AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene42428

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene42428.t1 MTR_7g077650 94.074 270 16 0 11 280 103 372 0.0 513
MS.gene42428.t1 MTR_7g077660 84.615 273 33 3 11 280 102 368 3.90e-160 450
MS.gene42428.t1 MTR_7g077620 68.382 272 73 7 11 276 104 368 9.07e-116 338
MS.gene42428.t1 MTR_7g076100 50.645 310 113 10 1 280 1 300 9.16e-85 256
MS.gene42428.t1 MTR_7g076110 52.500 280 114 7 14 280 40 313 1.46e-83 253
MS.gene42428.t1 MTR_1g108740 43.416 281 123 14 8 278 90 344 3.32e-54 179
MS.gene42428.t1 MTR_5g038260 41.503 306 120 16 14 280 98 383 2.92e-50 170
MS.gene42428.t1 MTR_5g038230 38.514 296 113 13 14 278 96 353 4.79e-46 158
MS.gene42428.t1 MTR_1g064570 37.994 329 118 18 14 280 96 400 5.27e-45 157
MS.gene42428.t1 MTR_5g082770 43.519 216 91 8 14 216 92 289 7.26e-40 140
MS.gene42428.t1 MTR_5g082780 40.408 245 96 10 21 245 1 215 1.13e-39 138
MS.gene42428.t1 MTR_7g076130 53.125 128 50 3 77 200 27 148 3.94e-36 127
MS.gene42428.t1 MTR_1g016150 49.412 85 39 3 14 95 108 191 3.91e-16 76.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 56 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACTGCATGCAACAATTT+TGG 0.088169 7.2:-28421794 MS.gene42428:CDS
TCTTATAGGCGTCCTTATTA+TGG 0.163187 7.2:-28422140 MS.gene42428:CDS
AAAGACCAAGCCAGTCATTT+TGG 0.211714 7.2:-28422355 MS.gene42428:CDS
CTCCAGAACTATATTCTTAT+AGG 0.226179 7.2:-28422154 MS.gene42428:CDS
GTTGCAGTGATTTACAATTT+TGG 0.255525 7.2:-28422392 MS.gene42428:CDS
CAAATTCAGAACTTCCTCTT+AGG 0.285333 7.2:-28422844 MS.gene42428:intron
CATGAACAAACTTGAGAGTT+TGG 0.291578 7.2:-28421988 MS.gene42428:CDS
GGAGCTATACTGCTCTTAAA+AGG 0.328493 7.2:+28422494 None:intergenic
ACCTCTCGAATCTCTCAAAA+AGG 0.330053 7.2:-28422459 MS.gene42428:CDS
AAATAAGCACGCCCATAATA+AGG 0.333798 7.2:+28422128 None:intergenic
TAATCACTTGGGCTTGTAAT+GGG 0.338599 7.2:+28422419 None:intergenic
CTTATAGGCGTCCTTATTAT+GGG 0.341054 7.2:-28422139 MS.gene42428:CDS
CGCCTATAAGAATATAGTTC+TGG 0.352063 7.2:+28422152 None:intergenic
TTCGAGAGGTGGCAGACTAA+TGG 0.374836 7.2:+28422472 None:intergenic
TAGCAATGAGGAAGGTTGAT+TGG 0.387641 7.2:-28422868 None:intergenic
CCATGGTTGGCTTGCATTGG+TGG 0.397590 7.2:-28422546 MS.gene42428:CDS
AATCATTGACCGGAGATATA+TGG 0.398581 7.2:-28422100 MS.gene42428:CDS
TGCTTTCTCCAAGTTGGAAA+AGG 0.401941 7.2:-28421910 MS.gene42428:CDS
CTGTGCTATCAACAAATATC+AGG 0.408578 7.2:+28422279 None:intergenic
AAAAGGATTCACTAGAGTTA+TGG 0.411464 7.2:+28422511 None:intergenic
CAGTTCCAATTTGAAAATGC+AGG 0.419394 7.2:+28422037 None:intergenic
AAATTGTTGCATGCAGTTGA+AGG 0.433203 7.2:+28421797 None:intergenic
TCGAGAGGTGGCAGACTAAT+GGG 0.438780 7.2:+28422473 None:intergenic
ACTAGCCATCTTCTCATAGT+AGG 0.443005 7.2:+28422193 None:intergenic
