AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84821

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84821.t1 MTR_6g032970 89.773 176 5 1 9 184 279 441 4.73e-106 317
MS.gene84821.t1 MTR_7g085500 64.516 186 60 4 3 184 288 471 1.02e-71 228
MS.gene84821.t1 MTR_8g088390 52.247 178 72 7 16 184 222 395 1.11e-43 153
MS.gene84821.t1 MTR_8g088390 52.247 178 72 7 16 184 287 460 1.42e-43 153
MS.gene84821.t1 MTR_4g005110 33.520 179 95 4 8 184 278 434 1.39e-19 85.9
MS.gene84821.t1 MTR_4g123630 35.484 186 84 5 5 184 216 371 2.98e-18 82.0
MS.gene84821.t1 MTR_2g032660 41.463 123 61 3 61 183 293 404 1.07e-17 80.5
MS.gene84821.t1 MTR_2g063460 43.750 112 37 3 79 184 322 413 2.00e-17 79.3
MS.gene84821.t1 MTR_2g063460 43.750 112 37 3 79 184 320 411 2.20e-17 79.3
MS.gene84821.t1 MTR_2g005840 60.000 55 22 0 130 184 236 290 4.60e-16 75.5
MS.gene84821.t1 MTR_2g005840 60.000 55 22 0 130 184 267 321 4.82e-16 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84821.t1 AT3G13460 48.619 181 77 7 15 184 306 481 2.56e-37 135
MS.gene84821.t1 AT3G13460 48.619 181 77 7 15 184 303 478 3.52e-37 135
MS.gene84821.t1 AT3G13460 48.619 181 77 7 15 184 306 481 3.94e-37 135
MS.gene84821.t1 AT3G13460 48.619 181 77 7 15 184 305 480 4.20e-37 135
MS.gene84821.t1 AT1G55500 45.963 161 74 4 31 184 243 397 4.24e-31 118
MS.gene84821.t1 AT1G55500 45.963 161 74 4 31 184 256 410 4.77e-31 118
MS.gene84821.t1 AT1G55500 44.444 162 75 4 31 184 286 440 5.23e-31 118
MS.gene84821.t1 AT1G55500 44.444 162 75 4 31 184 299 453 5.30e-31 118
MS.gene84821.t1 AT1G55500 44.444 162 75 4 31 184 299 453 5.52e-31 118
MS.gene84821.t1 AT1G55500 44.444 162 75 4 31 184 299 453 5.92e-31 118
MS.gene84821.t1 AT5G61020 39.247 186 101 6 2 184 122 298 7.34e-25 100
MS.gene84821.t1 AT5G61020 39.247 186 101 6 2 184 124 300 8.67e-25 100
MS.gene84821.t1 AT3G03950 40.351 171 78 6 22 184 130 284 5.92e-24 97.8
MS.gene84821.t1 AT3G03950 40.351 171 78 6 22 184 127 281 5.97e-24 97.4
MS.gene84821.t1 AT3G03950 40.351 171 78 6 22 184 126 280 6.05e-24 97.4
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 218 415 2.16e-20 88.2
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 218 415 2.16e-20 88.2
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 240 437 2.20e-20 88.2
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 230 427 2.34e-20 88.2
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 240 437 2.34e-20 87.8
MS.gene84821.t1 AT3G13060 36.816 201 99 7 9 184 240 437 2.65e-20 87.8
MS.gene84821.t1 AT1G48110 71.698 53 15 0 132 184 308 360 1.43e-18 82.8
MS.gene84821.t1 AT1G48110 71.698 53 15 0 132 184 308 360 1.43e-18 82.8
MS.gene84821.t1 AT1G27960 40.351 114 43 2 71 184 281 369 3.73e-18 81.3
MS.gene84821.t1 AT3G17330 58.209 67 26 1 118 184 143 207 3.91e-18 81.6
MS.gene84821.t1 AT3G17330 58.209 67 26 1 118 184 245 309 5.70e-18 81.3
MS.gene84821.t1 AT3G17330 58.209 67 26 1 118 184 245 309 5.70e-18 81.3
MS.gene84821.t1 AT1G09810 65.455 55 19 0 130 184 216 270 6.05e-18 80.9
MS.gene84821.t1 AT1G09810 65.455 55 19 0 130 184 197 251 6.29e-18 80.9
MS.gene84821.t1 AT1G27960 40.351 114 43 2 71 184 207 295 6.54e-18 80.9
MS.gene84821.t1 AT1G09810 65.455 55 19 0 130 184 174 228 6.64e-18 80.9
MS.gene84821.t1 AT1G27960 40.351 114 43 2 71 184 281 369 7.88e-18 80.9
MS.gene84821.t1 AT1G79270 67.273 55 18 0 130 184 306 360 3.64e-17 79.0
MS.gene84821.t1 AT1G79270 67.273 55 18 0 130 184 291 345 3.74e-17 78.6
MS.gene84821.t1 AT1G79270 67.273 55 18 0 130 184 291 345 3.74e-17 78.6
MS.gene84821.t1 AT1G79270 67.273 55 18 0 130 184 291 345 3.74e-17 78.6
MS.gene84821.t1 AT5G58190 42.000 100 48 3 85 184 274 363 2.24e-16 76.6
MS.gene84821.t1 AT5G58190 42.000 100 48 3 85 184 275 364 2.26e-16 76.6

Find 51 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGTATGTGTTTCCATAT+TGG 0.246769 6.3:+50096146 None:intergenic
TCTGGACTGGGACCGTATTC+TGG 0.259091 6.3:-50096208 MS.gene84821:CDS
TCTTACTATGGATCTACTTA+TGG 0.285566 6.3:-50096118 MS.gene84821:CDS
TCTAGCTTCTTGTTGCCATT+AGG 0.298283 6.3:+50095740 None:intergenic
CTAGCTTCTTGTTGCCATTA+GGG 0.298390 6.3:+50095741 None:intergenic
GAAGCTAGATGCGGCATATC+AGG 0.346860 6.3:-50095726 MS.gene84821:CDS
CCGTATTCTGGATATCCTAA+TGG 0.351387 6.3:-50096196 MS.gene84821:CDS
CCGGTGTATTGTTGCTTGTC+AGG 0.354452 6.3:+50095869 None:intergenic
GTTATCATAGGAACCTGTTC+TGG 0.374797 6.3:+50096093 None:intergenic
TTATCATCATCACTCTTGAT+AGG 0.378740 6.3:+50095908 None:intergenic
AACACGATGTACAGCCAATA+TGG 0.389273 6.3:-50096160 MS.gene84821:CDS
TTGCTTGGGTACATCCCATT+AGG 0.407428 6.3:+50096181 None:intergenic
TATTGTTGCTTGTCAGGAAT+TGG 0.409859 6.3:+50095875 None:intergenic
AACTTGCATGGCTATTCATC+TGG 0.421844 6.3:-50096226 MS.gene84821:CDS
TACAGAGGCAGGTCTTACTA+TGG 0.435477 6.3:-50096130 MS.gene84821:CDS
CGTATTCTGGATATCCTAAT+GGG 0.442464 6.3:-50096195 MS.gene84821:CDS
CATGGCTATTCATCTGGACT+GGG 0.442552 6.3:-50096220 MS.gene84821:CDS
TGGCTGTACATCGTGTTGCT+TGG 0.469761 6.3:+50096166 None:intergenic
AAAAGAAATGTGGATGGCTT+TGG 0.470712 6.3:-50096028 MS.gene84821:CDS
GGCTGTACATCGTGTTGCTT+GGG 0.474945 6.3:+50096167 None:intergenic
GCATGGCTATTCATCTGGAC+TGG 0.477233 6.3:-50096221 MS.gene84821:CDS
GGATCTATACTTGTTATCAT+AGG 0.478586 6.3:+50096081 None:intergenic
TCTACTTATGGATCCAGAAC+AGG 0.481498 6.3:-50096106 MS.gene84821:CDS
CACATTATTACTCAAGGGTC+AGG 0.490934 6.3:-50095936 MS.gene84821:CDS
GTGTGGACAAGTACCCCTAA+TGG 0.497541 6.3:-50095755 MS.gene84821:CDS
CCATTAGGATATCCAGAATA+CGG 0.504485 6.3:+50096196 None:intergenic
ACCTGTCACATTATTACTCA+AGG 0.514931 6.3:-50095942 MS.gene84821:CDS
AAGTATAGATCCACACGCTA+TGG 0.515371 6.3:-50096070 MS.gene84821:CDS
CCCTTGAGTAATAATGTGAC+AGG 0.522853 6.3:+50095941 None:intergenic
TAGCTTCTTGTTGCCATTAG+GGG 0.524738 6.3:+50095742 None:intergenic
CATCATCACTCTTGATAGGA+AGG 0.537515 6.3:+50095912 None:intergenic
TCTAGGTTGCAGAACTTGCA+TGG 0.539046 6.3:-50096238 MS.gene84821:intron
ATGGAAACACATACAGAGGC+AGG 0.547380 6.3:-50096141 MS.gene84821:CDS
CTGACAAGCAACAATACACC+GGG 0.567226 6.3:-50095868 MS.gene84821:CDS
ATTCTCAGATAAATCTTCCC+CGG 0.595705 6.3:+50095850 None:intergenic
TTAGAACTATTGGAACCTCT+CGG 0.606436 6.3:+50095989 None:intergenic
TGGCTTTGGTGAGCTGAACA+AGG 0.609686 6.3:-50096014 MS.gene84821:CDS
TGTCATCAAATCTTATAGCG+AGG 0.611587 6.3:-50095807 MS.gene84821:CDS
AGAGTATGAAATATAATGTG+TGG 0.612407 6.3:-50095772 MS.gene84821:CDS
TGACCATGTCAAAAGAAATG+TGG 0.616421 6.3:-50096038 MS.gene84821:CDS
AGATCCACACGCTATGGACG+TGG 0.617909 6.3:-50096064 MS.gene84821:CDS
TGCGGCATATCAGGAAGCCT+AGG 0.627415 6.3:-50095717 None:intergenic
CCTGACAAGCAACAATACAC+CGG 0.631302 6.3:-50095869 MS.gene84821:CDS
AAAACCACGTCCATAGCGTG+TGG 0.643915 6.3:+50096060 None:intergenic
CCTGTCACATTATTACTCAA+GGG 0.647177 6.3:-50095941 MS.gene84821:CDS
GGCTTTGGTGAGCTGAACAA+GGG 0.653383 6.3:-50096013 MS.gene84821:CDS
CATGTCAAAAGAAATGTGGA+TGG 0.682176 6.3:-50096034 MS.gene84821:CDS
CAATATGGAAACACATACAG+AGG 0.684546 6.3:-50096145 MS.gene84821:CDS
GAGCTGAACAAGGGACCGAG+AGG 0.693881 6.3:-50096004 MS.gene84821:CDS
TGGCAACAAGAAGCTAGATG+CGG 0.702216 6.3:-50095735 MS.gene84821:CDS
TGACAAGCAACAATACACCG+GGG 0.819631 6.3:-50095867 MS.gene84821:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTCATGATTTTTGATTT+TGG - chr6.3:50095785-50095804 MS.gene84821:CDS 15.0%
!!! ATTTTTATCATTAGAACTAT+TGG + chr6.3:50096217-50096236 None:intergenic 15.0%
! AGAGTATGAAATATAATGTG+TGG - chr6.3:50096421-50096440 MS.gene84821:intron 25.0%
! GATAAAAATGACAAAAGTCT+TGG - chr6.3:50096228-50096247 MS.gene84821:CDS 25.0%
TCTTACTATGGATCTACTTA+TGG - chr6.3:50096075-50096094 MS.gene84821:CDS 30.0%
TTATCATCATCACTCTTGAT+AGG + chr6.3:50096288-50096307 None:intergenic 30.0%
TTCAATTGTGAACTTACGAT+AGG + chr6.3:50095732-50095751 None:intergenic 30.0%
!! GGATCTATACTTGTTATCAT+AGG + chr6.3:50096115-50096134 None:intergenic 30.0%
AAAAGAAATGTGGATGGCTT+TGG - chr6.3:50096165-50096184 MS.gene84821:CDS 35.0%
ACCTGTCACATTATTACTCA+AGG - chr6.3:50096251-50096270 MS.gene84821:intron 35.0%
ATTCTCAGATAAATCTTCCC+CGG + chr6.3:50096346-50096365 None:intergenic 35.0%
