AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53899

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53899.t1 MTR_1g087870 82.915 199 34 0 1 199 31 229 6.66e-124 350
MS.gene53899.t1 MTR_7g110090 43.814 194 104 1 2 195 84 272 3.17e-57 182
MS.gene53899.t1 MTR_3g452180 43.850 187 100 1 9 195 7 188 4.28e-56 176
MS.gene53899.t1 MTR_4g032560 40.513 195 111 1 1 195 112 301 5.71e-51 166
MS.gene53899.t1 MTR_4g032580 40.513 195 111 1 1 195 112 301 1.64e-50 165
MS.gene53899.t1 MTR_2g100360 44.000 175 98 0 1 175 83 257 4.79e-50 163
MS.gene53899.t1 MTR_3g070250 39.896 193 116 0 1 193 88 280 9.51e-50 163
MS.gene53899.t1 MTR_3g048970 42.268 194 110 2 1 193 83 275 1.25e-49 162
MS.gene53899.t1 MTR_1g084880 42.268 194 110 2 1 193 83 275 3.24e-49 161
MS.gene53899.t1 MTR_1g105780 41.026 195 110 1 1 195 84 273 1.02e-44 149
MS.gene53899.t1 MTR_1g105765 41.026 195 110 1 1 195 84 273 1.05e-44 149
MS.gene53899.t1 MTR_4g121040 39.053 169 98 1 21 189 7 170 6.42e-40 135
MS.gene53899.t1 MTR_1g047540 39.683 189 94 3 2 190 84 252 2.26e-38 137
MS.gene53899.t1 MTR_2g038740 42.138 159 92 0 1 159 83 241 3.87e-38 139
MS.gene53899.t1 MTR_1g069260 37.912 182 96 3 24 193 111 287 1.89e-36 129
MS.gene53899.t1 MTR_4g062370 38.068 176 104 2 1 176 87 257 6.10e-36 133
MS.gene53899.t1 MTR_3g449750 40.426 141 82 2 13 152 31 170 1.25e-32 116
MS.gene53899.t1 MTR_5g094740 36.129 155 90 1 39 193 673 818 1.51e-28 112
MS.gene53899.t1 MTR_3g085990 34.031 191 84 2 1 191 84 232 2.51e-28 106
MS.gene53899.t1 MTR_1g019580 40.164 122 70 1 77 195 9 130 1.42e-26 99.0
MS.gene53899.t1 MTR_4g081330 64.516 62 22 0 113 174 1084 1145 9.13e-26 104
MS.gene53899.t1 MTR_8g042540 48.235 85 44 0 111 195 3 87 3.51e-25 94.0
MS.gene53899.t1 MTR_5g066660 32.105 190 97 3 1 190 83 240 7.16e-25 98.2
MS.gene53899.t1 MTR_8g042540 48.780 82 42 0 114 195 18 99 1.40e-24 92.8
MS.gene53899.t1 MTR_4g117740 32.857 140 60 2 1 140 94 199 1.33e-22 90.5
MS.gene53899.t1 MTR_0521s0010 37.008 127 78 2 14 139 76 201 1.20e-21 89.0
MS.gene53899.t1 MTR_2g016390 38.235 102 63 0 78 179 593 694 4.21e-19 85.1
MS.gene53899.t1 MTR_6g465600 29.381 194 126 2 2 191 90 276 7.28e-19 82.8
MS.gene53899.t1 MTR_5g075200 40.000 100 55 2 1 100 96 190 1.13e-17 77.8
MS.gene53899.t1 MTR_1g052720 27.041 196 128 4 2 192 87 272 7.13e-17 77.4
MS.gene53899.t1 MTR_1g037600 36.842 95 60 0 78 172 60 154 2.02e-16 75.5
MS.gene53899.t1 MTR_4g057880 47.692 65 34 0 129 193 7 71 1.67e-15 68.6
MS.gene53899.t1 MTR_0091s0090 27.461 193 120 6 2 192 6 180 3.78e-15 72.0
MS.gene53899.t1 MTR_0152s0060 38.636 88 53 1 92 179 221 307 1.32e-14 71.6
MS.gene53899.t1 MTR_6g016445 42.373 59 34 0 115 173 10 68 1.48e-12 61.6
MS.gene53899.t1 MTR_1g045920 76.190 42 10 0 1 42 42 83 6.60e-12 63.2
MS.gene53899.t1 MTR_1g054585 30.172 116 61 1 78 193 11 106 1.25e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 46 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAATTGCATCACAATATT+TGG 0.142675 5.2:-68904431 MS.gene53899:CDS
TGATGTTAGCTCTGGATTTC+TGG 0.165668 5.2:-68904628 MS.gene53899:intron
CTTCTCAATTTCAAACTTCA+TGG 0.267710 5.2:+68904764 None:intergenic
TGATGGAATGAGAGGATTTC+GGG 0.294439 5.2:+68904699 None:intergenic
TCTCAAACTCAAACAACTAT+TGG 0.300126 5.2:+68904266 None:intergenic
TTTACTGGTAATGGTCAGTT+TGG 0.323884 5.2:-68904843 MS.gene53899:CDS
ACGTTTCACTTCAATGTAGA+TGG 0.346590 5.2:+68904289 None:intergenic
ATGATGGAATGAGAGGATTT+CGG 0.364690 5.2:+68904698 None:intergenic
TTCATGGGAGGTATAAATAA+AGG 0.396538 5.2:+68904780 None:intergenic
GTGCCATCGTTTGTTTATCA+AGG 0.414248 5.2:-68904735 MS.gene53899:CDS
TTACTGGTAATGGTCAGTTT+GGG 0.414794 5.2:-68904842 MS.gene53899:CDS
ACTATCGTCATGGTGTTTAC+TGG 0.438683 5.2:-68904858 MS.gene53899:CDS
GAGAGGATTTCGGGTGTGAC+TGG 0.444509 5.2:+68904708 None:intergenic
ACTGGATATGATGTTAGCTC+TGG 0.447476 5.2:-68904636 MS.gene53899:CDS
GCATCACAATATTTGGAACT+AGG 0.455508 5.2:-68904424 MS.gene53899:CDS
TTCTCAATTTCAAACTTCAT+GGG 0.459280 5.2:+68904765 None:intergenic
GGACTATGTGACGTGACAAT+TGG 0.459653 5.2:-68904500 MS.gene53899:CDS
AGCTTGGAGGAGGGTGGAAA+AGG 0.464293 5.2:-68904385 MS.gene53899:CDS
GTCATGGTGTTTACTGGTAA+TGG 0.491948 5.2:-68904852 MS.gene53899:CDS
TGGAGGAGGGTGGAAAAGGA+TGG 0.500308 5.2:-68904381 MS.gene53899:CDS
GAAGGTGTCGTGGTCAAGGT+TGG 0.513832 5.2:-68904338 MS.gene53899:CDS
CCACACCACCACATCAAGCT+TGG 0.515731 5.2:-68904401 MS.gene53899:CDS
GAAAATTGATCTCATCATGA+TGG 0.516547 5.2:+68904682 None:intergenic
CTCCTCCAAGCTTGATGTGG+TGG 0.531491 5.2:+68904396 None:intergenic
CACCACATCAAGCTTGGAGG+AGG 0.534818 5.2:-68904395 MS.gene53899:CDS
