AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0132540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0132540 MtrunA17_Chr1g0158041 51.887 106 37 5 1 94 190 293 1.00e-23 93.6
Msa0132540 MtrunA17_Chr1g0157791 60.000 70 16 2 1 60 184 251 8.48e-21 85.1
Msa0132540 MtrunA17_Chr1g0157961 44.762 105 43 4 1 94 192 292 5.86e-20 81.6
Msa0132540 MtrunA17_Chr1g0158131 42.593 108 45 5 1 94 1 105 3.66e-19 80.1
Msa0132540 MtrunA17_Chr1g0157991 48.039 102 34 5 1 87 191 288 1.09e-18 79.3
Msa0132540 MtrunA17_Chr1g0158151 45.918 98 37 5 1 86 187 280 8.68e-17 73.9
Msa0132540 MtrunA17_Chr1g0158191 42.991 107 45 5 1 94 187 290 1.47e-16 73.2
Msa0132540 MtrunA17_Chr1g0158061 42.268 97 42 4 1 86 183 276 4.53e-16 70.9
Msa0132540 MtrunA17_Chr1g0157811 45.918 98 36 6 1 86 1 93 3.40e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATGAAAATTAGTTGTAAT+TGG 0.211481 1_3:-63611605 None:intergenic
CGGATTAATTTGAGGTTTCA+TGG 0.300380 1_3:+63611428 Msa0132540:intron
AGTTGGTTACTCTCACTTCT+TGG 0.363695 1_3:+63611343 Msa0132540:CDS
CTTGCTTGTAATAATCTTTG+TGG 0.380478 1_3:+63611457 Msa0132540:CDS
TTTGCTGGATATGGGACCTC+TGG 0.414584 1_3:+63611559 Msa0132540:CDS
GCATGCTACTTTAACGCTTC+CGG 0.415182 1_3:+63611496 Msa0132540:CDS
GGTTACTCTCACTTCTTGGT+CGG 0.458556 1_3:+63611347 Msa0132540:CDS
GTTACTCTCACTTCTTGGTC+GGG 0.468860 1_3:+63611348 Msa0132540:CDS
GGATATGGGACCTCTGGTTG+TGG 0.514857 1_3:+63611565 Msa0132540:CDS
GGGTATATTTATGCTATGGC+TGG 0.533069 1_3:+63611279 None:intergenic
AGTTGGTTGCCATGTGAAGT+TGG 0.556564 1_3:+63611326 Msa0132540:CDS
CTTTGTGGAGATCAAACACT+AGG 0.568601 1_3:+63611472 Msa0132540:CDS
ACATTGAAGCACTACGTGGC+CGG 0.574800 1_3:-63611515 None:intergenic
GGCTGGTGATTTATATGCTG+AGG 0.629303 1_3:+63611296 Msa0132540:CDS
TATGCTGAGGACATGCAAGT+TGG 0.631139 1_3:+63611309 Msa0132540:CDS
TCCAGCAAAAGCAATGCAAG+AGG 0.635322 1_3:-63611545 None:intergenic
CCAGCAAAAGCAATGCAAGA+GGG 0.650005 1_3:-63611544 None:intergenic
TGAGAGTAACCAACTTCACA+TGG 0.683411 1_3:-63611335 None:intergenic
GTTTGCATTACCACAACCAG+AGG 0.692170 1_3:-63611575 None:intergenic
GAGAACATTGAAGCACTACG+TGG 0.756280 1_3:-63611519 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTCATAAAGCATTAGTCTA+CGG + chr1_3:63611408-63611427 Msa0132540:intron 25.0%
! TTAGTCTACGGATTAATTTG+AGG + chr1_3:63611420-63611439 Msa0132540:intron 30.0%
CTTGCTTGTAATAATCTTTG+TGG + chr1_3:63611457-63611476 Msa0132540:CDS 30.0%
! CGGATTAATTTGAGGTTTCA+TGG + chr1_3:63611428-63611447 Msa0132540:intron 35.0%
TGAGAGTAACCAACTTCACA+TGG - chr1_3:63611338-63611357 None:intergenic 40.0%
AGTTGGTTACTCTCACTTCT+TGG + chr1_3:63611343-63611362 Msa0132540:CDS 40.0%
CTTTGTGGAGATCAAACACT+AGG + chr1_3:63611472-63611491 Msa0132540:CDS 40.0%
!! TGCATTGCTTTTGCTGGATA+TGG + chr1_3:63611550-63611569 Msa0132540:CDS 40.0%
!! GCATTGCTTTTGCTGGATAT+GGG + chr1_3:63611551-63611570 Msa0132540:CDS 40.0%
GGCTGGTGATTTATATGCTG+AGG + chr1_3:63611296-63611315 Msa0132540:CDS 45.0%
TATGCTGAGGACATGCAAGT+TGG + chr1_3:63611309-63611328 Msa0132540:CDS 45.0%
AGTTGGTTGCCATGTGAAGT+TGG + chr1_3:63611326-63611345 Msa0132540:CDS 45.0%
GGTTACTCTCACTTCTTGGT+CGG + chr1_3:63611347-63611366 Msa0132540:CDS 45.0%
GTTACTCTCACTTCTTGGTC+GGG + chr1_3:63611348-63611367 Msa0132540:CDS 45.0%
!! GCATGCTACTTTAACGCTTC+CGG + chr1_3:63611496-63611515 Msa0132540:CDS 45.0%
! GAGAACATTGAAGCACTACG+TGG - chr1_3:63611522-63611541 None:intergenic 45.0%
CCAGCAAAAGCAATGCAAGA+GGG - chr1_3:63611547-63611566 None:intergenic 45.0%
TCCAGCAAAAGCAATGCAAG+AGG - chr1_3:63611548-63611567 None:intergenic 45.0%
GTTTGCATTACCACAACCAG+AGG - chr1_3:63611578-63611597 None:intergenic 45.0%
! ACATTGAAGCACTACGTGGC+CGG - chr1_3:63611518-63611537 None:intergenic 50.0%
!! CCCTCTTGCATTGCTTTTGC+TGG + chr1_3:63611544-63611563 Msa0132540:CDS 50.0%
TTTGCTGGATATGGGACCTC+TGG + chr1_3:63611559-63611578 Msa0132540:CDS 50.0%
GGATATGGGACCTCTGGTTG+TGG + chr1_3:63611565-63611584 Msa0132540:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 63611294 63611618 63611294 ID=Msa0132540;Name=Msa0132540
chr1_3 mRNA 63611294 63611618 63611294 ID=Msa0132540-mRNA-1;Parent=Msa0132540;Name=Msa0132540-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|0|0|2|0|95
chr1_3 exon 63611294 63611404 63611294 ID=Msa0132540-mRNA-1:exon:21323;Parent=Msa0132540-mRNA-1
chr1_3 exon 63611442 63611618 63611442 ID=Msa0132540-mRNA-1:exon:21324;Parent=Msa0132540-mRNA-1
chr1_3 CDS 63611294 63611404 63611294 ID=Msa0132540-mRNA-1:cds;Parent=Msa0132540-mRNA-1
chr1_3 CDS 63611442 63611618 63611442 ID=Msa0132540-mRNA-1:cds;Parent=Msa0132540-mRNA-1
Gene Sequence

>Msa0132540

ATGGCTGGTGATTTATATGCTGAGGACATGCAAGTTGGTTGCCATGTGAAGTTGGTTACTCTCACTTCTTGGTCGGGTTTGCAAAGAAATCAAGTAGTACTTTCATATGATGTTTCATGGTTGCGTCTTGCTTGTAATAATCTTTGTGGAGATCAAACACTAGGAGCATGCTACTTTAACGCTTCCGGCCACGTAGTGCTTCAATGTTCTCTACCCTCTTGCATTGCTTTTGCTGGATATGGGACCTCTGGTTGTGGTAATGCAAACATCGTTACCAATTACAACTAA
Protein sequence

>Msa0132540

MAGDLYAEDMQVGCHVKLVTLTSWSGLQRNQVVLSYDVSWLRLACNNLCGDQTLGACYFNASGHVVLQCSLPSCIAFAGYGTSGCGNANIVTNYN*