AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1445040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1445040 MtrunA17_Chr5g0437611 95.610 205 9 0 1 205 1 205 1.98e-146 405
Msa1445040 MtrunA17_Chr3g0114121 62.946 224 62 5 1 204 1 223 4.31e-84 248
Msa1445040 MtrunA17_Chr4g0005501 64.327 171 54 4 39 205 42 209 9.23e-72 216
Msa1445040 MtrunA17_Chr7g0243271 68.000 175 46 4 39 205 6 178 1.56e-70 213
Msa1445040 MtrunA17_Chr5g0411391 55.488 164 66 3 46 203 44 206 1.70e-60 188
Msa1445040 MtrunA17_Chr8g0347191 52.353 170 73 4 41 205 66 232 9.87e-58 182
Msa1445040 MtrunA17_Chr3g0126471 51.534 163 73 3 44 203 19 178 2.31e-57 179
Msa1445040 MtrunA17_Chr1g0158871 50.909 165 75 2 44 205 17 178 6.83e-57 178
Msa1445040 MtrunA17_Chr1g0151661 52.795 161 69 3 46 202 39 196 1.47e-54 172
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1445040 AT2G40330.1 58.571 210 79 3 1 203 1 209 1.63e-81 242
Msa1445040 AT5G05440.1 60.396 202 74 3 1 200 1 198 7.90e-77 229
Msa1445040 AT2G38310.1 65.285 193 60 3 13 203 8 195 2.27e-73 221
Msa1445040 AT1G01360.1 52.147 163 72 2 46 205 21 180 1.86e-60 187
Msa1445040 AT4G27920.1 50.909 165 76 2 44 205 12 174 1.16e-57 180
Msa1445040 AT4G01026.1 52.201 159 70 3 50 205 27 182 3.58e-56 177
Msa1445040 AT5G53160.2 50.909 165 75 3 44 205 17 178 3.98e-56 176
Msa1445040 AT4G17870.1 50.610 164 77 2 45 205 16 178 3.94e-53 169
Msa1445040 AT2G26040.1 49.383 162 75 3 46 202 22 181 1.39e-50 162
Msa1445040 AT1G73000.1 47.619 168 77 3 46 202 37 204 1.03e-49 160
Msa1445040 AT5G46790.2 51.765 170 75 2 42 205 40 208 9.28e-49 159
Msa1445040 AT5G46790.1 51.765 170 75 2 42 205 40 208 9.28e-49 159
Msa1445040 AT5G45860.1 58.389 149 58 3 59 205 10 156 1.20e-46 151
Msa1445040 AT5G45870.1 56.954 151 62 3 56 205 7 155 2.18e-45 148
Msa1445040 AT4G18620.1 46.914 162 79 2 51 205 1 162 1.23e-35 123
Msa1445040 AT5G53160.1 46.667 105 53 2 44 148 17 118 5.55e-28 103

Find 59 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGTGGTTTGCAACCGTTTC+TGG 0.080678 tig0030914:-5597 None:intergenic
CGTGAAGTTCGACTTGTTTC+CGG 0.131980 tig0030914:+5795 Msa1445040:CDS
AAACGGAGGCCTTGATGGTT+TGG 0.349101 tig0030914:-5662 None:intergenic
GTGTTGTTGGTGGTGTTCAT+AGG 0.363891 tig0030914:+5886 Msa1445040:CDS
TCTAACACCGCCATGACTAA+TGG 0.405607 tig0030914:+5504 Msa1445040:CDS
GTTATTAGTTTCAGTGTTGT+TGG 0.408321 tig0030914:+5873 Msa1445040:CDS
TTCATAGGTGTAGGAATTAC+CGG 0.411086 tig0030914:+5901 Msa1445040:CDS
AGGCCTCCGTTTCAACTGTC+TGG 0.430513 tig0030914:+5673 Msa1445040:CDS
CGACACGCTTGAATTTGTTT+CGG 0.430906 tig0030914:-5537 None:intergenic
AGTTGAAACGGAGGCCTTGA+TGG 0.442287 tig0030914:-5667 None:intergenic
TAGGTGTAATTTGCAGTCAC+TGG 0.448044 tig0030914:+6043 Msa1445040:CDS
GGTGGTTTGCAACCGTTTCT+GGG 0.462922 tig0030914:-5596 None:intergenic
AACGTAGTTGCCTCCGGTGA+TGG 0.485651 tig0030914:+5753 Msa1445040:CDS
AACCGTTTCTGTCCCAGAAA+CGG 0.488981 tig0030914:+5584 Msa1445040:CDS
AGCTGCAACGTAGTTGCCTC+CGG 0.500297 tig0030914:+5747 Msa1445040:CDS
GCTTGAAACGGCAGGTAGAC+CGG 0.502003 tig0030914:-5814 None:intergenic
CAACCTCTCCATGCTTGAAA+CGG 0.516613 tig0030914:-5826 None:intergenic
GGATCACGACGGAGTAGCAC+TGG 0.520709 tig0030914:-5641 None:intergenic
AACCGTTTCTGGGACAGAAA+CGG 0.521454 tig0030914:-5586 None:intergenic
GTGACGACGTTGCACGGTGA+TGG 0.524987 tig0030914:+5927 Msa1445040:CDS
CGTTTCAAGCATGGAGAGGT+TGG 0.529991 tig0030914:+5827 Msa1445040:CDS
TCGAACCGTTGAAATTGAAC+CGG 0.530260 tig0030914:-5480 None:intergenic
CGTTGAAATTGAACCGGTGA+AGG 0.532412 tig0030914:-5474 None:intergenic
ACCGACACGAATGCCATCAC+CGG 0.534492 tig0030914:-5766 None:intergenic
AACGGACCAGACAGTTGAAA+CGG 0.535986 tig0030914:-5679 None:intergenic
CAAAATAGAAATGCCTTCAC+CGG 0.537348 tig0030914:+5461 None:intergenic
CTTCACCGGTTCAATTTCAA+CGG 0.537786 tig0030914:+5475 Msa1445040:CDS
CTCTCCATGCTTGAAACGGC+AGG 0.544665 tig0030914:-5822 None:intergenic
ACAAAGTGTTTGTAGCCTTG+TGG 0.546590 tig0030914:-5720 None:intergenic
TCTACCTGCCGTTTCAAGCA+TGG 0.550915 tig0030914:+5818 Msa1445040:CDS
CGGTCAGTGACGACGTTGCA+CGG 0.551799 tig0030914:+5921 Msa1445040:CDS
ATACGTTGTTGATGTACCAC+AGG 0.556769 tig0030914:+5977 Msa1445040:CDS
TTGGTGGTGTTCATAGGTGT+AGG 0.559793 tig0030914:+5892 Msa1445040:CDS
ATTAGTTTCAGTGTTGTTGG+TGG 0.561597 tig0030914:+5876 Msa1445040:CDS
CGTCGTGATCCAAACCATCA+AGG 0.571418 tig0030914:+5653 Msa1445040:CDS
CGTGCAACGTCGTCACTGAC+CGG 0.576112 tig0030914:-5920 None:intergenic
CAACACTGAAACTAATAACA+TGG 0.585088 tig0030914:-5869 None:intergenic
ACAGTTAATGCCATTAGTCA+TGG 0.586782 tig0030914:-5514 None:intergenic
AGCCTTGTGGATTGTCGAAG+CGG 0.601019 tig0030914:-5707 None:intergenic
AACCACCACATGCACGTGGT+GGG 0.602296 tig0030914:+5612 Msa1445040:CDS
ACGTTGCACGGTGATGGAAA+CGG 0.604152 tig0030914:+5933 Msa1445040:CDS
TCCGGTGATGGCATTCGTGT+CGG 0.606951 tig0030914:+5765 Msa1445040:CDS
TGTACCACAGGGTAACACTA+AGG 0.609377 tig0030914:+5989 Msa1445040:CDS
CGCCGCTTCGACAATCCACA+AGG 0.611657 tig0030914:+5705 Msa1445040:CDS
AAACCACCACATGCACGTGG+TGG 0.622421 tig0030914:+5611 Msa1445040:CDS
GTCCCACCACGTGCATGTGG+TGG 0.623392 tig0030914:-5614 None:intergenic
CTGCCGTTTCAAGCATGGAG+AGG 0.630256 tig0030914:+5823 Msa1445040:CDS
ATTGTCGAAGCGGCGGACAA+CGG 0.630831 tig0030914:-5697 None:intergenic
CTGCAAATTACACCTAACAA+TGG 0.632688 tig0030914:-6036 None:intergenic
TGCAAACCACCACATGCACG+TGG 0.642151 tig0030914:+5608 Msa1445040:CDS
TTTGTCCCACCACGTGCATG+TGG 0.645948 tig0030914:-5617 None:intergenic
TCTTCCTTAGTGTTACCCTG+TGG 0.656284 tig0030914:-5993 None:intergenic
GACACGAATGCCATCACCGG+AGG 0.657865 tig0030914:-5763 None:intergenic
CTTGTGGATTGTCGAAGCGG+CGG 0.689521 tig0030914:-5704 None:intergenic
CTTGATGGTTTGGATCACGA+CGG 0.697791 tig0030914:-5652 None:intergenic
GGACCAGACAGTTGAAACGG+AGG 0.712986 tig0030914:-5676 None:intergenic
TACGTTGTTGATGTACCACA+GGG 0.714710 tig0030914:+5978 Msa1445040:CDS
TTGCACGGTGATGGAAACGG+AGG 0.721827 tig0030914:+5936 Msa1445040:CDS
GTTAATGCCATTAGTCATGG+CGG 0.726535 tig0030914:-5511 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAACACTGAAACTAATAACA+TGG - tig0030914:5872-5891 None:intergenic 30.0%
! GTTATTAGTTTCAGTGTTGT+TGG + tig0030914:5873-5892 Msa1445040:CDS 30.0%
!! GTTTTGTTGATACCATTGTT+AGG + tig0030914:6024-6043 Msa1445040:CDS 30.0%
ACAGTTAATGCCATTAGTCA+TGG - tig0030914:5517-5536 None:intergenic 35.0%
! ATTAGTTTCAGTGTTGTTGG+TGG + tig0030914:5876-5895 Msa1445040:CDS 35.0%
TTCATAGGTGTAGGAATTAC+CGG + tig0030914:5901-5920 Msa1445040:CDS 35.0%
CTGCAAATTACACCTAACAA+TGG - tig0030914:6039-6058 None:intergenic 35.0%
!! CTTCACCGGTTCAATTTCAA+CGG + tig0030914:5475-5494 Msa1445040:CDS 40.0%
TCGAACCGTTGAAATTGAAC+CGG - tig0030914:5483-5502 None:intergenic 40.0%
GTTAATGCCATTAGTCATGG+CGG - tig0030914:5514-5533 None:intergenic 40.0%
! CGACACGCTTGAATTTGTTT+CGG - tig0030914:5540-5559 None:intergenic 40.0%
! ACAAAGTGTTTGTAGCCTTG+TGG - tig0030914:5723-5742 None:intergenic 40.0%
ATACGTTGTTGATGTACCAC+AGG + tig0030914:5977-5996 Msa1445040:CDS 40.0%
TACGTTGTTGATGTACCACA+GGG + tig0030914:5978-5997 Msa1445040:CDS 40.0%
! TAGGTGTAATTTGCAGTCAC+TGG + tig0030914:6043-6062 Msa1445040:CDS 40.0%
CGTTGAAATTGAACCGGTGA+AGG - tig0030914:5477-5496 None:intergenic 45.0%
TCTAACACCGCCATGACTAA+TGG + tig0030914:5504-5523 Msa1445040:CDS 45.0%
AACCGTTTCTGTCCCAGAAA+CGG + tig0030914:5584-5603 Msa1445040:CDS 45.0%
!! AACCGTTTCTGGGACAGAAA+CGG - tig0030914:5589-5608 None:intergenic 45.0%
! CTTGATGGTTTGGATCACGA+CGG - tig0030914:5655-5674 None:intergenic 45.0%
AACGGACCAGACAGTTGAAA+CGG - tig0030914:5682-5701 None:intergenic 45.0%
! CGTGAAGTTCGACTTGTTTC+CGG + tig0030914:5795-5814 Msa1445040:CDS 45.0%
CAACCTCTCCATGCTTGAAA+CGG - tig0030914:5829-5848 None:intergenic 45.0%
!! GTGTTGTTGGTGGTGTTCAT+AGG + tig0030914:5886-5905 Msa1445040:CDS 45.0%
!! TTGGTGGTGTTCATAGGTGT+AGG + tig0030914:5892-5911 Msa1445040:CDS 45.0%
TGTACCACAGGGTAACACTA+AGG + tig0030914:5989-6008 Msa1445040:CDS 45.0%
TCTTCCTTAGTGTTACCCTG+TGG - tig0030914:5996-6015 None:intergenic 45.0%
! GGTGGTTTGCAACCGTTTCT+GGG - tig0030914:5599-5618 None:intergenic 50.0%
! TGGTGGTTTGCAACCGTTTC+TGG - tig0030914:5600-5619 None:intergenic 50.0%
CGTCGTGATCCAAACCATCA+AGG + tig0030914:5653-5672 Msa1445040:CDS 50.0%
! AAACGGAGGCCTTGATGGTT+TGG - tig0030914:5665-5684 None:intergenic 50.0%
AGTTGAAACGGAGGCCTTGA+TGG - tig0030914:5670-5689 None:intergenic 50.0%
! AGCCTTGTGGATTGTCGAAG+CGG - tig0030914:5710-5729 None:intergenic 50.0%
! TCTACCTGCCGTTTCAAGCA+TGG + tig0030914:5818-5837 Msa1445040:CDS 50.0%
CGTTTCAAGCATGGAGAGGT+TGG + tig0030914:5827-5846 Msa1445040:CDS 50.0%
!! ACGTTGCACGGTGATGGAAA+CGG + tig0030914:5933-5952 Msa1445040:CDS 50.0%
TGCAAACCACCACATGCACG+TGG + tig0030914:5608-5627 Msa1445040:CDS 55.0%
AAACCACCACATGCACGTGG+TGG + tig0030914:5611-5630 Msa1445040:CDS 55.0%
AACCACCACATGCACGTGGT+GGG + tig0030914:5612-5631 Msa1445040:CDS 55.0%
TTTGTCCCACCACGTGCATG+TGG - tig0030914:5620-5639 None:intergenic 55.0%
AGGCCTCCGTTTCAACTGTC+TGG + tig0030914:5673-5692 Msa1445040:CDS 55.0%
GGACCAGACAGTTGAAACGG+AGG - tig0030914:5679-5698 None:intergenic 55.0%
ATTGTCGAAGCGGCGGACAA+CGG - tig0030914:5700-5719 None:intergenic 55.0%
! CTTGTGGATTGTCGAAGCGG+CGG - tig0030914:5707-5726 None:intergenic 55.0%
AGCTGCAACGTAGTTGCCTC+CGG + tig0030914:5747-5766 Msa1445040:CDS 55.0%
AACGTAGTTGCCTCCGGTGA+TGG + tig0030914:5753-5772 Msa1445040:CDS 55.0%
! TCCGGTGATGGCATTCGTGT+CGG + tig0030914:5765-5784 Msa1445040:CDS 55.0%
ACCGACACGAATGCCATCAC+CGG - tig0030914:5769-5788 None:intergenic 55.0%
GCTTGAAACGGCAGGTAGAC+CGG - tig0030914:5817-5836 None:intergenic 55.0%
CTCTCCATGCTTGAAACGGC+AGG - tig0030914:5825-5844 None:intergenic 55.0%
! CTGCCGTTTCAAGCATGGAG+AGG + tig0030914:5823-5842 Msa1445040:CDS 55.0%
!! TTGCACGGTGATGGAAACGG+AGG + tig0030914:5936-5955 Msa1445040:CDS 55.0%
GGATCACGACGGAGTAGCAC+TGG - tig0030914:5644-5663 None:intergenic 60.0%
CGCCGCTTCGACAATCCACA+AGG + tig0030914:5705-5724 Msa1445040:CDS 60.0%
GACACGAATGCCATCACCGG+AGG - tig0030914:5766-5785 None:intergenic 60.0%
CGTGCAACGTCGTCACTGAC+CGG - tig0030914:5923-5942 None:intergenic 60.0%
CGGTCAGTGACGACGTTGCA+CGG + tig0030914:5921-5940 Msa1445040:CDS 60.0%
GTGACGACGTTGCACGGTGA+TGG + tig0030914:5927-5946 Msa1445040:CDS 60.0%
GTCCCACCACGTGCATGTGG+TGG - tig0030914:5617-5636 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0030914 gene 5471 6088 5471 ID=Msa1445040;Name=Msa1445040
tig0030914 mRNA 5471 6088 5471 ID=Msa1445040-mRNA-1;Parent=Msa1445040;Name=Msa1445040-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|205
tig0030914 exon 5471 6088 5471 ID=Msa1445040-mRNA-1:exon:14794;Parent=Msa1445040-mRNA-1
tig0030914 CDS 5471 6088 5471 ID=Msa1445040-mRNA-1:cds;Parent=Msa1445040-mRNA-1
Gene Sequence

>Msa1445040

ATGCCTTCACCGGTTCAATTTCAACGGTTCGATTCTAACACCGCCATGACTAATGGCATTAACTGTCCGAAACAAATTCAAGCGTGTCGTTACGCGCTTTCTTCTTTAAAATCAACCGTTTCTGTCCCAGAAACGGTTGCAAACCACCACATGCACGTGGTGGGACAAAACCAGTGCTACTCCGTCGTGATCCAAACCATCAAGGCCTCCGTTTCAACTGTCTGGTCCGTTGTCCGCCGCTTCGACAATCCACAAGGCTACAAACACTTTGTTAAAAGCTGCAACGTAGTTGCCTCCGGTGATGGCATTCGTGTCGGTGCTCTTCGTGAAGTTCGACTTGTTTCCGGTCTACCTGCCGTTTCAAGCATGGAGAGGTTGGATATTCTTGATGAAGAACGCCATGTTATTAGTTTCAGTGTTGTTGGTGGTGTTCATAGGTGTAGGAATTACCGGTCAGTGACGACGTTGCACGGTGATGGAAACGGAGGAACAGTTGTCATTGAATCATACGTTGTTGATGTACCACAGGGTAACACTAAGGAAGAAACATGTAGTTTTGTTGATACCATTGTTAGGTGTAATTTGCAGTCACTGGCTCAGATCGCAGAGAAACTGTGA

Protein sequence

>Msa1445040

MPSPVQFQRFDSNTAMTNGINCPKQIQACRYALSSLKSTVSVPETVANHHMHVVGQNQCYSVVIQTIKASVSTVWSVVRRFDNPQGYKHFVKSCNVVASGDGIRVGALREVRLVSGLPAVSSMERLDILDEERHVISFSVVGGVHRCRNYRSVTTLHGDGNGGTVVIESYVVDVPQGNTKEETCSFVDTIVRCNLQSLAQIAEKL*