AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480020867.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480020867.01.T01 MTR_4g123470 92.405 79 6 0 29 107 146 224 5.29e-51 160
MsG0480020867.01.T01 MTR_7g113060 86.842 38 5 0 69 106 2 39 7.73e-18 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAACCTTAGTGGTAAAATT+TGG 0.131735 4:-49870423 None:intergenic
TAACCTTAGTGGTAAAATTT+GGG 0.245976 4:-49870422 None:intergenic
CACAGTGCATGTACAAAATC+AGG 0.330296 4:+49870458 MsG0480020867.01.T01:CDS
CATAAGGTCCGCACAACATT+AGG 0.337570 4:-49871404 None:intergenic
TAGGGACTACCTCATACTTT+TGG 0.338565 4:+49871351 MsG0480020867.01.T01:intron
AATCGTGATGTTTCACTCTA+AGG 0.342040 4:-49871380 None:intergenic
GAACGAACATTTAACCTTAG+TGG 0.367361 4:-49870433 None:intergenic
TCCGAACATCACATTTGGTA+TGG 0.417548 4:-49871466 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 4:-49871465 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 4:+49871506 MsG0480020867.01.T01:CDS
CCAAATGTGATGTTCGGAAA+AGG 0.475440 4:+49871471 MsG0480020867.01.T01:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 4:+49871465 MsG0480020867.01.T01:CDS
AGGAATTTGCCAAAAGTATG+AGG 0.497368 4:-49871360 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 4:+49871507 MsG0480020867.01.T01:CDS
AACCTTAGTGGTAAAATTTG+GGG 0.519564 4:-49870421 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 4:-49871420 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 4:-49871464 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 4:-49871438 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 4:+49871545 MsG0480020867.01.T01:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 4:-49871514 None:intergenic
ACCTTAGTGGTAAAATTTGG+GGG 0.592838 4:-49870420 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4:+49871475 MsG0480020867.01.T01:CDS
CACGATTACCTAATGTTGTG+CGG 0.637450 4:+49871396 MsG0480020867.01.T01:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 4:+49871510 MsG0480020867.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAATTATTGAATAAGT+AGG + Chr4:49870964-49870983 MsG0480020867.01.T01:intron 10.0%
!!! ATTTTATTTTGCTTTATATA+TGG + Chr4:49871193-49871212 MsG0480020867.01.T01:intron 10.0%
!!! GTTTTTTTTTTCTTTTTTTT+AGG + Chr4:49871332-49871351 MsG0480020867.01.T01:intron 10.0%
!! TTCTATTTAAATAAGATGAA+CGG + Chr4:49870508-49870527 MsG0480020867.01.T01:intron 15.0%
!!! AATAATTTTTTTTCTCTTTG+GGG - Chr4:49870956-49870975 None:intergenic 15.0%
!!! CAATAATTTTTTTTCTCTTT+GGG - Chr4:49870957-49870976 None:intergenic 15.0%
!!! TCAATAATTTTTTTTCTCTT+TGG - Chr4:49870958-49870977 None:intergenic 15.0%
!! ATTCTACCTAAAATTAAACT+TGG - Chr4:49871036-49871055 None:intergenic 20.0%
!! CCAATAAACAAAAAAAATCA+TGG - Chr4:49871146-49871165 None:intergenic 20.0%
!! TAGCCAACTATATATTATTA+GGG - Chr4:49871011-49871030 None:intergenic 20.0%
!! TTCTACCTAAAATTAAACTT+GGG - Chr4:49871035-49871054 None:intergenic 20.0%
!!! AAGCTATCAAATTTTTTATG+AGG - Chr4:49871222-49871241 None:intergenic 20.0%
!!! ATTGCTATTTTATGGTTTTT+AGG - Chr4:49871120-49871139 None:intergenic 20.0%
!!! CCATGATTTTTTTTGTTTAT+TGG + Chr4:49871143-49871162 MsG0480020867.01.T01:intron 20.0%
! AAATATTCAACAACGAAGAA+TGG - Chr4:49870583-49870602 None:intergenic 25.0%
! AGCCAACTATATATTATTAG+GGG - Chr4:49871010-49871029 None:intergenic 25.0%
! GTAGCCAACTATATATTATT+AGG - Chr4:49871012-49871031 None:intergenic 25.0%
! TAACCTTAGTGGTAAAATTT+GGG - Chr4:49870425-49870444 None:intergenic 25.0%
! TACCCCTAATAATATATAGT+TGG + Chr4:49871005-49871024 MsG0480020867.01.T01:intron 25.0%
! TCTACCTAAAATTAAACTTG+GGG - Chr4:49871034-49871053 None:intergenic 25.0%
! TTAACCTTAGTGGTAAAATT+TGG - Chr4:49870426-49870445 None:intergenic 25.0%
!!! ATTTTATGGTTTTTAGGAGA+CGG - Chr4:49871114-49871133 None:intergenic 25.0%
!!! CATGGAATATTGCTATTTTA+TGG - Chr4:49871128-49871147 None:intergenic 25.0%
!!! CTATCAAATTTTTTATGAGG+TGG - Chr4:49871219-49871238 None:intergenic 25.0%
AACCTTAGTGGTAAAATTTG+GGG - Chr4:49870424-49870443 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - Chr4:49871423-49871442 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG - Chr4:49870537-49870556 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + Chr4:49870662-49870681 MsG0480020867.01.T01:intron 30.0%
!! CTTACTTTTCAATCGAACTT+TGG + Chr4:49871077-49871096 MsG0480020867.01.T01:intron 30.0%
!! TTTTATGGTTTTTAGGAGAC+GGG - Chr4:49871113-49871132 None:intergenic 30.0%
AATCGTGATGTTTCACTCTA+AGG - Chr4:49871383-49871402 None:intergenic 35.0%
ACCTTAGTGGTAAAATTTGG+GGG - Chr4:49870423-49870442 None:intergenic 35.0%
ATTATTGCTTTCCAGTACCT+TGG + Chr4:49870745-49870764 MsG0480020867.01.T01:intron 35.0%
CTGCCTAACTTATATGATGT+CGG + Chr4:49870547-49870566 MsG0480020867.01.T01:intron 35.0%
GAACGAACATTTAACCTTAG+TGG - Chr4:49870436-49870455 None:intergenic 35.0%
TCAGCTAGAGTAATGTTATG+AGG - Chr4:49870799-49870818 None:intergenic 35.0%
TCTCCGACATCATATAAGTT+AGG - Chr4:49870553-49870572 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - Chr4:49871441-49871460 None:intergenic 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - Chr4:49871363-49871382 None:intergenic 35.0%
! TTTGAAATCTACTTCCACCA+AGG - Chr4:49870765-49870784 None:intergenic 35.0%
!! GCTACCCCAAGTTTAATTTT+AGG + Chr4:49871027-49871046 MsG0480020867.01.T01:intron 35.0%
ATGTGATGTTCGGAAAAGGT+TGG + Chr4:49871475-49871494 MsG0480020867.01.T01:CDS 40.0%
CACAGTGCATGTACAAAATC+AGG + Chr4:49870458-49870477 MsG0480020867.01.T01:CDS 40.0%
CACGATTACCTAATGTTGTG+CGG + Chr4:49871396-49871415 MsG0480020867.01.T01:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + Chr4:49871471-49871490 MsG0480020867.01.T01:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + Chr4:49871465-49871484 MsG0480020867.01.T01:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - Chr4:49871468-49871487 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - Chr4:49871467-49871486 None:intergenic 40.0%
GAAGTTCCTATCGTTGGATA+TGG + Chr4:49870871-49870890 MsG0480020867.01.T01:intron 40.0%
TAAACAACCTTCGATGACAG+CGG - Chr4:49871247-49871266 None:intergenic 40.0%
TCCAACGATAGGAACTTCAA+AGG - Chr4:49870869-49870888 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG - Chr4:49871469-49871488 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - Chr4:49871474-49871493 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + Chr4:49871351-49871370 MsG0480020867.01.T01:intron 40.0%
! TCCCCCAAATTTTACCACTA+AGG + Chr4:49870419-49870438 MsG0480020867.01.T01:CDS 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + Chr4:49870865-49870884 MsG0480020867.01.T01:intron 40.0%
ACCCTATCATTCCATGAGTG+CGG + Chr4:49870825-49870844 MsG0480020867.01.T01:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG - Chr4:49870759-49870778 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + Chr4:49870748-49870767 MsG0480020867.01.T01:intron 45.0%
CATAAGGTCCGCACAACATT+AGG - Chr4:49871407-49871426 None:intergenic 45.0%
CGTATGCTTTCATGACCATG+GGG + Chr4:49870918-49870937 MsG0480020867.01.T01:intron 45.0%
CTCCAACCATCTGTCAACAA+CGG - Chr4:49870688-49870707 None:intergenic 45.0%
GCGTATGCTTTCATGACCAT+GGG + Chr4:49870917-49870936 MsG0480020867.01.T01:intron 45.0%
GTCGATCCATATCCAACGAT+AGG - Chr4:49870880-49870899 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG + Chr4:49871506-49871525 MsG0480020867.01.T01:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + Chr4:49871498-49871517 MsG0480020867.01.T01:CDS 45.0%
! GACACTTGCTAGATGGTGAT+GGG + Chr4:49870623-49870642 MsG0480020867.01.T01:intron 45.0%
! GAGCAATGACACTTGCTAGA+TGG + Chr4:49870616-49870635 MsG0480020867.01.T01:intron 45.0%
! TCTAGCAAGTGTCATTGCTC+TGG - Chr4:49870616-49870635 None:intergenic 45.0%
! TGACACTTGCTAGATGGTGA+TGG + Chr4:49870622-49870641 MsG0480020867.01.T01:intron 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + Chr4:49871507-49871526 MsG0480020867.01.T01:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + Chr4:49871545-49871564 MsG0480020867.01.T01:CDS 45.0%
!!! TTTTTTTTTTCTTTTTTTTA+GGG + Chr4:49871333-49871352 MsG0480020867.01.T01:intron 5.0%
ATCGACGATGTCACCGAACA+GGG + Chr4:49870894-49870913 MsG0480020867.01.T01:intron 50.0%
ATGCTTTCATGACCATGGGG+TGG + Chr4:49870921-49870940 MsG0480020867.01.T01:intron 50.0%
GCACTCATGGAATGATAGGG+TGG - Chr4:49870826-49870845 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - Chr4:49870829-49870848 None:intergenic 50.0%
GGCGTATGCTTTCATGACCA+TGG + Chr4:49870916-49870935 MsG0480020867.01.T01:intron 50.0%
TGCCGCACTCATGGAATGAT+AGG - Chr4:49870830-49870849 None:intergenic 50.0%
! TGAAAGCATACGCCCCTGTT+CGG - Chr4:49870910-49870929 None:intergenic 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + Chr4:49870679-49870698 MsG0480020867.01.T01:intron 55.0%
GATCGACGATGTCACCGAAC+AGG + Chr4:49870893-49870912 MsG0480020867.01.T01:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG + Chr4:49870683-49870702 MsG0480020867.01.T01:intron 55.0%
GTCTCCGCCCTCAATACCAT+TGG - Chr4:49871517-49871536 None:intergenic 55.0%
TCATGACCATGGGGTGGCTA+TGG + Chr4:49870927-49870946 MsG0480020867.01.T01:intron 55.0%
TCGACGATGTCACCGAACAG+GGG + Chr4:49870895-49870914 MsG0480020867.01.T01:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + Chr4:49871510-49871529 MsG0480020867.01.T01:CDS 55.0%
ACACGATGCTGCCGCACTCA+TGG - Chr4:49870839-49870858 None:intergenic 60.0%
AGCTTCGCCGCTGTCATCGA+AGG + Chr4:49871237-49871256 MsG0480020867.01.T01:intron 60.0%
GGGTAGCCATAGCCACCCCA+TGG - Chr4:49870936-49870955 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 49870399 49871599 49870399 ID=MsG0480020867.01;Name=MsG0480020867.01
Chr4 mRNA 49870399 49871599 49870399 ID=MsG0480020867.01.T01;Parent=MsG0480020867.01;Name=MsG0480020867.01.T01;_AED=0.61;_eAED=0.61;_QI=0|0|0|0.5|0|0|2|0|108
Chr4 exon 49870399 49870479 49870399 ID=MsG0480020867.01.T01:exon:258;Parent=MsG0480020867.01.T01
Chr4 exon 49871354 49871599 49871354 ID=MsG0480020867.01.T01:exon:259;Parent=MsG0480020867.01.T01
Chr4 CDS 49870399 49870479 49870399 ID=MsG0480020867.01.T01:cds;Parent=MsG0480020867.01.T01
Chr4 CDS 49871354 49871599 49871354 ID=MsG0480020867.01.T01:cds;Parent=MsG0480020867.01.T01
Gene Sequence

>MsG0480020867.01.T01

ATGCGTTTTAAGGTGAAGTTTCCCCCAAATTTTACCACTAAGGTTAAATGTTCGTTCTTCACAGTGCATGTACAAAATCAGGGACTACCTCATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACCTAATGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGTGTTAA
Protein sequence

>MsG0480020867.01.T01

MRFKVKFPPNFTTKVKCSFFTVHVQNQGLPHTFGKFLRVKHHDYLMLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKC*