AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380017015.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380017015.01.T01 MTR_3g099400 100.000 48 0 0 6 53 162 209 7.51e-27 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 58 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTTGCTGTGGTTGCTTC+TGG 0.235109 3:+90736669 None:intergenic
AAACCCTAAATTCCCTGAAT+TGG 0.308517 3:+90736481 None:intergenic
CCGTCTTCTCCAGGTCCATT+TGG 0.337805 3:-90736563 MsG0380017015.01.T01:CDS
AACCCTAAATTCCCTGAATT+GGG 0.343019 3:+90736482 None:intergenic
CGTCTTCTCCAGGTCCATTT+GGG 0.351852 3:-90736562 MsG0380017015.01.T01:CDS
CCGCCACCACCACCGGCGAC+GGG 0.357471 3:-90736614 MsG0380017015.01.T01:CDS
AGTCAAATTTGTCTCCATCT+TGG 0.370849 3:+90736419 None:intergenic
CCCGTCGCCGGTGGTGGTGG+CGG 0.388345 3:+90736614 None:intergenic
ATCGATTCCAAGGGTTTCTC+TGG 0.399491 3:-90736732 MsG0380017015.01.T01:CDS
TAACAACAACTTTCCTGGTT+AGG 0.410191 3:-90736864 MsG0380017015.01.T01:CDS
GAATCAACCGCCACCGCAGC+AGG 0.412117 3:-90736648 MsG0380017015.01.T01:CDS
TGAGACCCCGTCGCCGGTGG+TGG 0.436857 3:+90736608 None:intergenic
GACCCCGTCGCCGGTGGTGG+TGG 0.440241 3:+90736611 None:intergenic
CTCCATCTTGGACTTGGTAC+AGG 0.441142 3:+90736431 None:intergenic
ATTTGTCTCCATCTTGGACT+TGG 0.443329 3:+90736425 None:intergenic
GCCGCCACCACCACCGGCGA+CGG 0.446995 3:-90736615 MsG0380017015.01.T01:CDS
GCTGTGGTTGCTTCTGGTTG+AGG 0.447947 3:+90736675 None:intergenic
ACAACTTCCTGCTGCGGTGG+CGG 0.450155 3:+90736641 None:intergenic
TTTCAGATGCCGTCTTCTCC+AGG 0.458680 3:-90736572 MsG0380017015.01.T01:CDS
GTCGCCGGTGGTGGTGGCGG+CGG 0.460770 3:+90736617 None:intergenic
GCGGCGTGAACGGTGGGAAA+CGG 0.462762 3:+90736810 None:intergenic
CTGCTCCACCATCGATTCCA+AGG 0.465145 3:-90736742 MsG0380017015.01.T01:CDS
ACAGGCACAGTTGGAGAAAG+AGG 0.475478 3:+90736449 None:intergenic
TCGCGCATGTAAGCTGAAAT+CGG 0.500612 3:+90736777 None:intergenic
GTCGATTGAGACCCCGTCGC+CGG 0.511197 3:+90736602 None:intergenic
AGATTCAGCGGCGGCGTGAA+CGG 0.513194 3:+90736800 None:intergenic
TCAGCGGCGGCGTGAACGGT+GGG 0.516055 3:+90736804 None:intergenic
TCTTATCCTTTGTTGTCACC+AGG 0.522307 3:-90736518 MsG0380017015.01.T01:CDS
TGTGCCGCCGCCACCACCAC+CGG 0.522332 3:-90736621 MsG0380017015.01.T01:CDS
GGCGGTTGATTCTCTTGCTG+TGG 0.528949 3:+90736659 None:intergenic
GGCACAACTTCCTGCTGCGG+TGG 0.532075 3:+90736638 None:intergenic
GGACTTGGTACAGGCACAGT+TGG 0.542926 3:+90736440 None:intergenic
TGTGAATTCAAACACCCAAA+TGG 0.545577 3:+90736548 None:intergenic
TGCTCCACCATCGATTCCAA+GGG 0.547232 3:-90736741 MsG0380017015.01.T01:CDS
CGCCACCACCACCGGCGACG+GGG 0.548896 3:-90736613 MsG0380017015.01.T01:CDS
AACGGTGGTAACGGAGATAA+CGG 0.553222 3:+90736828 None:intergenic
CCAAATGGACCTGGAGAAGA+CGG 0.556750 3:+90736563 None:intergenic
GGTTGAGGTGGTAAAACAGT+AGG 0.558870 3:+90736690 None:intergenic
TTCAGCGGCGGCGTGAACGG+TGG 0.559116 3:+90736803 None:intergenic
TTCAAACACCCAAATGGACC+TGG 0.560912 3:+90736554 None:intergenic
ACCCTAAATTCCCTGAATTG+GGG 0.570439 3:+90736483 None:intergenic
GATTGAGACCCCGTCGCCGG+TGG 0.573393 3:+90736605 None:intergenic
TGCTTGAGGTCTACCTAACC+AGG 0.578253 3:+90736851 None:intergenic
GTGGTTGCTTCTGGTTGAGG+TGG 0.578994 3:+90736678 None:intergenic
AACGGAGATAACGGTGCTTG+AGG 0.579544 3:+90736837 None:intergenic
CCCTAAATTCCCTGAATTGG+GGG 0.583945 3:+90736484 None:intergenic
AGAGAAACCCTTGGAATCGA+TGG 0.585883 3:+90736734 None:intergenic
GGCGGCACAACTTCCTGCTG+CGG 0.586848 3:+90736635 None:intergenic
ACGGTGGGAAACGGTGGTAA+CGG 0.589742 3:+90736819 None:intergenic
TGCCTGTACCAAGTCCAAGA+TGG 0.594045 3:-90736433 MsG0380017015.01.T01:CDS
GAAACCCTTGGAATCGATGG+TGG 0.604021 3:+90736737 None:intergenic
GTTGGAGAAAGAGGAAGTTG+AGG 0.605702 3:+90736458 None:intergenic
GGTGGTAAAACAGTAGGAAG+AGG 0.610301 3:+90736696 None:intergenic
AAAACAGTAGGAAGAGGCAA+AGG 0.615327 3:+90736702 None:intergenic
AGCTGAAATCGGAGATTCAG+CGG 0.616371 3:+90736788 None:intergenic
GCGTGAACGGTGGGAAACGG+TGG 0.624404 3:+90736813 None:intergenic
AATAAACCTGGTGACAACAA+AGG 0.646817 3:+90736512 None:intergenic
TGAAATCGGAGATTCAGCGG+CGG 0.730011 3:+90736791 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAACCCTAAATTCCCTGAAT+TGG + Chr3:90736799-90736818 None:intergenic 35.0%
AACCCTAAATTCCCTGAATT+GGG + Chr3:90736798-90736817 None:intergenic 35.0%
AATAAACCTGGTGACAACAA+AGG + Chr3:90736768-90736787 None:intergenic 35.0%
AGTCAAATTTGTCTCCATCT+TGG + Chr3:90736861-90736880 None:intergenic 35.0%
TGTGAATTCAAACACCCAAA+TGG + Chr3:90736732-90736751 None:intergenic 35.0%
! TATTGTTTTCCCCCAATTCA+GGG - Chr3:90736784-90736803 MsG0380017015.01.T01:CDS 35.0%
! TTATTGTTTTCCCCCAATTC+AGG - Chr3:90736783-90736802 MsG0380017015.01.T01:CDS 35.0%
AAAACAGTAGGAAGAGGCAA+AGG + Chr3:90736578-90736597 None:intergenic 40.0%
ACCCTAAATTCCCTGAATTG+GGG + Chr3:90736797-90736816 None:intergenic 40.0%
AGAAAAACCAGAGAAACCCT+TGG + Chr3:90736555-90736574 None:intergenic 40.0%
ATTTGTCTCCATCTTGGACT+TGG + Chr3:90736855-90736874 None:intergenic 40.0%
TTGGGGGAAAACAATAAACC+TGG + Chr3:90736780-90736799 None:intergenic 40.0%
! TCTTATCCTTTGTTGTCACC+AGG - Chr3:90736759-90736778 MsG0380017015.01.T01:CDS 40.0%
AGAGAAACCCTTGGAATCGA+TGG + Chr3:90736546-90736565 None:intergenic 45.0%
AGCTGAAATCGGAGATTCAG+CGG + Chr3:90736492-90736511 None:intergenic 45.0%
CCCCCAATTCAGGGAATTTA+GGG - Chr3:90736793-90736812 MsG0380017015.01.T01:CDS 45.0%
CCCTAAATTCCCTGAATTGG+GGG + Chr3:90736796-90736815 None:intergenic 45.0%
GGTGGTAAAACAGTAGGAAG+AGG + Chr3:90736584-90736603 None:intergenic 45.0%
GGTTGAGGTGGTAAAACAGT+AGG + Chr3:90736590-90736609 None:intergenic 45.0%
GTTGGAGAAAGAGGAAGTTG+AGG + Chr3:90736822-90736841 None:intergenic 45.0%
TCCCCCAATTCAGGGAATTT+AGG - Chr3:90736792-90736811 MsG0380017015.01.T01:CDS 45.0%
TCGCGCATGTAAGCTGAAAT+CGG + Chr3:90736503-90736522 None:intergenic 45.0%
TTCAAACACCCAAATGGACC+TGG + Chr3:90736726-90736745 None:intergenic 45.0%
! ATCGATTCCAAGGGTTTCTC+TGG - Chr3:90736545-90736564 MsG0380017015.01.T01:CDS 45.0%
!! AACGGTGGTAACGGAGATAA+CGG + Chr3:90736452-90736471 None:intergenic 45.0%
ACAGGCACAGTTGGAGAAAG+AGG + Chr3:90736831-90736850 None:intergenic 50.0%
CCAAATGGACCTGGAGAAGA+CGG + Chr3:90736717-90736736 None:intergenic 50.0%
CGTCTTCTCCAGGTCCATTT+GGG - Chr3:90736715-90736734 MsG0380017015.01.T01:CDS 50.0%
GAAACCCTTGGAATCGATGG+TGG + Chr3:90736543-90736562 None:intergenic 50.0%
TGAAATCGGAGATTCAGCGG+CGG + Chr3:90736489-90736508 None:intergenic 50.0%
TGCCTGTACCAAGTCCAAGA+TGG - Chr3:90736844-90736863 MsG0380017015.01.T01:CDS 50.0%
TGCTTGAGGTCTACCTAACC+AGG + Chr3:90736429-90736448 None:intergenic 50.0%
TTTCAGATGCCGTCTTCTCC+AGG - Chr3:90736705-90736724 MsG0380017015.01.T01:CDS 50.0%
! AACGGAGATAACGGTGCTTG+AGG + Chr3:90736443-90736462 None:intergenic 50.0%
! CTCCATCTTGGACTTGGTAC+AGG + Chr3:90736849-90736868 None:intergenic 50.0%
! TCTCTTGCTGTGGTTGCTTC+TGG + Chr3:90736611-90736630 None:intergenic 50.0%
!! TGCTCCACCATCGATTCCAA+GGG - Chr3:90736536-90736555 MsG0380017015.01.T01:CDS 50.0%
ACGGTGGGAAACGGTGGTAA+CGG + Chr3:90736461-90736480 None:intergenic 55.0%
CCGTCTTCTCCAGGTCCATT+TGG - Chr3:90736714-90736733 MsG0380017015.01.T01:CDS 55.0%
! GCTGTGGTTGCTTCTGGTTG+AGG + Chr3:90736605-90736624 None:intergenic 55.0%
! GGACTTGGTACAGGCACAGT+TGG + Chr3:90736840-90736859 None:intergenic 55.0%
! GGCGGTTGATTCTCTTGCTG+TGG + Chr3:90736621-90736640 None:intergenic 55.0%
! GTGGTTGCTTCTGGTTGAGG+TGG + Chr3:90736602-90736621 None:intergenic 55.0%
!! CTGCTCCACCATCGATTCCA+AGG - Chr3:90736535-90736554 MsG0380017015.01.T01:CDS 55.0%
ACAACTTCCTGCTGCGGTGG+CGG + Chr3:90736639-90736658 None:intergenic 60.0%
AGATTCAGCGGCGGCGTGAA+CGG + Chr3:90736480-90736499 None:intergenic 60.0%
GAATCAACCGCCACCGCAGC+AGG - Chr3:90736629-90736648 MsG0380017015.01.T01:CDS 65.0%
GCGGCGTGAACGGTGGGAAA+CGG + Chr3:90736470-90736489 None:intergenic 65.0%
GCGTGAACGGTGGGAAACGG+TGG + Chr3:90736467-90736486 None:intergenic 65.0%
GGCACAACTTCCTGCTGCGG+TGG + Chr3:90736642-90736661 None:intergenic 65.0%
GGCGGCACAACTTCCTGCTG+CGG + Chr3:90736645-90736664 None:intergenic 65.0%
GTCGATTGAGACCCCGTCGC+CGG + Chr3:90736678-90736697 None:intergenic 65.0%
GATTGAGACCCCGTCGCCGG+TGG + Chr3:90736675-90736694 None:intergenic 70.0%
TCAGCGGCGGCGTGAACGGT+GGG + Chr3:90736476-90736495 None:intergenic 70.0%
TTCAGCGGCGGCGTGAACGG+TGG + Chr3:90736477-90736496 None:intergenic 70.0%
TGAGACCCCGTCGCCGGTGG+TGG + Chr3:90736672-90736691 None:intergenic 75.0%
TGTGCCGCCGCCACCACCAC+CGG - Chr3:90736656-90736675 MsG0380017015.01.T01:CDS 75.0%
! CCGCCACCACCACCGGCGAC+GGG - Chr3:90736663-90736682 MsG0380017015.01.T01:CDS 80.0%
! CGCCACCACCACCGGCGACG+GGG - Chr3:90736664-90736683 MsG0380017015.01.T01:CDS 80.0%
! GCCGCCACCACCACCGGCGA+CGG - Chr3:90736662-90736681 MsG0380017015.01.T01:CDS 80.0%
!! GACCCCGTCGCCGGTGGTGG+TGG + Chr3:90736669-90736688 None:intergenic 80.0%
!!! CCCGTCGCCGGTGGTGGTGG+CGG + Chr3:90736666-90736685 None:intergenic 80.0%
!!! GTCGCCGGTGGTGGTGGCGG+CGG + Chr3:90736663-90736682 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
Chr3 gene 90736416 90736883 90736416 ID=MsG0380017015.01;Name=MsG0380017015.01
Chr3 mRNA 90736416 90736883 90736416 ID=MsG0380017015.01.T01;Parent=MsG0380017015.01;Name=MsG0380017015.01.T01;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|0|1|0|155
Chr3 exon 90736416 90736883 90736416 ID=MsG0380017015.01.T01:exon:30888;Parent=MsG0380017015.01.T01
Chr3 CDS 90736416 90736883 90736416 ID=MsG0380017015.01.T01:cds;Parent=MsG0380017015.01.T01
Gene Sequence

>MsG0380017015.01.T01

CAACAACTTTCCTGGTTAGGTAGACCTCAAGCACCGTTATCTCCGTTACCACCGTTTCCCACCGTTCACGCCGCCGCTGAATCTCCGATTTCAGCTTACATGCGCGATCTGCAGAATTTCTGCTCCACCATCGATTCCAAGGGTTTCTCTGGTTTTTCTCCTTTGCCTCTTCCTACTGTTTTACCACCTCAACCAGAAGCAACCACAGCAAGAGAATCAACCGCCACCGCAGCAGGAAGTTGTGCCGCCGCCACCACCACCGGCGACGGGGTCTCAATCGACTTCTTCATTTCAGATGCCGTCTTCTCCAGGTCCATTTGGGTGTTTGAATTCACAGCTAGCATCTTATCCTTTGTTGTCACCAGGTTTATTGTTTTCCCCCAATTCAGGGAATTTAGGGTTTCCTCAACTTCCTCTTTCTCCAACTGTGCCTGTACCAAGTCCAAGATGGAGACAAATTTGACTTGA
Protein sequence

>MsG0380017015.01.T01

QQLSWLGRPQAPLSPLPPFPTVHAAAESPISAYMRDLQNFCSTIDSKGFSGFSPLPLPTVLPPQPEATTARESTATAAGSCAAATTTGDGVSIDFFISDAVFSRSIWVFEFTASILSFVVTRFIVFPQFREFRVSSTSSFSNCACTKSKMETNLT*