AACGCACATTGTAAAAGTCT+CGG 0.537561 5.2:+68904889 None:intergenic
ACCCTCCTCCAAGCTTGATG+TGG 0.545430 5.2:+68904393 None:intergenic
TGAAGAAGGTGTCGTGGTCA+AGG 0.545787 5.2:-68904342 MS.gene53899:CDS
CCAAGCTTGATGTGGTGGTG+TGG 0.547240 5.2:+68904401 None:intergenic
CACCACCACATCAAGCTTGG+AGG 0.557816 5.2:-68904398 MS.gene53899:CDS
GTCATGGTGGAAAGGATAAG+TGG 0.571095 5.2:-68904945 MS.gene53899:CDS
TTGCAGATGCTTATTTACAA+AGG 0.583138 5.2:-68904521 MS.gene53899:intron
AGTTTGATGTCATGGTGGAA+AGG 0.589089 5.2:-68904953 None:intergenic
TCTCATCATGATGGAATGAG+AGG 0.601577 5.2:+68904691 None:intergenic
TCAATTTCAAACTTCATGGG+AGG 0.602862 5.2:+68904768 None:intergenic
ACATCAAGCTTGGAGGAGGG+TGG 0.613250 5.2:-68904391 MS.gene53899:CDS
AAGGTTGGATTTCGACACGC+TGG 0.618883 5.2:-68904323 MS.gene53899:CDS
TTGACGATTGTGGGAACAAG+TGG 0.630425 5.2:-68904451 MS.gene53899:CDS
ACCACATCAAGCTTGGAGGA+GGG 0.639220 5.2:-68904394 MS.gene53899:CDS
GCTGCGCGGAGACTTGAAGA+AGG 0.643869 5.2:-68904356 MS.gene53899:CDS
TTTAGGCGGAACTATCGTCA+TGG 0.647378 5.2:-68904868 MS.gene53899:CDS
ATTAACGTACTTGATCGAGC+AGG 0.652929 5.2:-68904819 MS.gene53899:CDS
ATGGGAGGTATAAATAAAGG+AGG 0.660218 5.2:+68904783 None:intergenic
GAGACTTGAAGAAGGTGTCG+TGG 0.672602 5.2:-68904348 MS.gene53899:CDS
ACACCTTGATAAACAAACGA+TGG 0.686570 5.2:+68904732 None:intergenic
GGAAAAGGATGGTTGCTGCG+CGG 0.715685 5.2:-68904370 MS.gene53899:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCTCAATTTCAAACTTCAT+GGG + chr5.2:68904454-68904473 None:intergenic 25.0%
CTTCTCAATTTCAAACTTCA+TGG + chr5.2:68904455-68904474 None:intergenic 30.0%
GAAAATTGATCTCATCATGA+TGG + chr5.2:68904537-68904556 None:intergenic 30.0%
TGGAATTGCATCACAATATT+TGG - chr5.2:68904785-68904804 MS.gene53899:CDS 30.0%
TTGCAGATGCTTATTTACAA+AGG - chr5.2:68904695-68904714 MS.gene53899:CDS 30.0%
! AGATCAATTTTCAGATAAGC+TGG - chr5.2:68904545-68904564 MS.gene53899:intron 30.0%
! GATCAATTTTCAGATAAGCT+GGG - chr5.2:68904546-68904565 MS.gene53899:intron 30.0%
! TTCATGGGAGGTATAAATAA+AGG + chr5.2:68904439-68904458 None:intergenic 30.0%
!!! GGAGTTGTTTTTTTAACAAC+TGG - chr5.2:68904292-68904311 MS.gene53899:CDS 30.0%
AACGCACATTGTAAAAGTCT+CGG + chr5.2:68904330-68904349 None:intergenic 35.0%
ACACCTTGATAAACAAACGA+TGG + chr5.2:68904487-68904506 None:intergenic 35.0%
ACGTTTCACTTCAATGTAGA+TGG + chr5.2:68904930-68904949 None:intergenic 35.0%
TCAATTTCAAACTTCATGGG+AGG + chr5.2:68904451-68904470 None:intergenic 35.0%
! ATGATGGAATGAGAGGATTT+CGG + chr5.2:68904521-68904540 None:intergenic 35.0%
! ATGGGAGGTATAAATAAAGG+AGG + chr5.2:68904436-68904455 None:intergenic 35.0%
! GACTTTTACAATGTGCGTTT+AGG - chr5.2:68904331-68904350 MS.gene53899:CDS 35.0%
! GCATCACAATATTTGGAACT+AGG - chr5.2:68904792-68904811 MS.gene53899:CDS 35.0%
! TGATTTTGCTTGACGATTGT+GGG - chr5.2:68904756-68904775 MS.gene53899:CDS 35.0%
! TTGATTTTGCTTGACGATTG+TGG - chr5.2:68904755-68904774 MS.gene53899:CDS 35.0%
! TTTTACAATGTGCGTTTAGG+CGG - chr5.2:68904334-68904353 MS.gene53899:CDS 35.0%
!! TTACTGGTAATGGTCAGTTT+GGG - chr5.2:68904374-68904393 MS.gene53899:CDS 35.0%
!! TTTACTGGTAATGGTCAGTT+TGG - chr5.2:68904373-68904392 MS.gene53899:CDS 35.0%
ACTATCGTCATGGTGTTTAC+TGG - chr5.2:68904358-68904377 MS.gene53899:CDS 40.0%
ACTGGATATGATGTTAGCTC+TGG - chr5.2:68904580-68904599 MS.gene53899:intron 40.0%
ATTAACGTACTTGATCGAGC+AGG - chr5.2:68904397-68904416 MS.gene53899:CDS 40.0%
GTCATGGTGTTTACTGGTAA+TGG - chr5.2:68904364-68904383 MS.gene53899:CDS 40.0%
GTGCCATCGTTTGTTTATCA+AGG - chr5.2:68904481-68904500 MS.gene53899:CDS 40.0%
TGATGGAATGAGAGGATTTC+GGG + chr5.2:68904520-68904539 None:intergenic 40.0%
! TCTCATCATGATGGAATGAG+AGG + chr5.2:68904528-68904547 None:intergenic 40.0%
!! TGATGTTAGCTCTGGATTTC+TGG - chr5.2:68904588-68904607 MS.gene53899:intron 40.0%
GGACTATGTGACGTGACAAT+TGG - chr5.2:68904716-68904735 MS.gene53899:CDS 45.0%
TTGACGATTGTGGGAACAAG+TGG - chr5.2:68904765-68904784 MS.gene53899:CDS 45.0%
TTTAGGCGGAACTATCGTCA+TGG - chr5.2:68904348-68904367 MS.gene53899:CDS 45.0%
!! AGCTGGGAAAAAGTGTTGAC+TGG - chr5.2:68904562-68904581 MS.gene53899:intron 45.0%
AAGGTTGGATTTCGACACGC+TGG - chr5.2:68904893-68904912 MS.gene53899:CDS 50.0%
ACCACATCAAGCTTGGAGGA+GGG - chr5.2:68904822-68904841 MS.gene53899:CDS 50.0%
!! GAGACTTGAAGAAGGTGTCG+TGG - chr5.2:68904868-68904887 MS.gene53899:CDS 50.0%
!! TGAAGAAGGTGTCGTGGTCA+AGG - chr5.2:68904874-68904893 MS.gene53899:CDS 50.0%
ACATCAAGCTTGGAGGAGGG+TGG - chr5.2:68904825-68904844 MS.gene53899:CDS 55.0%
ACCCTCCTCCAAGCTTGATG+TGG + chr5.2:68904826-68904845 None:intergenic 55.0%
AGCTTGGAGGAGGGTGGAAA+AGG - chr5.2:68904831-68904850 MS.gene53899:CDS 55.0%
CACCACATCAAGCTTGGAGG+AGG - chr5.2:68904821-68904840 MS.gene53899:CDS 55.0%
CACCACCACATCAAGCTTGG+AGG - chr5.2:68904818-68904837 MS.gene53899:CDS 55.0%
CCACACCACCACATCAAGCT+TGG - chr5.2:68904815-68904834 MS.gene53899:CDS 55.0%
CTCCTCCAAGCTTGATGTGG+TGG + chr5.2:68904823-68904842 None:intergenic 55.0%
GGAAAAGGATGGTTGCTGCG+CGG - chr5.2:68904846-68904865 MS.gene53899:CDS 55.0%
TGGAGGAGGGTGGAAAAGGA+TGG - chr5.2:68904835-68904854 MS.gene53899:CDS 55.0%
! CCAAGCTTGATGTGGTGGTG+TGG + chr5.2:68904818-68904837 None:intergenic 55.0%
! GAGAGGATTTCGGGTGTGAC+TGG + chr5.2:68904511-68904530 None:intergenic 55.0%
!! GAAGGTGTCGTGGTCAAGGT+TGG - chr5.2:68904878-68904897 MS.gene53899:CDS 55.0%
GCTGCGCGGAGACTTGAAGA+AGG - chr5.2:68904860-68904879 MS.gene53899:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 68904274 68904964 68904274 ID=MS.gene53899
chr5.2 mRNA 68904274 68904964 68904274 ID=MS.gene53899.t1;Parent=MS.gene53899
chr5.2 exon 68904629 68904964 68904629 ID=MS.gene53899.t1.exon1;Parent=MS.gene53899.t1
chr5.2 CDS 68904629 68904964 68904629 ID=cds.MS.gene53899.t1;Parent=MS.gene53899.t1
chr5.2 exon 68904274 68904537 68904274 ID=MS.gene53899.t1.exon2;Parent=MS.gene53899.t1
chr5.2 CDS 68904274 68904537 68904274 ID=cds.MS.gene53899.t1;Parent=MS.gene53899.t1
Gene Sequence

>MS.gene53899

ATGGTGGAAAGGATAAGTGGAGTTGTTTTTTTAACAACTGGATTCAATGCGATCCGAGACTTTTACAATGTGCGTTTAGGCGGAACTATCGTCATGGTGTTTACTGGTAATGGTCAGTTTGGGATTAACGTACTTGATCGAGCAGGACGTGTTGTTGATCCTCCTTTATTTATACCTCCCATGAAGTTTGAAATTGAGAAGACAATTGTGCCATCGTTTGTTTATCAAGGTGTGCCAGTCACACCCGAAATCCTCTCATTCCATCATGATGAGATCAATTTTCAGATAAGCTGGGAAAAAGTGTTGACTGGATATGATGTTAGCTCTGGATTTCTGGTATAAGTTTGATGTATTAGTATTGCTCACATAAACAGTTACTTTTAGCATATATACATTTGTTTGTATTAACACATCTTGATGTTTGCAGATGCTTATTTACAAAGGACTATGTGACGTGACAATTGGCAAGAAGACAACTTCATTGATTTTGCTTGACGATTGTGGGAACAAGTGGAATTGCATCACAATATTTGGAACTAGGCCACACCACCACATCAAGCTTGGAGGAGGGTGGAAAAGGATGGTTGCTGCGCGGAGACTTGAAGAAGGTGTCGTGGTCAAGGTTGGATTTCGACACGCTGGAAAGAACGATACCATCTACATTGAAGTGAAACGTCCAATAGTTGTTTGA
Protein sequence

>MS.gene53899.t1

MVERISGVVFLTTGFNAIRDFYNVRLGGTIVMVFTGNGQFGINVLDRAGRVVDPPLFIPPMKFEIEKTIVPSFVYQGVPVTPEILSFHHDEINFQISWEKVLTGYDVSSGFLMLIYKGLCDVTIGKKTTSLILLDDCGNKWNCITIFGTRPHHHIKLGGGWKRMVAARRLEEGVVVKVGFRHAGKNDTIYIEVKRPIVV