AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG004927

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG004927 MtrunA17_Chr1g0202341 91.367 139 7 2 1 138 1 135 2.09e-85 267
MsaG004927 MtrunA17_Chr1g0202341 80.315 127 24 1 108 233 560 686 1.23e-59 199
MsaG004927 MtrunA17_Chr3g0077241 61.702 94 32 2 14 106 1 91 8.52e-31 110
MsaG004927 MtrunA17_Chr4g0052331 55.914 93 41 0 13 105 5 97 2.88e-30 108
MsaG004927 MtrunA17_Chr2g0329361 36.634 101 61 2 49 148 59 157 2.19e-15 73.2
MsaG004927 MtrunA17_Chr2g0329421 39.286 84 39 2 50 128 26 102 5.19e-12 63.2
MsaG004927 MtrunA17_Chr4g0033611 33.028 109 61 2 25 128 50 151 3.06e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATTGTTTAATAGTATTA+TGG 0.227693 1:-75826461 MsaT004927.1:CDS
TTCCTTGTTTCACATACTTT+TGG 0.229711 1:+75828033 None:intergenic
CATTCCTTCAATGGGCTCTA+AGG 0.236305 1:+75828205 None:intergenic
AACTGTGTTCCTAAAGAAAA+AGG 0.312218 1:-75826599 MsaT004927.1:CDS
TTTAAACTCCATTCCTTCAA+TGG 0.364249 1:+75828196 None:intergenic
AGAACAAACGGTATGATAAT+TGG 0.370543 1:-75828089 MsaT004927.1:CDS
ATTCCTTCAATGGGCTCTAA+GGG 0.384475 1:+75828206 None:intergenic
TTAAACTCCATTCCTTCAAT+GGG 0.435121 1:+75828197 None:intergenic
TTGACAATTGAAGAATTTGA+AGG 0.456352 1:-75826505 MsaT004927.1:CDS
TCCTTCAATGGGCTCTAAGG+GGG 0.466966 1:+75828208 None:intergenic
TCAAGAAATTCTTTGTTCCA+AGG 0.511520 1:-75828066 MsaT004927.1:CDS
CCTTCAATGGGCTCTAAGGG+GGG 0.511902 1:+75828209 None:intergenic
GAAATTCTTTGTTCCAAGGA+GGG 0.512083 1:-75828062 MsaT004927.1:CDS
CACAGTATGTTCTACAACGA+TGG 0.518628 1:-75826561 MsaT004927.1:CDS
CTTAGAGCCCATTGAAGGAA+TGG 0.526994 1:-75828204 MsaT004927.1:CDS
ACAATTGAAGAATTTGAAGG+AGG 0.530417 1:-75826502 MsaT004927.1:CDS
GTTACTAAGTCAAGAACAAA+CGG 0.531428 1:-75828101 MsaT004927.1:CDS
AGGTCATGAGATGACAGATA+TGG 0.541561 1:-75828318 MsaT004927.1:CDS
GATGGTGGTTCACTATTGAG+AGG 0.542446 1:+75828236 None:intergenic
CGAGAAAATGAAAGACGATT+CGG 0.551598 1:-75829788 None:intergenic
TGAAACCAGGGTGGGATGCA+AGG 0.555494 1:-75827988 MsaT004927.1:CDS
TTCCTTCAATGGGCTCTAAG+GGG 0.577393 1:+75828207 None:intergenic
CCGTGCCTTGCATCCCACCC+TGG 0.580963 1:+75827983 None:intergenic
CGTTGTAGAACATACTGTGA+AGG 0.588365 1:+75826565 None:intergenic
CATGAGATGACAGATATGGA+TGG 0.601625 1:-75828314 MsaT004927.1:CDS
AGAAATTCTTTGTTCCAAGG+AGG 0.607187 1:-75828063 MsaT004927.1:CDS
AGCCAAAAGTATGTGAAACA+AGG 0.613058 1:-75828035 MsaT004927.1:CDS
GTTGTAGAACATACTGTGAA+GGG 0.621697 1:+75826566 None:intergenic
AGAGCTTGAAGAATCAAATG+AGG 0.626048 1:-75826338 MsaT004927.1:CDS
TTATTACACATGATGAAACC+AGG 0.637175 1:-75828001 MsaT004927.1:CDS
ACAAGGTACGCTCAGAACAA+AGG 0.639870 1:-75828146 MsaT004927.1:CDS
CCAGGGTGGGATGCAAGGCA+CGG 0.641442 1:-75827983 MsaT004927.1:intron
ACACATGATGAAACCAGGGT+GGG 0.653979 1:-75827996 MsaT004927.1:CDS
ACTTAGTAACACGGCCCATG+CGG 0.656322 1:+75828114 None:intergenic
AAGCGAAGAGTTACTACACA+AGG 0.658359 1:-75828163 MsaT004927.1:CDS
TTGTTCTTGACTTAGTAACA+CGG 0.665948 1:+75828105 None:intergenic
TACACATGATGAAACCAGGG+TGG 0.688016 1:-75827997 MsaT004927.1:CDS
TATTACACATGATGAAACCA+GGG 0.694710 1:-75828000 MsaT004927.1:CDS
TGTATCATTTGAGACAACCA+TGG 0.701765 1:+75828283 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 75826315 75829803 75826315 ID=MsaG004927
Chr1 mRNA 75826315 75829803 75826315 ID=MsaT004927.1;Parent=MsaG004927
Chr1 exon 75826315 75826630 75826315 ID=MsaT004927.1.exon3;Parent=MsaT004927.1
Chr1 CDS 75826315 75826630 75826315 ID=cds.MsaT004927.1;Parent=MsaT004927.1
Chr1 exon 75827984 75828338 75827984 ID=MsaT004927.1.exon2;Parent=MsaT004927.1
Chr1 CDS 75827984 75828338 75827984 ID=cds.MsaT004927.1;Parent=MsaT004927.1
Chr1 exon 75829773 75829803 75829773 ID=MsaT004927.1.exon1;Parent=MsaT004927.1
Chr1 CDS 75829773 75829803 75829773 ID=cds.MsaT004927.1;Parent=MsaT004927.1
Gene Sequence

>MsaT004927.1

ATGAAAGACGATTCGGTGCACTCAAAACCTTGTCATGAGATGACAGATATGGATGGAGATTTTACCATGGTTGTCTCAAATGATACACATGTCAGTGCTCTTGATGTGAAGCCTCTCAATAGTGAACCACCATCAGAGCCCCCCTTAGAGCCCATTGAAGGAATGGAGTTTAAATCATTTGAAGAAGCGAAGAGTTACTACACAAGGTACGCTCAGAACAAAGGTTTTAGTTTCCGCATGGGCCGTGTTACTAAGTCAAGAACAAACGGTATGATAATTGGTCAAGAAATTCTTTGTTCCAAGGAGGGTTTGAGCCAAAAGTATGTGAAACAAGGAAATAGTAGTCTTATTACACATGATGAAACCAGGGTGGGATGCAAGGCACGGCATATCTTAACTGTGTTCCTAAAGAAAAAGGTACGTTATCTCCCTTCACAGTATGTTCTACAACGATGGACCCGAAATGCTAAGAAAGAAAAATTTGAAGGATTGACAATTGAAGAATTTGAAGGAGGAAACAAAGCTTCTAGCACTTCATTGTTTAATAGTATTATGGTTCGTTCACTTGAATTTTCTGAAAGAGCTTCATGGTCAAAAAAACATCATGATATTGCAATTCAATGTTTGCAAAATGCAATTGCAAAACTTGATCTATTAGAGCTTGAAGAATCAAATGAGGAGTTTGTTAATTTGACATCTTAA
Protein sequence

>MsaT004927.1

MKDDSVHSKPCHEMTDMDGDFTMVVSNDTHVSALDVKPLNSEPPSEPPLEPIEGMEFKSFEEAKSYYTRYAQNKGFSFRMGRVTKSRTNGMIIGQEILCSKEGLSQKYVKQGNSSLITHDETRVGCKARHILTVFLKKKVRYLPSQYVLQRWTRNAKKEKFEGLTIEEFEGGNKASSTSLFNSIMVRSLEFSERASWSKKHHDIAIQCLQNAIAKLDLLELEESNEEFVNLTS*