AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068578

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068578.t1 MTR_1g054525 95.833 192 8 0 1 192 1 192 4.62e-134 373
MS.gene068578.t1 MTR_4g013345 56.322 174 74 1 21 192 23 196 3.93e-67 204
MS.gene068578.t1 MTR_4g013335 58.788 165 64 2 30 192 34 196 8.09e-67 203
MS.gene068578.t1 MTR_4g013350 59.394 165 65 1 30 192 33 197 1.36e-66 202
MS.gene068578.t1 MTR_4g013320 54.098 183 74 2 20 192 17 199 3.68e-66 201
MS.gene068578.t1 MTR_4g013330 56.287 167 69 2 30 192 33 199 4.39e-64 196
MS.gene068578.t1 MTR_4g013325 62.759 145 52 1 50 192 55 199 5.23e-62 191
MS.gene068578.t1 MTR_4g013310 50.610 164 81 0 29 192 34 197 1.66e-59 184
MS.gene068578.t1 MTR_7g093820 50.526 190 89 4 6 192 7 194 4.08e-59 183
MS.gene068578.t1 MTR_7g093850 48.500 200 89 6 1 192 1 194 9.87e-59 182
MS.gene068578.t1 MTR_7g093830 49.231 195 94 4 1 192 1 193 4.45e-58 181
MS.gene068578.t1 MTR_7g070390 48.168 191 90 5 10 192 3 192 3.95e-57 178
MS.gene068578.t1 MTR_7g093870 52.353 170 73 4 30 192 25 193 1.64e-55 175
MS.gene068578.t1 MTR_7g093790 46.154 195 98 4 1 192 1 191 4.43e-55 173
MS.gene068578.t1 MTR_4g013385 46.277 188 91 5 12 192 6 190 1.83e-54 172
MS.gene068578.t1 MTR_0433s0040 46.277 188 91 5 12 192 6 190 1.83e-54 172
MS.gene068578.t1 MTR_4g073950 46.196 184 94 4 14 192 9 192 3.04e-50 161
MS.gene068578.t1 MTR_4g013770 48.485 165 80 3 31 192 29 191 6.24e-50 160
MS.gene068578.t1 MTR_4g013355 44.809 183 82 4 17 192 9 179 2.22e-46 150
MS.gene068578.t1 MTR_4g078885 48.322 149 73 3 46 192 39 185 1.70e-45 149
MS.gene068578.t1 MTR_3g034030 48.322 149 73 3 46 192 39 185 9.37e-45 147
MS.gene068578.t1 MTR_3g105630 43.850 187 92 5 14 192 8 189 1.10e-43 144
MS.gene068578.t1 MTR_1g056370 47.682 151 75 3 44 191 36 185 9.05e-43 142
MS.gene068578.t1 MTR_5g096120 42.246 187 95 5 15 192 7 189 1.38e-41 139
MS.gene068578.t1 MTR_3g105640 45.513 156 79 4 42 192 34 188 7.03e-39 132
MS.gene068578.t1 MTR_4g122110 36.301 146 91 1 49 192 35 180 4.02e-26 99.0
MS.gene068578.t1 MTR_4g122130 36.601 153 91 2 46 192 28 180 2.09e-25 97.1
MS.gene068578.t1 MTR_4g049570 33.824 136 90 0 43 178 27 162 2.42e-18 78.6
MS.gene068578.t1 MTR_4g049550 28.652 178 106 2 7 176 4 168 4.60e-17 75.5
MS.gene068578.t1 MTR_1g046490 37.778 90 55 1 81 170 121 209 1.72e-14 69.7
MS.gene068578.t1 MTR_1g046800 35.780 109 67 2 62 170 118 223 3.24e-14 68.9
MS.gene068578.t1 MTR_8g099115 32.394 142 85 4 42 175 32 170 4.44e-14 67.8
MS.gene068578.t1 MTR_1g046500 38.889 90 54 1 81 170 135 223 6.59e-14 68.2
MS.gene068578.t1 MTR_1g115510 31.765 170 99 6 37 191 186 353 7.91e-13 66.2
MS.gene068578.t1 MTR_7g021300 30.986 142 84 5 60 189 248 387 6.39e-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.gene068578.t1 AT1G55210 49.744 195 87 5 1 192 1 187 5.08e-60 186
MS.gene068578.t1 AT1G55210 49.744 195 87 5 1 192 1 187 5.08e-60 186
MS.gene068578.t1 AT1G58170 55.263 152 66 1 43 192 34 185 2.22e-59 184
MS.gene068578.t1 AT1G65870 52.907 172 76 3 22 191 21 189 1.48e-58 182
MS.gene068578.t1 AT5G49040 47.778 180 92 1 15 192 12 191 1.69e-57 179
MS.gene068578.t1 AT5G42500 53.020 149 70 0 43 191 37 185 3.95e-57 178
MS.gene068578.t1 AT5G42510 51.678 149 72 0 43 191 34 182 2.20e-55 174
MS.gene068578.t1 AT1G22900 47.126 174 89 1 18 191 23 193 3.22e-54 171
MS.gene068578.t1 AT2G21100 43.005 193 102 3 1 191 1 187 2.36e-51 164
MS.gene068578.t1 AT2G21100 43.005 193 102 3 1 191 1 187 2.36e-51 164
MS.gene068578.t1 AT3G13650 47.179 195 91 6 1 192 1 186 3.66e-51 163
MS.gene068578.t1 AT3G13662 53.103 145 65 2 33 177 27 168 4.24e-51 162
MS.gene068578.t1 AT5G49030 46.821 173 92 0 15 187 12 184 6.68e-48 167
MS.gene068578.t1 AT3G13660 58.120 117 47 1 78 192 9 125 9.97e-43 139
MS.gene068578.t1 AT4G38700 37.766 188 105 6 14 192 6 190 3.00e-39 133
MS.gene068578.t1 AT2G21110 38.919 185 101 3 14 192 8 186 4.56e-39 132
MS.gene068578.t1 AT3G58090 55.046 109 47 1 85 191 163 271 2.77e-36 127
MS.gene068578.t1 AT3G24020 29.630 135 86 3 61 189 110 241 3.01e-13 66.2
MS.gene068578.t1 AT4G13580 29.630 135 86 3 61 189 111 242 1.19e-12 64.7
MS.gene068578.t1 AT4G11190 28.571 140 93 3 36 169 20 158 1.90e-11 60.5

Find 56 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAGTAATCTCAGTGTTT+TGG 0.259860 1.1:-41843304 MS.gene068578:CDS
TGTGGAGTCCTAGGGTTGTT+GGG 0.287660 1.1:+41843598 None:intergenic
AGGAAGTAGATGAGGGATAA+GGG 0.337506 1.1:+41843675 None:intergenic
TCCTAGGGTTGTTGGGGAGA+TGG 0.354171 1.1:+41843605 None:intergenic
GAGGAAGTAGATGAGGGATA+AGG 0.362909 1.1:+41843674 None:intergenic
TTGTGGAGTCCTAGGGTTGT+TGG 0.373760 1.1:+41843597 None:intergenic
TTTGAGGTTTGTGGAGTCCT+AGG 0.379817 1.1:+41843589 None:intergenic
AATCCGGACGCGCTGTTAAC+GGG 0.381175 1.1:+41843436 None:intergenic
ATGCCGGTTGTGGGTGGTAG+TGG 0.389118 1.1:-41843249 MS.gene068578:CDS
GAATCCGGACGCGCTGTTAA+CGG 0.397594 1.1:+41843435 None:intergenic
TTCACACGAGGGAAGTATAA+TGG 0.406207 1.1:-41843324 MS.gene068578:CDS
GGATGTTGAGAAGAAAAGTT+TGG 0.430943 1.1:+41843701 None:intergenic
AGGCGACCCGAACAGCAGTT+TGG 0.431782 1.1:+41843517 None:intergenic
GGATTCAAACTCCGAGGTTG+TGG 0.443331 1.1:-41843418 MS.gene068578:CDS
CGACCCGTTAACAGCGCGTC+CGG 0.452836 1.1:-41843439 MS.gene068578:CDS
CGTGAGAGAGATGCCGGTTG+TGG 0.463566 1.1:-41843259 MS.gene068578:CDS
AACCCACTACCACCCACAAC+CGG 0.476541 1.1:+41843246 None:intergenic
TTGAGGTTTGTGGAGTCCTA+GGG 0.486598 1.1:+41843590 None:intergenic
GTGGAGTCCTAGGGTTGTTG+GGG 0.490912 1.1:+41843599 None:intergenic
TGGGTTGTTCAGATTTGCAA+GGG 0.492504 1.1:-41843229 MS.gene068578:CDS
AGTAGATGAGGGATAAGGGA+AGG 0.507437 1.1:+41843679 None:intergenic
CGTGGAAGTAGAAGCGGATG+TGG 0.512512 1.1:+41843559 None:intergenic
TGCCGGTTGTGGGTGGTAGT+GGG 0.514800 1.1:-41843248 MS.gene068578:CDS
GATGAAGAGGAAGTAGATGA+GGG 0.521113 1.1:+41843668 None:intergenic
TCAGCTTCACAGAGTGAAGT+GGG 0.523071 1.1:-41843372 MS.gene068578:CDS
TTCTACTTCCACGACATCAT+CGG 0.523779 1.1:-41843549 MS.gene068578:CDS
GTGGGTTGTTCAGATTTGCA+AGG 0.530567 1.1:-41843230 MS.gene068578:CDS
GTGAGAGAGATGCCGGTTGT+GGG 0.540631 1.1:-41843258 MS.gene068578:CDS
ACAACCTCGGAGTTTGAATC+CGG 0.544334 1.1:+41843420 None:intergenic
ACCATCTCCCCAACAACCCT+AGG 0.552762 1.1:-41843606 MS.gene068578:CDS
AAATGCATTAGAAGCTATTG+TGG 0.554492 1.1:-41843178 MS.gene068578:CDS
GAGTGAAGTGGGGTTTCTCA+TGG 0.555374 1.1:-41843361 MS.gene068578:CDS
TTGTGCTCTTCCCACAACCT+CGG 0.556899 1.1:+41843407 None:intergenic
TGATGAAGAGGAAGTAGATG+AGG 0.561084 1.1:+41843667 None:intergenic
GATTCAAACTCCGAGGTTGT+GGG 0.568747 1.1:-41843417 MS.gene068578:CDS
GTAGATGAGGGATAAGGGAA+GGG 0.571545 1.1:+41843680 None:intergenic
ATCCGCCGTGAGAGAGATGC+CGG 0.574343 1.1:-41843265 MS.gene068578:CDS
CTTAACTTTGCATTCACACG+AGG 0.574668 1.1:-41843336 MS.gene068578:CDS
TGGTAATGGTGGTGATGAAG+AGG 0.589837 1.1:+41843655 None:intergenic
GAGGTTGTGGGAAGAGCACA+AGG 0.595582 1.1:-41843405 MS.gene068578:CDS
AACCACTGAACCAAAACCCG+TGG 0.598362 1.1:+41843470 None:intergenic
ACCACTGAACCAAAACCCGT+GGG 0.602599 1.1:+41843471 None:intergenic
TTCAGCTTCACAGAGTGAAG+TGG 0.609451 1.1:-41843373 MS.gene068578:CDS
CACAACCGGCATCTCTCTCA+CGG 0.612074 1.1:+41843260 None:intergenic
TACTTCCACGACATCATCGG+TGG 0.615547 1.1:-41843546 MS.gene068578:CDS
CACTGAACCAAAACCCGTGG+GGG 0.622706 1.1:+41843473 None:intergenic
TGATGTCGTGGAAGTAGAAG+CGG 0.627685 1.1:+41843553 None:intergenic
CAGCTTCACAGAGTGAAGTG+GGG 0.638369 1.1:-41843371 MS.gene068578:CDS
TGAGAAGAAAAGTTTGGCCA+TGG 0.638924 1.1:+41843707 None:intergenic
AGAGAGATGCCGGTTGTGGG+TGG 0.647672 1.1:-41843255 MS.gene068578:CDS
GGGTTGTTCAGATTTGCAAG+GGG 0.683015 1.1:-41843228 MS.gene068578:CDS
GGTTGTTCAGATTTGCAAGG+GGG 0.683578 1.1:-41843227 MS.gene068578:CDS
CCACTGAACCAAAACCCGTG+GGG 0.704423 1.1:+41843472 None:intergenic
TTAACTTTGCATTCACACGA+GGG 0.712435 1.1:-41843335 MS.gene068578:CDS
AACCGGCATCTCTCTCACGG+CGG 0.738069 1.1:+41843263 None:intergenic
GCGTCCGGATTCAAACTCCG+AGG 0.763343 1.1:-41843424 MS.gene068578:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATGGTTTTTATGAAAGAA+TGG + chr1.1:41843235-41843254 None:intergenic 25.0%
AAATGCATTAGAAGCTATTG+TGG - chr1.1:41843676-41843695 MS.gene068578:CDS 30.0%
AAAAAACCAAACTGCTGTTC+GGG - chr1.1:41843331-41843350 MS.gene068578:CDS 35.0%
GAAAAAACCAAACTGCTGTT+CGG - chr1.1:41843330-41843349 MS.gene068578:CDS 35.0%
GGATGTTGAGAAGAAAAGTT+TGG + chr1.1:41843156-41843175 None:intergenic 35.0%
TTAACTTTGCATTCACACGA+GGG - chr1.1:41843519-41843538 MS.gene068578:CDS 35.0%
! GGAAGTAATCTCAGTGTTTT+GGG - chr1.1:41843551-41843570 MS.gene068578:CDS 35.0%
! TGGAAGTAATCTCAGTGTTT+TGG - chr1.1:41843550-41843569 MS.gene068578:CDS 35.0%
!!! TTTTGGTTCAGTGGTTATGA+TGG - chr1.1:41843391-41843410 MS.gene068578:CDS 35.0%
AGGAAGTAGATGAGGGATAA+GGG + chr1.1:41843182-41843201 None:intergenic 40.0%
CTTAACTTTGCATTCACACG+AGG - chr1.1:41843518-41843537 MS.gene068578:CDS 40.0%
GATGAAGAGGAAGTAGATGA+GGG + chr1.1:41843189-41843208 None:intergenic 40.0%
TGATGAAGAGGAAGTAGATG+AGG + chr1.1:41843190-41843209 None:intergenic 40.0%
TGGGTTGTTCAGATTTGCAA+GGG - chr1.1:41843625-41843644 MS.gene068578:CDS 40.0%
TTCTACTTCCACGACATCAT+CGG - chr1.1:41843305-41843324 MS.gene068578:CDS 40.0%
! GAAAGAATGGAGTTTTGCTG+TGG + chr1.1:41843222-41843241 None:intergenic 40.0%
! TTCACACGAGGGAAGTATAA+TGG - chr1.1:41843530-41843549 MS.gene068578:CDS 40.0%
!! ATGGAGTTTTGCTGTGGTAA+TGG + chr1.1:41843216-41843235 None:intergenic 40.0%
!! TTTTTCAGTGGTTGGAGATG+AGG + chr1.1:41843360-41843379 None:intergenic 40.0%
!!! GGCTTAGTTTTTGAGGTTTG+TGG + chr1.1:41843277-41843296 None:intergenic 40.0%
!!! GTAATCTCAGTGTTTTGGGA+AGG - chr1.1:41843555-41843574 MS.gene068578:CDS 40.0%
AACCACTGAAAAATCCCCCA+CGG - chr1.1:41843367-41843386 MS.gene068578:CDS 45.0%
ACAACCTCGGAGTTTGAATC+CGG + chr1.1:41843437-41843456 None:intergenic 45.0%
AGTAGATGAGGGATAAGGGA+AGG + chr1.1:41843178-41843197 None:intergenic 45.0%
GAGGAAGTAGATGAGGGATA+AGG + chr1.1:41843183-41843202 None:intergenic 45.0%
GATTCAAACTCCGAGGTTGT+GGG - chr1.1:41843437-41843456 MS.gene068578:CDS 45.0%
GGGTTGTTCAGATTTGCAAG+GGG - chr1.1:41843626-41843645 MS.gene068578:CDS 45.0%
GGTTGTTCAGATTTGCAAGG+GGG - chr1.1:41843627-41843646 MS.gene068578:CDS 45.0%
GTAGATGAGGGATAAGGGAA+GGG + chr1.1:41843177-41843196 None:intergenic 45.0%
TCAGCTTCACAGAGTGAAGT+GGG - chr1.1:41843482-41843501 MS.gene068578:CDS 45.0%
TGATGTCGTGGAAGTAGAAG+CGG + chr1.1:41843304-41843323 None:intergenic 45.0%
TTCAGCTTCACAGAGTGAAG+TGG - chr1.1:41843481-41843500 MS.gene068578:CDS 45.0%
TTGAGGTTTGTGGAGTCCTA+GGG + chr1.1:41843267-41843286 None:intergenic 45.0%
! GTGGGTTGTTCAGATTTGCA+AGG - chr1.1:41843624-41843643 MS.gene068578:CDS 45.0%
! TTTGAGGTTTGTGGAGTCCT+AGG + chr1.1:41843268-41843287 None:intergenic 45.0%
! TTTTTCCACCGATGATGTCG+TGG + chr1.1:41843316-41843335 None:intergenic 45.0%
!! CGGATGTGGCTTAGTTTTTG+AGG + chr1.1:41843284-41843303 None:intergenic 45.0%
!! TGGTAATGGTGGTGATGAAG+AGG + chr1.1:41843202-41843221 None:intergenic 45.0%
!!! GAGTTTTGCTGTGGTAATGG+TGG + chr1.1:41843213-41843232 None:intergenic 45.0%
AACCACTGAACCAAAACCCG+TGG + chr1.1:41843387-41843406 None:intergenic 50.0%
ACCACTGAAAAATCCCCCAC+GGG - chr1.1:41843368-41843387 MS.gene068578:CDS 50.0%
ACCACTGAACCAAAACCCGT+GGG + chr1.1:41843386-41843405 None:intergenic 50.0%
CAGCTTCACAGAGTGAAGTG+GGG - chr1.1:41843483-41843502 MS.gene068578:CDS 50.0%
GAGTGAAGTGGGGTTTCTCA+TGG - chr1.1:41843493-41843512 MS.gene068578:CDS 50.0%
GGATTCAAACTCCGAGGTTG+TGG - chr1.1:41843436-41843455 MS.gene068578:CDS 50.0%
TACTTCCACGACATCATCGG+TGG - chr1.1:41843308-41843327 MS.gene068578:CDS 50.0%
TGTGGAGTCCTAGGGTTGTT+GGG + chr1.1:41843259-41843278 None:intergenic 50.0%
TTGTGCTCTTCCCACAACCT+CGG + chr1.1:41843450-41843469 None:intergenic 50.0%
TTGTGGAGTCCTAGGGTTGT+TGG + chr1.1:41843260-41843279 None:intergenic 50.0%
! GAAAAATCCCCCACGGGTTT+TGG - chr1.1:41843374-41843393 MS.gene068578:CDS 50.0%
!! GTGGGGGATTTTTCAGTGGT+TGG + chr1.1:41843368-41843387 None:intergenic 50.0%
AACCCACTACCACCCACAAC+CGG + chr1.1:41843611-41843630 None:intergenic 55.0%
AATCCGGACGCGCTGTTAAC+GGG + chr1.1:41843421-41843440 None:intergenic 55.0%
ACCATCTCCCCAACAACCCT+AGG - chr1.1:41843248-41843267 MS.gene068578:CDS 55.0%
CACAACCGGCATCTCTCTCA+CGG + chr1.1:41843597-41843616 None:intergenic 55.0%
CACTGAACCAAAACCCGTGG+GGG + chr1.1:41843384-41843403 None:intergenic 55.0%
CCACTGAACCAAAACCCGTG+GGG + chr1.1:41843385-41843404 None:intergenic 55.0%
CGTGGAAGTAGAAGCGGATG+TGG + chr1.1:41843298-41843317 None:intergenic 55.0%
GAATCCGGACGCGCTGTTAA+CGG + chr1.1:41843422-41843441 None:intergenic 55.0%
GTGGAGTCCTAGGGTTGTTG+GGG + chr1.1:41843258-41843277 None:intergenic 55.0%
TCCTAGGGTTGTTGGGGAGA+TGG + chr1.1:41843252-41843271 None:intergenic 55.0%
! GAGGTTGTGGGAAGAGCACA+AGG - chr1.1:41843449-41843468 MS.gene068578:CDS 55.0%
! GTGAGAGAGATGCCGGTTGT+GGG - chr1.1:41843596-41843615 MS.gene068578:CDS 55.0%
!! ACCCGTGGGGGATTTTTCAG+TGG + chr1.1:41843372-41843391 None:intergenic 55.0%
AACCGGCATCTCTCTCACGG+CGG + chr1.1:41843594-41843613 None:intergenic 60.0%
AGGCGACCCGAACAGCAGTT+TGG + chr1.1:41843340-41843359 None:intergenic 60.0%
ATCCGCCGTGAGAGAGATGC+CGG - chr1.1:41843589-41843608 MS.gene068578:CDS 60.0%
GCGTCCGGATTCAAACTCCG+AGG - chr1.1:41843430-41843449 MS.gene068578:CDS 60.0%
! AGAGAGATGCCGGTTGTGGG+TGG - chr1.1:41843599-41843618 MS.gene068578:CDS 60.0%
! ATGCCGGTTGTGGGTGGTAG+TGG - chr1.1:41843605-41843624 MS.gene068578:CDS 60.0%
! CGTGAGAGAGATGCCGGTTG+TGG - chr1.1:41843595-41843614 MS.gene068578:CDS 60.0%
! TGCCGGTTGTGGGTGGTAGT+GGG - chr1.1:41843606-41843625 MS.gene068578:CDS 60.0%
!!! CCCCACGGGTTTTGGTTCAG+TGG - chr1.1:41843382-41843401 MS.gene068578:CDS 60.0%
CGACCCGTTAACAGCGCGTC+CGG - chr1.1:41843415-41843434 MS.gene068578:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 41843149 41843727 41843149 ID=MS.gene068578
chr1.1 mRNA 41843149 41843727 41843149 ID=MS.gene068578.t1;Parent=MS.gene068578
chr1.1 exon 41843149 41843727 41843149 ID=MS.gene068578.t1.exon1;Parent=MS.gene068578.t1
chr1.1 CDS 41843149 41843727 41843149 ID=cds.MS.gene068578.t1;Parent=MS.gene068578.t1
Gene Sequence

>MS.gene068578

ATGGCCAAACTTTTCTTCTCAACATCCCTTCCCTTATCCCTCATCTACTTCCTCTTCATCACCACCATTACCACAGCAAAACTCCATTCTTTCATAAAAACCATCTCCCCAACAACCCTAGGACTCCACAAACCTCAAAAACTAAGCCACATCCGCTTCTACTTCCACGACATCATCGGTGGAAAAAACCAAACTGCTGTTCGGGTCGCCTCATCTCCAACCACTGAAAAATCCCCCACGGGTTTTGGTTCAGTGGTTATGATGGACGACCCGTTAACAGCGCGTCCGGATTCAAACTCCGAGGTTGTGGGAAGAGCACAAGGAATCTATGCTTCAGCTTCACAGAGTGAAGTGGGGTTTCTCATGGTGCTTAACTTTGCATTCACACGAGGGAAGTATAATGGAAGTAATCTCAGTGTTTTGGGAAGGAATACGATCGAATCCGCCGTGAGAGAGATGCCGGTTGTGGGTGGTAGTGGGTTGTTCAGATTTGCAAGGGGGTATGCTCAAGCTTCAACTCATTCTATAAATGCATTAGAAGCTATTGTGGAGTATAATGTTTATGTGTTTCATTATTAA
Protein sequence

>MS.gene068578.t1

MAKLFFSTSLPLSLIYFLFITTITTAKLHSFIKTISPTTLGLHKPQKLSHIRFYFHDIIGGKNQTAVRVASSPTTEKSPTGFGSVVMMDDPLTARPDSNSEVVGRAQGIYASASQSEVGFLMVLNFAFTRGKYNGSNLSVLGRNTIESAVREMPVVGGSGLFRFARGYAQASTHSINALEAIVEYNVYVFHY