AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0771820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0771820 MtrunA17_Chr5g0424931 50.000 156 40 3 2 119 154 309 8.97e-44 149
Msa0771820 MtrunA17_Chr1g0178011 54.887 133 45 3 1 118 148 280 2.41e-39 136
Msa0771820 MtrunA17_Chr5g0417211 50.000 130 53 4 2 119 149 278 4.54e-37 129
Msa0771820 MtrunA17_Chr2g0289221 50.000 128 54 4 2 119 158 285 3.33e-36 126
Msa0771820 MtrunA17_Chr5g0417281 47.244 127 58 4 2 119 149 275 5.36e-34 122
Msa0771820 MtrunA17_Chr5g0424741 52.239 134 48 4 1 118 174 307 1.18e-33 122
Msa0771820 MtrunA17_Chr5g0436761 46.565 131 58 4 1 119 149 279 5.52e-33 119
Msa0771820 MtrunA17_Chr5g0425661 92.453 53 4 0 1 53 172 224 1.13e-30 109
Msa0771820 MtrunA17_Chr5g0424801 45.865 133 53 5 3 119 144 273 6.15e-28 104
Msa0771820 MtrunA17_Chr2g0277531 46.457 127 58 5 3 119 160 286 6.51e-28 103
Msa0771820 MtrunA17_Chr5g0425261 45.865 133 53 5 3 119 144 273 1.63e-26 101
Msa0771820 MtrunA17_Chr2g0277461 44.697 132 58 5 3 119 153 284 2.05e-25 99.0
Msa0771820 MtrunA17_Chr2g0326761 35.088 171 58 3 2 119 144 314 2.48e-25 99.4
Msa0771820 MtrunA17_Chr1g0199681 35.714 168 58 5 2 119 229 396 6.55e-25 97.8
Msa0771820 MtrunA17_Chr3g0115271 37.725 167 55 4 2 119 153 319 1.36e-24 97.1
Msa0771820 MtrunA17_Chr7g0264161 37.313 134 68 3 2 119 128 261 7.40e-23 90.1
Msa0771820 MtrunA17_Chr2g0282961 35.821 134 70 3 2 119 194 327 2.97e-21 87.4
Msa0771820 MtrunA17_Chr5g0425651 80.435 46 8 1 75 119 1 46 1.12e-19 78.2
Msa0771820 MtrunA17_Chr4g0046371 34.483 116 61 2 2 102 184 299 1.29e-18 80.1
Msa0771820 MtrunA17_Chr4g0029671 40.171 117 53 4 2 102 202 317 4.66e-18 78.6
Msa0771820 MtrunA17_Chr4g0028971 55.738 61 27 0 2 62 145 205 5.82e-18 78.2
Msa0771820 MtrunA17_Chr2g0285461 38.793 116 56 4 2 102 163 278 8.68e-18 77.8
Msa0771820 MtrunA17_Chr8g0376771 37.931 116 57 4 2 102 162 277 9.12e-18 77.8
Msa0771820 MtrunA17_Chr2g0326281 39.316 117 54 4 2 102 217 332 9.78e-18 77.4
Msa0771820 MtrunA17_Chr8g0389081 37.069 116 58 2 2 102 172 287 1.35e-17 77.0
Msa0771820 MtrunA17_Chr7g0264171 27.778 180 68 4 2 119 167 346 3.96e-17 75.9
Msa0771820 MtrunA17_Chr1g0156321 35.345 116 60 3 2 102 182 297 8.89e-17 74.7
Msa0771820 MtrunA17_Chr2g0276781 36.975 119 60 3 2 105 161 279 1.16e-16 74.3
Msa0771820 MtrunA17_Chr3g0109391 36.207 116 59 3 2 102 166 281 1.18e-16 74.3
Msa0771820 MtrunA17_Chr5g0433301 36.207 116 59 3 2 102 164 279 1.70e-16 73.9
Msa0771820 MtrunA17_Chr8g0385791 32.090 134 75 4 2 119 198 331 2.50e-16 73.6
Msa0771820 MtrunA17_Chr1g0181211 53.846 52 24 0 2 53 165 216 3.96e-16 72.8
Msa0771820 MtrunA17_Chr7g0239061 34.821 112 58 3 2 98 152 263 2.04e-15 70.9
Msa0771820 MtrunA17_Chr2g0301251 33.621 116 62 3 2 102 162 277 3.62e-15 70.1
Msa0771820 MtrunA17_Chr8g0346711 51.923 52 25 0 2 53 167 218 4.10e-15 70.1
Msa0771820 MtrunA17_Chr4g0070181 33.621 116 62 3 2 102 162 277 5.44e-15 69.7
Msa0771820 MtrunA17_Chr4g0009751 34.821 112 58 3 2 98 157 268 1.25e-14 68.6
Msa0771820 MtrunA17_Chr8g0356211 32.203 118 63 2 2 102 30 147 2.75e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0771820 AT1G77850.1 36.196 163 59 3 2 119 155 317 1.52e-28 108
Msa0771820 AT1G77850.2 36.196 163 59 3 2 119 155 317 1.91e-28 108
Msa0771820 AT4G30080.1 35.329 167 59 4 2 119 156 322 2.26e-25 99.8
Msa0771820 AT2G28350.2 34.706 170 59 5 2 119 151 320 9.85e-21 86.7
Msa0771820 AT2G28350.1 34.706 170 59 5 2 119 151 320 1.10e-20 86.3
Msa0771820 AT2G33860.1 37.190 121 55 5 2 104 195 312 4.02e-20 84.7
Msa0771820 AT2G33860.2 36.975 119 58 4 2 104 38 155 8.05e-20 83.6
Msa0771820 AT1G30330.1 37.069 116 58 4 2 102 163 278 4.33e-17 76.3
Msa0771820 AT1G30330.3 37.069 116 58 4 2 102 165 280 4.33e-17 76.3
Msa0771820 AT1G30330.2 37.069 116 58 4 2 102 165 280 4.33e-17 76.3
Msa0771820 AT5G60450.2 38.261 115 57 3 2 102 189 303 7.85e-17 75.5
Msa0771820 AT5G60450.1 38.261 115 57 3 2 102 213 327 8.50e-17 75.1
Msa0771820 AT5G37020.2 33.621 116 62 3 2 102 162 277 1.76e-16 74.3
Msa0771820 AT5G37020.1 33.621 116 62 3 2 102 162 277 1.77e-16 74.3
Msa0771820 AT5G37020.3 33.621 116 62 3 2 102 67 182 2.45e-16 73.9
Msa0771820 AT1G59750.4 34.454 119 63 3 2 105 160 278 2.81e-16 73.9
Msa0771820 AT1G59750.2 34.454 119 63 3 2 105 160 278 2.81e-16 73.9
Msa0771820 AT1G59750.1 34.454 119 63 3 2 105 160 278 2.82e-16 73.9
Msa0771820 AT1G59750.3 34.454 119 63 3 2 105 160 278 2.82e-16 73.9
Msa0771820 AT5G20730.3 50.769 65 30 1 2 64 163 227 8.55e-16 72.4
Msa0771820 AT5G20730.2 50.769 65 30 1 2 64 163 227 8.56e-16 72.4
Msa0771820 AT5G20730.1 50.769 65 30 1 2 64 163 227 8.56e-16 72.4
Msa0771820 AT1G19850.2 34.483 116 61 3 2 102 183 298 2.05e-15 71.2
Msa0771820 AT1G19850.1 34.483 116 61 3 2 102 194 309 2.06e-15 71.2
Msa0771820 AT3G61830.2 32.090 134 73 4 2 119 113 244 2.62e-15 70.9
Msa0771820 AT3G61830.1 32.090 134 73 4 2 119 164 295 2.65e-15 70.9
Msa0771820 AT5G62000.4 33.621 116 62 3 2 102 200 315 2.99e-15 70.9
Msa0771820 AT5G62000.2 33.621 116 62 3 2 102 200 315 3.05e-15 70.9
Msa0771820 AT5G62000.5 33.621 116 62 3 2 102 200 315 3.05e-15 70.9
Msa0771820 AT5G62000.3 33.621 116 62 3 2 102 200 315 3.05e-15 70.9
Msa0771820 AT5G62000.1 33.621 116 62 3 2 102 200 315 3.05e-15 70.9
Msa0771820 AT1G34390.1 33.607 122 66 3 1 107 159 280 3.54e-15 70.5
Msa0771820 AT2G46530.2 37.778 90 53 2 2 90 73 160 4.87e-15 70.1
Msa0771820 AT2G46530.3 37.778 90 53 2 2 90 181 268 5.67e-15 70.1
Msa0771820 AT2G46530.1 37.778 90 53 2 2 90 160 247 5.76e-15 70.1
Msa0771820 AT4G23980.2 45.902 61 33 0 2 62 152 212 1.15e-14 69.3
Msa0771820 AT4G23980.1 45.902 61 33 0 2 62 152 212 1.17e-14 69.3
Msa0771820 AT1G34310.1 34.426 122 65 4 1 107 161 282 1.56e-14 68.9
Msa0771820 AT1G19220.1 32.479 117 62 3 2 102 162 277 2.50e-14 68.2
Msa0771820 AT1G35540.1 31.148 122 69 3 1 107 161 282 4.64e-14 67.4
Msa0771820 AT1G35520.1 33.607 122 66 4 1 107 161 282 2.39e-13 65.5
Msa0771820 AT1G35240.1 32.787 122 67 4 1 107 161 282 7.80e-13 63.9
Msa0771820 AT1G34410.1 31.967 122 68 5 1 107 161 282 1.68e-11 60.1

Find 28 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATGTCCAACTAATCTTTA+TGG 0.182838 5_2:-45310484 None:intergenic
GGTAACAGAGAAGGCGGTTA+TGG 0.361245 5_2:+45310362 Msa0771820:CDS
GGTTATGGATGCGGTGGAAT+TGG 0.365128 5_2:+45310377 Msa0771820:CDS
CTGACATTCAAGGCCGAGTC+TGG 0.403843 5_2:+45310171 Msa0771820:CDS
ATAAAGATTAGTTGGACATC+TGG 0.409167 5_2:+45310486 Msa0771820:CDS
GGAAGATATTCGTTGGAACT+TGG 0.410564 5_2:+45310318 Msa0771820:CDS
ATGATGCCATAAAGATTAGT+TGG 0.424164 5_2:+45310478 Msa0771820:CDS
TGTATTATCCGAGAGCGAAT+TGG 0.460538 5_2:+45310427 Msa0771820:CDS
CTCTCCGTCACTGACATTCA+AGG 0.461163 5_2:+45310161 Msa0771820:CDS
CCTACTGAAAAGGTGTCTCT+TGG 0.480185 5_2:-45310222 None:intergenic
AAGTCCATCCCCTACTGAAA+AGG 0.489646 5_2:-45310232 None:intergenic
CGTTGGAACTTGGAATATGC+CGG 0.508373 5_2:+45310328 Msa0771820:CDS
CTTGGAATATGCCGGAAAAG+TGG 0.525958 5_2:+45310336 Msa0771820:CDS
AGAGAAGGCGGTTATGGATG+CGG 0.535241 5_2:+45310368 Msa0771820:CDS
AAATCAAACCAATTCGCTCT+CGG 0.544399 5_2:-45310435 None:intergenic
TATGGATGCGGTGGAATTGG+CGG 0.548189 5_2:+45310380 Msa0771820:CDS
TTGGAATATGCCGGAAAAGT+GGG 0.561394 5_2:+45310337 Msa0771820:CDS
AACAACAAGAAACTCGTCGC+TGG 0.566110 5_2:+45310263 Msa0771820:CDS
TATGCGTGTACTGCCAGACT+CGG 0.574777 5_2:-45310184 None:intergenic
TCAGCTGGGAAGATATTCGT+TGG 0.583376 5_2:+45310311 Msa0771820:intron
AAGTGGGAAGGTAACAGAGA+AGG 0.628618 5_2:+45310353 Msa0771820:CDS
GAAGGCGGTTATGGATGCGG+TGG 0.634390 5_2:+45310371 Msa0771820:CDS
GTGACGGAGAGTGTCTGAGA+TGG 0.649352 5_2:-45310149 None:intergenic
TCGGCCTTGAATGTCAGTGA+CGG 0.654538 5_2:-45310165 None:intergenic
TGGGAAGGTAACAGAGAAGG+CGG 0.684452 5_2:+45310356 Msa0771820:CDS
GGTGTCTCTTGGATTTACCG+CGG 0.703682 5_2:-45310211 None:intergenic
AATATGCCGGAAAAGTGGGA+AGG 0.715565 5_2:+45310341 Msa0771820:CDS
CAGTACACGCATATTTACCG+CGG 0.765088 5_2:+45310194 Msa0771820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTTTCGTTAAAAACTCAGCT+GGG + chr5_2:45310297-45310316 Msa0771820:intron 30.0%
!!! GAATTGGTTTGATTTTGTAG+TGG + chr5_2:45310443-45310462 Msa0771820:CDS 30.0%
ATGATGCCATAAAGATTAGT+TGG + chr5_2:45310478-45310497 Msa0771820:CDS 30.0%
AGATGTCCAACTAATCTTTA+TGG - chr5_2:45310487-45310506 None:intergenic 30.0%
! ATAAAGATTAGTTGGACATC+TGG + chr5_2:45310486-45310505 Msa0771820:CDS 30.0%
! GTTTTCGTTAAAAACTCAGC+TGG + chr5_2:45310296-45310315 Msa0771820:intron 35.0%
AAATCAAACCAATTCGCTCT+CGG - chr5_2:45310438-45310457 None:intergenic 35.0%
! CAAGAGACACCTTTTCAGTA+GGG + chr5_2:45310223-45310242 Msa0771820:CDS 40.0%
! AAGAGACACCTTTTCAGTAG+GGG + chr5_2:45310224-45310243 Msa0771820:CDS 40.0%
GGAAGATATTCGTTGGAACT+TGG + chr5_2:45310318-45310337 Msa0771820:CDS 40.0%
TTGGAATATGCCGGAAAAGT+GGG + chr5_2:45310337-45310356 Msa0771820:CDS 40.0%
TGTATTATCCGAGAGCGAAT+TGG + chr5_2:45310427-45310446 Msa0771820:CDS 40.0%
CAGTACACGCATATTTACCG+CGG + chr5_2:45310194-45310213 Msa0771820:CDS 45.0%
!! CCTACTGAAAAGGTGTCTCT+TGG - chr5_2:45310225-45310244 None:intergenic 45.0%
! CCAAGAGACACCTTTTCAGT+AGG + chr5_2:45310222-45310241 Msa0771820:CDS 45.0%
AAGTCCATCCCCTACTGAAA+AGG - chr5_2:45310235-45310254 None:intergenic 45.0%
AACAACAAGAAACTCGTCGC+TGG + chr5_2:45310263-45310282 Msa0771820:CDS 45.0%
TCAGCTGGGAAGATATTCGT+TGG + chr5_2:45310311-45310330 Msa0771820:intron 45.0%
CGTTGGAACTTGGAATATGC+CGG + chr5_2:45310328-45310347 Msa0771820:CDS 45.0%
CTTGGAATATGCCGGAAAAG+TGG + chr5_2:45310336-45310355 Msa0771820:CDS 45.0%
AATATGCCGGAAAAGTGGGA+AGG + chr5_2:45310341-45310360 Msa0771820:CDS 45.0%
!! CTGTTACCTTCCCACTTTTC+CGG - chr5_2:45310350-45310369 None:intergenic 45.0%
AAGTGGGAAGGTAACAGAGA+AGG + chr5_2:45310353-45310372 Msa0771820:CDS 45.0%
GGAATTGGCGGTGAAAAACA+TGG + chr5_2:45310392-45310411 Msa0771820:CDS 45.0%
CTCTCCGTCACTGACATTCA+AGG + chr5_2:45310161-45310180 Msa0771820:CDS 50.0%
TCGGCCTTGAATGTCAGTGA+CGG - chr5_2:45310168-45310187 None:intergenic 50.0%
TATGCGTGTACTGCCAGACT+CGG - chr5_2:45310187-45310206 None:intergenic 50.0%
GGTGTCTCTTGGATTTACCG+CGG - chr5_2:45310214-45310233 None:intergenic 50.0%
! GACACCTTTTCAGTAGGGGA+TGG + chr5_2:45310228-45310247 Msa0771820:CDS 50.0%
TGGGAAGGTAACAGAGAAGG+CGG + chr5_2:45310356-45310375 Msa0771820:CDS 50.0%
GGTAACAGAGAAGGCGGTTA+TGG + chr5_2:45310362-45310381 Msa0771820:CDS 50.0%
AGAGAAGGCGGTTATGGATG+CGG + chr5_2:45310368-45310387 Msa0771820:CDS 50.0%
GGTTATGGATGCGGTGGAAT+TGG + chr5_2:45310377-45310396 Msa0771820:CDS 50.0%
TATGGATGCGGTGGAATTGG+CGG + chr5_2:45310380-45310399 Msa0771820:CDS 50.0%
!! GTGACGGAGAGTGTCTGAGA+TGG - chr5_2:45310152-45310171 None:intergenic 55.0%
CTGACATTCAAGGCCGAGTC+TGG + chr5_2:45310171-45310190 Msa0771820:CDS 55.0%
GAAGGCGGTTATGGATGCGG+TGG + chr5_2:45310371-45310390 Msa0771820:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 45310146 45310515 45310146 ID=Msa0771820;Name=Msa0771820
chr5_2 mRNA 45310146 45310515 45310146 ID=Msa0771820-mRNA-1;Parent=Msa0771820;Name=Msa0771820-mRNA-1;_AED=0.24;_eAED=0.24;_QI=0|0|0|1|0|0|2|0|119
chr5_2 exon 45310146 45310301 45310146 ID=Msa0771820-mRNA-1:exon:13710;Parent=Msa0771820-mRNA-1
chr5_2 exon 45310315 45310515 45310315 ID=Msa0771820-mRNA-1:exon:13711;Parent=Msa0771820-mRNA-1
chr5_2 CDS 45310146 45310301 45310146 ID=Msa0771820-mRNA-1:cds;Parent=Msa0771820-mRNA-1
chr5_2 CDS 45310315 45310515 45310315 ID=Msa0771820-mRNA-1:cds;Parent=Msa0771820-mRNA-1
Gene Sequence

>Msa0771820

ATGCCATCTCAGACACTCTCCGTCACTGACATTCAAGGCCGAGTCTGGCAGTACACGCATATTTACCGCGGTAAATCCAAGAGACACCTTTTCAGTAGGGGATGGACTTCATTTGTCAACAACAAGAAACTCGTCGCTGGTGATTCAGTTGTTTTCCTGGGAAGATATTCGTTGGAACTTGGAATATGCCGGAAAAGTGGGAAGGTAACAGAGAAGGCGGTTATGGATGCGGTGGAATTGGCGGTGAAAAACATGGCATTTGAAGTTTTGTATTATCCGAGAGCGAATTGGTTTGATTTTGTAGTGGATGCAAATGTTGATGATGCCATAAAGATTAGTTGGACATCTGGAATTCAA
Protein sequence

>Msa0771820

MPSQTLSVTDIQGRVWQYTHIYRGKSKRHLFSRGWTSFVNNKKLVAGDSVVFLGRYSLELGICRKSGKVTEKAVMDAVELAVKNMAFEVLYYPRANWFDFVVDANVDDAIKISWTSGIQ