AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene66447

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66447.t1 MTR_1g018420 94.538 238 6 3 1 237 1 232 6.26e-167 460
MS.gene66447.t1 MTR_3g102980 56.627 249 79 9 1 235 1 234 1.85e-81 243
MS.gene66447.t1 MTR_1g106730 42.697 267 85 13 1 226 3 242 1.23e-46 155
MS.gene66447.t1 MTR_1g062780 36.082 194 90 9 43 205 81 271 1.30e-20 88.6
MS.gene66447.t1 MTR_4g027440 50.000 86 41 1 80 165 220 303 3.20e-18 82.8
MS.gene66447.t1 MTR_0160s0030 39.007 141 59 5 71 211 231 344 3.13e-17 80.1
MS.gene66447.t1 MTR_1g090703 28.829 222 112 7 21 198 81 300 2.85e-16 77.0
MS.gene66447.t1 MTR_7g100100 36.364 121 66 2 80 200 34 143 6.29e-16 73.2
MS.gene66447.t1 MTR_5g062300 36.879 141 81 3 29 164 71 208 1.34e-15 73.9
MS.gene66447.t1 MTR_1g067650 29.070 172 89 4 32 196 3 148 6.96e-15 70.5
MS.gene66447.t1 MTR_1g115345 35.075 134 70 4 29 162 2 118 1.01e-14 70.9
MS.gene66447.t1 MTR_1g067640 29.070 172 89 4 32 196 2 147 1.19e-14 69.7
MS.gene66447.t1 MTR_5g099040 41.441 111 38 3 80 166 130 237 2.21e-14 71.2
MS.gene66447.t1 MTR_7g023560 33.333 138 68 4 32 169 2 115 7.22e-14 68.2
MS.gene66447.t1 MTR_1g067660 32.609 138 64 3 38 173 6 116 1.69e-13 66.6
MS.gene66447.t1 MTR_4g057230 29.878 164 70 4 44 162 67 230 1.55e-12 65.9
MS.gene66447.t1 MTR_4g100860 29.000 200 99 6 14 198 130 301 9.42e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene66447.t1 AT1G27730 49.194 248 90 10 1 233 1 227 3.71e-60 189
MS.gene66447.t1 AT5G04340 50.870 230 97 8 1 217 1 227 5.32e-51 166
MS.gene66447.t1 AT3G19580 40.392 255 104 7 1 214 1 248 1.23e-46 156
MS.gene66447.t1 AT3G19580 40.392 255 104 7 1 214 1 248 1.23e-46 156
MS.gene66447.t1 AT5G43170 46.414 237 70 12 1 225 1 192 1.91e-42 143
MS.gene66447.t1 AT5G67450 39.834 241 98 7 1 198 1 237 1.06e-36 129
MS.gene66447.t1 AT3G49930 43.069 202 69 8 25 211 36 206 1.07e-35 126
MS.gene66447.t1 AT2G28200 37.113 194 92 7 37 201 70 262 1.23e-24 99.4
MS.gene66447.t1 AT3G60580 37.500 184 83 5 38 211 122 283 2.41e-23 95.9
MS.gene66447.t1 AT2G45120 39.286 168 82 5 38 198 146 300 3.78e-22 93.2
MS.gene66447.t1 AT1G49900 51.111 90 36 2 80 169 193 274 3.03e-20 89.7
MS.gene66447.t1 AT1G49900 45.192 104 44 2 79 181 749 840 1.66e-19 87.4
MS.gene66447.t1 AT5G03510 31.250 192 102 4 39 201 69 259 4.51e-19 84.3
MS.gene66447.t1 AT5G04390 29.310 232 112 8 39 233 96 312 6.03e-18 82.0
MS.gene66447.t1 AT1G02040 32.105 190 96 7 5 163 61 248 4.51e-17 79.3
MS.gene66447.t1 AT5G56200 41.880 117 55 2 82 187 344 458 5.10e-17 80.1
MS.gene66447.t1 AT4G35280 39.231 130 54 5 39 164 138 246 1.61e-16 77.0
MS.gene66447.t1 AT2G37430 38.519 135 59 4 32 162 2 116 9.78e-16 73.2
MS.gene66447.t1 AT3G46090 34.848 132 59 3 38 169 11 115 4.55e-15 70.9
MS.gene66447.t1 AT1G02030 36.066 122 55 4 80 201 160 258 1.70e-14 71.2
MS.gene66447.t1 AT2G17180 30.303 165 77 5 39 198 121 252 2.65e-14 70.9
MS.gene66447.t1 AT3G53600 30.409 171 91 6 32 196 2 150 2.97e-14 68.9
MS.gene66447.t1 AT2G28710 35.000 120 45 3 43 162 14 100 5.87e-14 67.8
MS.gene66447.t1 AT3G10470 31.111 180 68 4 39 162 104 283 3.26e-13 68.6
MS.gene66447.t1 AT3G46080 43.023 86 37 2 77 162 34 107 4.78e-13 65.5
MS.gene66447.t1 AT5G61470 40.000 85 35 2 80 163 228 297 2.05e-12 65.9
MS.gene66447.t1 AT5G59820 35.514 107 50 3 72 176 31 120 2.09e-11 60.8
MS.gene66447.t1 AT3G46070 35.870 92 49 2 71 162 27 108 4.83e-11 60.1

Find 60 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.179252 1.4:+4799960 None:intergenic
CGTTTAGTCCAAGGAAGATT+AGG 0.313549 1.4:+4799939 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1.4:+4799314 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1.4:+4799773 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1.4:-4799402 MS.gene66447:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1.4:+4799300 None:intergenic
GTTCATCGAAGGTGAATTTA+GGG 0.339272 1.4:+4799961 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1.4:+4799807 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1.4:-4799555 MS.gene66447:CDS
AAATTCGGAATTTCAATCTT+GGG 0.411878 1.4:+4799315 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1.4:-4799421 MS.gene66447:CDS
AACTCCGTCGGTGGCGGTGT+TGG 0.416768 1.4:-4799687 MS.gene66447:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1.4:-4799556 MS.gene66447:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1.4:+4799829 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1.4:+4799360 None:intergenic
TCGATGAACCTAATCTTCCT+TGG 0.468846 1.4:-4799947 MS.gene66447:CDS
TTGTTGTTGTCAATGGTTGT+TGG 0.473433 1.4:+4799801 None:intergenic
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1.4:+4799354 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1.4:+4799411 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1.4:-4799581 MS.gene66447:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1.4:+4799719 None:intergenic
GTCGGTGGCGGTGTTGGTGT+TGG 0.503000 1.4:-4799681 MS.gene66447:CDS
TGAAATCATGGCGGCTGGTG+TGG 0.505659 1.4:+4799841 None:intergenic
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1.4:-4799567 MS.gene66447:CDS
TTGTTGTCAATGGTTGTTGG+TGG 0.511574 1.4:+4799804 None:intergenic
GAATTTAGGGGTAGTAGAAG+TGG 0.512596 1.4:+4799974 None:intergenic
GTGGCAGCTGAGGAAGTTGA+TGG 0.530856 1.4:+4799645 None:intergenic
GGTGGCGGTGTTGGTGTTGG+TGG 0.533807 1.4:-4799678 MS.gene66447:CDS
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1.4:+4799816 None:intergenic
AGGCTTGAAATCATGGCGGC+TGG 0.543417 1.4:+4799836 None:intergenic
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1.4:-4799519 MS.gene66447:CDS
AATTTAGGGGTAGTAGAAGT+GGG 0.550780 1.4:+4799975 None:intergenic
CCAATCTTATTAGCAAACTC+CGG 0.554584 1.4:+4799402 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1.4:+4799552 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.560111 1.4:-4799516 MS.gene66447:CDS
TACGAAGGTGTTGTTGGTGG+TGG 0.560220 1.4:-4799513 MS.gene66447:CDS
AACACCGCCACCGTTTGTGT+TGG 0.560436 1.4:+4799611 None:intergenic
ACTAGCTCAGCCAACACAAA+CGG 0.565002 1.4:-4799621 MS.gene66447:CDS
GAACGTTTACGTTTAGTCCA+AGG 0.565959 1.4:+4799930 None:intergenic
TGAGCTAGTGGTGGCAGCTG+AGG 0.573892 1.4:+4799635 None:intergenic
TGATTTCGATCTGAATATCC+CGG 0.576158 1.4:-4799430 MS.gene66447:CDS
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1.4:-4799552 MS.gene66447:CDS
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1.4:+4799412 None:intergenic
TCTGCTATAACTGTCTCTGA+AGG 0.590024 1.4:-4799480 MS.gene66447:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1.4:-4799864 MS.gene66447:CDS
TATAACTGTCTCTGAAGGTG+TGG 0.592472 1.4:-4799475 MS.gene66447:CDS
AACACCAACACCGCCACCGA+CGG 0.603987 1.4:+4799683 None:intergenic
ATAACTGTCTCTGAAGGTGT+GGG 0.609017 1.4:-4799474 MS.gene66447:CDS
TCAGCCAACACAAACGGTGG+CGG 0.610808 1.4:-4799615 MS.gene66447:CDS
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1.4:+4799718 None:intergenic
GTTTGTGTTGGCTGAGCTAG+TGG 0.622781 1.4:+4799623 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1.4:-4799732 MS.gene66447:CDS
ATCACGTTGATGACTATGTG+TGG 0.647702 1.4:+4799449 None:intergenic
AGGAAGATTAGGTTCATCGA+AGG 0.659843 1.4:+4799950 None:intergenic
TGTGTTGGCTGAGCTAGTGG+TGG 0.672396 1.4:+4799626 None:intergenic
TGGCAGCTGAGGAAGTTGAT+GGG 0.673304 1.4:+4799646 None:intergenic
TTCATCGAAGGTGAATTTAG+GGG 0.676237 1.4:+4799962 None:intergenic
CACAAACGTTGTCACTACGA+AGG 0.683725 1.4:-4799528 MS.gene66447:CDS
AGCTCAGCCAACACAAACGG+TGG 0.690830 1.4:-4799618 MS.gene66447:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.768132 1.4:+4799832 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCGGAATTTCAATCT+TGG + chr1.4:4799996-4800015 None:intergenic 25.0%
! AAATTCGGAATTTCAATCTT+GGG + chr1.4:4799995-4800014 None:intergenic 25.0%
AGAACATTTGTAACTGAGTT+TGG + chr1.4:4799537-4799556 None:intergenic 30.0%
AATTTAGGGGTAGTAGAAGT+GGG + chr1.4:4799335-4799354 None:intergenic 35.0%
CCAATCTTATTAGCAAACTC+CGG + chr1.4:4799908-4799927 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG + chr1.4:4799481-4799500 None:intergenic 35.0%
GTTCATCGAAGGTGAATTTA+GGG + chr1.4:4799349-4799368 None:intergenic 35.0%
TGATTTCGATCTGAATATCC+CGG - chr1.4:4799877-4799896 MS.gene66447:CDS 35.0%
TTCATCGAAGGTGAATTTAG+GGG + chr1.4:4799348-4799367 None:intergenic 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG - chr1.4:4799726-4799745 MS.gene66447:CDS 35.0%
! TTGTTGTTGTCAATGGTTGT+TGG + chr1.4:4799509-4799528 None:intergenic 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG - chr1.4:4799572-4799591 MS.gene66447:CDS 35.0%
AGGAAGATTAGGTTCATCGA+AGG + chr1.4:4799360-4799379 None:intergenic 40.0%
CGTTTAGTCCAAGGAAGATT+AGG + chr1.4:4799371-4799390 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+AGG + chr1.4:4799380-4799399 None:intergenic 40.0%
GAATTTAGGGGTAGTAGAAG+TGG + chr1.4:4799336-4799355 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG + chr1.4:4799956-4799975 None:intergenic 40.0%
GGTTCATCGAAGGTGAATTT+AGG + chr1.4:4799350-4799369 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG + chr1.4:4799478-4799497 None:intergenic 40.0%
TCGATGAACCTAATCTTCCT+TGG - chr1.4:4799360-4799379 MS.gene66447:CDS 40.0%
TCTGCTATAACTGTCTCTGA+AGG - chr1.4:4799827-4799846 MS.gene66447:CDS 40.0%
TTCTTCATCATCACAGGATG+AGG + chr1.4:4799950-4799969 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG + chr1.4:4799506-4799525 None:intergenic 40.0%
! ATAACTGTCTCTGAAGGTGT+GGG - chr1.4:4799833-4799852 MS.gene66447:CDS 40.0%
! TATAACTGTCTCTGAAGGTG+TGG - chr1.4:4799832-4799851 MS.gene66447:CDS 40.0%
!! ATCACGTTGATGACTATGTG+TGG + chr1.4:4799861-4799880 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG - chr1.4:4799905-4799924 MS.gene66447:CDS 40.0%
!! GGTGTTGTTGTTGTTGTCAA+TGG + chr1.4:4799516-4799535 None:intergenic 40.0%
ACTAGCTCAGCCAACACAAA+CGG - chr1.4:4799686-4799705 MS.gene66447:CDS 45.0%
CACAAACGTTGTCACTACGA+AGG - chr1.4:4799779-4799798 MS.gene66447:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG - chr1.4:4799886-4799905 MS.gene66447:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG + chr1.4:4799899-4799918 None:intergenic 45.0%
TTTCCGACAGGACAAGCTTT+GGG - chr1.4:4799752-4799771 MS.gene66447:CDS 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG - chr1.4:4799967-4799986 MS.gene66447:CDS 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG + chr1.4:4799503-4799522 None:intergenic 45.0%
!! GTTGTTGGTGGTGGATTCAA+AGG + chr1.4:4799494-4799513 None:intergenic 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG - chr1.4:4799788-4799807 MS.gene66447:CDS 45.0%
ACTTGCTTTGTGTCCACCGA+GGG + chr1.4:4799591-4799610 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG - chr1.4:4799608-4799627 MS.gene66447:CDS 50.0%
GTTTCCGACAGGACAAGCTT+TGG - chr1.4:4799751-4799770 MS.gene66447:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG + chr1.4:4799898-4799917 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG - chr1.4:4799575-4799594 MS.gene66447:CDS 50.0%
TGTCATAGGTCGTTTCCGAC+AGG - chr1.4:4799740-4799759 MS.gene66447:CDS 50.0%
! TGGCAGCTGAGGAAGTTGAT+GGG + chr1.4:4799664-4799683 None:intergenic 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG - chr1.4:4799791-4799810 MS.gene66447:CDS 50.0%
!! GTTTGTGTTGGCTGAGCTAG+TGG + chr1.4:4799687-4799706 None:intergenic 50.0%
!! TACGAAGGTGTTGTTGGTGG+TGG - chr1.4:4799794-4799813 MS.gene66447:CDS 50.0%
AACACCGCCACCGTTTGTGT+TGG + chr1.4:4799699-4799718 None:intergenic 55.0%
AGCTCAGCCAACACAAACGG+TGG - chr1.4:4799689-4799708 MS.gene66447:CDS 55.0%
AGGCTTGAAATCATGGCGGC+TGG + chr1.4:4799474-4799493 None:intergenic 55.0%
CCACCCAAAGCTTGTCCTGT+CGG + chr1.4:4799758-4799777 None:intergenic 55.0%
GTGGCAGCTGAGGAAGTTGA+TGG + chr1.4:4799665-4799684 None:intergenic 55.0%
TCAGCCAACACAAACGGTGG+CGG - chr1.4:4799692-4799711 MS.gene66447:CDS 55.0%
TGAAATCATGGCGGCTGGTG+TGG + chr1.4:4799469-4799488 None:intergenic 55.0%
TGTCTCATCATGCTCGCTCG+TGG - chr1.4:4799443-4799462 MS.gene66447:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG + chr1.4:4799592-4799611 None:intergenic 55.0%
!! TGTGTTGGCTGAGCTAGTGG+TGG + chr1.4:4799684-4799703 None:intergenic 55.0%
AACACCAACACCGCCACCGA+CGG + chr1.4:4799627-4799646 None:intergenic 60.0%
CACCGCAAAAACTCCGTCGG+TGG - chr1.4:4799611-4799630 MS.gene66447:CDS 60.0%
CGCAAAAACTCCGTCGGTGG+CGG - chr1.4:4799614-4799633 MS.gene66447:CDS 60.0%
TGAGCTAGTGGTGGCAGCTG+AGG + chr1.4:4799675-4799694 None:intergenic 60.0%
! CGCCACCGACGGAGTTTTTG+CGG + chr1.4:4799616-4799635 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG - chr1.4:4799755-4799774 MS.gene66447:CDS 60.0%
! AACTCCGTCGGTGGCGGTGT+TGG - chr1.4:4799620-4799639 MS.gene66447:CDS 65.0%
!! GGTGGCGGTGTTGGTGTTGG+TGG - chr1.4:4799629-4799648 MS.gene66447:CDS 65.0%
!! GTCGGTGGCGGTGTTGGTGT+TGG - chr1.4:4799626-4799645 MS.gene66447:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 4799308 4800021 4799308 ID=MS.gene66447
chr1.4 mRNA 4799308 4800021 4799308 ID=MS.gene66447.t1;Parent=MS.gene66447
chr1.4 exon 4799308 4800021 4799308 ID=MS.gene66447.t1.exon1;Parent=MS.gene66447.t1
chr1.4 CDS 4799308 4800021 4799308 ID=cds.MS.gene66447.t1;Parent=MS.gene66447.t1
Gene Sequence

>MS.gene66447

ATGGCTCTAGAAGCACTTAACTCACCCACTTCTACTACCCCTAAATTCACCTTCGATGAACCTAATCTTCCTTGGACTAAACGTAAACGTTCTAAACGTTCACGTTCATGCACTGAAGAAGAGTATCTTGCTCTCTGTCTCATCATGCTCGCTCGTGGCCACACCAGCCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGTTGGTGTTGGTGGTGATGATCACCCATCAACTTCCTCAGCTGCCACCACTAGCTCAGCCAACACAAACGGTGGCGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGTGGTGCTTCTGCTTCTGCTATAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA
Protein sequence

>MS.gene66447.t1

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTSRHDFKPLNPPPTTIDNNNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGVGVGGDDHPSTSSAATTSSANTNGGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAITVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