AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1458100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1458100 MtrunA17_Chr3g0136801 99.000 100 1 0 1 100 1 100 5.00e-70 204
Msa1458100 MtrunA17_Chr6g0460501 54.082 98 45 0 2 99 77 174 9.57e-37 122
Msa1458100 MtrunA17_Chr6g0470661 53.608 97 45 0 2 98 72 168 2.40e-33 115
Msa1458100 MtrunA17_Chr1g0203511 53.608 97 45 0 2 98 107 203 9.31e-33 114
Msa1458100 MtrunA17_Chr3g0120151 44.330 97 54 0 3 99 35 131 8.69e-24 90.9
Msa1458100 MtrunA17_Chr6g0460431 49.180 61 31 0 36 96 26 86 1.12e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1458100 AT2G24940.1 81.000 100 19 0 1 100 1 100 4.17e-57 171
Msa1458100 AT5G52240.2 53.608 97 45 0 2 98 74 170 6.13e-35 118
Msa1458100 AT5G52240.1 53.608 97 45 0 2 98 74 170 2.37e-34 117
Msa1458100 AT3G48890.1 52.577 97 46 0 2 98 70 166 1.72e-32 113
Msa1458100 AT4G14965.1 42.268 97 56 0 3 99 42 138 1.21e-20 83.2
Msa1458100 AT4G14965.2 45.783 83 45 0 3 85 42 124 4.43e-20 80.5

Find 26 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCTTCACCGCCACGTAGA+TGG 0.304041 tig0039409:+7469 None:intergenic
TGCTCTGCTAGCGTCTTTGC+CGG 0.356636 tig0039409:+7382 None:intergenic
AGATCGGAGTTCTCAATGAT+TGG 0.393020 tig0039409:-7295 Msa1458100:CDS
CTAACGATGGTGGCAACAAC+AGG 0.396192 tig0039409:+7248 None:intergenic
GAGAACTCCGATCTCTTTCT+CGG 0.397488 tig0039409:+7304 None:intergenic
GCCCATCTACGTGGCGGTGA+AGG 0.412629 tig0039409:-7471 Msa1458100:CDS
AGCGTCTTTGCCGGCGAACA+TGG 0.474656 tig0039409:+7391 None:intergenic
GATCGGAGTTCTCAATGATT+GGG 0.479187 tig0039409:-7294 Msa1458100:CDS
AGGGTACTTAGCTACGAACT+TGG 0.494927 tig0039409:+7268 None:intergenic
GCCACGTAGATGGGCTTCGA+TGG 0.508678 tig0039409:+7479 None:intergenic
GGTAAATCGTTCTACGGTCC+AGG 0.513945 tig0039409:-7425 Msa1458100:CDS
GGAGCCTACGCCATGTTCGC+CGG 0.517126 tig0039409:-7401 Msa1458100:CDS
GATATCACCTCGTCGCTCGA+TGG 0.532549 tig0039409:-7332 Msa1458100:CDS
TGGACCGTAGAACGATTTAC+CGG 0.538773 tig0039409:+7427 None:intergenic
CCCATCTACGTGGCGGTGAA+GGG 0.540433 tig0039409:-7470 Msa1458100:CDS
CCACGTAGATGGGCTTCGAT+GGG 0.568442 tig0039409:+7480 None:intergenic
GGACTCACCGAGAAAGAGAT+CGG 0.584108 tig0039409:-7311 Msa1458100:CDS
ACCACCGGTAAATCGTTCTA+CGG 0.585309 tig0039409:-7431 Msa1458100:CDS
TTGAATTAATTAGCTAACGA+TGG 0.596468 tig0039409:+7235 None:intergenic
AATTAATTAGCTAACGATGG+TGG 0.596842 tig0039409:+7238 None:intergenic
TTTGCCGGCGAACATGGCGT+AGG 0.602453 tig0039409:+7397 None:intergenic
AAATCGTTCTACGGTCCAGG+TGG 0.624678 tig0039409:-7422 Msa1458100:CDS
TAACGATGGTGGCAACAACA+GGG 0.689123 tig0039409:+7249 None:intergenic
ATCGAAGCCCATCTACGTGG+CGG 0.707583 tig0039409:-7477 Msa1458100:CDS
ACCGTAGAACGATTTACCGG+TGG 0.721812 tig0039409:+7430 None:intergenic
CAACAACTGAGCGAATACAA+CGG 0.745415 tig0039409:-7509 Msa1458100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAACAACTGAGCGAATACAA+CGG - tig0039409:7259-7278 Msa1458100:CDS 40.0%
AGATCGGAGTTCTCAATGAT+TGG - tig0039409:7473-7492 Msa1458100:CDS 40.0%
GATCGGAGTTCTCAATGATT+GGG - tig0039409:7474-7493 Msa1458100:CDS 40.0%
ACCACCGGTAAATCGTTCTA+CGG - tig0039409:7337-7356 Msa1458100:CDS 45.0%
TGGACCGTAGAACGATTTAC+CGG + tig0039409:7344-7363 None:intergenic 45.0%
GAGAACTCCGATCTCTTTCT+CGG + tig0039409:7467-7486 None:intergenic 45.0%
! AGGGTACTTAGCTACGAACT+TGG + tig0039409:7503-7522 None:intergenic 45.0%
! TAACGATGGTGGCAACAACA+GGG + tig0039409:7522-7541 None:intergenic 45.0%
ACCGTAGAACGATTTACCGG+TGG + tig0039409:7341-7360 None:intergenic 50.0%
GGTAAATCGTTCTACGGTCC+AGG - tig0039409:7343-7362 Msa1458100:CDS 50.0%
AAATCGTTCTACGGTCCAGG+TGG - tig0039409:7346-7365 Msa1458100:CDS 50.0%
GGACTCACCGAGAAAGAGAT+CGG - tig0039409:7457-7476 Msa1458100:CDS 50.0%
! CTAACGATGGTGGCAACAAC+AGG + tig0039409:7523-7542 None:intergenic 50.0%
! CCACGTAGATGGGCTTCGAT+GGG + tig0039409:7291-7310 None:intergenic 55.0%
ATCGAAGCCCATCTACGTGG+CGG - tig0039409:7291-7310 Msa1458100:CDS 55.0%
TGCTCTGCTAGCGTCTTTGC+CGG + tig0039409:7389-7408 None:intergenic 55.0%
GATATCACCTCGTCGCTCGA+TGG - tig0039409:7436-7455 Msa1458100:CDS 55.0%
CCCATCGAAGCCCATCTACG+TGG - tig0039409:7288-7307 Msa1458100:CDS 60.0%
! GCCACGTAGATGGGCTTCGA+TGG + tig0039409:7292-7311 None:intergenic 60.0%
CCCTTCACCGCCACGTAGAT+GGG + tig0039409:7301-7320 None:intergenic 60.0%
CCCATCTACGTGGCGGTGAA+GGG - tig0039409:7298-7317 Msa1458100:CDS 60.0%
ACCCTTCACCGCCACGTAGA+TGG + tig0039409:7302-7321 None:intergenic 60.0%
! CGCGTTTTCGACGTCACCAC+CGG - tig0039409:7322-7341 Msa1458100:CDS 60.0%
AACATGGCGTAGGCTCCACC+TGG + tig0039409:7364-7383 None:intergenic 60.0%
TTTGCCGGCGAACATGGCGT+AGG + tig0039409:7374-7393 None:intergenic 60.0%
AGCGTCTTTGCCGGCGAACA+TGG + tig0039409:7380-7399 None:intergenic 60.0%
GCCCATCTACGTGGCGGTGA+AGG - tig0039409:7297-7316 Msa1458100:CDS 65.0%
GGAGCCTACGCCATGTTCGC+CGG - tig0039409:7367-7386 Msa1458100:CDS 65.0%
GGTGAGTCCATCGAGCGACG+AGG + tig0039409:7446-7465 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0039409 gene 7244 7546 7244 ID=Msa1458100;Name=Msa1458100
tig0039409 mRNA 7244 7546 7244 ID=Msa1458100-mRNA-1;Parent=Msa1458100;Name=Msa1458100-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|100
tig0039409 exon 7244 7546 7244 ID=Msa1458100-mRNA-1:exon:21601;Parent=Msa1458100-mRNA-1
tig0039409 CDS 7244 7546 7244 ID=Msa1458100-mRNA-1:cds;Parent=Msa1458100-mRNA-1
Gene Sequence

>Msa1458100

ATGGAGATGACAGCACAACAACTGAGCGAATACAACGGTACAGACCCATCGAAGCCCATCTACGTGGCGGTGAAGGGTCGCGTTTTCGACGTCACCACCGGTAAATCGTTCTACGGTCCAGGTGGAGCCTACGCCATGTTCGCCGGCAAAGACGCTAGCAGAGCACTTGCAAAGATGAGCAAGAACGAAGAAGATATCACCTCGTCGCTCGATGGACTCACCGAGAAAGAGATCGGAGTTCTCAATGATTGGGAAACCAAGTTCGTAGCTAAGTACCCTGTTGTTGCCACCATCGTTAGCTAA
Protein sequence

>Msa1458100

MEMTAQQLSEYNGTDPSKPIYVAVKGRVFDVTTGKSFYGPGGAYAMFAGKDASRALAKMSKNEEDITSSLDGLTEKEIGVLNDWETKFVAKYPVVATIVS*