AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0905030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905030 MtrunA17_Chr1g0212471 85.106 188 26 1 1 186 1 188 1.89e-117 332
Msa0905030 MtrunA17_Chr4g0022641 62.736 212 71 3 1 204 1 212 1.58e-90 271
Msa0905030 MtrunA17_Chr4g0059631 54.955 222 82 4 1 204 1 222 1.31e-77 233
Msa0905030 MtrunA17_Chr2g0303981 45.026 191 96 3 3 192 5 187 7.13e-54 171
Msa0905030 MtrunA17_Chr6g0457851 37.975 158 95 1 1 155 11 168 2.77e-37 132
Msa0905030 MtrunA17_Chr1g0212151 38.608 158 94 1 1 155 1 158 9.04e-36 128
Msa0905030 MtrunA17_Chr6g0449851 36.842 171 105 1 1 168 1 171 5.38e-35 125
Msa0905030 MtrunA17_Chr6g0449861 33.520 179 116 1 1 176 9 187 1.59e-33 122
Msa0905030 MtrunA17_Chr3g0107381 28.000 175 111 5 1 165 1 170 1.45e-13 67.0
Msa0905030 MtrunA17_Chr3g0107461 29.448 163 103 4 1 154 1 160 7.84e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0905030 AT5G55690.1 34.416 154 84 4 1 147 1 144 3.56e-16 75.5
Msa0905030 AT5G55690.2 34.416 154 84 4 1 147 1 144 3.56e-16 75.5
Msa0905030 AT1G22590.2 30.625 160 99 6 1 153 1 155 1.61e-11 60.8
Msa0905030 AT3G05860.2 41.429 70 39 1 1 70 1 68 4.29e-11 60.5
Msa0905030 AT2G28700.1 37.333 75 44 2 1 75 1 72 5.18e-11 61.2
Msa0905030 AT3G05860.1 41.429 70 39 1 1 70 1 68 6.72e-11 60.5
Msa0905030 AT3G05860.3 41.429 70 39 1 1 70 1 68 7.09e-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 6_2:+2906481 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 6_2:-2906494 Msa0905030:CDS
CGGTCTTCGGGCCATGTTAT+TGG 0.257464 6_2:+2906670 None:intergenic
TTTACCATTGTACGGTCTTC+GGG 0.322440 6_2:+2906658 None:intergenic
GTTTACCATTGTACGGTCTT+CGG 0.346180 6_2:+2906657 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 6_2:+2906591 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 6_2:+2906741 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 6_2:+2906740 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 6_2:+2906423 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 6_2:+2906349 None:intergenic
ATGAGGCAAACCAGCATGAT+TGG 0.434094 6_2:+2906270 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.436280 6_2:+2906233 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 6_2:+2906320 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 6_2:+2906528 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 6_2:+2906489 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 6_2:+2906493 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 6_2:+2906319 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 6_2:-2906742 Msa0905030:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 6_2:-2906781 Msa0905030:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 6_2:+2906253 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 6_2:-2906485 Msa0905030:CDS
CTTTGAAATTAAGAAAGCTA+AGG 0.524267 6_2:-2906566 Msa0905030:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 6_2:-2906850 None:intergenic
TTGATTGTGTATGATGATGA+TGG 0.527956 6_2:-2906706 Msa0905030:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 6_2:+2906592 None:intergenic
GCATGGAGTTTACCATTGTA+CGG 0.551323 6_2:+2906650 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 6_2:+2906633 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 6_2:-2906299 Msa0905030:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 6_2:-2906302 Msa0905030:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 6_2:-2906392 Msa0905030:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 6_2:-2906395 Msa0905030:CDS
TGATGATGATGGCAATAATG+TGG 0.626471 6_2:-2906695 Msa0905030:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 6_2:+2906455 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 6_2:-2906507 Msa0905030:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 6_2:-2906681 Msa0905030:CDS
GATGATGATGGCAATAATGT+GGG 0.653668 6_2:-2906694 Msa0905030:CDS
GTGGATATGACCAATCATGC+TGG 0.656704 6_2:-2906280 Msa0905030:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 6_2:+2906344 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 6_2:+2906343 None:intergenic
ATGGCCCGAAGACCGTACAA+TGG 0.720674 6_2:-2906662 Msa0905030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+AGG - chr6_2:2906506-2906525 Msa0905030:CDS 25.0%
! TTGATTGTGTATGATGATGA+TGG - chr6_2:2906366-2906385 Msa0905030:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG + chr6_2:2906483-2906502 None:intergenic 30.0%
GATGATATCTTTATGCACTT+TGG + chr6_2:2906547-2906566 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG - chr6_2:2906565-2906584 Msa0905030:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG + chr6_2:2906822-2906841 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG - chr6_2:2906291-2906310 Msa0905030:CDS 35.0%
! AATCAAACAAGCTTTTGCAC+CGG + chr6_2:2906352-2906371 None:intergenic 35.0%
!! TGATGATGATGGCAATAATG+TGG - chr6_2:2906377-2906396 Msa0905030:CDS 35.0%
!! GATGATGATGGCAATAATGT+GGG - chr6_2:2906378-2906397 Msa0905030:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG - chr6_2:2906391-2906410 Msa0905030:CDS 35.0%
GTCGTTGACATCAAATATCT+TGG + chr6_2:2906484-2906503 None:intergenic 35.0%
GCATCCAAATTTGGTTAACA+TGG - chr6_2:2906587-2906606 Msa0905030:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG + chr6_2:2906594-2906613 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG + chr6_2:2906652-2906671 None:intergenic 35.0%
CAACATGTTGAAAAGTGAGA+TGG - chr6_2:2906677-2906696 Msa0905030:CDS 35.0%
! TGATGTGTTGTTGCATTTGA+GGG + chr6_2:2906755-2906774 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG + chr6_2:2906756-2906775 None:intergenic 35.0%
CATCAATCATGTTAGTGAGA+TGG - chr6_2:2906770-2906789 Msa0905030:CDS 35.0%
TTTACCATTGTACGGTCTTC+GGG + chr6_2:2906417-2906436 None:intergenic 40.0%
GTTTACCATTGTACGGTCTT+CGG + chr6_2:2906418-2906437 None:intergenic 40.0%
GCATGGAGTTTACCATTGTA+CGG + chr6_2:2906425-2906444 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG + chr6_2:2906442-2906461 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG + chr6_2:2906586-2906605 None:intergenic 40.0%
CATGTTGAAAAGTGAGATGG+TGG - chr6_2:2906680-2906699 Msa0905030:CDS 40.0%
TGCTATGTATGACACTGAGT+GGG + chr6_2:2906731-2906750 None:intergenic 40.0%
ATGCTATGTATGACACTGAG+TGG + chr6_2:2906732-2906751 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG - chr6_2:2906773-2906792 Msa0905030:CDS 40.0%
TCCCAATACACTGTCAAGTC+CGG - chr6_2:2906330-2906349 Msa0905030:CDS 45.0%
ACCGGACTTGACAGTGTATT+GGG + chr6_2:2906334-2906353 None:intergenic 45.0%
TCCAACCTGGCATCCAAATT+TGG - chr6_2:2906578-2906597 Msa0905030:CDS 45.0%
ACCAAATTTGGATGCCAGGT+TGG + chr6_2:2906582-2906601 None:intergenic 45.0%
GTGGATATGACCAATCATGC+TGG - chr6_2:2906792-2906811 Msa0905030:CDS 45.0%
ATGAGGCAAACCAGCATGAT+TGG + chr6_2:2906805-2906824 None:intergenic 45.0%
CACCGGACTTGACAGTGTAT+TGG + chr6_2:2906335-2906354 None:intergenic 50.0%
CAGCACTTAAGTCTCTGAGC+TGG + chr6_2:2906620-2906639 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG + chr6_2:2906726-2906745 None:intergenic 50.0%
CGGTCTTCGGGCCATGTTAT+TGG + chr6_2:2906405-2906424 None:intergenic 55.0%
ATGGCCCGAAGACCGTACAA+TGG - chr6_2:2906410-2906429 Msa0905030:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 2906234 2906860 2906234 ID=Msa0905030;Name=Msa0905030
chr6_2 mRNA 2906234 2906860 2906234 ID=Msa0905030-mRNA-1;Parent=Msa0905030;Name=Msa0905030-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|208
chr6_2 exon 2906234 2906860 2906234 ID=Msa0905030-mRNA-1:exon:923;Parent=Msa0905030-mRNA-1
chr6_2 CDS 2906234 2906860 2906234 ID=Msa0905030-mRNA-1:cds;Parent=Msa0905030-mRNA-1
Gene Sequence

>Msa0905030

ATGGGTCGTGGAAAAATAAATATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCCGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTAAGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGGTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>Msa0905030

MGRGKINMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKAKVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAGLPHNSSTNQLDLNI*