AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0485740

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0485740 MtrunA17_Chr3g0110091 93.724 239 14 1 1 239 1 238 3.37e-160 443
Msa0485740 MtrunA17_Chr5g0434121 61.538 247 77 9 1 239 1 237 6.90e-86 254
Msa0485740 MtrunA17_Chr1g0161901 43.426 251 124 7 3 239 5 251 2.80e-60 190
Msa0485740 MtrunA17_Chr8g0376021 45.205 219 112 5 27 239 1 217 2.24e-55 176
Msa0485740 MtrunA17_Chr2g0333741 65.432 81 20 3 81 154 76 155 5.45e-27 104
Msa0485740 MtrunA17_Chr1g0149811 52.000 100 30 3 74 155 80 179 1.19e-25 101
Msa0485740 MtrunA17_Chr1g0207691 40.299 134 74 4 70 202 47 175 2.12e-24 96.3
Msa0485740 MtrunA17_Chr3g0137111 49.541 109 30 6 72 159 60 164 2.56e-20 86.3
Msa0485740 MtrunA17_Chr4g0001081 62.857 70 18 3 87 155 67 129 1.03e-18 81.6
Msa0485740 MtrunA17_Chr4g0072571 66.071 56 18 1 86 140 44 99 2.97e-17 76.6
Msa0485740 MtrunA17_Chr4g0053691 40.650 123 54 5 79 199 59 164 1.67e-15 72.0
Msa0485740 MtrunA17_Chr7g0251581 75.758 33 8 0 87 119 39 71 1.82e-12 63.9
Msa0485740 MtrunA17_Chr7g0250871 59.574 47 19 0 75 121 37 83 3.64e-12 63.2
Msa0485740 MtrunA17_Chr7g0254221 67.568 37 12 0 87 123 33 69 4.10e-12 62.4
Msa0485740 MtrunA17_Chr5g0396031 44.186 86 38 4 87 165 46 128 1.56e-11 63.2
Msa0485740 MtrunA17_Chr3g0081131 42.353 85 38 3 87 165 98 177 3.32e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0485740 AT1G66140.1 50.000 184 57 8 86 239 82 260 1.29e-46 155
Msa0485740 AT1G24625.1 40.865 208 81 12 46 239 30 209 2.88e-31 114
Msa0485740 AT1G80730.1 53.261 92 25 2 82 155 61 152 1.11e-23 95.5
Msa0485740 AT5G10970.1 45.902 122 50 5 47 155 56 174 1.80e-22 93.2
Msa0485740 AT5G25160.1 56.410 78 28 2 84 155 56 133 7.67e-22 90.9
Msa0485740 AT5G57520.1 52.113 71 34 0 87 157 50 120 3.63e-16 73.6
Msa0485740 AT5G14010.1 66.667 39 13 0 86 124 35 73 1.21e-13 67.0
Msa0485740 AT3G58070.1 55.357 56 21 1 67 122 73 124 8.16e-12 63.5
Msa0485740 AT5G01860.1 48.214 56 29 0 71 126 49 104 1.18e-11 62.8

Find 41 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCCTCTTAATGGTTCTTTC+AGG 0.209061 3_4:+3523132 Msa0485740:CDS
CTTGCATCTCTGCCTCTTAA+TGG 0.234261 3_4:+3523122 Msa0485740:CDS
CAAAGTTTCAATGTTAATTC+AGG 0.241054 3_4:-3523419 None:intergenic
AATGGTTCTTTCAGGTCATT+AGG 0.297972 3_4:+3523140 Msa0485740:CDS
AATTGCAAGAGAAAATTCTT+TGG 0.318566 3_4:-3522977 None:intergenic
TTTCTCTCTTGTGTGCGTTT+TGG 0.337168 3_4:-3523043 None:intergenic
AACCTGGAGAGGTTTCAATT+TGG 0.372940 3_4:-3522812 None:intergenic
GCAAAGCGAGCTATGCGAAT+TGG 0.384062 3_4:+3523074 Msa0485740:CDS
TATCGGTCATCCGATATTCT+TGG 0.398517 3_4:+3523259 Msa0485740:CDS
GGGCTAGGCCTTATTGTTGA+TGG 0.404082 3_4:-3523200 None:intergenic
ATTAGAAAGGCTGTTACTAT+AGG 0.421832 3_4:-3522835 None:intergenic
CTGGAGAGGTTTCAATTTGG+TGG 0.433921 3_4:-3522809 None:intergenic
TCATCGTCCTCCAAGAATAT+CGG 0.434665 3_4:-3523269 None:intergenic
AATTTGGTGGGTGGATATAG+TGG 0.440124 3_4:-3522796 None:intergenic
TAATTCAGATTCCATCTCAC+TGG 0.457739 3_4:+3522854 Msa0485740:CDS
AAGTTCATTGCTGCTCTCAC+TGG 0.464380 3_4:-3522949 None:intergenic
GCAAGAGAAAATTCTTTGGA+TGG 0.480537 3_4:-3522973 None:intergenic
TTGGTTGCAAGAGATTCAAC+AGG 0.483148 3_4:+3522909 Msa0485740:CDS
AGCAGTGCTAGATTCAAGTT+AGG 0.490778 3_4:+3523233 Msa0485740:CDS
GACCTGAAAGAACCATTAAG+AGG 0.490795 3_4:-3523134 None:intergenic
TATAGCTCGCAGGCACTTGG+TGG 0.518085 3_4:+3523017 Msa0485740:CDS
CTTCAACAAGGACAATGACT+TGG 0.521722 3_4:+3522890 Msa0485740:CDS
TGGAGAGGTTTCAATTTGGT+GGG 0.530109 3_4:-3522808 None:intergenic
CACCAAATTGAAACCTCTCC+AGG 0.534773 3_4:+3522810 Msa0485740:CDS
AGATGGAATCTGAATTAGAA+AGG 0.546754 3_4:-3522848 None:intergenic
AGATTCAAGTTAGGATCTAT+CGG 0.563874 3_4:+3523242 Msa0485740:CDS
CGGTCATCCGATATTCTTGG+AGG 0.568620 3_4:+3523262 Msa0485740:CDS
GAATTCTCTATGTCAACCAA+TGG 0.572984 3_4:-3523392 None:intergenic
AGAGGTTTCAATTTGGTGGG+TGG 0.575688 3_4:-3522805 None:intergenic
GAGTGTTAAGTCCAGTGAGA+TGG 0.580909 3_4:-3522865 None:intergenic
ATCAGATTCATATTCTTCTG+TGG 0.583159 3_4:-3522754 None:intergenic
TTTCATCAGGTTACTGAGGG+AGG 0.597854 3_4:+3523317 Msa0485740:CDS
TGGATATAGTGGAAGCAACA+TGG 0.607959 3_4:-3522785 None:intergenic
AGGCTGTTACTATAGGAACC+TGG 0.608616 3_4:-3522828 None:intergenic
TGAGGTGAATGTGAAACCAT+TGG 0.612040 3_4:+3523376 Msa0485740:CDS
ACGATGAGACAGAACTGATG+TGG 0.646574 3_4:+3523285 Msa0485740:CDS
GAGACAGAACTGATGTGGCA+AGG 0.647919 3_4:+3523290 Msa0485740:CDS
CTTAACACTCAACTTCAACA+AGG 0.655631 3_4:+3522878 Msa0485740:CDS
GTTACTATAGGAACCTGGAG+AGG 0.688967 3_4:-3522823 None:intergenic
ACACACTCTTCACTACACCA+TGG 0.697590 3_4:+3523170 Msa0485740:CDS
GAATTGGACTATTCACTGAG+AGG 0.709982 3_4:+3523090 Msa0485740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCTACTTCAAGATCAAAAAT+TGG - chr3_4:3522732-3522751 None:intergenic 25.0%
!! AATTTTTGATCTTGAAGTAG+AGG + chr3_4:3522731-3522750 Msa0485740:CDS 25.0%
! AATTGCAAGAGAAAATTCTT+TGG - chr3_4:3522980-3522999 None:intergenic 25.0%
!! TTCAAATATGTGTTTTACTG+AGG + chr3_4:3523358-3523377 Msa0485740:CDS 25.0%
! CAAAGTTTCAATGTTAATTC+AGG - chr3_4:3523422-3523441 None:intergenic 25.0%
ATCAGATTCATATTCTTCTG+TGG - chr3_4:3522757-3522776 None:intergenic 30.0%
ATTAGAAAGGCTGTTACTAT+AGG - chr3_4:3522838-3522857 None:intergenic 30.0%
AGATGGAATCTGAATTAGAA+AGG - chr3_4:3522851-3522870 None:intergenic 30.0%
! TTTTCTCTTGCAATTACTGT+CGG + chr3_4:3522985-3523004 Msa0485740:CDS 30.0%
! AGATTCAAGTTAGGATCTAT+CGG + chr3_4:3523242-3523261 Msa0485740:CDS 30.0%
TAATTCAGATTCCATCTCAC+TGG + chr3_4:3522854-3522873 Msa0485740:CDS 35.0%
CTTAACACTCAACTTCAACA+AGG + chr3_4:3522878-3522897 Msa0485740:CDS 35.0%
GCAAGAGAAAATTCTTTGGA+TGG - chr3_4:3522976-3522995 None:intergenic 35.0%
! AATGGTTCTTTCAGGTCATT+AGG + chr3_4:3523140-3523159 Msa0485740:CDS 35.0%
! GTTTTTCGCCATCAACAATA+AGG + chr3_4:3523192-3523211 Msa0485740:CDS 35.0%
!!! TAGCACTGCTTTTTATCTCA+GGG - chr3_4:3523223-3523242 None:intergenic 35.0%
! TAGTTTTCATCAGGTTACTG+AGG + chr3_4:3523313-3523332 Msa0485740:CDS 35.0%
! AGTTTTCATCAGGTTACTGA+GGG + chr3_4:3523314-3523333 Msa0485740:CDS 35.0%
GAATTCTCTATGTCAACCAA+TGG - chr3_4:3523395-3523414 None:intergenic 35.0%
! TGGATATAGTGGAAGCAACA+TGG - chr3_4:3522788-3522807 None:intergenic 40.0%
! AATTTGGTGGGTGGATATAG+TGG - chr3_4:3522799-3522818 None:intergenic 40.0%
TGGAGAGGTTTCAATTTGGT+GGG - chr3_4:3522811-3522830 None:intergenic 40.0%
AACCTGGAGAGGTTTCAATT+TGG - chr3_4:3522815-3522834 None:intergenic 40.0%
CTTCAACAAGGACAATGACT+TGG + chr3_4:3522890-3522909 Msa0485740:CDS 40.0%
TTGGTTGCAAGAGATTCAAC+AGG + chr3_4:3522909-3522928 Msa0485740:CDS 40.0%
! TTTCTCTCTTGTGTGCGTTT+TGG - chr3_4:3523046-3523065 None:intergenic 40.0%
GAATTGGACTATTCACTGAG+AGG + chr3_4:3523090-3523109 Msa0485740:CDS 40.0%
TGCCTCTTAATGGTTCTTTC+AGG + chr3_4:3523132-3523151 Msa0485740:CDS 40.0%
GACCTGAAAGAACCATTAAG+AGG - chr3_4:3523137-3523156 None:intergenic 40.0%
!! TTGTTGATGGCGAAAAACCA+TGG - chr3_4:3523190-3523209 None:intergenic 40.0%
!!! CTAGCACTGCTTTTTATCTC+AGG - chr3_4:3523224-3523243 None:intergenic 40.0%
! AGCAGTGCTAGATTCAAGTT+AGG + chr3_4:3523233-3523252 Msa0485740:CDS 40.0%
TATCGGTCATCCGATATTCT+TGG + chr3_4:3523259-3523278 Msa0485740:CDS 40.0%
TCATCGTCCTCCAAGAATAT+CGG - chr3_4:3523272-3523291 None:intergenic 40.0%
TGAGGTGAATGTGAAACCAT+TGG + chr3_4:3523376-3523395 Msa0485740:CDS 40.0%
! AGAGGTTTCAATTTGGTGGG+TGG - chr3_4:3522808-3522827 None:intergenic 45.0%
CTGGAGAGGTTTCAATTTGG+TGG - chr3_4:3522812-3522831 None:intergenic 45.0%
CACCAAATTGAAACCTCTCC+AGG + chr3_4:3522810-3522829 Msa0485740:CDS 45.0%
GTTACTATAGGAACCTGGAG+AGG - chr3_4:3522826-3522845 None:intergenic 45.0%
AGGCTGTTACTATAGGAACC+TGG - chr3_4:3522831-3522850 None:intergenic 45.0%
GAGTGTTAAGTCCAGTGAGA+TGG - chr3_4:3522868-3522887 None:intergenic 45.0%
AAGTTCATTGCTGCTCTCAC+TGG - chr3_4:3522952-3522971 None:intergenic 45.0%
! GCGCAAATTTTATAGCTCGC+AGG + chr3_4:3523007-3523026 Msa0485740:CDS 45.0%
! TTTTATAGCTCGCAGGCACT+TGG + chr3_4:3523014-3523033 Msa0485740:CDS 45.0%
CTTGCATCTCTGCCTCTTAA+TGG + chr3_4:3523122-3523141 Msa0485740:CDS 45.0%
ACACACTCTTCACTACACCA+TGG + chr3_4:3523170-3523189 Msa0485740:CDS 45.0%
!!! CTGCTTTTTATCTCAGGGCT+AGG - chr3_4:3523218-3523237 None:intergenic 45.0%
ACGATGAGACAGAACTGATG+TGG + chr3_4:3523285-3523304 Msa0485740:CDS 45.0%
! GTGGCAAGGTAGTTTTCATC+AGG + chr3_4:3523304-3523323 Msa0485740:CDS 45.0%
TTTCATCAGGTTACTGAGGG+AGG + chr3_4:3523317-3523336 Msa0485740:CDS 45.0%
GCAAAGCGAGCTATGCGAAT+TGG + chr3_4:3523074-3523093 Msa0485740:CDS 50.0%
!! GGGCTAGGCCTTATTGTTGA+TGG - chr3_4:3523203-3523222 None:intergenic 50.0%
CGGTCATCCGATATTCTTGG+AGG + chr3_4:3523262-3523281 Msa0485740:CDS 50.0%
GAGACAGAACTGATGTGGCA+AGG + chr3_4:3523290-3523309 Msa0485740:CDS 50.0%
TATAGCTCGCAGGCACTTGG+TGG + chr3_4:3523017-3523036 Msa0485740:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 3522723 3523442 3522723 ID=Msa0485740;Name=Msa0485740
chr3_4 mRNA 3522723 3523442 3522723 ID=Msa0485740-mRNA-1;Parent=Msa0485740;Name=Msa0485740-mRNA-1;_AED=0.25;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|239
chr3_4 exon 3522723 3523442 3522723 ID=Msa0485740-mRNA-1:exon:1305;Parent=Msa0485740-mRNA-1
chr3_4 CDS 3522723 3523442 3522723 ID=Msa0485740-mRNA-1:cds;Parent=Msa0485740-mRNA-1
Gene Sequence

>Msa0485740

ATGAAACCAATTTTTGATCTTGAAGTAGAGGCCACAGAAGAATATGAATCTGATGTTAGTAGCCATGTTGCTTCCACTATATCCACCCACCAAATTGAAACCTCTCCAGGTTCCTATAGTAACAGCCTTTCTAATTCAGATTCCATCTCACTGGACTTAACACTCAACTTCAACAAGGACAATGACTTGGTTGCAAGAGATTCAACAGGATTCTCATTCTCAAGCACCAGTGAGAGCAGCAATGAACTTACCATCCAAAGAATTTTCTCTTGCAATTACTGTCGGCGCAAATTTTATAGCTCGCAGGCACTTGGTGGTCACCAAAACGCACACAAGAGAGAAAGAACGTTAGCAAAGCGAGCTATGCGAATTGGACTATTCACTGAGAGGTATGCAAGTCTTGCATCTCTGCCTCTTAATGGTTCTTTCAGGTCATTAGGTATAAAGACACACTCTTCACTACACCATGGTTTTTCGCCATCAACAATAAGGCCTAGCCCTGAGATAAAAAGCAGTGCTAGATTCAAGTTAGGATCTATCGGTCATCCGATATTCTTGGAGGACGATGAGACAGAACTGATGTGGCAAGGTAGTTTTCATCAGGTTACTGAGGGAGGTAGTAACACTTATCAGAGTTCAAATATGTGTTTTACTGAGGTGAATGTGAAACCATTGGTTGACATAGAGAATTCAGCACCTGAATTAACATTGAAACTTTGA
Protein sequence

>Msa0485740

MKPIFDLEVEATEEYESDVSSHVASTISTHQIETSPGSYSNSLSNSDSISLDLTLNFNKDNDLVARDSTGFSFSSTSESSNELTIQRIFSCNYCRRKFYSSQALGGHQNAHKRERTLAKRAMRIGLFTERYASLASLPLNGSFRSLGIKTHSSLHHGFSPSTIRPSPEIKSSARFKLGSIGHPIFLEDDETELMWQGSFHQVTEGGSNTYQSSNMCFTEVNVKPLVDIENSAPELTLKL*