AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0344910


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0344910 MtrunA17_Chr3g0136441 94.915 118 6 0 1 118 1 118 3.21e-82 236
Msa0344910 MtrunA17_Chr1g0150711 53.509 114 46 2 12 118 17 130 3.07e-36 120
Msa0344910 MtrunA17_Chr8g0344381 55.208 96 41 1 8 101 27 122 2.49e-34 116
Msa0344910 MtrunA17_Chr4g0070351 55.102 98 42 1 10 105 29 126 4.26e-32 109
Msa0344910 MtrunA17_Chr4g0070371 46.957 115 55 3 5 115 18 130 4.40e-28 100
Msa0344910 MtrunA17_Chr5g0394601 47.297 74 38 1 10 82 1 74 1.17e-22 85.1
Msa0344910 MtrunA17_Chr2g0331111 52.778 72 33 1 1 72 52 122 6.23e-21 83.2
Msa0344910 MtrunA17_Chr8g0340421 57.143 63 26 1 11 73 62 123 9.07e-21 82.8
Msa0344910 MtrunA17_Chr3g0140381 36.111 108 68 1 11 117 36 143 4.93e-20 79.7
Msa0344910 MtrunA17_Chr1g0205251 45.946 74 38 2 10 81 1 74 1.03e-19 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0344910 AT1G72510.1 57.447 94 38 1 14 105 36 129 1.72e-34 117
Msa0344910 AT1G72510.2 57.447 94 38 1 14 105 36 129 1.72e-34 117
Msa0344910 AT2G09970.1 48.980 98 47 2 11 105 33 130 1.56e-27 99.8
Msa0344910 AT5G20670.1 47.959 98 46 3 12 106 23 118 3.15e-23 88.2
Msa0344910 AT1G54095.1 45.192 104 52 3 1 101 6 107 1.88e-21 83.6
Msa0344910 AT4G14819.1 36.697 109 62 3 10 118 1 102 2.71e-19 77.0
Msa0344910 AT3G22540.1 38.462 91 51 3 10 99 1 87 5.55e-18 73.6
Msa0344910 AT1G79770.1 43.878 98 47 3 7 100 47 140 8.45e-16 69.7
Msa0344910 AT5G25840.1 42.391 92 38 3 3 82 34 122 1.07e-13 64.3
Msa0344910 AT2G25780.1 38.202 89 51 3 15 100 39 126 1.49e-12 60.8

Find 28 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATCAACCGTAGGTTTATT+AGG 0.246906 3_1:+3832318 None:intergenic
CTCCATCGTCGCCGCGGTTT+CGG 0.297193 3_1:+3832551 None:intergenic
TTTCAAAGCTTCTTCTTTCA+CGG 0.372656 3_1:+3832413 None:intergenic
TACCTGGGTCGTTGGATTTG+TGG 0.383506 3_1:-3832450 Msa0344910:CDS
ACCTGGGTCGTTGGATTTGT+GGG 0.391134 3_1:-3832449 Msa0344910:CDS
GTGCTACTGTTGCGGCTTAA+CGG 0.404880 3_1:-3832514 Msa0344910:CDS
AAACTCAAAGGTTGTTTCCT+CGG 0.484002 3_1:+3832252 None:intergenic
CCATGTTCGTGAGAAATACC+TGG 0.494919 3_1:-3832466 Msa0344910:CDS
GCCGCAACAGTAGCACTTCA+CGG 0.509628 3_1:+3832521 None:intergenic
GTGAGAAATACCTGGGTCGT+TGG 0.543743 3_1:-3832458 Msa0344910:CDS
GTGTTGATTAAGAGCTTCAT+CGG 0.550067 3_1:+3832371 None:intergenic
AACCGCGGCGACGATGGAGG+TGG 0.571492 3_1:-3832547 Msa0344910:CDS
AACCGAAACCGCGGCGACGA+TGG 0.582114 3_1:-3832553 Msa0344910:CDS
AAGTCCTCCTAATAAACCTA+CGG 0.601557 3_1:-3832325 Msa0344910:CDS
TCAACCGTAGGTTTATTAGG+AGG 0.609122 3_1:+3832321 None:intergenic
CCAGGTATTTCTCACGAACA+TGG 0.611108 3_1:+3832466 None:intergenic
TTCGGTCTTTGGATTCTCCG+AGG 0.613420 3_1:-3832269 Msa0344910:CDS
CGAAACCGCGGCGACGATGG+AGG 0.615356 3_1:-3832550 Msa0344910:CDS
GCCCACAAATCCAACGACCC+AGG 0.634250 3_1:+3832448 None:intergenic
CCAACCGTTCGAAAACTCAA+AGG 0.637318 3_1:+3832240 None:intergenic
GCAAGAATCAAATCAACCGT+AGG 0.641034 3_1:+3832309 None:intergenic
CATGTTCGTGAGAAATACCT+GGG 0.642264 3_1:-3832465 Msa0344910:CDS
GATTTGTGGGCTATGTGCAG+AGG 0.661005 3_1:-3832436 Msa0344910:CDS
GCCGTGAAGTGCTACTGTTG+CGG 0.673482 3_1:-3832522 Msa0344910:CDS
CTACTGTTGCGGCTTAACGG+AGG 0.677501 3_1:-3832511 Msa0344910:CDS
TACCACCTCCATCGTCGCCG+CGG 0.680469 3_1:+3832545 None:intergenic
GATGGCTTTAACCGAAACCG+CGG 0.711918 3_1:-3832562 Msa0344910:CDS
CGAACATGGTCAATATACGA+CGG 0.745897 3_1:+3832480 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TTTCAAAGCTTCTTCTTTCA+CGG + chr3_1:3832375-3832394 None:intergenic 30.0%
AAATCAACCGTAGGTTTATT+AGG + chr3_1:3832470-3832489 None:intergenic 30.0%
! CTGTGAAACATCTTCTTTTT+CGG - chr3_1:3832498-3832517 Msa0344910:CDS 30.0%
!! GTGTTGATTAAGAGCTTCAT+CGG + chr3_1:3832417-3832436 None:intergenic 35.0%
AAGTCCTCCTAATAAACCTA+CGG - chr3_1:3832460-3832479 Msa0344910:CDS 35.0%
!!! ACATCTTCTTTTTCGGTCTT+TGG - chr3_1:3832505-3832524 Msa0344910:CDS 35.0%
! AAACTCAAAGGTTGTTTCCT+CGG + chr3_1:3832536-3832555 None:intergenic 35.0%
!! ACAACCTTTGAGTTTTCGAA+CGG - chr3_1:3832541-3832560 Msa0344910:CDS 35.0%
CGAACATGGTCAATATACGA+CGG + chr3_1:3832308-3832327 None:intergenic 40.0%
CATGTTCGTGAGAAATACCT+GGG - chr3_1:3832320-3832339 Msa0344910:CDS 40.0%
TCAACCGTAGGTTTATTAGG+AGG + chr3_1:3832467-3832486 None:intergenic 40.0%
GCAAGAATCAAATCAACCGT+AGG + chr3_1:3832479-3832498 None:intergenic 40.0%
CCAGGTATTTCTCACGAACA+TGG + chr3_1:3832322-3832341 None:intergenic 45.0%
CCATGTTCGTGAGAAATACC+TGG - chr3_1:3832319-3832338 Msa0344910:CDS 45.0%
CCAACCGTTCGAAAACTCAA+AGG + chr3_1:3832548-3832567 None:intergenic 45.0%
!! CCTTTGAGTTTTCGAACGGT+TGG - chr3_1:3832545-3832564 Msa0344910:CDS 45.0%
! GTGCTACTGTTGCGGCTTAA+CGG - chr3_1:3832271-3832290 Msa0344910:CDS 50.0%
GTGAGAAATACCTGGGTCGT+TGG - chr3_1:3832327-3832346 Msa0344910:CDS 50.0%
TACCTGGGTCGTTGGATTTG+TGG - chr3_1:3832335-3832354 Msa0344910:CDS 50.0%
ACCTGGGTCGTTGGATTTGT+GGG - chr3_1:3832336-3832355 Msa0344910:CDS 50.0%
! GATTTGTGGGCTATGTGCAG+AGG - chr3_1:3832349-3832368 Msa0344910:CDS 50.0%
TTCGGTCTTTGGATTCTCCG+AGG - chr3_1:3832516-3832535 Msa0344910:CDS 50.0%
! GCCGTGAAGTGCTACTGTTG+CGG - chr3_1:3832263-3832282 Msa0344910:CDS 55.0%
GCCGCAACAGTAGCACTTCA+CGG + chr3_1:3832267-3832286 None:intergenic 55.0%
CTACTGTTGCGGCTTAACGG+AGG - chr3_1:3832274-3832293 Msa0344910:CDS 55.0%
GCCCACAAATCCAACGACCC+AGG + chr3_1:3832340-3832359 None:intergenic 60.0%
AACCGAAACCGCGGCGACGA+TGG - chr3_1:3832232-3832251 Msa0344910:CDS 65.0%
CTCCATCGTCGCCGCGGTTT+CGG + chr3_1:3832237-3832256 None:intergenic 65.0%
TACCACCTCCATCGTCGCCG+CGG + chr3_1:3832243-3832262 None:intergenic 65.0%
CGAAACCGCGGCGACGATGG+AGG - chr3_1:3832235-3832254 Msa0344910:CDS 70.0%
AACCGCGGCGACGATGGAGG+TGG - chr3_1:3832238-3832257 Msa0344910:CDS 70.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 3832224 3832583 3832224 ID=Msa0344910;Name=Msa0344910
chr3_1 mRNA 3832224 3832583 3832224 ID=Msa0344910-mRNA-1;Parent=Msa0344910;Name=Msa0344910-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|119
chr3_1 exon 3832224 3832583 3832224 ID=Msa0344910-mRNA-1:exon:1227;Parent=Msa0344910-mRNA-1
chr3_1 CDS 3832224 3832583 3832224 ID=Msa0344910-mRNA-1:cds;Parent=Msa0344910-mRNA-1
Gene Sequence

>Msa0344910

ATGGCTTTAACCGAAACCGCGGCGACGATGGAGGTGGTAGCCGTGAAGTGCTACTGTTGCGGCTTAACGGAGGAGTGCACTCCGTCGTATATTGACCATGTTCGTGAGAAATACCTGGGTCGTTGGATTTGTGGGCTATGTGCAGAGGCCGTGAAAGAAGAAGCTTTGAAATCGAAAAGAGATATTAGCACCGATGAAGCTCTTAATCAACACATGAATTTCAGAACTTTAACATCAAGTCCTCCTAATAAACCTACGGTTGATTTGATTCTTGCTGTGAAACATCTTCTTTTTCGGTCTTTGGATTCTCCGAGGAAACAACCTTTGAGTTTTCGAACGGTTGGTAGATCGCATAGATAA

Protein sequence

>Msa0344910

MALTETAATMEVVAVKCYCCGLTEECTPSYIDHVREKYLGRWICGLCAEAVKEEALKSKRDISTDEALNQHMNFRTLTSSPPNKPTVDLILAVKHLLFRSLDSPRKQPLSFRTVGRSHR*