AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00489

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00489.t1 MTR_1g018420 94.915 236 5 3 1 233 1 232 9.54e-166 456
MS.gene00489.t1 MTR_3g102980 61.633 245 69 10 1 231 1 234 3.17e-83 248
MS.gene00489.t1 MTR_1g106730 43.726 263 84 13 1 222 3 242 3.29e-48 159
MS.gene00489.t1 MTR_1g062780 35.938 192 89 7 43 201 81 271 3.25e-22 92.8
MS.gene00489.t1 MTR_4g027440 50.000 84 42 0 78 161 220 303 5.89e-20 87.8
MS.gene00489.t1 MTR_4g028610 28.807 243 94 5 25 200 134 364 1.52e-18 84.3
MS.gene00489.t1 MTR_1g090703 29.279 222 107 6 21 194 81 300 3.19e-17 79.7
MS.gene00489.t1 MTR_0160s0030 32.039 206 79 7 38 207 164 344 5.43e-17 79.0
MS.gene00489.t1 MTR_4g109340 39.355 155 56 8 73 197 343 489 1.33e-16 78.6
MS.gene00489.t1 MTR_7g100100 36.134 119 67 2 78 196 34 143 3.59e-16 73.6
MS.gene00489.t1 MTR_5g099040 44.954 109 35 3 78 162 130 237 6.30e-16 75.1
MS.gene00489.t1 MTR_5g062300 48.352 91 40 3 77 160 118 208 1.16e-15 73.9
MS.gene00489.t1 MTR_1g067650 30.588 170 85 6 32 192 3 148 9.48e-15 70.1
MS.gene00489.t1 MTR_1g067640 30.588 170 85 6 32 192 2 147 1.20e-14 69.7
MS.gene00489.t1 MTR_1g115345 43.902 82 37 2 78 158 45 118 2.20e-14 69.7
MS.gene00489.t1 MTR_7g023560 34.286 140 60 5 32 165 2 115 2.48e-14 69.3
MS.gene00489.t1 MTR_1g067660 37.500 96 46 2 76 169 33 116 4.18e-13 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00489.t1 AT1G27730 52.245 245 83 11 1 229 1 227 9.02e-62 193
MS.gene00489.t1 AT5G04340 52.193 228 93 8 1 213 1 227 2.79e-52 169
MS.gene00489.t1 AT3G19580 42.520 254 96 9 1 210 1 248 1.09e-46 156
MS.gene00489.t1 AT3G19580 42.520 254 96 9 1 210 1 248 1.09e-46 156
MS.gene00489.t1 AT5G43170 47.210 233 70 11 1 221 1 192 3.92e-44 147
MS.gene00489.t1 AT5G67450 40.167 239 96 7 1 194 1 237 4.42e-36 128
MS.gene00489.t1 AT3G49930 40.887 203 68 6 25 207 36 206 6.84e-36 126
MS.gene00489.t1 AT2G28200 35.897 195 89 8 37 197 70 262 3.07e-24 98.2
MS.gene00489.t1 AT3G60580 39.011 182 79 6 38 207 122 283 4.93e-23 94.7
MS.gene00489.t1 AT2G45120 37.349 166 84 4 38 194 146 300 6.08e-22 92.4
MS.gene00489.t1 AT1G49900 45.872 109 47 3 63 165 172 274 1.03e-21 94.0
MS.gene00489.t1 AT1G49900 48.544 103 40 3 77 177 749 840 3.71e-20 89.4
MS.gene00489.t1 AT5G03510 31.250 192 98 4 39 197 69 259 4.52e-19 84.3
MS.gene00489.t1 AT1G02040 32.804 189 92 6 5 159 61 248 6.45e-18 81.3
MS.gene00489.t1 AT5G04390 28.696 230 112 7 39 229 96 312 2.59e-17 80.1
MS.gene00489.t1 AT5G56200 42.735 117 52 3 80 183 344 458 2.98e-16 77.8
MS.gene00489.t1 AT2G37430 38.168 131 61 4 32 158 2 116 5.41e-16 73.6
MS.gene00489.t1 AT4G35280 39.844 128 52 6 39 160 138 246 1.12e-15 74.7
MS.gene00489.t1 AT1G02030 37.600 125 66 2 34 158 119 231 1.76e-15 73.9
MS.gene00489.t1 AT3G53600 31.138 167 91 5 32 192 2 150 5.57e-15 70.9
MS.gene00489.t1 AT3G46090 35.938 128 59 4 38 165 11 115 9.74e-15 70.1
MS.gene00489.t1 AT2G28710 38.136 118 40 4 43 158 14 100 1.63e-14 68.9
MS.gene00489.t1 AT2G17180 30.675 163 75 5 39 194 121 252 3.03e-14 70.5
MS.gene00489.t1 AT3G46080 44.186 86 34 2 75 158 34 107 1.13e-12 64.3
MS.gene00489.t1 AT5G61470 40.000 85 33 2 78 159 228 297 1.26e-12 66.2
MS.gene00489.t1 AT3G46070 39.773 88 45 2 71 158 29 108 7.42e-12 62.4
MS.gene00489.t1 AT3G10470 37.255 102 43 3 78 158 182 283 1.83e-11 63.5
MS.gene00489.t1 AT5G59820 34.091 132 60 4 46 176 18 123 1.86e-11 60.8

Find 59 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTCATCGAAGGTGAATTT+AGG 0.257514 1.3:+4667801 None:intergenic
CGTTTAGTCCATGGAAGATT+TGG 0.286174 1.3:+4667780 None:intergenic
AAAATTCGGAATTTCAATCT+TGG 0.317164 1.3:+4667167 None:intergenic
AGAACATTTGTAACTGAGTT+TGG 0.333314 1.3:+4667620 None:intergenic
CCGGAGTTTGCTAATAAGAT+TGG 0.334097 1.3:-4667255 MS.gene00489:CDS
AACTCCGTCGGTGGCGGTGG+CGG 0.338111 1.3:-4667534 MS.gene00489:CDS
ATTATTCATCACTGAAAATT+CGG 0.339013 1.3:+4667153 None:intergenic
TTGTCAATGGTTGTTGGTGG+TGG 0.368111 1.3:+4667648 None:intergenic
TTTCCGACAGGACAAGCTTT+GGG 0.386450 1.3:-4667408 MS.gene00489:CDS
TCCGTCGGTGGCGGTGGCGG+TGG 0.387651 1.3:-4667531 MS.gene00489:CDS
AAATTCGGAATTTCAATCTT+GGG 0.411878 1.3:+4667168 None:intergenic
TCTGAATATCCCGGCTTATC+CGG 0.414206 1.3:-4667274 MS.gene00489:CDS
GTTTCCGACAGGACAAGCTT+TGG 0.428305 1.3:-4667409 MS.gene00489:CDS
GATTCAAAGGCTTGAAATCA+TGG 0.448405 1.3:+4667670 None:intergenic
TTCTTCATCATCACAGGATG+AGG 0.458403 1.3:+4667213 None:intergenic
GAGTTTGGTGTTGTTGTCAA+TGG 0.463877 1.3:+4667635 None:intergenic
