AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59239.t1 MTR_1g087870 82.915 199 34 0 1 199 31 229 6.66e-124 350
MS.gene59239.t1 MTR_7g110090 43.814 194 104 1 2 195 84 272 3.17e-57 182
MS.gene59239.t1 MTR_3g452180 43.850 187 100 1 9 195 7 188 4.28e-56 176
MS.gene59239.t1 MTR_4g032560 40.513 195 111 1 1 195 112 301 5.71e-51 166
MS.gene59239.t1 MTR_4g032580 40.513 195 111 1 1 195 112 301 1.64e-50 165
MS.gene59239.t1 MTR_2g100360 44.000 175 98 0 1 175 83 257 4.79e-50 163
MS.gene59239.t1 MTR_3g070250 39.896 193 116 0 1 193 88 280 9.51e-50 163
MS.gene59239.t1 MTR_3g048970 42.268 194 110 2 1 193 83 275 1.25e-49 162
MS.gene59239.t1 MTR_1g084880 42.268 194 110 2 1 193 83 275 3.24e-49 161
MS.gene59239.t1 MTR_1g105780 41.026 195 110 1 1 195 84 273 1.02e-44 149
MS.gene59239.t1 MTR_1g105765 41.026 195 110 1 1 195 84 273 1.05e-44 149
MS.gene59239.t1 MTR_4g121040 39.053 169 98 1 21 189 7 170 6.42e-40 135
MS.gene59239.t1 MTR_1g047540 39.683 189 94 3 2 190 84 252 2.26e-38 137
MS.gene59239.t1 MTR_2g038740 42.138 159 92 0 1 159 83 241 3.87e-38 139
MS.gene59239.t1 MTR_1g069260 37.912 182 96 3 24 193 111 287 1.89e-36 129
MS.gene59239.t1 MTR_4g062370 38.068 176 104 2 1 176 87 257 6.10e-36 133
MS.gene59239.t1 MTR_3g449750 40.426 141 82 2 13 152 31 170 1.25e-32 116
MS.gene59239.t1 MTR_5g094740 36.129 155 90 1 39 193 673 818 1.51e-28 112
MS.gene59239.t1 MTR_3g085990 34.031 191 84 2 1 191 84 232 2.51e-28 106
MS.gene59239.t1 MTR_1g019580 40.164 122 70 1 77 195 9 130 1.42e-26 99.0
MS.gene59239.t1 MTR_4g081330 64.516 62 22 0 113 174 1084 1145 9.13e-26 104
MS.gene59239.t1 MTR_8g042540 48.235 85 44 0 111 195 3 87 3.51e-25 94.0
MS.gene59239.t1 MTR_5g066660 32.105 190 97 3 1 190 83 240 7.16e-25 98.2
MS.gene59239.t1 MTR_8g042540 48.780 82 42 0 114 195 18 99 1.40e-24 92.8
MS.gene59239.t1 MTR_4g117740 32.857 140 60 2 1 140 94 199 1.33e-22 90.5
MS.gene59239.t1 MTR_0521s0010 37.008 127 78 2 14 139 76 201 1.20e-21 89.0
MS.gene59239.t1 MTR_2g016390 38.235 102 63 0 78 179 593 694 4.21e-19 85.1
MS.gene59239.t1 MTR_6g465600 29.381 194 126 2 2 191 90 276 7.28e-19 82.8
MS.gene59239.t1 MTR_5g075200 40.000 100 55 2 1 100 96 190 1.13e-17 77.8
MS.gene59239.t1 MTR_1g052720 27.041 196 128 4 2 192 87 272 7.13e-17 77.4
MS.gene59239.t1 MTR_1g037600 36.842 95 60 0 78 172 60 154 2.02e-16 75.5
MS.gene59239.t1 MTR_4g057880 47.692 65 34 0 129 193 7 71 1.67e-15 68.6
MS.gene59239.t1 MTR_0091s0090 27.461 193 120 6 2 192 6 180 3.78e-15 72.0
MS.gene59239.t1 MTR_0152s0060 38.636 88 53 1 92 179 221 307 1.32e-14 71.6
MS.gene59239.t1 MTR_6g016445 42.373 59 34 0 115 173 10 68 1.48e-12 61.6
MS.gene59239.t1 MTR_1g045920 76.190 42 10 0 1 42 42 83 6.60e-12 63.2
MS.gene59239.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:+68781170 MS.gene59239:CDS
TGATGTTAGCTCTGGATTTC+TGG 0.165668 5.2:+68780973 MS.gene59239:CDS
CTTCTCAATTTCAAACTTCA+TGG 0.267710 5.2:-68780837 None:intergenic
TGATGGAATGAGAGGATTTC+GGG 0.294439 5.2:-68780902 None:intergenic
TCTCAAACTCAAACAACTAT+TGG 0.300126 5.2:-68781335 None:intergenic
TTTACTGGTAATGGTCAGTT+TGG 0.323884 5.2:+68780758 MS.gene59239:CDS
ACGTTTCACTTCAATGTAGA+TGG 0.346590 5.2:-68781312 None:intergenic
ATGATGGAATGAGAGGATTT+CGG 0.364690 5.2:-68780903 None:intergenic
TTCATGGGAGGTATAAATAA+AGG 0.396538 5.2:-68780821 None:intergenic
GTGCCATCGTTTGTTTATCA+AGG 0.414248 5.2:+68780866 MS.gene59239:CDS
TTACTGGTAATGGTCAGTTT+GGG 0.414794 5.2:+68780759 MS.gene59239:CDS
ACTATCGTCATGGTGTTTAC+TGG 0.438683 5.2:+68780743 MS.gene59239:CDS
GAGAGGATTTCGGGTGTGAC+TGG 0.444509 5.2:-68780893 None:intergenic
ACTGGATATGATGTTAGCTC+TGG 0.447476 5.2:+68780965 MS.gene59239:CDS
GCATCACAATATTTGGAACT+AGG 0.455508 5.2:+68781177 MS.gene59239:CDS
TTCTCAATTTCAAACTTCAT+GGG 0.459280 5.2:-68780836 None:intergenic
GGACTATGTGACGTGACAAT+TGG 0.459653 5.2:+68781101 MS.gene59239:CDS
AGCTTGGAGGAGGGTGGAAA+AGG 0.464293 5.2:+68781216 MS.gene59239:CDS
GTCATGGTGTTTACTGGTAA+TGG 0.491948 5.2:+68780749 MS.gene59239:CDS
TGGAGGAGGGTGGAAAAGGA+TGG 0.500308 5.2:+68781220 MS.gene59239:CDS
GAAGGTGTCGTGGTCAAGGT+TGG 0.513832 5.2:+68781263 MS.gene59239:CDS
CCACACCACCACATCAAGCT+TGG 0.515731 5.2:+68781200 MS.gene59239:CDS
GAAAATTGATCTCATCATGA+TGG 0.516547 5.2:-68780919 None:intergenic
CTCCTCCAAGCTTGATGTGG+TGG 0.531491 5.2:-68781205 None:intergenic
CACCACATCAAGCTTGGAGG+AGG 0.534818 5.2:+68781206 MS.gene59239:CDS
AACGCACATTGTAAAAGTCT+CGG 0.537561 5.2:-68780712 None:intergenic
ACCCTCCTCCAAGCTTGATG+TGG 0.545430 5.2:-68781208 None:intergenic
TGAAGAAGGTGTCGTGGTCA+AGG 0.545787 5.2:+68781259 MS.gene59239:CDS
CCAAGCTTGATGTGGTGGTG+TGG 0.547240 5.2:-68781200 None:intergenic
CACCACCACATCAAGCTTGG+AGG 0.557816 5.2:+68781203 MS.gene59239:CDS
GTCATGGTGGAAAGGATAAG+TGG 0.571095 5.2:+68780656 None:intergenic
TTGCAGATGCTTATTTACAA+AGG 0.583138 5.2:+68781080 MS.gene59239:intron
AGTTTGATGTCATGGTGGAA+AGG 0.589089 5.2:+68780648 None:intergenic
TCTCATCATGATGGAATGAG+AGG 0.601577 5.2:-68780910 None:intergenic
TCAATTTCAAACTTCATGGG+AGG 0.602862 5.2:-68780833 None:intergenic
ACATCAAGCTTGGAGGAGGG+TGG 0.613250 5.2:+68781210 MS.gene59239:CDS
AAGGTTGGATTTCGACACGC+TGG 0.618883 5.2:+68781278 MS.gene59239:CDS
TTGACGATTGTGGGAACAAG+TGG 0.630425 5.2:+68781150 MS.gene59239:CDS
ACCACATCAAGCTTGGAGGA+GGG 0.639220 5.2:+68781207 MS.gene59239:CDS
GCTGCGCGGAGACTTGAAGA+AGG 0.643869 5.2:+68781245 MS.gene59239:CDS
TTTAGGCGGAACTATCGTCA+TGG 0.647378 5.2:+68780733 MS.gene59239:CDS
ATTAACGTACTTGATCGAGC+AGG 0.652929 5.2:+68780782 MS.gene59239:CDS
ATGGGAGGTATAAATAAAGG+AGG 0.660218 5.2:-68780818 None:intergenic
GAGACTTGAAGAAGGTGTCG+TGG 0.672602 5.2:+68781253 MS.gene59239:CDS
ACACCTTGATAAACAAACGA+TGG 0.686570 5.2:-68780869 None:intergenic
GGAAAAGGATGGTTGCTGCG+CGG 0.715685 5.2:+68781231 MS.gene59239:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTCTCAATTTCAAACTTCAT+GGG - chr5.2:68780839-68780858 None:intergenic 25.0%
CTTCTCAATTTCAAACTTCA+TGG - chr5.2:68780840-68780859 None:intergenic 30.0%
GAAAATTGATCTCATCATGA+TGG - chr5.2:68780922-68780941 None:intergenic 30.0%
TGGAATTGCATCACAATATT+TGG + chr5.2:68781170-68781189 MS.gene59239:CDS 30.0%
TTGCAGATGCTTATTTACAA+AGG + chr5.2:68781080-68781099 MS.gene59239:intron 30.0%
! AGATCAATTTTCAGATAAGC+TGG + chr5.2:68780930-68780949 MS.gene59239:CDS 30.0%
! GATCAATTTTCAGATAAGCT+GGG + chr5.2:68780931-68780950 MS.gene59239:CDS 30.0%
! TTCATGGGAGGTATAAATAA+AGG - chr5.2:68780824-68780843 None:intergenic 30.0%
!!! GGAGTTGTTTTTTTAACAAC+TGG + chr5.2:68780677-68780696 MS.gene59239:CDS 30.0%
AACGCACATTGTAAAAGTCT+CGG - chr5.2:68780715-68780734 None:intergenic 35.0%
ACACCTTGATAAACAAACGA+TGG - chr5.2:68780872-68780891 None:intergenic 35.0%
ACGTTTCACTTCAATGTAGA+TGG - chr5.2:68781315-68781334 None:intergenic 35.0%
TCAATTTCAAACTTCATGGG+AGG - chr5.2:68780836-68780855 None:intergenic 35.0%
! ATGATGGAATGAGAGGATTT+CGG - chr5.2:68780906-68780925 None:intergenic 35.0%
! ATGGGAGGTATAAATAAAGG+AGG - chr5.2:68780821-68780840 None:intergenic 35.0%
! GACTTTTACAATGTGCGTTT+AGG + chr5.2:68780716-68780735 MS.gene59239:CDS 35.0%
! GCATCACAATATTTGGAACT+AGG + chr5.2:68781177-68781196 MS.gene59239:CDS 35.0%
! TGATTTTGCTTGACGATTGT+GGG + chr5.2:68781141-68781160 MS.gene59239:CDS 35.0%
! TTGATTTTGCTTGACGATTG+TGG + chr5.2:68781140-68781159 MS.gene59239:CDS 35.0%
! TTTTACAATGTGCGTTTAGG+CGG + chr5.2:68780719-68780738 MS.gene59239:CDS 35.0%
!! TTACTGGTAATGGTCAGTTT+GGG + chr5.2:68780759-68780778 MS.gene59239:CDS 35.0%
!! TTTACTGGTAATGGTCAGTT+TGG + chr5.2:68780758-68780777 MS.gene59239:CDS 35.0%
ACTATCGTCATGGTGTTTAC+TGG + chr5.2:68780743-68780762 MS.gene59239:CDS 40.0%
ACTGGATATGATGTTAGCTC+TGG + chr5.2:68780965-68780984 MS.gene59239:CDS 40.0%
ATTAACGTACTTGATCGAGC+AGG + chr5.2:68780782-68780801 MS.gene59239:CDS 40.0%
GTCATGGTGTTTACTGGTAA+TGG + chr5.2:68780749-68780768 MS.gene59239:CDS 40.0%
GTGCCATCGTTTGTTTATCA+AGG + chr5.2:68780866-68780885 MS.gene59239:CDS 40.0%
TGATGGAATGAGAGGATTTC+GGG - chr5.2:68780905-68780924 None:intergenic 40.0%
! TCTCATCATGATGGAATGAG+AGG - chr5.2:68780913-68780932 None:intergenic 40.0%
!! TGATGTTAGCTCTGGATTTC+TGG + chr5.2:68780973-68780992 MS.gene59239:CDS 40.0%
GGACTATGTGACGTGACAAT+TGG + chr5.2:68781101-68781120 MS.gene59239:CDS 45.0%
TTGACGATTGTGGGAACAAG+TGG + chr5.2:68781150-68781169 MS.gene59239:CDS 45.0%
TTTAGGCGGAACTATCGTCA+TGG + chr5.2:68780733-68780752 MS.gene59239:CDS 45.0%
!! AGCTGGGAAAAAGTGTTGAC+TGG + chr5.2:68780947-68780966 MS.gene59239:CDS 45.0%
AAGGTTGGATTTCGACACGC+TGG + chr5.2:68781278-68781297 MS.gene59239:CDS 50.0%
ACCACATCAAGCTTGGAGGA+GGG + chr5.2:68781207-68781226 MS.gene59239:CDS 50.0%
!! GAGACTTGAAGAAGGTGTCG+TGG + chr5.2:68781253-68781272 MS.gene59239:CDS 50.0%
!! TGAAGAAGGTGTCGTGGTCA+AGG + chr5.2:68781259-68781278 MS.gene59239:CDS 50.0%
ACATCAAGCTTGGAGGAGGG+TGG + chr5.2:68781210-68781229 MS.gene59239:CDS 55.0%
ACCCTCCTCCAAGCTTGATG+TGG - chr5.2:68781211-68781230 None:intergenic 55.0%
AGCTTGGAGGAGGGTGGAAA+AGG + chr5.2:68781216-68781235 MS.gene59239:CDS 55.0%
CACCACATCAAGCTTGGAGG+AGG + chr5.2:68781206-68781225 MS.gene59239:CDS 55.0%
CACCACCACATCAAGCTTGG+AGG + chr5.2:68781203-68781222 MS.gene59239:CDS 55.0%
CCACACCACCACATCAAGCT+TGG + chr5.2:68781200-68781219 MS.gene59239:CDS 55.0%
CTCCTCCAAGCTTGATGTGG+TGG - chr5.2:68781208-68781227 None:intergenic 55.0%
GGAAAAGGATGGTTGCTGCG+CGG + chr5.2:68781231-68781250 MS.gene59239:CDS 55.0%
TGGAGGAGGGTGGAAAAGGA+TGG + chr5.2:68781220-68781239 MS.gene59239:CDS 55.0%
! CCAAGCTTGATGTGGTGGTG+TGG - chr5.2:68781203-68781222 None:intergenic 55.0%
! GAGAGGATTTCGGGTGTGAC+TGG - chr5.2:68780896-68780915 None:intergenic 55.0%
!! GAAGGTGTCGTGGTCAAGGT+TGG + chr5.2:68781263-68781282 MS.gene59239:CDS 55.0%
GCTGCGCGGAGACTTGAAGA+AGG + chr5.2:68781245-68781264 MS.gene59239:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 68780659 68781349 68780659 ID=MS.gene59239
chr5.2 mRNA 68780659 68781349 68780659 ID=MS.gene59239.t1;Parent=MS.gene59239
chr5.2 exon 68780659 68780994 68780659 ID=MS.gene59239.t1.exon1;Parent=MS.gene59239.t1
chr5.2 CDS 68780659 68780994 68780659 ID=cds.MS.gene59239.t1;Parent=MS.gene59239.t1
chr5.2 exon 68781086 68781349 68781086 ID=MS.gene59239.t1.exon2;Parent=MS.gene59239.t1
chr5.2 CDS 68781086 68781349 68781086 ID=cds.MS.gene59239.t1;Parent=MS.gene59239.t1
Gene Sequence

>MS.gene59239

ATGGTGGAAAGGATAAGTGGAGTTGTTTTTTTAACAACTGGATTCAATGCGATCCGAGACTTTTACAATGTGCGTTTAGGCGGAACTATCGTCATGGTGTTTACTGGTAATGGTCAGTTTGGGATTAACGTACTTGATCGAGCAGGACGTGTTGTTGATCCTCCTTTATTTATACCTCCCATGAAGTTTGAAATTGAGAAGACAATTGTGCCATCGTTTGTTTATCAAGGTGTGCCAGTCACACCCGAAATCCTCTCATTCCATCATGATGAGATCAATTTTCAGATAAGCTGGGAAAAAGTGTTGACTGGATATGATGTTAGCTCTGGATTTCTGGTATAAGTTTGATGTATTAGTATTGCTCACATAAACAGTTACTTTTAGCATATATACATTTGTTTGTATTAACACATCTTGATGTTTGCAGATGCTTATTTACAAAGGACTATGTGACGTGACAATTGGCAAGAAGACAACTTCATTGATTTTGCTTGACGATTGTGGGAACAAGTGGAATTGCATCACAATATTTGGAACTAGGCCACACCACCACATCAAGCTTGGAGGAGGGTGGAAAAGGATGGTTGCTGCGCGGAGACTTGAAGAAGGTGTCGTGGTCAAGGTTGGATTTCGACACGCTGGAAAGAACGATACCATCTACATTGAAGTGAAACGTCCAATAGTTGTTTGA
Protein sequence

>MS.gene59239.t1

MVERISGVVFLTTGFNAIRDFYNVRLGGTIVMVFTGNGQFGINVLDRAGRVVDPPLFIPPMKFEIEKTIVPSFVYQGVPVTPEILSFHHDEINFQISWEKVLTGYDVSSGFLMLIYKGLCDVTIGKKTTSLILLDDCGNKWNCITIFGTRPHHHIKLGGGWKRMVAARRLEEGVVVKVGFRHAGKNDTIYIEVKRPIVV