AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071844

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071844.t1 MTR_2g035190 95.541 157 7 0 1 157 1 157 3.48e-106 300
MS.gene071844.t1 MTR_2g035320 94.268 157 9 0 1 157 1 157 6.44e-106 299
MS.gene071844.t1 MTR_2g035210 89.809 157 16 0 1 157 1 157 1.82e-100 285
MS.gene071844.t1 MTR_2g035220 88.535 157 18 0 1 157 1 157 8.20e-98 278
MS.gene071844.t1 MTR_6g033450 66.879 157 52 0 1 157 1 157 5.58e-70 208
MS.gene071844.t1 MTR_4g120970 66.879 157 52 0 1 157 1 157 5.58e-70 208
MS.gene071844.t1 MTR_2g035100 62.420 157 59 0 1 157 1 157 6.74e-67 201
MS.gene071844.t1 MTR_2g035105 61.783 157 60 0 1 157 1 157 5.57e-66 198
MS.gene071844.t1 MTR_2g035150 62.420 157 59 0 1 157 1 157 8.08e-66 198
MS.gene071844.t1 MTR_2g035130 60.510 157 62 0 1 157 1 157 1.25e-64 195
MS.gene071844.t1 MTR_2g035120 57.962 157 66 0 1 157 1 157 2.20e-61 186
MS.gene071844.t1 MTR_2g035320 88.000 100 12 0 58 157 23 122 2.80e-60 182
MS.gene071844.t1 MTR_2g035170 47.771 157 82 0 1 157 1 157 1.18e-48 154
MS.gene071844.t1 MTR_4g120950 41.615 161 87 5 1 157 1 158 1.82e-31 110
MS.gene071844.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 2.58e-29 105
MS.gene071844.t1 MTR_4g120760 33.121 157 104 1 1 156 1 157 2.58e-29 105
MS.gene071844.t1 MTR_2g435310 31.410 156 106 1 1 155 1 156 2.60e-29 105
MS.gene071844.t1 MTR_4g120940 63.014 73 27 0 85 157 47 119 1.41e-23 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTTAATTTGCTAGTAATT+AGG 0.154148 2.2:+53687876 None:intergenic
GTTTAATTTGCTAGTAATTA+GGG 0.258519 2.2:+53687877 None:intergenic
GGATAGCTTCTTAATAGTTC+CGG 0.311830 2.2:+53688765 None:intergenic
TACAGCTTAGTGGGAGGAAC+AGG 0.324066 2.2:-53688092 MS.gene071844:CDS
CTTGATAAGTCCAGTTCCTT+TGG 0.329858 2.2:+53687926 None:intergenic
TTCAACAATTTCAACACTTT+GGG 0.350751 2.2:+53688801 None:intergenic
CTTCAACAATTTCAACACTT+TGG 0.364915 2.2:+53688800 None:intergenic
TGGGCAGCAGAAATCACCTT+TGG 0.387864 2.2:+53688820 None:intergenic
AGATAGAGTTGCATCACCTT+TGG 0.394288 2.2:+53687974 None:intergenic
GATAGCTTCTTAATAGTTCC+GGG 0.397748 2.2:+53688766 None:intergenic
GTTGAAATTGTTGAAGGAAA+TGG 0.402462 2.2:-53688793 MS.gene071844:CDS
GAGACTAAGGCCAAAGGAAC+TGG 0.415366 2.2:-53687936 MS.gene071844:CDS
AGAGCCTTGTAGAGTTTAGC+TGG 0.426244 2.2:+53688868 None:intergenic
GGGCAGCAGAAATCACCTTT+GGG 0.449440 2.2:+53688821 None:intergenic
TGGATATAACTACAGCTTAG+TGG 0.476164 2.2:-53688102 MS.gene071844:CDS
AAAATTGTTGCTGGCTCTGA+TGG 0.476544 2.2:-53688032 MS.gene071844:CDS
GCAGTGGATGAGGCAAACTT+TGG 0.494243 2.2:-53688122 MS.gene071844:CDS
CAAATTAGATGCAGTGGATG+AGG 0.499478 2.2:-53688132 MS.gene071844:CDS
TAATTTGTGTAGCACAAAGT+TGG 0.501990 2.2:+53688148 None:intergenic
CAAAGTGTTGAAATTGTTGA+AGG 0.502542 2.2:-53688799 MS.gene071844:CDS
GGATATAACTACAGCTTAGT+GGG 0.506709 2.2:-53688101 MS.gene071844:CDS
ATCTGAATTACCTTCAACAA+TGG 0.509250 2.2:+53688744 None:intergenic
GGACTTATCAAGGCCATTGA+GGG 0.514208 2.2:-53687915 MS.gene071844:CDS
CAAAGGAACTGGACTTATCA+AGG 0.516806 2.2:-53687925 MS.gene071844:CDS
AAGAAGCTATCCATTGTTGA+AGG 0.523757 2.2:-53688754 MS.gene071844:intron
AGCAGTACGTGAGGAGACTA+AGG 0.536209 2.2:-53687949 MS.gene071844:CDS
GAGTTGCATCACCTTTGGTA+TGG 0.537356 2.2:+53687979 None:intergenic
TGCCACGACGTAGCCCTCAA+TGG 0.549026 2.2:+53687902 None:intergenic
GGCTCCAGCTAAACTCTACA+AGG 0.556705 2.2:-53688872 MS.gene071844:CDS
ATTGTTGCTGGCTCTGATGG+TGG 0.570543 2.2:-53688029 MS.gene071844:CDS
TGGACTTATCAAGGCCATTG+AGG 0.572485 2.2:-53687916 MS.gene071844:CDS
GTTGAAGGAAATGGAGGACC+CGG 0.599694 2.2:-53688784 MS.gene071844:CDS
GTAGAGTTTAGCTGGAGCCA+CGG 0.602676 2.2:+53688876 None:intergenic
TGCTGATGAAATCGTCCCAA+AGG 0.606260 2.2:-53688836 MS.gene071844:CDS
CTTAGTGGGAGGAACAGGGT+TGG 0.609437 2.2:-53688087 MS.gene071844:CDS
GAAATTGTTGAAGGAAATGG+AGG 0.626795 2.2:-53688790 MS.gene071844:CDS
GCTACACAAATTAGATGCAG+TGG 0.633814 2.2:-53688138 MS.gene071844:CDS
TTTCACTGAAATCTTAACAA+CGG 0.637000 2.2:+53688004 None:intergenic
GGCCATTGAGGGCTACGTCG+TGG 0.646344 2.2:-53687904 MS.gene071844:CDS
TCAGTGAAATACCATACCAA+AGG 0.652605 2.2:-53687990 MS.gene071844:CDS
CGTGAGGAGACTAAGGCCAA+AGG 0.670663 2.2:-53687942 MS.gene071844:CDS
TCTATCTGAAGCAGTACGTG+AGG 0.676642 2.2:-53687958 MS.gene071844:CDS
ACAGCTTAGTGGGAGGAACA+GGG 0.680453 2.2:-53688091 MS.gene071844:CDS
TATAACTACAGCTTAGTGGG+AGG 0.697586 2.2:-53688098 MS.gene071844:CDS
TGACGAACATGTCTCAACCG+TGG 0.725590 2.2:-53688893 MS.gene071844:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTATATAAATAATTATAA+TGG - chr2.2:53688609-53688628 MS.gene071844:intron 0.0%
!!! AAATAAAAGTATAACATAAA+TGG + chr2.2:53688413-53688432 None:intergenic 10.0%
!!! TTTGTCAATTTTTAAATAAA+AGG + chr2.2:53688200-53688219 None:intergenic 10.0%
!!! TTTTATACCAAAAAAAAAAA+AGG - chr2.2:53688326-53688345 MS.gene071844:intron 10.0%
!!! TAATTTAACTTTCTTTTCTT+TGG + chr2.2:53688305-53688324 None:intergenic 15.0%
!!! TTAACTTCCTTTTTTTTTTT+TGG + chr2.2:53688336-53688355 None:intergenic 15.0%
!! AATAGTAATCCAATTCTATT+TGG - chr2.2:53688375-53688394 MS.gene071844:intron 20.0%
! AATAGAATCTTGAGAAATGA+AGG - chr2.2:53688436-53688455 MS.gene071844:intron 25.0%
! AGGGTTATGTCTAATAATTA+TGG - chr2.2:53688481-53688500 MS.gene071844:intron 25.0%
! ATAATTATTAGACATAACCC+TGG + chr2.2:53688482-53688501 None:intergenic 25.0%
! TATAATGGTTATATTGCAGA+TGG - chr2.2:53688624-53688643 MS.gene071844:intron 25.0%
! TTCAACAATTTCAACACTTT+GGG + chr2.2:53688002-53688021 None:intergenic 25.0%
! TTCAGATGATTATTGATACT+CGG - chr2.2:53688520-53688539 MS.gene071844:intron 25.0%
! TTTCACTGAAATCTTAACAA+CGG + chr2.2:53688799-53688818 None:intergenic 25.0%
!!! CATCTGAATCATTTTTTTGA+AGG + chr2.2:53688508-53688527 None:intergenic 25.0%
ATCTGAATTACCTTCAACAA+TGG + chr2.2:53688059-53688078 None:intergenic 30.0%
CATGACTATCCAAATAGAAT+TGG + chr2.2:53688387-53688406 None:intergenic 30.0%
CTTCAACAATTTCAACACTT+TGG + chr2.2:53688003-53688022 None:intergenic 30.0%
GTTGAAATTGTTGAAGGAAA+TGG - chr2.2:53688007-53688026 MS.gene071844:CDS 30.0%
! TAATTTGTGTAGCACAAAGT+TGG + chr2.2:53688655-53688674 None:intergenic 30.0%
! TTTGAGACAAAAATTGTTGC+TGG - chr2.2:53688759-53688778 MS.gene071844:CDS 30.0%
!! CAAAGTGTTGAAATTGTTGA+AGG - chr2.2:53688001-53688020 MS.gene071844:CDS 30.0%
AAGAAGCTATCCATTGTTGA+AGG - chr2.2:53688046-53688065 MS.gene071844:CDS 35.0%
ATAATACATAAGCTCGTTCC+AGG - chr2.2:53688461-53688480 MS.gene071844:intron 35.0%
GAAATTGTTGAAGGAAATGG+AGG - chr2.2:53688010-53688029 MS.gene071844:CDS 35.0%
GACAAACATGATGTGACAAA+TGG - chr2.2:53688214-53688233 MS.gene071844:intron 35.0%
GATAGCTTCTTAATAGTTCC+GGG + chr2.2:53688037-53688056 None:intergenic 35.0%
GGATAGCTTCTTAATAGTTC+CGG + chr2.2:53688038-53688057 None:intergenic 35.0%
GGATATAACTACAGCTTAGT+GGG - chr2.2:53688699-53688718 MS.gene071844:intron 35.0%
TAATACATAAGCTCGTTCCA+GGG - chr2.2:53688462-53688481 MS.gene071844:intron 35.0%
TCAGTGAAATACCATACCAA+AGG - chr2.2:53688810-53688829 MS.gene071844:CDS 35.0%
TGGATATAACTACAGCTTAG+TGG - chr2.2:53688698-53688717 MS.gene071844:intron 35.0%
! GTTGTACCGACAAATTTGAT+CGG + chr2.2:53688160-53688179 None:intergenic 35.0%
!! CGGTCTAAAACAATTTTACG+CGG + chr2.2:53688133-53688152 None:intergenic 35.0%
AGATAGAGTTGCATCACCTT+TGG + chr2.2:53688829-53688848 None:intergenic 40.0%
CAAAGGAACTGGACTTATCA+AGG - chr2.2:53688875-53688894 MS.gene071844:CDS 40.0%
CAAATTAGATGCAGTGGATG+AGG - chr2.2:53688668-53688687 MS.gene071844:intron 40.0%
CGACAAATTTGATCGGTTGT+CGG + chr2.2:53688153-53688172 None:intergenic 40.0%
CGACAACCGATCAAATTTGT+CGG - chr2.2:53688151-53688170 MS.gene071844:CDS 40.0%
CTTGATAAGTCCAGTTCCTT+TGG + chr2.2:53688877-53688896 None:intergenic 40.0%
GCTACACAAATTAGATGCAG+TGG - chr2.2:53688662-53688681 MS.gene071844:intron 40.0%
TATAACTACAGCTTAGTGGG+AGG - chr2.2:53688702-53688721 MS.gene071844:intron 40.0%
!! AAAATTGTTGCTGGCTCTGA+TGG - chr2.2:53688768-53688787 MS.gene071844:CDS 40.0%
GAGTTGCATCACCTTTGGTA+TGG + chr2.2:53688824-53688843 None:intergenic 45.0%
GGACTTATCAAGGCCATTGA+GGG - chr2.2:53688885-53688904 MS.gene071844:CDS 45.0%
TGCTGATGAAATCGTCCCAA+AGG - chr2.2:53687964-53687983 MS.gene071844:CDS 45.0%
TGGACTTATCAAGGCCATTG+AGG - chr2.2:53688884-53688903 MS.gene071844:CDS 45.0%
! AGAGCCTTGTAGAGTTTAGC+TGG + chr2.2:53687935-53687954 None:intergenic 45.0%
! TCTATCTGAAGCAGTACGTG+AGG - chr2.2:53688842-53688861 MS.gene071844:CDS 45.0%
ACAGCTTAGTGGGAGGAACA+GGG - chr2.2:53688709-53688728 MS.gene071844:intron 50.0%
AGCAGTACGTGAGGAGACTA+AGG - chr2.2:53688851-53688870 MS.gene071844:CDS 50.0%
GAGACTAAGGCCAAAGGAAC+TGG - chr2.2:53688864-53688883 MS.gene071844:CDS 50.0%
GCAGTGGATGAGGCAAACTT+TGG - chr2.2:53688678-53688697 MS.gene071844:intron 50.0%
GGCTCCAGCTAAACTCTACA+AGG - chr2.2:53687928-53687947 MS.gene071844:CDS 50.0%
GGGCAGCAGAAATCACCTTT+GGG + chr2.2:53687982-53688001 None:intergenic 50.0%
GTAGAGTTTAGCTGGAGCCA+CGG + chr2.2:53687927-53687946 None:intergenic 50.0%
GTTGAAGGAAATGGAGGACC+CGG - chr2.2:53688016-53688035 MS.gene071844:CDS 50.0%
TACAGCTTAGTGGGAGGAAC+AGG - chr2.2:53688708-53688727 MS.gene071844:intron 50.0%
TGACGAACATGTCTCAACCG+TGG - chr2.2:53687907-53687926 MS.gene071844:CDS 50.0%
TGGGCAGCAGAAATCACCTT+TGG + chr2.2:53687983-53688002 None:intergenic 50.0%
!! ATTGTTGCTGGCTCTGATGG+TGG - chr2.2:53688771-53688790 MS.gene071844:CDS 50.0%
CGTGAGGAGACTAAGGCCAA+AGG - chr2.2:53688858-53688877 MS.gene071844:CDS 55.0%
CTTAGTGGGAGGAACAGGGT+TGG - chr2.2:53688713-53688732 MS.gene071844:intron 55.0%
TGCCACGACGTAGCCCTCAA+TGG + chr2.2:53688901-53688920 None:intergenic 60.0%
GGCCATTGAGGGCTACGTCG+TGG - chr2.2:53688896-53688915 MS.gene071844:CDS 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53687887 53688935 53687887 ID=MS.gene071844
chr2.2 mRNA 53687887 53688935 53687887 ID=MS.gene071844.t1;Parent=MS.gene071844
chr2.2 exon 53688755 53688935 53688755 ID=MS.gene071844.t1.exon1;Parent=MS.gene071844.t1
chr2.2 CDS 53688755 53688935 53688755 ID=cds.MS.gene071844.t1;Parent=MS.gene071844.t1
chr2.2 exon 53687887 53688179 53687887 ID=MS.gene071844.t1.exon2;Parent=MS.gene071844.t1
chr2.2 CDS 53687887 53688179 53687887 ID=cds.MS.gene071844.t1;Parent=MS.gene071844.t1
Gene Sequence

>MS.gene071844

ATGGGTGTTTTTACTTTCAATGACGAACATGTCTCAACCGTGGCTCCAGCTAAACTCTACAAGGCTCTTGCAAAAGATGCTGATGAAATCGTCCCAAAGGTGATTTCTGCTGCCCAAAGTGTTGAAATTGTTGAAGGAAATGGAGGACCCGGAACTATTAAGAAGCTATCCATTGTTGAAGGTAATTCAGATCATATACTATGTAGAAATATATAATACTTGAGATCAAATGATACATAGTGTCCGCGTAAAATTGTTTTAGACCGACAACCGATCAAATTTGTCGGTACAACAAAGAATAGTGTAACTACCTTTTATTTAAAAATTGACAAACATGATGTGACAAATGGAAGAGTTGCAATTGATTAATAATTTGATTAAATGATTCACAAATATGTAAGTTAAATTCATTATACCAAAGAAAAGAAAGTTAAATTAATTTTATACCAAAAAAAAAAAAGGAAGTTAAATACAACTGTAGCAAAAAAAATAGTAATCCAATTCTATTTGGATAGTCATGAAGCCATTTATGTTATACTTTTATTTTAAAATAGAATCTTGAGAAATGAAGGAGATAATACATAAGCTCGTTCCAGGGTTATGTCTAATAATTATGGACCTTCAAAAAAATGATTCAGATGATTATTGATACTCGGTAAAGTTCAAATCGATCTTTAACATAAAGAGTTTTTAGTCAAACTTTACTTATATTGAAAAAAAAATATTATATAAATAATTATAATGGTTATATTGCAGATGGCAAAACCAACTTTGTGCTACACAAATTAGATGCAGTGGATGAGGCAAACTTTGGATATAACTACAGCTTAGTGGGAGGAACAGGGTTGGATGAAAATTTAGAGAAAGTTGAATTTGAGACAAAAATTGTTGCTGGCTCTGATGGTGGATCCGTTGTTAAGATTTCAGTGAAATACCATACCAAAGGTGATGCAACTCTATCTGAAGCAGTACGTGAGGAGACTAAGGCCAAAGGAACTGGACTTATCAAGGCCATTGAGGGCTACGTCGTGGCAAACCCTAATTACTAG
Protein sequence

>MS.gene071844.t1

MGVFTFNDEHVSTVAPAKLYKALAKDADEIVPKVISAAQSVEIVEGNGGPGTIKKLSIVEDGKTNFVLHKLDAVDEANFGYNYSLVGGTGLDENLEKVEFETKIVAGSDGGSVVKISVKYHTKGDATLSEAVREETKAKGTGLIKAIEGYVVANPNY