AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0914280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0914280 MtrunA17_Chr6g0469541 91.209 91 8 0 1 91 20 110 1.19e-56 170
Msa0914280 MtrunA17_Chr7g0233251 74.444 90 23 0 1 90 20 109 6.32e-46 143
Msa0914280 MtrunA17_Chr7g0233191 72.527 91 25 0 1 91 20 110 1.28e-45 142
Msa0914280 MtrunA17_Chr7g0233201 71.429 91 26 0 1 91 20 110 5.23e-45 140
Msa0914280 MtrunA17_Chr7g0233211 70.330 91 27 0 1 91 20 110 2.53e-44 139
Msa0914280 MtrunA17_Chr7g0233231 69.231 91 28 0 1 91 20 110 4.20e-43 135
Msa0914280 MtrunA17_Chr7g0233181 71.765 85 24 0 1 85 20 104 2.26e-40 128
Msa0914280 MtrunA17_Chr6g0469571 58.889 90 31 2 1 86 20 107 1.07e-25 92.4
Msa0914280 MtrunA17_Chr6g0469591 58.889 90 31 2 1 86 20 107 2.96e-25 91.3
Msa0914280 MtrunA17_Chr6g0469551 57.778 90 32 2 1 86 20 107 3.48e-25 90.9
Msa0914280 MtrunA17_Chr1g0202541 70.000 50 15 0 1 50 20 69 1.54e-20 79.3
Msa0914280 MtrunA17_Chr1g0202561 70.000 50 15 0 1 50 20 69 8.23e-20 77.8
Msa0914280 MtrunA17_Chr6g0469651 72.000 50 14 0 1 50 20 69 1.83e-19 76.6
Msa0914280 MtrunA17_Chr6g0469671 64.000 50 18 0 1 50 20 69 8.15e-19 74.3
Msa0914280 MtrunA17_Chr6g0469681 64.000 50 18 0 1 50 20 69 3.92e-18 73.2
Msa0914280 MtrunA17_Chr8g0387471 62.264 53 20 0 1 53 20 72 4.09e-18 73.2
Msa0914280 MtrunA17_Chr1g0202581 68.000 50 15 1 1 50 20 68 1.15e-16 69.3
Msa0914280 MtrunA17_Chr1g0204291 66.000 50 16 1 1 50 20 68 1.63e-16 68.9
Msa0914280 MtrunA17_Chr1g0202501 63.265 49 18 0 1 49 20 68 7.53e-16 67.4
Msa0914280 MtrunA17_Chr8g0348361 63.830 47 17 0 3 49 22 68 3.32e-15 66.2
Msa0914280 MtrunA17_Chr7g0248671 59.184 49 20 0 1 49 20 68 3.56e-15 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0914280 AT1G01490.4 58.824 51 20 1 1 50 47 97 6.40e-12 58.9
Msa0914280 AT1G01490.1 58.824 51 20 1 1 50 20 70 6.56e-12 58.5
Msa0914280 AT1G01490.2 58.824 51 20 1 1 50 20 70 6.56e-12 58.5
Msa0914280 AT5G52740.1 50.980 51 23 1 1 51 20 68 4.08e-11 55.1

Find 26 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGACAGTGTCCAGCCTTTC+AGG 0.233115 6_2:-27733635 Msa0914280:intron
GAGAAGAAACTAACGTTAAC+AGG 0.281909 6_2:-27733040 Msa0914280:CDS
TCTTTCTTCTCCTCATTTAG+AGG 0.286030 6_2:+27732947 None:intergenic
TAGTAGTAATCTCGAATATA+AGG 0.349148 6_2:+27732848 None:intergenic
AATGGGTTCATTTGCATTTG+TGG 0.362031 6_2:+27732922 None:intergenic
ACAAACCTCAACAATAATAA+AGG 0.376511 6_2:-27733889 Msa0914280:intron
TTTATTATTGTTGAGGTTTG+TGG 0.386086 6_2:+27733891 None:intergenic
TTAACAGAAAGTAGTGTTGA+AGG 0.397592 6_2:-27733696 Msa0914280:intron
TTATTATTGTTGAGGTTTGT+GGG 0.419362 6_2:+27733892 None:intergenic
ATATATATTACCTGAAAGGC+TGG 0.445809 6_2:+27733625 None:intergenic
ATTATTGATGCCAAATGTAA+AGG 0.458445 6_2:+27733927 None:intergenic
TCAAATGACGGAAGTGGAAT+GGG 0.484078 6_2:+27732905 None:intergenic
TTCAAATGACGGAAGTGGAA+TGG 0.494749 6_2:+27732904 None:intergenic
TAATGATAGAACCAAGCAAA+AGG 0.516485 6_2:-27733663 Msa0914280:five_prime_UTR
AATGTAAAGGATTTCAAAAG+AGG 0.521012 6_2:+27733940 None:intergenic
TAGGATTCAAATGACGGAAG+TGG 0.521164 6_2:+27732899 None:intergenic
TTTAATATATATTACCTGAA+AGG 0.535056 6_2:+27733621 None:intergenic
GGTGTCATCTGATAATAGAA+TGG 0.567883 6_2:+27732875 None:intergenic
AATGGATAGGATTCAAATGA+CGG 0.583871 6_2:+27732893 None:intergenic
TAATCTCGAATATAAGGTGG+TGG 0.598290 6_2:+27732854 None:intergenic
TTCAGTCGGACCTCTAAATG+AGG 0.598439 6_2:-27732957 Msa0914280:CDS
CAAACAGAATTAGTTTCAGT+CGG 0.600751 6_2:-27732971 Msa0914280:CDS
AGAAGAAACTAACGTTAACA+GGG 0.635019 6_2:-27733039 Msa0914280:CDS
TAGTAATCTCGAATATAAGG+TGG 0.681154 6_2:+27732851 None:intergenic
CATCTGATAATAGAATGGAT+AGG 0.681841 6_2:+27732880 None:intergenic
GAAGAAACTAACGTTAACAG+GGG 0.736906 6_2:-27733038 Msa0914280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAATATATATTACCTGAA+AGG + chr6_2:27733209-27733228 None:intergenic 15.0%
!!! TTTTTTTTTATCAATACTGT+AGG - chr6_2:27733736-27733755 Msa0914280:intron 15.0%
!!! TTTTTTTTATCAATACTGTA+GGG - chr6_2:27733737-27733756 Msa0914280:intron 15.0%
!! TTTAATATATATTACCTGAA+AGG + chr6_2:27733209-27733228 None:intergenic 15.0%
!!! TTTTTTTTTATCAATACTGT+AGG - chr6_2:27733736-27733755 Msa0914280:intron 15.0%
!!! TTTTTTTTATCAATACTGTA+GGG - chr6_2:27733737-27733756 Msa0914280:intron 15.0%
!!! TTTTACCTTTATTATTGTTG+AGG + chr6_2:27732946-27732965 None:intergenic 20.0%
!! AAAAAATAGGTTTCATAACT+AGG + chr6_2:27733438-27733457 None:intergenic 20.0%
!! TTTAACATATCAAATGTTCT+CGG - chr6_2:27733468-27733487 Msa0914280:intron 20.0%
!!! TCTAGCATTTTTTTTTAAAG+AGG + chr6_2:27733656-27733675 None:intergenic 20.0%
!!! ATTTACGAATTATTTCAAGT+AGG - chr6_2:27733701-27733720 Msa0914280:intron 20.0%
!!! TTTTTTTATCAATACTGTAG+GGG - chr6_2:27733738-27733757 Msa0914280:intron 20.0%
!!! TTTTACCTTTATTATTGTTG+AGG + chr6_2:27732946-27732965 None:intergenic 20.0%
!! AAAAAATAGGTTTCATAACT+AGG + chr6_2:27733438-27733457 None:intergenic 20.0%
!! TTTAACATATCAAATGTTCT+CGG - chr6_2:27733468-27733487 Msa0914280:intron 20.0%
!!! TCTAGCATTTTTTTTTAAAG+AGG + chr6_2:27733656-27733675 None:intergenic 20.0%
!!! ATTTACGAATTATTTCAAGT+AGG - chr6_2:27733701-27733720 Msa0914280:intron 20.0%
!!! TTTTTTTATCAATACTGTAG+GGG - chr6_2:27733738-27733757 Msa0914280:intron 20.0%
! AATGTAAAGGATTTCAAAAG+AGG + chr6_2:27732890-27732909 None:intergenic 25.0%
!!! CTTTTGAAATCCTTTACATT+TGG - chr6_2:27732890-27732909 Msa0914280:CDS 25.0%
! ATTATTGATGCCAAATGTAA+AGG + chr6_2:27732903-27732922 None:intergenic 25.0%
! TTATTATTGTTGAGGTTTGT+GGG + chr6_2:27732938-27732957 None:intergenic 25.0%
! TTTATTATTGTTGAGGTTTG+TGG + chr6_2:27732939-27732958 None:intergenic 25.0%
! ACAAACCTCAACAATAATAA+AGG - chr6_2:27732938-27732957 Msa0914280:CDS 25.0%
! AAATGAGAAAAGTGAGAAAA+TGG + chr6_2:27732985-27733004 None:intergenic 25.0%
! AAATCACGTGATCAAAAAAT+AGG + chr6_2:27733451-27733470 None:intergenic 25.0%
! TAGTAGTAATCTCGAATATA+AGG + chr6_2:27733982-27734001 None:intergenic 25.0%
! AATGTAAAGGATTTCAAAAG+AGG + chr6_2:27732890-27732909 None:intergenic 25.0%
!!! CTTTTGAAATCCTTTACATT+TGG - chr6_2:27732890-27732909 Msa0914280:CDS 25.0%
! ATTATTGATGCCAAATGTAA+AGG + chr6_2:27732903-27732922 None:intergenic 25.0%
! TTATTATTGTTGAGGTTTGT+GGG + chr6_2:27732938-27732957 None:intergenic 25.0%
! TTTATTATTGTTGAGGTTTG+TGG + chr6_2:27732939-27732958 None:intergenic 25.0%
! ACAAACCTCAACAATAATAA+AGG - chr6_2:27732938-27732957 Msa0914280:CDS 25.0%
! AAATGAGAAAAGTGAGAAAA+TGG + chr6_2:27732985-27733004 None:intergenic 25.0%
! AAATCACGTGATCAAAAAAT+AGG + chr6_2:27733451-27733470 None:intergenic 25.0%
! TAGTAGTAATCTCGAATATA+AGG + chr6_2:27733982-27734001 None:intergenic 25.0%
! TTAACAGAAAGTAGTGTTGA+AGG - chr6_2:27733131-27733150 Msa0914280:intron 30.0%
TAATGATAGAACCAAGCAAA+AGG - chr6_2:27733164-27733183 Msa0914280:intron 30.0%
ATATATATTACCTGAAAGGC+TGG + chr6_2:27733205-27733224 None:intergenic 30.0%
AGTACTACTACAATGTAATG+TGG - chr6_2:27733245-27733264 Msa0914280:intron 30.0%
!!! ATGTGGACTTTTTTTTTGAG+AGG - chr6_2:27733262-27733281 Msa0914280:intron 30.0%
!!! TGTGGACTTTTTTTTTGAGA+GGG - chr6_2:27733263-27733282 Msa0914280:intron 30.0%
AGAAGAAACTAACGTTAACA+GGG - chr6_2:27733788-27733807 Msa0914280:intron 30.0%
! CAAACAGAATTAGTTTCAGT+CGG - chr6_2:27733856-27733875 Msa0914280:intron 30.0%
AATGGATAGGATTCAAATGA+CGG + chr6_2:27733937-27733956 None:intergenic 30.0%
CATCTGATAATAGAATGGAT+AGG + chr6_2:27733950-27733969 None:intergenic 30.0%
TAGTAATCTCGAATATAAGG+TGG + chr6_2:27733979-27733998 None:intergenic 30.0%
! TTAACAGAAAGTAGTGTTGA+AGG - chr6_2:27733131-27733150 Msa0914280:intron 30.0%
TAATGATAGAACCAAGCAAA+AGG - chr6_2:27733164-27733183 Msa0914280:intron 30.0%
ATATATATTACCTGAAAGGC+TGG + chr6_2:27733205-27733224 None:intergenic 30.0%
AGTACTACTACAATGTAATG+TGG - chr6_2:27733245-27733264 Msa0914280:intron 30.0%
!!! ATGTGGACTTTTTTTTTGAG+AGG - chr6_2:27733262-27733281 Msa0914280:intron 30.0%
!!! TGTGGACTTTTTTTTTGAGA+GGG - chr6_2:27733263-27733282 Msa0914280:intron 30.0%
AGAAGAAACTAACGTTAACA+GGG - chr6_2:27733788-27733807 Msa0914280:intron 30.0%
! CAAACAGAATTAGTTTCAGT+CGG - chr6_2:27733856-27733875 Msa0914280:intron 30.0%
AATGGATAGGATTCAAATGA+CGG + chr6_2:27733937-27733956 None:intergenic 30.0%
CATCTGATAATAGAATGGAT+AGG + chr6_2:27733950-27733969 None:intergenic 30.0%
TAGTAATCTCGAATATAAGG+TGG + chr6_2:27733979-27733998 None:intergenic 30.0%
! TGTCTTCATAACCTTTTGCT+TGG + chr6_2:27733178-27733197 None:intergenic 35.0%
!! TTTTTGAGAGGGATGTAATG+TGG - chr6_2:27733274-27733293 Msa0914280:intron 35.0%
GAGAAGAAACTAACGTTAAC+AGG - chr6_2:27733787-27733806 Msa0914280:intron 35.0%
GAAGAAACTAACGTTAACAG+GGG - chr6_2:27733789-27733808 Msa0914280:intron 35.0%
!! AGCTTAGAGACTACTTTTAC+TGG + chr6_2:27733823-27733842 None:intergenic 35.0%
TCTTTCTTCTCCTCATTTAG+AGG + chr6_2:27733883-27733902 None:intergenic 35.0%
! AATGGGTTCATTTGCATTTG+TGG + chr6_2:27733908-27733927 None:intergenic 35.0%
! GGTGTCATCTGATAATAGAA+TGG + chr6_2:27733955-27733974 None:intergenic 35.0%
TAATCTCGAATATAAGGTGG+TGG + chr6_2:27733976-27733995 None:intergenic 35.0%
! TGTCTTCATAACCTTTTGCT+TGG + chr6_2:27733178-27733197 None:intergenic 35.0%
!! TTTTTGAGAGGGATGTAATG+TGG - chr6_2:27733274-27733293 Msa0914280:intron 35.0%
GAGAAGAAACTAACGTTAAC+AGG - chr6_2:27733787-27733806 Msa0914280:intron 35.0%
GAAGAAACTAACGTTAACAG+GGG - chr6_2:27733789-27733808 Msa0914280:intron 35.0%
!! AGCTTAGAGACTACTTTTAC+TGG + chr6_2:27733823-27733842 None:intergenic 35.0%
TCTTTCTTCTCCTCATTTAG+AGG + chr6_2:27733883-27733902 None:intergenic 35.0%
! AATGGGTTCATTTGCATTTG+TGG + chr6_2:27733908-27733927 None:intergenic 35.0%
! GGTGTCATCTGATAATAGAA+TGG + chr6_2:27733955-27733974 None:intergenic 35.0%
TAATCTCGAATATAAGGTGG+TGG + chr6_2:27733976-27733995 None:intergenic 35.0%
! TCAAATGACGGAAGTGGAAT+GGG + chr6_2:27733925-27733944 None:intergenic 40.0%
! TTCAAATGACGGAAGTGGAA+TGG + chr6_2:27733926-27733945 None:intergenic 40.0%
! TAGGATTCAAATGACGGAAG+TGG + chr6_2:27733931-27733950 None:intergenic 40.0%
! TCAAATGACGGAAGTGGAAT+GGG + chr6_2:27733925-27733944 None:intergenic 40.0%
! TTCAAATGACGGAAGTGGAA+TGG + chr6_2:27733926-27733945 None:intergenic 40.0%
! TAGGATTCAAATGACGGAAG+TGG + chr6_2:27733931-27733950 None:intergenic 40.0%
TTCAGTCGGACCTCTAAATG+AGG - chr6_2:27733870-27733889 Msa0914280:intron 45.0%
TTCAGTCGGACCTCTAAATG+AGG - chr6_2:27733870-27733889 Msa0914280:intron 45.0%
!! TTTAATAATAGATATAATTA+TGG - chr6_2:27733076-27733095 Msa0914280:intron 5.0%
!! TTAATAATAGATATAATTAT+GGG - chr6_2:27733077-27733096 Msa0914280:intron 5.0%
!! TTTAATAATAGATATAATTA+TGG - chr6_2:27733076-27733095 Msa0914280:intron 5.0%
!! TTAATAATAGATATAATTAT+GGG - chr6_2:27733077-27733096 Msa0914280:intron 5.0%
AAGACAGTGTCCAGCCTTTC+AGG - chr6_2:27733192-27733211 Msa0914280:intron 50.0%
AAGACAGTGTCCAGCCTTTC+AGG - chr6_2:27733192-27733211 Msa0914280:intron 50.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 27732841 27734008 27732841 ID=Msa0914280;Name=Msa0914280
chr6_2 mRNA 27732841 27734008 27732841 ID=Msa0914280-mRNA-1;Parent=Msa0914280;Name=Msa0914280-mRNA-1;_AED=0.09;_eAED=0.09;_QI=170|0.5|0.33|1|0.5|0.66|3|0|91
chr6_2 exon 27732841 27733091 27732841 ID=Msa0914280-mRNA-1:exon:5143;Parent=Msa0914280-mRNA-1
chr6_2 exon 27733636 27733711 27733636 ID=Msa0914280-mRNA-1:exon:5142;Parent=Msa0914280-mRNA-1
chr6_2 exon 27733890 27734008 27733890 ID=Msa0914280-mRNA-1:exon:5141;Parent=Msa0914280-mRNA-1
chr6_2 five_prime_UTR 27733890 27734008 27733890 ID=Msa0914280-mRNA-1:five_prime_utr;Parent=Msa0914280-mRNA-1
chr6_2 five_prime_UTR 27733661 27733711 27733661 ID=Msa0914280-mRNA-1:five_prime_utr;Parent=Msa0914280-mRNA-1
chr6_2 CDS 27733636 27733660 27733636 ID=Msa0914280-mRNA-1:cds;Parent=Msa0914280-mRNA-1
chr6_2 CDS 27732841 27733091 27732841 ID=Msa0914280-mRNA-1:cds;Parent=Msa0914280-mRNA-1
Gene Sequence

>Msa0914280

ATGAAGACAGTGTCCAGCCTTTCAGGGGTTGAATCAGTATCAATAGACACTAATGAGAAGAAACTAACGTTAACAGGGGATGTTGATCCAGTAAAAGTAGTCTCTAAGCTACGAAAATTGTGTCAAACAGAATTAGTTTCAGTCGGACCTCTAAATGAGGAGAAGAAAGAGACCACAAATGCAAATGAACCCATTCCACTTCCGTCATTTGAATCCTATCCATTCTATTATCAGATGACACCACCACCTTATATTCGAGATTACTACTATGTTTGA

Protein sequence

>Msa0914280

MKTVSSLSGVESVSIDTNEKKLTLTGDVDPVKVVSKLRKLCQTELVSVGPLNEEKKETTNANEPIPLPSFESYPFYYQMTPPPYIRDYYYV*