AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0096250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0096250 MtrunA17_Chr4g0062691 47.973 148 60 5 1 137 145 286 1.99e-25 99.4
Msa0096250 MtrunA17_Chr6g0456881 40.299 134 65 3 1 119 139 272 8.30e-19 81.6
Msa0096250 MtrunA17_Chr7g0220931 57.692 52 22 0 1 52 133 184 4.44e-16 73.6
Msa0096250 MtrunA17_Chr1g0205131 50.000 50 25 0 1 50 122 171 2.09e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0096250 AT3G18550.2 39.583 144 50 4 2 116 162 297 7.32e-18 79.3
Msa0096250 AT1G67260.2 36.842 133 69 1 1 118 100 232 2.58e-17 77.4
Msa0096250 AT1G67260.3 36.842 133 69 1 1 118 100 232 2.58e-17 77.4
Msa0096250 AT3G18550.1 38.514 148 50 4 2 116 162 301 2.69e-17 77.8
Msa0096250 AT3G18550.4 38.514 148 50 4 2 116 162 301 2.69e-17 77.8
Msa0096250 AT1G67260.1 36.842 133 69 1 1 118 100 232 2.76e-17 77.4
Msa0096250 AT3G18550.3 38.514 148 50 4 2 116 162 301 3.42e-17 77.4
Msa0096250 AT1G68800.2 58.929 56 19 1 2 53 126 181 6.13e-16 73.6
Msa0096250 AT1G68800.1 58.929 56 19 1 2 53 126 181 6.20e-16 73.6
Msa0096250 AT4G18390.1 36.975 119 62 4 2 116 56 165 1.91e-13 66.6
Msa0096250 AT4G18390.2 36.975 119 62 4 2 116 56 165 1.91e-13 66.6
Msa0096250 AT1G30210.2 33.813 139 71 3 1 138 63 181 2.62e-13 65.9
Msa0096250 AT1G30210.1 33.813 139 71 3 1 138 63 181 2.62e-13 65.9

Find 40 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATAAGCTTATTTGTTTATT+GGG 0.218118 1_3:-1952934 Msa0096250:three_prime_UTR
TTATAAGCTTATTTGTTTAT+TGG 0.219253 1_3:-1952935 Msa0096250:three_prime_UTR
TGCAAGAGGATTATGTATTC+TGG 0.269182 1_3:+1953553 None:intergenic
TTTCAGTTCAAGTTGCTAAA+AGG 0.272883 1_3:-1953817 Msa0096250:CDS
TTGATAAAATCATAATAAAT+AGG 0.299310 1_3:+1953003 None:intergenic
ACATCTTGTACGGCCTTTGC+AGG 0.339389 1_3:+1953219 None:intergenic
TCGTTGACTGCAATCTCTTC+AGG 0.355340 1_3:+1953647 None:intergenic
TCACAAAATTTAATGGAGTA+AGG 0.374776 1_3:-1953143 Msa0096250:three_prime_UTR
CAGCTAGAGGAATGAGAGAT+AGG 0.396710 1_3:-1953850 None:intergenic
TGGGTGTGAAGAGAATTATT+AGG 0.425176 1_3:-1953586 Msa0096250:CDS
TTCCGTTTGCAAGACATGTT+AGG 0.439649 1_3:-1953791 Msa0096250:CDS
AGCTTATTTGTTTATTGGGA+GGG 0.440796 1_3:-1952930 Msa0096250:three_prime_UTR
AGAGTTTCAATCATTGAAGA+AGG 0.450602 1_3:-1953283 Msa0096250:CDS
CTTTGAAACCACATCTTGTA+CGG 0.457874 1_3:+1953209 None:intergenic
AAAATAATTTCTCAGATTCG+TGG 0.480399 1_3:+1953108 None:intergenic
ATTTCTCAGATTCGTGGATG+TGG 0.488045 1_3:+1953114 None:intergenic
GAGGATTATGTATTCTGGAA+TGG 0.490957 1_3:+1953558 None:intergenic
CATCTTGTACGGCCTTTGCA+GGG 0.499196 1_3:+1953220 None:intergenic
TGCAAGGGAGTTGAGAGAAA+AGG 0.502844 1_3:-1953534 Msa0096250:CDS
ACAAATCATATCTAATTGTA+CGG 0.507959 1_3:-1953250 Msa0096250:three_prime_UTR
TTACATTCATAAGTATAACT+TGG 0.515465 1_3:-1952898 Msa0096250:three_prime_UTR
AGCCTAACATGTCTTGCAAA+CGG 0.523751 1_3:+1953789 None:intergenic
GAGAGAAAAGGCAAGGGAAA+GGG 0.530804 1_3:-1953522 Msa0096250:CDS
TGAGAGAAAAGGCAAGGGAA+AGG 0.535173 1_3:-1953523 Msa0096250:CDS
TCTCTCAACTCCCTTGCAAG+AGG 0.544135 1_3:+1953539 None:intergenic
TGGTTACTAAATCAAGCAAA+AGG 0.545110 1_3:-1953740 Msa0096250:CDS
ATAATTCTCTTCACACCCAA+AGG 0.549718 1_3:+1953590 None:intergenic
AAGCTTATTTGTTTATTGGG+AGG 0.553506 1_3:-1952931 Msa0096250:three_prime_UTR
TGCAAAGGCCGTACAAGATG+TGG 0.583040 1_3:-1953217 Msa0096250:three_prime_UTR
GGGAGTTGAGAGAAAAGGCA+AGG 0.592316 1_3:-1953529 Msa0096250:CDS
ATCTTGTACGGCCTTTGCAG+GGG 0.594028 1_3:+1953221 None:intergenic
CAAGGGAAAGGGCAAGAGAG+AGG 0.597351 1_3:-1953511 Msa0096250:CDS
TACGGACATATCCCCTGCAA+AGG 0.613514 1_3:-1953232 Msa0096250:three_prime_UTR
GAATACATAATCCTCTTGCA+AGG 0.618391 1_3:-1953550 Msa0096250:CDS
AATACTATTAAACAAGCTTG+CGG 0.620564 1_3:+1953178 None:intergenic
AATACATAATCCTCTTGCAA+GGG 0.622939 1_3:-1953549 Msa0096250:CDS
TAGGTATAAGAGCAGAAACA+AGG 0.625010 1_3:+1953022 None:intergenic
GGAGTTGAGAGAAAAGGCAA+GGG 0.625355 1_3:-1953528 Msa0096250:CDS
CTGTAGAGAACTGAAAACCA+TGG 0.627809 1_3:+1953463 None:intergenic
AAGCTAGCAAAACAGTGGAG+TGG 0.654481 1_3:-1953760 Msa0096250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATAAAATCATAATAAAT+AGG + chr1_3:1953709-1953728 None:intergenic 10.0%
!! TTGATAAAATCATAATAAAT+AGG + chr1_3:1953709-1953728 None:intergenic 10.0%
!!! AATTATTTTTCTTAAACGTA+CGG - chr1_3:1953615-1953634 Msa0096250:CDS 15.0%
!! TTATAAGCTTATTTGTTTAT+TGG - chr1_3:1953774-1953793 Msa0096250:CDS 15.0%
!! TATAAGCTTATTTGTTTATT+GGG - chr1_3:1953775-1953794 Msa0096250:CDS 15.0%
!!! AATTATTTTTCTTAAACGTA+CGG - chr1_3:1953615-1953634 Msa0096250:CDS 15.0%
!! TTATAAGCTTATTTGTTTAT+TGG - chr1_3:1953774-1953793 Msa0096250:CDS 15.0%
!! TATAAGCTTATTTGTTTATT+GGG - chr1_3:1953775-1953794 Msa0096250:CDS 15.0%
!! ACAAATCATATCTAATTGTA+CGG - chr1_3:1953459-1953478 Msa0096250:intron 20.0%
!!! ACTTTTCTCACAAAATTTAA+TGG - chr1_3:1953559-1953578 Msa0096250:CDS 20.0%
!!! TATGATTTTATCAAATGACA+TGG - chr1_3:1953715-1953734 Msa0096250:CDS 20.0%
!! TTACATTCATAAGTATAACT+TGG - chr1_3:1953811-1953830 Msa0096250:CDS 20.0%
!! ACAAATCATATCTAATTGTA+CGG - chr1_3:1953459-1953478 Msa0096250:intron 20.0%
!!! ACTTTTCTCACAAAATTTAA+TGG - chr1_3:1953559-1953578 Msa0096250:CDS 20.0%
!!! TATGATTTTATCAAATGACA+TGG - chr1_3:1953715-1953734 Msa0096250:CDS 20.0%
!! TTACATTCATAAGTATAACT+TGG - chr1_3:1953811-1953830 Msa0096250:CDS 20.0%
! AGTAAGTCTCAATTAATTTC+TGG - chr1_3:1953271-1953290 Msa0096250:exon 25.0%
! AATACTATTAAACAAGCTTG+CGG + chr1_3:1953534-1953553 None:intergenic 25.0%
! TCACAAAATTTAATGGAGTA+AGG - chr1_3:1953566-1953585 Msa0096250:CDS 25.0%
! AAAATAATTTCTCAGATTCG+TGG + chr1_3:1953604-1953623 None:intergenic 25.0%
! AGTAAGTCTCAATTAATTTC+TGG - chr1_3:1953271-1953290 Msa0096250:exon 25.0%
! AATACTATTAAACAAGCTTG+CGG + chr1_3:1953534-1953553 None:intergenic 25.0%
! TCACAAAATTTAATGGAGTA+AGG - chr1_3:1953566-1953585 Msa0096250:CDS 25.0%
! AAAATAATTTCTCAGATTCG+TGG + chr1_3:1953604-1953623 None:intergenic 25.0%
!! TTTCAGTTCAAGTTGCTAAA+AGG - chr1_3:1952892-1952911 Msa0096250:three_prime_UTR 30.0%
TGGTTACTAAATCAAGCAAA+AGG - chr1_3:1952969-1952988 Msa0096250:three_prime_UTR 30.0%
AAGAAAAAGAAGAAGCCTTT+GGG - chr1_3:1953104-1953123 Msa0096250:three_prime_UTR 30.0%
AATACATAATCCTCTTGCAA+GGG - chr1_3:1953160-1953179 Msa0096250:three_prime_UTR 30.0%
CAAAAATATGAGAAGATCCA+TGG - chr1_3:1953229-1953248 Msa0096250:three_prime_UTR 30.0%
CTGTACATACTAGAATTGAA+TGG + chr1_3:1953366-1953385 None:intergenic 30.0%
AGAGTTTCAATCATTGAAGA+AGG - chr1_3:1953426-1953445 Msa0096250:intron 30.0%
! TTTTTCTTAAACGTACGGTA+CGG - chr1_3:1953620-1953639 Msa0096250:CDS 30.0%
AAGCTTATTTGTTTATTGGG+AGG - chr1_3:1953778-1953797 Msa0096250:CDS 30.0%
AGCTTATTTGTTTATTGGGA+GGG - chr1_3:1953779-1953798 Msa0096250:CDS 30.0%
!! TTTCAGTTCAAGTTGCTAAA+AGG - chr1_3:1952892-1952911 Msa0096250:three_prime_UTR 30.0%
TGGTTACTAAATCAAGCAAA+AGG - chr1_3:1952969-1952988 Msa0096250:three_prime_UTR 30.0%
AAGAAAAAGAAGAAGCCTTT+GGG - chr1_3:1953104-1953123 Msa0096250:three_prime_UTR 30.0%
AATACATAATCCTCTTGCAA+GGG - chr1_3:1953160-1953179 Msa0096250:three_prime_UTR 30.0%
CAAAAATATGAGAAGATCCA+TGG - chr1_3:1953229-1953248 Msa0096250:three_prime_UTR 30.0%
CTGTACATACTAGAATTGAA+TGG + chr1_3:1953366-1953385 None:intergenic 30.0%
AGAGTTTCAATCATTGAAGA+AGG - chr1_3:1953426-1953445 Msa0096250:intron 30.0%
! TTTTTCTTAAACGTACGGTA+CGG - chr1_3:1953620-1953639 Msa0096250:CDS 30.0%
AAGCTTATTTGTTTATTGGG+AGG - chr1_3:1953778-1953797 Msa0096250:CDS 30.0%
AGCTTATTTGTTTATTGGGA+GGG - chr1_3:1953779-1953798 Msa0096250:CDS 30.0%
TGAAAAAGCTAGCAAAACAG+TGG - chr1_3:1952944-1952963 Msa0096250:three_prime_UTR 35.0%
GAAGAAAAAGAAGAAGCCTT+TGG - chr1_3:1953103-1953122 Msa0096250:three_prime_UTR 35.0%
ATAATTCTCTTCACACCCAA+AGG + chr1_3:1953122-1953141 None:intergenic 35.0%
TGGGTGTGAAGAGAATTATT+AGG - chr1_3:1953123-1953142 Msa0096250:three_prime_UTR 35.0%
! GAGGATTATGTATTCTGGAA+TGG + chr1_3:1953154-1953173 None:intergenic 35.0%
TGCAAGAGGATTATGTATTC+TGG + chr1_3:1953159-1953178 None:intergenic 35.0%
GAATACATAATCCTCTTGCA+AGG - chr1_3:1953159-1953178 Msa0096250:three_prime_UTR 35.0%
!! CTTTGAAACCACATCTTGTA+CGG + chr1_3:1953503-1953522 None:intergenic 35.0%
TAGGTATAAGAGCAGAAACA+AGG + chr1_3:1953690-1953709 None:intergenic 35.0%
TGAAAAAGCTAGCAAAACAG+TGG - chr1_3:1952944-1952963 Msa0096250:three_prime_UTR 35.0%
GAAGAAAAAGAAGAAGCCTT+TGG - chr1_3:1953103-1953122 Msa0096250:three_prime_UTR 35.0%
ATAATTCTCTTCACACCCAA+AGG + chr1_3:1953122-1953141 None:intergenic 35.0%
TGGGTGTGAAGAGAATTATT+AGG - chr1_3:1953123-1953142 Msa0096250:three_prime_UTR 35.0%
! GAGGATTATGTATTCTGGAA+TGG + chr1_3:1953154-1953173 None:intergenic 35.0%
TGCAAGAGGATTATGTATTC+TGG + chr1_3:1953159-1953178 None:intergenic 35.0%
GAATACATAATCCTCTTGCA+AGG - chr1_3:1953159-1953178 Msa0096250:three_prime_UTR 35.0%
!! CTTTGAAACCACATCTTGTA+CGG + chr1_3:1953503-1953522 None:intergenic 35.0%
TAGGTATAAGAGCAGAAACA+AGG + chr1_3:1953690-1953709 None:intergenic 35.0%
TTCCGTTTGCAAGACATGTT+AGG - chr1_3:1952918-1952937 Msa0096250:three_prime_UTR 40.0%
AGCCTAACATGTCTTGCAAA+CGG + chr1_3:1952923-1952942 None:intergenic 40.0%
CTGTAGAGAACTGAAAACCA+TGG + chr1_3:1953249-1953268 None:intergenic 40.0%
! CATGGTTTTCAGTTCTCTAC+AGG - chr1_3:1953247-1953266 Msa0096250:three_prime_UTR 40.0%
ATTTCTCAGATTCGTGGATG+TGG + chr1_3:1953598-1953617 None:intergenic 40.0%
TTCCGTTTGCAAGACATGTT+AGG - chr1_3:1952918-1952937 Msa0096250:three_prime_UTR 40.0%
AGCCTAACATGTCTTGCAAA+CGG + chr1_3:1952923-1952942 None:intergenic 40.0%
CTGTAGAGAACTGAAAACCA+TGG + chr1_3:1953249-1953268 None:intergenic 40.0%
! CATGGTTTTCAGTTCTCTAC+AGG - chr1_3:1953247-1953266 Msa0096250:three_prime_UTR 40.0%
ATTTCTCAGATTCGTGGATG+TGG + chr1_3:1953598-1953617 None:intergenic 40.0%
AAGCTAGCAAAACAGTGGAG+TGG - chr1_3:1952949-1952968 Msa0096250:three_prime_UTR 45.0%
! TCGTTGACTGCAATCTCTTC+AGG + chr1_3:1953065-1953084 None:intergenic 45.0%
TGCAAGGGAGTTGAGAGAAA+AGG - chr1_3:1953175-1953194 Msa0096250:three_prime_UTR 45.0%
GGAGTTGAGAGAAAAGGCAA+GGG - chr1_3:1953181-1953200 Msa0096250:three_prime_UTR 45.0%
TGAGAGAAAAGGCAAGGGAA+AGG - chr1_3:1953186-1953205 Msa0096250:three_prime_UTR 45.0%
GAGAGAAAAGGCAAGGGAAA+GGG - chr1_3:1953187-1953206 Msa0096250:three_prime_UTR 45.0%
AAGCTAGCAAAACAGTGGAG+TGG - chr1_3:1952949-1952968 Msa0096250:three_prime_UTR 45.0%
! TCGTTGACTGCAATCTCTTC+AGG + chr1_3:1953065-1953084 None:intergenic 45.0%
TGCAAGGGAGTTGAGAGAAA+AGG - chr1_3:1953175-1953194 Msa0096250:three_prime_UTR 45.0%
GGAGTTGAGAGAAAAGGCAA+GGG - chr1_3:1953181-1953200 Msa0096250:three_prime_UTR 45.0%
TGAGAGAAAAGGCAAGGGAA+AGG - chr1_3:1953186-1953205 Msa0096250:three_prime_UTR 45.0%
GAGAGAAAAGGCAAGGGAAA+GGG - chr1_3:1953187-1953206 Msa0096250:three_prime_UTR 45.0%
TCTCTCAACTCCCTTGCAAG+AGG + chr1_3:1953173-1953192 None:intergenic 50.0%
GGGAGTTGAGAGAAAAGGCA+AGG - chr1_3:1953180-1953199 Msa0096250:three_prime_UTR 50.0%
TACGGACATATCCCCTGCAA+AGG - chr1_3:1953477-1953496 Msa0096250:CDS 50.0%
ATCTTGTACGGCCTTTGCAG+GGG + chr1_3:1953491-1953510 None:intergenic 50.0%
CATCTTGTACGGCCTTTGCA+GGG + chr1_3:1953492-1953511 None:intergenic 50.0%
ACATCTTGTACGGCCTTTGC+AGG + chr1_3:1953493-1953512 None:intergenic 50.0%
TGCAAAGGCCGTACAAGATG+TGG - chr1_3:1953492-1953511 Msa0096250:CDS 50.0%
TCTCTCAACTCCCTTGCAAG+AGG + chr1_3:1953173-1953192 None:intergenic 50.0%
GGGAGTTGAGAGAAAAGGCA+AGG - chr1_3:1953180-1953199 Msa0096250:three_prime_UTR 50.0%
TACGGACATATCCCCTGCAA+AGG - chr1_3:1953477-1953496 Msa0096250:CDS 50.0%
ATCTTGTACGGCCTTTGCAG+GGG + chr1_3:1953491-1953510 None:intergenic 50.0%
CATCTTGTACGGCCTTTGCA+GGG + chr1_3:1953492-1953511 None:intergenic 50.0%
ACATCTTGTACGGCCTTTGC+AGG + chr1_3:1953493-1953512 None:intergenic 50.0%
TGCAAAGGCCGTACAAGATG+TGG - chr1_3:1953492-1953511 Msa0096250:CDS 50.0%
CAAGGGAAAGGGCAAGAGAG+AGG - chr1_3:1953198-1953217 Msa0096250:three_prime_UTR 55.0%
CAAGGGAAAGGGCAAGAGAG+AGG - chr1_3:1953198-1953217 Msa0096250:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 1952870 1953861 1952870 ID=Msa0096250;Name=Msa0096250
chr1_3 mRNA 1952870 1953861 1952870 ID=Msa0096250-mRNA-1;Parent=Msa0096250;Name=Msa0096250-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0.5|0.33|1|0|0|3|402|146
chr1_3 exon 1952870 1953316 1952870 ID=Msa0096250-mRNA-1:exon:412;Parent=Msa0096250-mRNA-1
chr1_3 exon 1953460 1953670 1953460 ID=Msa0096250-mRNA-1:exon:411;Parent=Msa0096250-mRNA-1
chr1_3 exon 1953677 1953861 1953677 ID=Msa0096250-mRNA-1:exon:410;Parent=Msa0096250-mRNA-1
chr1_3 CDS 1953677 1953861 1953677 ID=Msa0096250-mRNA-1:cds;Parent=Msa0096250-mRNA-1
chr1_3 CDS 1953460 1953670 1953460 ID=Msa0096250-mRNA-1:cds;Parent=Msa0096250-mRNA-1
chr1_3 CDS 1953272 1953316 1953272 ID=Msa0096250-mRNA-1:cds;Parent=Msa0096250-mRNA-1
chr1_3 three_prime_UTR 1952870 1953271 1952870 ID=Msa0096250-mRNA-1:three_prime_utr;Parent=Msa0096250-mRNA-1
Gene Sequence

>Msa0096250

ATGAGAGATAGGAGAATGAGACTTTCAGTTCAAGTTGCTAAAAGGTTTTTCCGTTTGCAAGACATGTTAGGCTTTGAAAAAGCTAGCAAAACAGTGGAGTGGTTACTAAATCAAGCAAAAGGTCAAATCAATCAAATAGCTGCATCAAAGAGTAATAATGTTTCTTCTTCAACTTTTGAATATATTCCTGAAGAGATTGCAGTCAACGAGATTAAGCAAGAACAAAAGAAGAAAAAGAAGAAGCCTTTGGGTGTGAAGAGAATTATTAGGAAAAACCATTCCAGAATACATAATCCTCTTGCAAGGGAGTTGAGAGAAAAGGCAAGGGAAAGGGCAAGAGAGAGGACTAAAGACAAAAATATGAGAAGATCCATGGTTTTCAGTTCTCTACAGGAACATCTAGTTGAAGAGTTTCAATCATTGAAGAAGGATTACATATAA
Protein sequence

>Msa0096250

MRDRRMRLSVQVAKRFFRLQDMLGFEKASKTVEWLLNQAKGQINQIAASKSNNVSSSTFEYIPEEIAVNEIKQEQKKKKKKPLGVKRIIRKNHSRIHNPLARELREKARERARERTKDKNMRRSMVFSSLQEHLVEEFQSLKKDYI*