AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0311790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311790 MtrunA17_Chr1g0149481 42.857 91 43 4 29 111 70 159 2.96e-14 65.1
Msa0311790 MtrunA17_Chr1g0149491 46.250 80 34 4 40 111 68 146 3.03e-14 64.7
Msa0311790 MtrunA17_Chr4g0056411 43.662 71 36 2 44 110 93 163 1.18e-13 63.5
Msa0311790 MtrunA17_Chr1g0149471 48.611 72 32 3 44 111 135 205 1.39e-13 63.9
Msa0311790 MtrunA17_Chr4g0056391 41.667 72 38 2 44 111 67 138 2.67e-13 62.0
Msa0311790 MtrunA17_Chr4g0056401 44.444 72 36 2 44 111 58 129 5.09e-13 61.2
Msa0311790 MtrunA17_Chr2g0290521 40.860 93 43 3 18 98 16 108 4.82e-12 58.5
Msa0311790 MtrunA17_Chr3g0137521 36.508 126 62 6 1 110 1 124 6.92e-11 55.5
Msa0311790 MtrunA17_Chr4g0056371 41.860 86 41 4 39 116 48 132 9.20e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311790 AT5G46900.1 39.344 122 58 4 5 111 2 122 1.60e-18 75.5
Msa0311790 AT5G46890.1 37.705 122 60 4 5 111 2 122 2.90e-17 72.0
Msa0311790 AT4G12500.1 46.753 77 37 2 44 116 101 177 7.37e-16 69.7
Msa0311790 AT4G12470.1 46.479 71 34 2 44 110 85 155 2.69e-15 68.2
Msa0311790 AT4G12490.1 49.296 71 32 2 44 110 106 176 4.52e-15 67.8
Msa0311790 AT4G12520.1 35.938 128 69 4 1 115 1 128 4.93e-15 66.6
Msa0311790 AT4G12510.1 35.938 128 69 4 1 115 1 128 4.93e-15 66.6
Msa0311790 AT4G12480.1 46.479 71 34 2 44 110 92 162 6.58e-15 67.0
Msa0311790 AT1G12090.1 43.662 71 36 2 44 110 62 132 1.89e-12 60.1
Msa0311790 AT1G12100.1 38.144 97 55 3 24 116 37 132 8.39e-12 58.2
Msa0311790 AT2G45180.1 35.385 130 64 5 1 111 1 129 8.83e-12 58.2
Msa0311790 AT1G62510.1 37.975 79 41 3 40 110 66 144 2.03e-11 57.8
Msa0311790 AT4G12545.1 37.143 105 51 6 12 110 7 102 3.60e-11 55.8
Msa0311790 AT4G12530.1 37.778 90 51 3 12 99 11 97 5.98e-11 55.8

Find 35 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACCTTGAATACTTCCTTTA+TGG 0.070526 2_4:+6679144 None:intergenic
TTCCTTTATGGGAACGTTAA+TGG 0.184558 2_4:+6679156 None:intergenic
GAAGAGGATGAGAATGTTAA+TGG 0.273547 2_4:+6679411 None:intergenic
AGTAATCAAGGAAAATGTTT+TGG 0.276850 2_4:-6679185 Msa0311790:CDS
TCCTTTATGGGAACGTTAAT+GGG 0.309759 2_4:+6679157 None:intergenic
ACCTTGAATACTTCCTTTAT+GGG 0.339267 2_4:+6679145 None:intergenic
ACCCATTAACGTTCCCATAA+AGG 0.367765 2_4:-6679158 Msa0311790:CDS
GCCGGCACAAGCACTCAAAT+CGG 0.396560 2_4:+6679309 None:intergenic
CGCCTTAACAGAGTTAAGAT+TGG 0.406690 2_4:+6679366 None:intergenic
CACCAATCTTAACTCTGTTA+AGG 0.416695 2_4:-6679368 Msa0311790:CDS
TCCCATAAAGGAAGTATTCA+AGG 0.434770 2_4:-6679146 Msa0311790:CDS
TATTGCAAAATGGGTTCAAA+GGG 0.459238 2_4:-6679442 None:intergenic
TTCTACAAGACCACCGATGA+TGG 0.461353 2_4:+6679234 None:intergenic
CATATTACAAGGGCTTGTTA+AGG 0.462777 2_4:-6679287 Msa0311790:CDS
TGAAGAAGAAGAAGATGCTA+AGG 0.465305 2_4:+6679389 None:intergenic
TTATTGCAAAATGGGTTCAA+AGG 0.479552 2_4:-6679443 None:intergenic
CCCGATTTGAGTGCTTGTGC+CGG 0.487660 2_4:-6679310 Msa0311790:CDS
GCTTGTGCCGGCATATTACA+AGG 0.494276 2_4:-6679298 Msa0311790:CDS
AAATCGGGACACTGCGGCAG+TGG 0.500290 2_4:+6679325 None:intergenic
TTACAAGGGCTTGTTAAGGT+TGG 0.517501 2_4:-6679283 Msa0311790:CDS
AGAAGAAGATGCTAAGGAAG+AGG 0.520181 2_4:+6679395 None:intergenic
TAACCGCATACGGAGACATT+GGG 0.521289 2_4:+6679106 None:intergenic
TATATGAAGTTAACCGCATA+CGG 0.528309 2_4:+6679096 None:intergenic
AACAAGCCCTTGTAATATGC+CGG 0.532336 2_4:+6679291 None:intergenic
CCGGCACAAGCACTCAAATC+GGG 0.536967 2_4:+6679310 None:intergenic
GTGCCTTTGTGCAGTAATCA+AGG 0.543284 2_4:-6679197 Msa0311790:CDS
GGACACTGCGGCAGTGGTGA+TGG 0.554933 2_4:+6679331 None:intergenic
AAGTCTTGTTGCTCCATCAT+CGG 0.569193 2_4:-6679247 Msa0311790:CDS
GAGCAACAAGACTTTGCTTG+TGG 0.570002 2_4:+6679256 None:intergenic
TTAACCGCATACGGAGACAT+TGG 0.573421 2_4:+6679105 None:intergenic
GCACCCAATGTCTCCGTATG+CGG 0.626914 2_4:-6679109 Msa0311790:CDS
TCTTGTTGCTCCATCATCGG+TGG 0.639422 2_4:-6679244 Msa0311790:CDS
TTTCCTTGATTACTGCACAA+AGG 0.652604 2_4:+6679194 None:intergenic
CTTGTGCCGGCATATTACAA+GGG 0.672505 2_4:-6679297 Msa0311790:CDS
GCACTCAAATCGGGACACTG+CGG 0.725988 2_4:+6679319 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAATCAAGGAAAATGTTT+TGG - chr2_4:6679353-6679372 Msa0311790:CDS 25.0%
!! GTAATCAAGGAAAATGTTTT+GGG - chr2_4:6679354-6679373 Msa0311790:CDS 25.0%
ACCTTGAATACTTCCTTTAT+GGG + chr2_4:6679396-6679415 None:intergenic 30.0%
AACCTTGAATACTTCCTTTA+TGG + chr2_4:6679397-6679416 None:intergenic 30.0%
GAAGAGGATGAGAATGTTAA+TGG + chr2_4:6679130-6679149 None:intergenic 35.0%
TGAAGAAGAAGAAGATGCTA+AGG + chr2_4:6679152-6679171 None:intergenic 35.0%
CACCAATCTTAACTCTGTTA+AGG - chr2_4:6679170-6679189 Msa0311790:CDS 35.0%
!! CATATTACAAGGGCTTGTTA+AGG - chr2_4:6679251-6679270 Msa0311790:CDS 35.0%
TTTCCTTGATTACTGCACAA+AGG + chr2_4:6679347-6679366 None:intergenic 35.0%
TCCTTTATGGGAACGTTAAT+GGG + chr2_4:6679384-6679403 None:intergenic 35.0%
TTCCTTTATGGGAACGTTAA+TGG + chr2_4:6679385-6679404 None:intergenic 35.0%
!! TCCCATAAAGGAAGTATTCA+AGG - chr2_4:6679392-6679411 Msa0311790:CDS 35.0%
AGAAGAAGATGCTAAGGAAG+AGG + chr2_4:6679146-6679165 None:intergenic 40.0%
CGCCTTAACAGAGTTAAGAT+TGG + chr2_4:6679175-6679194 None:intergenic 40.0%
AACAAGCCCTTGTAATATGC+CGG + chr2_4:6679250-6679269 None:intergenic 40.0%
!! TTACAAGGGCTTGTTAAGGT+TGG - chr2_4:6679255-6679274 Msa0311790:CDS 40.0%
!! AAGTCTTGTTGCTCCATCAT+CGG - chr2_4:6679291-6679310 Msa0311790:CDS 40.0%
ACCCATTAACGTTCCCATAA+AGG - chr2_4:6679380-6679399 Msa0311790:CDS 40.0%
! CTTGTGCCGGCATATTACAA+GGG - chr2_4:6679241-6679260 Msa0311790:CDS 45.0%
GAGCAACAAGACTTTGCTTG+TGG + chr2_4:6679285-6679304 None:intergenic 45.0%
TTCTACAAGACCACCGATGA+TGG + chr2_4:6679307-6679326 None:intergenic 45.0%
GTGCCTTTGTGCAGTAATCA+AGG - chr2_4:6679341-6679360 Msa0311790:CDS 45.0%
TAACCGCATACGGAGACATT+GGG + chr2_4:6679435-6679454 None:intergenic 45.0%
TTAACCGCATACGGAGACAT+TGG + chr2_4:6679436-6679455 None:intergenic 45.0%
! GCTTGTGCCGGCATATTACA+AGG - chr2_4:6679240-6679259 Msa0311790:CDS 50.0%
TCTTGTTGCTCCATCATCGG+TGG - chr2_4:6679294-6679313 Msa0311790:CDS 50.0%
GCACTCAAATCGGGACACTG+CGG + chr2_4:6679222-6679241 None:intergenic 55.0%
CCGGCACAAGCACTCAAATC+GGG + chr2_4:6679231-6679250 None:intergenic 55.0%
! CCCGATTTGAGTGCTTGTGC+CGG - chr2_4:6679228-6679247 Msa0311790:CDS 55.0%
GCCGGCACAAGCACTCAAAT+CGG + chr2_4:6679232-6679251 None:intergenic 55.0%
GCACCCAATGTCTCCGTATG+CGG - chr2_4:6679429-6679448 Msa0311790:CDS 55.0%
AAATCGGGACACTGCGGCAG+TGG + chr2_4:6679216-6679235 None:intergenic 60.0%
GGACACTGCGGCAGTGGTGA+TGG + chr2_4:6679210-6679229 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 6679105 6679455 6679105 ID=Msa0311790;Name=Msa0311790
chr2_4 mRNA 6679105 6679455 6679105 ID=Msa0311790-mRNA-1;Parent=Msa0311790;Name=Msa0311790-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|116
chr2_4 exon 6679105 6679455 6679105 ID=Msa0311790-mRNA-1:exon:2576;Parent=Msa0311790-mRNA-1
chr2_4 CDS 6679105 6679455 6679105 ID=Msa0311790-mRNA-1:cds;Parent=Msa0311790-mRNA-1
Gene Sequence

>Msa0311790

ATGGGTTCAAAGGGTTTTGCATCCATTAACATTCTCATCCTCTTCCTTAGCATCTTCTTCTTCTTCACCAATCTTAACTCTGTTAAGGCGCAAATCGCTTCACCATCACCACTGCCGCAGTGTCCCGATTTGAGTGCTTGTGCCGGCATATTACAAGGGCTTGTTAAGGTTGGTTCTCCACAAGCAAAGTCTTGTTGCTCCATCATCGGTGGTCTTGTAGAAGTTGATGCTGTTGTGTGCCTTTGTGCAGTAATCAAGGAAAATGTTTTGGGAATACCCATTAACGTTCCCATAAAGGAAGTATTCAAGGTTTGTGAACGTGAAGCACCCAATGTCTCCGTATGCGGTTAA
Protein sequence

>Msa0311790

MGSKGFASINILILFLSIFFFFTNLNSVKAQIASPSPLPQCPDLSACAGILQGLVKVGSPQAKSCCSIIGGLVEVDAVVCLCAVIKENVLGIPINVPIKEVFKVCEREAPNVSVCG*