AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38356

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38356.t1 MTR_3g101810 97.059 272 5 3 1 270 1 271 0.0 528
MS.gene38356.t1 MTR_5g017210 65.714 140 45 2 110 248 75 212 1.04e-46 156
MS.gene38356.t1 MTR_8g093500 75.824 91 22 0 144 234 87 177 7.26e-46 155
MS.gene38356.t1 MTR_2g100490 63.441 93 33 1 143 234 261 353 1.58e-27 109
MS.gene38356.t1 MTR_8g015450 55.769 104 42 1 143 242 296 399 3.31e-27 109
MS.gene38356.t1 MTR_7g069590 68.519 54 17 0 177 230 32 85 1.73e-21 88.2
MS.gene38356.t1 MTR_5g079500 62.500 56 21 0 178 233 225 280 1.57e-18 84.0
MS.gene38356.t1 MTR_1g018090 62.963 54 20 0 180 233 283 336 9.57e-18 82.4
MS.gene38356.t1 MTR_1g106460 50.746 67 33 0 167 233 234 300 2.19e-17 80.9
MS.gene38356.t1 MTR_1g106470 46.914 81 43 0 180 260 205 285 2.54e-17 80.1
MS.gene38356.t1 MTR_5g005110 61.111 54 21 0 180 233 233 286 4.53e-17 80.1
MS.gene38356.t1 MTR_3g103030 53.968 63 29 0 171 233 229 291 4.83e-16 77.0
MS.gene38356.t1 MTR_4g131160 54.545 66 29 1 178 242 203 268 6.32e-15 74.3
MS.gene38356.t1 MTR_4g131160 54.545 66 29 1 178 242 206 271 6.57e-15 74.3
MS.gene38356.t1 MTR_1g080890 46.250 80 42 1 164 242 186 265 1.09e-14 73.2
MS.gene38356.t1 MTR_1g106480 58.000 50 21 0 184 233 82 131 1.29e-13 67.4
MS.gene38356.t1 MTR_2g067000 48.684 76 32 1 166 234 145 220 3.06e-13 68.6
MS.gene38356.t1 MTR_1g060700 57.407 54 23 0 181 234 357 410 2.59e-12 66.6
MS.gene38356.t1 MTR_4g033295 56.140 57 24 1 181 236 128 184 7.40e-12 63.2
MS.gene38356.t1 MTR_1g052470 41.304 92 49 2 146 236 277 364 8.08e-12 65.1
MS.gene38356.t1 MTR_2g089070 51.852 54 26 0 181 234 146 199 1.79e-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.gene38356.t1 AT3G50330 60.000 165 55 3 99 252 37 201 2.99e-48 160
MS.gene38356.t1 AT5G67060 86.170 94 13 0 144 237 83 176 1.17e-45 153
MS.gene38356.t1 AT5G67060 86.170 94 13 0 144 237 95 188 1.98e-45 153
MS.gene38356.t1 AT4G00120 68.539 89 28 0 146 234 87 175 8.11e-37 129
MS.gene38356.t1 AT3G21330 65.217 92 32 0 143 234 241 332 8.31e-37 134
MS.gene38356.t1 AT5G09750 74.444 90 23 0 144 233 92 181 8.52e-34 122
MS.gene38356.t1 AT5G01305 67.797 59 19 0 172 230 38 96 3.26e-21 88.2
MS.gene38356.t1 AT5G43175 50.725 69 34 0 165 233 126 194 1.34e-18 82.4
MS.gene38356.t1 AT4G33880 64.815 54 19 0 180 233 275 328 1.84e-18 84.3
MS.gene38356.t1 AT5G37800 53.333 75 28 1 166 233 189 263 3.40e-18 82.8
MS.gene38356.t1 AT1G27740 52.941 68 32 0 166 233 162 229 4.29e-18 81.6
