AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59535

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59535.t1 MTR_3g101810 93.145 248 14 3 8 254 26 271 3.17e-165 457
MS.gene59535.t1 MTR_5g017210 61.677 167 55 4 73 238 56 214 1.50e-49 163
MS.gene59535.t1 MTR_8g093500 76.923 91 21 0 128 218 87 177 3.57e-46 155
MS.gene59535.t1 MTR_2g100490 63.441 93 33 1 127 218 261 353 3.16e-27 108
MS.gene59535.t1 MTR_8g015450 55.769 104 42 1 127 226 296 399 5.57e-27 108
MS.gene59535.t1 MTR_7g069590 70.370 54 16 0 161 214 32 85 1.02e-21 88.6
MS.gene59535.t1 MTR_5g079500 64.286 56 20 0 162 217 225 280 1.17e-18 84.0
MS.gene59535.t1 MTR_1g106470 45.679 81 44 0 164 244 205 285 1.08e-17 80.9
MS.gene59535.t1 MTR_1g018090 62.963 54 20 0 164 217 283 336 1.26e-17 81.6
MS.gene59535.t1 MTR_1g106460 52.239 67 32 0 151 217 234 300 1.59e-17 80.9
MS.gene59535.t1 MTR_5g005110 46.154 78 42 0 164 241 233 310 2.04e-17 80.5
MS.gene59535.t1 MTR_3g103030 53.968 63 29 0 155 217 229 291 6.81e-16 76.3
MS.gene59535.t1 MTR_4g131160 53.030 66 30 1 162 226 203 268 1.23e-14 73.2
MS.gene59535.t1 MTR_4g131160 53.030 66 30 1 162 226 206 271 1.31e-14 73.2
MS.gene59535.t1 MTR_1g080890 45.000 80 43 1 148 226 186 265 2.62e-14 72.0
MS.gene59535.t1 MTR_1g106480 62.222 45 17 0 173 217 87 131 1.78e-13 66.6
MS.gene59535.t1 MTR_2g067000 47.368 76 33 1 150 218 145 220 6.08e-13 67.4
MS.gene59535.t1 MTR_1g060700 57.407 54 23 0 165 218 357 410 3.05e-12 66.2
MS.gene59535.t1 MTR_4g033295 54.386 57 25 1 165 220 128 184 9.47e-12 62.8
MS.gene59535.t1 MTR_2g089070 51.852 54 26 0 165 218 146 199 1.01e-11 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59535.t1 AT3G50330 58.788 165 42 4 90 235 35 192 1.61e-46 155
MS.gene59535.t1 AT5G67060 87.234 94 12 0 128 221 83 176 8.44e-46 153
MS.gene59535.t1 AT5G67060 87.234 94 12 0 128 221 95 188 1.12e-45 153
MS.gene59535.t1 AT4G00120 69.663 89 27 0 130 218 87 175 4.08e-37 130
MS.gene59535.t1 AT3G21330 56.303 119 43 2 127 242 241 353 8.49e-37 134
MS.gene59535.t1 AT5G09750 75.556 90 22 0 128 217 92 181 3.27e-34 123
MS.gene59535.t1 AT5G01305 69.492 59 18 0 156 214 38 96 1.81e-21 88.6
MS.gene59535.t1 AT5G43175 50.725 69 34 0 149 217 126 194 1.78e-18 81.6
MS.gene59535.t1 AT4G33880 64.815 54 19 0 164 217 275 328 3.20e-18 83.2
MS.gene59535.t1 AT1G27740 44.318 88 49 0 150 237 162 249 4.13e-18 81.6
MS.gene59535.t1 AT5G37800 53.333 75 28 1 150 217 189 263 5.72e-18 82.0
MS.gene59535.t1 AT1G66470 63.636 55 20 0 163 217 203 257 1.07e-17 80.9