AGCCTCTGCTTTCTCCAAGT+TGG 0.444570 7.2:-28421916 MS.gene42428:CDS
GGGTTCTACCACAACTTAAG+TGG 0.451369 7.2:-28421773 MS.gene42428:CDS
TAGCCATGGTTGGCTTGCAT+TGG 0.461010 7.2:-28422549 MS.gene42428:CDS
AGCAATGAGGAAGGTTGATT+GGG 0.467550 7.2:-28422867 None:intergenic
ATAATCACTTGGGCTTGTAA+TGG 0.476686 7.2:+28422418 None:intergenic
ATGATGAAAAGATTCTTAAT+CGG 0.482155 7.2:-28422077 MS.gene42428:CDS
AGAAGGATTGTTCAACTTGA+AGG 0.483358 7.2:+28422244 None:intergenic
TACAAGCCCAAGTGATTATG+TGG 0.499442 7.2:-28422414 MS.gene42428:CDS
TTTCATCATCCATATATCTC+CGG 0.517323 7.2:+28422091 None:intergenic
GTTTGGGCTGTAGCCATGGT+TGG 0.525841 7.2:-28422559 MS.gene42428:intron
CGAATCCAAAATGACTGGCT+TGG 0.533467 7.2:+28422350 None:intergenic
AGTTCCAATTTGAAAATGCA+GGG 0.535496 7.2:+28422038 None:intergenic
AACTTGGAGAAAGCAGAGGC+TGG 0.538703 7.2:+28421918 None:intergenic
TATATCTTTAATGTGAAGGA+TGG 0.540947 7.2:-28421849 MS.gene42428:CDS
ACTGCAACCACATAATCACT+TGG 0.547627 7.2:+28422407 None:intergenic
TCAAATGAGTCATCAGAAGA+AGG 0.554017 7.2:+28422227 None:intergenic
GGTTCTACCACAACTTAAGT+GGG 0.555055 7.2:-28421772 MS.gene42428:CDS
TATCTATATCTTTAATGTGA+AGG 0.560244 7.2:-28421853 MS.gene42428:CDS
TGTAATGGGGTCAGCAGACA+AGG 0.568289 7.2:+28422433 None:intergenic
CAGTTGAAGGAAAGCACTGA+AGG 0.581076 7.2:+28421810 None:intergenic
CTATAAGAATATAGTTCTGG+AGG 0.587258 7.2:+28422155 None:intergenic
TTCCAACTTGGAGAAAGCAG+AGG 0.596419 7.2:+28421914 None:intergenic
GTTCAACTTGAAGGATACAA+TGG 0.598885 7.2:+28422253 None:intergenic
CTACACGAATCCAAAATGAC+TGG 0.605238 7.2:+28422345 None:intergenic
AATCACTTGGGCTTGTAATG+GGG 0.606028 7.2:+28422420 None:intergenic
GATCAATCCCACTTAAGTTG+TGG 0.623118 7.2:+28421765 None:intergenic
TATAAGAATATAGTTCTGGA+GGG 0.624070 7.2:+28422156 None:intergenic
ATGAAAAGATTCTTAATCGG+CGG 0.627273 7.2:-28422074 MS.gene42428:CDS
CTGCAACCACATAATCACTT+GGG 0.636696 7.2:+28422408 None:intergenic
AAGGCTCTTAGCAATGAGGA+AGG 0.657532 7.2:-28422876 None:intergenic
CCACCAATGCAAGCCAACCA+TGG 0.665097 7.2:+28422546 None:intergenic
TTGGAACTGGATGCCCAGAG+TGG 0.674354 7.2:-28422023 MS.gene42428:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTCAATTTATTTTGTTAA+TGG - chr7.2:28422742-28422761 MS.gene42428:intron 15.0%
!! AATACAATGAAATTGTGTTT+GGG - chr7.2:28422055-28422074 MS.gene42428:CDS 20.0%
!! ACCATAAATATCATCAATTT+AGG - chr7.2:28421894-28421913 MS.gene42428:CDS 20.0%
!! ATGATGAAAAGATTCTTAAT+CGG - chr7.2:28422553-28422572 MS.gene42428:intron 20.0%
!! TATCTATATCTTTAATGTGA+AGG - chr7.2:28422777-28422796 MS.gene42428:intron 20.0%
!!! ACTGATGTTGTATTTTATAA+AGG - chr7.2:28422328-28422347 MS.gene42428:CDS 20.0%
!!! TCCTAAATTGATGATATTTA+TGG + chr7.2:28421898-28421917 None:intergenic 20.0%
! ACACAATTTCATTGTATTGA+TGG + chr7.2:28422053-28422072 None:intergenic 25.0%
! CAATACAATGAAATTGTGTT+TGG - chr7.2:28422054-28422073 MS.gene42428:CDS 25.0%
! TATATCTTTAATGTGAAGGA+TGG - chr7.2:28422781-28422800 MS.gene42428:intron 25.0%
! TTCTCATAGTAGGAAAAATT+AGG + chr7.2:28422430-28422449 None:intergenic 25.0%
!! AATTTCATTGTATTGATGGA+AGG + chr7.2:28422049-28422068 None:intergenic 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.2:28422520-28422539 MS.gene42428:CDS 25.0%
!!! TATAAGAATATAGTTCTGGA+GGG + chr7.2:28422477-28422496 None:intergenic 25.0%
AAAAGGATTCACTAGAGTTA+TGG + chr7.2:28422122-28422141 None:intergenic 30.0%
AACTACAAACAGACTATGTT+AGG - chr7.2:28421828-28421847 MS.gene42428:CDS 30.0%
AGTTCCAATTTGAAAATGCA+GGG + chr7.2:28422595-28422614 None:intergenic 30.0%
ATGAAAAGATTCTTAATCGG+CGG - chr7.2:28422556-28422575 MS.gene42428:intron 30.0%
CTCCAGAACTATATTCTTAT+AGG - chr7.2:28422476-28422495 MS.gene42428:CDS 30.0%
TTTCATCATCCATATATCTC+CGG + chr7.2:28422542-28422561 None:intergenic 30.0%
! AATTGAATCCTTTTCCAACT+TGG + chr7.2:28422731-28422750 None:intergenic 30.0%
! GTTGCAGTGATTTACAATTT+TGG - chr7.2:28422238-28422257 MS.gene42428:CDS 30.0%
! TTTTTCCTACTATGAGAAGA+TGG - chr7.2:28422432-28422451 MS.gene42428:CDS 30.0%
!! ATTTTATTTGTCGGAAGTGT+TGG - chr7.2:28422673-28422692 MS.gene42428:intron 30.0%
!! CTATAAGAATATAGTTCTGG+AGG + chr7.2:28422478-28422497 None:intergenic 30.0%
!! GAAGACAGCATTTTATTTGT+CGG - chr7.2:28422664-28422683 MS.gene42428:intron 30.0%
!!! TATGCGACAATTTTTTTGAG+AGG + chr7.2:28421946-28421965 None:intergenic 30.0%
AAATAAGCACGCCCATAATA+AGG + chr7.2:28422505-28422524 None:intergenic 35.0%
AAATTGTTGCATGCAGTTGA+AGG + chr7.2:28422836-28422855 None:intergenic 35.0%
AAGGATGGGAGAATTGAATA+GGG + chr7.2:28422030-28422049 None:intergenic 35.0%
AATCATTGACCGGAGATATA+TGG - chr7.2:28422530-28422549 MS.gene42428:CDS 35.0%
AGAAGGATTGTTCAACTTGA+AGG + chr7.2:28422389-28422408 None:intergenic 35.0%
ATAATCACTTGGGCTTGTAA+TGG + chr7.2:28422215-28422234 None:intergenic 35.0%
CAAACAGACTATGTTAGGTT+CGG - chr7.2:28421833-28421852 MS.gene42428:CDS 35.0%
CAAATTCAGAACTTCCTCTT+AGG - chr7.2:28421786-28421805 MS.gene42428:CDS 35.0%
CAGTTCCAATTTGAAAATGC+AGG + chr7.2:28422596-28422615 None:intergenic 35.0%
CATGAACAAACTTGAGAGTT+TGG - chr7.2:28422642-28422661 MS.gene42428:intron 35.0%
CGCCTATAAGAATATAGTTC+TGG + chr7.2:28422481-28422500 None:intergenic 35.0%
CTGTGCTATCAACAAATATC+AGG + chr7.2:28422354-28422373 None:intergenic 35.0%
CTTATAGGCGTCCTTATTAT+GGG - chr7.2:28422491-28422510 MS.gene42428:CDS 35.0%
GTTCAACTTGAAGGATACAA+TGG + chr7.2:28422380-28422399 None:intergenic 35.0%
TAATCACTTGGGCTTGTAAT+GGG + chr7.2:28422214-28422233 None:intergenic 35.0%
TCAAATGAGTCATCAGAAGA+AGG + chr7.2:28422406-28422425 None:intergenic 35.0%
TCTTATAGGCGTCCTTATTA+TGG - chr7.2:28422490-28422509 MS.gene42428:CDS 35.0%
! CAAACCCTGCATTTTCAAAT+TGG - chr7.2:28422588-28422607 MS.gene42428:intron 35.0%
! CAACTGCATGCAACAATTTT+GGG - chr7.2:28422837-28422856 MS.gene42428:intron 35.0%
! CATTGTATTGATGGAAGGAT+GGG + chr7.2:28422044-28422063 None:intergenic 35.0%
! CTGCATTTTCAAATTGGAAC+TGG - chr7.2:28422594-28422613 MS.gene42428:intron 35.0%
! TAGGGTACTCTTTCTTACTT+AGG + chr7.2:28422012-28422031 None:intergenic 35.0%
! TCAACTGCATGCAACAATTT+TGG - chr7.2:28422836-28422855 MS.gene42428:intron 35.0%
! TCATTGTATTGATGGAAGGA+TGG + chr7.2:28422045-28422064 None:intergenic 35.0%
!! AGTTCTGGAGGGAAAAAATA+TGG + chr7.2:28422466-28422485 None:intergenic 35.0%
!! TAGGTTGGTTCTTGAAAAGT+TGG - chr7.2:28421805-28421824 MS.gene42428:CDS 35.0%
!! TTTTCAAGAACCAACCTAAG+AGG + chr7.2:28421803-28421822 None:intergenic 35.0%
AATCACTTGGGCTTGTAATG+GGG + chr7.2:28422213-28422232 None:intergenic 40.0%
ACCTCTCGAATCTCTCAAAA+AGG - chr7.2:28422171-28422190 MS.gene42428:CDS 40.0%
ACTAGCCATCTTCTCATAGT+AGG + chr7.2:28422440-28422459 None:intergenic 40.0%
ACTGCAACCACATAATCACT+TGG + chr7.2:28422226-28422245 None:intergenic 40.0%
CTACACGAATCCAAAATGAC+TGG + chr7.2:28422288-28422307 None:intergenic 40.0%
CTGCAACCACATAATCACTT+GGG + chr7.2:28422225-28422244 None:intergenic 40.0%
GAAGGATGGGAGAATTGAAT+AGG + chr7.2:28422031-28422050 None:intergenic 40.0%
GGAGCTATACTGCTCTTAAA+AGG + chr7.2:28422139-28422158 None:intergenic 40.0%
GGTTCTACCACAACTTAAGT+GGG - chr7.2:28422858-28422877 MS.gene42428:CDS 40.0%
TACAAGCCCAAGTGATTATG+TGG - chr7.2:28422216-28422235 MS.gene42428:CDS 40.0%
TTCAGAACTTCCTCTTAGGT+TGG - chr7.2:28421790-28421809 MS.gene42428:CDS 40.0%
TTTGAGAGGATCATCAGCAT+AGG + chr7.2:28421932-28421951 None:intergenic 40.0%
! AAAGACCAAGCCAGTCATTT+TGG - chr7.2:28422275-28422294 MS.gene42428:CDS 40.0%
! TGCTTTCTCCAAGTTGGAAA+AGG - chr7.2:28422720-28422739 MS.gene42428:intron 40.0%
!! ACCTTTTTGAGAGATTCGAG+AGG + chr7.2:28422175-28422194 None:intergenic 40.0%
!! TCGGTGTTGTGTGTAAGAAT+TGG - chr7.2:28421852-28421871 MS.gene42428:CDS 40.0%
!! TTTTTGAGAGATTCGAGAGG+TGG + chr7.2:28422172-28422191 None:intergenic 40.0%
!!! GTGTTCTAGTTTTCCACTCT+GGG + chr7.2:28422623-28422642 None:intergenic 40.0%
!!! TGTGTTCTAGTTTTCCACTC+TGG + chr7.2:28422624-28422643 None:intergenic 40.0%
GGGTTCTACCACAACTTAAG+TGG - chr7.2:28422857-28422876 MS.gene42428:CDS 45.0%
TTCCAACTTGGAGAAAGCAG+AGG + chr7.2:28422719-28422738 None:intergenic 45.0%
! CGAATCCAAAATGACTGGCT+TGG + chr7.2:28422283-28422302 None:intergenic 45.0%
!! CAGTTGAAGGAAAGCACTGA+AGG + chr7.2:28422823-28422842 None:intergenic 45.0%
AACTTGGAGAAAGCAGAGGC+TGG + chr7.2:28422715-28422734 None:intergenic 50.0%
AGCCTCTGCTTTCTCCAAGT+TGG - chr7.2:28422714-28422733 MS.gene42428:intron 50.0%
TCGAGAGGTGGCAGACTAAT+GGG + chr7.2:28422160-28422179 None:intergenic 50.0%
TTCGAGAGGTGGCAGACTAA+TGG + chr7.2:28422161-28422180 None:intergenic 50.0%
TTGTGTTTGGGCTGTAGCCA+TGG - chr7.2:28422067-28422086 MS.gene42428:CDS 50.0%
! TGTAATGGGGTCAGCAGACA+AGG + chr7.2:28422200-28422219 None:intergenic 50.0%
!! TAGCCATGGTTGGCTTGCAT+TGG - chr7.2:28422081-28422100 MS.gene42428:CDS 50.0%
CCACCAATGCAAGCCAACCA+TGG + chr7.2:28422087-28422106 None:intergenic 55.0%
GTTTGGGCTGTAGCCATGGT+TGG - chr7.2:28422071-28422090 MS.gene42428:CDS 55.0%
TTGGAACTGGATGCCCAGAG+TGG - chr7.2:28422607-28422626 MS.gene42428:intron 55.0%
!! CCATGGTTGGCTTGCATTGG+TGG - chr7.2:28422084-28422103 MS.gene42428:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 28421767 28422885 28421767 ID=MS.gene42428
chr7.2 mRNA 28421767 28422885 28421767 ID=MS.gene42428.t1;Parent=MS.gene42428
chr7.2 exon 28422845 28422885 28422845 ID=MS.gene42428.t1.exon1;Parent=MS.gene42428.t1
chr7.2 CDS 28422845 28422885 28422845 ID=cds.MS.gene42428.t1;Parent=MS.gene42428.t1
chr7.2 exon 28421767 28422568 28421767 ID=MS.gene42428.t1.exon2;Parent=MS.gene42428.t1
chr7.2 CDS 28421767 28422568 28421767 ID=cds.MS.gene42428.t1;Parent=MS.gene42428.t1
Gene Sequence

>MS.gene42428

ATGAGGAAGGTTGATTGGGCAAATTCAGAACTTCCTCTTAGGTTGGTTCTTGAAAAGTTGGAACTACAAACAGACTATGTTAGGTTCGGTGTTGTGTGTAAGAATTGGCTATCAATTGCAAAGCTTAACCATAAATATCATCAATTTAGGATTAATGTACTGCCTATGCTGATGATCCTCTCAAAAAAATTGTCGCATATACATACAATATCACAGACAAAGAAGATATCATTGTATAATATCCTAAGTAAGAAAGAGTACCCTATTCAATTCTCCCATCCTTCCATCAATACAATGAAATTGTGTTTGGGCTGTAGCCATGGTTGGCTTGCATTGGTGGATGATAACAATGCCATAACTCTAGTGAATCCTTTTAAGAGCAGTATAGCTCCCATTAGTCTGCCACCTCTCGAATCTCTCAAAAAGGTTACCTTGTCTGCTGACCCCATTACAAGCCCAAGTGATTATGTGGTTGCAGTGATTTACAATTTTGGTTCTCTCGCTTTCAAAAGACCAAGCCAGTCATTTTGGATTCGTGTAGACACAAATGAATTTTCTTTCACTGATGTTGTATTTTATAAAGGCCTGATATTTGTTGATAGCACAGATACCATTGTATCCTTCAAGTTGAACAATCCTTCTTCTGATGACTCATTTGATCCTAATTTTTCCTACTATGAGAAGATGGCTAGTACTCCATATTTTTTCCCTCCAGAACTATATTCTTATAGGCGTCCTTATTATGGGCGTGCTTATTTTGTGAAATCATTGACCGGAGATATATGGATGATGAAAAGATTCTTAATCGGCGGAAATTTAATCAAACCCTGCATTTTCAAATTGGAACTGGATGCCCAGAGTGGAAAACTAGAACACATGAACAAACTTGAGAGTTTGGAAGACAGCATTTTATTTGTCGGAAGTGTTGGTGATTCAATATCTGTGCCAGCCTCTGCTTTCTCCAAGTTGGAAAAGGATTCAATTTATTTTGTTAATGGTATAGAGATAGATATCTATATCTTTAATGTGAAGGATGGAAGCGTTCAGAGATCACCTTCAGTGCTTTCCTTCAACTGCATGCAACAATTTTGGGTTCTACCACAACTTAAGTGGGATTGA
Protein sequence

>MS.gene42428.t1

MRKVDWANSELPLSHGWLALVDDNNAITLVNPFKSSIAPISLPPLESLKKVTLSADPITSPSDYVVAVIYNFGSLAFKRPSQSFWIRVDTNEFSFTDVVFYKGLIFVDSTDTIVSFKLNNPSSDDSFDPNFSYYEKMASTPYFFPPELYSYRRPYYGRAYFVKSLTGDIWMMKRFLIGGNLIKPCIFKLELDAQSGKLEHMNKLESLEDSILFVGSVGDSISVPASAFSKLEKDSIYFVNGIEIDIYIFNVKDGSVQRSPSVLSFNCMQQFWVLPQLKWD