AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0588820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0588820 MtrunA17_Chr4g0005031 93.500 200 12 1 1 200 23 221 1.55e-131 368
Msa0588820 MtrunA17_Chr4g0005081 77.500 200 42 2 1 200 1 197 1.53e-110 314
Msa0588820 MtrunA17_Chr4g0005071 76.500 200 43 2 1 200 1 196 8.60e-108 307
Msa0588820 MtrunA17_Chr4g0005041 72.727 187 44 3 16 200 17 198 7.10e-102 292
Msa0588820 MtrunA17_Chr4g0005011 73.000 200 51 2 1 200 1 197 2.00e-99 286
Msa0588820 MtrunA17_Chr7g0243501 71.512 172 46 2 30 200 23 192 1.88e-80 238
Msa0588820 MtrunA17_Chr4g0005111 57.812 192 72 3 9 200 8 190 1.05e-74 223
Msa0588820 MtrunA17_Chr1g0175911 55.682 176 75 2 25 200 20 192 2.25e-67 204
Msa0588820 MtrunA17_Chr4g0005131 57.059 170 71 1 31 200 24 191 6.85e-66 201
Msa0588820 MtrunA17_Chr4g0037481 53.947 152 70 0 49 200 41 192 6.23e-58 181
Msa0588820 MtrunA17_Chr7g0259091 48.677 189 91 5 13 200 11 194 7.80e-55 172
Msa0588820 MtrunA17_Chr7g0259071 49.102 167 82 3 35 200 27 191 1.49e-54 172
Msa0588820 MtrunA17_Chr4g0005091 51.562 192 71 6 9 200 6 175 2.97e-54 171
Msa0588820 MtrunA17_Chr7g0259121 53.846 156 68 2 49 200 38 193 3.01e-54 172
Msa0588820 MtrunA17_Chr7g0259101 48.148 189 92 5 13 200 11 194 1.45e-52 173
Msa0588820 MtrunA17_Chr7g0259101 46.561 189 95 5 13 200 210 393 1.57e-51 170
Msa0588820 MtrunA17_Chr1g0177051 50.980 153 69 3 51 199 35 185 4.01e-49 158
Msa0588820 MtrunA17_Chr3g0136641 46.584 161 85 1 41 200 28 188 2.08e-47 154
Msa0588820 MtrunA17_Chr4g0040551 46.358 151 78 1 50 200 38 185 5.44e-44 145
Msa0588820 MtrunA17_Chr3g0090231 46.358 151 78 1 50 200 38 185 1.13e-43 144
Msa0588820 MtrunA17_Chr3g0085301 41.919 198 103 4 2 199 8 193 1.58e-43 144
Msa0588820 MtrunA17_Chr3g0085311 47.651 149 75 1 51 199 43 188 3.59e-43 143
Msa0588820 MtrunA17_Chr3g0085291 47.651 149 73 1 51 199 43 186 7.32e-43 142
Msa0588820 MtrunA17_Chr3g0136631 44.654 159 86 2 44 200 31 189 9.43e-43 142
Msa0588820 MtrunA17_Chr3g0085321 42.487 193 96 5 11 199 7 188 3.54e-42 140
Msa0588820 MtrunA17_Chr5g0446751 41.401 157 79 3 52 200 38 189 5.89e-38 129
Msa0588820 MtrunA17_Chr4g0068381 38.095 147 90 1 54 200 35 180 7.97e-28 103
Msa0588820 MtrunA17_Chr4g0068391 38.462 143 87 1 58 200 39 180 2.59e-26 99.4
Msa0588820 MtrunA17_Chr4g0024951 30.921 152 96 2 48 195 27 173 3.32e-18 78.2
Msa0588820 MtrunA17_Chr4g0024961 31.081 148 93 2 52 195 31 173 1.09e-17 77.0
Msa0588820 MtrunA17_Chr8g0387701 32.857 140 86 3 51 183 34 172 5.25e-17 75.5
Msa0588820 MtrunA17_Chr4g0005061 71.429 42 8 1 159 200 189 226 1.20e-16 75.1
Msa0588820 MtrunA17_Chr4g0005061 65.854 41 14 0 82 122 3 43 4.59e-13 65.5
Msa0588820 MtrunA17_Chr8g0387711 32.576 132 81 3 59 183 38 168 4.26e-15 70.1
Msa0588820 MtrunA17_Chr8g0370591 31.944 144 92 4 55 196 42 181 1.14e-13 66.6
Msa0588820 MtrunA17_Chr8g0370501 31.944 144 92 4 55 196 42 181 1.27e-13 66.2
Msa0588820 MtrunA17_Chr1g0212861 34.426 122 67 5 88 199 235 353 7.53e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0588820 AT1G55210.1 63.253 166 57 1 35 200 26 187 8.66e-77 228
Msa0588820 AT1G55210.2 63.253 166 57 1 35 200 26 187 8.66e-77 228
Msa0588820 AT1G58170.1 64.052 153 54 1 48 200 34 185 5.48e-74 221
Msa0588820 AT5G49040.1 54.737 190 84 2 11 200 4 191 2.22e-73 220
Msa0588820 AT3G13650.1 53.158 190 82 3 11 200 4 186 2.75e-68 207
Msa0588820 AT5G49030.3 53.933 178 78 2 9 186 4 177 7.63e-57 193
Msa0588820 AT3G13662.1 56.667 150 61 2 38 187 27 172 9.27e-56 175
Msa0588820 AT3G13660.1 66.102 118 40 0 83 200 8 125 5.73e-53 166
Msa0588820 AT2G21100.1 53.333 150 69 1 50 199 39 187 6.68e-53 168
Msa0588820 AT2G21100.2 53.333 150 69 1 50 199 39 187 6.68e-53 168
Msa0588820 AT1G65870.1 49.342 152 76 1 48 199 39 189 2.06e-52 167
Msa0588820 AT1G22900.1 49.342 152 74 2 48 199 45 193 3.38e-47 154
Msa0588820 AT5G42500.1 43.931 173 89 3 27 199 21 185 7.00e-46 150
Msa0588820 AT5G42510.1 48.684 152 73 3 49 199 35 182 1.35e-45 149
Msa0588820 AT4G38700.1 45.912 159 80 4 47 200 33 190 6.38e-42 140
Msa0588820 AT2G21110.1 41.860 172 91 2 32 200 21 186 3.68e-40 135
Msa0588820 AT3G58090.1 55.046 109 49 0 91 199 163 271 1.21e-39 137
Msa0588820 AT4G23690.1 34.286 140 84 3 47 182 34 169 1.90e-16 74.3
Msa0588820 AT1G64160.1 29.286 140 91 3 48 183 30 165 1.67e-14 68.9
Msa0588820 AT4G11210.1 27.841 176 114 3 8 183 4 166 1.82e-14 68.9

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGGCATCACAAGATGATTT+TGG 0.214860 4_2:-11290622 Msa0588820:CDS
TTTGATGACCCTTTGACTTT+AGG 0.248779 4_2:-11290694 Msa0588820:CDS
ACTATCTTGGGGAGGAATTC+TGG 0.259975 4_2:-11290541 Msa0588820:CDS
ATAAACACAACCACTTCTTT+TGG 0.334067 4_2:-11290730 Msa0588820:CDS
CATTGGTTTGATCTCAAAAC+TGG 0.336336 4_2:-11290436 Msa0588820:CDS
GGTAGTACTATTACTATCTT+GGG 0.346488 4_2:-11290553 Msa0588820:CDS
CCTAACAACTTGCGGTCTAT+TGG 0.349675 4_2:+11290859 None:intergenic
CAATTGAGTTCTAAGCTTGT+TGG 0.353319 4_2:-11290667 Msa0588820:CDS
GAGGAATTCTGGTATTAATA+AGG 0.355147 4_2:-11290530 Msa0588820:CDS
TTCATTGAAGGAAAGTATAA+TGG 0.359474 4_2:-11290574 Msa0588820:CDS
CCAATAGACCGCAAGTTGTT+AGG 0.362080 4_2:-11290859 Msa0588820:CDS
TGGTAGTACTATTACTATCT+TGG 0.363892 4_2:-11290554 Msa0588820:CDS
TAAGTCACTTCAGATTCTAT+TGG 0.373289 4_2:-11290816 Msa0588820:CDS
ATGCCTATTGTTGGTGGTAG+TGG 0.375988 4_2:-11290499 Msa0588820:CDS
AAGTGAGAGTGTTGCAAGAG+AGG 0.407219 4_2:+11290932 None:intergenic
GAGTGTTGCAAGAGAGGAGA+AGG 0.459092 4_2:+11290938 None:intergenic
AGTCCACTACCACCAACAAT+AGG 0.461846 4_2:+11290496 None:intergenic
AGAACAAATTGAGAAAATGA+TGG 0.464684 4_2:+11290965 None:intergenic
ATGCTCAAGCTAGTACTCAT+TGG 0.468719 4_2:-11290453 Msa0588820:CDS
AATTGAGGTCCTAAAGTCAA+AGG 0.495751 4_2:+11290685 None:intergenic
GGAACAATTGTTATTGCAGT+GGG 0.508564 4_2:+11290769 None:intergenic
AAGCTTGTTGGAAAAGCTCA+AGG 0.509980 4_2:-11290655 Msa0588820:CDS
GTTGTGTTTATAAACTTCAA+TGG 0.515154 4_2:+11290742 None:intergenic
CGTTTAGGCCTAACAACTTG+CGG 0.520020 4_2:+11290851 None:intergenic
TTTATAAACTTCAATGGTGG+TGG 0.522057 4_2:+11290748 None:intergenic
AGGGAGATGCCTATTGTTGG+TGG 0.523499 4_2:-11290505 Msa0588820:CDS
GAACAAATTGAGAAAATGAT+GGG 0.523672 4_2:+11290966 None:intergenic
AGCTCAAGGTTTCTATGCAT+CGG 0.530517 4_2:-11290641 Msa0588820:CDS
GCTAGGGAGATGCCTATTGT+TGG 0.537497 4_2:-11290508 Msa0588820:CDS
TGGAACAATTGTTATTGCAG+TGG 0.544715 4_2:+11290768 None:intergenic
ATTGAGGTCCTAAAGTCAAA+GGG 0.547522 4_2:+11290686 None:intergenic
TATTGGCATGACATCTTGAG+TGG 0.547551 4_2:-11290799 Msa0588820:CDS
TTCTGGTATTAATAAGGCTA+GGG 0.556111 4_2:-11290524 Msa0588820:CDS
ATTCTGGTATTAATAAGGCT+AGG 0.573511 4_2:-11290525 Msa0588820:CDS
GTTGATTGAACCAAAAGAAG+TGG 0.598684 4_2:+11290720 None:intergenic
ACAAGCTTAGAACTCAATTG+AGG 0.620077 4_2:+11290670 None:intergenic
GTGTTTATAAACTTCAATGG+TGG 0.627180 4_2:+11290745 None:intergenic
GTACTATTACTATCTTGGGG+AGG 0.673978 4_2:-11290549 Msa0588820:CDS
GTAGTACTATTACTATCTTG+GGG 0.684734 4_2:-11290552 Msa0588820:CDS
GAACAATTGTTATTGCAGTG+GGG 0.694795 4_2:+11290770 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAACAAATTGAGAAAATGAT+GGG + chr4_2:11290403-11290422 None:intergenic 25.0%
! AGAACAAATTGAGAAAATGA+TGG + chr4_2:11290404-11290423 None:intergenic 25.0%
!!! TTAGTTTTTCTTTCTCGTTT+AGG + chr4_2:11290533-11290552 None:intergenic 25.0%
! GTTGTGTTTATAAACTTCAA+TGG + chr4_2:11290627-11290646 None:intergenic 25.0%
!! ATGAATTTTGCTTTCATTGA+AGG - chr4_2:11290780-11290799 Msa0588820:CDS 25.0%
!! TTCATTGAAGGAAAGTATAA+TGG - chr4_2:11290792-11290811 Msa0588820:CDS 25.0%
TAAGTCACTTCAGATTCTAT+TGG - chr4_2:11290550-11290569 Msa0588820:CDS 30.0%
TTTATAAACTTCAATGGTGG+TGG + chr4_2:11290621-11290640 None:intergenic 30.0%
GTGTTTATAAACTTCAATGG+TGG + chr4_2:11290624-11290643 None:intergenic 30.0%
! ATAAACACAACCACTTCTTT+TGG - chr4_2:11290636-11290655 Msa0588820:CDS 30.0%
!!! AGATGATTTTGGTTTTCTCA+TGG - chr4_2:11290755-11290774 Msa0588820:CDS 30.0%
TGGTAGTACTATTACTATCT+TGG - chr4_2:11290812-11290831 Msa0588820:CDS 30.0%
GGTAGTACTATTACTATCTT+GGG - chr4_2:11290813-11290832 Msa0588820:CDS 30.0%
GTAGTACTATTACTATCTTG+GGG - chr4_2:11290814-11290833 Msa0588820:CDS 30.0%
GAGGAATTCTGGTATTAATA+AGG - chr4_2:11290836-11290855 Msa0588820:CDS 30.0%
ATTCTGGTATTAATAAGGCT+AGG - chr4_2:11290841-11290860 Msa0588820:CDS 30.0%
TTCTGGTATTAATAAGGCTA+GGG - chr4_2:11290842-11290861 Msa0588820:CDS 30.0%
! GAACAATTGTTATTGCAGTG+GGG + chr4_2:11290599-11290618 None:intergenic 35.0%
! GGAACAATTGTTATTGCAGT+GGG + chr4_2:11290600-11290619 None:intergenic 35.0%
! TGGAACAATTGTTATTGCAG+TGG + chr4_2:11290601-11290620 None:intergenic 35.0%
GTTGATTGAACCAAAAGAAG+TGG + chr4_2:11290649-11290668 None:intergenic 35.0%
! TTTGATGACCCTTTGACTTT+AGG - chr4_2:11290672-11290691 Msa0588820:CDS 35.0%
ATTGAGGTCCTAAAGTCAAA+GGG + chr4_2:11290683-11290702 None:intergenic 35.0%
AATTGAGGTCCTAAAGTCAA+AGG + chr4_2:11290684-11290703 None:intergenic 35.0%
ACAAGCTTAGAACTCAATTG+AGG + chr4_2:11290699-11290718 None:intergenic 35.0%
!! CAATTGAGTTCTAAGCTTGT+TGG - chr4_2:11290699-11290718 Msa0588820:CDS 35.0%
!!! GACTTTTCAGATTTGCTAGA+GGG - chr4_2:11290889-11290908 Msa0588820:CDS 35.0%
!! CATTGGTTTGATCTCAAAAC+TGG - chr4_2:11290930-11290949 Msa0588820:CDS 35.0%
TATTGGCATGACATCTTGAG+TGG - chr4_2:11290567-11290586 Msa0588820:CDS 40.0%
!! AAGCTTGTTGGAAAAGCTCA+AGG - chr4_2:11290711-11290730 Msa0588820:CDS 40.0%
AGCTCAAGGTTTCTATGCAT+CGG - chr4_2:11290725-11290744 Msa0588820:CDS 40.0%
! TCGGCATCACAAGATGATTT+TGG - chr4_2:11290744-11290763 Msa0588820:CDS 40.0%
GTACTATTACTATCTTGGGG+AGG - chr4_2:11290817-11290836 Msa0588820:CDS 40.0%
!!! GGACTTTTCAGATTTGCTAG+AGG - chr4_2:11290888-11290907 Msa0588820:CDS 40.0%
ATGCTCAAGCTAGTACTCAT+TGG - chr4_2:11290913-11290932 Msa0588820:CDS 40.0%
!! AAGTGAGAGTGTTGCAAGAG+AGG + chr4_2:11290437-11290456 None:intergenic 45.0%
CCTAACAACTTGCGGTCTAT+TGG + chr4_2:11290510-11290529 None:intergenic 45.0%
CCAATAGACCGCAAGTTGTT+AGG - chr4_2:11290507-11290526 Msa0588820:CDS 45.0%
CGTTTAGGCCTAACAACTTG+CGG + chr4_2:11290518-11290537 None:intergenic 45.0%
ACTATCTTGGGGAGGAATTC+TGG - chr4_2:11290825-11290844 Msa0588820:CDS 45.0%
!! ATGCCTATTGTTGGTGGTAG+TGG - chr4_2:11290867-11290886 Msa0588820:CDS 45.0%
AGTCCACTACCACCAACAAT+AGG + chr4_2:11290873-11290892 None:intergenic 45.0%
! GAGTGTTGCAAGAGAGGAGA+AGG + chr4_2:11290431-11290450 None:intergenic 50.0%
GCTAGGGAGATGCCTATTGT+TGG - chr4_2:11290858-11290877 Msa0588820:CDS 50.0%
AGGGAGATGCCTATTGTTGG+TGG - chr4_2:11290861-11290880 Msa0588820:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 11290393 11290995 11290393 ID=Msa0588820;Name=Msa0588820
chr4_2 mRNA 11290393 11290995 11290393 ID=Msa0588820-mRNA-1;Parent=Msa0588820;Name=Msa0588820-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|200
chr4_2 exon 11290393 11290995 11290393 ID=Msa0588820-mRNA-1:exon:3302;Parent=Msa0588820-mRNA-1
chr4_2 CDS 11290393 11290995 11290393 ID=Msa0588820-mRNA-1:cds;Parent=Msa0588820-mRNA-1
Gene Sequence

>Msa0588820

ATGCTTTCCCATCATTTTCTCAATTTGTTCTTCTTCCTTCTCCTCTCTTGCAACACTCTCACTTCAACTTCATTACAATCTTTAGAAAAACAAGAAACTTTTGATTTTGTTCGTCCAATAGACCGCAAGTTGTTAGGCCTAAACGAGAAAGAAAAACTAAGTCACTTCAGATTCTATTGGCATGACATCTTGAGTGGAAAAAACCCCACTGCAATAACAATTGTTCCACCACCATTGAAGTTTATAAACACAACCACTTCTTTTGGTTCAATCAACATGTTTGATGACCCTTTGACTTTAGGACCTCAATTGAGTTCTAAGCTTGTTGGAAAAGCTCAAGGTTTCTATGCATCGGCATCACAAGATGATTTTGGTTTTCTCATGGCTATGAATTTTGCTTTCATTGAAGGAAAGTATAATGGTAGTACTATTACTATCTTGGGGAGGAATTCTGGTATTAATAAGGCTAGGGAGATGCCTATTGTTGGTGGTAGTGGACTTTTCAGATTTGCTAGAGGGTATGCTCAAGCTAGTACTCATTGGTTTGATCTCAAAACTGGAGATGCTATTGTTGAGTACAATGTTTATGTTTTTCACTATTGA
Protein sequence

>Msa0588820

MLSHHFLNLFFFLLLSCNTLTSTSLQSLEKQETFDFVRPIDRKLLGLNEKEKLSHFRFYWHDILSGKNPTAITIVPPPLKFINTTTSFGSINMFDDPLTLGPQLSSKLVGKAQGFYASASQDDFGFLMAMNFAFIEGKYNGSTITILGRNSGINKAREMPIVGGSGLFRFARGYAQASTHWFDLKTGDAIVEYNVYVFHY*