MS.gene38356.t1 AT1G66470 63.636 55 20 0 179 233 203 257 5.84e-18 82.0
MS.gene38356.t1 AT2G14760 62.963 54 20 0 180 233 246 299 2.04e-17 80.9
MS.gene38356.t1 AT4G30980 53.947 76 34 1 168 242 127 202 2.91e-16 77.4
MS.gene38356.t1 AT2G24260 53.086 81 30 3 169 242 28 107 3.00e-16 76.6
MS.gene38356.t1 AT4G30980 53.247 77 35 1 167 242 174 250 5.89e-16 77.0
MS.gene38356.t1 AT2G24260 53.086 81 30 3 169 242 131 210 8.54e-16 76.6
MS.gene38356.t1 AT5G58010 51.316 76 36 1 168 242 96 171 6.36e-15 73.6
MS.gene38356.t1 AT2G14760 50.746 67 20 1 180 233 246 312 4.04e-14 71.6

Find 54 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTGACGTTTCTTCTCTT+TGG 0.218574 3.2:+84763954 None:intergenic
ACAGTTGCTGGTTCAGGATT+AGG 0.247420 3.2:-84763729 MS.gene38356:CDS
GATTCTGGGTCTATGTAAAT+TGG 0.284997 3.2:+84763987 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 3.2:+84764380 None:intergenic
GATCGTAATGTTGATCGTTA+TGG 0.304956 3.2:-84763675 MS.gene38356:CDS
GTTTGTTGTTGGAACATTAA+TGG 0.311513 3.2:+84764146 None:intergenic
AACAGGACAGTTGCTGGTTC+AGG 0.321831 3.2:-84763735 MS.gene38356:CDS
CAGTTGCTGGTTCAGGATTA+GGG 0.322129 3.2:-84763728 MS.gene38356:CDS
GAAGACCATGGTATTTGATT+AGG 0.333202 3.2:+84764248 None:intergenic
TAATGGTGTAGAGTTGTTAT+TGG 0.339297 3.2:+84764163 None:intergenic
AGAGATTGTGTTTGTGTTTG+TGG 0.340639 3.2:+84764190 None:intergenic
TCACTGCAGGAACGTGCTTC+AGG 0.355705 3.2:-84763768 MS.gene38356:CDS
CCGTCAGATCAACAATTCTA+TGG 0.368765 3.2:-84764326 MS.gene38356:CDS
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 3.2:+84763702 None:intergenic
CTTCAGGAGCCAACAGTAAC+AGG 0.378388 3.2:-84763752 MS.gene38356:CDS
ATCGTAATGTTGATCGTTAT+GGG 0.398296 3.2:-84763674 MS.gene38356:CDS
ATGATGAAGATGACTTTAAC+TGG 0.403724 3.2:+84764450 None:intergenic
GCTCCGAATGCGAACCATTA+CGG 0.404632 3.2:-84764086 MS.gene38356:CDS
TTGACGTTTCTTCTCTTTGG+TGG 0.422338 3.2:+84763957 None:intergenic
AACGATCAACATTACGATCT+TGG 0.428866 3.2:+84763679 None:intergenic
CTCGAATTTGAAAACATTAG+CGG 0.440870 3.2:+84764119 None:intergenic
GACCATGGTATTTGATTAGG+AGG 0.444146 3.2:+84764251 None:intergenic
AACAGTAACAGGACAGTTGC+TGG 0.445444 3.2:-84763741 MS.gene38356:CDS
ATCGAGTTTCGTTTCTCTGA+TGG 0.446419 3.2:+84764053 None:intergenic
TTAGCGGTGTTGTTTGTTGT+TGG 0.484736 3.2:+84764135 None:intergenic
GTACCGTAATGGTTCGCATT+CGG 0.489297 3.2:+84764083 None:intergenic
CGTTAGATGAAGAAAATTCA+GGG 0.499125 3.2:+84764381 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 3.2:-84763874 MS.gene38356:CDS
TGTGTTTGTGGTGGATTGTG+AGG 0.519086 3.2:+84764202 None:intergenic
GGTACCAGGTGGAACTAAGA+TGG 0.521420 3.2:-84763853 MS.gene38356:CDS
GTGTTTGTGGTGGATTGTGA+GGG 0.523310 3.2:+84764203 None:intergenic
TGACGGTGGAAATTGATTGA+TGG 0.535291 3.2:+84764343 None:intergenic
GATTGTGTTTGTGTTTGTGG+TGG 0.537734 3.2:+84764193 None:intergenic
TTACGATCTTGGTAAGGCTT+AGG 0.545623 3.2:+84763690 None:intergenic
ATGGCGATGCAGTACCGTAA+TGG 0.554413 3.2:+84764072 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 3.2:-84763835 MS.gene38356:CDS
GAAACTCGATGGCGACGATG+AGG 0.573917 3.2:-84764040 MS.gene38356:CDS
TCAACATTACGATCTTGGTA+AGG 0.575828 3.2:+84763684 None:intergenic
GACACAACTTAAGTCACTGC+AGG 0.578655 3.2:-84763781 MS.gene38356:CDS
AGCAACTGTCCTGTTACTGT+TGG 0.580375 3.2:+84763743 None:intergenic
ACCATGGTATTTGATTAGGA+GGG 0.602997 3.2:+84764252 None:intergenic
AAACTCGATGGCGACGATGA+GGG 0.604342 3.2:-84764039 MS.gene38356:CDS
ATCAGAGAAACGAAACTCGA+TGG 0.615534 3.2:-84764051 MS.gene38356:CDS
GTCATCTTCATCATCATCAG+AGG 0.630073 3.2:-84764441 MS.gene38356:CDS
TGTCTAGCTGCTATACTCTG+AGG 0.634069 3.2:+84763921 None:intergenic
GTATCCATCTTAGTTCCACC+TGG 0.642640 3.2:+84763849 None:intergenic
CCATAGAATTGTTGATCTGA+CGG 0.644487 3.2:+84764326 None:intergenic
TTATCTATTAAATATGCAAG+AGG 0.650233 3.2:+84764275 None:intergenic
AAGGCTTAGGCAATGAAACA+GGG 0.655130 3.2:+84763703 None:intergenic
ACCCTCCTAATCAAATACCA+TGG 0.671083 3.2:-84764253 MS.gene38356:CDS
ATACTGCAAAGAATGGTACC+AGG 0.680757 3.2:-84763867 MS.gene38356:CDS
CTGCAAAGAATGGTACCAGG+TGG 0.704915 3.2:-84763864 MS.gene38356:CDS
TAGAATTGTTGATCTGACGG+TGG 0.709109 3.2:+84764329 None:intergenic
AATGATGAAGATGAAGACCA+TGG 0.757666 3.2:+84764236 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATCTATTAAATATGCAAG+AGG + chr3.2:84763860-84763879 None:intergenic 20.0%
! AATAAGAATACTGCAAAGAA+TGG - chr3.2:84764258-84764277 MS.gene38356:CDS 25.0%
ATCGTAATGTTGATCGTTAT+GGG - chr3.2:84764458-84764477 MS.gene38356:CDS 30.0%
ATGATGAAGATGACTTTAAC+TGG + chr3.2:84763685-84763704 None:intergenic 30.0%
CGTTAGATGAAGAAAATTCA+GGG + chr3.2:84763754-84763773 None:intergenic 30.0%
CTCGAATTTGAAAACATTAG+CGG + chr3.2:84764016-84764035 None:intergenic 30.0%
TAATGGTGTAGAGTTGTTAT+TGG + chr3.2:84763972-84763991 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG - chr3.2:84763752-84763771 MS.gene38356:CDS 30.0%
!! GTTTGTTGTTGGAACATTAA+TGG + chr3.2:84763989-84764008 None:intergenic 30.0%
AACGATCAACATTACGATCT+TGG + chr3.2:84764456-84764475 None:intergenic 35.0%
AATGATGAAGATGAAGACCA+TGG + chr3.2:84763899-84763918 None:intergenic 35.0%
ACCATGGTATTTGATTAGGA+GGG + chr3.2:84763883-84763902 None:intergenic 35.0%
AGAGATTGTGTTTGTGTTTG+TGG + chr3.2:84763945-84763964 None:intergenic 35.0%
ATCTTGACGTTTCTTCTCTT+TGG + chr3.2:84764181-84764200 None:intergenic 35.0%
CCATAGAATTGTTGATCTGA+CGG + chr3.2:84763809-84763828 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG + chr3.2:84763755-84763774 None:intergenic 35.0%
GAAGACCATGGTATTTGATT+AGG + chr3.2:84763887-84763906 None:intergenic 35.0%
GATCGTAATGTTGATCGTTA+TGG - chr3.2:84764457-84764476 MS.gene38356:CDS 35.0%
GATTCTGGGTCTATGTAAAT+TGG + chr3.2:84764148-84764167 None:intergenic 35.0%
TCAACATTACGATCTTGGTA+AGG + chr3.2:84764451-84764470 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG + chr3.2:84764162-84764181 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG + chr3.2:84764163-84764182 None:intergenic 35.0%
AAGGCTTAGGCAATGAAACA+GGG + chr3.2:84764432-84764451 None:intergenic 40.0%
ACCCTCCTAATCAAATACCA+TGG - chr3.2:84763879-84763898 MS.gene38356:CDS 40.0%
ATACTGCAAAGAATGGTACC+AGG - chr3.2:84764265-84764284 MS.gene38356:CDS 40.0%
ATCAGAGAAACGAAACTCGA+TGG - chr3.2:84764081-84764100 MS.gene38356:CDS 40.0%
ATCGAGTTTCGTTTCTCTGA+TGG + chr3.2:84764082-84764101 None:intergenic 40.0%
CCGTCAGATCAACAATTCTA+TGG - chr3.2:84763806-84763825 MS.gene38356:CDS 40.0%
GACCATGGTATTTGATTAGG+AGG + chr3.2:84763884-84763903 None:intergenic 40.0%
GATGGATACTGCATCAATGT+TGG - chr3.2:84764297-84764316 MS.gene38356:CDS 40.0%
GATTGTGTTTGTGTTTGTGG+TGG + chr3.2:84763942-84763961 None:intergenic 40.0%
GTCATCTTCATCATCATCAG+AGG - chr3.2:84763691-84763710 MS.gene38356:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG + chr3.2:84764433-84764452 None:intergenic 40.0%
TAGAATTGTTGATCTGACGG+TGG + chr3.2:84763806-84763825 None:intergenic 40.0%
TGACGGTGGAAATTGATTGA+TGG + chr3.2:84763792-84763811 None:intergenic 40.0%
TTACGATCTTGGTAAGGCTT+AGG + chr3.2:84764445-84764464 None:intergenic 40.0%
TTGACGTTTCTTCTCTTTGG+TGG + chr3.2:84764178-84764197 None:intergenic 40.0%
!! TTAGCGGTGTTGTTTGTTGT+TGG + chr3.2:84764000-84764019 None:intergenic 40.0%
AACAGTAACAGGACAGTTGC+TGG - chr3.2:84764391-84764410 MS.gene38356:CDS 45.0%
AGCAACTGTCCTGTTACTGT+TGG + chr3.2:84764392-84764411 None:intergenic 45.0%
GACACAACTTAAGTCACTGC+AGG - chr3.2:84764351-84764370 MS.gene38356:CDS 45.0%
GTACCGTAATGGTTCGCATT+CGG + chr3.2:84764052-84764071 None:intergenic 45.0%
GTATCCATCTTAGTTCCACC+TGG + chr3.2:84764286-84764305 None:intergenic 45.0%
TGTCTAGCTGCTATACTCTG+AGG + chr3.2:84764214-84764233 None:intergenic 45.0%
!! ACAGTTGCTGGTTCAGGATT+AGG - chr3.2:84764403-84764422 MS.gene38356:CDS 45.0%
!! CAGTTGCTGGTTCAGGATTA+GGG - chr3.2:84764404-84764423 MS.gene38356:CDS 45.0%
!! GTGTTTGTGGTGGATTGTGA+GGG + chr3.2:84763932-84763951 None:intergenic 45.0%
!! TGTGTTTGTGGTGGATTGTG+AGG + chr3.2:84763933-84763952 None:intergenic 45.0%
AAACTCGATGGCGACGATGA+GGG - chr3.2:84764093-84764112 MS.gene38356:CDS 50.0%
ATGGCGATGCAGTACCGTAA+TGG + chr3.2:84764063-84764082 None:intergenic 50.0%
CTGCAAAGAATGGTACCAGG+TGG - chr3.2:84764268-84764287 MS.gene38356:CDS 50.0%
CTTCAGGAGCCAACAGTAAC+AGG - chr3.2:84764380-84764399 MS.gene38356:CDS 50.0%
GCTCCGAATGCGAACCATTA+CGG - chr3.2:84764046-84764065 MS.gene38356:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG - chr3.2:84764279-84764298 MS.gene38356:CDS 50.0%
!! AACAGGACAGTTGCTGGTTC+AGG - chr3.2:84764397-84764416 MS.gene38356:CDS 50.0%
GAAACTCGATGGCGACGATG+AGG - chr3.2:84764092-84764111 MS.gene38356:CDS 55.0%
TCACTGCAGGAACGTGCTTC+AGG - chr3.2:84764364-84764383 MS.gene38356:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 84763671 84764483 84763671 ID=MS.gene38356
chr3.2 mRNA 84763671 84764483 84763671 ID=MS.gene38356.t1;Parent=MS.gene38356
chr3.2 exon 84763671 84764483 84763671 ID=MS.gene38356.t1.exon1;Parent=MS.gene38356.t1
chr3.2 CDS 84763671 84764483 84763671 ID=cds.MS.gene38356.t1;Parent=MS.gene38356.t1
Gene Sequence

>MS.gene38356

ATGGACTGTAACCAGTTAAAGTCATCTTCATCATCATCAGAGGATCAAATTGACATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAACAACAACACCATCAATCAATTTCCACCGTCAGATCAACAATTCTATGGCACTTCAAATGCTTCTAACAATACACGTCCTCTTGCATATTTAATAGATAACCCTCCTAATCAAATACCATGGTCTTCATCTTCATCATTCACTCACTTACCCTCACAATCCACCACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACACCATTAATGTTCCAACAACAAACAACACCGCTAATGTTTTCAAATTCGAGCAACGAGATTGCTCCGAATGCGAACCATTACGGTACTGCATCGCCATCAGAGAAACGAAACTCGATGGCGACGATGAGGGAGATGATATTCAGAATAGCAGCTATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAGAGAAGAAACGTCAAGATTTCAAAAGATCCTCAGAGTATAGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAACTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAGTAACAGGACAGTTGCTGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGATCGTAATGTTGATCGTTATGGGTGA
Protein sequence

>MS.gene38356.t1

MDCNQLKSSSSSSEDQIDMMLMMMMQLPEFSSSNGNNNNTINQFPPSDQQFYGTSNASNNTRPLAYLIDNPPNQIPWSSSSSFTHLPSQSTTNTNTISFTNNNSTPLMFQQQTTPLMFSNSSNEIAPNANHYGTASPSEKRNSMATMREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSIAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANSNRTVAGSGLGFPVSLPKPYQDRNVDRYG