AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580025567.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580025567.01.T01 MTR_5g430710 72.500 40 9 1 18 57 393 430 4.81e-12 60.1
MsG0580025567.01.T01 MTR_5g030610 72.500 40 9 1 18 57 393 430 8.93e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAAATACTGTAAAATTTA+TGG 0.103463 5:+20570552 None:intergenic
ATCGTAATGGGCATATTTCT+TGG 0.309165 5:+20571770 None:intergenic
TGATGACGACGACTCCAATA+TGG 0.352130 5:-20571748 MsG0580025567.01.T01:CDS
TCGTAATGGGCATATTTCTT+GGG 0.365503 5:+20571771 None:intergenic
ATCGAAGCCTGCCTCCATAT+TGG 0.385208 5:+20571734 None:intergenic
ATAATTGTAAACTTCCAAAT+GGG 0.412530 5:-20571890 MsG0580025567.01.T01:CDS
CATAACCGGTTTGATTATCA+TGG 0.415922 5:-20570750 MsG0580025567.01.T01:three_prime_UTR
GATAATTGTAAACTTCCAAA+TGG 0.416994 5:-20571891 MsG0580025567.01.T01:CDS
TTACAAAGAGGGCAAATGTT+GGG 0.433247 5:-20570603 MsG0580025567.01.T01:three_prime_UTR
AGCGAGGTTGTTAGCGGAGG+AGG 0.438735 5:-20570832 MsG0580025567.01.T01:CDS
TTGCTCAAATTCAGTCCAAT+GGG 0.446177 5:-20570719 MsG0580025567.01.T01:three_prime_UTR
GTCGTCGTCATCATCGTAAT+GGG 0.451701 5:+20571758 None:intergenic
CATGTGTGCAGTGCGAAAAT+TGG 0.456022 5:-20570876 MsG0580025567.01.T01:intron
TGTAACATGAAAGACATAAC+CGG 0.502361 5:-20570764 MsG0580025567.01.T01:exon
AGTCGTCGTCATCATCGTAA+TGG 0.503707 5:+20571757 None:intergenic
GGATTCCATGATAATCAAAC+CGG 0.522134 5:+20570745 None:intergenic
GAGGTTGTTAGCGGAGGAGG+AGG 0.524671 5:-20570829 MsG0580025567.01.T01:CDS
CTTGCTCAAATTCAGTCCAA+TGG 0.528600 5:-20570720 MsG0580025567.01.T01:three_prime_UTR
AAGGCAAAGAAGCGTAAGGT+TGG 0.536360 5:-20570789 MsG0580025567.01.T01:CDS
ACTGTAAAATTTATGGTCGA+AGG 0.541432 5:+20570559 None:intergenic
ATATCCAAAAGGAGGAAAAG+AGG 0.543025 5:-20571710 MsG0580025567.01.T01:CDS
GTTACAAAGAGGGCAAATGT+TGG 0.554743 5:-20570604 MsG0580025567.01.T01:three_prime_UTR
ACGTGAAGCGAGGTTGTTAG+CGG 0.563091 5:-20570838 MsG0580025567.01.T01:CDS
TGACAAAACATCATCCCCAT+TGG 0.565371 5:+20570704 None:intergenic
GACGACTCCAATATGGAGGC+AGG 0.569894 5:-20571741 MsG0580025567.01.T01:CDS
AGGCTTCGATGATATCCAAA+AGG 0.570810 5:-20571721 MsG0580025567.01.T01:CDS
CGTAATGGGCATATTTCTTG+GGG 0.571677 5:+20571772 None:intergenic
TGGACTGAATTTGAGCAAGT+CGG 0.577046 5:+20570724 None:intergenic
TGTTAGCGGAGGAGGAGGCA+AGG 0.580011 5:-20570824 MsG0580025567.01.T01:CDS
TACAAAGAGGGCAAATGTTG+GGG 0.582610 5:-20570602 MsG0580025567.01.T01:three_prime_UTR
AAACAAGGCAAAGAAGCGTA+AGG 0.611154 5:-20570793 MsG0580025567.01.T01:CDS
GGCAAGGAAAGAAAGAAACA+AGG 0.615016 5:-20570808 MsG0580025567.01.T01:CDS
CAGTGCGAAAATTGGTAGAG+CGG 0.624100 5:-20570868 MsG0580025567.01.T01:CDS
TAATTGTAAACTTCCAAATG+GGG 0.636786 5:-20571889 MsG0580025567.01.T01:CDS
TGCGAAAATTGGTAGAGCGG+AGG 0.640714 5:-20570865 MsG0580025567.01.T01:CDS
CGGAGGATGAACGTGAAGCG+AGG 0.646245 5:-20570848 MsG0580025567.01.T01:CDS
TGAAGCGAGGTTGTTAGCGG+AGG 0.648929 5:-20570835 MsG0580025567.01.T01:CDS
CTTCGATGATATCCAAAAGG+AGG 0.651494 5:-20571718 MsG0580025567.01.T01:CDS
AATTGTAAACTTCCAAATGG+GGG 0.651565 5:-20571888 MsG0580025567.01.T01:CDS
TTTACAATTATCAGTACACA+CGG 0.670506 5:+20571902 None:intergenic
TCCAAAAGGAGGAAAAGAGG+AGG 0.696978 5:-20571707 MsG0580025567.01.T01:intron
TGACGACGACTCCAATATGG+AGG 0.702574 5:-20571745 MsG0580025567.01.T01:CDS
TGCTCAAATTCAGTCCAATG+GGG 0.731099 5:-20570718 MsG0580025567.01.T01:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGAAAATATTACATTTTTT+TGG + Chr5:20571489-20571508 None:intergenic 10.0%
!! AAATATGAAATACAAGTAAA+GGG + Chr5:20571363-20571382 None:intergenic 15.0%
!! ACTAAATACTGTAAAATTTA+TGG + Chr5:20571856-20571875 None:intergenic 15.0%
!! TAAATATGAAATACAAGTAA+AGG + Chr5:20571364-20571383 None:intergenic 15.0%
!! TAATAATCATATGTAATGAA+AGG + Chr5:20570573-20570592 None:intergenic 15.0%
!! TCATAAAAATAAATAGATGA+AGG + Chr5:20570880-20570899 None:intergenic 15.0%
!! TTACTTGTATTTCATATTTA+GGG - Chr5:20571364-20571383 MsG0580025567.01.T01:intron 15.0%
!! TTTACTTGTATTTCATATTT+AGG - Chr5:20571363-20571382 MsG0580025567.01.T01:intron 15.0%
!! TTTATTCATTGAAATACATA+TGG + Chr5:20571195-20571214 None:intergenic 15.0%
!!! AAAGATTTTTATAATCAAGT+AGG + Chr5:20570791-20570810 None:intergenic 15.0%
!!! AGTTTTAAATAAGAATAAAC+TGG + Chr5:20570852-20570871 None:intergenic 15.0%
!!! ATTTTCTATTTAAATGCAAA+TGG - Chr5:20571166-20571185 MsG0580025567.01.T01:intron 15.0%
!!! ATTTTTTGAGTTCAATAATT+TGG - Chr5:20571895-20571914 MsG0580025567.01.T01:CDS 15.0%
!!! TTATTGATTACACTTATAAA+TGG - Chr5:20571329-20571348 MsG0580025567.01.T01:intron 15.0%
!!! TTTTCTATTTAAATGCAAAT+GGG - Chr5:20571167-20571186 MsG0580025567.01.T01:intron 15.0%
!! AAATGTTATGAAGCAATATT+TGG - Chr5:20571449-20571468 MsG0580025567.01.T01:intron 20.0%
!! AATGTTATGAAGCAATATTT+GGG - Chr5:20571450-20571469 MsG0580025567.01.T01:intron 20.0%
!! ATAATTGTAAACTTCCAAAT+GGG - Chr5:20570515-20570534 MsG0580025567.01.T01:three_prime_UTR 20.0%
!! CAAAAGAAATAAATAGATGA+AGG + Chr5:20570910-20570929 None:intergenic 20.0%
!! TTGATAAAAATGTTTACACT+TGG - Chr5:20571024-20571043 MsG0580025567.01.T01:intron 20.0%
!!! AAACATTTTTATCAAGTCTT+AGG + Chr5:20571019-20571038 None:intergenic 20.0%
!!! CAATTTTTATGTTACAAAGA+GGG - Chr5:20571791-20571810 MsG0580025567.01.T01:intron 20.0%
! ACACAAAATCTTCAATCATA+TGG + Chr5:20571245-20571264 None:intergenic 25.0%
! AGTCTGTATGAAAAGAAAAT+GGG + Chr5:20570960-20570979 None:intergenic 25.0%
! GATAATTGTAAACTTCCAAA+TGG - Chr5:20570514-20570533 MsG0580025567.01.T01:three_prime_UTR 25.0%
! TAATTGTAAACTTCCAAATG+GGG - Chr5:20570516-20570535 MsG0580025567.01.T01:three_prime_UTR 25.0%
! TAGTCTGTATGAAAAGAAAA+TGG + Chr5:20570961-20570980 None:intergenic 25.0%
! TTTACAATTATCAGTACACA+CGG + Chr5:20570506-20570525 None:intergenic 25.0%
!! ATGATTGAAGATTTTGTGTT+AGG - Chr5:20571246-20571265 MsG0580025567.01.T01:intron 25.0%
!! GCAATTTTTATGTTACAAAG+AGG - Chr5:20571790-20571809 MsG0580025567.01.T01:intron 25.0%
AATTGTAAACTTCCAAATGG+GGG - Chr5:20570517-20570536 MsG0580025567.01.T01:three_prime_UTR 30.0%
ACTGTAAAATTTATGGTCGA+AGG + Chr5:20571849-20571868 None:intergenic 30.0%
TGTAACATGAAAGACATAAC+CGG - Chr5:20571641-20571660 MsG0580025567.01.T01:intron 30.0%
TGTCCTGCTAAAAAAACTAA+AGG + Chr5:20571069-20571088 None:intergenic 30.0%
TTAAGTGAATATCACAGTGT+AGG + Chr5:20570739-20570758 None:intergenic 30.0%
! ACTCTCTTTGTTTGGTAATT+AGG - Chr5:20571088-20571107 MsG0580025567.01.T01:intron 30.0%
! GCTAAAAAAACTAAAGGTGT+TGG + Chr5:20571063-20571082 None:intergenic 30.0%
! TTGAAGATTTTGTGTTAGGA+AGG - Chr5:20571250-20571269 MsG0580025567.01.T01:intron 30.0%
!!! ACACCTTTAGTTTTTTTAGC+AGG - Chr5:20571063-20571082 MsG0580025567.01.T01:intron 30.0%
AAAATACTGTGTCGAGAAGT+GGG + Chr5:20571151-20571170 None:intergenic 35.0%
AGTCTCATTCTAATGACTGA+AGG - Chr5:20570540-20570559 MsG0580025567.01.T01:three_prime_UTR 35.0%
ATATCCAAAAGGAGGAAAAG+AGG - Chr5:20570695-20570714 MsG0580025567.01.T01:three_prime_UTR 35.0%
GGATTCCATGATAATCAAAC+CGG + Chr5:20571663-20571682 None:intergenic 35.0%
TCATATGTAATGAAAGGACG+AGG + Chr5:20570567-20570586 None:intergenic 35.0%
TTACAAAGAGGGCAAATGTT+GGG - Chr5:20571802-20571821 MsG0580025567.01.T01:intron 35.0%
TTGCTCAAATTCAGTCCAAT+GGG - Chr5:20571686-20571705 MsG0580025567.01.T01:intron 35.0%
! TTCCATTCCTTTCTGAAAAC+AGG - Chr5:20570812-20570831 MsG0580025567.01.T01:CDS 35.0%
!! ATCGTAATGGGCATATTTCT+TGG + Chr5:20570638-20570657 None:intergenic 35.0%
!! CATAACCGGTTTGATTATCA+TGG - Chr5:20571655-20571674 MsG0580025567.01.T01:intron 35.0%
!! TCGTAATGGGCATATTTCTT+GGG + Chr5:20570637-20570656 None:intergenic 35.0%
AGGCTTCGATGATATCCAAA+AGG - Chr5:20570684-20570703 MsG0580025567.01.T01:three_prime_UTR 40.0%
ATTAGGAAAAGACGAGTGCT+AGG - Chr5:20571105-20571124 MsG0580025567.01.T01:intron 40.0%
CTTCGATGATATCCAAAAGG+AGG - Chr5:20570687-20570706 MsG0580025567.01.T01:three_prime_UTR 40.0%
CTTGCTCAAATTCAGTCCAA+TGG - Chr5:20571685-20571704 MsG0580025567.01.T01:intron 40.0%
GAAAATACTGTGTCGAGAAG+TGG + Chr5:20571152-20571171 None:intergenic 40.0%
GGCAAGGAAAGAAAGAAACA+AGG - Chr5:20571597-20571616 MsG0580025567.01.T01:intron 40.0%
GTTACAAAGAGGGCAAATGT+TGG - Chr5:20571801-20571820 MsG0580025567.01.T01:intron 40.0%
TACAAAGAGGGCAAATGTTG+GGG - Chr5:20571803-20571822 MsG0580025567.01.T01:intron 40.0%
TGACAAAACATCATCCCCAT+TGG + Chr5:20571704-20571723 None:intergenic 40.0%
TGCTCAAATTCAGTCCAATG+GGG - Chr5:20571687-20571706 MsG0580025567.01.T01:intron 40.0%
TGGACTGAATTTGAGCAAGT+CGG + Chr5:20571684-20571703 None:intergenic 40.0%
! AAACAAGGCAAAGAAGCGTA+AGG - Chr5:20571612-20571631 MsG0580025567.01.T01:intron 40.0%
! AAGACGTCCTGTTTTCAGAA+AGG + Chr5:20570822-20570841 None:intergenic 40.0%
! GTCCTGTTTTCAGAAAGGAA+TGG + Chr5:20570817-20570836 None:intergenic 40.0%
!! CGTAATGGGCATATTTCTTG+GGG + Chr5:20570636-20570655 None:intergenic 40.0%
AAAGGAGGAAAAGAGGAGGT+TGG - Chr5:20570702-20570721 MsG0580025567.01.T01:three_prime_UTR 45.0%
AGCAGGACACTCTCTTTGTT+TGG - Chr5:20571080-20571099 MsG0580025567.01.T01:intron 45.0%
AGTCGTCGTCATCATCGTAA+TGG + Chr5:20570651-20570670 None:intergenic 45.0%
CAGTGCGAAAATTGGTAGAG+CGG - Chr5:20571537-20571556 MsG0580025567.01.T01:intron 45.0%
CATGTGTGCAGTGCGAAAAT+TGG - Chr5:20571529-20571548 MsG0580025567.01.T01:intron 45.0%
GTCGTCGTCATCATCGTAAT+GGG + Chr5:20570650-20570669 None:intergenic 45.0%
TAGAATGAGACTCCCCCATT+TGG + Chr5:20570532-20570551 None:intergenic 45.0%
TCCAAAAGGAGGAAAAGAGG+AGG - Chr5:20570698-20570717 MsG0580025567.01.T01:three_prime_UTR 45.0%
! AAGGCAAAGAAGCGTAAGGT+TGG - Chr5:20571616-20571635 MsG0580025567.01.T01:intron 45.0%
! ACCTCCTCTTTTCCTCCTTT+TGG + Chr5:20570702-20570721 None:intergenic 45.0%
! TGATGACGACGACTCCAATA+TGG - Chr5:20570657-20570676 MsG0580025567.01.T01:three_prime_UTR 45.0%
ACGTGAAGCGAGGTTGTTAG+CGG - Chr5:20571567-20571586 MsG0580025567.01.T01:intron 50.0%
ATCGAAGCCTGCCTCCATAT+TGG + Chr5:20570674-20570693 None:intergenic 50.0%
TGACGACGACTCCAATATGG+AGG - Chr5:20570660-20570679 MsG0580025567.01.T01:three_prime_UTR 50.0%
TGCGAAAATTGGTAGAGCGG+AGG - Chr5:20571540-20571559 MsG0580025567.01.T01:intron 50.0%
GACGACTCCAATATGGAGGC+AGG - Chr5:20570664-20570683 MsG0580025567.01.T01:three_prime_UTR 55.0%
TGAAGCGAGGTTGTTAGCGG+AGG - Chr5:20571570-20571589 MsG0580025567.01.T01:intron 55.0%
AGCGAGGTTGTTAGCGGAGG+AGG - Chr5:20571573-20571592 MsG0580025567.01.T01:intron 60.0%
CGGAGGATGAACGTGAAGCG+AGG - Chr5:20571557-20571576 MsG0580025567.01.T01:intron 60.0%
CTGTGTCGAGAAGTGGGTGC+TGG + Chr5:20571145-20571164 None:intergenic 60.0%
GAGGTTGTTAGCGGAGGAGG+AGG - Chr5:20571576-20571595 MsG0580025567.01.T01:intron 60.0%
TGTTAGCGGAGGAGGAGGCA+AGG - Chr5:20571581-20571600 MsG0580025567.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr5 gene 20570487 20571940 20570487 ID=MsG0580025567.01;Name=MsG0580025567.01
Chr5 mRNA 20570487 20571940 20570487 ID=MsG0580025567.01.T01;Parent=MsG0580025567.01;Name=MsG0580025567.01.T01;_AED=0.50;_eAED=0.55;_QI=0|0.5|0.66|1|0|0.33|3|295|83
Chr5 exon 20570487 20570887 20570487 ID=MsG0580025567.01.T01:exon:8993;Parent=MsG0580025567.01.T01
Chr5 exon 20571708 20571799 20571708 ID=MsG0580025567.01.T01:exon:8992;Parent=MsG0580025567.01.T01
Chr5 exon 20571887 20571940 20571887 ID=MsG0580025567.01.T01:exon:8991;Parent=MsG0580025567.01.T01
Chr5 CDS 20571887 20571940 20571887 ID=MsG0580025567.01.T01:cds;Parent=MsG0580025567.01.T01
Chr5 CDS 20571708 20571799 20571708 ID=MsG0580025567.01.T01:cds;Parent=MsG0580025567.01.T01
Chr5 CDS 20570782 20570887 20570782 ID=MsG0580025567.01.T01:cds;Parent=MsG0580025567.01.T01
Chr5 three_prime_UTR 20570487 20570781 20570487 ID=MsG0580025567.01.T01:three_prime_utr;Parent=MsG0580025567.01.T01
Gene Sequence

>MsG0580025567.01.T01

ATGCTTGATTTCTGTGCCGTGTGTACTGATAATTGTAAACTTCCAAATGGGGGATTACACCCCAAGAAATATGCCCATTACGATGATGACGACGACTCCAATATGGAGGCAGGCTTCGATGATATCCAAAAGGAGGAAAAGAGGAGTGCGAAAATTGGTAGAGCGGAGGATGAACGTGAAGCGAGGTTGTTAGCGGAGGAGGAGGCAAGGAAAGAAAGAAACAAGGCAAAGAAGCGTAAGGTTGGATTGTAA
Protein sequence

>MsG0580025567.01.T01

MLDFCAVCTDNCKLPNGGLHPKKYAHYDDDDDSNMEAGFDDIQKEEKRSAKIGRAEDEREARLLAEEEARKERNKAKKRKVGL*