AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96386

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96386.t1 MTR_1g048720 93.117 247 17 0 1 247 1 247 1.42e-167 462
MS.gene96386.t1 MTR_1g048720 92.713 247 17 1 1 247 1 246 3.93e-165 456
MS.gene96386.t1 MTR_1g048720 94.064 219 13 0 1 219 1 219 6.29e-150 417
MS.gene96386.t1 MTR_1g048720 93.607 219 13 1 1 219 1 218 1.72e-147 410
MS.gene96386.t1 MTR_1g048710 87.705 244 21 2 1 244 1 235 4.80e-143 400
MS.gene96386.t1 MTR_1g048750 84.862 218 25 1 1 218 1 210 8.85e-133 375
MS.gene96386.t1 MTR_7g090410 56.972 251 89 7 1 241 1 242 2.87e-64 201
MS.gene96386.t1 MTR_0007s0330 30.357 168 101 5 65 227 6 162 3.97e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96386.t1 AT3G56970 41.365 249 135 5 1 240 1 247 4.17e-54 175
MS.gene96386.t1 AT3G56980 39.560 273 115 6 1 242 1 254 1.30e-46 156
MS.gene96386.t1 AT2G41240 38.400 250 134 5 1 242 1 238 3.19e-45 152
MS.gene96386.t1 AT2G41240 38.000 250 134 6 1 242 1 237 7.83e-43 145
MS.gene96386.t1 AT5G04150 45.806 155 82 1 65 219 86 238 7.94e-36 127
MS.gene96386.t1 AT5G04150 44.000 175 93 3 65 237 86 257 1.68e-35 127

Find 41 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACTTGTTTCTGTAATTC+TGG 0.201065 1.1:-33332009 None:intergenic
TGTAACTATGCTTCTTCCTT+TGG 0.251062 1.1:-33332110 None:intergenic
CTTCTATAATTTGCATTTCC+AGG 0.265122 1.1:+33332302 MS.gene96386:CDS
TTCTGAGATCTTGATATGTT+TGG 0.287728 1.1:+33332221 MS.gene96386:CDS
GTAACTATGCTTCTTCCTTT+GGG 0.307422 1.1:-33332109 None:intergenic
TGAGAAGCTCTTATCAATAA+TGG 0.319674 1.1:+33332906 MS.gene96386:CDS
CTTTCTTCATCTCAGACCTT+TGG 0.339976 1.1:+33332270 MS.gene96386:CDS
AGGACTCTTGAAATTGTTGC+TGG 0.367920 1.1:-33331976 None:intergenic
GATCGCGTTCACTAGCATTA+TGG 0.375108 1.1:-33331665 None:intergenic
TCTTCATCTCAGACCTTTGG+AGG 0.399010 1.1:+33332273 MS.gene96386:CDS
TCTTCCTGTTTCTGATCAAA+TGG 0.413993 1.1:+33331731 MS.gene96386:CDS
AGTACCATTTGATCAGAAAC+AGG 0.414053 1.1:-33331735 None:intergenic
AACAATTGGATGGCCCTTTG+AGG 0.464251 1.1:+33331491 MS.gene96386:CDS
TGAAGGACTAAGTAAGAGAA+AGG 0.469978 1.1:+33332029 MS.gene96386:CDS
CATATCAAGATCTCAGAAAG+TGG 0.493296 1.1:-33332216 None:intergenic
AAGAAAGATTAAGAAGCAAA+AGG 0.505181 1.1:-33332254 None:intergenic
AGAATAACCTCTTCTTCTTG+AGG 0.516991 1.1:-33332075 None:intergenic
CATGCTAAGGTCACTGCTTG+TGG 0.529098 1.1:-33331628 None:intergenic
TGTAGAATGAATTCTGATGA+TGG 0.529120 1.1:-33331530 None:intergenic
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.1:-33331689 None:intergenic
TTGATATGTTTGGAAAATGA+TGG 0.537710 1.1:+33332231 MS.gene96386:CDS
CTTCATCTCAGACCTTTGGA+GGG 0.548412 1.1:+33332274 MS.gene96386:CDS
AAGAAGCATAGTTACAACTC+TGG 0.551749 1.1:+33332117 MS.gene96386:CDS
ACTTTATCCTCAAGAAGAAG+AGG 0.554683 1.1:+33332068 MS.gene96386:CDS
GCTCTTATCAATAATGGAGA+AGG 0.554810 1.1:+33332912 MS.gene96386:CDS
GAATTACAGAAACAAGTTGA+AGG 0.556198 1.1:+33332012 MS.gene96386:CDS
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.1:-33331480 None:intergenic
TCTCAGAAAGTGGAATCTTG+TGG 0.569417 1.1:-33332206 None:intergenic
AGTGTAACATGATATCTGAA+TGG 0.570967 1.1:-33332181 None:intergenic
TTCTGCAGGTGGATAAAGCA+CGG 0.571707 1.1:+33332860 MS.gene96386:intron
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.1:-33331477 None:intergenic
ATGAATTCTGATGATGGGTA+TGG 0.589276 1.1:-33331524 None:intergenic
GTAGAATGAATTCTGATGAT+GGG 0.591780 1.1:-33331529 None:intergenic
ATAGAAGACTCTCCCTCCAA+AGG 0.594272 1.1:-33332286 None:intergenic
GTCACTGCTTGTGGATTGTG+AGG 0.596424 1.1:-33331619 None:intergenic
AGGAAGAAGTGAACGAAGTG+AGG 0.599839 1.1:-33331715 None:intergenic
CAAGCTTCTTGACCATGCTA+AGG 0.604223 1.1:-33331641 None:intergenic
CACAAGCAGTGACCTTAGCA+TGG 0.613188 1.1:+33331629 MS.gene96386:CDS
TTCTAAGCAAAGAATCCCAA+AGG 0.620328 1.1:+33332094 MS.gene96386:CDS
TTATCAATAATGGAGAAGGA+AGG 0.636620 1.1:+33332916 MS.gene96386:CDS
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1.1:-33331618 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAACATGTAAGAAATA+AGG + chr1.1:33332675-33332694 MS.gene96386:intron 15.0%
!! TTACAAATAGTTGATTACTT+GGG + chr1.1:33332737-33332756 MS.gene96386:intron 20.0%
!! TTTACAAATAGTTGATTACT+TGG + chr1.1:33332736-33332755 MS.gene96386:intron 20.0%
! AAGAAAGATTAAGAAGCAAA+AGG - chr1.1:33332257-33332276 None:intergenic 25.0%
! ACAAATTATTGATCTTCTTG+CGG - chr1.1:33331692-33331711 None:intergenic 25.0%
! ACAATTAGAAACAGAAAGAA+GGG - chr1.1:33331769-33331788 None:intergenic 25.0%
! TCTAATTGTCAATAATGCTT+TGG + chr1.1:33331780-33331799 MS.gene96386:intron 25.0%
! TTGATATGTTTGGAAAATGA+TGG + chr1.1:33332231-33332250 MS.gene96386:CDS 25.0%
!! GTAATTCTGGTATGTATTTT+AGG - chr1.1:33331999-33332018 None:intergenic 25.0%
!!! TAATTTTCATGATCAAGTTG+AGG + chr1.1:33331575-33331594 MS.gene96386:CDS 25.0%
AGTGTAACATGATATCTGAA+TGG - chr1.1:33332184-33332203 None:intergenic 30.0%
CATCCAATTGTTGAAAACAT+AGG - chr1.1:33331483-33331502 None:intergenic 30.0%
GAAAACACATAAGTGCTTTA+AGG - chr1.1:33332843-33332862 None:intergenic 30.0%
GACAATTAGAAACAGAAAGA+AGG - chr1.1:33331770-33331789 None:intergenic 30.0%
GATGTATAGACTCATATAAG+AGG + chr1.1:33332802-33332821 MS.gene96386:intron 30.0%
GTAGAATGAATTCTGATGAT+GGG - chr1.1:33331532-33331551 None:intergenic 30.0%
TGAGAAGCTCTTATCAATAA+TGG + chr1.1:33332906-33332925 MS.gene96386:CDS 30.0%
TGTAGAATGAATTCTGATGA+TGG - chr1.1:33331533-33331552 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG + chr1.1:33331481-33331500 MS.gene96386:CDS 30.0%
! CTTCTATAATTTGCATTTCC+AGG + chr1.1:33332302-33332321 MS.gene96386:CDS 30.0%
! GAATTACAGAAACAAGTTGA+AGG + chr1.1:33332012-33332031 MS.gene96386:CDS 30.0%
! TTATCAATAATGGAGAAGGA+AGG + chr1.1:33332916-33332935 MS.gene96386:CDS 30.0%
!! GTTTTGTAGTTTCAAGTAGT+AGG + chr1.1:33332139-33332158 MS.gene96386:CDS 30.0%
!! TCAACTTGTTTCTGTAATTC+TGG - chr1.1:33332012-33332031 None:intergenic 30.0%
!! TTCTGAGATCTTGATATGTT+TGG + chr1.1:33332221-33332240 MS.gene96386:CDS 30.0%
!!! TCTAATTGTGATGTCGTTTT+TGG + chr1.1:33331877-33331896 MS.gene96386:intron 30.0%
ACTTTATCCTCAAGAAGAAG+AGG + chr1.1:33332068-33332087 MS.gene96386:CDS 35.0%
AGAATAACCTCTTCTTCTTG+AGG - chr1.1:33332078-33332097 None:intergenic 35.0%
AGTACCATTTGATCAGAAAC+AGG - chr1.1:33331738-33331757 None:intergenic 35.0%
CATATCAAGATCTCAGAAAG+TGG - chr1.1:33332219-33332238 None:intergenic 35.0%
CCAATTGTTGAAAACATAGG+AGG - chr1.1:33331480-33331499 None:intergenic 35.0%
GTAACTATGCTTCTTCCTTT+GGG - chr1.1:33332112-33332131 None:intergenic 35.0%
TGAAGGACTAAGTAAGAGAA+AGG + chr1.1:33332029-33332048 MS.gene96386:CDS 35.0%
TGTAACTATGCTTCTTCCTT+TGG - chr1.1:33332113-33332132 None:intergenic 35.0%
TTCTAAGCAAAGAATCCCAA+AGG + chr1.1:33332094-33332113 MS.gene96386:CDS 35.0%
! AAGAAGCATAGTTACAACTC+TGG + chr1.1:33332117-33332136 MS.gene96386:CDS 35.0%
! CCTCCTATGTTTTCAACAAT+TGG + chr1.1:33331477-33331496 MS.gene96386:CDS 35.0%
! CTTGAAAACCTTGTGTTTTG+AGG + chr1.1:33331838-33331857 MS.gene96386:intron 35.0%
! GCTCTTATCAATAATGGAGA+AGG + chr1.1:33332912-33332931 MS.gene96386:CDS 35.0%
!! ATGAATTCTGATGATGGGTA+TGG - chr1.1:33331527-33331546 None:intergenic 35.0%
!! TCTTCCTGTTTCTGATCAAA+TGG + chr1.1:33331731-33331750 MS.gene96386:CDS 35.0%
ACCATACTCCTCAAAACACA+AGG - chr1.1:33331849-33331868 None:intergenic 40.0%
AGGACTCTTGAAATTGTTGC+TGG - chr1.1:33331979-33331998 None:intergenic 40.0%
CCAGGTGTGTTAATTTCACT+AGG + chr1.1:33332320-33332339 MS.gene96386:intron 40.0%
CCTAGTGAAATTAACACACC+TGG - chr1.1:33332323-33332342 None:intergenic 40.0%
CTTTCTTCATCTCAGACCTT+TGG + chr1.1:33332270-33332289 MS.gene96386:CDS 40.0%
TCTCAGAAAGTGGAATCTTG+TGG - chr1.1:33332209-33332228 None:intergenic 40.0%
! ACTTATGTGTTTTCTGCAGG+TGG + chr1.1:33332849-33332868 MS.gene96386:intron 40.0%
! AGCACTTATGTGTTTTCTGC+AGG + chr1.1:33332846-33332865 MS.gene96386:intron 40.0%
!!! ACCTTGTGTTTTGAGGAGTA+TGG + chr1.1:33331845-33331864 MS.gene96386:intron 40.0%
!!! TGATGATGGGTATGGCTTTT+TGG - chr1.1:33331519-33331538 None:intergenic 40.0%
AACAATTGGATGGCCCTTTG+AGG + chr1.1:33331491-33331510 MS.gene96386:CDS 45.0%
AGGAAGAAGTGAACGAAGTG+AGG - chr1.1:33331718-33331737 None:intergenic 45.0%
ATAGAAGACTCTCCCTCCAA+AGG - chr1.1:33332289-33332308 None:intergenic 45.0%
CAAGCTTCTTGACCATGCTA+AGG - chr1.1:33331644-33331663 None:intergenic 45.0%
CTTCATCTCAGACCTTTGGA+GGG + chr1.1:33332274-33332293 MS.gene96386:CDS 45.0%
GATCGCGTTCACTAGCATTA+TGG - chr1.1:33331668-33331687 None:intergenic 45.0%
TCTTCATCTCAGACCTTTGG+AGG + chr1.1:33332273-33332292 MS.gene96386:CDS 45.0%
TTCTGCAGGTGGATAAAGCA+CGG + chr1.1:33332860-33332879 MS.gene96386:intron 45.0%
! TCACTGCTTGTGGATTGTGA+GGG - chr1.1:33331621-33331640 None:intergenic 45.0%
!!! ATGGCTTTTTGGCTCCTCAA+AGG - chr1.1:33331508-33331527 None:intergenic 45.0%
!!! TGGCTTTTTGGCTCCTCAAA+GGG - chr1.1:33331507-33331526 None:intergenic 45.0%
CACAAGCAGTGACCTTAGCA+TGG + chr1.1:33331629-33331648 MS.gene96386:CDS 50.0%
CATGCTAAGGTCACTGCTTG+TGG - chr1.1:33331631-33331650 None:intergenic 50.0%
! GTCACTGCTTGTGGATTGTG+AGG - chr1.1:33331622-33331641 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 33331462 33332957 33331462 ID=MS.gene96386
chr1.1 mRNA 33331462 33332957 33331462 ID=MS.gene96386.t1;Parent=MS.gene96386
chr1.1 exon 33331462 33331752 33331462 ID=MS.gene96386.t1.exon1;Parent=MS.gene96386.t1
chr1.1 CDS 33331462 33331752 33331462 ID=cds.MS.gene96386.t1;Parent=MS.gene96386.t1
chr1.1 exon 33331961 33332323 33331961 ID=MS.gene96386.t1.exon2;Parent=MS.gene96386.t1
chr1.1 CDS 33331961 33332323 33331961 ID=cds.MS.gene96386.t1;Parent=MS.gene96386.t1
chr1.1 exon 33332868 33332957 33332868 ID=MS.gene96386.t1.exon3;Parent=MS.gene96386.t1
chr1.1 CDS 33332868 33332957 33332868 ID=cds.MS.gene96386.t1;Parent=MS.gene96386.t1
Gene Sequence

>MS.gene96386

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAGGAGCCAAAAAGCCATACCCATCATCAGAATTCATTCTACAAAGACACTGTTGATCAATTATTTAATTTTCATGATCAAGTTGAGGCAGAAATTAATTCAACAGATCCCTCACAATCCACAAGCAGTGACCTTAGCATGGTCAAGAAGCTTGTCCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCCTCACTTCGTTCACTTCTTCCTGTTTCTGATCAAATGGTACTTAATTAATCCCTTCTTTCTGTTTCTAATTGTCAATAATGCTTTGGTCATTTCTTTATCTTTTTTTTTTTTTTTTTTTAATCTTGAAAACCTTGTGTTTTGAGGAGTATGGTTGCAATTGTCTAATTGTGATGTCGTTTTTGGAACTTGCATATCTCTTGTTAGAACTATTGTCTTAGTATTAATATATACATATATGTTGCAGAAGAAATTGAGCATTCCAGCAACAATTTCAAGAGTCCTAAAATACATACCAGAATTACAGAAACAAGTTGAAGGACTAAGTAAGAGAAAGGATGAGATCTTATTGAGACTTTATCCTCAAGAAGAAGAGGTTATTCTAAGCAAAGAATCCCAAAGGAAGAAGCATAGTTACAACTCTGGTTTTGTAGTTTCAAGTAGTAGGCTCAATGATAGTGAAATTACCATTCAGATATCATGTTACACTGTCCACAAGATTCCACTTTCTGAGATCTTGATATGTTTGGAAAATGATGGCCTTTTGCTTCTTAATCTTTCTTCATCTCAGACCTTTGGAGGGAGAGTCTTCTATAATTTGCATTTCCAGGTGTGTTAATTTCACTAGGCTTGTTTACTTTTTAAATATTTTGTCATTTATTATCGAGTGAACTCTTTATTGAATATTTTTTTAAATTATAAATTATTGAGTGAACTCTTTATTGAATATTTTTTTAAATTATAAAATAAGCTTAATAACTATTTCATATATTTTTGAAAGAAAAAACTATTTTGATCATATATAATTATGATTTGTTTTTTTTGAAGCATCATACATAATTATGATGTTACTTTATTATATTTATTATAAAATTATTTTCACAAATATTAAATTTAGAAATACTCTTAGATGCATATTTAATTATTTTTTTTATCATTCAATTATTTTAAGAATATTATTTTAAAAACATGTAAGAAATAAGGAACTAAAAATATAAGAAATTATGAAAACTATATTTTATTTTACAAATAGTTGATTACTTGGGAAAAAATAAAAAAAAATAATTTAAAAGTTAACTTTTTCTCAAGATGTATAGACTCATATAAGAGGTACAACAAACATTTTCCTTAAAGCACTTATGTGTTTTCTGCAGGTGGATAAAGCACGGAGATTAGAATATCATATTCTAAATGAGAAGCTCTTATCAATAATGGAGAAGGAAGGAGAGTTTTTAAAACAATAA
Protein sequence

>MS.gene96386.t1

MLAISPPMFSTIGWPFEEPKSHTHHQNSFYKDTVDQLFNFHDQVEAEINSTDPSQSTSSDLSMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPELQKQVEGLSKRKDEILLRLYPQEEEVILSKESQRKKHSYNSGFVVSSSRLNDSEITIQISCYTVHKIPLSEILICLENDGLLLLNLSSSQTFGGRVFYNLHFQVDKARRLEYHILNEKLLSIMEKEGEFLKQ