AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67211

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67211.t1 MTR_8g089170 88.462 156 18 0 1 156 1 156 3.79e-95 272
MS.gene67211.t1 MTR_8g089130 81.646 158 27 2 1 156 1 158 1.71e-87 253
MS.gene67211.t1 MTR_8g089145 86.301 73 10 0 1 73 1 73 1.78e-41 133
MS.gene67211.t1 MTR_1g089830 39.456 147 60 5 4 150 3 120 1.51e-21 85.1
MS.gene67211.t1 MTR_4g028990 53.425 73 32 1 81 151 20 92 1.02e-17 73.9
MS.gene67211.t1 MTR_1g045040 38.621 145 63 5 7 150 6 125 1.56e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATACCTTCAAATGAAAT+TGG 0.206576 4.2:-12353962 MS.gene67211:CDS
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.2:+12354976 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.2:+12354932 None:intergenic
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.2:+12355003 None:intergenic
ATCCTCAAACAACGTCTCTT+TGG 0.317203 4.2:+12354109 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.2:-12354817 MS.gene67211:intron
CTGTTAGTAACAAGTTCTTT+TGG 0.373720 4.2:+12354886 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.2:+12354994 None:intergenic
CTCCAAAGAGACGTTGTTTG+AGG 0.374170 4.2:-12354111 MS.gene67211:CDS
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.2:+12354908 None:intergenic
CCTTCAAATGAAATTGGCCT+TGG 0.396727 4.2:-12353956 MS.gene67211:CDS
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.2:-12354945 MS.gene67211:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.2:+12354964 None:intergenic
CCAAGGCCAATTTCATTTGA+AGG 0.421742 4.2:+12353956 None:intergenic
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.2:-12355001 MS.gene67211:CDS
TCCCTTCTACATAGAAGAAC+CGG 0.461538 4.2:+12353913 None:intergenic
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.2:+12354917 None:intergenic
TCTTCTGAGGATGACTCATC+TGG 0.485391 4.2:+12354013 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.2:+12354822 None:intergenic
GCAGTTCTTCTTAAACCAGC+CGG 0.561335 4.2:-12353932 MS.gene67211:CDS
GAACAATAAGGCCTCTTCTG+AGG 0.569819 4.2:+12354000 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.2:-12355000 MS.gene67211:CDS
AGATGAGTCATCCTCAGAAG+AGG 0.600054 4.2:-12354011 MS.gene67211:CDS
AAAGAACTTGTTACTAACAG+TGG 0.608058 4.2:-12354883 MS.gene67211:CDS
TTCTACATAGAAGAACCGGC+TGG 0.612139 4.2:+12353917 None:intergenic
CAATCAGAAGATGACACCGA+TGG 0.614691 4.2:-12354083 MS.gene67211:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.2:-12354944 MS.gene67211:CDS
GTTTAAGAAGAACTGCTCCA+AGG 0.642127 4.2:+12353939 None:intergenic
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.2:-12355008 MS.gene67211:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.2:-12354943 MS.gene67211:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAAAATTCTAATTTTTCT+TGG - chr4.2:12354534-12354553 MS.gene67211:intron 10.0%
!!! AAAAAATTCTAATTTTTCTT+GGG - chr4.2:12354535-12354554 MS.gene67211:intron 10.0%
!!! CAAAAATTAACTTTAAAATA+AGG - chr4.2:12354613-12354632 MS.gene67211:intron 10.0%
!!! TTATTAACAGTTTAAAATAA+GGG + chr4.2:12354747-12354766 None:intergenic 10.0%
!!! TTTATTAACAGTTTAAAATA+AGG + chr4.2:12354748-12354767 None:intergenic 10.0%
!! TATAAATGAGTTTACTTTAA+AGG + chr4.2:12354360-12354379 None:intergenic 15.0%
!!! ATGAATTTTCATATTTTTGA+CGG - chr4.2:12354480-12354499 MS.gene67211:intron 15.0%
!!! GAAAAGTTGATATATTTATA+GGG - chr4.2:12354704-12354723 MS.gene67211:intron 15.0%
!!! TAGTGATTGAAAATTTTATA+GGG - chr4.2:12354644-12354663 MS.gene67211:intron 15.0%
!! TTTATACCTTCAAATGAAAT+TGG - chr4.2:12354972-12354991 MS.gene67211:CDS 20.0%
!!! AAAATTTTCATCTTCACTTT+TGG - chr4.2:12354329-12354348 MS.gene67211:intron 20.0%
!!! AAATTTTCAATCACTACTTT+TGG + chr4.2:12354640-12354659 None:intergenic 20.0%
!!! ATAAGGGTTAAATATGTTTT+TGG + chr4.2:12354731-12354750 None:intergenic 20.0%
!!! ATACTACTTTAATTTTGTGA+GGG - chr4.2:12354192-12354211 MS.gene67211:intron 20.0%
!!! CGAAAAGTTGATATATTTAT+AGG - chr4.2:12354703-12354722 MS.gene67211:intron 20.0%
!!! GTAGTGATTGAAAATTTTAT+AGG - chr4.2:12354643-12354662 MS.gene67211:intron 20.0%
!!! TAAGGGTTAAAATATGTTTT+TGG - chr4.2:12354238-12354257 MS.gene67211:intron 20.0%
!!! TATACTACTTTAATTTTGTG+AGG - chr4.2:12354191-12354210 MS.gene67211:intron 20.0%
!!! TGAAGATGAAAATTTTTTGA+TGG + chr4.2:12354325-12354344 None:intergenic 20.0%
!!! TGCGTGAATATTTATTTTAA+GGG - chr4.2:12354221-12354240 MS.gene67211:intron 20.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.2:12354165-12354184 None:intergenic 25.0%
!! AAATGAGTTTACTTTAAAGG+AGG + chr4.2:12354357-12354376 None:intergenic 25.0%
!! AAGTTGAAGGAAAATTTTAG+AGG - chr4.2:12354672-12354691 MS.gene67211:intron 25.0%
!! AATGAGTTTACTTTAAAGGA+GGG + chr4.2:12354356-12354375 None:intergenic 25.0%
!! AGTTGAAGGAAAATTTTAGA+GGG - chr4.2:12354673-12354692 MS.gene67211:intron 25.0%
!! GTTCACATTTTTGAACAATA+AGG + chr4.2:12354949-12354968 None:intergenic 25.0%
!!! AAGTTGAAGAAATTTTTTCG+AGG + chr4.2:12354297-12354316 None:intergenic 25.0%
!!! AGTTGAAGAAATTTTTTCGA+GGG + chr4.2:12354296-12354315 None:intergenic 25.0%
!!! GTGCGTGAATATTTATTTTA+AGG - chr4.2:12354220-12354239 MS.gene67211:intron 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.2:12354115-12354134 None:intergenic 30.0%
TTATAGGGACTAAAAGTTGA+AGG - chr4.2:12354659-12354678 MS.gene67211:intron 30.0%
! CTGTTAGTAACAAGTTCTTT+TGG + chr4.2:12354051-12354070 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.2:12354117-12354136 MS.gene67211:CDS 30.0%
! TCTTGTTGAAACTTTTCCAT+CGG + chr4.2:12354870-12354889 None:intergenic 30.0%
!! AAAGAACTTGTTACTAACAG+TGG - chr4.2:12354051-12354070 MS.gene67211:CDS 30.0%
!! TACTTTAATTTTGTGAGGGT+GGG - chr4.2:12354196-12354215 MS.gene67211:intron 30.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.2:12354029-12354048 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.2:12353990-12354009 MS.gene67211:CDS 35.0%
!! CTACTTTAATTTTGTGAGGG+TGG - chr4.2:12354195-12354214 MS.gene67211:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.2:12353961-12353980 None:intergenic 35.0%
ATCCTCAAACAACGTCTCTT+TGG + chr4.2:12354828-12354847 None:intergenic 40.0%
CCAAGGCCAATTTCATTTGA+AGG + chr4.2:12354981-12355000 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.2:12353973-12353992 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.2:12353991-12354010 MS.gene67211:CDS 40.0%
GTTTAAGAAGAACTGCTCCA+AGG + chr4.2:12354998-12355017 None:intergenic 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.2:12354020-12354039 None:intergenic 40.0%
! CCTTCAAATGAAATTGGCCT+TGG - chr4.2:12354978-12354997 MS.gene67211:CDS 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.2:12353989-12354008 MS.gene67211:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.2:12353970-12353989 MS.gene67211:CDS 40.0%
AGATGAGTCATCCTCAGAAG+AGG - chr4.2:12354923-12354942 MS.gene67211:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.2:12354851-12354870 MS.gene67211:CDS 45.0%
CTCCAAAGAGACGTTGTTTG+AGG - chr4.2:12354823-12354842 MS.gene67211:CDS 45.0%
GAACAATAAGGCCTCTTCTG+AGG + chr4.2:12354937-12354956 None:intergenic 45.0%
GCAGTTCTTCTTAAACCAGC+CGG - chr4.2:12355002-12355021 MS.gene67211:CDS 45.0%
! TCTTCTGAGGATGACTCATC+TGG + chr4.2:12354924-12354943 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.2:12354005-12354024 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.2:12353926-12353945 MS.gene67211:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.2:12353954-12353973 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.2:12353933-12353952 MS.gene67211:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.2:12353934-12353953 MS.gene67211:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.2:12353934-12353953 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.2:12353943-12353962 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 12353919 12355037 12353919 ID=MS.gene67211
chr4.2 mRNA 12353919 12355037 12353919 ID=MS.gene67211.t1;Parent=MS.gene67211
chr4.2 exon 12354818 12355037 12354818 ID=MS.gene67211.t1.exon1;Parent=MS.gene67211.t1
chr4.2 CDS 12354818 12355037 12354818 ID=cds.MS.gene67211.t1;Parent=MS.gene67211.t1
chr4.2 exon 12353919 12354169 12353919 ID=MS.gene67211.t1.exon2;Parent=MS.gene67211.t1
chr4.2 CDS 12353919 12354169 12353919 ID=cds.MS.gene67211.t1;Parent=MS.gene67211.t1
Gene Sequence

>MS.gene67211

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACTAACAGTGGCAACAGTAGCAACAAGAGTCTCAACGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTCATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGCTATATACTACTTTAATTTTGTGAGGGTGGGTGTGCGTGAATATTTATTTTAAGGGTTAAAATATGTTTTTGGTCTCTATAAATATGTCAACTTTTCTTTTTAGTCCCTCGAAAAAATTTCTTCAACTTTTAGTCCATCAAAAAATTTTCATCTTCACTTTTGGTCCCTCCTTTAAAGTAAACTCATTTATAAAACTCATATTTTTGAATAAAATTTTGCAGAAAAATTCATAATATTATAAGAATCTCTTCAAAAAAAAATTAGAATTTTTTAACAAAACATGAATTTAATATGAATTTTCATATTTTTGACGGTTAAAAATTCATATTTAATCTGTGTTTTGCTAAAAAAATTCTAATTTTTCTTGGGATTTTTTTACAATATTCTACACAATTCTGCACAATTTCATTATAAAAAAAAAATACAAAAATTAACTTTAAAATAAGGACCAAAAGTAGTGATTGAAAATTTTATAGGGACTAAAAGTTGAAGGAAAATTTTAGAGGGACTAAAACGAAAAGTTGATATATTTATAGGGACCAAAAACATATTTAACCCTTATTTTAAACTGTTAATAAATTAGAGAATTTTTACTTAGATGAAAAAGATTCAGATTCTTGCAAGTCTGCAGTCTCTCCAAAGAGACGTTGTTTGAGGATTATCAATCAGAAGATGACACCGATGGAAAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCCTCAGAAGAGGCCTTATTGTTCAAAAATGTGAACAACTTTATACCTTCAAATGAAATTGGCCTTGGAGCAGTTCTTCTTAAACCAGCCGGTTCTTCTATGTAG
Protein sequence

>MS.gene67211.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNKSLNESSSTIDVSDSDNDEKDSDSCKSAVSPKRRCLRIINQKMTPMEKFQQELLDELKNHEIPDESSSEEALLFKNVNNFIPSNEIGLGAVLLKPAGSSM