AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0833640


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0833640 MtrunA17_Chr5g0398871 96.939 196 6 0 1 196 22 217 1.16e-141 393
Msa0833640 MtrunA17_Chr4g0056601 63.402 194 60 2 9 191 10 203 9.06e-85 249
Msa0833640 MtrunA17_Chr3g0079401 53.571 168 77 1 23 190 21 187 1.47e-64 197
Msa0833640 MtrunA17_Chr3g0079381 51.190 168 81 1 23 190 20 186 6.93e-62 190
Msa0833640 MtrunA17_Chr4g0018281 43.030 165 91 1 27 191 36 197 4.90e-45 147
Msa0833640 MtrunA17_Chr4g0018241 38.191 199 111 2 1 190 1 196 7.63e-42 139
Msa0833640 MtrunA17_Chr4g0018251 42.073 164 92 1 27 190 36 196 2.02e-41 138
Msa0833640 MtrunA17_Chr4g0011681 38.308 201 106 6 9 195 10 206 1.48e-38 132
Msa0833640 MtrunA17_Chr4g0011711 37.245 196 115 4 7 195 12 206 1.00e-37 129
Msa0833640 MtrunA17_Chr4g0011701 37.186 199 107 6 9 193 10 204 4.97e-37 127
Msa0833640 MtrunA17_Chr4g0011721 35.567 194 113 4 7 191 12 202 1.19e-35 124
Msa0833640 MtrunA17_Chr8g0391341 38.596 171 96 3 25 187 42 211 1.97e-33 119
Msa0833640 MtrunA17_Chr4g0067891 38.596 171 96 3 25 187 33 202 3.57e-33 117
Msa0833640 MtrunA17_Chr7g0230391 38.824 170 91 6 26 184 42 209 9.22e-31 112
Msa0833640 MtrunA17_Chr7g0269361 35.802 162 99 2 28 189 34 190 2.55e-30 110
Msa0833640 MtrunA17_Chr3g0079371 34.161 161 102 2 27 185 66 224 9.74e-29 107
Msa0833640 MtrunA17_Chr2g0301381 35.912 181 95 6 16 189 23 189 9.38e-26 98.6
Msa0833640 MtrunA17_Chr1g0195561 31.481 162 106 2 28 189 33 189 1.75e-25 97.8
Msa0833640 MtrunA17_Chr4g0070161 31.606 193 115 5 8 189 13 199 4.62e-24 94.4
Msa0833640 MtrunA17_Chr4g0018231 31.056 161 110 1 27 187 43 202 8.29e-23 90.9
Msa0833640 MtrunA17_Chr3g0126771 30.864 162 107 2 24 182 74 233 1.19e-17 80.1
Msa0833640 MtrunA17_Chr1g0147051 29.762 168 106 3 24 182 78 242 8.29e-17 77.8
Msa0833640 MtrunA17_Chr8g0345281 25.478 157 113 2 28 182 68 222 7.38e-15 72.0
Msa0833640 MtrunA17_Chr8g0345211 29.341 167 108 5 20 183 69 228 2.95e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0833640 AT1G62770.1 50.244 205 92 6 1 196 1 204 8.13e-61 188
Msa0833640 AT4G12390.1 56.805 169 69 2 27 192 39 206 3.89e-60 187
Msa0833640 AT4G25260.1 46.409 181 96 1 11 190 21 201 3.45e-55 174
Msa0833640 AT5G62350.1 47.273 165 86 1 27 190 38 202 2.19e-54 172
Msa0833640 AT3G47380.1 42.784 194 101 2 7 190 9 202 1.16e-51 165
Msa0833640 AT5G62360.1 41.818 165 92 2 26 190 42 202 3.46e-45 149
Msa0833640 AT1G62760.1 43.182 176 90 2 20 191 140 309 1.56e-41 142
Msa0833640 AT1G14890.1 41.566 166 90 2 26 189 57 217 9.31e-39 132
Msa0833640 AT2G01610.1 40.113 177 93 3 26 189 43 219 2.95e-37 129
Msa0833640 AT5G20740.1 40.361 166 90 3 26 186 32 193 1.73e-35 124
Msa0833640 AT5G20740.2 40.361 166 90 3 26 186 66 227 5.94e-35 123
Msa0833640 AT4G00080.1 36.683 199 111 6 1 185 1 198 4.57e-34 120
Msa0833640 AT4G25250.1 34.969 163 104 2 27 188 37 198 4.59e-34 120
Msa0833640 AT1G70720.1 34.254 181 110 3 12 187 18 194 4.62e-29 107
Msa0833640 AT1G70720.2 34.254 181 110 3 12 187 30 206 4.91e-29 107
Msa0833640 AT5G51520.1 33.929 168 101 2 27 186 37 202 7.98e-28 104
Msa0833640 AT1G23205.1 35.870 184 105 4 11 184 17 197 3.14e-25 97.8
Msa0833640 AT3G62820.1 32.796 186 115 5 8 188 11 191 2.23e-22 89.7
Msa0833640 AT3G14310.1 27.933 179 124 3 14 189 43 219 9.88e-21 89.7
Msa0833640 AT2G47670.1 30.675 163 109 2 25 187 46 204 1.18e-19 83.2
Msa0833640 AT1G53830.1 28.235 170 119 2 21 189 55 222 9.40e-18 80.9
Msa0833640 AT3G49220.2 32.184 174 92 7 24 190 128 282 3.24e-15 73.6
Msa0833640 AT3G49220.3 32.184 174 92 7 24 190 128 282 5.30e-15 73.2
Msa0833640 AT3G49220.1 32.184 174 92 7 24 190 83 237 5.56e-15 72.8
Msa0833640 AT5G53370.2 27.500 160 108 4 24 182 107 259 4.95e-13 67.4
Msa0833640 AT5G53370.1 27.500 160 108 4 24 182 71 223 5.11e-13 67.4
Msa0833640 AT3G14300.1 26.136 176 123 2 22 191 265 439 3.61e-12 64.7
Msa0833640 AT5G62340.1 24.623 199 127 5 9 190 14 206 4.36e-11 60.1

Find 52 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATGCGTTCAATGTCTTA+TGG 0.188587 5_4:+6748427 Msa0833640:CDS
GATGATAACACTTGTCTTGA+TGG 0.271370 5_4:+6748740 Msa0833640:CDS
ACTTGTCTTGATGGCTTTGC+TGG 0.284433 5_4:+6748749 Msa0833640:CDS
TAGAGCAGGGGTTTATTTGC+TGG 0.342763 5_4:+6748319 Msa0833640:CDS
AGAAAACATGGGTGACAGTT+TGG 0.352972 5_4:+6748607 Msa0833640:CDS
TTATGCGTTCAATGTCTTAT+GGG 0.361779 5_4:+6748428 Msa0833640:CDS
ATTGACAACCCTGTCCTTGA+TGG 0.385514 5_4:-6748801 None:intergenic
ACAGTCTTAGCCAATCGGTT+AGG 0.388918 5_4:+6748630 Msa0833640:CDS
TACCAGCAACACACTCGCTT+TGG 0.400248 5_4:+6748835 Msa0833640:CDS
ATGGGGTATGCGAGCGTGAT+TGG 0.403801 5_4:+6748446 Msa0833640:CDS
AACCAAAGCGAGTGTGTTGC+TGG 0.408904 5_4:-6748837 None:intergenic
TTCCATGAATGGAATTGTTA+AGG 0.412818 5_4:+6748775 Msa0833640:CDS
TCGTTAGTTGTCGCTCGCTT+TGG 0.415738 5_4:-6748469 None:intergenic
AGCCTTAACAATTCCATTCA+TGG 0.416556 5_4:-6748777 None:intergenic
ACATGAACAACGTGCAGACT+TGG 0.438369 5_4:+6748699 Msa0833640:CDS
AGCCAATCGGTTAGGGAGTT+AGG 0.439103 5_4:+6748638 Msa0833640:CDS
GTAAACATGGCGGCTAGAGC+AGG 0.443562 5_4:+6748305 None:intergenic
TTTGCTGGTCCTTCCATGAA+TGG 0.446590 5_4:+6748764 Msa0833640:CDS
CGATGCACTCGATCGTGTCC+TGG 0.450154 5_4:-6748516 None:intergenic
CAGTCTTAGCCAATCGGTTA+GGG 0.452763 5_4:+6748631 Msa0833640:CDS
GGCAGTATTGGTCATGCTGT+TGG 0.460878 5_4:+6748659 Msa0833640:CDS
GTTAGGGAGTTAGGCAGTAT+TGG 0.470731 5_4:+6748647 Msa0833640:CDS
GAACTCTGATGGGGTTATAG+AGG 0.476311 5_4:-6748369 None:intergenic
TTAAGGCTGCCATCAAGGAC+AGG 0.476862 5_4:+6748792 Msa0833640:CDS
TGTACGGCTCTGTACTCCCT+TGG 0.486585 5_4:-6748575 None:intergenic
CTCTATCAGTGAGCATATCC+AGG 0.495431 5_4:+6748498 Msa0833640:CDS
TTTGGACAGTCTTAGCCAAT+CGG 0.504656 5_4:+6748625 Msa0833640:CDS
GGCAAGAGGCATCAAGCCAA+GGG 0.526611 5_4:+6748559 Msa0833640:CDS
TATGCGTTCAATGTCTTATG+GGG 0.527485 5_4:+6748429 Msa0833640:CDS
TTCTGCAGTTCGATGGCTTG+AGG 0.534233 5_4:-6748870 None:intergenic
TAAACATGGCGGCTAGAGCA+GGG 0.538519 5_4:+6748306 None:intergenic
AATTGTTAAGGCTGCCATCA+AGG 0.538854 5_4:+6748787 Msa0833640:CDS
TGCCTAACTCCCTAACCGAT+TGG 0.544285 5_4:-6748640 None:intergenic
AGGCAAGAGGCATCAAGCCA+AGG 0.545433 5_4:+6748558 Msa0833640:CDS
GAGGACTTGATGAACTCTGA+TGG 0.549989 5_4:-6748380 None:intergenic
AGGACTTGATGAACTCTGAT+GGG 0.550827 5_4:-6748379 None:intergenic
AAGGAGTTTCTGCAGTTCGA+TGG 0.560457 5_4:-6748877 None:intergenic
CTGCAGTGACAAGGCTCATG+AGG 0.569036 5_4:-6748343 None:intergenic
ACAAGACTGCATAGAAAACA+TGG 0.577763 5_4:+6748595 Msa0833640:CDS
CATGAACAACGTGCAGACTT+GGG 0.585314 5_4:+6748700 Msa0833640:CDS
TTAACAATTCCATTCATGGA+AGG 0.596367 5_4:-6748773 None:intergenic
TAAGGCTGCCATCAAGGACA+GGG 0.619720 5_4:+6748793 Msa0833640:CDS
TATTGGTCATGCTGTTGGAG+AGG 0.620267 5_4:+6748664 Msa0833640:CDS
TAGAGGATTCTGCAGTGACA+AGG 0.636790 5_4:-6748352 None:intergenic
CAGAAGATATCAAAGGCAAG+AGG 0.641738 5_4:+6748545 Msa0833640:CDS
GTTTGTACAGAAGATATCAA+AGG 0.649432 5_4:+6748538 Msa0833640:CDS
AAACATGGCGGCTAGAGCAG+GGG 0.661918 5_4:+6748307 None:intergenic
ATAGCGAGTAGCTCTACATG+AGG 0.683240 5_4:-6748399 None:intergenic
GGATATGCTCACTGATAGAG+CGG 0.692375 5_4:-6748495 None:intergenic
GGACTTGATGAACTCTGATG+GGG 0.708124 5_4:-6748378 None:intergenic
CAAGACTGCATAGAAAACAT+GGG 0.713583 5_4:+6748596 Msa0833640:CDS
CTGTTGGAGAGGACTTCGTG+TGG 0.729717 5_4:+6748675 Msa0833640:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGACATTGAACGCATAAAAA+AGG - chr5_4:6748425-6748444 None:intergenic 30.0%
TTTATGCGTTCAATGTCTTA+TGG + chr5_4:6748427-6748446 Msa0833640:CDS 30.0%
TTATGCGTTCAATGTCTTAT+GGG + chr5_4:6748428-6748447 Msa0833640:CDS 30.0%
GTTTGTACAGAAGATATCAA+AGG + chr5_4:6748538-6748557 Msa0833640:CDS 30.0%
TTAACAATTCCATTCATGGA+AGG - chr5_4:6748776-6748795 None:intergenic 30.0%
TTCCATGAATGGAATTGTTA+AGG + chr5_4:6748775-6748794 Msa0833640:CDS 30.0%
TATGCGTTCAATGTCTTATG+GGG + chr5_4:6748429-6748448 Msa0833640:CDS 35.0%
!! GTTTTCTATGCAGTCTTGTA+CGG - chr5_4:6748594-6748613 None:intergenic 35.0%
ACAAGACTGCATAGAAAACA+TGG + chr5_4:6748595-6748614 Msa0833640:CDS 35.0%
CAAGACTGCATAGAAAACAT+GGG + chr5_4:6748596-6748615 Msa0833640:CDS 35.0%
GATGATAACACTTGTCTTGA+TGG + chr5_4:6748740-6748759 Msa0833640:CDS 35.0%
AGCCTTAACAATTCCATTCA+TGG - chr5_4:6748780-6748799 None:intergenic 35.0%
AGGACTTGATGAACTCTGAT+GGG - chr5_4:6748382-6748401 None:intergenic 40.0%
CAGAAGATATCAAAGGCAAG+AGG + chr5_4:6748545-6748564 Msa0833640:CDS 40.0%
AGAAAACATGGGTGACAGTT+TGG + chr5_4:6748607-6748626 Msa0833640:CDS 40.0%
TTTGGACAGTCTTAGCCAAT+CGG + chr5_4:6748625-6748644 Msa0833640:CDS 40.0%
AATTGTTAAGGCTGCCATCA+AGG + chr5_4:6748787-6748806 Msa0833640:CDS 40.0%
TAGAGCAGGGGTTTATTTGC+TGG + chr5_4:6748319-6748338 Msa0833640:CDS 45.0%
TAGAGGATTCTGCAGTGACA+AGG - chr5_4:6748355-6748374 None:intergenic 45.0%
GAACTCTGATGGGGTTATAG+AGG - chr5_4:6748372-6748391 None:intergenic 45.0%
GGACTTGATGAACTCTGATG+GGG - chr5_4:6748381-6748400 None:intergenic 45.0%
GAGGACTTGATGAACTCTGA+TGG - chr5_4:6748383-6748402 None:intergenic 45.0%
! ATAGCGAGTAGCTCTACATG+AGG - chr5_4:6748402-6748421 None:intergenic 45.0%
GGATATGCTCACTGATAGAG+CGG - chr5_4:6748498-6748517 None:intergenic 45.0%
CTCTATCAGTGAGCATATCC+AGG + chr5_4:6748498-6748517 Msa0833640:CDS 45.0%
ACAGTCTTAGCCAATCGGTT+AGG + chr5_4:6748630-6748649 Msa0833640:CDS 45.0%
CAGTCTTAGCCAATCGGTTA+GGG + chr5_4:6748631-6748650 Msa0833640:CDS 45.0%
GTTAGGGAGTTAGGCAGTAT+TGG + chr5_4:6748647-6748666 Msa0833640:CDS 45.0%
TATTGGTCATGCTGTTGGAG+AGG + chr5_4:6748664-6748683 Msa0833640:CDS 45.0%
ACATGAACAACGTGCAGACT+TGG + chr5_4:6748699-6748718 Msa0833640:CDS 45.0%
CATGAACAACGTGCAGACTT+GGG + chr5_4:6748700-6748719 Msa0833640:CDS 45.0%
! ACTTGTCTTGATGGCTTTGC+TGG + chr5_4:6748749-6748768 Msa0833640:CDS 45.0%
TTTGCTGGTCCTTCCATGAA+TGG + chr5_4:6748764-6748783 Msa0833640:CDS 45.0%
ATTGACAACCCTGTCCTTGA+TGG - chr5_4:6748804-6748823 None:intergenic 45.0%
AAGGAGTTTCTGCAGTTCGA+TGG - chr5_4:6748880-6748899 None:intergenic 45.0%
TCGTTAGTTGTCGCTCGCTT+TGG - chr5_4:6748472-6748491 None:intergenic 50.0%
AGCCAATCGGTTAGGGAGTT+AGG + chr5_4:6748638-6748657 Msa0833640:CDS 50.0%
TGCCTAACTCCCTAACCGAT+TGG - chr5_4:6748643-6748662 None:intergenic 50.0%
!! GGCAGTATTGGTCATGCTGT+TGG + chr5_4:6748659-6748678 Msa0833640:CDS 50.0%
TTAAGGCTGCCATCAAGGAC+AGG + chr5_4:6748792-6748811 Msa0833640:CDS 50.0%
TAAGGCTGCCATCAAGGACA+GGG + chr5_4:6748793-6748812 Msa0833640:CDS 50.0%
TACCAGCAACACACTCGCTT+TGG + chr5_4:6748835-6748854 Msa0833640:CDS 50.0%
AACCAAAGCGAGTGTGTTGC+TGG - chr5_4:6748840-6748859 None:intergenic 50.0%
TTCTGCAGTTCGATGGCTTG+AGG - chr5_4:6748873-6748892 None:intergenic 50.0%
CTGCAGTGACAAGGCTCATG+AGG - chr5_4:6748346-6748365 None:intergenic 55.0%
ATGGGGTATGCGAGCGTGAT+TGG + chr5_4:6748446-6748465 Msa0833640:CDS 55.0%
!! AGGCAAGAGGCATCAAGCCA+AGG + chr5_4:6748558-6748577 Msa0833640:CDS 55.0%
!! GGCAAGAGGCATCAAGCCAA+GGG + chr5_4:6748559-6748578 Msa0833640:CDS 55.0%
TGTACGGCTCTGTACTCCCT+TGG - chr5_4:6748578-6748597 None:intergenic 55.0%
CTGTTGGAGAGGACTTCGTG+TGG + chr5_4:6748675-6748694 Msa0833640:CDS 55.0%
CGATGCACTCGATCGTGTCC+TGG - chr5_4:6748519-6748538 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 6748311 6748901 6748311 ID=Msa0833640;Name=Msa0833640
chr5_4 mRNA 6748311 6748901 6748311 ID=Msa0833640-mRNA-1;Parent=Msa0833640;Name=Msa0833640-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|196
chr5_4 exon 6748311 6748901 6748311 ID=Msa0833640-mRNA-1:exon:2950;Parent=Msa0833640-mRNA-1
chr5_4 CDS 6748311 6748901 6748311 ID=Msa0833640-mRNA-1:cds;Parent=Msa0833640-mRNA-1
Gene Sequence

>Msa0833640

ATGGCGGCTAGAGCAGGGGTTTATTTGCTGGTCCTCATGAGCCTTGTCACTGCAGAATCCTCTATAACCCCATCAGAGTTCATCAAGTCCTCATGTAGAGCTACTCGCTATCCTTTTTTATGCGTTCAATGTCTTATGGGGTATGCGAGCGTGATTGGCCAAAGCGAGCGACAACTAACGATAACCGCTCTATCAGTGAGCATATCCAGGACACGATCGAGTGCATCGTTTGTACAGAAGATATCAAAGGCAAGAGGCATCAAGCCAAGGGAGTACAGAGCCGTACAAGACTGCATAGAAAACATGGGTGACAGTTTGGACAGTCTTAGCCAATCGGTTAGGGAGTTAGGCAGTATTGGTCATGCTGTTGGAGAGGACTTCGTGTGGCACATGAACAACGTGCAGACTTGGGTCAGTGCTGCACTTACTGATGATAACACTTGTCTTGATGGCTTTGCTGGTCCTTCCATGAATGGAATTGTTAAGGCTGCCATCAAGGACAGGGTTGTCAATGTTGCTCAAGTTACCAGCAACACACTCGCTTTGGTTAATCACTTCGCCTCAAGCCATCGAACTGCAGAAACTCCTTAA

Protein sequence

>Msa0833640

MAARAGVYLLVLMSLVTAESSITPSEFIKSSCRATRYPFLCVQCLMGYASVIGQSERQLTITALSVSISRTRSSASFVQKISKARGIKPREYRAVQDCIENMGDSLDSLSQSVRELGSIGHAVGEDFVWHMNNVQTWVSAALTDDNTCLDGFAGPSMNGIVKAAIKDRVVNVAQVTSNTLALVNHFASSHRTAETP*