AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG005498

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005498 MtrunA17_Chr1g0209041 99.160 357 3 0 1 357 1 357 0.0 738
MsaG005498 MtrunA17_Chr5g0442111 82.432 74 4 1 272 345 24 88 2.09e-39 135
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG005498 AT1G68200.1 49.020 306 109 8 62 352 29 302 5.93e-85 260
MsaG005498 AT1G68200.5 49.020 306 109 8 62 352 29 302 5.93e-85 260
MsaG005498 AT1G68200.2 48.693 306 109 8 62 352 29 301 2.10e-83 256
MsaG005498 AT1G68200.6 48.693 306 109 8 62 352 29 301 2.10e-83 256
MsaG005498 AT1G66810.1 61.644 146 47 1 200 345 168 304 2.41e-55 184
MsaG005498 AT1G66810.3 61.644 146 47 1 200 345 168 304 2.41e-55 184
MsaG005498 AT1G68200.4 41.026 156 72 5 62 217 29 164 4.70e-22 92.8
MsaG005498 AT1G68200.3 41.026 156 72 5 62 217 29 164 4.70e-22 92.8

Find 103 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCTGCAGGATGGTCCTTGC+TGG 0.159266 1:-82076135 MsaT005498.1:CDS
CTGCAGAGCTTCAACTTCTT+TGG 0.179049 1:+82078674 None:intergenic
TCTTTCCAGCTTCATTGATC+TGG 0.216499 1:+82076032 None:intergenic
GCCGCCGTTGCTGCTGTTTC+CGG 0.266911 1:+82078815 None:intergenic
GCCGATGCCGTAACCGCTTT+TGG 0.267264 1:+82078926 None:intergenic
CAACTTCTTTGGAACTTTCC+AGG 0.279329 1:+82078685 None:intergenic
TAGCGTGGGTGGCGGATCAC+TGG 0.295264 1:+82076168 None:intergenic
GATCTAACAGAAATGCTCTT+TGG 0.302932 1:+82078345 None:intergenic
GCGGGAGCGAGTAGCGCTTT+TGG 0.327959 1:+82078260 None:intergenic
GTCAATTCGCTCATGGCATT+GGG 0.349776 1:-82076200 MsaT005498.1:CDS
GGTTTCCGTGGCTTGAATCT+TGG 0.355570 1:-82078510 MsaT005498.1:CDS
CTTTCCAGCTTCATTGATCT+GGG 0.356760 1:+82076033 None:intergenic
CATGACGGAAATGGCATCTA+TGG 0.367595 1:+82076094 None:intergenic
CTTTATCCTTACTCTGACCT+TGG 0.377357 1:-82078783 MsaT005498.1:CDS
GAAACTGGCACATGCCCTTA+TGG 0.383739 1:-82076231 MsaT005498.1:CDS
TAATAATAACAAGGAGTTGC+AGG 0.387088 1:-82078442 MsaT005498.1:CDS
CCGTCATCCAAAAGCGGTTA+CGG 0.390482 1:-82078933 MsaT005498.1:CDS
GATACAGAAGCATCAGGATA+TGG 0.396830 1:-82078739 MsaT005498.1:CDS
CTGTTTCCGGCGAGCGATGA+TGG 0.396990 1:+82078828 None:intergenic
TGTAACAAATGGCAGGAAAC+TGG 0.399409 1:-82076246 MsaT005498.1:CDS
TCTGCAGGATGGTCCTTGCT+GGG 0.402584 1:-82076134 MsaT005498.1:CDS
CTTCTGCAACTCTTTGTTCA+CGG 0.410248 1:+82078629 None:intergenic
CAGTAAGTGCATGACGGAAA+TGG 0.414882 1:+82076085 None:intergenic
CCTTCTCGTTCAAGCTTCGC+TGG 0.421155 1:-82078598 MsaT005498.1:CDS
TATGTTTCTCAGTCGTCTCC+TGG 0.438714 1:-82078703 MsaT005498.1:CDS
CAAACGGAGTTGATTGAGTC+TGG 0.444450 1:+82078544 None:intergenic
TGTCAATTCGCTCATGGCAT+TGG 0.444853 1:-82076201 MsaT005498.1:CDS
CTTGAAGCTTGCTCCGCCTC+CGG 0.468503 1:-82078313 MsaT005498.1:CDS
AATTGACAGTGGTCTCCATA+AGG 0.472418 1:+82076216 None:intergenic
CGTGGCTTGAATCTTGGAGA+TGG 0.475661 1:-82078504 MsaT005498.1:CDS
GAAAGGAAAACTGTGCTGAT+TGG 0.476246 1:-82078482 MsaT005498.1:CDS
GGCGTTCGACTGCATGTGAC+CGG 0.476954 1:+82078893 None:intergenic
AGCATTTCTGTTAGATCCAA+TGG 0.486635 1:-82078339 MsaT005498.1:CDS
TCCAAAAGCGGTTACGGCAT+CGG 0.490846 1:-82078927 MsaT005498.1:CDS
CGTCGGACTCTCATCAGATT+CGG 0.492348 1:+82078413 None:intergenic
GAAGCTCTGCAGCAGGAAAA+CGG 0.500754 1:-82078663 MsaT005498.1:CDS
AAACCTTGCAACACATCAAA+CGG 0.507246 1:+82078528 None:intergenic
TGAGAATAACGGTGTTGAAA+CGG 0.507485 1:-82078382 MsaT005498.1:CDS
AGCGTGGGTGGCGGATCACT+GGG 0.510898 1:+82076169 None:intergenic
AAATGGCATCTATGGCCATA+CGG 0.511220 1:+82076102 None:intergenic
GCTGGGGTTGTGTGCCCGTA+TGG 0.512898 1:-82076117 MsaT005498.1:CDS
ATGCGTGATACAGAAGCATC+AGG 0.518868 1:-82078745 MsaT005498.1:CDS
TCGCTGGAGAACCGATTCAA+TGG 0.519751 1:-82078582 MsaT005498.1:CDS
CTCGCCGGAAACAGCAGCAA+CGG 0.524709 1:-82078819 MsaT005498.1:CDS
GGAAACAGCAGCAACGGCGG+CGG 0.524773 1:-82078813 MsaT005498.1:CDS
GCCGGAAACAGCAGCAACGG+CGG 0.525054 1:-82078816 MsaT005498.1:CDS
GCTACAAAACTGAGGTCTGC+AGG 0.527724 1:-82076149 MsaT005498.1:CDS
TTAGTTACGACGGCCGGAGG+CGG 0.529646 1:+82078300 None:intergenic
AGAAGTTGAAGCTCTGCAGC+AGG 0.529958 1:-82078670 MsaT005498.1:CDS
ATTGACAGTGGTCTCCATAA+GGG 0.530052 1:+82076217 None:intergenic
TAAGCCCAGATCAATGAAGC+TGG 0.530814 1:-82076037 MsaT005498.1:CDS
AGCAAGCTTCAAGTAGCCAT+TGG 0.531440 1:+82078323 None:intergenic
AGACTGAGCTCTGTAACAAA+TGG 0.531908 1:-82076257 MsaT005498.1:CDS
AATGGCATCTATGGCCATAC+GGG 0.531942 1:+82076103 None:intergenic
AGGATCCGCCACCATTGAAT+CGG 0.534519 1:+82078571 None:intergenic
GCTCAGTCTTGAACATCCCC+TGG 0.541107 1:+82076271 None:intergenic
TCTGTTCCAAGGTCAGAGTA+AGG 0.546191 1:+82078777 None:intergenic
GATCTTCCATCATCGCTCGC+CGG 0.559218 1:-82078834 MsaT005498.1:CDS
ACTCCGTTTGATGTGTTGCA+AGG 0.560653 1:-82078531 MsaT005498.1:CDS
TGAGCTCTGTAACAAATGGC+AGG 0.566245 1:-82076253 MsaT005498.1:CDS
AGCATTGTTGTTAGTTACGA+CGG 0.567553 1:+82078290 None:intergenic
CATCTCCAAGATTCAAGCCA+CGG 0.567612 1:+82078505 None:intergenic
TGTGCGAGGAGGGCAGAAAG+AGG 0.570699 1:-82076322 MsaT005498.1:CDS
GACCACTGTCAATTCGCTCA+TGG 0.571725 1:-82076207 MsaT005498.1:CDS
CTGCAGGATGGTCCTTGCTG+GGG 0.572424 1:-82076133 MsaT005498.1:CDS
AGAGGAAGAGCCTCTTGAGA+TGG 0.573431 1:-82076304 MsaT005498.1:CDS
AAAAGGTATTTGTGCGAGGA+GGG 0.574881 1:-82076332 MsaT005498.1:CDS
GAGAACCGATTCAATGGTGG+CGG 0.578241 1:-82078576 MsaT005498.1:CDS
CCAGCGAAGCTTGAACGAGA+AGG 0.578885 1:+82078598 None:intergenic
TACAACTGTATCAGATTGAG+TGG 0.578967 1:+82078230 None:intergenic
TGAGATGGTTGTGTACAACC+AGG 0.582022 1:-82076289 MsaT005498.1:CDS
CTTGAATCTTGGAGATGGAA+AGG 0.582921 1:-82078499 MsaT005498.1:CDS
CAGATTGAGTGGAGGAAGCG+CGG 0.588323 1:+82078241 None:intergenic
CGGAGTTGATTGAGTCTGGA+CGG 0.589982 1:+82078548 None:intergenic
GCAACTCTTTGTTCACGGCA+CGG 0.595404 1:+82078634 None:intergenic
AGATTGAGTGGAGGAAGCGC+GGG 0.600576 1:+82078242 None:intergenic
CAAAAGGTATTTGTGCGAGG+AGG 0.603500 1:-82076333 MsaT005498.1:CDS
TTGTTGTTAGTTACGACGGC+CGG 0.605294 1:+82078294 None:intergenic
GATGTGTTGCAAGGTTTCCG+TGG 0.607851 1:-82078522 MsaT005498.1:CDS
GGTCACATGCAGTCGAACGC+CGG 0.607925 1:-82078891 MsaT005498.1:CDS
CTTGTTCAGTAAGTGCATGA+CGG 0.608476 1:+82076079 None:intergenic
CAAAACTGAGGTCTGCAGGA+TGG 0.616724 1:-82076145 MsaT005498.1:CDS
ACGAGTGTGATTGAGAATAA+CGG 0.622937 1:-82078393 MsaT005498.1:CDS
ATGAGTCGTACTCTGTTCCA+AGG 0.623681 1:+82078766 None:intergenic
ACGGGCACACAACCCCAGCA+AGG 0.626804 1:+82076121 None:intergenic
CTGGAGAACCGATTCAATGG+TGG 0.634958 1:-82078579 MsaT005498.1:CDS
TGTTCTCCGTCATCCAAAAG+CGG 0.637659 1:-82078939 MsaT005498.1:CDS
GAGATGGTTGTGTACAACCA+GGG 0.638365 1:-82076288 MsaT005498.1:CDS
TTGTTAGTTACGACGGCCGG+AGG 0.641381 1:+82078297 None:intergenic
CAGCAAAAGGTATTTGTGCG+AGG 0.645044 1:-82076336 MsaT005498.1:CDS
GGCATCGGCGTCAACAACGC+CGG 0.645707 1:-82078912 MsaT005498.1:CDS
TCAATTCGCTCATGGCATTG+GGG 0.646224 1:-82076199 MsaT005498.1:CDS
TTGTACACAACCATCTCAAG+AGG 0.647753 1:+82076294 None:intergenic
ACCGATCAAAATGCATAACA+AGG 0.654571 1:-82078967 None:intergenic
AACTGTATCAGATTGAGTGG+AGG 0.659126 1:+82078233 None:intergenic
TAACATCAATAATAATAACA+AGG 0.675567 1:-82078451 MsaT005498.1:CDS
TGCCATGAGCGAATTGACAG+TGG 0.682669 1:+82076205 None:intergenic
TTATTCTCAATCACACTCGT+CGG 0.688787 1:+82078396 None:intergenic
AGTTGATTGAGTCTGGACGG+AGG 0.689033 1:+82078551 None:intergenic
ATAACGGTGTTGAAACGGAG+AGG 0.717587 1:-82078377 MsaT005498.1:CDS
CCACCCACGCTACAAAACTG+AGG 0.721664 1:-82076157 MsaT005498.1:CDS
AGATGGTTGTGTACAACCAG+GGG 0.741581 1:-82076287 MsaT005498.1:CDS
GTACAACGAAGCAAACACGC+CGG 0.782658 1:+82078872 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 82076029 82078979 82076029 ID=MsaG005498
Chr1 mRNA 82076029 82078979 82076029 ID=MsaT005498.1;Parent=MsaG005498
Chr1 exon 82076029 82076355 82076029 ID=MsaT005498.1.exon2;Parent=MsaT005498.1
Chr1 CDS 82076029 82076355 82076029 ID=cds.MsaT005498.1;Parent=MsaT005498.1
Chr1 exon 82078233 82078979 82078233 ID=MsaT005498.1.exon1;Parent=MsaT005498.1
Chr1 CDS 82078233 82078979 82078233 ID=cds.MsaT005498.1;Parent=MsaT005498.1
Gene Sequence

>MsaT005498.1

ATGCATAACAAGGACGTTTGTTCTCCGTCATCCAAAAGCGGTTACGGCATCGGCGTCAACAACGCCGGTCACATGCAGTCGAACGCCGGCGTGTTTGCTTCGTTGTACTCTGCTCTGAGTAATGATCTTCCATCATCGCTCGCCGGAAACAGCAGCAACGGCGGCGGATTTTCGCTTTATCCTTACTCTGACCTTGGAACAGAGTACGACTCATGCGTGATACAGAAGCATCAGGATATGGTGAATCGTCACAGTATGTTTCTCAGTCGTCTCCTGGAAAGTTCCAAAGAAGTTGAAGCTCTGCAGCAGGAAAACGGACAGCTCCGTGCCGTGAACAAAGAGTTGCAGAAGAATCTGAACCTTCTCGTTCAAGCTTCGCTGGAGAACCGATTCAATGGTGGCGGATCCTCCGTCCAGACTCAATCAACTCCGTTTGATGTGTTGCAAGGTTTCCGTGGCTTGAATCTTGGAGATGGAAAGGAAAACTGTGCTGATTGGAATAGCAATAACATCAATAATAATAACAAGGAGTTGCAGGAAGCTTCCGAATCTGATGAGAGTCCGACGAGTGTGATTGAGAATAACGGTGTTGAAACGGAGAGGTTCTCGCTTCCAAAGAGCATTTCTGTTAGATCCAATGGCTACTTGAAGCTTGCTCCGCCTCCGGCCGTCGTAACTAACAACAATGCTTGCCGCACCAAAAGCGCTACTCGCTCCCGCGCTTCCTCCACTCAATCTGATACAGTTCAAAAGGTATTTGTGCGAGGAGGGCAGAAAGAGGAAGAGCCTCTTGAGATGGTTGTGTACAACCAGGGGATGTTCAAGACTGAGCTCTGTAACAAATGGCAGGAAACTGGCACATGCCCTTATGGAGACCACTGTCAATTCGCTCATGGCATTGGGGAGCTTCGCCCAGTGATCCGCCACCCACGCTACAAAACTGAGGTCTGCAGGATGGTCCTTGCTGGGGTTGTGTGCCCGTATGGCCATAGATGCCATTTCCGTCATGCACTTACTGAACAAGAGAAAGCTGTGTCACAATCTAAGCCCAGATCAATGAAGCTGGAAAGATGA
Protein sequence

>MsaT005498.1

MHNKDVCSPSSKSGYGIGVNNAGHMQSNAGVFASLYSALSNDLPSSLAGNSSNGGGFSLYPYSDLGTEYDSCVIQKHQDMVNRHSMFLSRLLESSKEVEALQQENGQLRAVNKELQKNLNLLVQASLENRFNGGGSSVQTQSTPFDVLQGFRGLNLGDGKENCADWNSNNINNNNKELQEASESDESPTSVIENNGVETERFSLPKSISVRSNGYLKLAPPPAVVTNNNACRTKSATRSRASSTQSDTVQKVFVRGGQKEEEPLEMVVYNQGMFKTELCNKWQETGTCPYGDHCQFAHGIGELRPVIRHPRYKTEVCRMVLAGVVCPYGHRCHFRHALTEQEKAVSQSKPRSMKLER*