CAACCTAGAAACAATAGTTG+AGG + chr6.3:50095944-50095963 None:intergenic 35.0%
CAATATGGAAACACATACAG+AGG - chr6.3:50096048-50096067 MS.gene84821:CDS 35.0%
CATGTCAAAAGAAATGTGGA+TGG - chr6.3:50096159-50096178 MS.gene84821:CDS 35.0%
CCATTAGGATATCCAGAATA+CGG + chr6.3:50096000-50096019 None:intergenic 35.0%
CCTGTCACATTATTACTCAA+GGG - chr6.3:50096252-50096271 MS.gene84821:intron 35.0%
CGTATTCTGGATATCCTAAT+GGG - chr6.3:50095998-50096017 MS.gene84821:CDS 35.0%
CTCTGTATGTGTTTCCATAT+TGG + chr6.3:50096050-50096069 None:intergenic 35.0%
TGACCATGTCAAAAGAAATG+TGG - chr6.3:50096155-50096174 MS.gene84821:CDS 35.0%
TGTCATCAAATCTTATAGCG+AGG - chr6.3:50096386-50096405 MS.gene84821:intron 35.0%
TTAGAACTATTGGAACCTCT+CGG + chr6.3:50096207-50096226 None:intergenic 35.0%
! CATCCACATTTCTTTTGACA+TGG + chr6.3:50096161-50096180 None:intergenic 35.0%
! TATTGTTGCTTGTCAGGAAT+TGG + chr6.3:50096321-50096340 None:intergenic 35.0%
! TCACCTCAACTATTGTTTCT+AGG - chr6.3:50095938-50095957 MS.gene84821:CDS 35.0%
AACACGATGTACAGCCAATA+TGG - chr6.3:50096033-50096052 MS.gene84821:CDS 40.0%
AACTTGCATGGCTATTCATC+TGG - chr6.3:50095967-50095986 MS.gene84821:CDS 40.0%
AAGTATAGATCCACACGCTA+TGG - chr6.3:50096123-50096142 MS.gene84821:CDS 40.0%
CACATTATTACTCAAGGGTC+AGG - chr6.3:50096257-50096276 MS.gene84821:intron 40.0%
CATCATCACTCTTGATAGGA+AGG + chr6.3:50096284-50096303 None:intergenic 40.0%
CCCTTGAGTAATAATGTGAC+AGG + chr6.3:50096255-50096274 None:intergenic 40.0%
CCGTATTCTGGATATCCTAA+TGG - chr6.3:50095997-50096016 MS.gene84821:CDS 40.0%
CTAGCTTCTTGTTGCCATTA+GGG + chr6.3:50096455-50096474 None:intergenic 40.0%
GTATCTGCTTACCTAATCGA+CGG - chr6.3:50095850-50095869 MS.gene84821:CDS 40.0%
GTTATCATAGGAACCTGTTC+TGG + chr6.3:50096103-50096122 None:intergenic 40.0%
TAGCTTCTTGTTGCCATTAG+GGG + chr6.3:50096454-50096473 None:intergenic 40.0%
TCTACTTATGGATCCAGAAC+AGG - chr6.3:50096087-50096106 MS.gene84821:CDS 40.0%
! TCTAGCTTCTTGTTGCCATT+AGG + chr6.3:50096456-50096475 None:intergenic 40.0%
ATGGAAACACATACAGAGGC+AGG - chr6.3:50096052-50096071 MS.gene84821:CDS 45.0%
CATGGCTATTCATCTGGACT+GGG - chr6.3:50095973-50095992 MS.gene84821:CDS 45.0%
CCTGACAAGCAACAATACAC+CGG - chr6.3:50096324-50096343 MS.gene84821:intron 45.0%
CTGACAAGCAACAATACACC+GGG - chr6.3:50096325-50096344 MS.gene84821:intron 45.0%
TACAGAGGCAGGTCTTACTA+TGG - chr6.3:50096063-50096082 MS.gene84821:CDS 45.0%
TCTAGGTTGCAGAACTTGCA+TGG - chr6.3:50095955-50095974 MS.gene84821:CDS 45.0%
TGACAAGCAACAATACACCG+GGG - chr6.3:50096326-50096345 MS.gene84821:intron 45.0%
TGGCAACAAGAAGCTAGATG+CGG - chr6.3:50096458-50096477 MS.gene84821:intron 45.0%
TTGCTTGGGTACATCCCATT+AGG + chr6.3:50096015-50096034 None:intergenic 45.0%
AAAACCACGTCCATAGCGTG+TGG + chr6.3:50096136-50096155 None:intergenic 50.0%
GAAGCTAGATGCGGCATATC+AGG - chr6.3:50096467-50096486 MS.gene84821:intron 50.0%
GCATGGCTATTCATCTGGAC+TGG - chr6.3:50095972-50095991 MS.gene84821:CDS 50.0%
GTGTGGACAAGTACCCCTAA+TGG - chr6.3:50096438-50096457 MS.gene84821:intron 50.0%
TACCTAATCGACGGTAGAGC+TGG - chr6.3:50095859-50095878 MS.gene84821:CDS 50.0%
! CCGGTGTATTGTTGCTTGTC+AGG + chr6.3:50096327-50096346 None:intergenic 50.0%
! GGCTTTGGTGAGCTGAACAA+GGG - chr6.3:50096180-50096199 MS.gene84821:CDS 50.0%
! TGGCTGTACATCGTGTTGCT+TGG + chr6.3:50096030-50096049 None:intergenic 50.0%
! TTCCAGCTCTACCGTCGATT+AGG + chr6.3:50095864-50095883 None:intergenic 50.0%
!! GGCTGTACATCGTGTTGCTT+GGG + chr6.3:50096029-50096048 None:intergenic 50.0%
!! TGGCTTTGGTGAGCTGAACA+AGG - chr6.3:50096179-50096198 MS.gene84821:CDS 50.0%
AGATCCACACGCTATGGACG+TGG - chr6.3:50096129-50096148 MS.gene84821:CDS 55.0%
! TCTGGACTGGGACCGTATTC+TGG - chr6.3:50095985-50096004 MS.gene84821:CDS 55.0%
GAGCTGAACAAGGGACCGAG+AGG - chr6.3:50096189-50096208 MS.gene84821:CDS 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 50095718 50096497 50095718 ID=MS.gene84821
chr6.3 mRNA 50095718 50096497 50095718 ID=MS.gene84821.t1;Parent=MS.gene84821
chr6.3 exon 50096481 50096497 50096481 ID=MS.gene84821.t1.exon1;Parent=MS.gene84821.t1
chr6.3 CDS 50096481 50096497 50096481 ID=cds.MS.gene84821.t1;Parent=MS.gene84821.t1
chr6.3 exon 50095718 50096255 50095718 ID=MS.gene84821.t1.exon2;Parent=MS.gene84821.t1
chr6.3 CDS 50095718 50096255 50095718 ID=cds.MS.gene84821.t1;Parent=MS.gene84821.t1
Gene Sequence

>MS.gene84821

ATGTATAGTTTCCTATCGTAAGTTCACAATTGAAGCTATTATACTCGATTATCTCTCTATATATGAAATTTTCATGATTTTTGATTTTGGCTATGACTATTGTTGTTGTGATACACATTTTGATAGTTCGTTGTATCTGCTTACCTAATCGACGGTAGAGCTGGAAGTTCTATTTTTGTTTTTGCACATACATTTATGCTTCTATTAATGTATTCAAAATTCACCTCAACTATTGTTTCTAGGTTGCAGAACTTGCATGGCTATTCATCTGGACTGGGACCGTATTCTGGATATCCTAATGGGATGTACCCAAGCAACACGATGTACAGCCAATATGGAAACACATACAGAGGCAGGTCTTACTATGGATCTACTTATGGATCCAGAACAGGTTCCTATGATAACAAGTATAGATCCACACGCTATGGACGTGGTTTTGACCATGTCAAAAGAAATGTGGATGGCTTTGGTGAGCTGAACAAGGGACCGAGAGGTTCCAATAGTTCTAATGATAAAAATGACAAAAGTCTTGGACCTGTCACATTATTACTCAAGGGTCAGGACCTTCCTATCAAGAGTGATGATGATAAAGAAGTGCTTCCAATTCCTGACAAGCAACAATACACCGGGGAAGATTTATCTGAGAATTATTCTGATGCAAAGTTTTTTGTCATCAAATCTTATAGCGAGGATGATATTCACAAGAGTATGAAATATAATGTGTGGACAAGTACCCCTAATGGCAACAAGAAGCTAGATGCGGCATATCAGGAAGCCTAG
Protein sequence

>MS.gene84821.t1

MYSFLSLQNLHGYSSGLGPYSGYPNGMYPSNTMYSQYGNTYRGRSYYGSTYGSRTGSYDNKYRSTRYGRGFDHVKRNVDGFGELNKGPRGSNSSNDKNDKSLGPVTLLLKGQDLPIKSDDDKEVLPIPDKQQYTGEDLSENYSDAKFFVIKSYSEDDIHKSMKYNVWTSTPNGNKKLDAAYQEA