AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068292

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068292.t1 MTR_4g013335 93.878 196 12 0 1 196 1 196 5.11e-130 363
MS.gene068292.t1 MTR_4g013350 76.263 198 44 2 1 196 1 197 7.71e-107 305
MS.gene068292.t1 MTR_4g013345 77.049 183 39 2 16 196 15 196 7.83e-103 295
MS.gene068292.t1 MTR_4g013325 81.095 201 31 4 1 196 1 199 5.69e-99 285
MS.gene068292.t1 MTR_4g013330 71.739 184 48 2 17 196 16 199 7.40e-99 285
MS.gene068292.t1 MTR_4g013320 70.109 184 51 2 17 196 16 199 9.35e-96 277
MS.gene068292.t1 MTR_4g013310 64.500 200 64 5 1 196 1 197 3.66e-85 250
MS.gene068292.t1 MTR_7g070390 68.235 170 52 2 29 196 23 192 1.63e-75 225
MS.gene068292.t1 MTR_4g013385 53.191 188 82 3 10 196 8 190 1.28e-67 205
MS.gene068292.t1 MTR_0433s0040 53.191 188 82 3 10 196 8 190 1.28e-67 205
MS.gene068292.t1 MTR_1g054525 53.061 196 80 3 3 196 7 192 1.17e-66 202
MS.gene068292.t1 MTR_4g013770 56.471 170 69 2 30 196 24 191 3.10e-61 189
MS.gene068292.t1 MTR_4g013355 47.619 189 82 4 10 196 6 179 5.39e-56 175
MS.gene068292.t1 MTR_7g093870 51.923 156 68 2 48 196 38 193 4.12e-54 172
MS.gene068292.t1 MTR_7g093820 45.699 186 96 4 14 196 11 194 8.73e-52 165
MS.gene068292.t1 MTR_7g093850 44.624 186 98 4 14 196 11 194 1.55e-51 164
MS.gene068292.t1 MTR_7g093790 43.976 166 89 3 34 196 27 191 1.87e-50 161
MS.gene068292.t1 MTR_7g093830 43.548 186 100 4 14 196 10 193 5.06e-50 160
MS.gene068292.t1 MTR_4g073950 47.368 152 77 1 48 196 41 192 2.43e-48 156
MS.gene068292.t1 MTR_4g078885 41.892 148 86 0 49 196 38 185 4.21e-40 135
MS.gene068292.t1 MTR_1g056370 44.000 150 82 2 48 195 36 185 5.64e-40 135
MS.gene068292.t1 MTR_3g105640 41.615 161 90 2 40 196 28 188 1.35e-39 134
MS.gene068292.t1 MTR_3g034030 41.892 148 86 0 49 196 38 185 1.58e-39 134
MS.gene068292.t1 MTR_3g105630 37.129 202 108 5 1 196 1 189 1.25e-38 131
MS.gene068292.t1 MTR_5g096120 42.105 152 82 2 51 196 38 189 2.90e-36 125
MS.gene068292.t1 MTR_4g122130 37.063 143 86 2 57 196 39 180 9.36e-26 98.2
MS.gene068292.t1 MTR_4g122110 37.324 142 87 1 57 196 39 180 1.70e-25 97.4
MS.gene068292.t1 MTR_4g049570 31.387 137 92 1 57 191 37 173 1.39e-16 74.3
MS.gene068292.t1 MTR_8g099115 31.429 140 85 3 50 179 34 172 2.67e-15 70.9
MS.gene068292.t1 MTR_4g049550 27.891 147 104 1 47 191 27 173 2.83e-15 70.9
MS.gene068292.t1 MTR_8g099135 29.252 147 98 2 38 179 23 168 4.24e-13 65.1
MS.gene068292.t1 MTR_1g046490 36.667 90 56 1 83 172 121 209 1.01e-12 65.1
MS.gene068292.t1 MTR_1g046800 36.667 90 56 1 83 172 135 223 4.59e-12 63.2
MS.gene068292.t1 MTR_1g046500 36.667 90 56 1 83 172 135 223 6.19e-12 62.8
MS.gene068292.t1 MTR_1g115510 31.405 121 72 4 84 195 235 353 8.98e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068292.t1 AT1G55210 57.368 190 78 2 7 196 1 187 2.04e-74 222
MS.gene068292.t1 AT1G55210 57.368 190 78 2 7 196 1 187 2.04e-74 222
MS.gene068292.t1 AT5G49040 53.061 196 84 2 3 196 2 191 1.19e-69 210
MS.gene068292.t1 AT1G58170 53.191 188 75 3 13 196 7 185 9.55e-68 205
MS.gene068292.t1 AT3G13650 52.577 194 83 4 3 196 2 186 1.50e-63 195
MS.gene068292.t1 AT5G49030 53.552 183 77 2 3 183 2 178 4.43e-57 194
MS.gene068292.t1 AT3G13662 56.849 146 62 1 37 182 27 171 7.34e-57 177
MS.gene068292.t1 AT1G65870 49.669 151 74 1 47 195 39 189 3.40e-49 158
MS.gene068292.t1 AT3G13660 61.864 118 45 0 79 196 8 125 1.78e-48 154
MS.gene068292.t1 AT2G21100 46.309 149 78 1 49 195 39 187 1.34e-45 149
MS.gene068292.t1 AT2G21100 46.309 149 78 1 49 195 39 187 1.34e-45 149
MS.gene068292.t1 AT1G22900 47.682 151 75 2 47 195 45 193 1.72e-44 146
MS.gene068292.t1 AT5G42510 45.333 150 78 2 48 195 35 182 1.33e-43 144
MS.gene068292.t1 AT5G42500 44.667 150 79 2 48 195 38 185 2.21e-42 141
MS.gene068292.t1 AT4G38700 38.974 195 101 7 10 196 6 190 2.06e-40 136
MS.gene068292.t1 AT2G21110 38.235 170 93 2 33 196 23 186 3.99e-37 127
MS.gene068292.t1 AT3G58090 47.706 109 57 0 87 195 163 271 7.32e-35 124
MS.gene068292.t1 AT4G23690 33.588 131 80 4 46 171 34 162 6.25e-15 70.1
MS.gene068292.t1 AT4G11210 27.841 176 109 3 8 179 5 166 6.42e-15 70.1
MS.gene068292.t1 AT4G11180 30.526 190 110 6 12 195 10 183 1.61e-14 68.9
MS.gene068292.t1 AT4G11190 26.230 183 114 4 1 179 1 166 2.50e-14 68.6
MS.gene068292.t1 AT1G64160 30.000 130 86 2 54 179 37 165 3.92e-13 65.1

Find 32 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAATACACTTACTATTT+TGG 0.028476 4.4:+86736901 MS.gene068292:CDS
AACTGTGGTCCTAAAGTTAA+AGG 0.173169 4.4:-86736770 None:intergenic
ATCAACAACCCTTTAACTTT+AGG 0.295206 4.4:+86736761 MS.gene068292:CDS
TTTACTGAAGGAAAGTATAA+TGG 0.321123 4.4:+86736881 MS.gene068292:CDS
CCTAACAACTTGCGATCTAT+TGG 0.340385 4.4:-86736605 None:intergenic
AGATGAAGTTGATTTGCTTA+TGG 0.369472 4.4:+86736844 MS.gene068292:CDS
CAAAGTGATGAGGAAATGTT+TGG 0.371335 4.4:-86736501 None:intergenic
CCAATAGATCGCAAGTTGTT+AGG 0.388446 4.4:+86736605 MS.gene068292:CDS
TTAAACTCTACCACTGCCTT+TGG 0.391230 4.4:+86736725 MS.gene068292:CDS
GGAATAACTATGATAGAAGT+AGG 0.416983 4.4:-86736695 None:intergenic
ATACCTGTTGTTGGTGGTAG+TGG 0.427470 4.4:+86736956 MS.gene068292:CDS
ACTGTGGTCCTAAAGTTAAA+GGG 0.432091 4.4:-86736769 None:intergenic
CAGTTGAATTCTAAGATTGT+TGG 0.460772 4.4:+86736788 MS.gene068292:CDS
AAGATTGTTGGAAAAGCTCA+AGG 0.501113 4.4:+86736800 MS.gene068292:CDS
AGTCCACTACCACCAACAAC+AGG 0.521446 4.4:-86736959 None:intergenic
GTTAGAGAGATACCTGTTGT+TGG 0.532991 4.4:+86736947 MS.gene068292:CDS
