGGATTATATT+GGG 0.360873 2.4:+355748 None:intergenic
AGAGATTAGGAGGAGAATTC+TGG 0.378079 2.4:+355663 None:intergenic
CCCGGGAAACTGAAAGAAAT+GGG 0.394159 2.4:-355895 MS.gene067489:CDS
CAGAGCGTCTGCGGCGGGAG+TGG 0.394365 2.4:+355802 None:intergenic
GTTGGGTTTCCAGAAGTTGC+TGG 0.414499 2.4:+355707 None:intergenic
AAAATATGTATCTGAGCTGT+TGG 0.415022 2.4:+355689 None:intergenic
CCCGGCGAATGGTGCGGAGG+TGG 0.417570 2.4:+355851 None:intergenic
CCTCCTCCCCAATATAATCC+TGG 0.422464 2.4:-355755 MS.gene067489:CDS
CCCATTTCTTTCAGTTTCCC+GGG 0.433130 2.4:+355895 None:intergenic
GAATGGTGCGGAGGTGGTGG+TGG 0.448834 2.4:+355857 None:intergenic
TATAATCCTGGGCCAACTCC+AGG 0.450650 2.4:-355743 MS.gene067489:CDS
GGAGAATTCAGTTTCTGAAC+TGG 0.452981 2.4:+355827 None:intergenic
AGAGCGTCTGCGGCGGGAGT+GGG 0.453808 2.4:+355803 None:intergenic
GGCGAATGGTGCGGAGGTGG+TGG 0.454424 2.4:+355854 None:intergenic
TTATATTGGGGAGGAGGTGG+TGG 0.459881 2.4:+355761 None:intergenic
ACCACCTCCGCACCATTCGC+CGG 0.460281 2.4:-355852 MS.gene067489:CDS
TTCAGTTTCTGAACTGGTCC+CGG 0.467126 2.4:+355833 None:intergenic
GGATTATATTGGGGAGGAGG+TGG 0.471962 2.4:+355758 None:intergenic
GCTGAAGCTGCAAAGAGATT+AGG 0.479618 2.4:+355650 None:intergenic
AAATATGTATCTGAGCTGTT+GGG 0.496619 2.4:+355690 None:intergenic
AAGAGCCCTGGAGTTGGCCC+AGG 0.496989 2.4:+355737 None:intergenic
TAGAAACAAACAGCAAGGCT+TGG 0.507692 2.4:+356519 None:intergenic
CTCCTCCCCAATATAATCCT+GGG 0.521004 2.4:-355754 MS.gene067489:CDS
TGTCTCAGAGCGTCTGCGGC+GGG 0.521606 2.4:+355797 None:intergenic
TCTGAACTGGTCCCGGCGAA+TGG 0.523874 2.4:+355840 None:intergenic
CCACCTCCGCACCATTCGCC+GGG 0.524394 2.4:-355851 MS.gene067489:CDS
GCTGGCACAGTTAAGAGCCC+TGG 0.549638 2.4:+355725 None:intergenic
CCAGGATTATATTGGGGAGG+AGG 0.552901 2.4:+355755 None:intergenic
CAGCAAGCATCTAGCTTCTG+TGG 0.554315 2.4:+356493 None:intergenic
TAGAAACTGAATTCTCCTCC+CGG 0.559431 2.4:-355913 MS.gene067489:CDS
GAAGCTGCAAAGAGATTAGG+AGG 0.563505 2.4:+355653 None:intergenic
ACAGTTAAGAGCCCTGGAGT+TGG 0.564303 2.4:+355731 None:intergenic
ACTGGTCCCGGCGAATGGTG+CGG 0.568557 2.4:+355845 None:intergenic
AGAAACTGAATTCTCCTCCC+GGG 0.573887 2.4:-355912 MS.gene067489:CDS
GCGTCTGCGGCGGGAGTGGG+AGG 0.581224 2.4:+355806 None:intergenic
CTGTTGCAGACTATGTCACT+AGG 0.582810 2.4:-356473 MS.gene067489:intron
ATGTCTCAGAGCGTCTGCGG+CGG 0.587729 2.4:+355796 None:intergenic
ATAATCCTGGGCCAACTCCA+GGG 0.596363 2.4:-355742 MS.gene067489:CDS
GGTCCCGGCGAATGGTGCGG+AGG 0.622064 2.4:+355848 None:intergenic
GTTGGCCCAGGATTATATTG+GGG 0.622956 2.4:+355749 None:intergenic
GGCCCAGGATTATATTGGGG+AGG 0.624273 2.4:+355752 None:intergenic
CCGGGAAACTGAAAGAAATG+GGG 0.639431 2.4:-355894 MS.gene067489:CDS
GGCAGTAGAAACAAACAGCA+AGG 0.643990 2.4:+356514 None:intergenic
ATGATGTCTCAGAGCGTCTG+CGG 0.676100 2.4:+355793 None:intergenic
CGGGAAACTGAAAGAAATGG+GGG 0.677386 2.4:-355893 MS.gene067489:CDS
ATTTCTTTCAGTTTCCCGGG+AGG 0.690454 2.4:+355898 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTCTTATTAGTTAT+TGG - chr2.4:355910-355929 MS.gene067489:CDS 10.0%
!! AATTATTCTTATTAGTTATT+GGG - chr2.4:355911-355930 MS.gene067489:CDS 10.0%
!!! TAAAAGAATTTTATTTGAAT+TGG + chr2.4:355830-355849 None:intergenic 10.0%
!! AAACAATATATTTATGTGAT+TGG + chr2.4:356186-356205 None:intergenic 15.0%
!! GTCTTGAAAATATAATATAA+TGG - chr2.4:355999-356018 MS.gene067489:intron 15.0%
!! ATATAATGGTTGAATTTAAG+TGG - chr2.4:356013-356032 MS.gene067489:intron 20.0%
!! TATTTATGTGATTGGAATAA+TGG + chr2.4:356178-356197 None:intergenic 20.0%
!!! AAGAATTTTATTTGAATTGG+AGG + chr2.4:355827-355846 None:intergenic 20.0%
!!! AATATTTTTTCAGTTACATG+AGG + chr2.4:356155-356174 None:intergenic 20.0%
!!! AGAATTTTATTTGAATTGGA+GGG + chr2.4:355826-355845 None:intergenic 20.0%
!!! TATTTTGTTTTGAATATGTG+CGG + chr2.4:355864-355883 None:intergenic 20.0%
AAAATATGTATCTGAGCTGT+TGG + chr2.4:356526-356545 None:intergenic 30.0%
AAATATGTATCTGAGCTGTT+GGG + chr2.4:356525-356544 None:intergenic 30.0%
AAGAGAGTAGAAAGACATAT+TGG + chr2.4:355660-355679 None:intergenic 30.0%
!!! GATATCTTTTTGAGTTCGAA+TGG + chr2.4:356124-356143 None:intergenic 30.0%
TCAGTTACATGAGGTGAAAA+AGG + chr2.4:356146-356165 None:intergenic 35.0%
AGAGATTAGGAGGAGAATTC+TGG + chr2.4:356552-356571 None:intergenic 40.0%
AGTTGGCCCAGGATTATATT+GGG + chr2.4:356467-356486 None:intergenic 40.0%
GGAGAATTCAGTTTCTGAAC+TGG + chr2.4:356388-356407 None:intergenic 40.0%
TAGAAACAAACAGCAAGGCT+TGG + chr2.4:355696-355715 None:intergenic 40.0%
TAGAAACTGAATTCTCCTCC+CGG - chr2.4:356299-356318 MS.gene067489:intron 40.0%
AGAAACTGAATTCTCCTCCC+GGG - chr2.4:356300-356319 MS.gene067489:intron 45.0%
ATTTCTTTCAGTTTCCCGGG+AGG + chr2.4:356317-356336 None:intergenic 45.0%
CCCATTTCTTTCAGTTTCCC+GGG + chr2.4:356320-356339 None:intergenic 45.0%
CCCCATTTCTTTCAGTTTCC+CGG + chr2.4:356321-356340 None:intergenic 45.0%
CCCGGGAAACTGAAAGAAAT+GGG - chr2.4:356317-356336 MS.gene067489:intron 45.0%
CCGGGAAACTGAAAGAAATG+GGG - chr2.4:356318-356337 MS.gene067489:intron 45.0%
CGGGAAACTGAAAGAAATGG+GGG - chr2.4:356319-356338 MS.gene067489:intron 45.0%
CTCCTCCCCAATATAATCCT+GGG - chr2.4:356458-356477 MS.gene067489:intron 45.0%
CTGTTGCAGACTATGTCACT+AGG - chr2.4:355739-355758 MS.gene067489:CDS 45.0%
GAAGCTGCAAAGAGATTAGG+AGG + chr2.4:356562-356581 None:intergenic 45.0%
GAGTTGGCCCAGGATTATAT+TGG + chr2.4:356468-356487 None:intergenic 45.0%
GCTGAAGCTGCAAAGAGATT+AGG + chr2.4:356565-356584 None:intergenic 45.0%
GGCAGTAGAAACAAACAGCA+AGG + chr2.4:355701-355720 None:intergenic 45.0%
GTTGGCCCAGGATTATATTG+GGG + chr2.4:356466-356485 None:intergenic 45.0%
TCCCGGGAAACTGAAAGAAA+TGG - chr2.4:356316-356335 MS.gene067489:intron 45.0%
TTAACTGTGCCAGCAACTTC+TGG - chr2.4:356496-356515 MS.gene067489:CDS 45.0%
TTCAGTTTCTGAACTGGTCC+CGG + chr2.4:356382-356401 None:intergenic 45.0%
!! AATTGGAGGGAGTACTGACT+AGG + chr2.4:355813-355832 None:intergenic 45.0%
!! TATAATATAATATAATTAGT+TGG - chr2.4:355946-355965 MS.gene067489:intron 5.0%
ACAGTTAAGAGCCCTGGAGT+TGG + chr2.4:356484-356503 None:intergenic 50.0%
ATAATCCTGGGCCAACTCCA+GGG - chr2.4:356470-356489 MS.gene067489:intron 50.0%
CCAGGATTATATTGGGGAGG+AGG + chr2.4:356460-356479 None:intergenic 50.0%
CCTCCTCCCCAATATAATCC+TGG - chr2.4:356457-356476 MS.gene067489:intron 50.0%
GGATTATATTGGGGAGGAGG+TGG + chr2.4:356457-356476 None:intergenic 50.0%
GTTGGGTTTCCAGAAGTTGC+TGG + chr2.4:356508-356527 None:intergenic 50.0%
TATAATCCTGGGCCAACTCC+AGG - chr2.4:356469-356488 MS.gene067489:intron 50.0%
TTATATTGGGGAGGAGGTGG+TGG + chr2.4:356454-356473 None:intergenic 50.0%
! ATGATGTCTCAGAGCGTCTG+CGG + chr2.4:356422-356441 None:intergenic 50.0%
! CAGCAAGCATCTAGCTTCTG+TGG + chr2.4:355722-355741 None:intergenic 50.0%
GGCCCAGGATTATATTGGGG+AGG + chr2.4:356463-356482 None:intergenic 55.0%
GCTGGCACAGTTAAGAGCCC+TGG + chr2.4:356490-356509 None:intergenic 60.0%
TCTGAACTGGTCCCGGCGAA+TGG + chr2.4:356375-356394 None:intergenic 60.0%
! ATGTCTCAGAGCGTCTGCGG+CGG + chr2.4:356419-356438 None:intergenic 60.0%
AAGAGCCCTGGAGTTGGCCC+AGG + chr2.4:356478-356497 None:intergenic 65.0%
ACCACCTCCGCACCATTCGC+CGG - chr2.4:356360-356379 MS.gene067489:intron 65.0%
ACTGGTCCCGGCGAATGGTG+CGG + chr2.4:356370-356389 None:intergenic 65.0%
! GAATGGTGCGGAGGTGGTGG+TGG + chr2.4:356358-356377 None:intergenic 65.0%
! TGTCTCAGAGCGTCTGCGGC+GGG + chr2.4:356418-356437 None:intergenic 65.0%
CCACCTCCGCACCATTCGCC+GGG - chr2.4:356361-356380 MS.gene067489:intron 70.0%
GGCGAATGGTGCGGAGGTGG+TGG + chr2.4:356361-356380 None:intergenic 70.0%
! AGAGCGTCTGCGGCGGGAGT+GGG + chr2.4:356412-356431 None:intergenic 70.0%
CCCGGCGAATGGTGCGGAGG+TGG + chr2.4:356364-356383 None:intergenic 75.0%
GGTCCCGGCGAATGGTGCGG+AGG + chr2.4:356367-356386 None:intergenic 75.0%
! CAGAGCGTCTGCGGCGGGAG+TGG + chr2.4:356413-356432 None:intergenic 75.0%
! GCGTCTGCGGCGGGAGTGGG+AGG + chr2.4:356409-356428 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 355646 356588 355646 ID=MS.gene067489
chr2.4 mRNA 355646 356588 355646 ID=MS.gene067489.t1;Parent=MS.gene067489
chr2.4 exon 356474 356588 356474 ID=MS.gene067489.t1.exon1;Parent=MS.gene067489.t1
chr2.4 CDS 356474 356588 356474 ID=cds.MS.gene067489.t1;Parent=MS.gene067489.t1
chr2.4 exon 355646 355932 355646 ID=MS.gene067489.t1.exon2;Parent=MS.gene067489.t1
chr2.4 CDS 355646 355932 355646 ID=cds.MS.gene067489.t1;Parent=MS.gene067489.t1
Gene Sequence

>MS.gene067489

ATGAAGACTCTCCAATATGTCTTTCTACTCTCTTCACTCTTTGCATTCCAAGCCTTGCTGTTTGTTTCTACTGCCACAGAAGCTAGATGCTTGCTGTTGCAGACTATGTCACTAGGTAAATTCTTTACTTATAGCTTATAACTTATATGTGCATGCACTTTGTACCTAGTCAGTACTCCCTCCAATTCAAATAAAATTCTTTTAAAGCTTTTTCGCCGCACATATTCAAAACAAAATAAATGAACAAAGTGTAATAATCTTTTAAAATTATTCTTATTAGTTATTGGGTTGTATAGTACGTATAATATAATATAATTAGTTGGACGTAAAATTGAAAAATTAATTAATTGATTGTCTTGAAAATATAATATAATGGTTGAATTTAAGTGGTTAATAAATTTTATTTTAAATAATTCAAAAGAACACGAATTTAAAATTTTAAATAAAATAATCATTGATCAAGCTATACTTATATCCATTCGAACTCAAAAAGATATCCTTTTTCACCTCATGTAACTGAAAAAATATTCCATTATTCCAATCACATAAATATATTGTTTAGAAAAAGAAAAGCATATCACAATGTCAGTTTGTCATACTAGTTATTAATATATTTTCACAAATATTTATACAACTAGACGTGATTTGATGTATAGAAACTGAATTCTCCTCCCGGGAAACTGAAAGAAATGGGGGAAGACATCATGCACCACCACCACCTCCGCACCATTCGCCGGGACCAGTTCAGAAACTGAATTCTCCTCCCACTCCCGCCGCAGACGCTCTGAGACATCATCGACACTCACCACCACCTCCTCCCCAATATAATCCTGGGCCAACTCCAGGGCTCTTAACTGTGCCAGCAACTTCTGGAAACCCAACAGCTCAGATACATATTTTGTACCAGAATTCTCCTCCTAATCTCTTTGCAGCTTCAGCCTGA
Protein sequence

>MS.gene067489.t1

MKTLQYVFLLSSLFAFQALLFVSTATEARCLLLQTMSLETEFSSRETERNGGRHHAPPPPPHHSPGPVQKLNSPPTPAADALRHHRHSPPPPPQYNPGPTPGLLTVPATSGNPTAQIHILYQNSPPNLFAASA