AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32959

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32959.t1 MTR_1g017000 93.452 168 10 1 20 187 86 252 6.34e-111 317
MS.gene32959.t1 MTR_6g009430 50.725 69 30 3 20 85 85 152 1.71e-12 65.1
MS.gene32959.t1 MTR_3g103570 41.096 73 43 0 20 92 86 158 1.99e-12 64.7
MS.gene32959.t1 MTR_7g102110 56.452 62 20 2 20 74 86 147 2.80e-12 63.9
MS.gene32959.t1 MTR_4g057635 70.588 34 10 0 20 53 86 119 2.04e-11 61.6
MS.gene32959.t1 MTR_6g090405 62.500 40 15 0 15 54 81 120 2.06e-11 61.2
MS.gene32959.t1 MTR_1g017140 67.647 34 11 0 20 53 86 119 5.14e-11 60.8
MS.gene32959.t1 MTR_5g014990 67.647 34 11 0 20 53 86 119 5.26e-11 60.5
MS.gene32959.t1 MTR_4g091490 53.333 45 19 1 20 64 86 128 5.85e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32959.t1 AT5G16770 38.136 118 60 6 20 134 85 192 1.34e-12 65.1
MS.gene32959.t1 AT5G16770 38.136 118 60 6 20 134 85 192 1.34e-12 65.1
MS.gene32959.t1 AT5G16770 38.136 118 60 6 20 134 85 192 2.20e-12 64.7
MS.gene32959.t1 AT5G16770 38.136 118 60 6 20 134 85 192 2.20e-12 64.7
MS.gene32959.t1 AT5G57620 53.846 52 21 1 20 71 86 134 1.65e-11 62.0
MS.gene32959.t1 AT4G37780 70.588 34 10 0 20 53 86 119 2.21e-11 61.6
MS.gene32959.t1 AT3G23250 45.000 80 41 2 15 92 23 101 3.65e-11 60.5
MS.gene32959.t1 AT5G23000 63.158 38 14 0 15 52 81 118 8.09e-11 60.1
MS.gene32959.t1 AT3G23250 45.000 80 41 2 15 92 80 158 9.21e-11 59.7
MS.gene32959.t1 AT5G65790 69.697 33 10 0 20 52 86 118 9.63e-11 60.1

Find 30 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTTATTGTCTAGCATAAT+TGG 0.238985 1.1:-5466717 None:intergenic
AAAACTGAAGAAGAAGATTT+TGG 0.243833 1.1:+5466551 MS.gene32959:CDS
CAGCAATATTATTAATCCTT+TGG 0.356887 1.1:+5466785 MS.gene32959:CDS
TCATTGATGGACTTTGGCTT+TGG 0.361801 1.1:+5466873 MS.gene32959:CDS
GATGCTGTAGTATCAGAAAT+TGG 0.363867 1.1:+5466753 MS.gene32959:CDS
TTTCACCCTCTATTCTCAAA+TGG 0.370485 1.1:+5465564 MS.gene32959:CDS
TCAAGCTGGTGATGAATCTA+TGG 0.374214 1.1:+5466848 MS.gene32959:CDS
ATGGAATCATTGATGGACTT+TGG 0.403753 1.1:+5466867 MS.gene32959:CDS
TGAGTTAGTGATGGAGTTGA+AGG 0.446977 1.1:-5466621 None:intergenic
TGAATCTATGGAATCATTGA+TGG 0.447988 1.1:+5466860 MS.gene32959:CDS
GCCAGGTAGTTTAGATGCTA+TGG 0.455877 1.1:-5466493 None:intergenic
TGCTACCCATTTGAGAATAG+AGG 0.456147 1.1:-5465570 None:intergenic
TTCACCCTCTATTCTCAAAT+GGG 0.465064 1.1:+5465565 MS.gene32959:CDS
ACATCATTGTCTGTTCTGCC+AGG 0.476737 1.1:-5466510 None:intergenic
TCTATTCTCAAATGGGTAGC+AGG 0.500149 1.1:+5465572 MS.gene32959:CDS
TCTTAACTGCTTTCCTGAGT+GGG 0.511907 1.1:+5466923 MS.gene32959:CDS
AGCATAATTGGAAGTGGTGA+AGG 0.515734 1.1:-5466705 None:intergenic
TTGTCTAGCATAATTGGAAG+TGG 0.518920 1.1:-5466711 None:intergenic
AGAATAGAGGGTGAAAATGA+TGG 0.524462 1.1:-5465557 None:intergenic
TTGGAACTTTGAGTTAGTGA+TGG 0.526757 1.1:-5466630 None:intergenic
GAGTTAGTGATGGAGTTGAA+GGG 0.551144 1.1:-5466620 None:intergenic
ATCTTAACTGCTTTCCTGAG+TGG 0.564962 1.1:+5466922 MS.gene32959:CDS
TGGAGGCTTCACTGAAGAAG+AGG 0.582932 1.1:+5465531 MS.gene32959:CDS
ATAATTGGAAGTGGTGAAGG+TGG 0.597724 1.1:-5466702 None:intergenic
GCTACCCATTTGAGAATAGA+GGG 0.601575 1.1:-5465569 None:intergenic
TCTTGAGAAATTGACACCAA+AGG 0.604458 1.1:-5466801 None:intergenic
TAACTAAAATCAACCCACTC+AGG 0.606546 1.1:-5466936 None:intergenic
GCCATAGCATCTAAACTACC+TGG 0.606568 1.1:+5466492 MS.gene32959:CDS
ATTGCAATTCAAGATCAAGC+TGG 0.635582 1.1:+5466834 MS.gene32959:CDS
TCATTGACATGATCATCATG+AGG 0.679338 1.1:-5466900 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAAAATCATGTTAT+TGG - chr1.1:5466275-5466294 None:intergenic 10.0%
!! ACTAAAATTTAAATTTCAGT+TGG + chr1.1:5465952-5465971 MS.gene32959:intron 15.0%
!! CGTTTATAATAATAACAATT+TGG - chr1.1:5465654-5465673 None:intergenic 15.0%
!! CTAAAATTTAAATTTCAGTT+GGG + chr1.1:5465953-5465972 MS.gene32959:intron 15.0%
!! TACAACTTAATTAAATAAGT+TGG - chr1.1:5465610-5465629 None:intergenic 15.0%
!! TTAAAAAAAGTGAGAAATTA+TGG + chr1.1:5466286-5466305 MS.gene32959:intron 15.0%
!!! ATATTCTATAACCATTTTTT+GGG - chr1.1:5466240-5466259 None:intergenic 15.0%
!!! TATATTCTATAACCATTTTT+TGG - chr1.1:5466241-5466260 None:intergenic 15.0%
!!! TGAAATTTAAATTTTAGTCT+CGG - chr1.1:5465950-5465969 None:intergenic 15.0%
!!! AAATTGATTTCTGAATTTTG+AGG - chr1.1:5466657-5466676 None:intergenic 20.0%
!!! AATTGATTTCTGAATTTTGA+GGG - chr1.1:5466656-5466675 None:intergenic 20.0%
!!! ATTTTTTATAGTCAGTTGAA+TGG + chr1.1:5466378-5466397 MS.gene32959:intron 20.0%
! ACAATGATGTGAAAAACTAT+TGG + chr1.1:5466523-5466542 MS.gene32959:CDS 25.0%
! ACAGAAAAAATGTGATTAGA+AGG + chr1.1:5466135-5466154 MS.gene32959:intron 25.0%
! ACTTTATTGTCTAGCATAAT+TGG - chr1.1:5466720-5466739 None:intergenic 25.0%
! AGAAATTATAACAACCAACT+GGG + chr1.1:5465872-5465891 MS.gene32959:intron 25.0%
! ATTCCTAGTTTATAACATCA+TGG - chr1.1:5465926-5465945 None:intergenic 25.0%
! CAGCAATATTATTAATCCTT+TGG + chr1.1:5466785-5466804 MS.gene32959:CDS 25.0%
! TTCCTAGTTTATAACATCAT+GGG - chr1.1:5465925-5465944 None:intergenic 25.0%
!! AAAACTGAAGAAGAAGATTT+TGG + chr1.1:5466551-5466570 MS.gene32959:CDS 25.0%
!! GATTTTTAATGTGTACAAGT+TGG + chr1.1:5465816-5465835 MS.gene32959:intron 25.0%
!!! ATTTTTTGGGTCTTAATCTT+GGG - chr1.1:5466227-5466246 None:intergenic 25.0%
CAAGATTAAGACCCAAAAAA+TGG + chr1.1:5466226-5466245 MS.gene32959:intron 30.0%
GAAATTATAACAACCAACTG+GGG + chr1.1:5465873-5465892 MS.gene32959:intron 30.0%
GAGAAATTATAACAACCAAC+TGG + chr1.1:5465871-5465890 MS.gene32959:intron 30.0%
GTACTATGAAACTAACTTTG+AGG - chr1.1:5466405-5466424 None:intergenic 30.0%
TAATTTCTCACTTTGACTGA+AGG - chr1.1:5466026-5466045 None:intergenic 30.0%
TAGTTTCATAGTACTTCAAG+AGG + chr1.1:5466411-5466430 MS.gene32959:intron 30.0%
TGAATCTATGGAATCATTGA+TGG + chr1.1:5466860-5466879 MS.gene32959:CDS 30.0%
TGAGAACTATTCAAACTTTG+AGG - chr1.1:5466443-5466462 None:intergenic 30.0%
TTCCCATGATGTTATAAACT+AGG + chr1.1:5465920-5465939 MS.gene32959:intron 30.0%
! AATTTGTGATTTTGTGCAGA+TGG + chr1.1:5466466-5466485 MS.gene32959:intron 30.0%
! ATGTCGTATTTAGAGTTTGA+TGG + chr1.1:5465980-5465999 MS.gene32959:intron 30.0%
!!! AATGTTGATTTTGTGAAGCA+GGG - chr1.1:5466680-5466699 None:intergenic 30.0%
!!! CATTTTTTGGGTCTTAATCT+TGG - chr1.1:5466228-5466247 None:intergenic 30.0%
!!! GTATTGTCATTTTCAGTCAA+TGG - chr1.1:5466597-5466616 None:intergenic 30.0%
!!! TTTTTTGGGTCTTAATCTTG+GGG - chr1.1:5466226-5466245 None:intergenic 30.0%
AGAATAGAGGGTGAAAATGA+TGG - chr1.1:5465560-5465579 None:intergenic 35.0%
ATTGCAATTCAAGATCAAGC+TGG + chr1.1:5466834-5466853 MS.gene32959:CDS 35.0%
CACTTAGACCAACATTATGT+CGG - chr1.1:5466060-5466079 None:intergenic 35.0%
GATGCTGTAGTATCAGAAAT+TGG + chr1.1:5466753-5466772 MS.gene32959:CDS 35.0%
GGAGAGAAACTACTAAATGT+TGG + chr1.1:5466156-5466175 MS.gene32959:intron 35.0%
TAACTAAAATCAACCCACTC+AGG - chr1.1:5466939-5466958 None:intergenic 35.0%
TCATTGACATGATCATCATG+AGG - chr1.1:5466903-5466922 None:intergenic 35.0%
TCTTGAGAAATTGACACCAA+AGG - chr1.1:5466804-5466823 None:intergenic 35.0%
TTCACCCTCTATTCTCAAAT+GGG + chr1.1:5465565-5465584 MS.gene32959:CDS 35.0%
TTGTCTAGCATAATTGGAAG+TGG - chr1.1:5466714-5466733 None:intergenic 35.0%
TTTCACCCTCTATTCTCAAA+TGG + chr1.1:5465564-5465583 MS.gene32959:CDS 35.0%
! AATGTTGGTCTAAGTGTAAC+TGG + chr1.1:5466064-5466083 MS.gene32959:intron 35.0%
! TTGGAACTTTGAGTTAGTGA+TGG - chr1.1:5466633-5466652 None:intergenic 35.0%
!! ATGGAATCATTGATGGACTT+TGG + chr1.1:5466867-5466886 MS.gene32959:CDS 35.0%
!! GATTTCTGAATTTTGAGGGT+TGG - chr1.1:5466652-5466671 None:intergenic 35.0%
!!! GAATGTTGATTTTGTGAAGC+AGG - chr1.1:5466681-5466700 None:intergenic 35.0%
AGCATAATTGGAAGTGGTGA+AGG - chr1.1:5466708-5466727 None:intergenic 40.0%
ATAATTGGAAGTGGTGAAGG+TGG - chr1.1:5466705-5466724 None:intergenic 40.0%
ATCTTAACTGCTTTCCTGAG+TGG + chr1.1:5466922-5466941 MS.gene32959:CDS 40.0%
GCTACCCATTTGAGAATAGA+GGG - chr1.1:5465572-5465591 None:intergenic 40.0%
GGAAAGACCATAATCATCAC+AGG - chr1.1:5466205-5466224 None:intergenic 40.0%
TCTATTCTCAAATGGGTAGC+AGG + chr1.1:5465572-5465591 MS.gene32959:CDS 40.0%
TCTTAACTGCTTTCCTGAGT+GGG + chr1.1:5466923-5466942 MS.gene32959:CDS 40.0%
TGCTACCCATTTGAGAATAG+AGG - chr1.1:5465573-5465592 None:intergenic 40.0%
TGGTCTAAGTGTAACTGGAT+TGG + chr1.1:5466069-5466088 MS.gene32959:intron 40.0%
TGTCGAACCTGTGATGATTA+TGG + chr1.1:5466195-5466214 MS.gene32959:intron 40.0%
! GAGTTAGTGATGGAGTTGAA+GGG - chr1.1:5466623-5466642 None:intergenic 40.0%
! TCAAGCTGGTGATGAATCTA+TGG + chr1.1:5466848-5466867 MS.gene32959:CDS 40.0%
! TGAGTTAGTGATGGAGTTGA+AGG - chr1.1:5466624-5466643 None:intergenic 40.0%
!! CTGAAGAAGAAGATTTTGGC+AGG + chr1.1:5466555-5466574 MS.gene32959:CDS 40.0%
!! TCATTGATGGACTTTGGCTT+TGG + chr1.1:5466873-5466892 MS.gene32959:CDS 40.0%
ACATCATTGTCTGTTCTGCC+AGG - chr1.1:5466513-5466532 None:intergenic 45.0%
CCAACATTATGTCGGACTGT+CGG - chr1.1:5466052-5466071 None:intergenic 45.0%
GCCAGGTAGTTTAGATGCTA+TGG - chr1.1:5466496-5466515 None:intergenic 45.0%
GCCATAGCATCTAAACTACC+TGG + chr1.1:5466492-5466511 MS.gene32959:CDS 45.0%
TGGGGTTGAGTCAACTTGAA+GGG + chr1.1:5465891-5465910 MS.gene32959:intron 45.0%
CCGACAGTCCGACATAATGT+TGG + chr1.1:5466049-5466068 MS.gene32959:intron 50.0%
CTGGGGTTGAGTCAACTTGA+AGG + chr1.1:5465890-5465909 MS.gene32959:intron 50.0%
GGGGTTGAGTCAACTTGAAG+GGG + chr1.1:5465892-5465911 MS.gene32959:intron 50.0%
TGGAGGCTTCACTGAAGAAG+AGG + chr1.1:5465531-5465550 MS.gene32959:CDS 50.0%
! CAAGTTGACTCAACCCCAGT+TGG - chr1.1:5465889-5465908 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 5465530 5466980 5465530 ID=MS.gene32959
chr1.1 mRNA 5465530 5466980 5465530 ID=MS.gene32959.t1;Parent=MS.gene32959
chr1.1 exon 5465530 5465597 5465530 ID=MS.gene32959.t1.exon1;Parent=MS.gene32959.t1
chr1.1 CDS 5465530 5465597 5465530 ID=cds.MS.gene32959.t1;Parent=MS.gene32959.t1
chr1.1 exon 5466485 5466980 5466485 ID=MS.gene32959.t1.exon2;Parent=MS.gene32959.t1
chr1.1 CDS 5466485 5466980 5466485 ID=cds.MS.gene32959.t1;Parent=MS.gene32959.t1
Gene Sequence

>MS.gene32959

ATGGAGGCTTCACTGAAGAAGAGGATGCCATCATTTTCACCCTCTATTCTCAAATGGGTAGCAGGCAAGTACTATTTCCAACTTATTTAATTAAGTTGTATCTATTTTCACTATATAATTTCCAAATTGTTATTATTATAAACGTTGATCATTGTTAACTGTTATAATCACTTTATTTAATTTAGTATTATATATAGTTTTTCATAAGAGTTGATCATTGTTAAGTGCTAACTATTACAACTTTATTTAATTTAGTACTATGTATTGTTTTTCTTTAAGAGTTGATGATTTTTAATGTGTACAAGTTGGAAAGATTTGTTTTTTCATATAGATAATAAATTGAGAAATTATAACAACCAACTGGGGTTGAGTCAACTTGAAGGGGATAACTTCCCATGATGTTATAAACTAGGAATTCCGAGACTAAAATTTAAATTTCAGTTGGGAGAGATGTCGTATTTAGAGTTTGATGGTGTTTTAAATAAAATTACAACCTTCAGTCAAAGTGAGAAATTATAACCGACAGTCCGACATAATGTTGGTCTAAGTGTAACTGGATTGGACTCAAATTTTTTTAAGCAATGTCTCATGTTCAAACTTTATCAACAGAAAAAATGTGATTAGAAGGAGAGAAACTACTAAATGTTGGATTTTATTTAATTATCTGTCGAACCTGTGATGATTATGGTCTTTCCCCAAGATTAAGACCCAAAAAATGGTTATAGAATATAGATGCTTGATACCAATAACATGATTTTAAAAAAAGTGAGAAATTATGGATTGATATTCTATCATTTAATTATGCATATATACAAAATAAATGTACTATCTATCTATTAGTAGTATTGATTTTTTATAGTCAGTTGAATGGTCCTCAAAGTTAGTTTCATAGTACTTCAAGAGGAATATGCCTCAAAGTTTGAATAGTTCTCATGAAATTTGTGATTTTGTGCAGATGGTCTGCCATAGCATCTAAACTACCTGGCAGAACAGACAATGATGTGAAAAACTATTGGAACACAAAACTGAAGAAGAAGATTTTGGCAGGAATAGTTAAGCTCAAACCATTGACTGAAAATGACAATACTATCCCTTCAACTCCATCACTAACTCAAAGTTCCAACCCTCAAAATTCAGAAATCAATTTCCCTGCTTCACAAAATCAACATTCTCCACCTTCACCACTTCCAATTATGCTAGACAATAAAGTTGACAAAATTCATGATGCTGTAGTATCAGAAATTGGTACAAGTAACAGCAATATTATTAATCCTTTGGTGTCAATTTCTCAAGACTCTTCAAGCATTGCAATTCAAGATCAAGCTGGTGATGAATCTATGGAATCATTGATGGACTTTGGCTTTGGATTTCCTCATGATGATCATGTCAATGATCTTAACTGCTTTCCTGAGTGGGTTGATTTTAGTTATGCTGACATTAAGCCAAATTGA
Protein sequence

>MS.gene32959.t1

MEASLKKRMPSFSPSILKWVAGKWSAIASKLPGRTDNDVKNYWNTKLKKKILAGIVKLKPLTENDNTIPSTPSLTQSSNPQNSEINFPASQNQHSPPSPLPIMLDNKVDKIHDAVVSEIGTSNSNIINPLVSISQDSSSIAIQDQAGDESMESLMDFGFGFPHDDHVNDLNCFPEWVDFSYADIKPN