AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene92827

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92827.t1 MTR_3g101810 95.588 272 9 3 1 271 1 270 0.0 517
MS.gene92827.t1 MTR_5g017210 60.870 161 58 3 91 250 56 212 7.78e-48 159
MS.gene92827.t1 MTR_8g093500 75.824 91 22 0 146 236 87 177 6.58e-46 155
MS.gene92827.t1 MTR_2g100490 63.441 93 33 1 145 236 261 353 2.15e-27 109
MS.gene92827.t1 MTR_8g015450 56.311 103 41 1 145 243 296 398 5.60e-27 108
MS.gene92827.t1 MTR_7g069590 68.519 54 17 0 179 232 32 85 1.72e-21 88.6
MS.gene92827.t1 MTR_5g079500 62.500 56 21 0 180 235 225 280 1.91e-18 83.6
MS.gene92827.t1 MTR_1g018090 62.963 54 20 0 182 235 283 336 1.14e-17 82.0
MS.gene92827.t1 MTR_1g106460 50.746 67 33 0 169 235 234 300 1.95e-17 80.9
MS.gene92827.t1 MTR_5g005110 61.111 54 21 0 182 235 233 286 5.72e-17 79.7
MS.gene92827.t1 MTR_1g106470 46.914 81 43 0 182 262 205 285 8.61e-17 78.6
MS.gene92827.t1 MTR_3g103030 53.968 63 29 0 173 235 229 291 5.74e-16 76.6
MS.gene92827.t1 MTR_4g131160 55.385 65 28 1 180 243 203 267 9.39e-15 73.9
MS.gene92827.t1 MTR_4g131160 55.385 65 28 1 180 243 206 270 9.66e-15 73.9
MS.gene92827.t1 MTR_1g080890 46.835 79 41 1 166 243 186 264 1.60e-14 72.8
MS.gene92827.t1 MTR_1g106480 58.000 50 21 0 186 235 82 131 1.77e-13 67.0
MS.gene92827.t1 MTR_2g067000 48.684 76 32 1 168 236 145 220 2.05e-13 69.3
MS.gene92827.t1 MTR_1g060700 57.407 54 23 0 183 236 357 410 1.81e-12 67.4
MS.gene92827.t1 MTR_4g033295 56.140 57 24 1 183 238 128 184 9.22e-12 63.2
MS.gene92827.t1 MTR_1g052470 41.573 89 47 2 151 238 280 364 1.63e-11 64.3
MS.gene92827.t1 MTR_2g089070 51.852 54 26 0 183 236 146 199 1.76e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92827.t1 AT3G50330 73.554 121 25 2 141 254 81 201 3.09e-46 155
MS.gene92827.t1 AT5G67060 86.170 94 13 0 146 239 83 176 1.18e-45 153
MS.gene92827.t1 AT5G67060 86.170 94 13 0 146 239 95 188 1.75e-45 153
MS.gene92827.t1 AT4G00120 69.318 88 27 0 149 236 88 175 1.00e-36 129
MS.gene92827.t1 AT3G21330 65.217 92 32 0 145 236 241 332 1.13e-36 134
MS.gene92827.t1 AT5G09750 74.444 90 23 0 146 235 92 181 8.30e-34 122
MS.gene92827.t1 AT5G01305 56.579 76 33 0 174 249 38 113 2.12e-21 88.6
MS.gene92827.t1 AT5G43175 50.725 69 34 0 167 235 126 194 1.45e-18 82.4
MS.gene92827.t1 AT4G33880 64.815 54 19 0 182 235 275 328 2.03e-18 84.0
MS.gene92827.t1 AT5G37800 53.333 75 28 1 168 235 189 263 3.26e-18 82.8
MS.gene92827.t1 AT1G27740 52.941 68 32 0 168 235 162 229 4.41e-18 81.6
MS.gene92827.t1 AT1G66470 63.636 55 20 0 181 235 203 257 7.33e-18 82.0
MS.gene92827.t1 AT2G14760 62.963 54 20 0 182 235 246 299 2.39e-17 80.9
MS.gene92827.t1 AT4G30980 54.054 74 33 1 170 242 127 200 5.54e-16 76.6
MS.gene92827.t1 AT2G24260 53.165 79 29 3 171 242 28 105 6.92e-16 75.5
MS.gene92827.t1 AT4G30980 53.333 75 34 1 169 242 174 248 1.07e-15 76.3
MS.gene92827.t1 AT2G24260 53.165 79 29 3 171 242 131 208 1.63e-15 75.9
MS.gene92827.t1 AT5G58010 50.000 76 37 1 170 244 96 171 1.87e-14 72.4
MS.gene92827.t1 AT2G14760 50.746 67 20 1 182 235 246 312 4.47e-14 71.6

Find 51 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGTTGCTGGTTCAGGATT+AGG 0.247420 5.2:-36387250 MS.gene92827:CDS
GATTCTGGGTCTATGTAAAT+TGG 0.284997 5.2:+36387508 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 5.2:+36387907 None:intergenic
GATCGTAATGTTGATCGTTA+TGG 0.304956 5.2:-36387196 MS.gene92827:CDS
TGTTGTTGTTGGAACATTAA+TGG 0.311513 5.2:+36387670 None:intergenic
AACAGGACAGTTGCTGGTTC+AGG 0.321831 5.2:-36387256 MS.gene92827:CDS
CAGTTGCTGGTTCAGGATTA+GGG 0.322129 5.2:-36387249 MS.gene92827:CDS
AGAGATTGTGTTTGTGTTTG+TGG 0.340639 5.2:+36387717 None:intergenic
TCACTGCAGGAACGTGCTTC+AGG 0.355705 5.2:-36387289 MS.gene92827:CDS
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 5.2:+36387223 None:intergenic
CTTCAGGAGCCAACAATAAC+AGG 0.382936 5.2:-36387273 MS.gene92827:CDS
GAAGACCATGGTATTGGATT+AGG 0.391268 5.2:+36387775 None:intergenic
CTCGAATTAGAAAACATTAA+CGG 0.391592 5.2:+36387640 None:intergenic
AACAATAACAGGACAGTTGC+TGG 0.393832 5.2:-36387262 MS.gene92827:CDS
TGGTGTAGTAGAGTTGTTAT+TGG 0.394604 5.2:+36387690 None:intergenic
ATCGTAATGTTGATCGTTAT+GGG 0.398296 5.2:-36387195 None:intergenic
ATGATGAAGATGACTTTAAC+TGG 0.403724 5.2:+36387977 None:intergenic
ACGGTGTTGTTTGTTGTTGT+TGG 0.421243 5.2:+36387659 None:intergenic
AACGATCAACATTACGATCT+TGG 0.428866 5.2:+36387200 None:intergenic
AGCAACTGTCCTGTTATTGT+TGG 0.439967 5.2:+36387264 None:intergenic
GACCATGGTATTGGATTAGG+AGG 0.459342 5.2:+36387778 None:intergenic
GAAGATGAAGACCATGGTAT+TGG 0.485579 5.2:+36387769 None:intergenic
GCTCAGAATACGAACCATTA+CGG 0.497476 5.2:-36387607 MS.gene92827:CDS
CGTTAGATGAAGAAAATTCA+GGG 0.499125 5.2:+36387908 None:intergenic
GTGTTTGTGGTGGATTGTGA+AGG 0.504020 5.2:+36387730 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 5.2:-36387395 MS.gene92827:CDS
GGTACCAGGTGGAACTAAGA+TGG 0.521420 5.2:-36387374 MS.gene92827:CDS
AAACTCGATGGCGGTGATGA+GGG 0.526683 5.2:-36387560 MS.gene92827:CDS
TGACGGTGGAAATTGATTGA+TGG 0.535291 5.2:+36387870 None:intergenic
GATTGTGTTTGTGTTTGTGG+TGG 0.537734 5.2:+36387720 None:intergenic
TTACGATCTTGGTAAGGCTT+AGG 0.545623 5.2:+36387211 None:intergenic
GAAACTCGATGGCGGTGATG+AGG 0.551248 5.2:-36387561 MS.gene92827:CDS
ATGACAACGCAGTACCGTAA+TGG 0.563084 5.2:+36387593 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 5.2:-36387356 MS.gene92827:CDS
TGGAAATTGATTGATGGTGT+TGG 0.574025 5.2:+36387876 None:intergenic
TCAACATTACGATCTTGGTA+AGG 0.575828 5.2:+36387205 None:intergenic
GACACAACTTAAGTCACTGC+AGG 0.578655 5.2:-36387302 MS.gene92827:CDS
ATCTGAGAAGAGAAACTCGA+TGG 0.628015 5.2:-36387572 MS.gene92827:CDS
GTCATCTTCATCATCATCAG+AGG 0.630073 5.2:-36387968 MS.gene92827:CDS
TTATCTATTAAATCTGCAAG+AGG 0.636966 5.2:+36387802 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 5.2:+36387370 None:intergenic
AAGGCTTAGGCAATGAAACA+GGG 0.655130 5.2:+36387224 None:intergenic
TCATAGAATTGTTGATCTGA+CGG 0.657239 5.2:+36387853 None:intergenic
ACCATGGTATTGGATTAGGA+GGG 0.660517 5.2:+36387779 None:intergenic
ATACTGCAAAGAATGGTACC+AGG 0.680757 5.2:-36387388 MS.gene92827:CDS
TGAGAAGAGAAACTCGATGG+CGG 0.681216 5.2:-36387569 MS.gene92827:CDS
ACCCTCCTAATCCAATACCA+TGG 0.687624 5.2:-36387780 MS.gene92827:CDS
TGTCTAGCTGCAATACTCTG+AGG 0.695596 5.2:+36387442 None:intergenic
TAGAATTGTTGATCTGACGG+TGG 0.700773 5.2:+36387856 None:intergenic
CTGCAAAGAATGGTACCAGG+TGG 0.704915 5.2:-36387385 MS.gene92827:CDS
AATGATGAAGATGAAGACCA+TGG 0.757666 5.2:+36387763 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAGAATACTGCAAAGAA+TGG - chr5.2:36387789-36387808 MS.gene92827:CDS 25.0%
! CTCGAATTAGAAAACATTAA+CGG + chr5.2:36387547-36387566 None:intergenic 25.0%
! TTATCTATTAAATCTGCAAG+AGG + chr5.2:36387385-36387404 None:intergenic 25.0%
!! ATCTTCACATTTCTTCTTTT+TGG + chr5.2:36387712-36387731 None:intergenic 25.0%
ATGATGAAGATGACTTTAAC+TGG + chr5.2:36387210-36387229 None:intergenic 30.0%
CGTTAGATGAAGAAAATTCA+GGG + chr5.2:36387279-36387298 None:intergenic 30.0%
TCATAGAATTGTTGATCTGA+CGG + chr5.2:36387334-36387353 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG - chr5.2:36387277-36387296 MS.gene92827:CDS 30.0%
! TGTTGTTGTTGGAACATTAA+TGG + chr5.2:36387517-36387536 None:intergenic 30.0%
! TTCACATTTCTTCTTTTTGG+TGG + chr5.2:36387709-36387728 None:intergenic 30.0%
AACGATCAACATTACGATCT+TGG + chr5.2:36387987-36388006 None:intergenic 35.0%
AATGATGAAGATGAAGACCA+TGG + chr5.2:36387424-36387443 None:intergenic 35.0%
AGAGATTGTGTTTGTGTTTG+TGG + chr5.2:36387470-36387489 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG + chr5.2:36387280-36387299 None:intergenic 35.0%
GATCGTAATGTTGATCGTTA+TGG - chr5.2:36387988-36388007 MS.gene92827:CDS 35.0%
GATTCTGGGTCTATGTAAAT+TGG + chr5.2:36387679-36387698 None:intergenic 35.0%
TCAACATTACGATCTTGGTA+AGG + chr5.2:36387982-36388001 None:intergenic 35.0%
TGGTGTAGTAGAGTTGTTAT+TGG + chr5.2:36387497-36387516 None:intergenic 35.0%
!! TGGAAATTGATTGATGGTGT+TGG + chr5.2:36387311-36387330 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG + chr5.2:36387693-36387712 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG + chr5.2:36387694-36387713 None:intergenic 35.0%
AACAATAACAGGACAGTTGC+TGG - chr5.2:36387922-36387941 MS.gene92827:CDS 40.0%
AAGGCTTAGGCAATGAAACA+GGG + chr5.2:36387963-36387982 None:intergenic 40.0%
AGCAACTGTCCTGTTATTGT+TGG + chr5.2:36387923-36387942 None:intergenic 40.0%
ATACTGCAAAGAATGGTACC+AGG - chr5.2:36387796-36387815 MS.gene92827:CDS 40.0%
ATCTGAGAAGAGAAACTCGA+TGG - chr5.2:36387612-36387631 MS.gene92827:CDS 40.0%
GAAGATGAAGACCATGGTAT+TGG + chr5.2:36387418-36387437 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr5.2:36387828-36387847 MS.gene92827:CDS 40.0%
GATTGTGTTTGTGTTTGTGG+TGG + chr5.2:36387467-36387486 None:intergenic 40.0%
GCTCAGAATACGAACCATTA+CGG - chr5.2:36387577-36387596 MS.gene92827:CDS 40.0%
GTCATCTTCATCATCATCAG+AGG - chr5.2:36387216-36387235 MS.gene92827:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG + chr5.2:36387964-36387983 None:intergenic 40.0%
TAGAATTGTTGATCTGACGG+TGG + chr5.2:36387331-36387350 None:intergenic 40.0%
TGACGGTGGAAATTGATTGA+TGG + chr5.2:36387317-36387336 None:intergenic 40.0%
TTACGATCTTGGTAAGGCTT+AGG + chr5.2:36387976-36387995 None:intergenic 40.0%
! ACCATGGTATTGGATTAGGA+GGG + chr5.2:36387408-36387427 None:intergenic 40.0%
! GAAGACCATGGTATTGGATT+AGG + chr5.2:36387412-36387431 None:intergenic 40.0%
!! ACGGTGTTGTTTGTTGTTGT+TGG + chr5.2:36387528-36387547 None:intergenic 40.0%
ACCCTCCTAATCCAATACCA+TGG - chr5.2:36387404-36387423 MS.gene92827:CDS 45.0%
ATGACAACGCAGTACCGTAA+TGG + chr5.2:36387594-36387613 None:intergenic 45.0%
CTTCAGGAGCCAACAATAAC+AGG - chr5.2:36387911-36387930 MS.gene92827:CDS 45.0%
GACACAACTTAAGTCACTGC+AGG - chr5.2:36387882-36387901 MS.gene92827:CDS 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr5.2:36387817-36387836 None:intergenic 45.0%
TGAGAAGAGAAACTCGATGG+CGG - chr5.2:36387615-36387634 MS.gene92827:CDS 45.0%
TGTCTAGCTGCAATACTCTG+AGG + chr5.2:36387745-36387764 None:intergenic 45.0%
! GACCATGGTATTGGATTAGG+AGG + chr5.2:36387409-36387428 None:intergenic 45.0%
!! ACAGTTGCTGGTTCAGGATT+AGG - chr5.2:36387934-36387953 MS.gene92827:CDS 45.0%
!! CAGTTGCTGGTTCAGGATTA+GGG - chr5.2:36387935-36387954 MS.gene92827:CDS 45.0%
!! GTGTTTGTGGTGGATTGTGA+AGG + chr5.2:36387457-36387476 None:intergenic 45.0%
CTGCAAAGAATGGTACCAGG+TGG - chr5.2:36387799-36387818 MS.gene92827:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr5.2:36387810-36387829 MS.gene92827:CDS 50.0%
! AAACTCGATGGCGGTGATGA+GGG - chr5.2:36387624-36387643 MS.gene92827:CDS 50.0%
!! AACAGGACAGTTGCTGGTTC+AGG - chr5.2:36387928-36387947 MS.gene92827:CDS 50.0%
TCACTGCAGGAACGTGCTTC+AGG - chr5.2:36387895-36387914 MS.gene92827:CDS 55.0%
! GAAACTCGATGGCGGTGATG+AGG - chr5.2:36387623-36387642 MS.gene92827:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 36387196 36388010 36387196 ID=MS.gene92827
chr5.2 mRNA 36387196 36388010 36387196 ID=MS.gene92827.t1;Parent=MS.gene92827
chr5.2 exon 36387196 36388010 36387196 ID=MS.gene92827.t1.exon1;Parent=MS.gene92827.t1
chr5.2 CDS 36387196 36388010 36387196 ID=cds.MS.gene92827.t1;Parent=MS.gene92827.t1
Gene Sequence

>MS.gene92827

ATGGACTGTAACCAGTTAAAGTCATCTTCATCATCATCAGAGGATCAAATTGACATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAATACCAACACCATCAATCAATTTCCACCGTCAGATCAACAATTCTATGACACTTCAAATGCTTCTAACAATACACGTCCTCTTGCAGATTTAATAGATAACCCTCCTAATCCAATACCATGGTCTTCATCTTCATCATTCACTCATTTACCTTCACAATCCACCACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACTACACCATTAATGTTCCAACAACAACAAACAACACCGTTAATGTTTTCTAATTCGAGCAACGAGATTGCTCAGAATACGAACCATTACGGTACTGCGTTGTCATCTGAGAAGAGAAACTCGATGGCGGTGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAAAGAAGAAATGTGAAGATTTCAAAAGATCCTCAGAGTATTGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAATAACAGGACAGTTGCTGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGATCGTAATGTTGATCGTTATGG
Protein sequence

>MS.gene92827.t1

MDCNQLKSSSSSSEDQIDMMLMMMMQLPEFSSSNGNNTNTINQFPPSDQQFYDTSNASNNTRPLADLIDNPPNPIPWSSSSSFTHLPSQSTTNTNTISFTNNNSTTPLMFQQQQTTPLMFSNSSNEIAQNTNHYGTALSSEKRNSMAVMREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANNNRTVAGSGLGFPVSLPKPYQDRNVDRY