AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49415

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49415.t1 MTR_1g115290 85.526 152 20 1 37 186 1 152 1.29e-92 268
MS.gene49415.t1 MTR_4g045977 62.736 212 71 3 1 204 1 212 2.00e-90 271
MS.gene49415.t1 MTR_4g107170 54.955 222 82 4 1 204 1 222 1.66e-77 233
MS.gene49415.t1 MTR_2g049610 47.959 196 93 3 1 194 1 189 1.72e-59 187
MS.gene49415.t1 MTR_2g049530 45.026 191 96 3 3 192 5 187 9.06e-54 171
MS.gene49415.t1 MTR_2g049630 51.974 152 71 2 2 152 4 154 5.55e-48 161
MS.gene49415.t1 MTR_6g018920 37.975 158 95 1 1 155 1 158 2.64e-37 132
MS.gene49415.t1 MTR_1g114730 38.608 158 94 1 1 155 1 158 1.15e-35 128
MS.gene49415.t1 MTR_6g005440 36.842 171 105 1 1 168 1 171 6.87e-35 125
MS.gene49415.t1 MTR_6g005450 33.520 179 116 1 1 176 1 179 1.90e-33 122
MS.gene49415.t1 MTR_3g466980 28.000 175 111 5 1 165 1 170 1.87e-13 67.0
MS.gene49415.t1 MTR_3g467080 29.448 163 103 4 1 154 1 160 1.01e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49415.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.47e-16 75.5
MS.gene49415.t1 AT5G55690 34.416 154 84 4 1 147 1 144 3.47e-16 75.5
MS.gene49415.t1 AT1G22590 30.625 160 99 6 1 153 1 155 1.58e-11 60.8
MS.gene49415.t1 AT3G05860 41.429 70 39 1 1 70 1 68 4.21e-11 60.5
MS.gene49415.t1 AT2G28700 37.333 75 44 2 1 75 1 72 5.08e-11 61.2
MS.gene49415.t1 AT3G05860 41.429 70 39 1 1 70 1 68 6.59e-11 60.5
MS.gene49415.t1 AT3G05860 41.429 70 39 1 1 70 1 68 6.96e-11 60.5

Find 40 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCCATGTTAACCAAATT+TGG 0.129467 1.2:-85129883 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 1.2:+85129870 MS.gene49415:CDS
CGGTCTTCGGGCCATGTTAT+TGG 0.257464 1.2:-85129694 None:intergenic
TTTACCATTGTACGGTCTTC+GGG 0.322440 1.2:-85129706 None:intergenic
GTTTACCATTGTACGGTCTT+CGG 0.346180 1.2:-85129707 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1.2:-85129773 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 1.2:-85129623 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 1.2:-85129624 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 1.2:-85129941 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 1.2:-85130015 None:intergenic
ATGAGGCAAACCAGCATGAT+TGG 0.434094 1.2:-85130094 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.436280 1.2:-85130131 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 1.2:-85130044 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 1.2:-85129836 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 1.2:-85129875 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 1.2:-85129871 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 1.2:-85130045 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 1.2:+85129622 MS.gene49415:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 1.2:+85129583 MS.gene49415:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 1.2:-85130111 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 1.2:+85129879 MS.gene49415:CDS
CTTTGAAATTAAGAAAGCTA+AGG 0.524267 1.2:+85129798 MS.gene49415:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 1.2:+85129514 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.527956 1.2:+85129658 MS.gene49415:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 1.2:-85129772 None:intergenic
GCATGGAGTTTACCATTGTA+CGG 0.551323 1.2:-85129714 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 1.2:-85129731 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 1.2:+85130065 MS.gene49415:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 1.2:+85130062 MS.gene49415:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 1.2:+85129972 MS.gene49415:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 1.2:+85129969 MS.gene49415:CDS
TGATGATGATGGCAATAATG+TGG 0.626471 1.2:+85129669 MS.gene49415:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 1.2:-85129909 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 1.2:+85129857 MS.gene49415:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 1.2:+85129683 MS.gene49415:CDS
GATGATGATGGCAATAATGT+GGG 0.653668 1.2:+85129670 MS.gene49415:CDS
GTGGATATGACCAATCATGC+TGG 0.656704 1.2:+85130084 MS.gene49415:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 1.2:-85130020 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 1.2:-85130021 None:intergenic
ATGGCCCGAAGACCGTACAA+TGG 0.720674 1.2:+85129702 MS.gene49415:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+AGG + chr1.2:85129798-85129817 MS.gene49415:CDS 25.0%
GATGATATCTTTATGCACTT+TGG - chr1.2:85129839-85129858 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG + chr1.2:85129857-85129876 MS.gene49415:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG - chr1.2:85129775-85129794 None:intergenic 30.0%
! TTGATTGTGTATGATGATGA+TGG + chr1.2:85129658-85129677 MS.gene49415:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG - chr1.2:85130114-85130133 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG + chr1.2:85129583-85129602 MS.gene49415:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG + chr1.2:85129683-85129702 MS.gene49415:CDS 35.0%
CAACATGTTGAAAAGTGAGA+TGG + chr1.2:85129969-85129988 MS.gene49415:CDS 35.0%
CATCAATCATGTTAGTGAGA+TGG + chr1.2:85130062-85130081 MS.gene49415:CDS 35.0%
GCATCCAAATTTGGTTAACA+TGG + chr1.2:85129879-85129898 MS.gene49415:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG - chr1.2:85129886-85129905 None:intergenic 35.0%
GTCGTTGACATCAAATATCT+TGG - chr1.2:85129776-85129795 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG - chr1.2:85129944-85129963 None:intergenic 35.0%
! AATCAAACAAGCTTTTGCAC+CGG - chr1.2:85129644-85129663 None:intergenic 35.0%
! TGATGTGTTGTTGCATTTGA+GGG - chr1.2:85130047-85130066 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG - chr1.2:85130048-85130067 None:intergenic 35.0%
!! GATGATGATGGCAATAATGT+GGG + chr1.2:85129670-85129689 MS.gene49415:CDS 35.0%
!! TGATGATGATGGCAATAATG+TGG + chr1.2:85129669-85129688 MS.gene49415:CDS 35.0%
ATGCTATGTATGACACTGAG+TGG - chr1.2:85130024-85130043 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG - chr1.2:85129734-85129753 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG + chr1.2:85130065-85130084 MS.gene49415:CDS 40.0%
CATGTTGAAAAGTGAGATGG+TGG + chr1.2:85129972-85129991 MS.gene49415:CDS 40.0%
GCATGGAGTTTACCATTGTA+CGG - chr1.2:85129717-85129736 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG - chr1.2:85129878-85129897 None:intergenic 40.0%
GTTTACCATTGTACGGTCTT+CGG - chr1.2:85129710-85129729 None:intergenic 40.0%
TGCTATGTATGACACTGAGT+GGG - chr1.2:85130023-85130042 None:intergenic 40.0%
TTTACCATTGTACGGTCTTC+GGG - chr1.2:85129709-85129728 None:intergenic 40.0%
ACCAAATTTGGATGCCAGGT+TGG - chr1.2:85129874-85129893 None:intergenic 45.0%
ACCGGACTTGACAGTGTATT+GGG - chr1.2:85129626-85129645 None:intergenic 45.0%
ATGAGGCAAACCAGCATGAT+TGG - chr1.2:85130097-85130116 None:intergenic 45.0%
GTGGATATGACCAATCATGC+TGG + chr1.2:85130084-85130103 MS.gene49415:CDS 45.0%
TCCAACCTGGCATCCAAATT+TGG + chr1.2:85129870-85129889 MS.gene49415:CDS 45.0%
TCCCAATACACTGTCAAGTC+CGG + chr1.2:85129622-85129641 MS.gene49415:CDS 45.0%
CACCGGACTTGACAGTGTAT+TGG - chr1.2:85129627-85129646 None:intergenic 50.0%
CAGCACTTAAGTCTCTGAGC+TGG - chr1.2:85129912-85129931 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG - chr1.2:85130018-85130037 None:intergenic 50.0%
ATGGCCCGAAGACCGTACAA+TGG + chr1.2:85129702-85129721 MS.gene49415:CDS 55.0%
CGGTCTTCGGGCCATGTTAT+TGG - chr1.2:85129697-85129716 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 85129526 85130152 85129526 ID=MS.gene49415
chr1.2 mRNA 85129526 85130152 85129526 ID=MS.gene49415.t1;Parent=MS.gene49415
chr1.2 exon 85129526 85130152 85129526 ID=MS.gene49415.t1.exon1;Parent=MS.gene49415.t1
chr1.2 CDS 85129526 85130152 85129526 ID=cds.MS.gene49415.t1;Parent=MS.gene49415.t1
Gene Sequence

>MS.gene49415

ATGGGTCGTGGAAAAATAAATATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCCGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTAAGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGGTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>MS.gene49415.t1

MGRGKINMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKAKVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAGLPHNSSTNQLDLNI