AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99864

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99864.t1 MTR_2g105850 94.309 246 11 2 1 243 1 246 1.21e-165 457
MS.gene99864.t1 MTR_2g105850 74.797 246 10 3 1 243 1 197 1.13e-124 352
MS.gene99864.t1 MTR_4g113520 29.900 301 136 8 13 242 15 311 1.87e-38 136
MS.gene99864.t1 MTR_3g087920 47.222 144 73 1 51 191 31 174 1.93e-36 131
MS.gene99864.t1 MTR_3g087920 42.500 80 38 2 171 242 245 324 5.20e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99864.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene99864.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene99864.t1 AT1G50440 69.444 252 66 3 1 243 1 250 1.57e-128 363
MS.gene99864.t1 AT1G50440 68.919 222 59 2 1 213 1 221 1.07e-112 322
MS.gene99864.t1 AT1G50440 58.294 211 76 3 1 202 1 208 1.85e-84 251
MS.gene99864.t1 AT1G11020 37.319 276 95 7 38 242 52 320 2.74e-46 157
MS.gene99864.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.00e-36 132
MS.gene99864.t1 AT2G22120 46.269 67 31 1 181 242 257 323 9.39e-11 61.2
MS.gene99864.t1 AT2G22120 43.421 152 79 2 24 172 7 154 1.20e-36 132
MS.gene99864.t1 AT2G22120 42.683 82 40 2 168 242 242 323 9.66e-11 61.2

Find 57 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAGTTCTCGCCATTATTT+TGG 0.183622 2.1:+232401 MS.gene99864:intron
TGCACAGGTTGTTGCTTTCT+TGG 0.234683 2.1:+232148 MS.gene99864:intron
TTCACAGAGGTGATTCAATA+TGG 0.242810 2.1:-231686 None:intergenic
ATGATCTGTGGACATACTTT+TGG 0.267771 2.1:-231858 None:intergenic
CTCAACCACCATCGATCTTT+AGG 0.272819 2.1:-231970 None:intergenic
GTGCTTATTTATAAATTCTA+TGG 0.292569 2.1:+232173 MS.gene99864:CDS
TTGTCAGACGTGGCAGAAAT+AGG 0.331431 2.1:-231715 None:intergenic
TTGGGTACCTTTGCAATGGC+AGG 0.331526 2.1:-231839 None:intergenic
GACCTTTGTCAATTCTTGTT+TGG 0.347635 2.1:-232499 None:intergenic
ACAGATCATGTCTCGATAAC+TGG 0.347729 2.1:+231872 MS.gene99864:CDS
GCACAGGTTGTTGCTTTCTT+GGG 0.351526 2.1:+232149 MS.gene99864:intron
CATCGATCTTTAGGGACATT+TGG 0.365167 2.1:-231961 None:intergenic
CCTTAGTTCTGTCACATGGC+TGG 0.365929 2.1:-232856 None:intergenic
TCAACCACCATCGATCTTTA+GGG 0.389036 2.1:-231969 None:intergenic
CTTAGTTCTGTCACATGGCT+GGG 0.400790 2.1:-232855 None:intergenic
TTTCTGAAGAAGAAGAATCT+TGG 0.402422 2.1:-231657 None:intergenic
GAGCAAACCCACCAAAATAA+TGG 0.405865 2.1:-232412 None:intergenic
TTCTTTATAGCAATAATATG+TGG 0.428860 2.1:+232441 MS.gene99864:CDS
TGCCGGATATGCCTTGATCT+TGG 0.432553 2.1:+231796 MS.gene99864:CDS
GATGAACTTAGAGAAATGTT+TGG 0.432617 2.1:+232197 MS.gene99864:CDS
ACATGGCTGGGGTCGAGTTC+AGG 0.434273 2.1:-232843 None:intergenic
GAGGTGATTCAATATGGGTT+GGG 0.457987 2.1:-231680 None:intergenic
CTCCAAGATCAAGGCATATC+CGG 0.463345 2.1:-231798 None:intergenic
GGGTACCTTTGCAATGGCAG+GGG 0.470794 2.1:-231837 None:intergenic
TCACAGAGGTGATTCAATAT+GGG 0.474068 2.1:-231685 None:intergenic
GTGACAGAACTAAGGATGTT+GGG 0.491109 2.1:+232864 MS.gene99864:CDS
TGGGTACCTTTGCAATGGCA+GGG 0.492265 2.1:-231838 None:intergenic
GAAAATGAATGCATGATCTC+TGG 0.494455 2.1:-232016 None:intergenic
CGGATATGCCTTGATCTTGG+AGG 0.499840 2.1:+231799 MS.gene99864:CDS
AGAGGTGATTCAATATGGGT+TGG 0.514100 2.1:-231681 None:intergenic
CAAGGCATATCCGGCATTGT+GGG 0.523063 2.1:-231789 None:intergenic
TGTGACAGAACTAAGGATGT+TGG 0.527888 2.1:+232863 MS.gene99864:CDS
AGTCTTCTCCTCCAAGATCA+AGG 0.530295 2.1:-231807 None:intergenic
TCTTTATAGCAATAATATGT+GGG 0.533500 2.1:+232442 MS.gene99864:CDS
AGAAGAAGAATCTTGGTTGT+CGG 0.545346 2.1:-231650 None:intergenic
TTAGTTCTGTCACATGGCTG+GGG 0.552531 2.1:-232854 None:intergenic
ATGCTGATCACCCACAATGC+CGG 0.553024 2.1:+231779 MS.gene99864:CDS
GTTTGGCAAGAACATGGTAG+TGG 0.554746 2.1:-232482 None:intergenic
CCAGCCATGTGACAGAACTA+AGG 0.558116 2.1:+232856 MS.gene99864:CDS
TCAAGGCATATCCGGCATTG+TGG 0.559551 2.1:-231790 None:intergenic
GCCATTGTGTAAAATCCGTA+TGG 0.559880 2.1:-232233 None:intergenic
ATACATATACCAGCTAGTAA+AGG 0.563392 2.1:-232887 None:intergenic
GGTACCTTTGCAATGGCAGG+GGG 0.567201 2.1:-231836 None:intergenic
AACTGGAGGTCTACCAAGGA+GGG 0.573090 2.1:+231889 MS.gene99864:CDS
AGAAGATCGAGAACATGTAA+AGG 0.577463 2.1:+232815 MS.gene99864:CDS
GGTTATGAAGAACATCCATA+CGG 0.581353 2.1:+232218 MS.gene99864:CDS
ATTCTTGTTTGGCAAGAACA+TGG 0.604029 2.1:-232488 None:intergenic
CAAATGTCCCTAAAGATCGA+TGG 0.630129 2.1:+231962 MS.gene99864:CDS
ACATCCTTAGTTCTGTCACA+TGG 0.650556 2.1:-232860 None:intergenic
CGATAACTGGAGGTCTACCA+AGG 0.652909 2.1:+231885 MS.gene99864:CDS
TGCCAAACAAGAATTGACAA+AGG 0.654420 2.1:+232497 MS.gene99864:CDS
AGTTATCGAGACATGATCTG+TGG 0.663655 2.1:-231870 None:intergenic
TAACTGGAGGTCTACCAAGG+AGG 0.663726 2.1:+231888 MS.gene99864:CDS
ATGTCCCTAAAGATCGATGG+TGG 0.685209 2.1:+231965 MS.gene99864:CDS
GATCATGTCTCGATAACTGG+AGG 0.685887 2.1:+231875 MS.gene99864:CDS
TATATCATGATTGTCAGACG+TGG 0.692189 2.1:-231725 None:intergenic
AAATAGGAATAATTTCACAG+AGG 0.778628 2.1:-231699 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACCTTAAATTTTTATAAAAA+AGG - chr2.1:232744-232763 None:intergenic 10.0%
!!! TCCTTTTTTATAAAAATTTA+AGG + chr2.1:232740-232759 MS.gene99864:intron 10.0%
!! ACATAAAATTATATTCGTAG+AGG - chr2.1:232075-232094 None:intergenic 20.0%
!! GTGCTTATTTATAAATTCTA+TGG + chr2.1:232173-232192 MS.gene99864:CDS 20.0%
!! TAAACAATACAATACAAGAA+CGG - chr2.1:232682-232701 None:intergenic 20.0%
!! TCTTTATAGCAATAATATGT+GGG + chr2.1:232442-232461 MS.gene99864:CDS 20.0%
!! TTCTTGTATTGTATTGTTTA+AGG + chr2.1:232682-232701 MS.gene99864:intron 20.0%
!! TTCTTTATAGCAATAATATG+TGG + chr2.1:232441-232460 MS.gene99864:CDS 20.0%
! AAAATTATATTCGTAGAGGA+TGG - chr2.1:232071-232090 None:intergenic 25.0%
! AAACAATACAATACAAGAAC+GGG - chr2.1:232681-232700 None:intergenic 25.0%
! AAATAGGAATAATTTCACAG+AGG - chr2.1:231702-231721 None:intergenic 25.0%
! GAAAAGGAAAAGAAATTAAC+AGG - chr2.1:232118-232137 None:intergenic 25.0%
!! AATTGATTCTGAGTCATATA+AGG + chr2.1:232710-232729 MS.gene99864:intron 25.0%
AAAAGCTGCAAACAAACATT+GGG - chr2.1:232295-232314 None:intergenic 30.0%
AACCAACTTATTACATGCAA+TGG + chr2.1:232354-232373 MS.gene99864:intron 30.0%
ATTTGAGAGTGGTGAATAAA+TGG - chr2.1:232267-232286 None:intergenic 30.0%
GATGAACTTAGAGAAATGTT+TGG + chr2.1:232197-232216 MS.gene99864:CDS 30.0%
GGTCATAAGATATGCAATTT+CGG + chr2.1:232636-232655 MS.gene99864:intron 30.0%
GTCATAAGATATGCAATTTC+GGG + chr2.1:232637-232656 MS.gene99864:intron 30.0%
TGTGCAATTAGAAAAGGAAA+AGG - chr2.1:232134-232153 None:intergenic 30.0%
TTCCATTGCATGTAATAAGT+TGG - chr2.1:232359-232378 None:intergenic 30.0%
TTTGAGAGTGGTGAATAAAT+GGG - chr2.1:232266-232285 None:intergenic 30.0%
! TTTCTGAAGAAGAAGAATCT+TGG - chr2.1:231660-231679 None:intergenic 30.0%
! TTTTCCTTTTCTAATTGCAC+AGG + chr2.1:232133-232152 MS.gene99864:intron 30.0%
!! TAACATGCTTCACTTTTATG+TGG - chr2.1:232577-232596 None:intergenic 30.0%
ACAACCTGTGCAATTAGAAA+AGG - chr2.1:232140-232159 None:intergenic 35.0%
ACGAAAAAGTCAGAAATGAG+TGG - chr2.1:232318-232337 None:intergenic 35.0%
AGAAGAAGAATCTTGGTTGT+CGG - chr2.1:231653-231672 None:intergenic 35.0%
AGAAGATCGAGAACATGTAA+AGG + chr2.1:232815-232834 MS.gene99864:CDS 35.0%
GAAAAGCTGCAAACAAACAT+TGG - chr2.1:232296-232315 None:intergenic 35.0%
GAAAATGAATGCATGATCTC+TGG - chr2.1:232019-232038 None:intergenic 35.0%
GACCTTTGTCAATTCTTGTT+TGG - chr2.1:232502-232521 None:intergenic 35.0%
GGTTATGAAGAACATCCATA+CGG + chr2.1:232218-232237 MS.gene99864:CDS 35.0%
TATATCATGATTGTCAGACG+TGG - chr2.1:231728-231747 None:intergenic 35.0%
TCACAGAGGTGATTCAATAT+GGG - chr2.1:231688-231707 None:intergenic 35.0%
TGCCAAACAAGAATTGACAA+AGG + chr2.1:232497-232516 MS.gene99864:CDS 35.0%
TTCACAGAGGTGATTCAATA+TGG - chr2.1:231689-231708 None:intergenic 35.0%
! ATGATCTGTGGACATACTTT+TGG - chr2.1:231861-231880 None:intergenic 35.0%
! ATTCTTGTTTGGCAAGAACA+TGG - chr2.1:232491-232510 None:intergenic 35.0%
! TCCATACGGATTTTACACAA+TGG + chr2.1:232232-232251 MS.gene99864:CDS 35.0%
! TGATCTGTGGACATACTTTT+GGG - chr2.1:231860-231879 None:intergenic 35.0%
!! TGCTTCACTTTTATGTGGAT+TGG - chr2.1:232572-232591 None:intergenic 35.0%
!!! CTGTTTACTTTTTTGACGTC+AGG + chr2.1:232782-232801 MS.gene99864:intron 35.0%
ACAGATCATGTCTCGATAAC+TGG + chr2.1:231872-231891 MS.gene99864:CDS 40.0%
AGAGGTGATTCAATATGGGT+TGG - chr2.1:231684-231703 None:intergenic 40.0%
AGTTATCGAGACATGATCTG+TGG - chr2.1:231873-231892 None:intergenic 40.0%
ATTGGGCATGAATTTGAGAG+TGG - chr2.1:232278-232297 None:intergenic 40.0%
CAAATGTCCCTAAAGATCGA+TGG + chr2.1:231962-231981 MS.gene99864:CDS 40.0%
GAGCAAACCCACCAAAATAA+TGG - chr2.1:232415-232434 None:intergenic 40.0%
GAGGTGATTCAATATGGGTT+GGG - chr2.1:231683-231702 None:intergenic 40.0%
GCCATTGTGTAAAATCCGTA+TGG - chr2.1:232236-232255 None:intergenic 40.0%
GTGACAGAACTAAGGATGTT+GGG + chr2.1:232864-232883 MS.gene99864:CDS 40.0%
TCAACCACCATCGATCTTTA+GGG - chr2.1:231972-231991 None:intergenic 40.0%
TGTGACAGAACTAAGGATGT+TGG + chr2.1:232863-232882 MS.gene99864:CDS 40.0%
! CATCGATCTTTAGGGACATT+TGG - chr2.1:231964-231983 None:intergenic 40.0%
! TACGGATTTTACACAATGGC+TGG + chr2.1:232236-232255 MS.gene99864:CDS 40.0%
! TGCAGTTCTCGCCATTATTT+TGG + chr2.1:232401-232420 MS.gene99864:intron 40.0%
!! ACATCCTTAGTTCTGTCACA+TGG - chr2.1:232863-232882 None:intergenic 40.0%
!! ACTTTTGGGTACCTTTGCAA+TGG - chr2.1:231846-231865 None:intergenic 40.0%
!! TTTTTGACGTCAGGAGTATG+TGG + chr2.1:232791-232810 MS.gene99864:intron 40.0%
!!! AGTTCTCGCCATTATTTTGG+TGG + chr2.1:232404-232423 MS.gene99864:intron 40.0%
!!! ATTTTGGTGGGTTTGCTCTA+TGG + chr2.1:232417-232436 MS.gene99864:CDS 40.0%
!!! GTTCTCGCCATTATTTTGGT+GGG + chr2.1:232405-232424 MS.gene99864:intron 40.0%
AGAAAAAGCAAAGCCCTCCT+TGG - chr2.1:231905-231924 None:intergenic 45.0%
AGTCTTCTCCTCCAAGATCA+AGG - chr2.1:231810-231829 None:intergenic 45.0%
ATGTCCCTAAAGATCGATGG+TGG + chr2.1:231965-231984 MS.gene99864:CDS 45.0%
CTCAACCACCATCGATCTTT+AGG - chr2.1:231973-231992 None:intergenic 45.0%
CTCCAAGATCAAGGCATATC+CGG - chr2.1:231801-231820 None:intergenic 45.0%
CTTGCTGCAAAACACGTCTT+TGG + chr2.1:232615-232634 MS.gene99864:intron 45.0%
GATCATGTCTCGATAACTGG+AGG + chr2.1:231875-231894 MS.gene99864:CDS 45.0%
GTTTGGCAAGAACATGGTAG+TGG - chr2.1:232485-232504 None:intergenic 45.0%
TTGTCAGACGTGGCAGAAAT+AGG - chr2.1:231718-231737 None:intergenic 45.0%
!! CTTAGTTCTGTCACATGGCT+GGG - chr2.1:232858-232877 None:intergenic 45.0%
!! GCACAGGTTGTTGCTTTCTT+GGG + chr2.1:232149-232168 MS.gene99864:intron 45.0%
!! TGCACAGGTTGTTGCTTTCT+TGG + chr2.1:232148-232167 MS.gene99864:intron 45.0%
!! TTAGTTCTGTCACATGGCTG+GGG - chr2.1:232857-232876 None:intergenic 45.0%
AACTGGAGGTCTACCAAGGA+GGG + chr2.1:231889-231908 MS.gene99864:CDS 50.0%
ATGCTGATCACCCACAATGC+CGG + chr2.1:231779-231798 MS.gene99864:CDS 50.0%
CAAGGCATATCCGGCATTGT+GGG - chr2.1:231792-231811 None:intergenic 50.0%
CCAGCCATGTGACAGAACTA+AGG + chr2.1:232856-232875 MS.gene99864:CDS 50.0%
CGATAACTGGAGGTCTACCA+AGG + chr2.1:231885-231904 MS.gene99864:CDS 50.0%
CGGATATGCCTTGATCTTGG+AGG + chr2.1:231799-231818 MS.gene99864:CDS 50.0%
TAACTGGAGGTCTACCAAGG+AGG + chr2.1:231888-231907 MS.gene99864:CDS 50.0%
TCAAGGCATATCCGGCATTG+TGG - chr2.1:231793-231812 None:intergenic 50.0%
TGCCGGATATGCCTTGATCT+TGG + chr2.1:231796-231815 MS.gene99864:CDS 50.0%
TGGGTACCTTTGCAATGGCA+GGG - chr2.1:231841-231860 None:intergenic 50.0%
TTGGGTACCTTTGCAATGGC+AGG - chr2.1:231842-231861 None:intergenic 50.0%
!! CCTTAGTTCTGTCACATGGC+TGG - chr2.1:232859-232878 None:intergenic 50.0%
ATTGCCCCCTGCCATTGCAA+AGG + chr2.1:231832-231851 MS.gene99864:CDS 55.0%
GGGTACCTTTGCAATGGCAG+GGG - chr2.1:231840-231859 None:intergenic 55.0%
GGTACCTTTGCAATGGCAGG+GGG - chr2.1:231839-231858 None:intergenic 55.0%
ACATGGCTGGGGTCGAGTTC+AGG - chr2.1:232846-232865 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 231631 232896 231631 ID=MS.gene99864
chr2.1 mRNA 231631 232896 231631 ID=MS.gene99864.t1;Parent=MS.gene99864
chr2.1 exon 231631 232053 231631 ID=MS.gene99864.t1.exon1;Parent=MS.gene99864.t1
chr2.1 CDS 231631 232053 231631 ID=cds.MS.gene99864.t1;Parent=MS.gene99864.t1
chr2.1 exon 232155 232257 232155 ID=MS.gene99864.t1.exon2;Parent=MS.gene99864.t1
chr2.1 CDS 232155 232257 232155 ID=cds.MS.gene99864.t1;Parent=MS.gene99864.t1
chr2.1 exon 232406 232518 232406 ID=MS.gene99864.t1.exon3;Parent=MS.gene99864.t1
chr2.1 CDS 232406 232518 232406 ID=cds.MS.gene99864.t1;Parent=MS.gene99864.t1
chr2.1 exon 232804 232896 232804 ID=MS.gene99864.t1.exon4;Parent=MS.gene99864.t1
chr2.1 CDS 232804 232896 232804 ID=cds.MS.gene99864.t1;Parent=MS.gene99864.t1
Gene Sequence

>MS.gene99864

ATGCAATTAGCTTCAAACACCGACAACCAAGATTCTTCTTCTTCAGAAACCCAACCCATATTGAATCACCTCTGTGAAATTATTCCTATTTCTGCCACGTCTGACAATCATGATATAGAGAATGAGTCTTCTCGTCTTGTTGTTGTAAATGCTGATCACCCACAATGCCGGATATGCCTTGATCTTGGAGGAGAAGACTTAATTGCCCCCTGCCATTGCAAAGGTACCCAAAAGTATGTCCACAGATCATGTCTCGATAACTGGAGGTCTACCAAGGAGGGCTTTGCTTTTTCTCACTGTACAGAATGCAGAGCTGTCTTCATAATTCGACCAAATGTCCCTAAAGATCGATGGTGGTTGAGATTGAAATTTCAGTTTCTTGTTGCCAGAGATCATGCATTCATTTTCATCATTGTTCAACTCGTATGTATATGCATCCATCCTCTACGAATATAATTTTATGTATTTCATTCAGAGAATATGTCCTGTTAATTTCTTTTCCTTTTCCTTTTCTAATTGCACAGGTTGTTGCTTTCTTGGGAGTGCTTATTTATAAATTCTATGGAGATGAACTTAGAGAAATGTTTGGTTATGAAGAACATCCATACGGATTTTACACAATGGCTGGTATTCCCATTTATTCACCACTCTCAAATTCATGCCCAATGTTTGTTTGCAGCTTTTCCACTCATTTCTGACTTTTTCGTAAATTCAATGTGTAACAACCAACTTATTACATGCAATGGAAACTTGATAATTTTGCTTTGTTTTGCAGTTCTCGCCATTATTTTGGTGGGTTTGCTCTATGGCTTCTTTATAGCAATAATATGTGGGCAAAGAATCAATGAACGCCACTACCATGTTCTTGCCAAACAAGAATTGACAAAGGTCTGCTATGTAATAGTAATAAATGCTTTCAAATTACTTTGACTTACAATCCAATCCACATAAAAGTGAAGCATGTTACTCAAAACTAGTAATATGCTTGCTGCAAAACACGTCTTTGGTCATAAGATATGCAATTTCGGGAAAACAATCATTTAACTACCCGTTCTTGTATTGTATTGTTTAAGGATTATAATTGATTCTGAGTCATATAAGGACTATATTCCTTTTTTATAAAAATTTAAGGTATTCAACTCTTCACTCTGCTGTTTACTTTTTTGACGTCAGGAGTATGTGGTAGAAGATCGAGAACATGTAAAGGATGTGCCTGAACTCGACCCCAGCCATGTGACAGAACTAAGGATGTTGGGCCTTTACTAG
Protein sequence

>MS.gene99864.t1

MQLASNTDNQDSSSSETQPILNHLCEIIPISATSDNHDIENESSRLVVVNADHPQCRICLDLGGEDLIAPCHCKGTQKYVHRSCLDNWRSTKEGFAFSHCTECRAVFIIRPNVPKDRWWLRLKFQFLVARDHAFIFIIVQLVVAFLGVLIYKFYGDELREMFGYEEHPYGFYTMAVLAIILVGLLYGFFIAIICGQRINERHYHVLAKQELTKEYVVEDREHVKDVPELDPSHVTELRMLGLY