AGAGTGTGTTGCAAGATATG+AGG 0.539071 4.4:-86736535 None:intergenic
GTGGTAGAGTTTAATGATGG+TGG 0.541569 4.4:-86736716 None:intergenic
TATTGGCATGGCATAGTGAG+TGG 0.558746 4.4:+86736665 MS.gene068292:CDS
AGAGAGATACCTGTTGTTGG+TGG 0.564352 4.4:+86736950 MS.gene068292:CDS
GGAAGAAGAACAAAGTGATG+AGG 0.576295 4.4:-86736511 None:intergenic
TTCGATTGATCTCAAATCTG+AGG 0.584967 4.4:+86737021 MS.gene068292:CDS
GAATAACTATGATAGAAGTA+GGG 0.585056 4.4:-86736694 None:intergenic
GTGTGTTGCAAGATATGAGG+AGG 0.585643 4.4:-86736532 None:intergenic
GTGATGAGGAAATGTTTGGA+AGG 0.586936 4.4:-86736497 None:intergenic
GTTGTTAGGCCTAAACAAGA+AGG 0.591926 4.4:+86736619 MS.gene068292:CDS
GCGGACTGAACCAAAGGCAG+TGG 0.603551 4.4:-86736735 None:intergenic
GCAGTGGTAGAGTTTAATGA+TGG 0.613743 4.4:-86736719 None:intergenic
TTAAAGGGTTGTTGATCATG+CGG 0.621737 4.4:-86736754 None:intergenic
GATCATGCGGACTGAACCAA+AGG 0.627284 4.4:-86736741 None:intergenic
AGATTGTTGGAAAAGCTCAA+GGG 0.648311 4.4:+86736801 MS.gene068292:CDS
ACAATCTTAGAATTCAACTG+TGG 0.718096 4.4:-86736785 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATCATTTCAAATTTTAT+TGG + chr4.4:86736648-86736667 MS.gene068292:CDS 10.0%
! GAATAACTATGATAGAAGTA+GGG - chr4.4:86736697-86736716 None:intergenic 25.0%
!! CATTTCAAATTTTATTGGCA+TGG + chr4.4:86736653-86736672 MS.gene068292:CDS 25.0%
!! GGAAATACACTTACTATTTT+GGG + chr4.4:86736902-86736921 MS.gene068292:CDS 25.0%
!! TGGAAATACACTTACTATTT+TGG + chr4.4:86736901-86736920 MS.gene068292:CDS 25.0%
!! TTTACTGAAGGAAAGTATAA+TGG + chr4.4:86736881-86736900 MS.gene068292:CDS 25.0%
!!! ATGAATTTTGCTTTTACTGA+AGG + chr4.4:86736869-86736888 MS.gene068292:CDS 25.0%
ACAATCTTAGAATTCAACTG+TGG - chr4.4:86736788-86736807 None:intergenic 30.0%
GGAATAACTATGATAGAAGT+AGG - chr4.4:86736698-86736717 None:intergenic 30.0%
! ATCAACAACCCTTTAACTTT+AGG + chr4.4:86736761-86736780 MS.gene068292:CDS 30.0%
!! AGATGAAGTTGATTTGCTTA+TGG + chr4.4:86736844-86736863 MS.gene068292:CDS 30.0%
!! ATACACTTACTATTTTGGGA+AGG + chr4.4:86736906-86736925 MS.gene068292:CDS 30.0%
!! CAGTTGAATTCTAAGATTGT+TGG + chr4.4:86736788-86736807 MS.gene068292:CDS 30.0%
!! TTAGCTTTTCCTTCTTGTTT+AGG - chr4.4:86736631-86736650 None:intergenic 30.0%
AACTGTGGTCCTAAAGTTAA+AGG - chr4.4:86736773-86736792 None:intergenic 35.0%
AAGATTGTTGGAAAAGCTCA+AGG + chr4.4:86736800-86736819 MS.gene068292:CDS 35.0%
ACTGTGGTCCTAAAGTTAAA+GGG - chr4.4:86736772-86736791 None:intergenic 35.0%
AGATTGTTGGAAAAGCTCAA+GGG + chr4.4:86736801-86736820 MS.gene068292:CDS 35.0%
CAAAGTGATGAGGAAATGTT+TGG - chr4.4:86736504-86736523 None:intergenic 35.0%
TTAAAGGGTTGTTGATCATG+CGG - chr4.4:86736757-86736776 None:intergenic 35.0%
TTCGATTGATCTCAAATCTG+AGG + chr4.4:86737021-86737040 MS.gene068292:CDS 35.0%
! GACTTTTCAGATTTGCAAGA+GGG + chr4.4:86736978-86736997 MS.gene068292:CDS 35.0%
AGAGTGTGTTGCAAGATATG+AGG - chr4.4:86736538-86736557 None:intergenic 40.0%
CCAATAGATCGCAAGTTGTT+AGG + chr4.4:86736605-86736624 MS.gene068292:CDS 40.0%
CCTAACAACTTGCGATCTAT+TGG - chr4.4:86736608-86736627 None:intergenic 40.0%
GCAGTGGTAGAGTTTAATGA+TGG - chr4.4:86736722-86736741 None:intergenic 40.0%
GGAAGAAGAACAAAGTGATG+AGG - chr4.4:86736514-86736533 None:intergenic 40.0%
GTGATGAGGAAATGTTTGGA+AGG - chr4.4:86736500-86736519 None:intergenic 40.0%
GTGGTAGAGTTTAATGATGG+TGG - chr4.4:86736719-86736738 None:intergenic 40.0%
GTTAGAGAGATACCTGTTGT+TGG + chr4.4:86736947-86736966 MS.gene068292:CDS 40.0%
GTTGTTAGGCCTAAACAAGA+AGG + chr4.4:86736619-86736638 MS.gene068292:CDS 40.0%
TTAAACTCTACCACTGCCTT+TGG + chr4.4:86736725-86736744 MS.gene068292:CDS 40.0%
! GGACTTTTCAGATTTGCAAG+AGG + chr4.4:86736977-86736996 MS.gene068292:CDS 40.0%
AGAGAGATACCTGTTGTTGG+TGG + chr4.4:86736950-86736969 MS.gene068292:CDS 45.0%
GTGTGTTGCAAGATATGAGG+AGG - chr4.4:86736535-86736554 None:intergenic 45.0%
TATTGGCATGGCATAGTGAG+TGG + chr4.4:86736665-86736684 MS.gene068292:CDS 45.0%
!! ATACCTGTTGTTGGTGGTAG+TGG + chr4.4:86736956-86736975 MS.gene068292:CDS 45.0%
AGTCCACTACCACCAACAAC+AGG - chr4.4:86736962-86736981 None:intergenic 50.0%
! GATCATGCGGACTGAACCAA+AGG - chr4.4:86736744-86736763 None:intergenic 50.0%
! GCGGACTGAACCAAAGGCAG+TGG - chr4.4:86736738-86736757 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 86736494 86737084 86736494 ID=MS.gene068292
chr4.4 mRNA 86736494 86737084 86736494 ID=MS.gene068292.t1;Parent=MS.gene068292
chr4.4 exon 86736494 86737084 86736494 ID=MS.gene068292.t1.exon1;Parent=MS.gene068292.t1
chr4.4 CDS 86736494 86737084 86736494 ID=cds.MS.gene068292.t1;Parent=MS.gene068292.t1
Gene Sequence

>MS.gene068292

ATGCCTTCCAAACATTTCCTCATCACTTTGTTCTTCTTCCTCCTCATATCTTGCAACACACTCTCTGCTTCAACTTCATCAGAAAAAGAAGACACTTTTGATTTTGTTCGTCCAATAGATCGCAAGTTGTTAGGCCTAAACAAGAAGGAAAAGCTAAATCATTTCAAATTTTATTGGCATGGCATAGTGAGTGGAAAAAACCCTACTTCTATCATAGTTATTCCACCATCATTAAACTCTACCACTGCCTTTGGTTCAGTCCGCATGATCAACAACCCTTTAACTTTAGGACCACAGTTGAATTCTAAGATTGTTGGAAAAGCTCAAGGGTTCTATGCATCTGCATGCAAAGATGAAGTTGATTTGCTTATGGCTATGAATTTTGCTTTTACTGAAGGAAAGTATAATGGAAATACACTTACTATTTTGGGAAGGAATGCTGTTTTTCATAAAGTTAGAGAGATACCTGTTGTTGGTGGTAGTGGACTTTTCAGATTTGCAAGAGGGTATGCTGAAGCTAATACTCATTCGATTGATCTCAAATCTGAGGATGCTTGTGTAGAGTACAATGTTCATGTTTTTCACTATTAA
Protein sequence

>MS.gene068292.t1

MPSKHFLITLFFFLLISCNTLSASTSSEKEDTFDFVRPIDRKLLGLNKKEKLNHFKFYWHGIVSGKNPTSIIVIPPSLNSTTAFGSVRMINNPLTLGPQLNSKIVGKAQGFYASACKDEVDLLMAMNFAFTEGKYNGNTLTILGRNAVFHKVREIPVVGGSGLFRFARGYAEANTHSIDLKSEDACVEYNVHVFHY