AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048249


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048249.t1 MTR_2g026710 100.000 164 0 0 1 164 1 164 8.51e-121 338
MS.gene048249.t1 MTR_5g095740 66.667 165 42 4 1 155 1 162 5.48e-69 207
MS.gene048249.t1 MTR_3g058980 73.944 142 22 3 1 132 1 137 3.68e-67 203
MS.gene048249.t1 MTR_8g091720 76.190 126 23 2 16 134 27 152 1.17e-63 194
MS.gene048249.t1 MTR_4g133938 73.846 130 29 2 1 125 1 130 2.02e-63 191
MS.gene048249.t1 MTR_7g061270 59.509 163 50 3 1 147 1 163 3.24e-62 189
MS.gene048249.t1 MTR_7g100650 73.950 119 22 1 1 110 1 119 1.28e-61 188
MS.gene048249.t1 MTR_1g072790 64.336 143 39 2 3 133 9 151 1.75e-61 188
MS.gene048249.t1 MTR_8g093920 77.778 108 22 1 16 121 39 146 6.51e-58 180
MS.gene048249.t1 MTR_4g133952 52.564 156 54 4 2 144 48 196 1.97e-52 167
MS.gene048249.t1 MTR_1g088860 75.000 96 24 0 16 111 35 130 1.58e-51 163
MS.gene048249.t1 MTR_0392s0020 66.667 108 32 1 4 111 9 112 1.04e-50 159
MS.gene048249.t1 MTR_4g119500 61.157 121 44 1 4 124 12 129 1.16e-50 159
MS.gene048249.t1 MTR_1g039040 62.745 102 38 0 13 114 2 103 2.43e-47 152
MS.gene048249.t1 MTR_1g083070 64.130 92 33 0 17 108 4 95 1.68e-40 133
MS.gene048249.t1 MTR_1g029070 54.839 93 42 0 22 114 57 149 1.54e-30 109
MS.gene048249.t1 MTR_5g095900 45.098 102 53 1 7 105 3 104 4.66e-23 90.5
MS.gene048249.t1 MTR_1g028480 46.429 84 44 1 47 129 19 102 2.41e-19 79.0
MS.gene048249.t1 MTR_1g029100 40.789 76 45 0 22 97 7 82 1.61e-18 76.3
MS.gene048249.t1 MTR_2g056000 33.333 78 52 0 18 95 42 119 2.85e-14 67.4
MS.gene048249.t1 MTR_4g112380 32.530 83 56 0 13 95 7 89 3.25e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048249.t1 AT4G14540 84.298 121 15 1 1 117 1 121 2.39e-71 213
MS.gene048249.t1 AT5G47640 83.929 112 16 2 16 127 26 135 9.24e-64 194
MS.gene048249.t1 AT2G38880 68.939 132 36 2 10 139 12 140 1.87e-60 184
MS.gene048249.t1 AT2G38880 70.312 128 33 2 10 135 12 136 2.41e-60 184
MS.gene048249.t1 AT2G38880 70.312 128 33 2 10 135 12 136 2.41e-60 184
MS.gene048249.t1 AT2G38880 70.312 128 33 2 10 135 12 136 2.41e-60 184
MS.gene048249.t1 AT2G37060 77.064 109 21 1 6 110 15 123 5.23e-59 182
MS.gene048249.t1 AT2G37060 77.064 109 21 1 6 110 15 123 5.23e-59 182
MS.gene048249.t1 AT2G37060 77.064 109 21 1 6 110 15 123 5.23e-59 182
MS.gene048249.t1 AT2G38880 69.531 128 32 2 10 135 12 134 1.04e-58 180
MS.gene048249.t1 AT3G53340 62.838 148 38 4 15 147 27 172 1.38e-57 178
