AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG025388

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025388 MtrunA17_Chr5g0401051 85.458 612 69 6 1 606 1 598 0.0 1026
MsaG025388 MtrunA17_Chr5g0401041 90.598 117 8 2 1 115 1 116 7.81e-70 221
MsaG025388 MtrunA17_Chr3g0138721 26.778 239 158 5 52 287 35 259 1.64e-11 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025388 AT4G37670.2 68.841 552 156 4 62 598 60 610 0.0 764
MsaG025388 AT2G22910.1 68.382 544 164 4 62 598 59 601 0.0 749
MsaG025388 AT4G37670.1 67.909 483 139 4 62 529 60 541 0.0 647

Find 134 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGCTTGTGCCTTGGCAAT+TGG 0.248266 5:+7697729 MsaT025388.1:CDS
ACAGTAATTCCACTCTTATT+TGG 0.256128 5:-7700313 None:intergenic
TACTGTTGGTGGAAACAAAT+TGG 0.281715 5:+7700330 MsaT025388.1:CDS
AGCACATGGCTGCTTGTTCT+TGG 0.283155 5:+7694046 None:intergenic
TCTCCTCAGGGTAAGGAAAA+AGG 0.290072 5:-7699354 None:intergenic
CAGCTTGTGCCTTGGCAATT+GGG 0.298414 5:+7697730 MsaT025388.1:CDS
CGCAATAAGACAACAATAAT+TGG 0.299636 5:-7694172 None:intergenic
ATCCACTTTGTTATTGTTCC+TGG 0.304270 5:+7696266 MsaT025388.1:CDS
GGTCCAATACTTGATGAAAA+TGG 0.316810 5:+7697780 MsaT025388.1:CDS
ACAATGTTTGAGTTTCTCTT+TGG 0.319692 5:-7694092 None:intergenic
GACAACATTCTCAAAGATAA+AGG 0.329004 5:+7696305 MsaT025388.1:CDS
AGCGAGCAAGGCTTTGCTAT+TGG 0.336026 5:+7698044 MsaT025388.1:CDS
TTAAAATTGTTATGCTCAAC+AGG 0.336039 5:-7697918 None:intergenic
TGAAATATGTGCAGATTATA+TGG 0.338432 5:+7699943 MsaT025388.1:intron
GTTTGAGTTTCTCTTTGGTT+TGG 0.360791 5:-7694087 None:intergenic
TTGCACAGAAAAGTAAGGTT+TGG 0.370369 5:-7694298 None:intergenic
TTGGAATTGTTTACAAGAGA+TGG 0.378945 5:+7698492 MsaT025388.1:CDS
AGCTGCTATTTCACTTTGCT+CGG 0.382328 5:-7697859 None:intergenic
TTGTTGGATGGCACTATTAG+TGG 0.387463 5:+7698459 MsaT025388.1:CDS
GCAGTCAAATCTCCACCTAA+TGG 0.388073 5:+7697945 MsaT025388.1:CDS
GGAATTGATTATGGGTCAAC+TGG 0.390661 5:+7697305 MsaT025388.1:CDS
CATATAATACTTAGAATTGC+GGG 0.398277 5:-7700278 None:intergenic
TTTGAGAATGGAGATGGCTT+AGG 0.403018 5:+7698017 MsaT025388.1:CDS
CAAACAACTTATCCAGCCTT+TGG 0.403846 5:+7699115 MsaT025388.1:CDS
CCTCTTTGCACAGAAAAGTA+AGG 0.410284 5:-7694303 None:intergenic
TTTGGAGGCATGTGGCATAC+TGG 0.410523 5:+7699133 MsaT025388.1:CDS
AACACCAAGTTTAAGGTAAG+AGG 0.412750 5:+7694204 MsaT025388.1:CDS
ACCTCTGCACACTTCTCCTC+AGG 0.437888 5:-7699367 None:intergenic
GTGGTCGGTGGAATTGATTA+TGG 0.441744 5:+7697296 MsaT025388.1:CDS
GTTGGATAATTTCGTTGTTG+TGG 0.449871 5:+7699300 MsaT025388.1:CDS
TTCTTTCTCCAGCACCTATG+AGG 0.453361 5:+7697701 MsaT025388.1:intron
TCAATTTGCACATGGGTGCC+AGG 0.453790 5:-7696284 None:intergenic
ACAAGCTGTTGCAACCTCAT+AGG 0.454255 5:-7697715 None:intergenic
ATGTCTACGAATATTGCATA+TGG 0.454955 5:-7697074 None:intergenic
TGCCACATGCCTCCAAAGGC+TGG 0.455867 5:-7699127 None:intergenic
ATTCAATACTTCACCAGAGC+TGG 0.458082 5:-7697411 None:intergenic
GTGAAAGCGGTTGAGGAAGA+AGG 0.459644 5:+7697888 MsaT025388.1:CDS
TGTCCTTGACCACGGCAATC+AGG 0.460303 5:-7699409 None:intergenic
AAGATTTGATGACAAGAAGT+AGG 0.463698 5:-7694126 None:intergenic
CGCATGCGTGAGAGACTTGA+TGG 0.466167 5:+7697353 MsaT025388.1:CDS
GAGAAGAAAGCAGCATCTCT+TGG 0.466675 5:+7699965 MsaT025388.1:CDS
GGTTCAAAGAGTTCACTTGT+TGG 0.467382 5:+7698443 MsaT025388.1:CDS
TTGAGAATGGAGATGGCTTA+GGG 0.472572 5:+7698018 MsaT025388.1:CDS
CAAGAGGCAAGAAACGAATT+AGG 0.474284 5:-7697806 None:intergenic
CTATATCTCCCAACATACTT+AGG 0.475306 5:-7696962 None:intergenic
GAACGGCTAAGTCGAATGAA+TGG 0.475981 5:+7698074 MsaT025388.1:CDS
TAACTATGTGAAAGCGGTTG+AGG 0.486501 5:+7697881 MsaT025388.1:CDS
AAGAGTGGAATTACTGTTGG+TGG 0.488225 5:+7700319 MsaT025388.1:CDS
GAATGGGTACCTGTCAGAAT+TGG 0.488645 5:+7698091 MsaT025388.1:CDS
TGATTGCCGTGGTCAAGGAC+AGG 0.489686 5:+7699411 MsaT025388.1:CDS
TGGTAACTTTCTTGCAGCCA+AGG 0.491225 5:+7697141 MsaT025388.1:CDS
GGAGCGAGCCTAAGTATGTT+GGG 0.492830 5:+7696954 MsaT025388.1:CDS
AGCTTGTGCCTTGGCAATTG+GGG 0.494564 5:+7697731 MsaT025388.1:CDS
GCACACTTCTCCTCAGGGTA+AGG 0.495453 5:-7699361 None:intergenic
AACGCTGCAATGTGTGCAGC+AGG 0.498191 5:+7697007 MsaT025388.1:CDS
AAGTTAATATGCGTTATAGA+TGG 0.498769 5:+7697759 MsaT025388.1:CDS
AAGTTTAAGGTAAGAGGGTG+TGG 0.498999 5:+7694210 MsaT025388.1:CDS
CAAAGAGTTCACTTGTTGGA+TGG 0.500446 5:+7698447 MsaT025388.1:CDS
AACATGTCTGCTTCTTCAAG+AGG 0.505053 5:-7697822 None:intergenic
GGATGTAATGAAGAAGAATA+TGG 0.505634 5:+7694231 MsaT025388.1:CDS
ATTGTTTACAAGAGATGGGA+TGG 0.511266 5:+7698497 MsaT025388.1:CDS
ACAACTTATCCAGCCTTTGG+AGG 0.513265 5:+7699118 MsaT025388.1:CDS
TGTTGTTCACATTTCTGCTG+AGG 0.514873 5:+7694335 MsaT025388.1:CDS
ACACCCTCTTACCTTAAACT+TGG 0.521900 5:-7694208 None:intergenic
TGGAATTGTTTACAAGAGAT+GGG 0.523017 5:+7698493 MsaT025388.1:CDS
AACTTGGGCTACTCCAGCTC+TGG 0.523097 5:+7697398 MsaT025388.1:CDS
GGGAGCGAGCCTAAGTATGT+TGG 0.523204 5:+7696953 MsaT025388.1:intron
CTGCTGTACGTGTTGTAAGT+AGG 0.526017 5:-7700003 None:intergenic
GGATGGGAACAATGGTGGCT+AGG 0.526598 5:+7698514 MsaT025388.1:CDS
TCTCCTGATTGCCGTGGTCA+AGG 0.528056 5:+7699406 MsaT025388.1:CDS
TTCGTTGTTGTGGAAAGAGA+AGG 0.528576 5:+7699310 MsaT025388.1:CDS
GAGCAAGGCTTTGCTATTGG+AGG 0.529772 5:+7698047 MsaT025388.1:CDS
TGGTCGGTGGAATTGATTAT+GGG 0.530856 5:+7697297 MsaT025388.1:CDS
CTGCAGCAGCCAATTCTGAC+AGG 0.535179 5:-7698100 None:intergenic
CTTGACAGGTTTGTGAGGCG+TGG 0.536755 5:+7700196 MsaT025388.1:intron
ATAGCAGCTAAACTTTCAGT+TGG 0.541876 5:+7697046 MsaT025388.1:CDS
AACGGCTAAGTCGAATGAAT+GGG 0.542375 5:+7698075 MsaT025388.1:CDS
GCAACTTTCCACAATGGTGT+TGG 0.543734 5:+7697993 MsaT025388.1:CDS
CAATTATTGTTGTCTTATTG+CGG 0.544662 5:+7694173 MsaT025388.1:CDS
TCATATAATACTTAGAATTG+CGG 0.547939 5:-7700279 None:intergenic
AGATTTGATGACAAGAAGTA+GGG 0.548479 5:-7694125 None:intergenic
TTTATAGCTGCTACAAACGT+TGG 0.550580 5:+7699282 MsaT025388.1:intron
GGCTTAGGGACTAGCGAGCA+AGG 0.560101 5:+7698032 MsaT025388.1:CDS
GGTGGGTGGTACCTTGAGAA+TGG 0.560737 5:-7694385 None:intergenic
TTACAACACGTACAGCAGAT+TGG 0.561074 5:+7700008 MsaT025388.1:CDS
CAATAACAAAGTGGATTCCA+AGG 0.563812 5:-7696259 None:intergenic
ATGGAAAACGCATTACAGAA+TGG 0.566481 5:+7697964 MsaT025388.1:CDS
TTGTGCCTTGGCAATTGGGG+CGG 0.568264 5:+7697734 MsaT025388.1:CDS
AACTTCTTGACAGGTTTGTG+AGG 0.570293 5:+7700191 MsaT025388.1:intron
GGACAGGGAGACAAATTGCT+TGG 0.571020 5:+7699427 MsaT025388.1:CDS
AGACATGTTAATTCGCAAGC+GGG 0.573614 5:+7697836 MsaT025388.1:CDS
GAATTGATTATGGGTCAACT+GGG 0.574055 5:+7697306 MsaT025388.1:CDS
GGTTAAGCGGTCTGATGAAG+AGG 0.575532 5:+7699154 MsaT025388.1:CDS
TTGCTATTGGAGGTCAAGAA+CGG 0.575766 5:+7698057 MsaT025388.1:CDS
CAGAGAAGAGGGGTGGTCGG+TGG 0.577629 5:+7697284 MsaT025388.1:intron
AGAATGGCATGGAAGTAACT+AGG 0.578075 5:-7694369 None:intergenic
CCTTTCGAGTGCCTTCGTAA+AGG 0.580703 5:-7699067 None:intergenic
TTACTTCCATGCCATTCTCA+AGG 0.583673 5:+7694374 MsaT025388.1:CDS
AGCAGCTAACTATGTGAAAG+CGG 0.584271 5:+7697875 MsaT025388.1:CDS
GATTGCCGTGGTCAAGGACA+GGG 0.586053 5:+7699412 MsaT025388.1:CDS
AATAAGAGTGGAATTACTGT+TGG 0.587427 5:+7700316 MsaT025388.1:CDS
CTTGTCCGCCCCAATTGCCA+AGG 0.592760 5:-7697739 None:intergenic
ACACCAAGTTTAAGGTAAGA+GGG 0.594258 5:+7694205 MsaT025388.1:CDS
TGACAGAGAAGAGGGGTGGT+CGG 0.595410 5:+7697281 MsaT025388.1:intron
TGTCTCCCTGTCCTTGACCA+CGG 0.601589 5:-7699417 None:intergenic
ATATGCAATATTCGTAGACA+TGG 0.605536 5:+7697076 MsaT025388.1:CDS
GGTTGCAACAGCTTGTGCCT+TGG 0.608428 5:+7697722 MsaT025388.1:CDS
CTACGAATATTGCATATGGA+AGG 0.610959 5:-7697070 None:intergenic
AAGAGATGGGATGGGAACAA+TGG 0.612647 5:+7698506 MsaT025388.1:CDS
TTGTTTACAAGAGATGGGAT+GGG 0.612686 5:+7698498 MsaT025388.1:CDS
TCTCAAAACCAACACCATTG+TGG 0.620130 5:-7698001 None:intergenic
ATCCAGCCTTTGGAGGCATG+TGG 0.622064 5:+7699125 MsaT025388.1:CDS
AAGCTTCTACCAAATAAGAG+TGG 0.625840 5:+7700304 MsaT025388.1:CDS
AGATGGGATGGGAACAATGG+TGG 0.628080 5:+7698509 MsaT025388.1:CDS
GAATGTTGTCAATTTGCACA+TGG 0.630324 5:-7696292 None:intergenic
AGAGCTGGAGTAGCCCAAGT+TGG 0.630783 5:-7697396 None:intergenic
AGTATGCCACATGCCTCCAA+AGG 0.632526 5:-7699131 None:intergenic
CATGTGGCATACTGGTTAAG+CGG 0.633218 5:+7699141 MsaT025388.1:CDS
CAGACATGTTAATTCGCAAG+CGG 0.635149 5:+7697835 MsaT025388.1:CDS
GCAGTATCTCCTGATTGCCG+TGG 0.637078 5:+7699400 MsaT025388.1:CDS
GAAGGTCAAATAATTGCATG+TGG 0.638311 5:+7699328 MsaT025388.1:CDS
CCTCTGCACACTTCTCCTCA+GGG 0.642147 5:-7699366 None:intergenic
CCTTTACGAAGGCACTCGAA+AGG 0.642671 5:+7699067 MsaT025388.1:CDS
GCTGCAATGTGTGCAGCAGG+AGG 0.644204 5:+7697010 MsaT025388.1:CDS
CCCTGAGGAGAAGTGTGCAG+AGG 0.655036 5:+7699366 MsaT025388.1:CDS
GGTCAAATAATTGCATGTGG+TGG 0.656987 5:+7699331 MsaT025388.1:CDS
GTTAGTGTCAGTGTTACAAG+TGG 0.659841 5:+7697121 MsaT025388.1:CDS
GTGGTACCTTGAGAATGGCA+TGG 0.663414 5:-7694380 None:intergenic
TGCCAGGAACAATAACAAAG+TGG 0.667425 5:-7696268 None:intergenic
CATAATGCAACTTTCCACAA+TGG 0.674650 5:+7697987 MsaT025388.1:CDS
AGAAGAATATGGTGTGACTG+AGG 0.686228 5:+7694242 MsaT025388.1:CDS
AATGTTGTCAATTTGCACAT+GGG 0.704234 5:-7696291 None:intergenic
AATTGATTATGGGTCAACTG+GGG 0.744930 5:+7697307 MsaT025388.1:CDS
ATGCGTGAGAGACTTGATGG+TGG 0.746452 5:+7697356 MsaT025388.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 7694051 7700363 7694051 ID=MsaG025388
Chr5 mRNA 7694051 7700363 7694051 ID=MsaT025388.1;Parent=MsaG025388
Chr5 exon 7694051 7694395 7694051 ID=MsaT025388.1.exon1;Parent=MsaT025388.1
Chr5 CDS 7694051 7694395 7694051 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7696239 7696326 7696239 ID=MsaT025388.1.exon2;Parent=MsaT025388.1
Chr5 CDS 7696239 7696326 7696239 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7696954 7697162 7696954 ID=MsaT025388.1.exon3;Parent=MsaT025388.1
Chr5 CDS 7696954 7697162 7696954 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7697287 7697438 7697287 ID=MsaT025388.1.exon4;Parent=MsaT025388.1
Chr5 CDS 7697287 7697438 7697287 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7697713 7698136 7697713 ID=MsaT025388.1.exon5;Parent=MsaT025388.1
Chr5 CDS 7697713 7698136 7697713 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7698438 7698535 7698438 ID=MsaT025388.1.exon6;Parent=MsaT025388.1
Chr5 CDS 7698438 7698535 7698438 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7699064 7699175 7699064 ID=MsaT025388.1.exon7;Parent=MsaT025388.1
Chr5 CDS 7699064 7699175 7699064 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7699289 7699448 7699289 ID=MsaT025388.1.exon8;Parent=MsaT025388.1
Chr5 CDS 7699289 7699448 7699289 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7699957 7700029 7699957 ID=MsaT025388.1.exon9;Parent=MsaT025388.1
Chr5 CDS 7699957 7700029 7699957 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Chr5 exon 7700204 7700363 7700204 ID=MsaT025388.1.exon10;Parent=MsaT025388.1
Chr5 CDS 7700204 7700363 7700204 ID=cds.MsaT025388.1;Parent=MsaT025388.1
Gene Sequence

>MsaT025388.1

ATGGCTGCTTGTTCTTGGAAGCTACACATGAATTTACCAAACCAAAGAGAAACTCAAACATTGTTTTCACGTGGCCCTACTTCTTGTCATCAAATCTTCAACTTTGCTTCAAGATCAGTGACCAATTATTGTTGTCTTATTGCGGCTGTCAAAAACACCAAGTTTAAGGTAAGAGGGTGTGGATGTAATGAAGAAGAATATGGTGTGACTGAGGAAGACAAAGATATTGTGAAAATTCTCTTTGAATCCAAACCTTACTTTTCTGTGCAAAGAGGTAGAGTCTTTGTTGTTCACATTTCTGCTGAGGTTATTGCTACTCCTAGTTACTTCCATGCCATTCTCAAGGATATAGCTTTTCTTCATCACCTTGGAATCCACTTTGTTATTGTTCCTGGCACCCATGTGCAAATTGACAACATTCTCAAAGATAAAGGGAGCGAGCCTAAGTATGTTGGGAGATATAGAATAACAGATGATGAATCTCTAAACGCTGCAATGTGTGCAGCAGGAGGAATAATGTCAATGATAGCAGCTAAACTTTCAGTTGGACCTTCCATATGCAATATTCGTAGACATGGTGATAATAGTCGATTGCATGACGTTAGTGTCAGTGTTACAAGTGGTAACTTTCTTGCAGCCAAGAGAAGAGGGGTGGTCGGTGGAATTGATTATGGGTCAACTGGGGAAGTTAAAAAAATAGACGCTACTCGCATGCGTGAGAGACTTGATGGTGGTTCTATAGTTATTTTAACCAACTTGGGCTACTCCAGCTCTGGTGAAGTATTGAATTGCAACACCTATGAGGTTGCAACAGCTTGTGCCTTGGCAATTGGGGCGGACAAGTTAATATGCGTTATAGATGGTCCAATACTTGATGAAAATGGACGCCTAATTCGTTTCTTGCCTCTTGAAGAAGCAGACATGTTAATTCGCAAGCGGGCCGAGCAAAGTGAAATAGCAGCTAACTATGTGAAAGCGGTTGAGGAAGAAGGTTTAAATCCTGTTGAGCATAACAATTTTAACGGGGCAGTCAAATCTCCACCTAATGGAAAACGCATTACAGAATGGCATAATGCAACTTTCCACAATGGTGTTGGTTTTGAGAATGGAGATGGCTTAGGGACTAGCGAGCAAGGCTTTGCTATTGGAGGTCAAGAACGGCTAAGTCGAATGAATGGGTACCTGTCAGAATTGGCTGCTGCAGCTTTTGTTTGCAGGGGAGGGGTTCAAAGAGTTCACTTGTTGGATGGCACTATTAGTGGAGTTTTATTGTTGGAATTGTTTACAAGAGATGGGATGGGAACAATGGTGGCTAGTGACCTTTACGAAGGCACTCGAAAGGCAGAGAAAGAAGATTTTTCTGGAATCAAACAACTTATCCAGCCTTTGGAGGCATGTGGCATACTGGTTAAGCGGTCTGATGAAGAGCTGCTACAAACGTTGGATAATTTCGTTGTTGTGGAAAGAGAAGGTCAAATAATTGCATGTGGTGGCCTTTTTCCTTACCCTGAGGAGAAGTGTGCAGAGGTTGCTGCTATTGCAGTATCTCCTGATTGCCGTGGTCAAGGACAGGGAGACAAATTGCTTGATTATATGGAGAAGAAAGCAGCATCTCTTGGATTCAATAAGCTTTTCCTACTTACAACACGTACAGCAGATTGGTTTGTGAGGCGTGGATTTTCAGAATGTTCAATTGATAATATCCCTGAAAAGAAAAAGAAAACAATCAACATGTCCCGCAATTCTAAGTATTATATGAAGAAGCTTCTACCAAATAAGAGTGGAATTACTGTTGGTGGAAACAAATTGGTTACAAATTAG
Protein sequence

>MsaT025388.1

MAACSWKLHMNLPNQRETQTLFSRGPTSCHQIFNFASRSVTNYCCLIAAVKNTKFKVRGCGCNEEEYGVTEEDKDIVKILFESKPYFSVQRGRVFVVHISAEVIATPSYFHAILKDIAFLHHLGIHFVIVPGTHVQIDNILKDKGSEPKYVGRYRITDDESLNAAMCAAGGIMSMIAAKLSVGPSICNIRRHGDNSRLHDVSVSVTSGNFLAAKRRGVVGGIDYGSTGEVKKIDATRMRERLDGGSIVILTNLGYSSSGEVLNCNTYEVATACALAIGADKLICVIDGPILDENGRLIRFLPLEEADMLIRKRAEQSEIAANYVKAVEEEGLNPVEHNNFNGAVKSPPNGKRITEWHNATFHNGVGFENGDGLGTSEQGFAIGGQERLSRMNGYLSELAAAAFVCRGGVQRVHLLDGTISGVLLLELFTRDGMGTMVASDLYEGTRKAEKEDFSGIKQLIQPLEACGILVKRSDEELLQTLDNFVVVEREGQIIACGGLFPYPEEKCAEVAAIAVSPDCRGQGQGDKLLDYMEKKAASLGFNKLFLLTTRTADWFVRRGFSECSIDNIPEKKKKTINMSRNSKYYMKKLLPNKSGITVGGNKLVTN*