AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0393850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0393850 MtrunA17_Chr3g0079381 95.699 186 8 0 1 186 1 186 2.03e-126 353
Msa0393850 MtrunA17_Chr3g0079401 89.535 172 18 0 15 186 16 187 4.99e-117 329
Msa0393850 MtrunA17_Chr5g0398871 48.649 185 93 2 4 186 27 211 3.60e-64 197
Msa0393850 MtrunA17_Chr4g0056601 46.597 191 93 2 5 186 12 202 1.18e-57 179
Msa0393850 MtrunA17_Chr4g0018281 48.466 163 82 1 24 186 36 196 6.60e-50 160
Msa0393850 MtrunA17_Chr4g0018241 46.012 163 86 1 24 186 36 196 8.82e-45 147
Msa0393850 MtrunA17_Chr4g0018251 45.399 163 87 1 24 186 36 196 1.17e-43 144
Msa0393850 MtrunA17_Chr4g0011681 41.538 195 102 6 3 186 8 201 1.03e-42 142
Msa0393850 MtrunA17_Chr4g0011711 40.000 195 105 6 3 186 8 201 1.47e-39 134
Msa0393850 MtrunA17_Chr4g0011701 41.489 188 100 6 7 186 16 201 2.92e-39 133
Msa0393850 MtrunA17_Chr4g0011721 38.614 202 107 6 1 186 1 201 2.11e-38 131
Msa0393850 MtrunA17_Chr4g0067891 35.897 195 105 4 8 183 9 202 2.78e-35 122
Msa0393850 MtrunA17_Chr8g0391341 36.571 175 101 3 18 183 38 211 6.30e-34 119
Msa0393850 MtrunA17_Chr7g0230391 42.353 170 84 7 23 180 42 209 1.85e-33 118
Msa0393850 MtrunA17_Chr3g0079371 35.165 182 104 4 12 181 45 224 2.70e-31 113
Msa0393850 MtrunA17_Chr2g0301381 37.952 166 87 4 23 183 33 187 3.20e-29 107
Msa0393850 MtrunA17_Chr7g0269361 32.121 165 108 3 17 181 26 186 8.20e-29 105
Msa0393850 MtrunA17_Chr1g0195561 29.348 184 124 3 3 184 9 188 8.65e-29 105
Msa0393850 MtrunA17_Chr4g0070161 32.447 188 113 5 5 183 15 197 9.00e-25 95.9
Msa0393850 MtrunA17_Chr4g0018231 32.335 167 99 5 24 183 43 202 9.52e-20 82.4
Msa0393850 MtrunA17_Chr1g0147051 29.444 180 108 5 19 185 76 249 4.58e-15 72.4
Msa0393850 MtrunA17_Chr8g0345281 27.564 156 110 2 25 178 68 222 4.34e-14 69.7
Msa0393850 MtrunA17_Chr8g0345211 30.120 166 105 5 20 181 72 230 1.34e-13 68.2
Msa0393850 MtrunA17_Chr3g0126771 29.341 167 112 3 21 183 74 238 2.45e-13 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0393850 AT5G62350.1 54.070 172 77 2 17 186 31 202 3.52e-66 201
Msa0393850 AT3G47380.1 48.454 194 88 4 5 186 9 202 2.90e-62 192
Msa0393850 AT4G25260.1 45.274 201 95 2 1 186 1 201 2.32e-58 182
Msa0393850 AT1G62770.1 47.872 188 89 4 5 183 9 196 6.63e-54 171
Msa0393850 AT4G12390.1 48.503 167 83 1 23 186 38 204 1.73e-49 159
Msa0393850 AT5G62360.1 43.902 164 89 2 23 186 42 202 5.75e-49 158
Msa0393850 AT5G20740.1 40.933 193 101 3 1 181 1 192 8.53e-42 139
Msa0393850 AT5G20740.2 45.062 162 85 2 23 181 66 226 2.76e-41 139
Msa0393850 AT1G14890.1 37.037 189 105 3 6 185 34 217 1.22e-39 134
Msa0393850 AT4G00080.1 38.693 199 100 8 2 181 3 198 1.45e-39 134
Msa0393850 AT2G01610.1 36.979 192 103 4 10 185 30 219 3.29e-37 128
Msa0393850 AT1G62760.1 43.452 168 88 3 20 184 143 306 5.93e-36 127
Msa0393850 AT4G25250.1 35.185 162 104 1 22 182 35 196 1.52e-35 123
Msa0393850 AT1G70720.1 35.567 194 110 5 1 183 5 194 4.03e-31 112
Msa0393850 AT1G70720.2 35.567 194 110 5 1 183 17 206 4.65e-31 112
Msa0393850 AT1G23205.1 34.031 191 111 4 5 181 9 198 4.32e-30 109
Msa0393850 AT5G51520.1 35.366 164 97 2 24 179 37 199 1.22e-28 106
Msa0393850 AT3G62820.1 27.895 190 123 6 3 185 10 192 5.73e-20 83.2
Msa0393850 AT3G14310.1 32.278 158 101 4 25 179 59 213 1.38e-19 85.9
Msa0393850 AT5G62340.1 29.902 204 109 8 6 186 14 206 4.25e-19 81.3
Msa0393850 AT2G47670.1 28.125 160 112 2 24 183 48 204 1.42e-17 77.4
Msa0393850 AT5G53370.2 29.448 163 108 4 18 179 104 260 2.34e-17 79.3
Msa0393850 AT5G53370.1 29.448 163 108 4 18 179 68 224 2.54e-17 79.3
Msa0393850 AT1G53830.1 28.221 163 115 2 18 179 55 216 3.98e-17 79.0
Msa0393850 AT3G49220.2 31.056 161 101 4 21 180 128 279 5.92e-17 78.2
Msa0393850 AT3G49220.3 31.250 160 100 4 21 179 128 278 7.31e-17 78.2
Msa0393850 AT3G49220.1 31.250 160 100 4 21 179 83 233 8.29e-17 77.8
Msa0393850 AT3G47670.1 29.851 201 112 8 1 181 76 267 4.50e-14 68.9
Msa0393850 AT3G14300.1 28.177 181 116 6 12 182 258 434 8.50e-13 66.2
Msa0393850 AT3G14300.1 29.070 172 104 6 20 181 454 617 2.18e-12 65.1

Find 30 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAATAGCAGCATATTCTTT+TGG 0.312148 3_2:+8059000 None:intergenic
CTTGCACTCATTAATCAATA+TGG 0.347778 3_2:-8058730 Msa0393850:CDS
CCAATTGATGAGGGTCTTGT+TGG 0.382982 3_2:+8059109 None:intergenic
TAGGCTTAGCCGTTCACTTA+AGG 0.410233 3_2:-8058944 Msa0393850:CDS
AACAAAACTCAATCCACAAA+AGG 0.414225 3_2:-8059060 Msa0393850:CDS
GAGGATTTGATGAAATTTGT+TGG 0.419280 3_2:+8059195 None:intergenic
TCAATGGTCAAGATTTCAAT+TGG 0.421550 3_2:-8058903 Msa0393850:CDS
CCAACAAGACCCTCATCAAT+TGG 0.429940 3_2:-8059109 Msa0393850:CDS
AAATTACTGATAGTGTTGAT+AGG 0.448838 3_2:-8058963 Msa0393850:CDS
CTTAAACTTTGCAAGATCAA+TGG 0.453176 3_2:-8058919 Msa0393850:CDS
AACCATTCTAGATCTAATAG+AGG 0.455384 3_2:+8058780 None:intergenic
GAGTTGAAGTTGCAATAGAT+AGG 0.465044 3_2:+8059217 None:intergenic
GAGATTCAACACAAAGTGTT+GGG 0.484787 3_2:+8059154 None:intergenic
AGTACTTGTAGTGATGGATT+TGG 0.488408 3_2:-8058832 Msa0393850:CDS
TAGAATGGTTAATCTTGCTC+AGG 0.489212 3_2:-8058767 Msa0393850:CDS
AACCTCTATTAGATCTAGAA+TGG 0.501103 3_2:-8058782 Msa0393850:CDS
AAGAAGAACATTTGTTGCCA+TGG 0.516513 3_2:+8059257 None:intergenic
AGAGATTCAACACAAAGTGT+TGG 0.533099 3_2:+8059153 None:intergenic
ACAAAACTCAATCCACAAAA+GGG 0.537573 3_2:-8059059 Msa0393850:CDS
TAGATAGGAGAGTTAAGAGA+AGG 0.542534 3_2:+8059232 None:intergenic
GTTTAAGCTCCTTAAGTGAA+CGG 0.545857 3_2:+8058935 None:intergenic
ACTTGTAGTGATGGATTTGG+TGG 0.550252 3_2:-8058829 Msa0393850:CDS
TCAATATGGTACTAATCACT+AGG 0.554200 3_2:-8058716 None:intergenic
GCTGTTTGAACCAATTGATG+AGG 0.568833 3_2:+8059099 None:intergenic
ATATAAGTAATGTTCAAACA+TGG 0.577147 3_2:-8058879 Msa0393850:CDS
CTGTTTGAACCAATTGATGA+GGG 0.590554 3_2:+8059100 None:intergenic
GATGCAAGTACTTGTAGTGA+TGG 0.592136 3_2:-8058838 Msa0393850:CDS
CAATATGGTACTAATCACTA+GGG 0.596788 3_2:-8058715 None:intergenic
TATAAGTAATGTTCAAACAT+GGG 0.606584 3_2:-8058878 Msa0393850:CDS
GTATGATGTTGTGCTACATG+AGG 0.681149 3_2:+8059176 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAGTAATGTTCAAACA+TGG - chr3_2:8059093-8059112 Msa0393850:CDS 20.0%
!! TATAAGTAATGTTCAAACAT+GGG - chr3_2:8059094-8059113 Msa0393850:CDS 20.0%
! ACAATGTGCAAAAAGTTTAA+AGG - chr3_2:8058942-8058961 Msa0393850:CDS 25.0%
!!! AAATTACTGATAGTGTTGAT+AGG - chr3_2:8059009-8059028 Msa0393850:CDS 25.0%
GAGGATTTGATGAAATTTGT+TGG + chr3_2:8058780-8058799 None:intergenic 30.0%
!!! TTGTGGATTGAGTTTTGTTT+AGG + chr3_2:8058911-8058930 None:intergenic 30.0%
AACAAAACTCAATCCACAAA+AGG - chr3_2:8058912-8058931 Msa0393850:CDS 30.0%
ACAAAACTCAATCCACAAAA+GGG - chr3_2:8058913-8058932 Msa0393850:CDS 30.0%
! TGAATAGCAGCATATTCTTT+TGG + chr3_2:8058975-8058994 None:intergenic 30.0%
CTTAAACTTTGCAAGATCAA+TGG - chr3_2:8059053-8059072 Msa0393850:CDS 30.0%
TCAATGGTCAAGATTTCAAT+TGG - chr3_2:8059069-8059088 Msa0393850:CDS 30.0%
AACCTCTATTAGATCTAGAA+TGG - chr3_2:8059190-8059209 Msa0393850:CDS 30.0%
AACCATTCTAGATCTAATAG+AGG + chr3_2:8059195-8059214 None:intergenic 30.0%
CTTGCACTCATTAATCAATA+TGG - chr3_2:8059242-8059261 Msa0393850:CDS 30.0%
TAGATAGGAGAGTTAAGAGA+AGG + chr3_2:8058743-8058762 None:intergenic 35.0%
GAGTTGAAGTTGCAATAGAT+AGG + chr3_2:8058758-8058777 None:intergenic 35.0%
! GAGATTCAACACAAAGTGTT+GGG + chr3_2:8058821-8058840 None:intergenic 35.0%
AGAGATTCAACACAAAGTGT+TGG + chr3_2:8058822-8058841 None:intergenic 35.0%
CTGTTTGAACCAATTGATGA+GGG + chr3_2:8058875-8058894 None:intergenic 35.0%
! CATTGTAACAAACCCTTTTG+TGG + chr3_2:8058928-8058947 None:intergenic 35.0%
GTTTAAGCTCCTTAAGTGAA+CGG + chr3_2:8059040-8059059 None:intergenic 35.0%
!! AGTACTTGTAGTGATGGATT+TGG - chr3_2:8059140-8059159 Msa0393850:CDS 35.0%
TTTGGTGGAAAAACACTTGA+TGG - chr3_2:8059158-8059177 Msa0393850:CDS 35.0%
TAGAATGGTTAATCTTGCTC+AGG - chr3_2:8059205-8059224 Msa0393850:CDS 35.0%
GTATGATGTTGTGCTACATG+AGG + chr3_2:8058799-8058818 None:intergenic 40.0%
GCTGTTTGAACCAATTGATG+AGG + chr3_2:8058876-8058895 None:intergenic 40.0%
GATGCAAGTACTTGTAGTGA+TGG - chr3_2:8059134-8059153 Msa0393850:CDS 40.0%
!! ACTTGTAGTGATGGATTTGG+TGG - chr3_2:8059143-8059162 Msa0393850:CDS 40.0%
! CCAATTGATGAGGGTCTTGT+TGG + chr3_2:8058866-8058885 None:intergenic 45.0%
CCAACAAGACCCTCATCAAT+TGG - chr3_2:8058863-8058882 Msa0393850:CDS 45.0%
TAGGCTTAGCCGTTCACTTA+AGG - chr3_2:8059028-8059047 Msa0393850:CDS 45.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 8058717 8059277 8058717 ID=Msa0393850;Name=Msa0393850
chr3_2 mRNA 8058717 8059277 8058717 ID=Msa0393850-mRNA-1;Parent=Msa0393850;Name=Msa0393850-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|186
chr3_2 exon 8058717 8059277 8058717 ID=Msa0393850-mRNA-1:exon:2091;Parent=Msa0393850-mRNA-1
chr3_2 CDS 8058717 8059277 8058717 ID=Msa0393850-mRNA-1:cds;Parent=Msa0393850-mRNA-1
Gene Sequence

>Msa0393850

ATGGCAACAAATGTTCTTCTTTTCCTTCTCTTAACTCTCCTATCTATTGCAACTTCAACTCCAACAAATTTCATCAAATCCTCATGTAGCACAACATCATACCCAACACTTTGTGTTGAATCTCTTTCTGTCTATGCAACAACAATCCAACAAGACCCTCATCAATTGGTTCAAACAGCTTTATCAATTAGCCTAAACAAAACTCAATCCACAAAAGGGTTTGTTACAATGTGCAAAAAGTTTAAAGGTCTTAAACCAAAAGAATATGCTGCTATTCATGATTGTGTTGAAGAAATTACTGATAGTGTTGATAGGCTTAGCCGTTCACTTAAGGAGCTTAAACTTTGCAAGATCAATGGTCAAGATTTCAATTGGCATATAAGTAATGTTCAAACATGGGTTAGCGCAGCTATGACTGATGCAAGTACTTGTAGTGATGGATTTGGTGGAAAAACACTTGATGGAAGAATGAAAACCTCTATTAGATCTAGAATGGTTAATCTTGCTCAGGTTACTAGTAATGCTCTTGCACTCATTAATCAATATGGTACTAATCACTAG
Protein sequence

>Msa0393850

MATNVLLFLLLTLLSIATSTPTNFIKSSCSTTSYPTLCVESLSVYATTIQQDPHQLVQTALSISLNKTQSTKGFVTMCKKFKGLKPKEYAAIHDCVEEITDSVDRLSRSLKELKLCKINGQDFNWHISNVQTWVSAAMTDASTCSDGFGGKTLDGRMKTSIRSRMVNLAQVTSNALALINQYGTNH*