AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24561


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24561.t1 MTR_1g016270 92.391 276 21 0 1 276 1 276 2.70e-148 416
MS.gene24561.t1 MTR_8g097140 48.188 276 91 10 4 271 3 234 1.60e-51 169
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24561.t1 AT5G60030 59.322 59 24 0 1 59 1 59 5.64e-17 79.0
MS.gene24561.t1 AT1G75335 59.322 59 24 0 1 59 1 59 9.39e-16 71.6

Find 64 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAAGAAGAAACTAGAATT+TGG 0.282317 1.2:-6231347 MS.gene24561:CDS
AAGAAGGAGAAGAGTGTAGA+AGG 0.312453 1.2:-6231233 MS.gene24561:CDS
AAGAAGAATGGAAGTGAGTT+AGG 0.374907 1.2:-6231314 MS.gene24561:CDS
TGAAAAGGAGAAGAATTTAG+AGG 0.379641 1.2:-6231126 MS.gene24561:CDS
GTTGTCAGCAGAGACAAATT+TGG 0.400587 1.2:+6231604 None:intergenic
ATTCTCGGGATGTAGAAATT+AGG 0.415570 1.2:-6231016 MS.gene24561:CDS
AGAAGGAGAAGAGTGTAGAA+GGG 0.423276 1.2:-6231232 MS.gene24561:CDS
GAAGACACGGAAGAGAGATC+TGG 0.440783 1.2:-6230909 MS.gene24561:CDS
GTGGAGGGCTAGTTGATTCT+CGG 0.450550 1.2:-6231031 MS.gene24561:CDS
AAGGAGAAGAATTTAGAGGT+TGG 0.455722 1.2:-6231122 MS.gene24561:CDS
TTAAACCGGCGCAGTCTCAT+AGG 0.455996 1.2:-6231502 MS.gene24561:CDS
TGAGCTTAATCAACTTCATA+AGG 0.457180 1.2:-6231528 MS.gene24561:CDS
AGTCTAAGAAGAAAATGAAA+AGG 0.460042 1.2:-6230881 MS.gene24561:CDS
ATGTGAAGGTTGAAAGTAAA+GGG 0.462456 1.2:-6231205 MS.gene24561:CDS
GGAGAGAGTGTAAAGAAGAA+TGG 0.469789 1.2:-6231326 MS.gene24561:CDS
CTCCTCAGGAGTTAGAAATT+AGG 0.475036 1.2:-6231175 MS.gene24561:CDS
GAGAAGCGTGATAAGAAAGA+TGG 0.475565 1.2:-6231368 MS.gene24561:CDS
AAATGAAGTGGGGAGTGAAA+AGG 0.480460 1.2:-6231141 MS.gene24561:CDS
AACAGATGATAGTGGTAGAT+TGG 0.498404 1.2:-6231459 MS.gene24561:CDS
TGGAGGGCTAGTTGATTCTC+GGG 0.502825 1.2:-6231030 MS.gene24561:CDS
AAGACACGGAAGAGAGATCT+GGG 0.505868 1.2:-6230908 MS.gene24561:CDS
ACTTCATAAGGAGCTTAAAC+CGG 0.507615 1.2:-6231516 MS.gene24561:CDS
GAATGGAAGTGAGTTAGGTC+AGG 0.510402 1.2:-6231309 MS.gene24561:CDS
GAAGTTGTTGGTTCTGTCGT+GGG 0.512214 1.2:-6231398 MS.gene24561:CDS
GAAGGAGAAGAGTGTAGAAG+GGG 0.517307 1.2:-6231231 MS.gene24561:CDS
CGAGAAGAAGAACAAGAAGA+AGG 0.521154 1.2:-6231249 MS.gene24561:CDS
TAAAGGGATAGTTCCTCCTC+AGG 0.521560 1.2:-6231189 MS.gene24561:CDS
TTTAGAGGTTGGAAATGTGA+AGG 0.536582 1.2:-6231111 MS.gene24561:CDS
