AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG029918

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG029918 MtrunA17_Chr5g0448611 61.585 328 50 14 16 340 25 279 4.73e-99 294
MsaG029918 MtrunA17_Chr5g0425411 65.414 266 29 9 19 282 16 220 6.14e-95 282
MsaG029918 MtrunA17_Chr4g0012791 24.484 339 155 8 41 315 79 380 2.41e-20 91.7
MsaG029918 MtrunA17_Chr4g0061301 31.100 209 89 5 124 331 347 501 1.39e-18 86.7
MsaG029918 MtrunA17_Chr1g0197281 30.198 202 84 5 125 322 156 304 1.37e-13 70.9
MsaG029918 MtrunA17_Chr4g0012691 30.256 195 71 5 121 315 216 345 9.63e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG029918 AT4G35280.1 40.727 275 79 6 35 296 71 274 1.01e-54 181
MsaG029918 AT2G17180.1 57.937 126 36 2 39 156 63 179 1.71e-39 140
MsaG029918 AT5G56200.1 31.746 189 74 5 123 311 340 473 1.33e-14 75.1
MsaG029918 AT1G02040.1 46.250 80 36 2 83 155 101 180 2.33e-11 64.3

Find 98 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAAGGTGTCATTGGGAAAA+AGG 0.228044 5:+83212020 MsaT029918.1:CDS
TCGTGTTGCAACAAAGTATT+TGG 0.254538 5:+83211615 MsaT029918.1:CDS
GCAGCACCTTCCTGTTCTTC+TGG 0.259557 5:-83211495 None:intergenic
TCTTCTTCATCTGTTGTTAC+TGG 0.269278 5:+83211264 MsaT029918.1:CDS
AGTTGTGGTCTTCTGAAATT+AGG 0.270404 5:-83211456 None:intergenic
CTCCCCTCAGCCTTGATTTG+AGG 0.284244 5:+83212222 MsaT029918.1:CDS
CTCAGCCTTGATTTGAGGTT+GGG 0.292402 5:+83212227 MsaT029918.1:CDS
CTGAATGCGGTAAGATATTC+TGG 0.313666 5:+83211364 MsaT029918.1:CDS
TCAGGAGGTGGTGGTGGAAA+AGG 0.369982 5:-83212170 None:intergenic
CCTCAGCCTTGATTTGAGGT+TGG 0.373861 5:+83212226 MsaT029918.1:CDS
AGCAGTACCCCTCAAGGAAT+TGG 0.378939 5:+83211735 MsaT029918.1:CDS
GTCTGAGGCACCATGATCAT+TGG 0.382607 5:-83211831 None:intergenic
AGCGGTTATTGTTGTTGTAT+TGG 0.394693 5:-83211697 None:intergenic
ACTACTAGACTTGTTGTTGT+TGG 0.399673 5:-83212120 None:intergenic
GTGGTCACAAAAGGTGTCAT+TGG 0.407889 5:+83212012 MsaT029918.1:CDS
AAGAAGAAGCGTAAGGAATT+CGG 0.417811 5:+83211288 MsaT029918.1:CDS
CTCCTCCTCCAATTCCTTGA+GGG 0.423809 5:-83211743 None:intergenic
AAGCGTAAGGAATTCGGCTC+CGG 0.438803 5:+83211294 MsaT029918.1:CDS
CAAAGTATTTGGATCTCATC+AGG 0.456499 5:+83211626 MsaT029918.1:CDS
GCTGAGGGGAGAAGAAGAAT+CGG 0.458860 5:-83212210 None:intergenic
ATTCCTCTCCATTGACGCTC+AGG 0.461015 5:-83211423 None:intergenic
GTTGTTGTTGTTGCAACTGC+TGG 0.463828 5:-83211567 None:intergenic
TGTTTGAGGGTATTCACCTC+TGG 0.465821 5:+83211978 MsaT029918.1:CDS
TACCGCGACTCCAGAAGAAC+AGG 0.473036 5:+83211485 MsaT029918.1:CDS
CAGGAGGTGGTGGTGGAAAA+GGG 0.474090 5:-83212169 None:intergenic
AATTCCTTGAGGGGTACTGC+TGG 0.478356 5:-83211733 None:intergenic
TCATTGGGTGTTGTTGATGA+TGG 0.481633 5:-83211815 None:intergenic
AACAATAACAATAACAATGT+TGG 0.482830 5:+83211876 MsaT029918.1:CDS
TCCGGGGAATCATCATCATC+TGG 0.485557 5:+83211312 MsaT029918.1:CDS
TCATCATCAGGAGGTGGTGG+TGG 0.489318 5:-83212176 None:intergenic
GGATGATGATCATCATCATC+AGG 0.494007 5:-83212188 None:intergenic
TCTGAGGCACCATGATCATT+GGG 0.496728 5:-83211830 None:intergenic
AGCGTAAGGAATTCGGCTCC+GGG 0.496896 5:+83211295 MsaT029918.1:CDS
AAGCACTCGGTGGTCACAAA+AGG 0.500352 5:+83212003 MsaT029918.1:CDS
TGGTCACAAAAGGTGTCATT+GGG 0.500704 5:+83212013 MsaT029918.1:CDS
TGGAAACGTGGAAGGGGAAG+CGG 0.512114 5:+83211899 MsaT029918.1:CDS
GGATCTCATCAGGCACTTGG+AGG 0.512393 5:+83211636 MsaT029918.1:CDS
GTTGTCATCCTGAGCGTCAA+TGG 0.514198 5:+83211415 MsaT029918.1:CDS
AAAGTCCCAACCTCAAATCA+AGG 0.519574 5:-83212232 None:intergenic
ACAAGTGTAGCATATGTTTG+AGG 0.520240 5:+83211964 MsaT029918.1:CDS
AATAACAATAACAATGTTGG+TGG 0.522015 5:+83211879 MsaT029918.1:CDS
TTTGGATCTCATCAGGCACT+TGG 0.527004 5:+83211633 MsaT029918.1:CDS
CCTCAGACTCGTGGTGGTGA+CGG 0.528908 5:+83211846 MsaT029918.1:CDS
TCAACAACACCCAATGATCA+TGG 0.533233 5:+83211821 MsaT029918.1:CDS
TCGAATGGTAATGTTGTTGA+TGG 0.537184 5:-83212056 None:intergenic
CTGAGGGGAGAAGAAGAATC+GGG 0.541339 5:-83212209 None:intergenic
TGTGGTCTTCTGAAATTAGG+AGG 0.542449 5:-83211453 None:intergenic
GCGGTAAGATATTCTGGTCA+TGG 0.544652 5:+83211370 MsaT029918.1:CDS
ATCAGGCACTTGGAGGACAC+AGG 0.546807 5:+83211643 MsaT029918.1:CDS
TCTCCTCCTCCAATTCCTTG+AGG 0.553008 5:-83211744 None:intergenic
ACCAGATGATGATGATTCCC+CGG 0.553428 5:-83211313 None:intergenic
CAAGTGTAGCATATGTTTGA+GGG 0.557225 5:+83211965 MsaT029918.1:CDS
TGCAACAACAACAACGGTGG+TGG 0.560440 5:+83211575 MsaT029918.1:CDS
GTCTTCTGAAATTAGGAGGA+GGG 0.563842 5:-83211449 None:intergenic
CCAACCTCAAATCAAGGCTG+AGG 0.568598 5:-83212226 None:intergenic
TTCACCTCTGGACAAGCACT+CGG 0.569437 5:+83211990 MsaT029918.1:CDS
AGTACCCCTCAAGGAATTGG+AGG 0.570140 5:+83211738 MsaT029918.1:CDS
ACCCCTCAAGGAATTGGAGG+AGG 0.572628 5:+83211741 MsaT029918.1:CDS
TGTTGGTGGAAACGTGGAAG+GGG 0.573504 5:+83211893 MsaT029918.1:CDS
TCCTCCTCCAATTCCTTGAG+GGG 0.573541 5:-83211742 None:intergenic
GGTCTTCTGAAATTAGGAGG+AGG 0.578908 5:-83211450 None:intergenic
TCATCATCATCAGGAGGTGG+TGG 0.579076 5:-83212179 None:intergenic
TAATGTTGTTGATGGTGTGG+TGG 0.579959 5:-83212048 None:intergenic
TGCAGTTGCAGTTGCAGTTG+CGG 0.585594 5:-83212090 None:intergenic
GGCTAGTCACAAGAATGTCA+AGG 0.586833 5:+83211665 MsaT029918.1:CDS
AATGTTGGTGGAAACGTGGA+AGG 0.586957 5:+83211891 MsaT029918.1:CDS
AATAACGAAATCATAAGCAT+CGG 0.587279 5:+83211933 MsaT029918.1:CDS
CAACCTCAAATCAAGGCTGA+GGG 0.588474 5:-83212225 None:intergenic
TAAGATATTCTGGTCATGGA+AGG 0.594766 5:+83211374 MsaT029918.1:CDS
AACGAAATCATAAGCATCGG+AGG 0.603782 5:+83211936 MsaT029918.1:CDS
CCGTCACCACCACGAGTCTG+AGG 0.606419 5:-83211846 None:intergenic
TTCCTGTTCTTCTGGAGTCG+CGG 0.607526 5:-83211487 None:intergenic
TACTGGTAAGAAGAAGCGTA+AGG 0.609817 5:+83211281 MsaT029918.1:CDS
GAAATCATAAGCATCGGAGG+AGG 0.616674 5:+83211939 MsaT029918.1:CDS
TGGACCAGCAGTACCCCTCA+AGG 0.619084 5:+83211729 MsaT029918.1:CDS
TGATCATCATCATCAGGAGG+TGG 0.620196 5:-83212182 None:intergenic
TGGTAATGTTGTTGATGGTG+TGG 0.620418 5:-83212051 None:intergenic
ATGTTGGTGGAAACGTGGAA+GGG 0.632193 5:+83211892 MsaT029918.1:CDS
GCTAGTCACAAGAATGTCAA+GGG 0.632503 5:+83211666 MsaT029918.1:CDS
CATCCTGAGCGTCAATGGAG+AGG 0.633209 5:+83211420 MsaT029918.1:CDS
TAACAATGTTGGTGGAAACG+TGG 0.636140 5:+83211887 MsaT029918.1:CDS
GTCGCGGTATTGATGAGTTG+TGG 0.636172 5:-83211471 None:intergenic
GCTCGTAGTTGCACTGAATG+CGG 0.637940 5:+83211351 MsaT029918.1:CDS
TCAGGCACTTGGAGGACACA+GGG 0.641355 5:+83211644 MsaT029918.1:CDS
CAATAACCGCTTCTTCTACG+TGG 0.643180 5:+83211709 MsaT029918.1:CDS
GCGGTAGAAGAAGAATCGAA+TGG 0.655654 5:-83212071 None:intergenic
GCTGGTCCACGTAGAAGAAG+CGG 0.656413 5:-83211715 None:intergenic
ATCATGGTGCCTCAGACTCG+TGG 0.664991 5:+83211837 MsaT029918.1:CDS
ACCTCTGGACAAGCACTCGG+TGG 0.666232 5:+83211993 MsaT029918.1:CDS
ACAACAGATGAAGAAGAACA+TGG 0.667372 5:-83211258 None:intergenic
AACCTCAAATCAAGGCTGAG+GGG 0.678963 5:-83212224 None:intergenic
TGATGATCATCATCATCAGG+AGG 0.687105 5:-83212185 None:intergenic
GCGTAAGGAATTCGGCTCCG+GGG 0.689557 5:+83211296 MsaT029918.1:CDS
AGCAGTTGCAACAACAACAA+CGG 0.693090 5:+83211569 MsaT029918.1:CDS
ACCACCGAGTGCTTGTCCAG+AGG 0.705617 5:-83211994 None:intergenic
ATGGTGCCTCAGACTCGTGG+TGG 0.717787 5:+83211840 MsaT029918.1:CDS
GCGACTCCAGAAGAACAGGA+AGG 0.732274 5:+83211489 MsaT029918.1:CDS
AGTTGCAACAACAACAACGG+TGG 0.749347 5:+83211572 MsaT029918.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 83211234 83212256 83211234 ID=MsaG029918
Chr5 mRNA 83211234 83212256 83211234 ID=MsaT029918.1;Parent=MsaG029918
Chr5 exon 83211234 83212256 83211234 ID=MsaT029918.1.exon1;Parent=MsaT029918.1
Chr5 CDS 83211234 83212256 83211234 ID=cds.MsaT029918.1;Parent=MsaT029918.1
Gene Sequence

>MsaT029918.1

ATGAAAGATCATCATCAACATCGTCCATGTTCTTCTTCATCTGTTGTTACTGGTAAGAAGAAGCGTAAGGAATTCGGCTCCGGGGAATCATCATCATCTGGTAATAACAACAACATTGCTCGTAGTTGCACTGAATGCGGTAAGATATTCTGGTCATGGAAGGCTCTTTTCGGTCACATGCGTTGTCATCCTGAGCGTCAATGGAGAGGAATTAACCCTCCTCCTAATTTCAGAAGACCACAACTCATCAATACCGCGACTCCAGAAGAACAGGAAGGTGCTGCTTCTTTGCTCTTACTTGCAAATTCAAATTCAAATTCAAAGAACAAGAAACCAGCAGTTGCAACAACAACAACGGTGGTGGATGATCAGTTTGTGTGTTCGTGTTGCAACAAAGTATTTGGATCTCATCAGGCACTTGGAGGACACAGGGCTAGTCACAAGAATGTCAAGGGTTGTTTCGCCAATACAACAACAATAACCGCTTCTTCTACGTGGACCAGCAGTACCCCTCAAGGAATTGGAGGAGGAGATCATGCTTTTGTTACTGCTGCTGCTGCTTCTGTTGATCACGATGACAACCATCATCAACAACACCCAATGATCATGGTGCCTCAGACTCGTGGTGGTGACGGTTATAATAACAATAACAATAACAATGTTGGTGGAAACGTGGAAGGGGAAGCGGTTAATAGCAGTAATAACGAAATCATAAGCATCGGAGGAGGACACAAGTGTAGCATATGTTTGAGGGTATTCACCTCTGGACAAGCACTCGGTGGTCACAAAAGGTGTCATTGGGAAAAAGGGGAAACCACCACACCATCAACAACATTACCATTCGATTCTTCTTCTACCGCAACTGCAACTGCAACTGCAACAACATCCAACAACAACAAGTCTAGTAGTGTTGTTAATGTCGTTGATTTGAATTTCCCTTTTCCACCACCACCTCCTGATGATGATGATCATCATCCCGATTCTTCTTCTCCCCTCAGCCTTGATTTGAGGTTGGGACTTTAA
Protein sequence

>MsaT029918.1

MKDHHQHRPCSSSSVVTGKKKRKEFGSGESSSSGNNNNIARSCTECGKIFWSWKALFGHMRCHPERQWRGINPPPNFRRPQLINTATPEEQEGAASLLLLANSNSNSKNKKPAVATTTTVVDDQFVCSCCNKVFGSHQALGGHRASHKNVKGCFANTTTITASSTWTSSTPQGIGGGDHAFVTAAAASVDHDDNHHQQHPMIMVPQTRGGDGYNNNNNNNVGGNVEGEAVNSSNNEIISIGGGHKCSICLRVFTSGQALGGHKRCHWEKGETTTPSTTLPFDSSSTATATATATTSNNNKSSSVVNVVDLNFPFPPPPPDDDDHHPDSSSPLSLDLRLGL*