AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene037406

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037406.t1 MTR_1g115290 84.868 152 21 1 37 186 1 152 7.93e-92 266
MS.gene037406.t1 MTR_4g045977 62.736 212 71 3 1 204 1 212 2.11e-90 271
MS.gene037406.t1 MTR_4g107170 54.505 222 83 4 1 204 1 222 2.13e-76 230
MS.gene037406.t1 MTR_2g049610 48.128 187 92 2 1 185 1 184 1.34e-58 184
MS.gene037406.t1 MTR_2g049530 44.503 191 97 3 3 192 5 187 4.07e-53 169
MS.gene037406.t1 MTR_2g049630 51.316 152 72 2 2 152 4 154 2.63e-47 159
MS.gene037406.t1 MTR_6g018920 37.342 158 96 1 1 155 1 158 1.46e-36 130
MS.gene037406.t1 MTR_1g114730 37.975 158 95 1 1 155 1 158 6.36e-35 126
MS.gene037406.t1 MTR_6g005440 36.257 171 106 1 1 168 1 171 3.36e-34 124
MS.gene037406.t1 MTR_6g005450 32.961 179 117 1 1 176 1 179 1.19e-32 120
MS.gene037406.t1 MTR_3g466980 27.429 175 112 5 1 165 1 170 8.13e-13 65.1
MS.gene037406.t1 MTR_3g467080 29.448 163 103 4 1 154 1 160 1.75e-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.gene037406.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.92e-16 75.1
MS.gene037406.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.92e-16 75.1
MS.gene037406.t1 AT1G22590 30.625 160 99 6 1 153 1 155 2.42e-11 60.1
MS.gene037406.t1 AT3G05860 41.429 70 39 1 1 70 1 68 5.05e-11 60.1
MS.gene037406.t1 AT2G28700 37.333 75 44 2 1 75 1 72 5.18e-11 61.2
MS.gene037406.t1 AT5G58890 25.561 223 132 9 6 208 6 214 5.73e-11 60.8
MS.gene037406.t1 AT3G05860 41.429 70 39 1 1 70 1 68 7.06e-11 60.5
MS.gene037406.t1 AT3G05860 41.429 70 39 1 1 70 1 68 7.46e-11 60.1

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 1.3:-78435389 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 1.3:+78435376 MS.gene037406:CDS
CGGTCTTCGGGCCATGTTAT+TGG 0.257464 1.3:-78435200 None:intergenic
TTTACCATTGTACGGTCTTC+GGG 0.322440 1.3:-78435212 None:intergenic
GTTTACCATTGTACGGTCTT+CGG 0.346180 1.3:-78435213 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1.3:-78435279 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 1.3:-78435129 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 1.3:-78435130 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 1.3:-78435447 None:intergenic
ATGAGGCAAAACAGCATGAT+TGG 0.423445 1.3:-78435600 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 1.3:-78435521 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.436280 1.3:-78435637 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 1.3:-78435550 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 1.3:-78435342 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 1.3:-78435381 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 1.3:-78435377 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 1.3:-78435551 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 1.3:+78435128 MS.gene037406:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 1.3:+78435089 MS.gene037406:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 1.3:-78435617 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 1.3:+78435385 MS.gene037406:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 1.3:+78435020 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.527956 1.3:+78435164 MS.gene037406:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 1.3:-78435278 None:intergenic
CTTTGAAATTAAGAAAGCTA+CGG 0.543256 1.3:+78435304 MS.gene037406:CDS
GCATGGAGTTTACCATTGTA+CGG 0.551323 1.3:-78435220 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 1.3:-78435237 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 1.3:+78435571 MS.gene037406:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 1.3:+78435568 MS.gene037406:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 1.3:+78435478 MS.gene037406:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 1.3:+78435475 MS.gene037406:CDS
TGATGATGATGGCAATAATG+TGG 0.626471 1.3:+78435175 MS.gene037406:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 1.3:-78435415 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 1.3:+78435363 MS.gene037406:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 1.3:+78435189 MS.gene037406:CDS
GATGATGATGGCAATAATGT+GGG 0.653668 1.3:+78435176 MS.gene037406:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 1.3:-78435526 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 1.3:-78435527 None:intergenic
ATGGCCCGAAGACCGTACAA+TGG 0.720674 1.3:+78435208 MS.gene037406:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+CGG + chr1.3:78435304-78435323 MS.gene037406:CDS 25.0%
GATGATATCTTTATGCACTT+TGG - chr1.3:78435345-78435364 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG + chr1.3:78435363-78435382 MS.gene037406:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG - chr1.3:78435281-78435300 None:intergenic 30.0%
! TTGATTGTGTATGATGATGA+TGG + chr1.3:78435164-78435183 MS.gene037406:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG - chr1.3:78435620-78435639 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG + chr1.3:78435089-78435108 MS.gene037406:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG + chr1.3:78435189-78435208 MS.gene037406:CDS 35.0%
CAACATGTTGAAAAGTGAGA+TGG + chr1.3:78435475-78435494 MS.gene037406:CDS 35.0%
CATCAATCATGTTAGTGAGA+TGG + chr1.3:78435568-78435587 MS.gene037406:CDS 35.0%
GCATCCAAATTTGGTTAACA+TGG + chr1.3:78435385-78435404 MS.gene037406:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG - chr1.3:78435392-78435411 None:intergenic 35.0%
GTCGTTGACATCAAATATCT+TGG - chr1.3:78435282-78435301 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG - chr1.3:78435450-78435469 None:intergenic 35.0%
! AATCAAACAAGCTTTTGCAC+CGG - chr1.3:78435150-78435169 None:intergenic 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr1.3:78435553-78435572 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr1.3:78435554-78435573 None:intergenic 35.0%
!! GATGATGATGGCAATAATGT+GGG + chr1.3:78435176-78435195 MS.gene037406:CDS 35.0%
!! TGATGATGATGGCAATAATG+TGG + chr1.3:78435175-78435194 MS.gene037406:CDS 35.0%
ATGAGGCAAAACAGCATGAT+TGG - chr1.3:78435603-78435622 None:intergenic 40.0%
ATGCTATGTATGACACTGAG+TGG - chr1.3:78435530-78435549 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG - chr1.3:78435240-78435259 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG + chr1.3:78435571-78435590 MS.gene037406:CDS 40.0%
CATGTTGAAAAGTGAGATGG+TGG + chr1.3:78435478-78435497 MS.gene037406:CDS 40.0%
GCATGGAGTTTACCATTGTA+CGG - chr1.3:78435223-78435242 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG - chr1.3:78435384-78435403 None:intergenic 40.0%
GTTTACCATTGTACGGTCTT+CGG - chr1.3:78435216-78435235 None:intergenic 40.0%
TGCTATGTATGACACTGAGT+GGG - chr1.3:78435529-78435548 None:intergenic 40.0%
TTTACCATTGTACGGTCTTC+GGG - chr1.3:78435215-78435234 None:intergenic 40.0%
ACCAAATTTGGATGCCAGGT+TGG - chr1.3:78435380-78435399 None:intergenic 45.0%
ACCGGACTTGACAGTGTATT+GGG - chr1.3:78435132-78435151 None:intergenic 45.0%
TCCAACCTGGCATCCAAATT+TGG + chr1.3:78435376-78435395 MS.gene037406:CDS 45.0%
TCCCAATACACTGTCAAGTC+CGG + chr1.3:78435128-78435147 MS.gene037406:CDS 45.0%
CACCGGACTTGACAGTGTAT+TGG - chr1.3:78435133-78435152 None:intergenic 50.0%
CAGCACTTAAGTCTCTGAGC+TGG - chr1.3:78435418-78435437 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG - chr1.3:78435524-78435543 None:intergenic 50.0%
ATGGCCCGAAGACCGTACAA+TGG + chr1.3:78435208-78435227 MS.gene037406:CDS 55.0%
CGGTCTTCGGGCCATGTTAT+TGG - chr1.3:78435203-78435222 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 78435032 78435658 78435032 ID=MS.gene037406
chr1.3 mRNA 78435032 78435658 78435032 ID=MS.gene037406.t1;Parent=MS.gene037406
chr1.3 exon 78435032 78435658 78435032 ID=MS.gene037406.t1.exon1;Parent=MS.gene037406.t1
chr1.3 CDS 78435032 78435658 78435032 ID=cds.MS.gene037406.t1;Parent=MS.gene037406.t1
Gene Sequence

>MS.gene037406

ATGGGTCGTGGAAAAATAAATATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCCGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTACGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGTTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>MS.gene037406.t1

MGRGKINMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKATVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAVLPHNSSTNQLDLNI