AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0680032327.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680032327.01.T01 MTR_6g034680 96.774 124 4 0 1 124 1 124 1.71e-85 248
MsG0680032327.01.T01 MTR_1g097400 63.855 83 29 1 42 124 24 105 2.09e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0680032327.01.T01 AT1G71780 60.504 119 35 2 6 124 22 128 1.03e-41 137

Find 35 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCGGTGTCGCCGTCGTTAC+CGG 0.272903 6:+38578210 None:intergenic
TTGCGTTATAGCCACGAATT+TGG 0.284047 6:-38576709 MsG0680032327.01.T01:CDS
GTGTTCGTGGTGTTCCTGTT+AGG 0.311079 6:-38578012 MsG0680032327.01.T01:CDS
GTGGTGTTCAAATCAGCTTT+AGG 0.376958 6:-38578121 MsG0680032327.01.T01:CDS
CAAATCAGCTTTAGGAGGTT+GGG 0.388837 6:-38578113 MsG0680032327.01.T01:CDS
TTCCTAGGATTAAACCTAAC+AGG 0.389199 6:+38577998 None:intergenic
AAGTAGAGATCCATTTATTC+CGG 0.389969 6:-38578162 MsG0680032327.01.T01:CDS
TTCGATTTCGGAAGTGAGTA+AGG 0.394764 6:+38578261 None:intergenic
CTACTTCCGGTACCTTTGTT+CGG 0.403909 6:+38578179 None:intergenic
GAAGAAATCACCACCGCAAC+CGG 0.422292 6:-38578229 MsG0680032327.01.T01:CDS
CATTTATTCCGGCAAGGAAA+AGG 0.432348 6:-38578151 MsG0680032327.01.T01:CDS
CTTTGTTCGGACATGCTTTG+CGG 0.448560 6:+38578192 None:intergenic
AATAAATGGATCTCTACTTC+CGG 0.450385 6:+38578166 None:intergenic
GGTGCTGTTGTTTATCTTGA+CGG 0.459045 6:-38577947 MsG0680032327.01.T01:CDS
TCAAATCAGCTTTAGGAGGT+TGG 0.462750 6:-38578114 MsG0680032327.01.T01:CDS
AAAACAGACCTTCCATTCCT+AGG 0.466614 6:+38577983 None:intergenic
GTCGCCGTCGTTACCGGTTG+CGG 0.484980 6:+38578216 None:intergenic
TTCCTGTTAGGTTTAATCCT+AGG 0.496073 6:-38578000 MsG0680032327.01.T01:CDS
AACACTATAAACCAAATTCG+TGG 0.505791 6:+38576698 None:intergenic
GTTAGGTTTAATCCTAGGAA+TGG 0.509296 6:-38577995 MsG0680032327.01.T01:CDS
AATCATCAGACACGTGTTCG+TGG 0.512446 6:-38578025 MsG0680032327.01.T01:CDS
GCTGATTTGAACACCACAAT+CGG 0.515089 6:+38578127 None:intergenic
TTATCTTGACGGAGAACCTA+AGG 0.518482 6:-38577936 MsG0680032327.01.T01:intron
GAACAAGATCAGCTTGAGGT+TGG 0.553586 6:-38578091 MsG0680032327.01.T01:CDS
GGTTTAATCCTAGGAATGGA+AGG 0.569067 6:-38577991 MsG0680032327.01.T01:CDS
GTGTTCAAATCAGCTTTAGG+AGG 0.571556 6:-38578118 MsG0680032327.01.T01:CDS
GCATGTCCGAACAAAGGTAC+CGG 0.584813 6:-38578185 MsG0680032327.01.T01:CDS
GAGATCCATTTATTCCGGCA+AGG 0.593898 6:-38578157 MsG0680032327.01.T01:CDS
GGTGATATTCTTGAGAAACA+TGG 0.594343 6:-38578070 MsG0680032327.01.T01:CDS
TCGATTTCGGAAGTGAGTAA+GGG 0.600648 6:+38578262 None:intergenic
GCCGTCGTTACCGGTTGCGG+TGG 0.600924 6:+38578219 None:intergenic
CGCAAAGCATGTCCGAACAA+AGG 0.608336 6:-38578191 MsG0680032327.01.T01:CDS
GCAAGGAAAAGGACCGATTG+TGG 0.632906 6:-38578140 MsG0680032327.01.T01:CDS
ACCACCGCAACCGGTAACGA+CGG 0.642588 6:-38578220 MsG0680032327.01.T01:CDS
TTGGGAACAAGATCAGCTTG+AGG 0.689710 6:-38578095 MsG0680032327.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTTAAAAAAATTTATT+TGG - Chr6:38577867-38577886 MsG0680032327.01.T01:intron 0.0%
!!! AATTTTAAAAAAATTTATTT+GGG - Chr6:38577868-38577887 MsG0680032327.01.T01:intron 0.0%
!! ATTATTTCCATAAATTTGAT+TGG - Chr6:38577651-38577670 MsG0680032327.01.T01:intron 15.0%
!! AAAACAAAAAAACAAACCTT+AGG + Chr6:38577071-38577090 None:intergenic 20.0%
!! AATTTAGTGTAATTATGTGT+TGG - Chr6:38577343-38577362 MsG0680032327.01.T01:intron 20.0%
!!! TGATTTTCTCAAATTATTAG+CGG + Chr6:38577320-38577339 None:intergenic 20.0%
! AATCTCACCAATCAAATTTA+TGG + Chr6:38577661-38577680 None:intergenic 25.0%
! ACAAAAACAAGATTTAGATG+AGG - Chr6:38577563-38577582 MsG0680032327.01.T01:intron 25.0%
! ACAATGACATAGAATCATAA+TGG - Chr6:38578079-38578098 MsG0680032327.01.T01:CDS 25.0%
! ATTTCAAATTTCCATGTTAG+AGG + Chr6:38577909-38577928 None:intergenic 25.0%
! CGTTTGACAATAATAATTTG+AGG - Chr6:38577719-38577738 MsG0680032327.01.T01:intron 25.0%
! GTATAGAATTATATATCGAG+TGG - Chr6:38577596-38577615 MsG0680032327.01.T01:intron 25.0%
! TGAAACATTGATATGGATAT+TGG - Chr6:38577163-38577182 MsG0680032327.01.T01:intron 25.0%
! TTGTGTGTACAATTTATTCT+TGG - Chr6:38577935-38577954 MsG0680032327.01.T01:intron 25.0%
!! AAACACGATATAATGGAAAT+AGG - Chr6:38578030-38578049 MsG0680032327.01.T01:CDS 25.0%
!! GCGATTAGTTATTTAGTAAA+GGG + Chr6:38578223-38578242 None:intergenic 25.0%
!! TGCGATTAGTTATTTAGTAA+AGG + Chr6:38578224-38578243 None:intergenic 25.0%
!!! TGTTGTTAATTTGTGTTCTT+AGG - Chr6:38577116-38577135 MsG0680032327.01.T01:intron 25.0%
AAGTAGAGATCCATTTATTC+CGG - Chr6:38576826-38576845 MsG0680032327.01.T01:intron 30.0%
AATAAATGGATCTCTACTTC+CGG + Chr6:38576825-38576844 None:intergenic 30.0%
AATTATTAACAGTCCGACAT+CGG + Chr6:38577376-38577395 None:intergenic 30.0%
ATTGATCATTGTTGTCAATC+AGG - Chr6:38578118-38578137 MsG0680032327.01.T01:CDS 30.0%
TCAGGGATTACAAAAAATAG+TGG - Chr6:38578136-38578155 MsG0680032327.01.T01:CDS 30.0%
TCGAAACAAACACGATATAA+TGG - Chr6:38578023-38578042 MsG0680032327.01.T01:CDS 30.0%
TTCTTCTTCTTCTTCGATTT+CGG + Chr6:38576742-38576761 None:intergenic 30.0%
TTGAATGTAACTATCTACGT+CGG - Chr6:38577756-38577775 MsG0680032327.01.T01:intron 30.0%
TTGATCATTGTTGTCAATCA+GGG - Chr6:38578119-38578138 MsG0680032327.01.T01:CDS 30.0%
! ATATAATGGAAATAGGTTGC+TGG - Chr6:38578037-38578056 MsG0680032327.01.T01:CDS 30.0%
! CTTTTAATCAAAGACATGTC+AGG + Chr6:38577504-38577523 None:intergenic 30.0%
! TATAATGGAAATAGGTTGCT+GGG - Chr6:38578038-38578057 MsG0680032327.01.T01:CDS 30.0%
! TTTTCTCAAATTATTAGCGG+TGG + Chr6:38577317-38577336 None:intergenic 30.0%
!! GTTAATTTGTGTTCTTAGGT+TGG - Chr6:38577120-38577139 MsG0680032327.01.T01:intron 30.0%
!! TTGTCTCTGAAACATTGATA+TGG - Chr6:38577156-38577175 MsG0680032327.01.T01:intron 30.0%
!!! AAGGTCTGTTTTGACTTATA+GGG - Chr6:38577016-38577035 MsG0680032327.01.T01:intron 30.0%
AAAGATATCGTCCTCTAACA+TGG - Chr6:38577895-38577914 MsG0680032327.01.T01:intron 35.0%
ATTATTAACAGTCCGACATC+GGG + Chr6:38577375-38577394 None:intergenic 35.0%
GGTGATATTCTTGAGAAACA+TGG - Chr6:38576918-38576937 MsG0680032327.01.T01:intron 35.0%
GTTAGGTTTAATCCTAGGAA+TGG - Chr6:38576993-38577012 MsG0680032327.01.T01:intron 35.0%
TTCCTAGGATTAAACCTAAC+AGG + Chr6:38576993-38577012 None:intergenic 35.0%
TTCCTGTTAGGTTTAATCCT+AGG - Chr6:38576988-38577007 MsG0680032327.01.T01:intron 35.0%
! GATATATAGGGGTAACTTGT+AGG - Chr6:38577844-38577863 MsG0680032327.01.T01:intron 35.0%
! TAGTAAAGGGTGTAGTCAAA+TGG + Chr6:38578210-38578229 None:intergenic 35.0%
!! ATCGAGTGTTGGTGATATAT+AGG - Chr6:38577831-38577850 MsG0680032327.01.T01:intron 35.0%
!! TCGAGTGTTGGTGATATATA+GGG - Chr6:38577832-38577851 MsG0680032327.01.T01:intron 35.0%
!!! GAAGGTCTGTTTTGACTTAT+AGG - Chr6:38577015-38577034 MsG0680032327.01.T01:intron 35.0%
!!! TCTGTTTTGACTTATAGGGA+TGG - Chr6:38577020-38577039 MsG0680032327.01.T01:intron 35.0%
AAAACAGACCTTCCATTCCT+AGG + Chr6:38577008-38577027 None:intergenic 40.0%
ACATGTCGATCTATGAAGCA+CGG + Chr6:38577469-38577488 None:intergenic 40.0%
ACTGAGACCTATGAAGCATA+CGG - Chr6:38577264-38577283 MsG0680032327.01.T01:intron 40.0%
CAAATTATTAGCGGTGGTGT+CGG + Chr6:38577311-38577330 None:intergenic 40.0%
CATTTATTCCGGCAAGGAAA+AGG - Chr6:38576837-38576856 MsG0680032327.01.T01:intron 40.0%
CTTCATAGATCGACATGTGT+CGG - Chr6:38577471-38577490 MsG0680032327.01.T01:intron 40.0%
GAAATACTGATCCTGATACC+AGG - Chr6:38577682-38577701 MsG0680032327.01.T01:intron 40.0%
GCTTCATAGGTCTCAGTAAA+TGG + Chr6:38577261-38577280 None:intergenic 40.0%
GGTTTAATCCTAGGAATGGA+AGG - Chr6:38576997-38577016 MsG0680032327.01.T01:intron 40.0%
GTGGTGTTCAAATCAGCTTT+AGG - Chr6:38576867-38576886 MsG0680032327.01.T01:intron 40.0%
TATCACCAACACTCGATTGA+AGG + Chr6:38577828-38577847 None:intergenic 40.0%
TCGATTTCGGAAGTGAGTAA+GGG + Chr6:38576729-38576748 None:intergenic 40.0%
TGTGTATCTTTGTGTCATCC+CGG - Chr6:38577425-38577444 MsG0680032327.01.T01:intron 40.0%
TTATCTTGACGGAGAACCTA+AGG - Chr6:38577052-38577071 MsG0680032327.01.T01:intron 40.0%
TTCGATTTCGGAAGTGAGTA+AGG + Chr6:38576730-38576749 None:intergenic 40.0%
TTGCGTTATAGCCACGAATT+TGG - Chr6:38578279-38578298 MsG0680032327.01.T01:CDS 40.0%
TTGTATTTGACATCGACACG+TGG - Chr6:38577787-38577806 MsG0680032327.01.T01:intron 40.0%
! CTTTTCCTTGCCGGAATAAA+TGG + Chr6:38576839-38576858 None:intergenic 40.0%
! TAAAGGGTGTAGTCAAATGG+CGG + Chr6:38578207-38578226 None:intergenic 40.0%
! TATCGAGTGGTGATGTTTGT+AGG - Chr6:38577609-38577628 MsG0680032327.01.T01:intron 40.0%
!! CAAATCAGCTTTAGGAGGTT+GGG - Chr6:38576875-38576894 MsG0680032327.01.T01:intron 40.0%
!! CGAGTGTTGGTGATATATAG+GGG - Chr6:38577833-38577852 MsG0680032327.01.T01:intron 40.0%
!! GCTGATTTGAACACCACAAT+CGG + Chr6:38576864-38576883 None:intergenic 40.0%
!! GGTGCTGTTGTTTATCTTGA+CGG - Chr6:38577041-38577060 MsG0680032327.01.T01:intron 40.0%
!! GTGTTCAAATCAGCTTTAGG+AGG - Chr6:38576870-38576889 MsG0680032327.01.T01:intron 40.0%
!! TCAAATCAGCTTTAGGAGGT+TGG - Chr6:38576874-38576893 MsG0680032327.01.T01:intron 40.0%
AATCATCAGACACGTGTTCG+TGG - Chr6:38576963-38576982 MsG0680032327.01.T01:intron 45.0%
ACACACCTTCAATCGAGTGT+TGG - Chr6:38577820-38577839 MsG0680032327.01.T01:intron 45.0%
ATAGATCGACATGTGTCGGA+CGG - Chr6:38577475-38577494 MsG0680032327.01.T01:intron 45.0%
ATTCGTGGCTATAACGCAAC+TGG + Chr6:38578278-38578297 None:intergenic 45.0%
CAGCATCATATCCTGGTATC+AGG + Chr6:38577696-38577715 None:intergenic 45.0%
CTACTTCCGGTACCTTTGTT+CGG + Chr6:38576812-38576831 None:intergenic 45.0%
CTGATACCAGGATATGATGC+TGG - Chr6:38577694-38577713 MsG0680032327.01.T01:intron 45.0%
CTTTGTTCGGACATGCTTTG+CGG + Chr6:38576799-38576818 None:intergenic 45.0%
GAACAAGATCAGCTTGAGGT+TGG - Chr6:38576897-38576916 MsG0680032327.01.T01:intron 45.0%
GAGATCCATTTATTCCGGCA+AGG - Chr6:38576831-38576850 MsG0680032327.01.T01:intron 45.0%
TTCGTGGCTATAACGCAACT+GGG + Chr6:38578277-38578296 None:intergenic 45.0%
TTGGGAACAAGATCAGCTTG+AGG - Chr6:38576893-38576912 MsG0680032327.01.T01:intron 45.0%
AACGTGCCAGCATCATATCC+TGG + Chr6:38577703-38577722 None:intergenic 50.0%
ACACTCCTCGGATTGAAACC+GGG + Chr6:38577446-38577465 None:intergenic 50.0%
CCTATGAAGCATACGGACAC+CGG - Chr6:38577271-38577290 MsG0680032327.01.T01:intron 50.0%
CGCAAAGCATGTCCGAACAA+AGG - Chr6:38576797-38576816 MsG0680032327.01.T01:intron 50.0%
CGCAACTGGGTAGCAGAATT+TGG + Chr6:38578264-38578283 None:intergenic 50.0%
GAAGAAATCACCACCGCAAC+CGG - Chr6:38576759-38576778 MsG0680032327.01.T01:intron 50.0%
GACACTCCTCGGATTGAAAC+CGG + Chr6:38577447-38577466 None:intergenic 50.0%
GCAAGGAAAAGGACCGATTG+TGG - Chr6:38576848-38576867 MsG0680032327.01.T01:intron 50.0%
GTGTTCGTGGTGTTCCTGTT+AGG - Chr6:38576976-38576995 MsG0680032327.01.T01:intron 50.0%
TAGTCAAATGGCGGCTAGAG+TGG + Chr6:38578198-38578217 None:intergenic 50.0%
TATGAAGCACGGACACTCCT+CGG + Chr6:38577458-38577477 None:intergenic 50.0%
! CAATCGGTCCTTTTCCTTGC+CGG + Chr6:38576848-38576867 None:intergenic 50.0%
! GCATGTCCGAACAAAGGTAC+CGG - Chr6:38576803-38576822 MsG0680032327.01.T01:intron 50.0%
!! TGTTGGTGTCATCCCGATGT+CGG - Chr6:38577360-38577379 MsG0680032327.01.T01:intron 50.0%
CCGGTGTCCGTATGCTTCAT+AGG + Chr6:38577274-38577293 None:intergenic 55.0%
GTCATCCCGGTTTCAATCCG+AGG - Chr6:38577438-38577457 MsG0680032327.01.T01:intron 55.0%
ACCACCGCAACCGGTAACGA+CGG - Chr6:38576768-38576787 MsG0680032327.01.T01:intron 60.0%
GAAGCATACGGACACCGGAC+AGG - Chr6:38577276-38577295 MsG0680032327.01.T01:intron 60.0%
TACGGACACCGGACAGGACA+TGG - Chr6:38577282-38577301 MsG0680032327.01.T01:intron 60.0%
! GTCGGTGTCCATGTCCTGTC+CGG + Chr6:38577293-38577312 None:intergenic 60.0%
! GTCGCCGTCGTTACCGGTTG+CGG + Chr6:38576775-38576794 None:intergenic 65.0%
!! TGCGGTGTCGCCGTCGTTAC+CGG + Chr6:38576781-38576800 None:intergenic 65.0%
! GCCGTCGTTACCGGTTGCGG+TGG + Chr6:38576772-38576791 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
Chr6 gene 38576702 38578308 38576702 ID=MsG0680032327.01;Name=MsG0680032327.01
Chr6 mRNA 38576702 38578308 38576702 ID=MsG0680032327.01.T01;Parent=MsG0680032327.01;Name=MsG0680032327.01.T01;_AED=0.46;_eAED=0.50;_QI=0|0|0|1|1|1|2|0|133
Chr6 exon 38577937 38578308 38577937 ID=MsG0680032327.01.T01:exon:21041;Parent=MsG0680032327.01.T01
Chr6 exon 38576702 38576731 38576702 ID=MsG0680032327.01.T01:exon:21040;Parent=MsG0680032327.01.T01
Chr6 CDS 38577937 38578308 38577937 ID=MsG0680032327.01.T01:cds;Parent=MsG0680032327.01.T01
Chr6 CDS 38576702 38576731 38576702 ID=MsG0680032327.01.T01:cds;Parent=MsG0680032327.01.T01
Gene Sequence

>MsG0680032327.01.T01

ATGGTTAACGAAAACGAAAACTCACCCTTACTCACTTCCGAAATCGAAGAAGAAGAAGAAGAAATCACCACCGCAACCGGTAACGACGGCGACACCGCAAAGCATGTCCGAACAAAGGTACCGGAAGTAGAGATCCATTTATTCCGGCAAGGAAAAGGACCGATTGTGGTGTTCAAATCAGCTTTAGGAGGTTGGGAACAAGATCAGCTTGAGGTTGGTGATATTCTTGAGAAACATGGATTGAAAACTGTGTTTGCTTTTAATCATCAGACACGTGTTCGTGGTGTTCCTGTTAGGTTTAATCCTAGGAATGGAAGGTCTGTTTTGACTTATAGGGATGGTGCTGTTGTTTATCTTGACGGAGAACCTAAGTTGCGTTATAGCCACGAATTTGGTTTATAG
Protein sequence

>MsG0680032327.01.T01

MVNENENSPLLTSEIEEEEEEITTATGNDGDTAKHVRTKVPEVEIHLFRQGKGPIVVFKSALGGWEQDQLEVGDILEKHGLKTVFAFNHQTRVRGVPVRFNPRNGRSVLTYRDGAVVYLDGEPKLRYSHEFGL*