AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27954

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27954.t1 MTR_8g089170 87.821 156 19 0 1 156 1 156 4.57e-94 269
MS.gene27954.t1 MTR_8g089130 81.013 158 28 2 1 156 1 158 2.04e-86 250
MS.gene27954.t1 MTR_8g089145 84.932 73 11 0 1 73 1 73 1.21e-40 131
MS.gene27954.t1 MTR_1g089830 38.095 147 62 4 4 150 3 120 3.96e-21 84.0
MS.gene27954.t1 MTR_4g028990 53.425 73 32 1 81 151 20 92 1.09e-17 73.6
MS.gene27954.t1 MTR_1g045040 38.194 144 65 4 7 150 6 125 1.27e-15 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATACCTTCAAATGAAAT+TGG 0.206576 4.4:-12018994 MS.gene27954:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.4:+12020005 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.4:+12019961 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.4:+12020032 None:intergenic
ATCCTCAAACAACGTCTCTT+TGG 0.317203 4.4:+12019141 None:intergenic
CTGTTAGTAACAAGTTCTTT+TGG 0.373720 4.4:+12019915 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.4:+12020023 None:intergenic
CTCCAAAGAGACGTTGTTTG+AGG 0.374170 4.4:-12019143 MS.gene27954:CDS
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.4:+12019937 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.396727 4.4:-12018988 MS.gene27954:CDS
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.4:-12019974 MS.gene27954:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.4:+12019993 None:intergenic
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.4:+12018988 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.4:-12020030 MS.gene27954:CDS
TCCCTTCTACATAGAAGAAC+CGG 0.461538 4.4:+12018945 None:intergenic
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.4:+12019946 None:intergenic
TCTTCTGAGGATGACTCATC+TGG 0.485391 4.4:+12019045 None:intergenic
GCAGTTCTTCTTAAACCAGC+CGG 0.561335 4.4:-12018964 MS.gene27954:CDS
GAACAATAAGGCCTCTTCTG+AGG 0.569819 4.4:+12019032 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.4:-12020029 MS.gene27954:CDS
AGATGAGTCATCCTCAGAAG+AGG 0.600054 4.4:-12019043 MS.gene27954:CDS
AAAGAACTTGTTACTAACAG+TGG 0.608058 4.4:-12019912 MS.gene27954:CDS
TTCTACATAGAAGAACCGGC+TGG 0.612139 4.4:+12018949 None:intergenic
CAATCAGAAGATGACACCGA+TGG 0.614691 4.4:-12019115 MS.gene27954:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.4:-12019973 MS.gene27954:CDS
GTTTAAGAAGAACTGCTCCA+AGG 0.642127 4.4:+12018971 None:intergenic
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.4:-12020037 MS.gene27954:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.4:-12019972 MS.gene27954:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAAAATTAACTTTAAAATA+AGG - chr4.4:12019641-12019660 MS.gene27954:intron 10.0%
!!! TTATTAACAGTTTAAAATAA+GGG + chr4.4:12019776-12019795 None:intergenic 10.0%
!!! TTTATTAACAGTTTAAAATA+AGG + chr4.4:12019777-12019796 None:intergenic 10.0%
!! TATAAATGAGTTTACTTTAA+AGG + chr4.4:12019390-12019409 None:intergenic 15.0%
!!! ATGAATTTTCATATTTTTGA+CGG - chr4.4:12019509-12019528 MS.gene27954:intron 15.0%
!!! GAAAAGTTGATATATTTATA+GGG - chr4.4:12019733-12019752 MS.gene27954:intron 15.0%
!!! TAGTGATTGAAAATTTTATA+GGG - chr4.4:12019672-12019691 MS.gene27954:intron 15.0%
!! TTTATACCTTCAAATGAAAT+TGG - chr4.4:12020001-12020020 MS.gene27954:CDS 20.0%
!!! AAAAATTTCATCTTCACTTT+TGG - chr4.4:12019359-12019378 MS.gene27954:intron 20.0%
!!! AAATTTTCAATCACTACTTT+TGG + chr4.4:12019668-12019687 None:intergenic 20.0%
!!! ATAAGGGTTAAATATGTTTT+TGG + chr4.4:12019760-12019779 None:intergenic 20.0%
!!! ATACTACTTTAATTTTGTGA+GGG - chr4.4:12019224-12019243 MS.gene27954:intron 20.0%
!!! CGAAAAGTTGATATATTTAT+AGG - chr4.4:12019732-12019751 MS.gene27954:intron 20.0%
!!! GTAGTGATTGAAAATTTTAT+AGG - chr4.4:12019671-12019690 MS.gene27954:intron 20.0%
!!! TATACTACTTTAATTTTGTG+AGG - chr4.4:12019223-12019242 MS.gene27954:intron 20.0%
!!! TGAAGATGAAATTTTTTTGA+TGG + chr4.4:12019355-12019374 None:intergenic 20.0%
!!! TGCGTGAATATTTATTTTAA+GGG - chr4.4:12019253-12019272 MS.gene27954:intron 20.0%
!!! TTTAAGGGTTAAATATGTTT+TGG - chr4.4:12019268-12019287 MS.gene27954:intron 20.0%
! ATCTGAATCAAAAACATCAA+TGG + chr4.4:12019147-12019166 None:intergenic 25.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.4:12019197-12019216 None:intergenic 25.0%
!! AAATGAGTTTACTTTAAAGG+AGG + chr4.4:12019387-12019406 None:intergenic 25.0%
!! AATGAGTTTACTTTAAAGGA+GGG + chr4.4:12019386-12019405 None:intergenic 25.0%
!! GTTCACATTTTTGAACAATA+AGG + chr4.4:12019978-12019997 None:intergenic 25.0%
!!! AAGTTGAAGAAATTTTTTCG+AGG + chr4.4:12019327-12019346 None:intergenic 25.0%
!!! AGTTGAAGAAATTTTTTCGA+GGG + chr4.4:12019326-12019345 None:intergenic 25.0%
!!! GATGTTTTTGATTCAGATAA+TGG - chr4.4:12019149-12019168 MS.gene27954:CDS 25.0%
!!! GTGCGTGAATATTTATTTTA+AGG - chr4.4:12019252-12019271 MS.gene27954:intron 25.0%
TATAGGGACTAAAAGTTGAA+GGG - chr4.4:12019688-12019707 MS.gene27954:intron 30.0%
TTATAGGGACTAAAAGTTGA+AGG - chr4.4:12019687-12019706 MS.gene27954:intron 30.0%
! CTGTTAGTAACAAGTTCTTT+TGG + chr4.4:12019083-12019102 None:intergenic 30.0%
! TCTTGTTGAAACTTTTCCAT+CGG + chr4.4:12019899-12019918 None:intergenic 30.0%
!! AAAGAACTTGTTACTAACAG+TGG - chr4.4:12019083-12019102 MS.gene27954:CDS 30.0%
!! AGTTGAAGGGAAATTTTTAG+AGG - chr4.4:12019701-12019720 MS.gene27954:intron 30.0%
!! GTTGAAGGGAAATTTTTAGA+GGG - chr4.4:12019702-12019721 MS.gene27954:intron 30.0%
!! TACTTTAATTTTGTGAGGGT+GGG - chr4.4:12019228-12019247 MS.gene27954:intron 30.0%
AGAAAAGAGTGAAAATGGCT+AGG + chr4.4:12019192-12019211 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.4:12019061-12019080 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.4:12019022-12019041 MS.gene27954:CDS 35.0%
!! CTACTTTAATTTTGTGAGGG+TGG - chr4.4:12019227-12019246 MS.gene27954:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.4:12018993-12019012 None:intergenic 35.0%
ATCCTCAAACAACGTCTCTT+TGG + chr4.4:12019857-12019876 None:intergenic 40.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.4:12020010-12020029 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.4:12019005-12019024 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.4:12019023-12019042 MS.gene27954:CDS 40.0%
GTTTAAGAAGAACTGCTCCA+AGG + chr4.4:12020027-12020046 None:intergenic 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.4:12019052-12019071 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.4:12020007-12020026 MS.gene27954:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.4:12019021-12019040 MS.gene27954:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.4:12019002-12019021 MS.gene27954:CDS 40.0%
AGATGAGTCATCCTCAGAAG+AGG - chr4.4:12019952-12019971 MS.gene27954:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.4:12019880-12019899 MS.gene27954:CDS 45.0%
CTCCAAAGAGACGTTGTTTG+AGG - chr4.4:12019852-12019871 MS.gene27954:CDS 45.0%
GAACAATAAGGCCTCTTCTG+AGG + chr4.4:12019966-12019985 None:intergenic 45.0%
GCAGTTCTTCTTAAACCAGC+CGG - chr4.4:12020031-12020050 MS.gene27954:CDS 45.0%
! TCTTCTGAGGATGACTCATC+TGG + chr4.4:12019953-12019972 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.4:12019037-12019056 None:intergenic 45.0%
!!! AAAAAAATTCTAATTTTTTT+TGG - chr4.4:12019563-12019582 MS.gene27954:intron 5.0%
!!! AAAAAATTCTAATTTTTTTT+GGG - chr4.4:12019564-12019583 MS.gene27954:intron 5.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.4:12018958-12018977 MS.gene27954:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.4:12018986-12019005 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.4:12018965-12018984 MS.gene27954:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.4:12018966-12018985 MS.gene27954:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.4:12018966-12018985 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.4:12018975-12018994 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 12018951 12020066 12018951 ID=MS.gene27954
chr4.4 mRNA 12018951 12020066 12018951 ID=MS.gene27954.t1;Parent=MS.gene27954
chr4.4 exon 12019847 12020066 12019847 ID=MS.gene27954.t1.exon1;Parent=MS.gene27954.t1
chr4.4 CDS 12019847 12020066 12019847 ID=cds.MS.gene27954.t1;Parent=MS.gene27954.t1
chr4.4 exon 12018951 12019201 12018951 ID=MS.gene27954.t1.exon2;Parent=MS.gene27954.t1
chr4.4 CDS 12018951 12019201 12018951 ID=cds.MS.gene27954.t1;Parent=MS.gene27954.t1
Gene Sequence

>MS.gene27954

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACTAACAGTGGCAACAGTAGCAACAAGAGTCTCAACGAAAGTTCATCAACCATTGATGTTTTTGATTCAGATAATGGTATGTGCTCATACTAGTCCTAGCCATTTTCACTCTTTTCTTTACAATGCTATATACTACTTTAATTTTGTGAGGGTGGGTGTGCGTGAATATTTATTTTAAGGGTTAAATATGTTTTGGTCTCTATAAATATGTCAACTTTTCGTTTTAGTCCCTCGAAAAAATTTCTTCAACTTTTAGTCCATCAAAAAAATTTCATCTTCACTTTTGGTCCCTCCTTTAAAGTAAACTCATTTATAAAACTCATATTTTTGAATAAAATTTTGCAGAAAAATTCATAATATTATAAGAATTTCTTCAAAAAAAATTAGAATTTTTTAACAAAACATGAATTTAATATGAATTTTCATATTTTTGACGGTTAAAAATTCATATTTAATCTGTGTTTTGCTAAAAAAATTCTAATTTTTTTTGGGATTTTTTTACAATATTCTACACAATTCTGCACAATTTCATTATAAAAAAAAATACAAAAATTAACTTTAAAATAAGGACCAAAAGTAGTGATTGAAAATTTTATAGGGACTAAAAGTTGAAGGGAAATTTTTAGAGGGACTAAAACGAAAAGTTGATATATTTATAGGGACCAAAAACATATTTAACCCTTATTTTAAACTGTTAATAAATTAGAGAATTTTTACTTAGATGAAAAAGATTCAGATTCTTGCAAGTCTGCAGTCTCTCCAAAGAGACGTTGTTTGAGGATTATCAATCAGAAGATGACACCGATGGAAAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCCTCAGAAGAGGCCTTATTGTTCAAAAATGTGAACAACTTTATACCTTCAAATGAAATTGGCCTTGGAGCAGTTCTTCTTAAACCAGCCGGTTCTTCTATGTAG
Protein sequence

>MS.gene27954.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNKSLNESSSTIDVFDSDNDEKDSDSCKSAVSPKRRCLRIINQKMTPMEKFQQELLDELKNHEIPDESSSEEALLFKNVNNFIPSNEIGLGAVLLKPAGSSM