AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG039212

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039212 MtrunA17_Chr7g0255811 96.622 444 14 1 1 443 1 444 0.0 882
MsaG039212 MtrunA17_Chr3g0129551 33.175 211 120 6 6 208 3 200 4.58e-23 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039212 AT5G05140.1 46.868 463 194 11 3 443 4 436 3.26e-120 358
MsaG039212 AT3G10820.1 41.898 432 204 9 3 433 7 392 1.43e-88 275
MsaG039212 AT3G10820.2 41.898 432 204 9 3 433 7 392 6.27e-86 274
MsaG039212 AT5G09850.1 30.769 221 113 5 6 208 3 201 7.20e-22 96.7
MsaG039212 AT5G09850.4 30.769 221 113 5 6 208 3 201 7.20e-22 96.7
MsaG039212 AT5G09850.2 30.769 221 113 5 6 208 3 201 7.20e-22 96.7
MsaG039212 AT5G09850.5 30.769 221 113 5 6 208 3 201 7.20e-22 96.7
MsaG039212 AT5G09850.3 30.769 221 113 5 6 208 3 201 2.14e-21 95.5

Find 112 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAAGCTGTAATTGCTAAT+AGG 0.172892 7:+86053109 None:intergenic
CCATTGCCGATTGTGATTTC+CGG 0.189148 7:+86050926 None:intergenic
TTCAACAACAGATGGATTTC+TGG 0.196234 7:+86051980 None:intergenic
TGGGCATTGAGAGGCCTCTT+AGG 0.273392 7:+86051332 None:intergenic
CGCTGAATGTTTGAGTTTAG+TGG 0.274638 7:+86051407 None:intergenic
CATTGCCGATTGTGATTTCC+GGG 0.275321 7:+86050927 None:intergenic
GCCGAAGATGCCTCTGAAAA+TGG 0.300933 7:-86051369 MsaT039212.1:CDS
CTCTTGAAGTCTTCGCTTAG+TGG 0.327399 7:+86051185 None:intergenic
CCTATTAGCAATTACAGCTT+TGG 0.340233 7:-86053109 MsaT039212.1:CDS
CAAAGCTGTAATTGCTAATA+GGG 0.344245 7:+86053110 None:intergenic
TCAGCCGCCATCGGTTTATT+AGG 0.348688 7:+86051446 None:intergenic
CTCCTAGACTTAAACTCCTT+TGG 0.357491 7:+86053322 None:intergenic
GCTTTCTTTGTTGCCCCAAC+TGG 0.358676 7:-86051906 MsaT039212.1:CDS
AGTTATCAACAAGCTGAAAA+TGG 0.359783 7:-86051162 MsaT039212.1:intron
TTGTATTGTCCTTTGCCTCT+TGG 0.365164 7:+86051010 None:intergenic
AGGACTCCCGTCACCTCCTT+TGG 0.378418 7:-86051937 MsaT039212.1:CDS
TTACTTTCGTTCATCGAATT+CGG 0.381995 7:-86053395 MsaT039212.1:CDS
AATTTGCAGTCAACTGAGAT+TGG 0.383050 7:-86052605 MsaT039212.1:intron
AAACCGATGGCGGCTGATAC+TGG 0.392097 7:-86051440 MsaT039212.1:CDS
CGTTGGACAGACCCTTGCTT+TGG 0.393563 7:+86050966 None:intergenic
TGTTATGCTGAATCGTTGTA+AGG 0.399819 7:-86053272 MsaT039212.1:CDS
GTGCTGACTCTTGTTGTCCT+TGG 0.405815 7:+86051496 None:intergenic
TTGTCACGGTTCTTGTTGAA+TGG 0.419455 7:+86051593 None:intergenic
GATTGCAGTAGGGAAGAAAA+TGG 0.423504 7:-86053148 MsaT039212.1:CDS
CGGAAATCACAATCGGCAAT+GGG 0.431117 7:-86050925 MsaT039212.1:CDS
AGAGTTCAATTGTACCAGTT+GGG 0.432169 7:+86051892 None:intergenic
TTGGGATTGAAGATGAAGTC+AGG 0.434760 7:-86053439 None:intergenic
AGCTCTTGGCACTCAAACTA+AGG 0.440911 7:-86051558 MsaT039212.1:CDS
GTCCAAGTGTTCAGATGATT+CGG 0.441028 7:-86051220 MsaT039212.1:CDS
CCGTCACCTCCTTTGGATGA+AGG 0.458747 7:-86051930 MsaT039212.1:CDS
CTGTCTTTCTTCCGTTGTCA+CGG 0.459719 7:+86051579 None:intergenic
TGAGAGTTCGTGCTAGTTGA+CGG 0.465786 7:+86052540 None:intergenic
CGTCACCTCCTTTGGATGAA+GGG 0.466548 7:-86051929 MsaT039212.1:CDS
ATGTTTGTAGCTTCAGAAGA+AGG 0.472561 7:-86052014 MsaT039212.1:intron
TCATCACCATTATCATCATC+AGG 0.473283 7:+86053223 None:intergenic
GTTTGAAATGTGTATTCCGT+TGG 0.475671 7:+86050949 None:intergenic
GGGCATTGAGAGGCCTCTTA+GGG 0.490032 7:+86051333 None:intergenic
GAGTTTAAGTCTAGGAGAGA+TGG 0.491402 7:-86053316 MsaT039212.1:CDS
AACGGAAGAAAGACAGCTCT+TGG 0.493030 7:-86051572 MsaT039212.1:CDS
ACAGATGGATTTCTGGAATC+CGG 0.496893 7:+86051987 None:intergenic
GCAAAGGACAATACAAGTAA+TGG 0.500794 7:-86051003 MsaT039212.1:CDS
CCGGAAATCACAATCGGCAA+TGG 0.503234 7:-86050926 MsaT039212.1:CDS
GAAAATGAAGAAGAGGAAGA+AGG 0.503793 7:-86051960 MsaT039212.1:CDS
CAAGAGAAGTTCTGTTAGAG+AGG 0.509666 7:-86053194 MsaT039212.1:CDS
AAGATTATACCTCATCTTCA+CGG 0.513302 7:+86053002 None:intergenic
TGCTGCTTCTGATTGTCCAA+AGG 0.514908 7:-86053338 MsaT039212.1:CDS
GCTGGTCAATGCGTGGGTGA+AGG 0.515961 7:-86052164 MsaT039212.1:CDS
AGAGCAAGGTGGATTGCAGT+AGG 0.520399 7:-86053159 MsaT039212.1:CDS
GCAATCACAACTTGCTGCTG+AGG 0.525782 7:-86053053 MsaT039212.1:CDS
CACAATCGGCAATGGGGCAA+CGG 0.528995 7:-86050918 MsaT039212.1:CDS
CTTGTTGTCCTTGGCAGTGA+CGG 0.530853 7:+86051505 None:intergenic
AGCCGAATCATCTGAACACT+TGG 0.534167 7:+86051218 None:intergenic
ATAAATGATCTTCCAAAGCA+AGG 0.538473 7:-86050978 MsaT039212.1:CDS
ACATCTTGCTGGGCATTGAG+AGG 0.541123 7:+86051323 None:intergenic
GTCACCTCCTTTGGATGAAG+GGG 0.541178 7:-86051928 MsaT039212.1:CDS
GTGAATCATCTAAGAAAGCA+TGG 0.544384 7:-86052575 MsaT039212.1:CDS
GGGTGCTAGCAAAGAGAGCA+AGG 0.546467 7:-86053173 MsaT039212.1:CDS
TAATTGCAGCCAAGAGGCAA+AGG 0.551496 7:-86051019 MsaT039212.1:intron
TCAAACCCGGAAATCACAAT+CGG 0.553682 7:-86050932 MsaT039212.1:CDS
TGTAAAGTTCTTCGATGGCA+TGG 0.555348 7:-86051760 MsaT039212.1:intron
TGTTGTTGAAAATGAAGAAG+AGG 0.557042 7:-86051967 MsaT039212.1:CDS
CATGTTGCTACAGTCTGACT+CGG 0.562250 7:-86052786 MsaT039212.1:intron
ACGGCTGTTTCATTAGATGC+CGG 0.562358 7:+86051524 None:intergenic
TAAATGATCTTCCAAAGCAA+GGG 0.564834 7:-86050977 MsaT039212.1:CDS
GAGAGTTCAATTGTACCAGT+TGG 0.566913 7:+86051891 None:intergenic
CCTTCATCCAAAGGAGGTGA+CGG 0.567401 7:+86051930 None:intergenic
CGGAATACACATTTCAAACC+CGG 0.569195 7:-86050945 MsaT039212.1:CDS
TTCGATGGCATGGATGATGA+TGG 0.571056 7:-86051750 MsaT039212.1:CDS
GAGTTCAATTGTACCAGTTG+GGG 0.574661 7:+86051893 None:intergenic
TAGGGAAGAAAATGGAGTGA+TGG 0.575118 7:-86053140 MsaT039212.1:CDS
CTTCATCCAAAGGAGGTGAC+GGG 0.575720 7:+86051931 None:intergenic
TGGTACAATTGAACTCTCAC+AGG 0.578719 7:-86051886 MsaT039212.1:intron
GTTATGCTGAATCGTTGTAA+GGG 0.581949 7:-86053271 MsaT039212.1:CDS
GAGCAAGGTGGATTGCAGTA+GGG 0.582197 7:-86053158 MsaT039212.1:CDS
AGGCATCTTCGGCTCCACAT+TGG 0.582725 7:+86051379 None:intergenic
AAAACAGTACTGTCCCTAAG+AGG 0.584288 7:-86051346 MsaT039212.1:CDS
AAGAAAGCCCCTTCATCCAA+AGG 0.586587 7:+86051921 None:intergenic
TTCTAGTGGATGGAAAGAGC+TGG 0.587363 7:-86052182 MsaT039212.1:intron
CAAAGCAAGGGTCTGTCCAA+CGG 0.592243 7:-86050965 MsaT039212.1:CDS
TGGGATTGAAGATGAAGTCA+GGG 0.594781 7:-86053438 None:intergenic
TCTAAGAAAGCATGGATCGA+AGG 0.595986 7:-86052567 MsaT039212.1:CDS
AATGAAGAAGAGGAAGAAGG+AGG 0.597918 7:-86051957 MsaT039212.1:CDS
AAGAGAAGTTCTGTTAGAGA+GGG 0.600208 7:-86053193 MsaT039212.1:CDS
ACTCTCTGTCGATCTTCTGA+AGG 0.600474 7:-86052726 MsaT039212.1:intron
GACGATGTAAAGTTCTTCGA+TGG 0.605011 7:-86051765 MsaT039212.1:intron
AATTATTAATTGCAGCCAAG+AGG 0.608124 7:-86051025 MsaT039212.1:intron
CGACCAGTATCAGCCGCCAT+CGG 0.609021 7:+86051437 None:intergenic
TCAACAACCACACCTGTCGC+AGG 0.609609 7:-86052139 MsaT039212.1:intron
TGAAACAGCCGTCACTGCCA+AGG 0.610149 7:-86051513 MsaT039212.1:CDS
GCAGTCAACTGAGATTGGAA+AGG 0.610845 7:-86052600 MsaT039212.1:intron
TGCTGTTTGAGTCTCTGAGG+AGG 0.611179 7:-86052763 MsaT039212.1:CDS
CATTCAGCGAAAAGCCAATG+TGG 0.612860 7:-86051393 MsaT039212.1:CDS
TCTCAATAACCGTGAAGATG+AGG 0.613333 7:-86053011 MsaT039212.1:intron
AATTCTACCTGCGACAGGTG+TGG 0.614711 7:+86052132 None:intergenic
CAGGGTCACTTGATCAGTGG+AGG 0.617583 7:-86053420 MsaT039212.1:CDS
TTCAACAAGAACCGTGACAA+CGG 0.624350 7:-86051590 MsaT039212.1:CDS
GGAAAGAGCTGGTCAATGCG+TGG 0.625905 7:-86052171 MsaT039212.1:CDS
GTCCAAAGGAGTTTAAGTCT+AGG 0.627009 7:-86053324 MsaT039212.1:CDS
TCTGTGCCTGATGATGATAA+TGG 0.629006 7:-86053229 MsaT039212.1:CDS
CGGTGCTGTTTGAGTCTCTG+AGG 0.632670 7:-86052766 MsaT039212.1:CDS
GAAAGAGCTGGTCAATGCGT+GGG 0.636719 7:-86052170 MsaT039212.1:CDS
TCGTTGTAAGGGGTGTGAGA+AGG 0.640457 7:-86053260 MsaT039212.1:CDS
AAGCAGCAACAACAATTGCA+TGG 0.641026 7:+86053353 None:intergenic
AGTCAGGGTCACTTGATCAG+TGG 0.646882 7:-86053423 MsaT039212.1:CDS
AGCTTCAGAAGAAGGCACAC+CGG 0.647483 7:-86052006 MsaT039212.1:CDS
GGTGAGGCCTAATAAACCGA+TGG 0.659654 7:-86051453 MsaT039212.1:CDS
TTATGCTGAATCGTTGTAAG+GGG 0.662020 7:-86053270 MsaT039212.1:CDS
GAGGCCTAATAAACCGATGG+CGG 0.667726 7:-86051450 MsaT039212.1:CDS
TTGGCACTCAAACTAAGGAG+AGG 0.668123 7:-86051553 MsaT039212.1:CDS
AAAGCCCCTTCATCCAAAGG+AGG 0.683333 7:+86051924 None:intergenic
GGAAATCACAATCGGCAATG+GGG 0.692012 7:-86050924 MsaT039212.1:CDS
TGCTAGCAAAGAGAGCAAGG+TGG 0.724881 7:-86053170 MsaT039212.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 86050908 86053449 86050908 ID=MsaG039212
Chr7 mRNA 86050908 86053449 86050908 ID=MsaT039212.1;Parent=MsaG039212
Chr7 exon 86050908 86051032 86050908 ID=MsaT039212.1.exon9;Parent=MsaT039212.1
Chr7 CDS 86050908 86051032 86050908 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86051163 86051244 86051163 ID=MsaT039212.1.exon8;Parent=MsaT039212.1
Chr7 CDS 86051163 86051244 86051163 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86051325 86051632 86051325 ID=MsaT039212.1.exon7;Parent=MsaT039212.1
Chr7 CDS 86051325 86051632 86051325 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86051748 86051775 86051748 ID=MsaT039212.1.exon6;Parent=MsaT039212.1
Chr7 CDS 86051748 86051775 86051748 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86051887 86052026 86051887 ID=MsaT039212.1.exon5;Parent=MsaT039212.1
Chr7 CDS 86051887 86052026 86051887 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86052140 86052198 86052140 ID=MsaT039212.1.exon4;Parent=MsaT039212.1
Chr7 CDS 86052140 86052198 86052140 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86052536 86052618 86052536 ID=MsaT039212.1.exon3;Parent=MsaT039212.1
Chr7 CDS 86052536 86052618 86052536 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86052727 86052795 86052727 ID=MsaT039212.1.exon2;Parent=MsaT039212.1
Chr7 CDS 86052727 86052795 86052727 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Chr7 exon 86053012 86053449 86053012 ID=MsaT039212.1.exon1;Parent=MsaT039212.1
Chr7 CDS 86053012 86053449 86053012 ID=cds.MsaT039212.1;Parent=MsaT039212.1
Gene Sequence

>MsaT039212.1

ATGAAGTCAGGGTCACTTGATCAGTGGAGGAGTTACTTTCGTTCATCGAATTCGGATATTTTCGATATAATTGACCATGCAATTGTTGTTGCTGCTTCTGATTGTCCAAAGGAGTTTAAGTCTAGGAGAGATGGTATTGCTGAGAGATTGTTTTCTGTTATGCTGAATCGTTGTAAGGGGTGTGAGAAGGTTGAAATATCTGTGCCTGATGATGATAATGGTGATGAACTTTGCAAGAGAAGTTCTGTTAGAGAGGGTGCTAGCAAAGAGAGCAAGGTGGATTGCAGTAGGGAAGAAAATGGAGTGATGGATGCTAACCCTATTAGCAATTACAGCTTTGGAGAAGCTGAAGCTTTAACTGATGAACTTGAAGAGCAATCACAACTTGCTGCTGAGGTTTTGAGGATTAAAGAGATTCTCAATAACCGTGAAGATGAGTCTGACTCGGTGCTGTTTGAGTCTCTGAGGAGGCTTCAACTGATGCAACTCTCTGTCGATCTTCTGAAGTCAACTGAGATTGGAAAGGCTGTGAATCATCTAAGAAAGCATGGATCGAAGGATATCCGTCAACTAGCACGAACTCTCATAGATGGATGGAAAGAGCTGGTCAATGCGTGGGTGAAGGCGTCAACAACCACACCTGTCGCAGCTTCAGAAGAAGGCACACCGGATTCCAGAAATCCATCTGTTGTTGAAAATGAAGAAGAGGAAGAAGGAGGACTCCCGTCACCTCCTTTGGATGAAGGGGCTTTCTTTGTTGCCCCAACTGGTACAATTGAACTCTCACAGTTCTTCGATGGCATGGATGATGATGGAAATATTCGAAAGAGTGCACCATTCAACAAGAACCGTGACAACGGAAGAAAGACAGCTCTTGGCACTCAAACTAAGGAGAGGAATTTTCCGGCATCTAATGAAACAGCCGTCACTGCCAAGGACAACAAGAGTCAGCACATGAAGAAAAACGAGGCTGTGGTGAGGCCTAATAAACCGATGGCGGCTGATACTGGTCGTGCAAGACCACTAAACTCAAACATTCAGCGAAAAGCCAATGTGGAGCCGAAGATGCCTCTGAAAATGGAAAACAGTACTGTCCCTAAGAGGCCTCTCAATGCCCAGCAAGATAAGTCCAAGTGTTCAGATGATTCGGCTAAGCTCGAAGCCACTAAGCGAAGACTTCAAGAGAGTTATCAACAAGCTGAAAATGCCAAGAGGCAAAGGACAATACAAGTAATGGAAATAAATGATCTTCCAAAGCAAGGGTCTGTCCAACGGAATACACATTTCAAACCCGGAAATCACAATCGGCAATGGGGCAACGGTCGAAGATAG
Protein sequence

>MsaT039212.1

MKSGSLDQWRSYFRSSNSDIFDIIDHAIVVAASDCPKEFKSRRDGIAERLFSVMLNRCKGCEKVEISVPDDDNGDELCKRSSVREGASKESKVDCSREENGVMDANPISNYSFGEAEALTDELEEQSQLAAEVLRIKEILNNREDESDSVLFESLRRLQLMQLSVDLLKSTEIGKAVNHLRKHGSKDIRQLARTLIDGWKELVNAWVKASTTTPVAASEEGTPDSRNPSVVENEEEEEGGLPSPPLDEGAFFVAPTGTIELSQFFDGMDDDGNIRKSAPFNKNRDNGRKTALGTQTKERNFPASNETAVTAKDNKSQHMKKNEAVVRPNKPMAADTGRARPLNSNIQRKANVEPKMPLKMENSTVPKRPLNAQQDKSKCSDDSAKLEATKRRLQESYQQAENAKRQRTIQVMEINDLPKQGSVQRNTHFKPGNHNRQWGNGRR*