MS.gene59535.t1 AT2G14760 62.963 54 20 0 164 217 246 299 3.33e-17 80.1
MS.gene59535.t1 AT4G30980 51.948 77 36 1 151 226 126 202 5.80e-16 76.3
MS.gene59535.t1 AT2G24260 51.852 81 31 3 153 226 28 107 6.61e-16 75.1
MS.gene59535.t1 AT4G30980 51.948 77 36 1 151 226 174 250 1.10e-15 75.9
MS.gene59535.t1 AT2G24260 51.852 81 31 3 153 226 131 210 1.60e-15 75.5
MS.gene59535.t1 AT5G58010 50.000 76 37 1 152 226 96 171 1.34e-14 72.4
MS.gene59535.t1 AT2G14760 50.746 67 20 1 164 217 246 312 6.45e-14 70.9
MS.gene59535.t1 AT1G35460 31.875 160 85 6 92 227 95 254 4.24e-11 62.0

Find 54 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTCACGTTTCTTCTCTT+TGG 0.198805 8.4:-68834622 None:intergenic
GATGAAGACCATGGTATTAT+TGG 0.220049 8.4:-68834325 None:intergenic
ACAGTTGATGGTTCAGGATT+AGG 0.252559 8.4:+68834847 MS.gene59535:CDS
TGTTGTTGTTGGAACCTTAA+TGG 0.283073 8.4:-68834427 None:intergenic
GATTCTGGGTCTATGTAAAT+TGG 0.284997 8.4:-68834589 None:intergenic
CCGTTAGATGAAGAAAATTC+AGG 0.301231 8.4:-68834190 None:intergenic
CAGTTGATGGTTCAGGATTA+GGG 0.305766 8.4:+68834848 MS.gene59535:CDS
CTTCAGGAGCCAACAGTAAA+AGG 0.313374 8.4:+68834824 MS.gene59535:CDS
GACCATGGTATTATTGGATT+AGG 0.338106 8.4:-68834319 None:intergenic
ACAACTCTACTGCACCATTA+AGG 0.339069 8.4:+68834413 MS.gene59535:CDS
GGTCGTAATGTTGATCGTTA+TGG 0.343129 8.4:+68834901 MS.gene59535:CDS
TCACTGCAGGAACGTGCTTC+AGG 0.355705 8.4:+68834808 MS.gene59535:CDS
CCGTCAGATCAACAATTCTA+TGG 0.368765 8.4:+68834241 MS.gene59535:CDS
GATTGTGTTTGTGTTTGTTA+TGG 0.370441 8.4:-68834377 None:intergenic
TAAGGCTTAGGCAATGAAAC+AGG 0.373028 8.4:-68834874 None:intergenic
CTCGAATTCGAAAACATTAA+CGG 0.373336 8.4:-68834457 None:intergenic
AAAAGGACAGTTGATGGTTC+AGG 0.375534 8.4:+68834841 MS.gene59535:CDS
TGGTGCAGTAGAGTTGTTAT+TGG 0.394604 8.4:-68834407 None:intergenic
GTCGTAATGTTGATCGTTAT+GGG 0.397591 8.4:+68834902 MS.gene59535:CDS
CCTCCGAATGCGAACCATTA+CGG 0.398684 8.4:+68834490 MS.gene59535:CDS
TTCACGTTTCTTCTCTTTGG+TGG 0.406987 8.4:-68834619 None:intergenic
ACGGTGTTGTTTGTTGTTGT+TGG 0.421243 8.4:-68834438 None:intergenic
ATCGAGTTTCTCTTCTCTGA+TGG 0.441629 8.4:-68834523 None:intergenic
AAACTCGATGGCGGCGTTGA+GGG 0.444275 8.4:+68834537 MS.gene59535:CDS
GTACCGTAATGGTTCGCATT+CGG 0.446982 8.4:-68834493 None:intergenic
CATGGTATTATTGGATTAGG+AGG 0.465821 8.4:-68834316 None:intergenic
TGACGGTTGAAATTGATTGA+TGG 0.483851 8.4:-68834224 None:intergenic
AACAGTAAAAGGACAGTTGA+TGG 0.491037 8.4:+68834835 MS.gene59535:CDS
CGTTAGATGAAGAAAATTCA+GGG 0.499125 8.4:-68834189 None:intergenic
AATAAGAATACTGCAAAGAA+TGG 0.517132 8.4:+68834702 MS.gene59535:CDS
GGTACCAGGTGGAACTAAGA+TGG 0.521420 8.4:+68834723 MS.gene59535:CDS
AACGATCAACATTACGACCT+TGG 0.536598 8.4:-68834897 None:intergenic
ATGGAGATGCAGTACCGTAA+TGG 0.553568 8.4:-68834504 None:intergenic
GAAACTCGATGGCGGCGTTG+AGG 0.556516 8.4:+68834536 MS.gene59535:CDS
TGTGTTTGTTATGGATTGTG+AGG 0.557974 8.4:-68834368 None:intergenic
TCAACATTACGACCTTGGTA+AGG 0.559092 8.4:-68834892 None:intergenic
GATGGATACTGCATCAATGT+TGG 0.564818 8.4:+68834741 MS.gene59535:CDS
GTGTTTGTTATGGATTGTGA+GGG 0.568107 8.4:-68834367 None:intergenic
CCGTAATGGTTCGCATTCGG+AGG 0.570332 8.4:-68834490 None:intergenic
GACACAGCTTAAGTCACTGC+AGG 0.580951 8.4:+68834795 MS.gene59535:CDS
TTACGACCTTGGTAAGGCTT+AGG 0.584405 8.4:-68834886 None:intergenic
ATGGTATTATTGGATTAGGA+GGG 0.600791 8.4:-68834315 None:intergenic
CTCCTAATCCAATAATACCA+TGG 0.613375 8.4:+68834317 MS.gene59535:CDS
TGTCTAGCTGCTACACTCTG+AGG 0.614013 8.4:-68834655 None:intergenic
CCATAGAATTGTTGATCTGA+CGG 0.627985 8.4:-68834241 None:intergenic
TTATCTATTAAATCTACAAG+AGG 0.640072 8.4:-68834292 None:intergenic
ATCAGAGAAGAGAAACTCGA+TGG 0.641186 8.4:+68834525 MS.gene59535:CDS
GTATCCATCTTAGTTCCACC+TGG 0.642640 8.4:-68834727 None:intergenic
TCATTGCCTAAGCCTTACCA+AGG 0.645634 8.4:+68834880 MS.gene59535:CDS
AAGGCTTAGGCAATGAAACA+GGG 0.655130 8.4:-68834873 None:intergenic
ATACTGCAAAGAATGGTACC+AGG 0.680757 8.4:+68834709 MS.gene59535:CDS
AGAGAAGAGAAACTCGATGG+CGG 0.694059 8.4:+68834528 MS.gene59535:CDS
CTGCAAAGAATGGTACCAGG+TGG 0.704915 8.4:+68834712 MS.gene59535:CDS
AATGATGAAGATGAAGACCA+TGG 0.757666 8.4:-68834334 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATCTATTAAATCTACAAG+AGG - chr8.4:68834295-68834314 None:intergenic 20.0%
! AATAAGAATACTGCAAAGAA+TGG + chr8.4:68834702-68834721 MS.gene59535:CDS 25.0%
CGTTAGATGAAGAAAATTCA+GGG - chr8.4:68834192-68834211 None:intergenic 30.0%
CTCGAATTCGAAAACATTAA+CGG - chr8.4:68834460-68834479 None:intergenic 30.0%
! ATGGTATTATTGGATTAGGA+GGG - chr8.4:68834318-68834337 None:intergenic 30.0%
! CCTGAATTTTCTTCATCTAA+CGG + chr8.4:68834190-68834209 MS.gene59535:CDS 30.0%
! GATTGTGTTTGTGTTTGTTA+TGG - chr8.4:68834380-68834399 None:intergenic 30.0%
AACAGTAAAAGGACAGTTGA+TGG + chr8.4:68834835-68834854 MS.gene59535:CDS 35.0%
AATGATGAAGATGAAGACCA+TGG - chr8.4:68834337-68834356 None:intergenic 35.0%
ATCTTCACGTTTCTTCTCTT+TGG - chr8.4:68834625-68834644 None:intergenic 35.0%
CCATAGAATTGTTGATCTGA+CGG - chr8.4:68834244-68834263 None:intergenic 35.0%
CCGTTAGATGAAGAAAATTC+AGG - chr8.4:68834193-68834212 None:intergenic 35.0%
CTCCTAATCCAATAATACCA+TGG + chr8.4:68834317-68834336 MS.gene59535:CDS 35.0%
GACCATGGTATTATTGGATT+AGG - chr8.4:68834322-68834341 None:intergenic 35.0%
GATGAAGACCATGGTATTAT+TGG - chr8.4:68834328-68834347 None:intergenic 35.0%
GATTCTGGGTCTATGTAAAT+TGG - chr8.4:68834592-68834611 None:intergenic 35.0%
GTCGTAATGTTGATCGTTAT+GGG + chr8.4:68834902-68834921 MS.gene59535:CDS 35.0%
TGACGGTTGAAATTGATTGA+TGG - chr8.4:68834227-68834246 None:intergenic 35.0%
! ATCAACTGTCCTTTTACTGT+TGG - chr8.4:68834836-68834855 None:intergenic 35.0%
! CATGGTATTATTGGATTAGG+AGG - chr8.4:68834319-68834338 None:intergenic 35.0%
! TGTTGTTGTTGGAACCTTAA+TGG - chr8.4:68834430-68834449 None:intergenic 35.0%
!! GTGTTTGTTATGGATTGTGA+GGG - chr8.4:68834370-68834389 None:intergenic 35.0%
!! TGTGTTTGTTATGGATTGTG+AGG - chr8.4:68834371-68834390 None:intergenic 35.0%
!!! TTGGTGGTTTTACTGATTCT+GGG - chr8.4:68834606-68834625 None:intergenic 35.0%
!!! TTTGGTGGTTTTACTGATTC+TGG - chr8.4:68834607-68834626 None:intergenic 35.0%
AACGATCAACATTACGACCT+TGG - chr8.4:68834900-68834919 None:intergenic 40.0%
AAGGCTTAGGCAATGAAACA+GGG - chr8.4:68834876-68834895 None:intergenic 40.0%
ACAACTCTACTGCACCATTA+AGG + chr8.4:68834413-68834432 MS.gene59535:CDS 40.0%
ATACTGCAAAGAATGGTACC+AGG + chr8.4:68834709-68834728 MS.gene59535:CDS 40.0%
ATCAGAGAAGAGAAACTCGA+TGG + chr8.4:68834525-68834544 MS.gene59535:CDS 40.0%
ATCGAGTTTCTCTTCTCTGA+TGG - chr8.4:68834526-68834545 None:intergenic 40.0%
CCGTCAGATCAACAATTCTA+TGG + chr8.4:68834241-68834260 MS.gene59535:CDS 40.0%
GATGGATACTGCATCAATGT+TGG + chr8.4:68834741-68834760 MS.gene59535:CDS 40.0%
GGTCGTAATGTTGATCGTTA+TGG + chr8.4:68834901-68834920 MS.gene59535:CDS 40.0%
TAAGGCTTAGGCAATGAAAC+AGG - chr8.4:68834877-68834896 None:intergenic 40.0%
TCAACATTACGACCTTGGTA+AGG - chr8.4:68834895-68834914 None:intergenic 40.0%
TGGTGCAGTAGAGTTGTTAT+TGG - chr8.4:68834410-68834429 None:intergenic 40.0%
TTCACGTTTCTTCTCTTTGG+TGG - chr8.4:68834622-68834641 None:intergenic 40.0%
!! AAAAGGACAGTTGATGGTTC+AGG + chr8.4:68834841-68834860 MS.gene59535:CDS 40.0%
!! ACAGTTGATGGTTCAGGATT+AGG + chr8.4:68834847-68834866 MS.gene59535:CDS 40.0%
!! ACGGTGTTGTTTGTTGTTGT+TGG - chr8.4:68834441-68834460 None:intergenic 40.0%
!! CAGTTGATGGTTCAGGATTA+GGG + chr8.4:68834848-68834867 MS.gene59535:CDS 40.0%
AGAGAAGAGAAACTCGATGG+CGG + chr8.4:68834528-68834547 MS.gene59535:CDS 45.0%
ATGGAGATGCAGTACCGTAA+TGG - chr8.4:68834507-68834526 None:intergenic 45.0%
CTTCAGGAGCCAACAGTAAA+AGG + chr8.4:68834824-68834843 MS.gene59535:CDS 45.0%
GTACCGTAATGGTTCGCATT+CGG - chr8.4:68834496-68834515 None:intergenic 45.0%
GTATCCATCTTAGTTCCACC+TGG - chr8.4:68834730-68834749 None:intergenic 45.0%
TCATTGCCTAAGCCTTACCA+AGG + chr8.4:68834880-68834899 MS.gene59535:CDS 45.0%
TTACGACCTTGGTAAGGCTT+AGG - chr8.4:68834889-68834908 None:intergenic 45.0%
CCTCCGAATGCGAACCATTA+CGG + chr8.4:68834490-68834509 MS.gene59535:CDS 50.0%
CTGCAAAGAATGGTACCAGG+TGG + chr8.4:68834712-68834731 MS.gene59535:CDS 50.0%
GACACAGCTTAAGTCACTGC+AGG + chr8.4:68834795-68834814 MS.gene59535:CDS 50.0%
GGTACCAGGTGGAACTAAGA+TGG + chr8.4:68834723-68834742 MS.gene59535:CDS 50.0%
TGTCTAGCTGCTACACTCTG+AGG - chr8.4:68834658-68834677 None:intergenic 50.0%
CCGTAATGGTTCGCATTCGG+AGG - chr8.4:68834493-68834512 None:intergenic 55.0%
TCACTGCAGGAACGTGCTTC+AGG + chr8.4:68834808-68834827 MS.gene59535:CDS 55.0%
! AAACTCGATGGCGGCGTTGA+GGG + chr8.4:68834537-68834556 MS.gene59535:CDS 55.0%
! GAAACTCGATGGCGGCGTTG+AGG + chr8.4:68834536-68834555 MS.gene59535:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 68834163 68834927 68834163 ID=MS.gene59535
chr8.4 mRNA 68834163 68834927 68834163 ID=MS.gene59535.t1;Parent=MS.gene59535
chr8.4 exon 68834163 68834927 68834163 ID=MS.gene59535.t1.exon1;Parent=MS.gene59535.t1
chr8.4 CDS 68834163 68834927 68834163 ID=cds.MS.gene59535.t1;Parent=MS.gene59535.t1
Gene Sequence

>MS.gene59535

ATGATGTTAATGATGATGATGCAACTCCCTGAATTTTCTTCATCTAACGGTAATAACAACACCATCAATCAATTTCAACCGTCAGATCAACAATTCTATGGCACTTCAAATGCTTCTAACAATACACATCCTCTTGTAGATTTAATAGATAACCCTCCTAATCCAATAATACCATGGTCTTCATCTTCATCATTCACTCACTTACCCTCACAATCCATAACAAACACAAACACAATCTCTTTCACCAATAACAACTCTACTGCACCATTAAGGTTCCAACAACAACAAACAACACCGTTAATGTTTTCGAATTCGAGCAATGAGATTCCTCCGAATGCGAACCATTACGGTACTGCATCTCCATCAGAGAAGAGAAACTCGATGGCGGCGTTGAGGGAGATGATATTCAGAATAGCAGCGATGCAACCAATTTACATAGACCCAGAATCAGTAAAACCACCAAAGAGAAGAAACGTGAAGATTTCAAAAGATCCTCAGAGTGTAGCAGCTAGACACAGAAGAGAAAGAATAAGCGAGAAAATAAGAATACTGCAAAGAATGGTACCAGGTGGAACTAAGATGGATACTGCATCAATGTTGGATGAAGCTATTCATTATGTTAAGTTTCTCAAGACACAGCTTAAGTCACTGCAGGAACGTGCTTCAGGAGCCAACAGTAAAAGGACAGTTGATGGTTCAGGATTAGGGTTCCCTGTTTCATTGCCTAAGCCTTACCAAGGTCGTAATGTTGATCGTTATGGGTGA
Protein sequence

>MS.gene59535.t1

MMLMMMMQLPEFSSSNGNNNTINQFQPSDQQFYGTSNASNNTHPLVDLIDNPPNPIIPWSSSSSFTHLPSQSITNTNTISFTNNNSTAPLRFQQQQTTPLMFSNSSNEIPPNANHYGTASPSEKRNSMAALREMIFRIAAMQPIYIDPESVKPPKRRNVKISKDPQSVAARHRRERISEKIRILQRMVPGGTKMDTASMLDEAIHYVKFLKTQLKSLQERASGANSKRTVDGSGLGFPVSLPKPYQGRNVDRYG