AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063976

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063976.t1 MTR_3g101810 95.604 273 9 3 1 272 1 271 0.0 520
MS.gene063976.t1 MTR_5g017210 60.870 161 58 3 91 250 56 212 8.19e-48 159
MS.gene063976.t1 MTR_8g093500 75.824 91 22 0 146 236 87 177 7.72e-46 155
MS.gene063976.t1 MTR_2g100490 63.441 93 33 1 145 236 261 353 2.07e-27 109
MS.gene063976.t1 MTR_8g015450 56.311 103 41 1 145 243 296 398 5.85e-27 108
MS.gene063976.t1 MTR_7g069590 68.519 54 17 0 179 232 32 85 1.79e-21 88.2
MS.gene063976.t1 MTR_5g079500 62.500 56 21 0 180 235 225 280 1.89e-18 83.6
MS.gene063976.t1 MTR_1g018090 62.963 54 20 0 182 235 283 336 1.14e-17 82.0
MS.gene063976.t1 MTR_1g106460 50.746 67 33 0 169 235 234 300 2.23e-17 80.9
MS.gene063976.t1 MTR_5g005110 61.111 54 21 0 182 235 233 286 5.49e-17 79.7
MS.gene063976.t1 MTR_1g106470 46.914 81 43 0 182 262 205 285 7.93e-17 79.0
MS.gene063976.t1 MTR_3g103030 53.968 63 29 0 173 235 229 291 5.78e-16 76.6
MS.gene063976.t1 MTR_4g131160 55.385 65 28 1 180 243 206 270 9.82e-15 73.9
MS.gene063976.t1 MTR_4g131160 55.385 65 28 1 180 243 203 267 1.01e-14 73.9
MS.gene063976.t1 MTR_1g080890 46.835 79 41 1 166 243 186 264 1.61e-14 72.8
MS.gene063976.t1 MTR_1g106480 58.000 50 21 0 186 235 82 131 1.69e-13 67.0
MS.gene063976.t1 MTR_2g067000 48.684 76 32 1 168 236 145 220 2.35e-13 68.9
MS.gene063976.t1 MTR_1g060700 57.407 54 23 0 183 236 357 410 2.10e-12 67.0
MS.gene063976.t1 MTR_4g033295 56.140 57 24 1 183 238 128 184 8.87e-12 63.2
MS.gene063976.t1 MTR_1g052470 41.573 89 47 2 151 238 280 364 1.57e-11 64.3
MS.gene063976.t1 MTR_2g089070 51.852 54 26 0 183 236 146 199 1.67e-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.gene063976.t1 AT3G50330 78.182 110 23 1 146 254 92 201 3.29e-46 155
MS.gene063976.t1 AT5G67060 86.170 94 13 0 146 239 83 176 1.34e-45 153
MS.gene063976.t1 AT5G67060 86.170 94 13 0 146 239 95 188 1.88e-45 153
MS.gene063976.t1 AT4G00120 69.318 88 27 0 149 236 88 175 1.05e-36 129
MS.gene063976.t1 AT3G21330 65.217 92 32 0 145 236 241 332 1.22e-36 134
MS.gene063976.t1 AT5G09750 74.444 90 23 0 146 235 92 181 9.28e-34 122
MS.gene063976.t1 AT5G01305 56.579 76 33 0 174 249 38 113 2.14e-21 88.6
MS.gene063976.t1 AT5G43175 50.725 69 34 0 167 235 126 194 1.45e-18 82.4
MS.gene063976.t1 AT4G33880 64.815 54 19 0 182 235 275 328 1.99e-18 84.0
MS.gene063976.t1 AT5G37800 53.333 75 28 1 168 235 189 263 3.46e-18 82.8
MS.gene063976.t1 AT1G27740 52.941 68 32 0 168 235 162 229 4.63e-18 81.6
MS.gene063976.t1 AT1G66470 63.636 55 20 0 181 235 203 257 7.17e-18 82.0
MS.gene063976.t1 AT2G14760 62.963 54 20 0 182 235 246 299 2.36e-17 80.9
MS.gene063976.t1 AT4G30980 54.054 74 33 1 170 242 127 200 5.91e-16 76.6
MS.gene063976.t1 AT2G24260 53.165 79 29 3 171 242 28 105 6.89e-16 75.5
MS.gene063976.t1 AT4G30980 53.333 75 34 1 169 242 174 248 1.08e-15 76.3
MS.gene063976.t1 AT2G24260 53.165 79 29 3 171 242 131 208 1.70e-15 75.9
MS.gene063976.t1 AT5G58010 50.000 76 37 1 170 244 96 171 1.88e-14 72.4
MS.gene063976.t1 AT2G14760 50.746 67 20 1 182 235 246 312 4.41e-14 71.6

Find 51 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGTTGCTGGTTCAGGATT+AGG 0.247420 5.2:-36436507 MS.gene063976:CDS
GATTCTGGGTCTATGTAAAT+TGG 0.284997 5.2:+36436765 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 5.2:+36437164 None:intergenic
GATCGTAATGTTGATCGTTA+TGG 0.304956 5.2:-36436453 MS.gene063976:CDS
TGTTGTTGTTGGAACATTAA+TGG 0.311513 5.2:+36436927 None:intergenic
AACAGGACAGTTGCTGGTTC+AGG 0.321831 5.2:-36436513 MS.gene063976:CDS
CAGTTGCTGGTTCAGGATTA+GGG 0.322129 5.2:-36436506 MS.gene063976:CDS
AGAGATTGTGTTTGTGTTTG+TGG 0.340639 5.2:+36436974 None:intergenic
TCACTGCAGGAACGTGCTTC+AGG 0.355705 5.2:-36436546 MS.gene063976:CDS
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 5.2:+36436480 None:intergenic
CTTCAGGAGCCAACAATAAC+AGG 0.382936 5.2:-36436530 MS.gene063976:CDS
GAAGACCATGGTATTGGATT+AGG 0.391268 5.2:+36437032 None:intergenic
CTCGAATTAGAAAACATTAA+CGG 0.391592 5.2:+36436897 None:intergenic
AACAATAACAGGACAGTTGC+TGG 0.393832 5.2:-36436519 MS.gene063976:CDS
TGGTGTAGTAGAGTTGTTAT+TGG 0.394604 5.2:+36436947 None:intergenic
ATCGTAATGTTGATCGTTAT+GGG 0.398296 5.2:-36436452 MS.gene063976:CDS
ATGATGAAGATGACTTTAAC+TGG 0.403724 5.2:+36437234 None:intergenic
ACGGTGTTGTTTGTTGTTGT+TGG 0.421243 5.2:+36436916 None:intergenic
AACGATCAACATTACGATCT+TGG 0.428866 5.2:+36436457 None:intergenic
AGCAACTGTCCTGTTATTGT+TGG 0.439967 5.2:+36436521 None:intergenic
GACCATGGTATTGGATTAGG+AGG 0.459342 5.2:+36437035 None:intergenic
GAAGATGAAGACCATGGTAT+TGG 0.485579 5.2:+36437026 None:intergenic
GCTCAGAATACGAACCATTA+CGG 0.497476 5.2:-36436864 MS.gene063976:CDS
CGTTAGATGAAGAAAATTCA+GGG 0.499125 5.2:+36437165 None:intergenic
GTGTTTGTGGTGGATTGTGA+AGG 0.504020 5.2:+36436987 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 5.2:-36436652 MS.gene063976:CDS
GGTACCAGGTGGAACTAAGA+TGG 0.521420 5.2:-36436631 MS.gene063976:CDS
AAACTCGATGGCGGTGATGA+GGG 0.526683 5.2:-36436817 MS.gene063976:CDS
TGACGGTGGAAATTGATTGA+TGG 0.535291 5.2:+36437127 None:intergenic
GATTGTGTTTGTGTTTGTGG+TGG 0.537734 5.2:+36436977 None:intergenic
TTACGATCTTGGTAAGGCTT+AGG 0.545623 5.2:+36436468 None:intergenic
GAAACTCGATGGCGGTGATG+AGG 0.551248 5.2:-36436818 MS.gene063976:CDS
ATGACAACGCAGTACCGTAA+TGG 0.563084 5.2:+36436850 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 5.2:-36436613 MS.gene063976:CDS
TGGAAATTGATTGATGGTGT+TGG 0.574025 5.2:+36437133 None:intergenic
TCAACATTACGATCTTGGTA+AGG 0.575828 5.2:+36436462 None:intergenic
GACACAACTTAAGTCACTGC+AGG 0.578655 5.2:-36436559 MS.gene063976:CDS
ATCTGAGAAGAGAAACTCGA+TGG 0.628015 5.2:-36436829 MS.gene063976:CDS
GTCATCTTCATCATCATCAG+AGG 0.630073 5.2:-36437225 MS.gene063976:CDS
TTATCTATTAAATCTGCAAG+AGG 0.636966 5.2:+36437059 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 5.2:+36436627 None:intergenic
AAGGCTTAGGCAATGAAACA+GGG 0.655130 5.2:+36436481 None:intergenic
TCATAGAATTGTTGATCTGA+CGG 0.657239 5.2:+36437110 None:intergenic
ACCATGGTATTGGATTAGGA+GGG 0.660517 5.2:+36437036 None:intergenic
ATACTGCAAAGAATGGTACC+AGG 0.680757 5.2:-36436645 MS.gene063976:CDS
TGAGAAGAGAAACTCGATGG+CGG 0.681216 5.2:-36436826 MS.gene063976:CDS
ACCCTCCTAATCCAATACCA+TGG 0.687624 5.2:-36437037 MS.gene063976:CDS
TGTCTAGCTGCAATACTCTG+AGG 0.695596 5.2:+36436699 None:intergenic
TAGAATTGTTGATCTGACGG+TGG 0.700773 5.2:+36437113 None:intergenic
CTGCAAAGAATGGTACCAGG+TGG 0.704915 5.2:-36436642 MS.gene063976:CDS
AATGATGAAGATGAAGACCA+TGG 0.757666 5.2:+36437020 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAGAATACTGCAAAGAA+TGG - chr5.2:36437042-36437061 MS.gene063976:CDS 25.0%
! CTCGAATTAGAAAACATTAA+CGG + chr5.2:36436800-36436819 None:intergenic 25.0%
! TTATCTATTAAATCTGCAAG+AGG + chr5.2:36436638-36436657 None:intergenic 25.0%
!! ATCTTCACATTTCTTCTTTT+TGG + chr5.2:36436965-36436984 None:intergenic 25.0%
ATCGTAATGTTGATCGTTAT+GGG - chr5.2:36437242-36437261 MS.gene063976:CDS 30.0%
ATGATGAAGATGACTTTAAC+TGG + chr5.2:36436463-36436482 None:intergenic 30.0%
CGTTAGATGAAGAAAATTCA+GGG + chr5.2:36436532-36436551 None:intergenic 30.0%
TCATAGAATTGTTGATCTGA+CGG + chr5.2:36436587-36436606 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG - chr5.2:36436530-36436549 MS.gene063976:CDS 30.0%
! TGTTGTTGTTGGAACATTAA+TGG + chr5.2:36436770-36436789 None:intergenic 30.0%
! TTCACATTTCTTCTTTTTGG+TGG + chr5.2:36436962-36436981 None:intergenic 30.0%
AACGATCAACATTACGATCT+TGG + chr5.2:36437240-36437259 None:intergenic 35.0%
AATGATGAAGATGAAGACCA+TGG + chr5.2:36436677-36436696 None:intergenic 35.0%
AGAGATTGTGTTTGTGTTTG+TGG + chr5.2:36436723-36436742 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG + chr5.2:36436533-36436552 None:intergenic 35.0%
GATCGTAATGTTGATCGTTA+TGG - chr5.2:36437241-36437260 MS.gene063976:CDS 35.0%
GATTCTGGGTCTATGTAAAT+TGG + chr5.2:36436932-36436951 None:intergenic 35.0%
TCAACATTACGATCTTGGTA+AGG + chr5.2:36437235-36437254 None:intergenic 35.0%
TGGTGTAGTAGAGTTGTTAT+TGG + chr5.2:36436750-36436769 None:intergenic 35.0%
!! TGGAAATTGATTGATGGTGT+TGG + chr5.2:36436564-36436583 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG + chr5.2:36436946-36436965 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG + chr5.2:36436947-36436966 None:intergenic 35.0%
AACAATAACAGGACAGTTGC+TGG - chr5.2:36437175-36437194 MS.gene063976:CDS 40.0%
AAGGCTTAGGCAATGAAACA+GGG + chr5.2:36437216-36437235 None:intergenic 40.0%
AGCAACTGTCCTGTTATTGT+TGG + chr5.2:36437176-36437195 None:intergenic 40.0%
ATACTGCAAAGAATGGTACC+AGG - chr5.2:36437049-36437068 MS.gene063976:CDS 40.0%
ATCTGAGAAGAGAAACTCGA+TGG - chr5.2:36436865-36436884 MS.gene063976:CDS 40.0%
GAAGATGAAGACCATGGTAT+TGG + chr5.2:36436671-36436690 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr5.2:36437081-36437100 MS.gene063976:CDS 40.0%
GATTGTGTTTGTGTTTGTGG+TGG + chr5.2:36436720-36436739 None:intergenic 40.0%
GCTCAGAATACGAACCATTA+CGG - chr5.2:36436830-36436849 MS.gene063976:CDS 40.0%
GTCATCTTCATCATCATCAG+AGG - chr5.2:36436469-36436488 MS.gene063976:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG + chr5.2:36437217-36437236 None:intergenic 40.0%
TAGAATTGTTGATCTGACGG+TGG + chr5.2:36436584-36436603 None:intergenic 40.0%
TGACGGTGGAAATTGATTGA+TGG + chr5.2:36436570-36436589 None:intergenic 40.0%
TTACGATCTTGGTAAGGCTT+AGG + chr5.2:36437229-36437248 None:intergenic 40.0%
! ACCATGGTATTGGATTAGGA+GGG + chr5.2:36436661-36436680 None:intergenic 40.0%
! GAAGACCATGGTATTGGATT+AGG + chr5.2:36436665-36436684 None:intergenic 40.0%
!! ACGGTGTTGTTTGTTGTTGT+TGG + chr5.2:36436781-36436800 None:intergenic 40.0%
ACCCTCCTAATCCAATACCA+TGG - chr5.2:36436657-36436676 MS.gene063976:CDS 45.0%
ATGACAACGCAGTACCGTAA+TGG + chr5.2:36436847-36436866 None:intergenic 45.0%
CTTCAGGAGCCAACAATAAC+AGG - chr5.2:36437164-36437183 MS.gene063976:CDS 45.0%
GACACAACTTAAGTCACTGC+AGG - chr5.2:36437135-36437154 MS.gene063976:CDS 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr5.2:36437070-36437089 None:intergenic 45.0%
TGAGAAGAGAAACTCGATGG+CGG - chr5.2:36436868-36436887 MS.gene063976:CDS 45.0%
TGTCTAGCTGCAATACTCTG+AGG + chr5.2:36436998-36437017 None:intergenic 45.0%
! GACCATGGTATTGGATTAGG+AGG + chr5.2:36436662-36436681 None:intergenic 45.0%
!! ACAGTTGCTGGTTCAGGATT+AGG - chr5.2:36437187-36437206 MS.gene063976:CDS 45.0%
!! CAGTTGCTGGTTCAGGATTA+GGG - chr5.2:36437188-36437207 MS.gene063976:CDS 45.0%
!! GTGTTTGTGGTGGATTGTGA+AGG + chr5.2:36436710-36436729 None:intergenic 45.0%
CTGCAAAGAATGGTACCAGG+TGG - chr5.2:36437052-36437071 MS.gene063976:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr5.2:36437063-36437082 MS.gene063976:CDS 50.0%
! AAACTCGATGGCGGTGATGA+GGG - chr5.2:36436877-36436896 MS.gene063976:CDS 50.0%
!! AACAGGACAGTTGCTGGTTC+AGG - chr5.2:36437181-36437200 MS.gene063976:CDS 50.0%
TCACTGCAGGAACGTGCTTC+AGG - chr5.2:36437148-36437167 MS.gene063976:CDS 55.0%
! GAAACTCGATGGCGGTGATG+AGG - chr5.2:36436876-36436895 MS.gene063976:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 36436449 36437267 36436449 ID=MS.gene063976
chr5.2 mRNA 36436449 36437267 36436449 ID=MS.gene063976.t1;Parent=MS.gene063976
chr5.2 exon 36436449 36437267 36436449 ID=MS.gene063976.t1.exon1;Parent=MS.gene063976.t1
chr5.2 CDS 36436449 36437267 36436449 ID=cds.MS.gene063976.t1;Parent=MS.gene063976.t1
Gene Sequence

>MS.gene063976

ATGGACTGTAACCAGTTAAAGTCATCTTCATCATCATCAGAGGATCAAATTGACATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAATACCAACACCATCAATCAATTTCCACCGTCAGATCAACAATTCTATGACACTTCAAATGCTTCTAACAATACACGTCCTCTTGCAGATTTAATAGATAACCCTCCTAATCCAATACCATGGTCTTCATCTTCATCATTCACTCATTTACCTTCACAATCCACCACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACTACACCATTAATGTTCCAACAACAACAAACAACACCGTTAATGTTTTCTAATTCGAGCAACGAGATTGCTCAGAATACGAACCATTACGGTACTGCGTTGTCATCTGAGAAGAGAAACTCGATGGCGGTGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAAAGAAGAAATGTGAAGATTTCAAAAGATCCTCAGAGTATTGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAATAACAGGACAGTTGCTGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGATCGTAATGTTGATCGTTATGGGTGA
Protein sequence

>MS.gene063976.t1

MDCNQLKSSSSSSEDQIDMMLMMMMQLPEFSSSNGNNTNTINQFPPSDQQFYDTSNASNNTRPLADLIDNPPNPIPWSSSSSFTHLPSQSTTNTNTISFTNNNSTTPLMFQQQQTTPLMFSNSSNEIAQNTNHYGTALSSEKRNSMAVMREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANNNRTVAGSGLGFPVSLPKPYQDRNVDRYG