AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90866

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90866.t1 MTR_1g115290 86.184 152 20 1 37 187 1 152 1.04e-93 270
MS.gene90866.t1 MTR_4g045977 62.441 213 71 4 1 205 1 212 1.93e-88 266
MS.gene90866.t1 MTR_4g107170 54.709 223 82 5 1 205 1 222 2.33e-75 228
MS.gene90866.t1 MTR_2g049610 47.872 188 92 2 1 186 1 184 1.02e-57 182
MS.gene90866.t1 MTR_2g049530 45.078 193 94 4 3 193 5 187 3.99e-53 169
MS.gene90866.t1 MTR_2g049630 51.948 154 69 3 2 153 4 154 2.40e-47 159
MS.gene90866.t1 MTR_6g018920 37.975 158 96 1 1 156 1 158 4.82e-37 132
MS.gene90866.t1 MTR_1g114730 39.130 161 90 2 1 156 1 158 2.41e-35 127
MS.gene90866.t1 MTR_6g005440 36.842 171 106 2 1 169 1 171 1.58e-34 125
MS.gene90866.t1 MTR_6g005450 33.520 179 117 2 1 177 1 179 1.50e-32 120
MS.gene90866.t1 MTR_3g466980 27.841 176 111 5 1 166 1 170 1.59e-13 67.0
MS.gene90866.t1 MTR_3g467080 29.268 164 103 4 1 155 1 160 1.52e-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.gene90866.t1 AT5G55690 34.899 149 81 4 1 143 1 139 1.81e-16 76.3
MS.gene90866.t1 AT5G55690 34.899 149 81 4 1 143 1 139 1.81e-16 76.3
MS.gene90866.t1 AT5G58890 25.561 223 133 9 6 209 6 214 5.77e-12 63.9
MS.gene90866.t1 AT3G05860 40.845 71 39 1 1 71 1 68 3.44e-11 60.5
MS.gene90866.t1 AT1G22590 30.435 161 99 6 1 154 1 155 4.11e-11 59.7
MS.gene90866.t1 AT2G28700 36.842 76 44 2 1 76 1 72 4.70e-11 61.2
MS.gene90866.t1 AT3G05860 40.845 71 39 1 1 71 1 68 5.00e-11 60.8
MS.gene90866.t1 AT3G05860 40.845 71 39 1 1 71 1 68 5.49e-11 60.5

Find 39 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCCATGTTAACCAAATT+TGG 0.129467 1.4:-87399324 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 1.4:+87399311 MS.gene90866:CDS
CGGTCTTCGGGCCATGTTAT+TGG 0.257464 1.4:-87399135 None:intergenic
TTTACCATTGTACGGTCTTC+GGG 0.322440 1.4:-87399147 None:intergenic
GTTTACCATTGTACGGTCTT+CGG 0.346180 1.4:-87399148 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1.4:-87399214 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 1.4:-87399061 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 1.4:-87399062 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 1.4:-87399382 None:intergenic
ATGAGGCAAAACAGCATGAT+TGG 0.423445 1.4:-87399535 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 1.4:-87399456 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.436280 1.4:-87399572 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 1.4:-87399485 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 1.4:-87399277 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 1.4:-87399316 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 1.4:-87399312 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 1.4:-87399486 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 1.4:+87399060 MS.gene90866:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 1.4:+87399021 MS.gene90866:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 1.4:-87399552 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 1.4:+87399320 MS.gene90866:CDS
CTTTGAAATTAAGAAAGCTA+AGG 0.524267 1.4:+87399239 MS.gene90866:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 1.4:+87398952 None:intergenic
TCGTTGACATCAAATATCTT+GGG 0.530959 1.4:-87399213 None:intergenic
GCATGGAGTTTACCATTGTA+CGG 0.551323 1.4:-87399155 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 1.4:-87399172 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 1.4:+87399506 MS.gene90866:CDS
ATTGTGTATGATGATGATGA+TGG 0.576451 1.4:+87399099 MS.gene90866:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 1.4:+87399503 MS.gene90866:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 1.4:+87399413 MS.gene90866:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 1.4:+87399410 MS.gene90866:CDS
TGATGATGATGGCAATAATG+TGG 0.630960 1.4:+87399110 MS.gene90866:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 1.4:-87399350 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 1.4:+87399298 MS.gene90866:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 1.4:+87399124 MS.gene90866:CDS
GATGATGATGGCAATAATGT+GGG 0.668464 1.4:+87399111 MS.gene90866:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 1.4:-87399461 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 1.4:-87399462 None:intergenic
ATGGCCCGAAGACCGTACAA+TGG 0.720674 1.4:+87399143 MS.gene90866:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+AGG + chr1.4:87399239-87399258 MS.gene90866:CDS 25.0%
GATGATATCTTTATGCACTT+TGG - chr1.4:87399280-87399299 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG + chr1.4:87399298-87399317 MS.gene90866:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG - chr1.4:87399216-87399235 None:intergenic 30.0%
! ATTGTGTATGATGATGATGA+TGG + chr1.4:87399099-87399118 MS.gene90866:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG - chr1.4:87399555-87399574 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG + chr1.4:87399021-87399040 MS.gene90866:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG + chr1.4:87399124-87399143 MS.gene90866:CDS 35.0%
CAACATGTTGAAAAGTGAGA+TGG + chr1.4:87399410-87399429 MS.gene90866:CDS 35.0%
CATCAATCATGTTAGTGAGA+TGG + chr1.4:87399503-87399522 MS.gene90866:CDS 35.0%
GCATCCAAATTTGGTTAACA+TGG + chr1.4:87399320-87399339 MS.gene90866:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG - chr1.4:87399327-87399346 None:intergenic 35.0%
GTCGTTGACATCAAATATCT+TGG - chr1.4:87399217-87399236 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG - chr1.4:87399385-87399404 None:intergenic 35.0%
! AATCAAACAAGCTTTTGCAC+CGG - chr1.4:87399082-87399101 None:intergenic 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr1.4:87399488-87399507 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr1.4:87399489-87399508 None:intergenic 35.0%
!! GATGATGATGGCAATAATGT+GGG + chr1.4:87399111-87399130 MS.gene90866:CDS 35.0%
!! TGATGATGATGGCAATAATG+TGG + chr1.4:87399110-87399129 MS.gene90866:CDS 35.0%
ATGAGGCAAAACAGCATGAT+TGG - chr1.4:87399538-87399557 None:intergenic 40.0%
ATGCTATGTATGACACTGAG+TGG - chr1.4:87399465-87399484 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG - chr1.4:87399175-87399194 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG + chr1.4:87399506-87399525 MS.gene90866:CDS 40.0%
CATGTTGAAAAGTGAGATGG+TGG + chr1.4:87399413-87399432 MS.gene90866:CDS 40.0%
GCATGGAGTTTACCATTGTA+CGG - chr1.4:87399158-87399177 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG - chr1.4:87399319-87399338 None:intergenic 40.0%
GTTTACCATTGTACGGTCTT+CGG - chr1.4:87399151-87399170 None:intergenic 40.0%
TGCTATGTATGACACTGAGT+GGG - chr1.4:87399464-87399483 None:intergenic 40.0%
TTTACCATTGTACGGTCTTC+GGG - chr1.4:87399150-87399169 None:intergenic 40.0%
ACCAAATTTGGATGCCAGGT+TGG - chr1.4:87399315-87399334 None:intergenic 45.0%
ACCGGACTTGACAGTGTATT+GGG - chr1.4:87399064-87399083 None:intergenic 45.0%
TCCAACCTGGCATCCAAATT+TGG + chr1.4:87399311-87399330 MS.gene90866:CDS 45.0%
TCCCAATACACTGTCAAGTC+CGG + chr1.4:87399060-87399079 MS.gene90866:CDS 45.0%
CACCGGACTTGACAGTGTAT+TGG - chr1.4:87399065-87399084 None:intergenic 50.0%
CAGCACTTAAGTCTCTGAGC+TGG - chr1.4:87399353-87399372 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG - chr1.4:87399459-87399478 None:intergenic 50.0%
ATGGCCCGAAGACCGTACAA+TGG + chr1.4:87399143-87399162 MS.gene90866:CDS 55.0%
CGGTCTTCGGGCCATGTTAT+TGG - chr1.4:87399138-87399157 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 87398964 87399593 87398964 ID=MS.gene90866
chr1.4 mRNA 87398964 87399593 87398964 ID=MS.gene90866.t1;Parent=MS.gene90866
chr1.4 exon 87398964 87399593 87398964 ID=MS.gene90866.t1.exon1;Parent=MS.gene90866.t1
chr1.4 CDS 87398964 87399593 87398964 ID=cds.MS.gene90866.t1;Parent=MS.gene90866.t1
Gene Sequence

>MS.gene90866

ATGGGTCGTGGAAAAATAAATATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCCGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTAAGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGTTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>MS.gene90866.t1

MGRGKINMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKAKVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAVLPHNSSTNQLDLNI