AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0037790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0037790 MtrunA17_Chr1g0212471 75.676 185 43 1 1 185 1 183 3.08e-100 287
Msa0037790 MtrunA17_Chr4g0022641 56.477 193 72 4 1 185 1 189 4.85e-68 213
Msa0037790 MtrunA17_Chr4g0059631 62.420 157 55 1 1 157 1 153 2.28e-63 196
Msa0037790 MtrunA17_Chr2g0303981 45.355 183 87 3 3 184 5 175 3.16e-49 158
Msa0037790 MtrunA17_Chr6g0457851 35.849 159 101 1 1 159 11 168 2.95e-34 124
Msa0037790 MtrunA17_Chr1g0212151 37.736 159 98 1 1 159 1 158 7.10e-34 123
Msa0037790 MtrunA17_Chr6g0449851 36.047 172 109 1 1 172 1 171 4.03e-33 120
Msa0037790 MtrunA17_Chr6g0449861 31.667 180 122 1 1 180 9 187 1.69e-30 114
Msa0037790 MtrunA17_Chr3g0107381 25.843 178 115 4 1 169 1 170 4.10e-13 65.5
Msa0037790 MtrunA17_Chr2g0283941 29.333 150 89 5 2 142 3 144 2.47e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0037790 AT5G55690.1 33.557 149 77 4 1 143 1 133 1.87e-15 72.8
Msa0037790 AT5G55690.2 33.557 149 77 4 1 143 1 133 1.87e-15 72.8

Find 26 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACAATTGTATGGTCTTC+TGG 0.253429 1_1:+66964726 None:intergenic
TGGTCTTCTGGCCATGTTAT+TGG 0.266179 1_1:+66964738 None:intergenic
TCCAGTCTTGTTAGTGTATT+GGG 0.267250 1_1:+66964821 None:intergenic
TCTTCCATCTTAATTAAATC+TGG 0.297958 1_1:+66964549 None:intergenic
CTCCAGTCTTGTTAGTGTAT+TGG 0.305175 1_1:+66964820 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1_1:+66964659 None:intergenic
TCCATGTGTTGTTGCATTTG+AGG 0.399480 1_1:+66964387 None:intergenic
GCATCCAGATTTAATTAAGA+TGG 0.417713 1_1:-66964553 Msa0037790:CDS
GCATAGAGTTTACAATTGTA+TGG 0.435000 1_1:+66964718 None:intergenic
TGGAATTTGTAGAATGGGTC+GGG 0.450805 1_1:-66964931 None:intergenic
ATTAAATCTGGATGCCAAGT+TGG 0.464493 1_1:+66964561 None:intergenic
GATGATAGCTTTATGCACTT+TGG 0.469421 1_1:+66964596 None:intergenic
TTGGAATTTGTAGAATGGGT+CGG 0.500741 1_1:-66964932 None:intergenic
TGAACGACACTAAGTGGGCT+TGG 0.514956 1_1:+66964417 None:intergenic
TCCCAATACACTAACAAGAC+TGG 0.520688 1_1:-66964822 Msa0037790:CDS
TCGTTGACATCAAATATCTT+GGG 0.530959 1_1:+66964660 None:intergenic
ACCTCAAATGCAACAACACA+TGG 0.539597 1_1:-66964388 Msa0037790:CDS
ATGCTATGAACGACACTAAG+TGG 0.542543 1_1:+66964411 None:intergenic
TCGATATCATGTATCCAACT+TGG 0.557370 1_1:-66964575 Msa0037790:CDS
GATTGCTGTTATAAATGCAA+AGG 0.578620 1_1:-66964508 Msa0037790:CDS
ATGATATTATAGTGAGACGA+TGG 0.597377 1_1:-66964365 Msa0037790:CDS
GATGATGGTGGTAATAATGC+GGG 0.602556 1_1:-66964762 Msa0037790:CDS
TAACATGTTGAAAAGTGAGA+TGG 0.625075 1_1:-66964463 Msa0037790:CDS
TGCTATGAACGACACTAAGT+GGG 0.625498 1_1:+66964412 None:intergenic
ATAATGCGGGACCAATAACA+TGG 0.644832 1_1:-66964749 Msa0037790:CDS
TGATGATGGTGGTAATAATG+CGG 0.705229 1_1:-66964763 Msa0037790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAAATAAGAAAAAAA+TGG - chr1_1:66964643-66964662 Msa0037790:CDS 15.0%
! TCTTCCATCTTAATTAAATC+TGG + chr1_1:66964731-66964750 None:intergenic 25.0%
GCAAAAATACTTTCAAGCAA+AGG - chr1_1:66964408-66964427 Msa0037790:CDS 30.0%
ACTTTCAAGCAAAGGAAAAA+TGG - chr1_1:66964416-66964435 Msa0037790:CDS 30.0%
! TATGATGATGATGATGATGA+TGG - chr1_1:66964500-66964519 Msa0037790:CDS 30.0%
TTTACAATTGTATGGTCTTC+TGG + chr1_1:66964554-66964573 None:intergenic 30.0%
GCATAGAGTTTACAATTGTA+TGG + chr1_1:66964562-66964581 None:intergenic 30.0%
TCGTTGACATCAAATATCTT+GGG + chr1_1:66964620-66964639 None:intergenic 30.0%
GCATCCAGATTTAATTAAGA+TGG - chr1_1:66964724-66964743 Msa0037790:CDS 30.0%
! GATTGCTGTTATAAATGCAA+AGG - chr1_1:66964769-66964788 Msa0037790:CDS 30.0%
TAACATGTTGAAAAGTGAGA+TGG - chr1_1:66964814-66964833 Msa0037790:CDS 30.0%
ATGATATTATAGTGAGACGA+TGG - chr1_1:66964912-66964931 Msa0037790:CDS 30.0%
!! TCCAGTCTTGTTAGTGTATT+GGG + chr1_1:66964459-66964478 None:intergenic 35.0%
!! TGATGATGGTGGTAATAATG+CGG - chr1_1:66964514-66964533 Msa0037790:CDS 35.0%
GTCGTTGACATCAAATATCT+TGG + chr1_1:66964621-66964640 None:intergenic 35.0%
!! GATGATAGCTTTATGCACTT+TGG + chr1_1:66964684-66964703 None:intergenic 35.0%
TCGATATCATGTATCCAACT+TGG - chr1_1:66964702-66964721 Msa0037790:CDS 35.0%
ATTAAATCTGGATGCCAAGT+TGG + chr1_1:66964719-66964738 None:intergenic 35.0%
TCCCAATACACTAACAAGAC+TGG - chr1_1:66964455-66964474 Msa0037790:CDS 40.0%
!! CTCCAGTCTTGTTAGTGTAT+TGG + chr1_1:66964460-66964479 None:intergenic 40.0%
!! GATGATGATGATGATGATGG+TGG - chr1_1:66964503-66964522 Msa0037790:CDS 40.0%
!! GATGATGGTGGTAATAATGC+GGG - chr1_1:66964515-66964534 Msa0037790:CDS 40.0%
ATAATGCGGGACCAATAACA+TGG - chr1_1:66964528-66964547 Msa0037790:CDS 40.0%
TGCTATGAACGACACTAAGT+GGG + chr1_1:66964868-66964887 None:intergenic 40.0%
ATGCTATGAACGACACTAAG+TGG + chr1_1:66964869-66964888 None:intergenic 40.0%
ACCTCAAATGCAACAACACA+TGG - chr1_1:66964889-66964908 Msa0037790:CDS 40.0%
! TCCATGTGTTGTTGCATTTG+AGG + chr1_1:66964893-66964912 None:intergenic 40.0%
TGGTCTTCTGGCCATGTTAT+TGG + chr1_1:66964542-66964561 None:intergenic 45.0%
! TGAACGACACTAAGTGGGCT+TGG + chr1_1:66964863-66964882 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 66964359 66964940 66964359 ID=Msa0037790;Name=Msa0037790
chr1_1 mRNA 66964359 66964940 66964359 ID=Msa0037790-mRNA-1;Parent=Msa0037790;Name=Msa0037790-mRNA-1;_AED=0.05;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|193
chr1_1 exon 66964359 66964940 66964359 ID=Msa0037790-mRNA-1:exon:21677;Parent=Msa0037790-mRNA-1
chr1_1 CDS 66964359 66964940 66964359 ID=Msa0037790-mRNA-1:cds;Parent=Msa0037790-mRNA-1
Gene Sequence

>Msa0037790

ATGGGTCGGGCGAAAATAACTATGAAATACATTAAAAATAAGAAAAATCGCAAAAATACTTTCAAGCAAAGGAAAAATGGACTCATAAAGAAAATTTCCCAATACACTAACAAGACTGGAGCAAAAGCTTGCTTGATTGTGTATGATGATGATGATGATGATGGTGGTAATAATGCGGGACCAATAACATGGCCAGAAGACCATACAATTGTAAACTCTATGCTTCAAGAGTATGTGCATCAAGAGATTGAGAAAACACCCAAGATATTTGATGTCAACGACTACTTTGAAAATAAGAAAAAAATGGTTGAAACTGAGATTACCAAAGTGCATAAAGCTATCATCGATATCATGTATCCAACTTGGCATCCAGATTTAATTAAGATGGAAGAGAGTGAACTCAAAGACTTGATTGCTGTTATAAATGCAAAGGTAGATGCTTGTAATCTCAAAATTAACATGTTGAAAAGTGAGATGGTGAAAGAGAATGTTGTTTTGAATCCAAGCCCACTTAGTGTCGTTCATAGCATACCTCAAATGCAACAACACATGGATGATATTATAGTGAGACGATGGATATGA
Protein sequence

>Msa0037790

MGRAKITMKYIKNKKNRKNTFKQRKNGLIKKISQYTNKTGAKACLIVYDDDDDDGGNNAGPITWPEDHTIVNSMLQEYVHQEIEKTPKIFDVNDYFENKKKMVETEITKVHKAIIDIMYPTWHPDLIKMEESELKDLIAVINAKVDACNLKINMLKSEMVKENVVLNPSPLSVVHSIPQMQQHMDDIIVRRWI*