AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051384

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051384.t1 MTR_1g062160 99.507 203 1 0 1 203 1 203 4.97e-154 424
MS.gene051384.t1 MTR_7g102790 78.431 204 41 2 1 202 1 203 2.02e-108 309
MS.gene051384.t1 MTR_5g007230 55.612 196 79 4 7 202 21 208 1.64e-72 219
MS.gene051384.t1 MTR_5g030130 54.680 203 79 4 7 202 35 231 2.44e-72 219
MS.gene051384.t1 MTR_4g078170 53.465 202 81 4 7 202 15 209 3.24e-70 213
MS.gene051384.t1 MTR_8g066820 55.340 206 73 5 7 202 33 229 3.55e-70 213
MS.gene051384.t1 MTR_5g030130 66.667 129 42 1 7 135 35 162 4.56e-59 184
MS.gene051384.t1 MTR_2g084495 38.136 236 100 7 4 201 2 229 5.84e-46 152
MS.gene051384.t1 MTR_2g060500 50.000 146 63 4 1 137 5 149 4.92e-42 139
MS.gene051384.t1 MTR_2g060540 51.408 142 59 4 1 133 5 145 1.01e-41 138
MS.gene051384.t1 MTR_2g084510 36.475 244 106 8 4 201 1 241 4.45e-39 134
MS.gene051384.t1 MTR_2g084525 48.299 147 67 4 4 141 1 147 7.48e-38 131
MS.gene051384.t1 MTR_2g055210 38.608 158 93 4 5 161 100 254 1.86e-33 122
MS.gene051384.t1 MTR_4g094680 33.641 217 120 6 7 201 22 236 2.73e-30 111
MS.gene051384.t1 MTR_4g116300 42.188 128 72 2 7 134 6 131 1.85e-29 110
MS.gene051384.t1 MTR_2g036170 31.250 224 118 6 7 202 37 252 2.49e-28 107
MS.gene051384.t1 MTR_8g105930 36.054 147 70 6 9 134 15 158 6.45e-20 84.7
MS.gene051384.t1 MTR_5g077740 29.744 195 106 6 7 201 23 186 2.96e-19 81.6
MS.gene051384.t1 MTR_8g097310 32.075 159 96 3 46 201 4 153 4.63e-19 80.5
MS.gene051384.t1 MTR_2g083710 49.206 63 30 2 1 62 1 62 1.82e-15 68.6
MS.gene051384.t1 MTR_1g032880 39.535 86 47 3 54 135 27 111 1.26e-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.gene051384.t1 AT1G32700 53.769 199 86 3 7 202 12 207 2.34e-71 216
MS.gene051384.t1 AT2G27930 54.327 208 66 3 4 202 1 188 6.42e-68 206
MS.gene051384.t1 AT2G27930 54.327 208 66 3 4 202 1 188 6.42e-68 206
MS.gene051384.t1 AT1G21000 45.923 233 86 5 7 201 13 243 3.25e-65 201
MS.gene051384.t1 AT1G21000 45.923 233 86 5 7 201 16 246 4.43e-65 201
MS.gene051384.t1 AT1G76590 46.957 230 85 4 7 201 18 245 5.64e-65 201
MS.gene051384.t1 AT4G17900 52.736 201 83 6 7 202 20 213 2.66e-64 198
MS.gene051384.t1 AT4G17900 51.471 204 81 7 7 202 34 227 3.54e-64 198
MS.gene051384.t1 AT1G43000 45.581 215 100 5 2 201 11 223 8.65e-60 187
MS.gene051384.t1 AT1G43000 45.581 215 100 5 2 201 4 216 8.67e-60 186
MS.gene051384.t1 AT2G27930 61.290 155 51 1 4 149 1 155 7.07e-59 182
MS.gene051384.t1 AT2G27930 61.290 155 51 1 4 149 1 155 7.07e-59 182
MS.gene051384.t1 AT5G46710 48.744 199 97 4 7 201 12 209 1.74e-57 180
MS.gene051384.t1 AT5G46710 48.744 199 97 4 7 201 28 225 3.49e-57 180
MS.gene051384.t1 AT1G32700 52.632 171 75 3 35 202 1 168 9.82e-56 175
MS.gene051384.t1 AT5G46710 58.140 129 52 2 7 134 28 155 3.21e-49 158
MS.gene051384.t1 AT2G27930 52.318 151 43 3 61 202 61 191 1.04e-41 139
MS.gene051384.t1 AT2G27930 52.318 151 43 3 61 202 61 191 1.04e-41 139
MS.gene051384.t1 AT1G31040 34.802 227 113 6 7 201 19 242 1.95e-34 122
MS.gene051384.t1 AT3G60670 39.024 164 91 4 1 157 1 162 1.22e-31 115
MS.gene051384.t1 AT2G12646 43.077 130 72 2 5 134 1 128 1.53e-29 110
MS.gene051384.t1 AT2G12646 43.750 128 70 2 7 134 6 131 1.86e-29 110
MS.gene051384.t1 AT2G12646 43.750 128 70 2 7 134 6 131 1.86e-29 110
MS.gene051384.t1 AT2G01818 31.280 211 125 7 9 201 13 221 1.15e-22 91.7

Find 43 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAGTTCGTTTCTGTTCTT+TGG 0.184177 1.1:+46909816 MS.gene051384:CDS
AGAAGTGGTTTGAGCCATTT+AGG 0.226031 1.1:-46909331 None:intergenic
AGAAACGAACTTGGTCTAAA+AGG 0.306972 1.1:-46909807 None:intergenic
ATTCCTCATAGGGCTCCTTT+TGG 0.317747 1.1:+46910432 MS.gene051384:CDS
ACACAATGTTGGTTCCTAAA+TGG 0.324494 1.1:+46909317 MS.gene051384:CDS
CAAGGATCATCAAGTCATTC+AGG 0.333682 1.1:+46909474 MS.gene051384:CDS
TTTCTTCTCCTTGCGTTTGA+AGG 0.347275 1.1:-46910405 None:intergenic
CAAGTTCGTTTCTGTTCTTT+GGG 0.351554 1.1:+46909817 MS.gene051384:CDS
CTTGTAGGAATAAAGAGAAA+TGG 0.373461 1.1:+46910249 MS.gene051384:CDS
TTTCTGTTCTTTGGGATGTA+AGG 0.374729 1.1:+46909825 MS.gene051384:CDS
CAGAAAATGTTGGACATTAG+TGG 0.376562 1.1:+46909676 MS.gene051384:CDS
GGAGGTGTTGGAGGAGTTGC+TGG 0.378339 1.1:-46910384 None:intergenic
GAGAGGCCTCAACCAAAATC+TGG 0.407501 1.1:+46909745 MS.gene051384:CDS
GAAGAAAAGGGATTCCTCAT+AGG 0.407985 1.1:+46910421 MS.gene051384:CDS
CAATGATTGAATTAGCTTGT+AGG 0.416656 1.1:+46910234 MS.gene051384:intron
TTGTAGGAATAAAGAGAAAT+GGG 0.420634 1.1:+46910250 MS.gene051384:CDS
TCAAACGCAAGGAGAAGAAA+AGG 0.442491 1.1:+46910408 MS.gene051384:CDS
CCTTACATTTGTGAGATTTG+TGG 0.451494 1.1:+46909778 MS.gene051384:CDS
CTTGCGTTTGAAGGAGGTGT+TGG 0.453994 1.1:-46910396 None:intergenic
CCAAAGAACAGAAACGAACT+TGG 0.484387 1.1:-46909816 None:intergenic
GAGGTATCAACAACGGAAGA+AGG 0.485618 1.1:+46910306 MS.gene051384:CDS
CCACAAATCTCACAAATGTA+AGG 0.486176 1.1:-46909778 None:intergenic
TAAAATGACTAGGGTCCAAA+AGG 0.492758 1.1:-46910447 None:intergenic
GCGTTTGAAGGAGGTGTTGG+AGG 0.501278 1.1:-46910393 None:intergenic
CTTCTCCTTGCGTTTGAAGG+AGG 0.504177 1.1:-46910402 None:intergenic
GGCTGAAATTCAGAAAATGT+TGG 0.529817 1.1:+46909666 MS.gene051384:CDS
ATTTGTGAGATTTGTGGAAG+AGG 0.530195 1.1:+46909784 MS.gene051384:CDS
AAGAAAAGGGATTCCTCATA+GGG 0.544259 1.1:+46910422 MS.gene051384:CDS
CAAACGCAAGGAGAAGAAAA+GGG 0.546728 1.1:+46910409 MS.gene051384:CDS
AGAACGACAATAGAAGCAAA+AGG 0.552138 1.1:-46909443 None:intergenic
AGGTATCAACAACGGAAGAA+GGG 0.587617 1.1:+46910307 MS.gene051384:CDS
GGTCCAAAAGGAGCCCTATG+AGG 0.587771 1.1:-46910435 None:intergenic
TTTAGATGCAAATAACAATG+AGG 0.589036 1.1:+46910287 MS.gene051384:CDS
CTTCATATCATGATGTAGTG+AGG 0.591334 1.1:+46909641 MS.gene051384:CDS
GGATTCACGCTGACGCCGCA+AGG 0.591752 1.1:+46909380 MS.gene051384:CDS
TTCATATCATGATGTAGTGA+GGG 0.599632 1.1:+46909642 MS.gene051384:CDS
TTGTCGTTCTTCAAAACACA+AGG 0.606276 1.1:+46909456 MS.gene051384:CDS
CAACACCTCCTTCAAACGCA+AGG 0.609547 1.1:+46910397 MS.gene051384:CDS
TTGCGTGAAGGCTCACAACA+AGG 0.621390 1.1:+46910354 MS.gene051384:CDS
CATGTTACATTCACTCCTTG+CGG 0.659509 1.1:-46909395 None:intergenic
CAAGAAGAAGAATTGCGTGA+AGG 0.666815 1.1:+46910342 MS.gene051384:CDS
ATATCATGATGTAGTGAGGG+TGG 0.676670 1.1:+46909645 MS.gene051384:CDS
TAACAATGAGGTATCAACAA+CGG 0.691354 1.1:+46910299 MS.gene051384:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAAAAATATATACTTT+AGG - chr1.1:46909599-46909618 None:intergenic 10.0%
!!! AAAGTATATATTTTTTTTGT+TGG + chr1.1:46909599-46909618 MS.gene051384:intron 10.0%
!! ATAATTATTGAATAGTAGAT+AGG + chr1.1:46910128-46910147 MS.gene051384:intron 15.0%
!!! TATGCACATTTTTTTATAAT+GGG + chr1.1:46909525-46909544 MS.gene051384:intron 15.0%
!!! TTATGCACATTTTTTTATAA+TGG + chr1.1:46909524-46909543 MS.gene051384:intron 15.0%
!! TAAGAAAATAATTTAGGAAC+CGG - chr1.1:46909507-46909526 None:intergenic 20.0%
!! TATATGAAGCATATAACTAT+AGG + chr1.1:46910018-46910037 MS.gene051384:intron 20.0%
!! TGTGCATAAGAAAATAATTT+AGG - chr1.1:46909513-46909532 None:intergenic 20.0%
!!! ATGCACATTTTTTTATAATG+GGG + chr1.1:46909526-46909545 MS.gene051384:intron 20.0%
!!! TTTAAAATTATGATGTGAAG+AGG - chr1.1:46909923-46909942 None:intergenic 20.0%
! ATACACATGATGATTAATGA+TGG - chr1.1:46910001-46910020 None:intergenic 25.0%
! ATTCTAATTAATTGTTGTGC+TGG + chr1.1:46910211-46910230 MS.gene051384:intron 25.0%
! TAAATGTGATGAAATGTCAA+TGG - chr1.1:46910053-46910072 None:intergenic 25.0%
! TGATGGAAGGAATATAATTA+TGG - chr1.1:46909984-46910003 None:intergenic 25.0%
! TTGTAGGAATAAAGAGAAAT+GGG + chr1.1:46910250-46910269 MS.gene051384:CDS 25.0%
! TTTAGATGCAAATAACAATG+AGG + chr1.1:46910287-46910306 MS.gene051384:CDS 25.0%
!!! ACATTTTTTTATAATGGGGT+TGG + chr1.1:46909530-46909549 MS.gene051384:intron 25.0%
!!! TTTGATTTTGATTTTTGAGC+AGG + chr1.1:46909294-46909313 MS.gene051384:intron 25.0%
AAAAATGGTGTACTAAGAAG+TGG - chr1.1:46909349-46909368 None:intergenic 30.0%
AAGTCATTCAGGTAAATTAC+CGG + chr1.1:46909485-46909504 MS.gene051384:intron 30.0%
ATGAGCTTTCCAAATAATGT+AGG - chr1.1:46909957-46909976 None:intergenic 30.0%
CTTGTAGGAATAAAGAGAAA+TGG + chr1.1:46910249-46910268 MS.gene051384:CDS 30.0%
TTCATATCATGATGTAGTGA+GGG + chr1.1:46909642-46909661 MS.gene051384:CDS 30.0%
TTGAATAGTAGATAGGAACA+TGG + chr1.1:46910135-46910154 MS.gene051384:intron 30.0%
! ACATGATGATTAATGATGGA+AGG - chr1.1:46909997-46910016 None:intergenic 30.0%
! TAACAATGAGGTATCAACAA+CGG + chr1.1:46910299-46910318 MS.gene051384:CDS 30.0%
!! CAATGATTGAATTAGCTTGT+AGG + chr1.1:46910234-46910253 MS.gene051384:intron 30.0%
!!! GAGTTTTATTTCTGAATGAG+AGG + chr1.1:46909728-46909747 MS.gene051384:CDS 30.0%
AAGAAAAGGGATTCCTCATA+GGG + chr1.1:46910422-46910441 MS.gene051384:CDS 35.0%
AGAAACGAACTTGGTCTAAA+AGG - chr1.1:46909810-46909829 None:intergenic 35.0%
AGAACGACAATAGAAGCAAA+AGG - chr1.1:46909446-46909465 None:intergenic 35.0%
AGCTTTCCAAATAATGTAGG+TGG - chr1.1:46909954-46909973 None:intergenic 35.0%
ATTTGTGAGATTTGTGGAAG+AGG + chr1.1:46909784-46909803 MS.gene051384:CDS 35.0%
CAAGTTCGTTTCTGTTCTTT+GGG + chr1.1:46909817-46909836 MS.gene051384:CDS 35.0%
CAGAAAATGTTGGACATTAG+TGG + chr1.1:46909676-46909695 MS.gene051384:CDS 35.0%
CCACAAATCTCACAAATGTA+AGG - chr1.1:46909781-46909800 None:intergenic 35.0%
CCTTACATTTGTGAGATTTG+TGG + chr1.1:46909778-46909797 MS.gene051384:CDS 35.0%
CTTCATATCATGATGTAGTG+AGG + chr1.1:46909641-46909660 MS.gene051384:CDS 35.0%
GGCTGAAATTCAGAAAATGT+TGG + chr1.1:46909666-46909685 MS.gene051384:CDS 35.0%
TTCCAAATAATGTAGGTGGT+GGG - chr1.1:46909950-46909969 None:intergenic 35.0%
TTGTCGTTCTTCAAAACACA+AGG + chr1.1:46909456-46909475 MS.gene051384:CDS 35.0%
TTTCCAAATAATGTAGGTGG+TGG - chr1.1:46909951-46909970 None:intergenic 35.0%
!! ACACAATGTTGGTTCCTAAA+TGG + chr1.1:46909317-46909336 MS.gene051384:CDS 35.0%
!! TTTCTGTTCTTTGGGATGTA+AGG + chr1.1:46909825-46909844 MS.gene051384:CDS 35.0%
AGAAGTGGTTTGAGCCATTT+AGG - chr1.1:46909334-46909353 None:intergenic 40.0%
AGGTATCAACAACGGAAGAA+GGG + chr1.1:46910307-46910326 MS.gene051384:CDS 40.0%
ATATCATGATGTAGTGAGGG+TGG + chr1.1:46909645-46909664 MS.gene051384:CDS 40.0%
ATCCGACACTCGTTGAAAAA+TGG - chr1.1:46909364-46909383 None:intergenic 40.0%
CAAACGCAAGGAGAAGAAAA+GGG + chr1.1:46910409-46910428 MS.gene051384:CDS 40.0%
CAAGAAGAAGAATTGCGTGA+AGG + chr1.1:46910342-46910361 MS.gene051384:CDS 40.0%
CAAGGATCATCAAGTCATTC+AGG + chr1.1:46909474-46909493 MS.gene051384:CDS 40.0%
CATGTTACATTCACTCCTTG+CGG - chr1.1:46909398-46909417 None:intergenic 40.0%
CCAAAGAACAGAAACGAACT+TGG - chr1.1:46909819-46909838 None:intergenic 40.0%
CCAAGTTCGTTTCTGTTCTT+TGG + chr1.1:46909816-46909835 MS.gene051384:CDS 40.0%
GAAGAAAAGGGATTCCTCAT+AGG + chr1.1:46910421-46910440 MS.gene051384:CDS 40.0%
TCAAACGCAAGGAGAAGAAA+AGG + chr1.1:46910408-46910427 MS.gene051384:CDS 40.0%
TTTCTTCTCCTTGCGTTTGA+AGG - chr1.1:46910408-46910427 None:intergenic 40.0%
! TTTTGAGCAGGACACAATGT+TGG + chr1.1:46909306-46909325 MS.gene051384:intron 40.0%
!! CACCATTTTTCAACGAGTGT+CGG + chr1.1:46909359-46909378 MS.gene051384:CDS 40.0%
!! GGAACTGCTTTTCCAGATTT+TGG - chr1.1:46909760-46909779 None:intergenic 40.0%
!!! GCTTTTCCAGATTTTGGTTG+AGG - chr1.1:46909754-46909773 None:intergenic 40.0%
CACCCACCACCTACATTATT+TGG + chr1.1:46909945-46909964 MS.gene051384:intron 45.0%
! ATTCCTCATAGGGCTCCTTT+TGG + chr1.1:46910432-46910451 MS.gene051384:CDS 45.0%
! GAGGTATCAACAACGGAAGA+AGG + chr1.1:46910306-46910325 MS.gene051384:CDS 45.0%
CAACACCTCCTTCAAACGCA+AGG + chr1.1:46910397-46910416 MS.gene051384:CDS 50.0%
CTTCTCCTTGCGTTTGAAGG+AGG - chr1.1:46910405-46910424 None:intergenic 50.0%
GAGAGGCCTCAACCAAAATC+TGG + chr1.1:46909745-46909764 MS.gene051384:CDS 50.0%
TTGCGTGAAGGCTCACAACA+AGG + chr1.1:46910354-46910373 MS.gene051384:CDS 50.0%
! CTTGCGTTTGAAGGAGGTGT+TGG - chr1.1:46910399-46910418 None:intergenic 50.0%
GGTCCAAAAGGAGCCCTATG+AGG - chr1.1:46910438-46910457 None:intergenic 55.0%
!! GCGTTTGAAGGAGGTGTTGG+AGG - chr1.1:46910396-46910415 None:intergenic 55.0%
!! GGAGGTGTTGGAGGAGTTGC+TGG - chr1.1:46910387-46910406 None:intergenic 60.0%
GGATTCACGCTGACGCCGCA+AGG + chr1.1:46909380-46909399 MS.gene051384:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 46909227 46910461 46909227 ID=MS.gene051384
chr1.1 mRNA 46909227 46910461 46909227 ID=MS.gene051384.t1;Parent=MS.gene051384
chr1.1 exon 46909227 46909229 46909227 ID=MS.gene051384.t1.exon1;Parent=MS.gene051384.t1
chr1.1 CDS 46909227 46909229 46909227 ID=cds.MS.gene051384.t1;Parent=MS.gene051384.t1
chr1.1 exon 46909316 46909495 46909316 ID=MS.gene051384.t1.exon2;Parent=MS.gene051384.t1
chr1.1 CDS 46909316 46909495 46909316 ID=cds.MS.gene051384.t1;Parent=MS.gene051384.t1
chr1.1 exon 46909631 46909846 46909631 ID=MS.gene051384.t1.exon3;Parent=MS.gene051384.t1
chr1.1 CDS 46909631 46909846 46909631 ID=cds.MS.gene051384.t1;Parent=MS.gene051384.t1
chr1.1 exon 46910249 46910461 46910249 ID=MS.gene051384.t1.exon4;Parent=MS.gene051384.t1
chr1.1 CDS 46910249 46910461 46910249 ID=cds.MS.gene051384.t1;Parent=MS.gene051384.t1
Gene Sequence

>MS.gene051384

ATGGTATGTATATGCACATATAACTTATGTTTTGAATTTAATATGTTCATATGATTTTGATTTTGATTTTGATTTTGATTTTTGAGCAGGACACAATGTTGGTTCCTAAATGGCTCAAACCACTTCTTAGTACACCATTTTTCAACGAGTGTCGGATTCACGCTGACGCCGCAAGGAGTGAATGTAACATGTTTTGTCTAGATTGCAATGTTGATGCCTTTTGCTTCTATTGTCGTTCTTCAAAACACAAGGATCATCAAGTCATTCAGGTAAATTACCGGTTCCTAAATTATTTTCTTATGCACATTTTTTTATAATGGGGTTGGTTAAATTTTGTGATTTTTTAATATGATCTTCATTTTTCTTTATCCTAAAGTATATATTTTTTTTGTTGGTTTAATTAGATAAGACGATCTTCATATCATGATGTAGTGAGGGTGGCTGAAATTCAGAAAATGTTGGACATTAGTGGAGTACAAACTTATGTGATCAATAGTGCTAGAGTTTTATTTCTGAATGAGAGGCCTCAACCAAAATCTGGAAAAGCAGTTCCTTACATTTGTGAGATTTGTGGAAGAGGCCTTTTAGACCAAGTTCGTTTCTGTTCTTTGGGATGTAAGGTGAGATTTTGTTTCATAAACATTTTTCATATCATCAAAATGTACATATAATTCACAAATCAAATAGCTTAGTCCTCTTCACATCATAATTTTAAAAACACCCACCACCTACATTATTTGGAAAGCTCATCACACCATAATTATATTCCTTCCATCATTAATCATCATGTGTATATGAAGCATATAACTATAGGCGCAGTACTCCATTGACATTTCATCACATTTATAAAAATAATCATATTATTATCTAGTTAATATTATTGATATATTTTTTTATAAAGATAATTATTGAATAGTAGATAGGAACATGGTATAATAATGTGTATAAAATAATAATGAATCAATATATGATTTGTTTAATTTGATTCTAATTAATTGTTGTGCTGGCAATGATTGAATTAGCTTGTAGGAATAAAGAGAAATGGGAATGCAAGCTTTGTTTTAGATGCAAATAACAATGAGGTATCAACAACGGAAGAAGGGATGTCAAGACAACAAGAAGAAGAATTGCGTGAAGGCTCACAACAAGGCATGTATCCAGCAACTCCTCCAACACCTCCTTCAAACGCAAGGAGAAGAAAAGGGATTCCTCATAGGGCTCCTTTTGGACCCTAG
Protein sequence

>MS.gene051384.t1

MDTMLVPKWLKPLLSTPFFNECRIHADAARSECNMFCLDCNVDAFCFYCRSSKHKDHQVIQIRRSSYHDVVRVAEIQKMLDISGVQTYVINSARVLFLNERPQPKSGKAVPYICEICGRGLLDQVRFCSLGCKLVGIKRNGNASFVLDANNNEVSTTEEGMSRQQEEELREGSQQGMYPATPPTPPSNARRRKGIPHRAPFGP