MS.gene048249.t1 AT3G53340 62.838 148 38 4 15 147 27 172 1.38e-57 178
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 1.81e-57 176
MS.gene048249.t1 AT2G13570 83.333 96 16 0 16 111 35 130 2.16e-57 179
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 6.47e-57 176
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 6.47e-57 176
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 6.47e-57 176
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 6.83e-57 176
MS.gene048249.t1 AT2G38880 81.000 100 17 1 10 107 12 111 6.83e-57 176
MS.gene048249.t1 AT3G53340 77.778 99 22 0 16 114 28 126 8.55e-56 173
MS.gene048249.t1 AT3G53340 77.778 99 22 0 16 114 28 126 8.55e-56 173
MS.gene048249.t1 AT3G53340 80.435 92 18 0 16 107 28 119 3.57e-55 170
MS.gene048249.t1 AT2G47810 72.549 102 28 0 16 117 50 151 9.01e-52 163
MS.gene048249.t1 AT5G47670 63.063 111 39 1 3 111 13 123 3.94e-51 163
MS.gene048249.t1 AT5G47670 63.063 111 39 1 3 111 42 152 8.75e-51 163
MS.gene048249.t1 AT5G47670 63.063 111 39 1 3 111 42 152 8.75e-51 163
MS.gene048249.t1 AT1G21970 52.273 132 60 2 12 140 52 183 1.46e-46 152
MS.gene048249.t1 AT1G09030 61.458 96 37 0 17 112 3 98 5.85e-43 140
MS.gene048249.t1 AT5G08190 34.286 105 63 2 13 113 7 109 1.92e-17 75.5
MS.gene048249.t1 AT5G23090 32.381 105 65 2 13 113 7 109 8.25e-17 73.6
MS.gene048249.t1 AT5G08190 37.349 83 52 0 13 95 7 89 1.99e-16 72.8
MS.gene048249.t1 AT5G23090 33.000 100 61 2 13 108 7 104 6.79e-16 71.2
MS.gene048249.t1 AT5G23090 33.000 100 61 2 13 108 7 104 6.79e-16 71.2
MS.gene048249.t1 AT5G23090 33.000 100 61 2 13 108 7 104 6.79e-16 71.2
MS.gene048249.t1 AT5G23090 32.911 79 47 2 34 108 15 91 2.48e-11 58.9

Find 39 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGGTAGTGGTGGAGTTTA+TGG 0.223086 2.3:-62569085 MS.gene048249:CDS
TCAACGGTGATGATCTTCTT+TGG 0.252720 2.3:-62569237 MS.gene048249:CDS
TTTGAGATCTTTGCGTTTGC+TGG 0.274169 2.3:+62569358 None:intergenic
ATCCTACTCACGTTTGCTAT+TGG 0.294063 2.3:+62569397 None:intergenic
CGTGAGTAGGATCATGAAAA+AGG 0.331544 2.3:-62569386 MS.gene048249:CDS
GGGAGTGGATCACCATCTTC+TGG 0.352082 2.3:-62569001 MS.gene048249:CDS
GGACATAATATGTATGGATC+TGG 0.358939 2.3:-62569022 MS.gene048249:CDS
GAGTTCATCAGTTTCATAAC+AGG 0.366706 2.3:-62569301 MS.gene048249:CDS
CTTTGGGCTATGACAACTCT+TGG 0.376889 2.3:-62569220 MS.gene048249:CDS
CAACGGTGATGATCTTCTTT+GGG 0.389396 2.3:-62569236 MS.gene048249:CDS
GGAGAGAAGAGTGCTATGAT+TGG 0.411557 2.3:-62569139 MS.gene048249:CDS
CAGGTTGCAGAGAGCAAGAT+AGG 0.412786 2.3:-62569426 MS.gene048249:CDS
GAGTCAGGAGGTGGTCAAAC+AGG 0.413478 2.3:-62569445 MS.gene048249:CDS
AGTGGTGGAGTTTATGGTCA+TGG 0.452362 2.3:-62569079 MS.gene048249:CDS
GGAGTTTATGGTCATGGAGT+TGG 0.458217 2.3:-62569073 MS.gene048249:CDS
CGAGTACTCCTTCCAGAAGA+TGG 0.483647 2.3:+62568989 None:intergenic
AGAAGAGTGCTATGATTGGT+AGG 0.483869 2.3:-62569135 MS.gene048249:CDS
ATCATCATCATCATAGAAGA+TGG 0.485382 2.3:+62569046 None:intergenic
ATCTTCTATGATGATGATGA+TGG 0.489435 2.3:-62569044 MS.gene048249:CDS
GGTAGGAGTGATCAGAGAGA+TGG 0.493822 2.3:-62569118 MS.gene048249:CDS
GGAAATGTTGGTGAGGGTAG+TGG 0.495110 2.3:-62569097 MS.gene048249:CDS
TTTGAGTAAGTATAGAGAGA+TGG 0.496858 2.3:-62569164 MS.gene048249:CDS
ATGATGGGACATAATATGTA+TGG 0.500614 2.3:-62569028 MS.gene048249:CDS
GCTGAATCAGACAATGAGTC+AGG 0.509383 2.3:-62569460 MS.gene048249:CDS
GATCAGAGAGATGGAAATGT+TGG 0.512395 2.3:-62569109 MS.gene048249:CDS
GACATAATATGTATGGATCT+GGG 0.545156 2.3:-62569021 MS.gene048249:CDS
AGAGATGGAAATGTTGGTGA+GGG 0.549342 2.3:-62569103 MS.gene048249:CDS
ATAAGTGTCAGAAAGAGAAG+AGG 0.567471 2.3:-62569267 MS.gene048249:CDS
AGTAAGTATAGAGAGATGGA+AGG 0.568189 2.3:-62569160 MS.gene048249:CDS
AATGTTGGTGAGGGTAGTGG+TGG 0.579830 2.3:-62569094 MS.gene048249:CDS
AATATGTATGGATCTGGGAG+TGG 0.582558 2.3:-62569016 MS.gene048249:CDS
TTCCAATAGCAAACGTGAGT+AGG 0.595976 2.3:-62569399 MS.gene048249:CDS
TCAGACAATGAGTCAGGAGG+TGG 0.599898 2.3:-62569454 MS.gene048249:CDS
TTACTCAAATAAATCTTGAG+TGG 0.610816 2.3:+62569178 None:intergenic
GAGAAGAGGAAAACAATCAA+CGG 0.615125 2.3:-62569253 MS.gene048249:CDS
GAGAGATGGAAATGTTGGTG+AGG 0.620088 2.3:-62569104 MS.gene048249:CDS
GTGGATCACCATCTTCTGGA+AGG 0.624829 2.3:-62568997 MS.gene048249:CDS
TCTTCTATGATGATGATGAT+GGG 0.641124 2.3:-62569043 MS.gene048249:CDS
GAATCAGACAATGAGTCAGG+AGG 0.682591 2.3:-62569457 MS.gene048249:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTCTTTTTATTTTTTG+TGG - chr2.3:62569033-62569052 MS.gene048249:CDS 10.0%
!!! TAATTTTTTTTTGTTCATTA+AGG - chr2.3:62569220-62569239 MS.gene048249:CDS 10.0%
!!! TTTTTCTTTTTATTTTTTGT+GGG - chr2.3:62569034-62569053 MS.gene048249:CDS 10.0%
!!! TTTAAAGTTTAAAAAGGAAA+CGG + chr2.3:62569440-62569459 None:intergenic 15.0%
!! AAAACATACCAATTAATAAC+AGG + chr2.3:62569292-62569311 None:intergenic 20.0%
!! AAATTGCAACAATATATCTA+GGG + chr2.3:62568951-62568970 None:intergenic 20.0%
!! ATTTCTTTCAGTTTAATCAT+AGG + chr2.3:62568836-62568855 None:intergenic 20.0%
!! GTTTATGAAAATTAACATTG+TGG + chr2.3:62569251-62569270 None:intergenic 20.0%
!! TAAATTGCAACAATATATCT+AGG + chr2.3:62568952-62568971 None:intergenic 20.0%
!! TAACAATTCCTGTTATTAAT+TGG - chr2.3:62569281-62569300 MS.gene048249:CDS 20.0%
!! TAACAGGAATTGTTATAAAT+AGG + chr2.3:62569276-62569295 None:intergenic 20.0%
!!! AACCTGTTTAAAGTTTAAAA+AGG + chr2.3:62569446-62569465 None:intergenic 20.0%
!!! ATAGTCTAGTTTCTAATTAA+AGG + chr2.3:62569160-62569179 None:intergenic 20.0%
!!! TTCCTTTTTAAACTTTAAAC+AGG - chr2.3:62569441-62569460 MS.gene048249:CDS 20.0%
!!! TTTTTTTGTTCATTAAGGAA+AGG - chr2.3:62569225-62569244 MS.gene048249:CDS 20.0%
! AGTATTTAGATGAGATAACT+CGG + chr2.3:62568859-62568878 None:intergenic 25.0%
! CTAATCACATTTAGTTATGA+TGG + chr2.3:62569409-62569428 None:intergenic 25.0%
! TACTCAATTCTAACTTCAAT+GGG + chr2.3:62569198-62569217 None:intergenic 25.0%
! TTACTCAAATAAATCTTGAG+TGG + chr2.3:62568546-62568565 None:intergenic 25.0%
! TTATCAACATGTTTCGAAAA+TGG - chr2.3:62569347-62569366 MS.gene048249:CDS 25.0%
! TTATCTCATCTAAATACTCT+TGG - chr2.3:62568861-62568880 MS.gene048249:intron 25.0%
!!! GCAATTTAATTTGTTGTTGA+GGG - chr2.3:62568964-62568983 MS.gene048249:intron 25.0%
!!! GTTTTGATCACACAATATAT+AGG - chr2.3:62569307-62569326 MS.gene048249:CDS 25.0%
!!! TGCAATTTAATTTGTTGTTG+AGG - chr2.3:62568963-62568982 MS.gene048249:intron 25.0%
!!! TTCTTTTTATTTTTTGTGGG+AGG - chr2.3:62569037-62569056 MS.gene048249:CDS 25.0%
ATCATCATCATCATAGAAGA+TGG + chr2.3:62568678-62568697 None:intergenic 30.0%
CTACTCAATTCTAACTTCAA+TGG + chr2.3:62569199-62569218 None:intergenic 30.0%
GACATAATATGTATGGATCT+GGG - chr2.3:62568700-62568719 MS.gene048249:intron 30.0%
GATCAATGTAACAAAGAAGT+AGG + chr2.3:62569129-62569148 None:intergenic 30.0%
TGATCACACAATATATAGGT+TGG - chr2.3:62569311-62569330 MS.gene048249:CDS 30.0%
TTTGAGTAAGTATAGAGAGA+TGG - chr2.3:62568557-62568576 MS.gene048249:intron 30.0%
! ATCTTCTATGATGATGATGA+TGG - chr2.3:62568677-62568696 MS.gene048249:intron 30.0%
! ATGATGGGACATAATATGTA+TGG - chr2.3:62568693-62568712 MS.gene048249:intron 30.0%
! TCTTCTATGATGATGATGAT+GGG - chr2.3:62568678-62568697 MS.gene048249:intron 30.0%
AGTAAGTATAGAGAGATGGA+AGG - chr2.3:62568561-62568580 MS.gene048249:intron 35.0%
ATAAGTGTCAGAAAGAGAAG+AGG - chr2.3:62568454-62568473 MS.gene048249:intron 35.0%
GAGAAGAGGAAAACAATCAA+CGG - chr2.3:62568468-62568487 MS.gene048249:intron 35.0%
GAGTTCATCAGTTTCATAAC+AGG - chr2.3:62568420-62568439 MS.gene048249:intron 35.0%
GGACATAATATGTATGGATC+TGG - chr2.3:62568699-62568718 MS.gene048249:intron 35.0%
GTACAGTGAAACATTATGGA+TGG - chr2.3:62568986-62569005 MS.gene048249:intron 35.0%
! AAACATTATGGATGGTGGTT+TGG - chr2.3:62568994-62569013 MS.gene048249:intron 35.0%
AATACTCTTGGCTAGACAAC+AGG - chr2.3:62568873-62568892 MS.gene048249:intron 40.0%
AATATGTATGGATCTGGGAG+TGG - chr2.3:62568705-62568724 MS.gene048249:intron 40.0%
CAACGGTGATGATCTTCTTT+GGG - chr2.3:62568485-62568504 MS.gene048249:intron 40.0%
CAGTGAAACATTATGGATGG+TGG - chr2.3:62568989-62569008 MS.gene048249:intron 40.0%
CGTGAGTAGGATCATGAAAA+AGG - chr2.3:62568335-62568354 MS.gene048249:intron 40.0%
GATCAGAGAGATGGAAATGT+TGG - chr2.3:62568612-62568631 MS.gene048249:intron 40.0%
TCAACGGTGATGATCTTCTT+TGG - chr2.3:62568484-62568503 MS.gene048249:intron 40.0%
TTCCAATAGCAAACGTGAGT+AGG - chr2.3:62568322-62568341 MS.gene048249:intron 40.0%
! AGAGATGGAAATGTTGGTGA+GGG - chr2.3:62568618-62568637 MS.gene048249:intron 40.0%
! GAGGGTACAGTGAAACATTA+TGG - chr2.3:62568982-62569001 MS.gene048249:intron 40.0%
! TTTGAGATCTTTGCGTTTGC+TGG + chr2.3:62568366-62568385 None:intergenic 40.0%
!! AGAAGAGTGCTATGATTGGT+AGG - chr2.3:62568586-62568605 MS.gene048249:intron 40.0%
!! ATCCTACTCACGTTTGCTAT+TGG + chr2.3:62568327-62568346 None:intergenic 40.0%
CTTTGGGCTATGACAACTCT+TGG - chr2.3:62568501-62568520 MS.gene048249:intron 45.0%
GAATCAGACAATGAGTCAGG+AGG - chr2.3:62568264-62568283 MS.gene048249:intron 45.0%
GAGAGATGGAAATGTTGGTG+AGG - chr2.3:62568617-62568636 MS.gene048249:intron 45.0%
GCTGAATCAGACAATGAGTC+AGG - chr2.3:62568261-62568280 MS.gene048249:CDS 45.0%
GGAGTTTATGGTCATGGAGT+TGG - chr2.3:62568648-62568667 MS.gene048249:intron 45.0%
! AGTGGTGGAGTTTATGGTCA+TGG - chr2.3:62568642-62568661 MS.gene048249:intron 45.0%
!! GGAGAGAAGAGTGCTATGAT+TGG - chr2.3:62568582-62568601 MS.gene048249:intron 45.0%
CAGGTTGCAGAGAGCAAGAT+AGG - chr2.3:62568295-62568314 MS.gene048249:intron 50.0%
CGAGTACTCCTTCCAGAAGA+TGG + chr2.3:62568735-62568754 None:intergenic 50.0%
GGTAGGAGTGATCAGAGAGA+TGG - chr2.3:62568603-62568622 MS.gene048249:intron 50.0%
GTGGATCACCATCTTCTGGA+AGG - chr2.3:62568724-62568743 MS.gene048249:intron 50.0%
TCAGACAATGAGTCAGGAGG+TGG - chr2.3:62568267-62568286 MS.gene048249:intron 50.0%
! AATGTTGGTGAGGGTAGTGG+TGG - chr2.3:62568627-62568646 MS.gene048249:intron 50.0%
! GAGGGTAGTGGTGGAGTTTA+TGG - chr2.3:62568636-62568655 MS.gene048249:intron 50.0%
! GGAAATGTTGGTGAGGGTAG+TGG - chr2.3:62568624-62568643 MS.gene048249:intron 50.0%
GAGTCAGGAGGTGGTCAAAC+AGG - chr2.3:62568276-62568295 MS.gene048249:intron 55.0%
GGGAGTGGATCACCATCTTC+TGG - chr2.3:62568720-62568739 MS.gene048249:intron 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 62568258 62569485 62568258 ID=MS.gene048249
chr2.3 mRNA 62568258 62569485 62568258 ID=MS.gene048249.t1;Parent=MS.gene048249
chr2.3 exon 62568996 62569485 62568996 ID=MS.gene048249.t1.exon1;Parent=MS.gene048249.t1
chr2.3 CDS 62568996 62569485 62568996 ID=cds.MS.gene048249.t1;Parent=MS.gene048249.t1
chr2.3 exon 62568258 62568280 62568258 ID=MS.gene048249.t1.exon2;Parent=MS.gene048249.t1
chr2.3 CDS 62568258 62568280 62568258 ID=cds.MS.gene048249.t1;Parent=MS.gene048249.t1
Gene Sequence

>MS.gene048249

ATGGCTGAATCAGACAATGAGTCAGGAGGTGGTCAAACAGGTTGCAGAGAGCAAGATAGGTTTCTTCCAATAGCAAACGTGAGTAGGATCATGAAAAAGGCTTTACCAGCAAACGCAAAGATCTCAAAAGAAGCAAAAGAAACAGTGCAAGAGTGTGTATCAGAGTTCATCAGTTTCATAACAGGAGAAGCTTCTGATAAGTGTCAGAAAGAGAAGAGGAAAACAATCAACGGTGATGATCTTCTTTGGGCTATGACAACTCTTGGATTTGAAGATTATGTTGAGCCACTCAAGATTTATTTGAGTAAGTATAGAGAGATGGAAGGAGAGAAGAGTGCTATGATTGGTAGGAGTGATCAGAGAGATGGAAATGTTGGTGAGGGTAGTGGTGGAGTTTATGGTCATGGAGTTGGAGTTCCATCTTCTATGATGATGATGATGGGACATAATATGTATGGATCTGGGAGTGGATCACCATCTTCTGGAAGGAGTACTCGATAGCAGAGACTAATCTCTCGAGTCAGATAATATCATAGTGAGCAGTAAACTTCTATCTTAAGAATACAAACTCAAGACCTATGATTAAACTGAAAGAAATCCGAGTTATCTCATCTAAATACTCTTGGCTAGACAACAGGTTTATGTATGCATATGTTTGATATAAATTCATGTATTTTTTAATTTAGAGTACCCTAGATATATTGTTGCAATTTAATTTGTTGTTGAGGGTACAGTGAAACATTATGGATGGTGGTTTGGAATTAATGCAAAAAGTATTTTTCTTTTTATTTTTTGTGGGAGGTGATAAATGTTGCATGTATAGTTTGCTTGTGTTGTGTACTATTTATGTCTTCATTGATTATATACACCTACTTCTTTGTTACATTGATCATATACTTCCTTTAATTAGAAACTAGACTATGAATTTATTGAAAAACCCATTGAAGTTAGAATTGAGTAGCTAATTTTTTTTTGTTCATTAAGGAAAGGCCACAATGTTAATTTTCATAAACTTCCTATTTATAACAATTCCTGTTATTAATTGGTATGTTTTGATCACACAATATATAGGTTGGTCTTATAAGTTTGTTATCAACATGTTTCGAAAATGGAAAACATTAAATATAGCGAGAATAATTATCACGAAGCCATCATAACTAAATGTGATTAGTTAGTTTGCCGTTTCCTTTTTAAACTTTAAACAGGTTTCGAGAGATTTCACGAATAA

Protein sequence

>MS.gene048249.t1

MAESDNESGGGQTGCREQDRFLPIANVSRIMKKALPANAKISKEAKETVQECVSEFISFITGEASDKCQKEKRKTINGDDLLWAMTTLGFEDYVEPLKIYLSKYREMEGEKSAMIGRSDQRDGNVGEGSGGVYGHGVGVPSSMMMMMGHNMYGSGSGSPSSGRSFERFHE