GTTGCAGCTGAGGAAGTTGT+TGG 0.467673 1.3:+4667498 None:intergenic
GTGTTGTTGTCAATGGTTGT+TGG 0.486272 1.3:+4667642 None:intergenic
AATTTAGGAGTAGTAGAAGT+GGG 0.488875 1.3:+4667816 None:intergenic
CACTACGAAGGTGTTGTTGG+TGG 0.490444 1.3:-4667369 MS.gene00489:CDS
GCTTTCTTCTTCATCATCAC+AGG 0.490449 1.3:+4667207 None:intergenic
TGAGCTTGTGGTTGCAGCTG+AGG 0.495728 1.3:+4667488 None:intergenic
TTAGCAAACTCCGGATAAGC+CGG 0.495798 1.3:+4667264 None:intergenic
GAATTTAGGAGTAGTAGAAG+TGG 0.499359 1.3:+4667815 None:intergenic
ATGAGTGTTCGATTTGTCAT+AGG 0.501927 1.3:-4667434 MS.gene00489:CDS
ACTTGCTTTGTGTCCACCGA+GGG 0.502207 1.3:+4667566 None:intergenic
ACTACGAAGGTGTTGTTGGT+GGG 0.505453 1.3:-4667368 MS.gene00489:CDS
TGTCATAGGTCGTTTCCGAC+AGG 0.511441 1.3:-4667420 MS.gene00489:CDS
CTACGAAGGTGTTGTTGGTG+GGG 0.511916 1.3:-4667367 MS.gene00489:CDS
GAACGTTTACGTTTAGTCCA+TGG 0.526324 1.3:+4667771 None:intergenic
TTGTTGTCAATGGTTGTTGG+TGG 0.527436 1.3:+4667645 None:intergenic
TTGCAGCTGAGGAAGTTGTT+GGG 0.534746 1.3:+4667499 None:intergenic
GTTGTTGGTGGTGGATTCAA+AGG 0.535966 1.3:+4667657 None:intergenic
TGTCACTACGAAGGTGTTGT+TGG 0.546239 1.3:-4667372 MS.gene00489:CDS
TCGATGAACCAAATCTTCCA+TGG 0.550148 1.3:-4667788 MS.gene00489:CDS
TACGAAGGTGTTGTTGGTGG+GGG 0.550558 1.3:-4667366 MS.gene00489:CDS
TGTAACTGTCTCTGAAGGTG+TGG 0.551186 1.3:-4667328 MS.gene00489:CDS
ACAAGCTCAGCCAACACAAA+CGG 0.552600 1.3:-4667474 MS.gene00489:CDS
CCAATCTTATTAGCAAACTC+CGG 0.554584 1.3:+4667255 None:intergenic
CCACCCAAAGCTTGTCCTGT+CGG 0.557784 1.3:+4667405 None:intergenic
AACACCGCCACCGTTTGTGT+TGG 0.560436 1.3:+4667464 None:intergenic
GTAACTGTCTCTGAAGGTGT+GGG 0.567359 1.3:-4667327 MS.gene00489:CDS
TGATTTCGATCTGAATATCC+CGG 0.576158 1.3:-4667283 MS.gene00489:CDS
CCGACAGGACAAGCTTTGGG+TGG 0.581171 1.3:-4667405 MS.gene00489:CDS
TGAAATCATGGCGGTTGGTG+TGG 0.583151 1.3:+4667682 None:intergenic
TAGCAAACTCCGGATAAGCC+GGG 0.583949 1.3:+4667265 None:intergenic
AGGCTTGAAATCATGGCGGT+TGG 0.583949 1.3:+4667677 None:intergenic
GTTTGTGTTGGCTGAGCTTG+TGG 0.588915 1.3:+4667476 None:intergenic
TCTGCTGTAACTGTCTCTGA+AGG 0.589059 1.3:-4667333 MS.gene00489:CDS
TGTCTCATCATGCTCGCTCG+TGG 0.591916 1.3:-4667705 MS.gene00489:CDS
TGGAAGATTTGGTTCATCGA+AGG 0.595055 1.3:+4667791 None:intergenic
TCAGCCAACACAAACGGTGG+CGG 0.606071 1.3:-4667468 MS.gene00489:CDS
ACCACCGCCACCGCCACCGA+CGG 0.606095 1.3:+4667530 None:intergenic
GACTTGCTTTGTGTCCACCG+AGG 0.621099 1.3:+4667565 None:intergenic
TCTTCTTATCAAGCCCTCGG+TGG 0.636904 1.3:-4667579 MS.gene00489:CDS
ATCACGTTGATGACTATGTG+TGG 0.647702 1.3:+4667302 None:intergenic
AGCTCAGCCAACACAAACGG+TGG 0.659448 1.3:-4667471 MS.gene00489:CDS
CACAAACGTTGTCACTACGA+AGG 0.683725 1.3:-4667381 MS.gene00489:CDS
TCAAAGGCTTGAAATCATGG+CGG 0.753429 1.3:+4667673 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCGGAATTTCAATCT+TGG + chr1.3:4667837-4667856 None:intergenic 25.0%
! AAATTCGGAATTTCAATCTT+GGG + chr1.3:4667836-4667855 None:intergenic 25.0%
AATTTAGGAGTAGTAGAAGT+GGG + chr1.3:4667188-4667207 None:intergenic 30.0%
AGAACATTTGTAACTGAGTT+TGG + chr1.3:4667384-4667403 None:intergenic 30.0%
CCAATCTTATTAGCAAACTC+CGG + chr1.3:4667749-4667768 None:intergenic 35.0%
GAATTTAGGAGTAGTAGAAG+TGG + chr1.3:4667189-4667208 None:intergenic 35.0%
GATTCAAAGGCTTGAAATCA+TGG + chr1.3:4667334-4667353 None:intergenic 35.0%
TGATTTCGATCTGAATATCC+CGG - chr1.3:4667718-4667737 MS.gene00489:CDS 35.0%
! ATGAGTGTTCGATTTGTCAT+AGG - chr1.3:4667567-4667586 MS.gene00489:CDS 35.0%
! TTTTCTTCTTATCAAGCCCT+CGG - chr1.3:4667419-4667438 MS.gene00489:CDS 35.0%
CGTTTAGTCCATGGAAGATT+TGG + chr1.3:4667224-4667243 None:intergenic 40.0%
GAACGTTTACGTTTAGTCCA+TGG + chr1.3:4667233-4667252 None:intergenic 40.0%
GCTTTCTTCTTCATCATCAC+AGG + chr1.3:4667797-4667816 None:intergenic 40.0%
GGTTCATCGAAGGTGAATTT+AGG + chr1.3:4667203-4667222 None:intergenic 40.0%
TCAAAGGCTTGAAATCATGG+CGG + chr1.3:4667331-4667350 None:intergenic 40.0%
TCGATGAACCAAATCTTCCA+TGG - chr1.3:4667213-4667232 MS.gene00489:CDS 40.0%
TTCTTCATCATCACAGGATG+AGG + chr1.3:4667791-4667810 None:intergenic 40.0%
TTGTTGTCAATGGTTGTTGG+TGG + chr1.3:4667359-4667378 None:intergenic 40.0%
! GTGTTGTTGTCAATGGTTGT+TGG + chr1.3:4667362-4667381 None:intergenic 40.0%
! TGGAAGATTTGGTTCATCGA+AGG + chr1.3:4667213-4667232 None:intergenic 40.0%
!! ATCACGTTGATGACTATGTG+TGG + chr1.3:4667702-4667721 None:intergenic 40.0%
!! CCGGAGTTTGCTAATAAGAT+TGG - chr1.3:4667746-4667765 MS.gene00489:CDS 40.0%
!! GAGTTTGGTGTTGTTGTCAA+TGG + chr1.3:4667369-4667388 None:intergenic 40.0%
ACAAGCTCAGCCAACACAAA+CGG - chr1.3:4667527-4667546 MS.gene00489:CDS 45.0%
CACAAACGTTGTCACTACGA+AGG - chr1.3:4667620-4667639 MS.gene00489:CDS 45.0%
TCTGAATATCCCGGCTTATC+CGG - chr1.3:4667727-4667746 MS.gene00489:CDS 45.0%
TCTGCTGTAACTGTCTCTGA+AGG - chr1.3:4667668-4667687 MS.gene00489:CDS 45.0%
TTAGCAAACTCCGGATAAGC+CGG + chr1.3:4667740-4667759 None:intergenic 45.0%
TTGCAGCTGAGGAAGTTGTT+GGG + chr1.3:4667505-4667524 None:intergenic 45.0%
TTTCCGACAGGACAAGCTTT+GGG - chr1.3:4667593-4667612 MS.gene00489:CDS 45.0%
! GAAGAAAGCTCGTGTTTTCG+TGG - chr1.3:4667808-4667827 MS.gene00489:CDS 45.0%
! GTAACTGTCTCTGAAGGTGT+GGG - chr1.3:4667674-4667693 MS.gene00489:CDS 45.0%
! TGTAACTGTCTCTGAAGGTG+TGG - chr1.3:4667673-4667692 MS.gene00489:CDS 45.0%
! TTGTCAATGGTTGTTGGTGG+TGG + chr1.3:4667356-4667375 None:intergenic 45.0%
!! ACTACGAAGGTGTTGTTGGT+GGG - chr1.3:4667633-4667652 MS.gene00489:CDS 45.0%
!! GTTGTTGGTGGTGGATTCAA+AGG + chr1.3:4667347-4667366 None:intergenic 45.0%
!! TGTCACTACGAAGGTGTTGT+TGG - chr1.3:4667629-4667648 MS.gene00489:CDS 45.0%
ACTTGCTTTGTGTCCACCGA+GGG + chr1.3:4667438-4667457 None:intergenic 50.0%
AGGCTTGAAATCATGGCGGT+TGG + chr1.3:4667327-4667346 None:intergenic 50.0%
AGTCACCGCAAAAACTCCGT+CGG - chr1.3:4667455-4667474 MS.gene00489:CDS 50.0%
GTTGCAGCTGAGGAAGTTGT+TGG + chr1.3:4667506-4667525 None:intergenic 50.0%
GTTTCCGACAGGACAAGCTT+TGG - chr1.3:4667592-4667611 MS.gene00489:CDS 50.0%
TAGCAAACTCCGGATAAGCC+GGG + chr1.3:4667739-4667758 None:intergenic 50.0%
TCTTCTTATCAAGCCCTCGG+TGG - chr1.3:4667422-4667441 MS.gene00489:CDS 50.0%
TGTCATAGGTCGTTTCCGAC+AGG - chr1.3:4667581-4667600 MS.gene00489:CDS 50.0%
! TGAAATCATGGCGGTTGGTG+TGG + chr1.3:4667322-4667341 None:intergenic 50.0%
!! CACTACGAAGGTGTTGTTGG+TGG - chr1.3:4667632-4667651 MS.gene00489:CDS 50.0%
!! CTACGAAGGTGTTGTTGGTG+GGG - chr1.3:4667634-4667653 MS.gene00489:CDS 50.0%
!! GTTTGTGTTGGCTGAGCTTG+TGG + chr1.3:4667528-4667547 None:intergenic 50.0%
!! TACGAAGGTGTTGTTGGTGG+GGG - chr1.3:4667635-4667654 MS.gene00489:CDS 50.0%
AACACCGCCACCGTTTGTGT+TGG + chr1.3:4667540-4667559 None:intergenic 55.0%
AGCTCAGCCAACACAAACGG+TGG - chr1.3:4667530-4667549 MS.gene00489:CDS 55.0%
CCACCCAAAGCTTGTCCTGT+CGG + chr1.3:4667599-4667618 None:intergenic 55.0%
TCAGCCAACACAAACGGTGG+CGG - chr1.3:4667533-4667552 MS.gene00489:CDS 55.0%
TGAGCTTGTGGTTGCAGCTG+AGG + chr1.3:4667516-4667535 None:intergenic 55.0%
TGTCTCATCATGCTCGCTCG+TGG - chr1.3:4667296-4667315 MS.gene00489:CDS 55.0%
! GACTTGCTTTGTGTCCACCG+AGG + chr1.3:4667439-4667458 None:intergenic 55.0%
CACCGCAAAAACTCCGTCGG+TGG - chr1.3:4667458-4667477 MS.gene00489:CDS 60.0%
CGCAAAAACTCCGTCGGTGG+CGG - chr1.3:4667461-4667480 MS.gene00489:CDS 60.0%
! AAAAACTCCGTCGGTGGCGG+TGG - chr1.3:4667464-4667483 MS.gene00489:CDS 60.0%
! CGCCACCGACGGAGTTTTTG+CGG + chr1.3:4667463-4667482 None:intergenic 60.0%
!! CCGACAGGACAAGCTTTGGG+TGG - chr1.3:4667596-4667615 MS.gene00489:CDS 60.0%
! AACTCCGTCGGTGGCGGTGG+CGG - chr1.3:4667467-4667486 MS.gene00489:CDS 70.0%
ACCACCGCCACCGCCACCGA+CGG + chr1.3:4667474-4667493 None:intergenic 75.0%
!! TCCGTCGGTGGCGGTGGCGG+TGG - chr1.3:4667470-4667489 MS.gene00489:CDS 80.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 4667161 4667862 4667161 ID=MS.gene00489
chr1.3 mRNA 4667161 4667862 4667161 ID=MS.gene00489.t1;Parent=MS.gene00489
chr1.3 exon 4667161 4667862 4667161 ID=MS.gene00489.t1.exon1;Parent=MS.gene00489.t1
chr1.3 CDS 4667161 4667862 4667161 ID=cds.MS.gene00489.t1;Parent=MS.gene00489.t1
Gene Sequence

>MS.gene00489

ATGGCTCTTGAAGCACTTAACTCACCCACTTCTACTACTCCTAAATTCACCTTCGATGAACCAAATCTTCCATGGACTAAACGTAAACGTTCTAAACGTTCACGTTCATGCACTGAAGAAGAGTATCTTGCTCTCTGTCTCATCATGCTCGCTCGTGGCCACACCAACCGCCATGATTTCAAGCCTTTGAATCCACCACCAACAACCATTGACAACAACACCAAACTCAGTTACAAATGTTCTGTCTGTAACAAAGAGTTTTCTTCTTATCAAGCCCTCGGTGGACACAAAGCAAGTCACCGCAAAAACTCCGTCGGTGGCGGTGGCGGTGGTGATGATCACCCAACAACTTCCTCAGCTGCAACCACAAGCTCAGCCAACACAAACGGTGGCGGTGTTAGATCTCATGAGTGTTCGATTTGTCATAGGTCGTTTCCGACAGGACAAGCTTTGGGTGGACACAAACGTTGTCACTACGAAGGTGTTGTTGGTGGGGGTGCTTCTGCTTCTGCTGTAACTGTCTCTGAAGGTGTGGGATCCACACATAGTCATCAACGTGATTTCGATCTGAATATCCCGGCTTATCCGGAGTTTGCTAATAAGATTGGAGAAGATGAAGTTGAAAGTCCTCATCCTGTGATGATGAAGAAGAAAGCTCGTGTTTTCGTGGTGCCCAAGATTGAAATTCCGAATTTTCAGTGA
Protein sequence

>MS.gene00489.t1

MALEALNSPTSTTPKFTFDEPNLPWTKRKRSKRSRSCTEEEYLALCLIMLARGHTNRHDFKPLNPPPTTIDNNTKLSYKCSVCNKEFSSYQALGGHKASHRKNSVGGGGGGDDHPTTSSAATTSSANTNGGGVRSHECSICHRSFPTGQALGGHKRCHYEGVVGGGASASAVTVSEGVGSTHSHQRDFDLNIPAYPEFANKIGEDEVESPHPVMMKKKARVFVVPKIEIPNFQ