AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1368700

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1368700 MtrunA17_Chr3g0136801 99.000 100 1 0 1 100 1 100 5.00e-70 204
Msa1368700 MtrunA17_Chr6g0460501 54.082 98 45 0 2 99 77 174 9.57e-37 122
Msa1368700 MtrunA17_Chr6g0470661 53.608 97 45 0 2 98 72 168 2.40e-33 115
Msa1368700 MtrunA17_Chr1g0203511 53.608 97 45 0 2 98 107 203 9.31e-33 114
Msa1368700 MtrunA17_Chr3g0120151 44.330 97 54 0 3 99 35 131 8.69e-24 90.9
Msa1368700 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
Msa1368700 AT2G24940.1 81.000 100 19 0 1 100 1 100 4.17e-57 171
Msa1368700 AT5G52240.2 53.608 97 45 0 2 98 74 170 6.13e-35 118
Msa1368700 AT5G52240.1 53.608 97 45 0 2 98 74 170 2.37e-34 117
Msa1368700 AT3G48890.1 52.577 97 46 0 2 98 70 166 1.72e-32 113
Msa1368700 AT4G14965.1 42.268 97 56 0 3 99 42 138 1.21e-20 83.2
Msa1368700 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 tig0018650:-167380 None:intergenic
TGCTCTGCTAGCGTCTTTGC+CGG 0.356636 tig0018650:-167467 None:intergenic
AGATCGGAGTTCTCAATGAT+TGG 0.393020 tig0018650:+167554 Msa1368700:CDS
CTAACGATGGTGGCAACAAC+AGG 0.396192 tig0018650:-167601 None:intergenic
GAGAACTCCGATCTCTTTCT+CGG 0.397488 tig0018650:-167545 None:intergenic
GCCCATCTACGTGGCGGTGA+AGG 0.412629 tig0018650:+167378 Msa1368700:CDS
AGCGTCTTTGCCGGCGAACA+TGG 0.474656 tig0018650:-167458 None:intergenic
GATCGGAGTTCTCAATGATT+GGG 0.479187 tig0018650:+167555 Msa1368700:CDS
AGGGTACTTAGCTACGAACT+TGG 0.494927 tig0018650:-167581 None:intergenic
GCCACGTAGATGGGCTTCGA+TGG 0.508678 tig0018650:-167370 None:intergenic
GGTAAATCGTTCTACGGTCC+AGG 0.513945 tig0018650:+167424 Msa1368700:CDS
GGAGCCTACGCCATGTTCGC+CGG 0.517126 tig0018650:+167448 Msa1368700:CDS
GATATCACCTCGTCGCTCGA+TGG 0.532549 tig0018650:+167517 Msa1368700:CDS
TGGACCGTAGAACGATTTAC+CGG 0.538773 tig0018650:-167422 None:intergenic
CCCATCTACGTGGCGGTGAA+GGG 0.540433 tig0018650:+167379 Msa1368700:CDS
CCACGTAGATGGGCTTCGAT+GGG 0.568442 tig0018650:-167369 None:intergenic
GGACTCACCGAGAAAGAGAT+CGG 0.584108 tig0018650:+167538 Msa1368700:CDS
ACCACCGGTAAATCGTTCTA+CGG 0.585309 tig0018650:+167418 Msa1368700:CDS
TTGAATTAATTAGCTAACGA+TGG 0.596468 tig0018650:-167614 None:intergenic
AATTAATTAGCTAACGATGG+TGG 0.596842 tig0018650:-167611 None:intergenic
TTTGCCGGCGAACATGGCGT+AGG 0.602453 tig0018650:-167452 None:intergenic
AAATCGTTCTACGGTCCAGG+TGG 0.624678 tig0018650:+167427 Msa1368700:CDS
TAACGATGGTGGCAACAACA+GGG 0.689123 tig0018650:-167600 None:intergenic
ATCGAAGCCCATCTACGTGG+CGG 0.707583 tig0018650:+167372 Msa1368700:CDS
ACCGTAGAACGATTTACCGG+TGG 0.721812 tig0018650:-167419 None:intergenic
CAACAACTGAGCGAATACAA+CGG 0.745415 tig0018650:+167340 Msa1368700:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAACAACTGAGCGAATACAA+CGG + tig0018650:167340-167359 Msa1368700:CDS 40.0%
AGATCGGAGTTCTCAATGAT+TGG + tig0018650:167554-167573 Msa1368700:CDS 40.0%
GATCGGAGTTCTCAATGATT+GGG + tig0018650:167555-167574 Msa1368700:CDS 40.0%
ACCACCGGTAAATCGTTCTA+CGG + tig0018650:167418-167437 Msa1368700:CDS 45.0%
TGGACCGTAGAACGATTTAC+CGG - tig0018650:167425-167444 None:intergenic 45.0%
GAGAACTCCGATCTCTTTCT+CGG - tig0018650:167548-167567 None:intergenic 45.0%
! AGGGTACTTAGCTACGAACT+TGG - tig0018650:167584-167603 None:intergenic 45.0%
! TAACGATGGTGGCAACAACA+GGG - tig0018650:167603-167622 None:intergenic 45.0%
ACCGTAGAACGATTTACCGG+TGG - tig0018650:167422-167441 None:intergenic 50.0%
GGTAAATCGTTCTACGGTCC+AGG + tig0018650:167424-167443 Msa1368700:CDS 50.0%
AAATCGTTCTACGGTCCAGG+TGG + tig0018650:167427-167446 Msa1368700:CDS 50.0%
GGACTCACCGAGAAAGAGAT+CGG + tig0018650:167538-167557 Msa1368700:CDS 50.0%
! CTAACGATGGTGGCAACAAC+AGG - tig0018650:167604-167623 None:intergenic 50.0%
! CCACGTAGATGGGCTTCGAT+GGG - tig0018650:167372-167391 None:intergenic 55.0%
ATCGAAGCCCATCTACGTGG+CGG + tig0018650:167372-167391 Msa1368700:CDS 55.0%
TGCTCTGCTAGCGTCTTTGC+CGG - tig0018650:167470-167489 None:intergenic 55.0%
GATATCACCTCGTCGCTCGA+TGG + tig0018650:167517-167536 Msa1368700:CDS 55.0%
CCCATCGAAGCCCATCTACG+TGG + tig0018650:167369-167388 Msa1368700:CDS 60.0%
! GCCACGTAGATGGGCTTCGA+TGG - tig0018650:167373-167392 None:intergenic 60.0%
CCCTTCACCGCCACGTAGAT+GGG - tig0018650:167382-167401 None:intergenic 60.0%
CCCATCTACGTGGCGGTGAA+GGG + tig0018650:167379-167398 Msa1368700:CDS 60.0%
ACCCTTCACCGCCACGTAGA+TGG - tig0018650:167383-167402 None:intergenic 60.0%
! CGCGTTTTCGACGTCACCAC+CGG + tig0018650:167403-167422 Msa1368700:CDS 60.0%
AACATGGCGTAGGCTCCACC+TGG - tig0018650:167445-167464 None:intergenic 60.0%
TTTGCCGGCGAACATGGCGT+AGG - tig0018650:167455-167474 None:intergenic 60.0%
AGCGTCTTTGCCGGCGAACA+TGG - tig0018650:167461-167480 None:intergenic 60.0%
GCCCATCTACGTGGCGGTGA+AGG + tig0018650:167378-167397 Msa1368700:CDS 65.0%
GGAGCCTACGCCATGTTCGC+CGG + tig0018650:167448-167467 Msa1368700:CDS 65.0%
GGTGAGTCCATCGAGCGACG+AGG - tig0018650:167527-167546 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0018650 gene 167325 167627 167325 ID=Msa1368700;Name=Msa1368700
tig0018650 mRNA 167325 167627 167325 ID=Msa1368700-mRNA-1;Parent=Msa1368700;Name=Msa1368700-mRNA-1;_AED=0.37;_eAED=0.39;_QI=0|-1|0|1|-1|1|1|0|100
tig0018650 exon 167325 167627 167325 ID=Msa1368700-mRNA-1:exon:587;Parent=Msa1368700-mRNA-1
tig0018650 CDS 167325 167627 167325 ID=Msa1368700-mRNA-1:cds;Parent=Msa1368700-mRNA-1
Gene Sequence

>Msa1368700

ATGGAGATGACAGCACAACAACTGAGCGAATACAACGGTACAGACCCATCGAAGCCCATCTACGTGGCGGTGAAGGGTCGCGTTTTCGACGTCACCACCGGTAAATCGTTCTACGGTCCAGGTGGAGCCTACGCCATGTTCGCCGGCAAAGACGCTAGCAGAGCACTTGCAAAGATGAGCAAGAACGAAGAAGATATCACCTCGTCGCTCGATGGACTCACCGAGAAAGAGATCGGAGTTCTCAATGATTGGGAAACCAAGTTCGTAGCTAAGTACCCTGTTGTTGCCACCATCGTTAGCTAA
Protein sequence

>Msa1368700

MEMTAQQLSEYNGTDPSKPIYVAVKGRVFDVTTGKSFYGPGGAYAMFAGKDASRALAKMSKNEEDITSSLDGLTEKEIGVLNDWETKFVAKYPVVATIVS*