AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99201

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99201.t1 MTR_5g017210 55.762 269 81 11 1 253 1 247 8.75e-64 199
MS.gene99201.t1 MTR_3g101810 56.109 221 63 9 21 214 40 253 1.88e-62 197
MS.gene99201.t1 MTR_8g093500 75.824 91 22 0 108 198 87 177 4.63e-46 155
MS.gene99201.t1 MTR_2g100490 52.027 148 62 4 91 229 242 389 1.03e-29 115
MS.gene99201.t1 MTR_8g015450 59.596 99 36 1 107 201 296 394 2.66e-27 108
MS.gene99201.t1 MTR_7g069590 66.667 60 20 0 141 200 32 91 8.48e-23 91.3
MS.gene99201.t1 MTR_5g079500 54.430 79 34 1 121 197 202 280 1.07e-19 86.7
MS.gene99201.t1 MTR_1g018090 60.714 56 22 0 142 197 281 336 4.80e-17 79.7
MS.gene99201.t1 MTR_1g106460 52.239 67 32 0 131 197 234 300 4.90e-17 79.3
MS.gene99201.t1 MTR_5g005110 62.963 54 20 0 144 197 233 286 6.64e-17 79.0
MS.gene99201.t1 MTR_1g106470 60.714 56 22 0 142 197 203 258 1.72e-16 77.4
MS.gene99201.t1 MTR_3g103030 55.556 63 28 0 135 197 229 291 4.43e-16 76.6
MS.gene99201.t1 MTR_1g080890 47.059 85 37 1 128 212 186 262 3.65e-15 74.3
MS.gene99201.t1 MTR_4g131160 52.778 72 26 1 142 213 203 266 1.01e-14 73.2
MS.gene99201.t1 MTR_4g131160 52.778 72 26 1 142 213 206 269 1.09e-14 73.2
MS.gene99201.t1 MTR_1g106480 64.444 45 16 0 153 197 87 131 1.81e-13 66.6
MS.gene99201.t1 MTR_2g067000 48.000 75 32 1 131 198 146 220 5.03e-13 67.8
MS.gene99201.t1 MTR_1g060700 57.407 54 23 0 145 198 357 410 2.61e-12 66.6
MS.gene99201.t1 MTR_4g033295 57.143 56 23 1 145 199 128 183 7.29e-12 63.2
MS.gene99201.t1 MTR_4g033295 57.407 54 22 1 145 197 128 181 1.99e-11 61.6
MS.gene99201.t1 MTR_2g089070 48.148 54 28 0 145 198 146 199 6.30e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99201.t1 AT5G67060 57.212 208 58 8 1 199 1 186 3.15e-50 165
MS.gene99201.t1 AT3G50330 55.769 208 67 7 17 216 11 201 6.57e-50 164
MS.gene99201.t1 AT5G67060 58.511 188 55 6 21 199 1 174 3.97e-48 159
MS.gene99201.t1 AT4G00120 68.750 96 27 1 110 202 87 182 4.13e-39 135
MS.gene99201.t1 AT3G21330 64.894 94 33 0 107 200 241 334 3.25e-36 132
MS.gene99201.t1 AT5G09750 76.667 90 21 0 108 197 92 181 1.70e-34 124
MS.gene99201.t1 AT5G01305 69.492 59 18 0 136 194 38 96 1.11e-21 89.0
MS.gene99201.t1 AT5G37800 35.542 166 78 5 35 197 124 263 1.46e-18 83.6
MS.gene99201.t1 AT5G43175 50.725 69 34 0 129 197 126 194 3.09e-18 81.3
MS.gene99201.t1 AT4G33880 59.677 62 25 0 136 197 267 328 3.23e-18 83.2
MS.gene99201.t1 AT1G66470 36.879 141 69 4 72 197 122 257 7.85e-18 81.3
MS.gene99201.t1 AT1G27740 52.941 68 32 0 130 197 162 229 8.23e-18 80.5
MS.gene99201.t1 AT2G14760 58.065 62 26 0 136 197 238 299 3.08e-17 80.1
MS.gene99201.t1 AT2G24260 41.071 112 47 3 133 226 28 138 1.75e-16 76.6
MS.gene99201.t1 AT2G24260 41.071 112 47 3 133 226 131 241 5.78e-16 76.6
MS.gene99201.t1 AT4G30980 41.584 101 51 1 131 231 126 218 1.28e-15 75.5
MS.gene99201.t1 AT4G30980 49.398 83 34 1 131 213 174 248 2.75e-15 74.7
MS.gene99201.t1 AT5G58010 47.674 86 36 2 132 216 96 173 1.50e-14 72.0
MS.gene99201.t1 AT2G14760 48.000 75 26 1 136 197 238 312 5.77e-14 70.9

Find 59 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGAAGCAGTGTCCATTT+TGG 0.223878 8.4:+26542622 None:intergenic
AATAATGTGAATTATAATTC+TGG 0.269339 8.4:-26542464 MS.gene99201:CDS
CTTCGGCGGCCTAACGGATT+CGG 0.285239 8.4:+26542754 None:intergenic
CACATTGGTGGTGGATTCAT+TGG 0.306846 8.4:-26542512 MS.gene99201:CDS
AAAGGTTGATCAGAGAATTC+AGG 0.327420 8.4:+26543064 None:intergenic
CAGTGTTGTTGGTGATTTCT+TGG 0.347528 8.4:+26543020 None:intergenic
GTGGAGATGATAGTGCATTT+TGG 0.349089 8.4:+26542978 None:intergenic
GTGTAGCTGCTAGGCATAGA+AGG 0.352095 8.4:-26542697 MS.gene99201:CDS
AAAGGATAAGTGAGAGGATA+AGG 0.357712 8.4:-26542673 MS.gene99201:CDS
TTCGGCGGCCTAACGGATTC+GGG 0.378261 8.4:+26542755 None:intergenic
AGTACCTGGTGGAACCAAAA+TGG 0.383832 8.4:-26542636 MS.gene99201:CDS
TAACTAGCTAAGCAATTGTT+TGG 0.384797 8.4:+26542394 None:intergenic
CCTTCTCTTCGGCGGCCTAA+CGG 0.391457 8.4:+26542748 None:intergenic
ATCTTCACATTCCTTCTCTT+CGG 0.392038 8.4:+26542737 None:intergenic
TGCCTAGCAGCTACACTTTG+TGG 0.400476 8.4:+26542704 None:intergenic
TCAATATTATTCAAACTTTG+TGG 0.420960 8.4:+26542959 None:intergenic
TAATTCTGGTTTGATGATGA+AGG 0.423318 8.4:-26542450 MS.gene99201:CDS
AAAGAATTCGACTGCGAGTA+AGG 0.432337 8.4:+26542854 None:intergenic
GATTCGGGATCGATATGTAT+AGG 0.452777 8.4:+26542770 None:intergenic
AAGGTTGATCAGAGAATTCA+GGG 0.455273 8.4:+26543065 None:intergenic
GCTAAGCAATTGTTTGGAAG+TGG 0.457304 8.4:+26542400 None:intergenic
GTTGGTGATTTCTTGGTAAG+TGG 0.468287 8.4:+26543027 None:intergenic
CCGTTAGGCCGCCGAAGAGA+AGG 0.485491 8.4:-26542748 MS.gene99201:CDS
AAATAATGGAACAGTGTTGT+TGG 0.485998 8.4:+26543009 None:intergenic
GATAGCAATGATGATGCAAA+TGG 0.487640 8.4:-26543095 MS.gene99201:CDS
GTGGAACCCACCATTTGAAA+AGG 0.490966 8.4:+26542419 None:intergenic
GTGGTGGGAGTGTTATAAAA+AGG 0.493586 8.4:+26543046 None:intergenic
ATATCGATCCCGAATCCGTT+AGG 0.506193 8.4:-26542763 MS.gene99201:CDS
GTGATTTCTTGGTAAGTGGT+GGG 0.510263 8.4:+26543031 None:intergenic
GTAAGGAAATGATGAAGAGT+TGG 0.515713 8.4:+26542871 None:intergenic
TTCACACGTTGGAACAAGTA+GGG 0.518979 8.4:-26542556 MS.gene99201:CDS
GAATTCGATGGCAGCGATGA+GGG 0.520911 8.4:-26542822 MS.gene99201:CDS
GTGTGATATTCAAGTGTTGT+TGG 0.525349 8.4:+26542909 None:intergenic
GGTGATTTCTTGGTAAGTGG+TGG 0.542766 8.4:+26543030 None:intergenic
AATGGACACTGCTTCAATGT+TGG 0.562917 8.4:-26542618 MS.gene99201:CDS
GAAGAGTTGGTTTGAAGAGA+TGG 0.565464 8.4:+26542884 None:intergenic
TTCACATTCCTTCTCTTCGG+CGG 0.566092 8.4:+26542740 None:intergenic
ATTGGTGGTGGATTCATTGG+AGG 0.568963 8.4:-26542509 MS.gene99201:CDS
GAAGGGAAAGGATAAGTGAG+AGG 0.571416 8.4:-26542679 MS.gene99201:CDS
TTGGTGGTGGATTCATTGGA+GGG 0.580871 8.4:-26542508 MS.gene99201:CDS
TTGACATTGGAGTGTAGAAG+TGG 0.581516 8.4:+26542935 None:intergenic
AATTCTGGTTTGATGATGAA+GGG 0.584821 8.4:-26542449 MS.gene99201:CDS
AGTGAAAACTGACGGAAGCA+TGG 0.586477 8.4:-26543122 MS.gene99201:CDS
GTTCACACGTTGGAACAAGT+AGG 0.594798 8.4:-26542557 MS.gene99201:CDS
TCACAATCACACATTGGTGG+TGG 0.595725 8.4:-26542521 MS.gene99201:CDS
GAAGAAACAAGTTCACACGT+TGG 0.614768 8.4:-26542567 MS.gene99201:CDS
AGAATTCGATGGCAGCGATG+AGG 0.615506 8.4:-26542823 MS.gene99201:CDS
TGTAGCTGCTAGGCATAGAA+GGG 0.616015 8.4:-26542696 MS.gene99201:CDS
CTGCTAGGCATAGAAGGGAA+AGG 0.619057 8.4:-26542691 MS.gene99201:CDS
ATCCACAAAGTGTAGCTGCT+AGG 0.619623 8.4:-26542706 MS.gene99201:CDS
AAGGAATGTGAAGATATCAA+AGG 0.620019 8.4:-26542729 MS.gene99201:CDS
GTGTTGTTGGAAATTGACAT+TGG 0.623317 8.4:+26542922 None:intergenic
GTCGACATAGTGAAAACTGA+CGG 0.646360 8.4:-26543130 MS.gene99201:CDS
GAGTTGGTTTGAAGAGATGG+TGG 0.649591 8.4:+26542887 None:intergenic
AATAGATCACAATCACACAT+TGG 0.653131 8.4:-26542527 MS.gene99201:CDS
AGATCACAATCACACATTGG+TGG 0.659957 8.4:-26542524 MS.gene99201:CDS
TTGCAAAGATTAGTACCTGG+TGG 0.666600 8.4:-26542647 MS.gene99201:CDS
TCACACGTTGGAACAAGTAG+GGG 0.679972 8.4:-26542555 MS.gene99201:CDS
ATATTGCAAAGATTAGTACC+TGG 0.688702 8.4:-26542650 MS.gene99201:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATGTGAATTATAATTC+TGG - chr8.4:26543069-26543088 MS.gene99201:CDS 15.0%
!! TCAATATTATTCAAACTTTG+TGG + chr8.4:26542577-26542596 None:intergenic 20.0%
!!! TTTTGGTTAAGGTTAAATAA+TGG + chr8.4:26542541-26542560 None:intergenic 20.0%
!!! TTTTGAAAAGAAGAATTCGA+TGG - chr8.4:26542699-26542718 MS.gene99201:CDS 25.0%
AAGGAATGTGAAGATATCAA+AGG - chr8.4:26542804-26542823 MS.gene99201:CDS 30.0%
AATAGATCACAATCACACAT+TGG - chr8.4:26543006-26543025 MS.gene99201:CDS 30.0%
ATATTGCAAAGATTAGTACC+TGG - chr8.4:26542883-26542902 MS.gene99201:CDS 30.0%
! AAATAATGGAACAGTGTTGT+TGG + chr8.4:26542527-26542546 None:intergenic 30.0%
!! AATTCTGGTTTGATGATGAA+GGG - chr8.4:26543084-26543103 MS.gene99201:CDS 30.0%
!! TAATTCTGGTTTGATGATGA+AGG - chr8.4:26543083-26543102 MS.gene99201:CDS 30.0%
!!! ATGATAGTGCATTTTGGTTA+AGG + chr8.4:26542552-26542571 None:intergenic 30.0%
AAAGGATAAGTGAGAGGATA+AGG - chr8.4:26542860-26542879 MS.gene99201:CDS 35.0%
ATCTTCACATTCCTTCTCTT+CGG + chr8.4:26542799-26542818 None:intergenic 35.0%
GTAAGGAAATGATGAAGAGT+TGG + chr8.4:26542665-26542684 None:intergenic 35.0%
! AAAGGTTGATCAGAGAATTC+AGG + chr8.4:26542472-26542491 None:intergenic 35.0%
! AAGGTTGATCAGAGAATTCA+GGG + chr8.4:26542471-26542490 None:intergenic 35.0%
! GATAGCAATGATGATGCAAA+TGG - chr8.4:26542438-26542457 MS.gene99201:CDS 35.0%
! GTGTGATATTCAAGTGTTGT+TGG + chr8.4:26542627-26542646 None:intergenic 35.0%
! GTGTTGTTGGAAATTGACAT+TGG + chr8.4:26542614-26542633 None:intergenic 35.0%
! TGTCAACCTTTTCAAATGGT+GGG - chr8.4:26543108-26543127 MS.gene99201:CDS 35.0%
! TTGTCAACCTTTTCAAATGG+TGG - chr8.4:26543107-26543126 MS.gene99201:CDS 35.0%
AAAGAATTCGACTGCGAGTA+AGG + chr8.4:26542682-26542701 None:intergenic 40.0%
AATGGACACTGCTTCAATGT+TGG - chr8.4:26542915-26542934 MS.gene99201:CDS 40.0%
AGATCACAATCACACATTGG+TGG - chr8.4:26543009-26543028 MS.gene99201:CDS 40.0%
GAAGAAACAAGTTCACACGT+TGG - chr8.4:26542966-26542985 MS.gene99201:CDS 40.0%
GATTCGGGATCGATATGTAT+AGG + chr8.4:26542766-26542785 None:intergenic 40.0%
GCTAAGCAATTGTTTGGAAG+TGG + chr8.4:26543136-26543155 None:intergenic 40.0%
GTCGACATAGTGAAAACTGA+CGG - chr8.4:26542403-26542422 MS.gene99201:CDS 40.0%
GTGATTTCTTGGTAAGTGGT+GGG + chr8.4:26542505-26542524 None:intergenic 40.0%
TTCACACGTTGGAACAAGTA+GGG - chr8.4:26542977-26542996 MS.gene99201:CDS 40.0%
TTGACATTGGAGTGTAGAAG+TGG + chr8.4:26542601-26542620 None:intergenic 40.0%
TTGCAAAGATTAGTACCTGG+TGG - chr8.4:26542886-26542905 MS.gene99201:CDS 40.0%
! CATTGAAGCAGTGTCCATTT+TGG + chr8.4:26542914-26542933 None:intergenic 40.0%
! GGGTTGTCAACCTTTTCAAA+TGG - chr8.4:26543104-26543123 MS.gene99201:CDS 40.0%
!! CAGTGTTGTTGGTGATTTCT+TGG + chr8.4:26542516-26542535 None:intergenic 40.0%
!! GAAGAGTTGGTTTGAAGAGA+TGG + chr8.4:26542652-26542671 None:intergenic 40.0%
!! GTGGAGATGATAGTGCATTT+TGG + chr8.4:26542558-26542577 None:intergenic 40.0%
!! GTGGTGGGAGTGTTATAAAA+AGG + chr8.4:26542490-26542509 None:intergenic 40.0%
!! GTTGGTGATTTCTTGGTAAG+TGG + chr8.4:26542509-26542528 None:intergenic 40.0%
AGTACCTGGTGGAACCAAAA+TGG - chr8.4:26542897-26542916 MS.gene99201:CDS 45.0%
AGTGAAAACTGACGGAAGCA+TGG - chr8.4:26542411-26542430 MS.gene99201:CDS 45.0%
ATATCGATCCCGAATCCGTT+AGG - chr8.4:26542770-26542789 MS.gene99201:CDS 45.0%
ATCCACAAAGTGTAGCTGCT+AGG - chr8.4:26542827-26542846 MS.gene99201:CDS 45.0%
GAAGGGAAAGGATAAGTGAG+AGG - chr8.4:26542854-26542873 MS.gene99201:CDS 45.0%
GGTGATTTCTTGGTAAGTGG+TGG + chr8.4:26542506-26542525 None:intergenic 45.0%
GTGGAACCCACCATTTGAAA+AGG + chr8.4:26543117-26543136 None:intergenic 45.0%
GTTCACACGTTGGAACAAGT+AGG - chr8.4:26542976-26542995 MS.gene99201:CDS 45.0%
TCACAATCACACATTGGTGG+TGG - chr8.4:26543012-26543031 MS.gene99201:CDS 45.0%
TCACACGTTGGAACAAGTAG+GGG - chr8.4:26542978-26542997 MS.gene99201:CDS 45.0%
TGTAGCTGCTAGGCATAGAA+GGG - chr8.4:26542837-26542856 MS.gene99201:CDS 45.0%
TTCACATTCCTTCTCTTCGG+CGG + chr8.4:26542796-26542815 None:intergenic 45.0%
!! ATTGGTGGTGGATTCATTGG+AGG - chr8.4:26543024-26543043 MS.gene99201:CDS 45.0%
!! CACATTGGTGGTGGATTCAT+TGG - chr8.4:26543021-26543040 MS.gene99201:CDS 45.0%
!! GAGTTGGTTTGAAGAGATGG+TGG + chr8.4:26542649-26542668 None:intergenic 45.0%
!! TTGGTGGTGGATTCATTGGA+GGG - chr8.4:26543025-26543044 MS.gene99201:CDS 45.0%
AGAATTCGATGGCAGCGATG+AGG - chr8.4:26542710-26542729 MS.gene99201:CDS 50.0%
CTGCTAGGCATAGAAGGGAA+AGG - chr8.4:26542842-26542861 MS.gene99201:CDS 50.0%
GAATTCGATGGCAGCGATGA+GGG - chr8.4:26542711-26542730 MS.gene99201:CDS 50.0%
GTGTAGCTGCTAGGCATAGA+AGG - chr8.4:26542836-26542855 MS.gene99201:CDS 50.0%
TGCCTAGCAGCTACACTTTG+TGG + chr8.4:26542832-26542851 None:intergenic 50.0%
!!! GTGTCCATTTTGGTTCCACC+AGG + chr8.4:26542904-26542923 None:intergenic 50.0%
CCTTCTCTTCGGCGGCCTAA+CGG + chr8.4:26542788-26542807 None:intergenic 60.0%
!! CTTCGGCGGCCTAACGGATT+CGG + chr8.4:26542782-26542801 None:intergenic 60.0%
!! TTCGGCGGCCTAACGGATTC+GGG + chr8.4:26542781-26542800 None:intergenic 60.0%
CCGTTAGGCCGCCGAAGAGA+AGG - chr8.4:26542785-26542804 MS.gene99201:CDS 65.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 26542397 26543158 26542397 ID=MS.gene99201
chr8.4 mRNA 26542397 26543158 26542397 ID=MS.gene99201.t1;Parent=MS.gene99201
chr8.4 exon 26542397 26543158 26542397 ID=MS.gene99201.t1.exon1;Parent=MS.gene99201.t1
chr8.4 CDS 26542397 26543158 26542397 ID=cds.MS.gene99201.t1;Parent=MS.gene99201.t1
Gene Sequence

>MS.gene99201

ATGGATGTCGACATAGTGAAAACTGACGGAAGCATGGACATGATAGCAATGATGATGCAAATGGAAAAGTTCCCTGAATTCTCTGATCAACCTTTTTATAACACTCCCACCACTTACCAAGAAATCACCAACAACACTGTTCCATTATTTAACCTTAACCAAAATGCACTATCATCTCCACAAAGTTTGAATAATATTGATCCACTTCTACACTCCAATGTCAATTTCCAACAACACTTGAATATCACACCACCATCTCTTCAAACCAACTCTTCATCATTTCCTTACTCGCAGTCGAATTCTTTTGAAAAGAAGAATTCGATGGCAGCGATGAGGGAAATGATATTTAGAATAGCAGTGATGCAACCTATACATATCGATCCCGAATCCGTTAGGCCGCCGAAGAGAAGGAATGTGAAGATATCAAAGGATCCACAAAGTGTAGCTGCTAGGCATAGAAGGGAAAGGATAAGTGAGAGGATAAGGATATTGCAAAGATTAGTACCTGGTGGAACCAAAATGGACACTGCTTCAATGTTGGATGAAGCTATACATTATGTGAAGTTTTTGAAGAAACAAGTTCACACGTTGGAACAAGTAGGGGCTAATAATAGATCACAATCACACATTGGTGGTGGATTCATTGGAGGGAATAATATGATGAACAATTTTAATAATGTGAATTATAATTCTGGTTTGATGATGAAGGGTTGTCAACCTTTTCAAATGGTGGGTTCCACTTCCAAACAATTGCTTAGCTAG
Protein sequence

>MS.gene99201.t1

MDVDIVKTDGSMDMIAMMMQMEKFPEFSDQPFYNTPTTYQEITNNTVPLFNLNQNALSSPQSLNNIDPLLHSNVNFQQHLNITPPSLQTNSSSFPYSQSNSFEKKNSMAAMREMIFRIAVMQPIHIDPESVRPPKRRNVKISKDPQSVAARHRRERISERIRILQRLVPGGTKMDTASMLDEAIHYVKFLKKQVHTLEQVGANNRSQSHIGGGFIGGNNMMNNFNNVNYNSGLMMKGCQPFQMVGSTSKQLLS