TGAAGTTGTTGGTTCTGTCG+TGG 0.542751 1.2:-6231399 MS.gene24561:CDS
AATGTGAAGGTTGAAAGTAA+AGG 0.544852 1.2:-6231206 MS.gene24561:CDS
AGACGGAGCAAAGGAAGAAG+AGG 0.546821 1.2:-6230938 MS.gene24561:CDS
CATTGAAAGCCGTGGATGCA+CGG 0.548708 1.2:+6231549 None:intergenic
AAGAGGGAAAGACGGAGCAA+AGG 0.550638 1.2:-6230947 MS.gene24561:CDS
AAACCTGGTCGTGAAGTTGT+TGG 0.551304 1.2:-6231410 MS.gene24561:CDS
GAGTTAGGTCAGGACGATGA+AGG 0.567638 1.2:-6231299 MS.gene24561:CDS
GAGTAAATTACATGCTGAAG+AGG 0.574245 1.2:-6230964 MS.gene24561:CDS
AATGGTGTGAAGAGTGAAAG+TGG 0.576054 1.2:-6231050 MS.gene24561:CDS
GGGACGAGAACAACAGAAAG+AGG 0.576625 1.2:-6231090 MS.gene24561:CDS
TGTAGAAGGGGAGAATGTGA+AGG 0.579317 1.2:-6231219 MS.gene24561:CDS
TTAGAGGTTGGAAATGTGAA+GGG 0.581388 1.2:-6231110 MS.gene24561:CDS
GATTGGTCGAAAGTACTGTT+CGG 0.581744 1.2:-6231442 MS.gene24561:CDS
TACCACTATCATCTGTTGCA+TGG 0.584555 1.2:+6231465 None:intergenic
AGCCATGCAACAGATGATAG+TGG 0.587057 1.2:-6231467 MS.gene24561:CDS
ATTAAGCTCATTGAAAGCCG+TGG 0.591302 1.2:+6231541 None:intergenic
GACGATGAAGGAAGAACGGA+GGG 0.595325 1.2:-6231287 MS.gene24561:CDS
TTATCTGCTCCGTGCATCCA+CGG 0.595538 1.2:-6231558 MS.gene24561:CDS
AGTAAATTACATGCTGAAGA+GGG 0.598011 1.2:-6230963 MS.gene24561:CDS
GACCTAATTTCTAACTCCTG+AGG 0.598620 1.2:+6231173 None:intergenic
GAACCAACAACTTCACGACC+AGG 0.602335 1.2:+6231407 None:intergenic
GTTCGGAGTGATGTTAAACC+TGG 0.607851 1.2:-6231425 MS.gene24561:CDS
GTTGTTGGTTCTGTCGTGGG+TGG 0.608189 1.2:-6231395 MS.gene24561:CDS
ACGAGAACAACAGAAAGAGG+TGG 0.612657 1.2:-6231087 MS.gene24561:CDS
TCAGGACGATGAAGGAAGAA+CGG 0.621358 1.2:-6231291 MS.gene24561:CDS
ACATGCTGAAGAGGGAAAGA+CGG 0.635975 1.2:-6230955 MS.gene24561:CDS
TTCTTCCTATGAGACTGCGC+CGG 0.636496 1.2:+6231497 None:intergenic
GAAGAGGAAGAATGAAGACA+CGG 0.643138 1.2:-6230922 MS.gene24561:CDS
AAATTTGTCTCTGCTGACAA+CGG 0.644626 1.2:-6231602 MS.gene24561:CDS
CTAATTTCTAACTCCTGAGG+AGG 0.647828 1.2:+6231176 None:intergenic
GTGTGAAGAGTGAAAGTGGA+GGG 0.650346 1.2:-6231046 MS.gene24561:CDS
GGACGATGAAGGAAGAACGG+AGG 0.651421 1.2:-6231288 MS.gene24561:CDS
GAAAATGAAAAGGAAACACG+AGG 0.691720 1.2:-6230871 MS.gene24561:CDS
AAAATGAAAAGGAAACACGA+GGG 0.733622 1.2:-6230870 MS.gene24561:CDS
AGACACGGAAGAGAGATCTG+GGG 0.742079 1.2:-6230907 MS.gene24561:CDS
GGTGTGAAGAGTGAAAGTGG+AGG 0.804724 1.2:-6231047 MS.gene24561:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTCTAAGAAGAAAATGAAA+AGG - chr1.2:6231659-6231678 MS.gene24561:CDS 25.0%
AAAATGAAAAGGAAACACGA+GGG - chr1.2:6231670-6231689 MS.gene24561:CDS 30.0%
AATGTGAAGGTTGAAAGTAA+AGG - chr1.2:6231334-6231353 MS.gene24561:CDS 30.0%
AGTAAATTACATGCTGAAGA+GGG - chr1.2:6231577-6231596 MS.gene24561:CDS 30.0%
ATGTGAAGGTTGAAAGTAAA+GGG - chr1.2:6231335-6231354 MS.gene24561:CDS 30.0%
GGAAAGAAGAAACTAGAATT+TGG - chr1.2:6231193-6231212 MS.gene24561:CDS 30.0%
TCGAAAAAGAGAAATGAAGT+GGG - chr1.2:6231388-6231407 MS.gene24561:CDS 30.0%
TGAAAAGGAGAAGAATTTAG+AGG - chr1.2:6231414-6231433 MS.gene24561:CDS 30.0%
TGAGCTTAATCAACTTCATA+AGG - chr1.2:6231012-6231031 MS.gene24561:CDS 30.0%
AAATTTGTCTCTGCTGACAA+CGG - chr1.2:6230938-6230957 MS.gene24561:CDS 35.0%
AAGAAGAATGGAAGTGAGTT+AGG - chr1.2:6231226-6231245 MS.gene24561:CDS 35.0%
AAGGAGAAGAATTTAGAGGT+TGG - chr1.2:6231418-6231437 MS.gene24561:CDS 35.0%
ACTTCATAAGGAGCTTAAAC+CGG - chr1.2:6231024-6231043 MS.gene24561:CDS 35.0%
ATTCTCGGGATGTAGAAATT+AGG - chr1.2:6231524-6231543 MS.gene24561:CDS 35.0%
CGAAAAAGAGAAATGAAGTG+GGG - chr1.2:6231389-6231408 MS.gene24561:CDS 35.0%
GAAAATGAAAAGGAAACACG+AGG - chr1.2:6231669-6231688 MS.gene24561:CDS 35.0%
GAGTAAATTACATGCTGAAG+AGG - chr1.2:6231576-6231595 MS.gene24561:CDS 35.0%
GTCGAAAAAGAGAAATGAAG+TGG - chr1.2:6231387-6231406 MS.gene24561:CDS 35.0%
GTGGAGAAAAAACTAAGCAA+TGG - chr1.2:6231472-6231491 MS.gene24561:CDS 35.0%
TTAGAGGTTGGAAATGTGAA+GGG - chr1.2:6231430-6231449 MS.gene24561:CDS 35.0%
TTTAGAGGTTGGAAATGTGA+AGG - chr1.2:6231429-6231448 MS.gene24561:CDS 35.0%
! CGAAAAAGAAGCATGAAACT+GGG - chr1.2:6231548-6231567 MS.gene24561:CDS 35.0%
! TCGAAAAAGAAGCATGAAAC+TGG - chr1.2:6231547-6231566 MS.gene24561:CDS 35.0%
!! AACAGATGATAGTGGTAGAT+TGG - chr1.2:6231081-6231100 MS.gene24561:CDS 35.0%
AAATGAAGTGGGGAGTGAAA+AGG - chr1.2:6231399-6231418 MS.gene24561:CDS 40.0%
AATGGTGTGAAGAGTGAAAG+TGG - chr1.2:6231490-6231509 MS.gene24561:CDS 40.0%
ATTAAGCTCATTGAAAGCCG+TGG + chr1.2:6231002-6231021 None:intergenic 40.0%
CGAGAAGAAGAACAAGAAGA+AGG - chr1.2:6231291-6231310 MS.gene24561:CDS 40.0%
CTAATTTCTAACTCCTGAGG+AGG + chr1.2:6231367-6231386 None:intergenic 40.0%
CTCCTCAGGAGTTAGAAATT+AGG - chr1.2:6231365-6231384 MS.gene24561:CDS 40.0%
GAAGAGGAAGAATGAAGACA+CGG - chr1.2:6231618-6231637 MS.gene24561:CDS 40.0%
GACCTAATTTCTAACTCCTG+AGG + chr1.2:6231370-6231389 None:intergenic 40.0%
GTTGTCAGCAGAGACAAATT+TGG + chr1.2:6230939-6230958 None:intergenic 40.0%
TACCACTATCATCTGTTGCA+TGG + chr1.2:6231078-6231097 None:intergenic 40.0%
! AAGAAGGAGAAGAGTGTAGA+AGG - chr1.2:6231307-6231326 MS.gene24561:CDS 40.0%
! AGAAGGAGAAGAGTGTAGAA+GGG - chr1.2:6231308-6231327 MS.gene24561:CDS 40.0%
! GAGAAGCGTGATAAGAAAGA+TGG - chr1.2:6231172-6231191 MS.gene24561:CDS 40.0%
! GGAGAGAGTGTAAAGAAGAA+TGG - chr1.2:6231214-6231233 MS.gene24561:CDS 40.0%
!! GATTGGTCGAAAGTACTGTT+CGG - chr1.2:6231098-6231117 MS.gene24561:CDS 40.0%
AAACCTGGTCGTGAAGTTGT+TGG - chr1.2:6231130-6231149 MS.gene24561:CDS 45.0%
AAGACACGGAAGAGAGATCT+GGG - chr1.2:6231632-6231651 MS.gene24561:CDS 45.0%
ACATGCTGAAGAGGGAAAGA+CGG - chr1.2:6231585-6231604 MS.gene24561:CDS 45.0%
ACGAGAACAACAGAAAGAGG+TGG - chr1.2:6231453-6231472 MS.gene24561:CDS 45.0%
AGCCATGCAACAGATGATAG+TGG - chr1.2:6231073-6231092 MS.gene24561:CDS 45.0%
GAATGGAAGTGAGTTAGGTC+AGG - chr1.2:6231231-6231250 MS.gene24561:CDS 45.0%
GTGTGAAGAGTGAAAGTGGA+GGG - chr1.2:6231494-6231513 MS.gene24561:CDS 45.0%
GTTCGGAGTGATGTTAAACC+TGG - chr1.2:6231115-6231134 MS.gene24561:CDS 45.0%
TAAAGGGATAGTTCCTCCTC+AGG - chr1.2:6231351-6231370 MS.gene24561:CDS 45.0%
TCAGGACGATGAAGGAAGAA+CGG - chr1.2:6231249-6231268 MS.gene24561:CDS 45.0%
TGTAGAAGGGGAGAATGTGA+AGG - chr1.2:6231321-6231340 MS.gene24561:CDS 45.0%
! GAAGGAGAAGAGTGTAGAAG+GGG - chr1.2:6231309-6231328 MS.gene24561:CDS 45.0%
!! GAAGTTGTTGGTTCTGTCGT+GGG - chr1.2:6231142-6231161 MS.gene24561:CDS 45.0%
!! TGAAGTTGTTGGTTCTGTCG+TGG - chr1.2:6231141-6231160 MS.gene24561:CDS 45.0%
AAGAGGGAAAGACGGAGCAA+AGG - chr1.2:6231593-6231612 MS.gene24561:CDS 50.0%
AGACACGGAAGAGAGATCTG+GGG - chr1.2:6231633-6231652 MS.gene24561:CDS 50.0%
AGACGGAGCAAAGGAAGAAG+AGG - chr1.2:6231602-6231621 MS.gene24561:CDS 50.0%
CATTGAAAGCCGTGGATGCA+CGG + chr1.2:6230994-6231013 None:intergenic 50.0%
GAACCAACAACTTCACGACC+AGG + chr1.2:6231136-6231155 None:intergenic 50.0%
GAAGACACGGAAGAGAGATC+TGG - chr1.2:6231631-6231650 MS.gene24561:CDS 50.0%
GACGATGAAGGAAGAACGGA+GGG - chr1.2:6231253-6231272 MS.gene24561:CDS 50.0%
GAGTTAGGTCAGGACGATGA+AGG - chr1.2:6231241-6231260 MS.gene24561:CDS 50.0%
GGGACGAGAACAACAGAAAG+AGG - chr1.2:6231450-6231469 MS.gene24561:CDS 50.0%
GGTGTGAAGAGTGAAAGTGG+AGG - chr1.2:6231493-6231512 MS.gene24561:CDS 50.0%
TTAAACCGGCGCAGTCTCAT+AGG - chr1.2:6231038-6231057 MS.gene24561:CDS 50.0%
TTATCTGCTCCGTGCATCCA+CGG - chr1.2:6230982-6231001 MS.gene24561:CDS 50.0%
TTCTTCCTATGAGACTGCGC+CGG + chr1.2:6231046-6231065 None:intergenic 50.0%
!! GTGGAGGGCTAGTTGATTCT+CGG - chr1.2:6231509-6231528 MS.gene24561:CDS 50.0%
!! TGGAGGGCTAGTTGATTCTC+GGG - chr1.2:6231510-6231529 MS.gene24561:CDS 50.0%
GGACGATGAAGGAAGAACGG+AGG - chr1.2:6231252-6231271 MS.gene24561:CDS 55.0%
!! GTTGTTGGTTCTGTCGTGGG+TGG - chr1.2:6231145-6231164 MS.gene24561:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 6230866 6231696 6230866 ID=MS.gene24561
chr1.2 mRNA 6230866 6231696 6230866 ID=MS.gene24561.t1;Parent=MS.gene24561
chr1.2 exon 6230866 6231696 6230866 ID=MS.gene24561.t1.exon1;Parent=MS.gene24561.t1
chr1.2 CDS 6230866 6231696 6230866 ID=cds.MS.gene24561.t1;Parent=MS.gene24561.t1
Gene Sequence

>MS.gene24561

ATGAAAACGATTACGGGACATTGTGAATCATCTAAAGAGATATCACTTTCAAAAGCTTCAAAAATTCTCTCCAAATTTGTCTCTGCTGACAACGGTGCTTCACATGTCATCAACGCTTATCTGCTCCGTGCATCCACGGCTTTCAATGAGCTTAATCAACTTCATAAGGAGCTTAAACCGGCGCAGTCTCATAGGAAGAATCGTCGAAGCCATGCAACAGATGATAGTGGTAGATTGGTCGAAAGTACTGTTCGGAGTGATGTTAAACCTGGTCGTGAAGTTGTTGGTTCTGTCGTGGGTGGAAGTGAGAAGCGTGATAAGAAAGATGGAAAGAAGAAACTAGAATTTGGAGAGAGTGTAAAGAAGAATGGAAGTGAGTTAGGTCAGGACGATGAAGGAAGAACGGAGGGAAAAAAGCAAAAGAGCGAGAAGAAGAACAAGAAGAAGGAGAAGAGTGTAGAAGGGGAGAATGTGAAGGTTGAAAGTAAAGGGATAGTTCCTCCTCAGGAGTTAGAAATTAGGTCGAAAAAGAGAAATGAAGTGGGGAGTGAAAAGGAGAAGAATTTAGAGGTTGGAAATGTGAAGGGACGAGAACAACAGAAAGAGGTGGAGAAAAAACTAAGCAATGGTGTGAAGAGTGAAAGTGGAGGGCTAGTTGATTCTCGGGATGTAGAAATTAGGTCGAAAAAGAAGCATGAAACTGGGAGTGAGAGTAAATTACATGCTGAAGAGGGAAAGACGGAGCAAAGGAAGAAGAGGAAGAATGAAGACACGGAAGAGAGATCTGGGGAGAAGTCTAAGAAGAAAATGAAAAGGAAACACGAGGGTTAA

Protein sequence

>MS.gene24561.t1

MKTITGHCESSKEISLSKASKILSKFVSADNGASHVINAYLLRASTAFNELNQLHKELKPAQSHRKNRRSHATDDSGRLVESTVRSDVKPGREVVGSVVGGSEKRDKKDGKKKLEFGESVKKNGSELGQDDEGRTEGKKQKSEKKNKKKEKSVEGENVKVESKGIVPPQELEIRSKKRNEVGSEKEKNLEVGNVKGREQQKEVEKKLSNGVKSESGGLVDSRDVEIRSKKKHETGSESKLHAEEGKTEQRKKRKNEDTEERSGEKSKKKMKRKHEG