AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1283980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1283980 MtrunA17_Chr8g0355741 93.571 140 9 0 1 140 1 140 1.85e-95 271
Msa1283980 MtrunA17_Chr8g0355721 82.143 140 25 0 1 140 1 140 3.13e-83 241
Msa1283980 MtrunA17_Chr8g0355811 80.714 140 26 1 1 140 1 139 5.29e-81 235
Msa1283980 MtrunA17_Chr8g0355661 81.429 140 25 1 1 140 1 139 6.38e-81 235
Msa1283980 MtrunA17_Chr8g0355761 74.286 140 36 0 1 140 1 140 3.33e-78 228
Msa1283980 MtrunA17_Chr8g0355781 75.000 140 35 0 1 140 1 140 1.78e-77 226
Msa1283980 MtrunA17_Chr8g0355801 77.857 140 30 1 1 140 1 139 9.99e-77 224
Msa1283980 MtrunA17_Chr8g0355821 74.286 140 35 1 1 140 1 139 1.97e-75 221
Msa1283980 MtrunA17_Chr8g0355791 75.000 140 34 1 1 140 1 139 1.21e-73 216
Msa1283980 MtrunA17_Chr8g0355641 71.429 140 40 0 1 140 1 140 2.17e-72 213
Msa1283980 MtrunA17_Chr8g0355771 72.857 140 37 1 1 140 1 139 7.64e-71 209
Msa1283980 MtrunA17_Chr1g0160371 40.141 142 82 2 1 140 1 141 1.87e-32 112
Msa1283980 MtrunA17_Chr1g0160381 35.915 142 88 2 1 140 5 145 8.39e-31 108
Msa1283980 MtrunA17_Chr8g0339261 33.071 127 82 3 6 131 8 132 6.88e-23 87.8
Msa1283980 MtrunA17_Chr1g0160391 34.014 147 89 4 1 140 1 146 7.07e-23 88.2
Msa1283980 MtrunA17_Chr1g0160801 33.333 135 81 5 7 139 7 134 7.82e-19 77.4
Msa1283980 MtrunA17_Chr1g0160351 42.683 82 45 1 61 140 1 82 4.86e-16 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1283980 AT1G70890.1 37.226 137 83 3 3 137 7 142 2.69e-22 86.7
Msa1283980 AT5G28010.1 33.571 140 90 3 3 140 15 153 5.84e-22 86.3
Msa1283980 AT5G28010.2 33.571 140 90 3 3 140 15 153 5.84e-22 86.3
Msa1283980 AT1G23120.1 32.558 129 82 3 10 138 10 133 2.36e-20 81.6
Msa1283980 AT1G70840.1 33.577 137 88 3 3 137 20 155 4.45e-20 81.3
Msa1283980 AT1G23120.2 32.558 129 82 3 10 138 60 183 6.92e-20 81.6
Msa1283980 AT1G70830.5 33.577 137 88 3 3 137 22 157 3.79e-19 79.0
Msa1283980 AT1G70830.3 33.577 137 88 3 3 137 22 157 7.37e-19 79.0
Msa1283980 AT1G70830.2 33.577 137 88 3 3 137 22 157 1.97e-18 79.0
Msa1283980 AT1G70870.1 36.496 137 74 4 1 137 1 124 2.25e-18 76.3
Msa1283980 AT5G28000.1 30.935 139 93 3 3 139 13 150 3.03e-18 76.6
Msa1283980 AT1G70830.4 33.577 137 88 3 3 137 137 272 3.48e-18 78.6
Msa1283980 AT1G70830.1 33.577 137 88 3 3 137 22 157 4.21e-18 79.0
Msa1283980 AT1G70830.1 33.577 137 88 3 3 137 184 319 8.81e-18 78.2
Msa1283980 AT1G70850.2 32.847 137 89 3 3 137 9 144 4.40e-18 77.8
Msa1283980 AT1G70850.3 32.847 137 89 3 3 137 9 144 1.12e-17 77.8
Msa1283980 AT1G70850.3 33.858 127 81 3 13 137 175 300 2.62e-17 76.6
Msa1283980 AT1G70850.1 32.847 137 89 3 3 137 9 144 1.12e-17 77.8
Msa1283980 AT1G70850.1 33.858 127 81 3 13 137 175 300 2.62e-17 76.6
Msa1283980 AT1G23130.1 27.338 139 99 2 3 140 10 147 2.21e-16 71.6
Msa1283980 AT4G23670.1 34.507 142 84 4 1 138 1 137 4.76e-16 70.5
Msa1283980 AT1G24020.1 31.690 142 93 3 1 140 1 140 7.20e-15 67.4
Msa1283980 AT1G24020.2 31.690 142 93 3 1 140 1 140 7.20e-15 67.4
Msa1283980 AT1G14930.1 30.216 139 94 3 1 138 1 137 9.19e-15 67.4
Msa1283980 AT4G23680.1 30.986 142 89 4 1 138 1 137 4.35e-14 65.5
Msa1283980 AT1G70880.1 29.771 131 89 3 3 131 8 137 6.58e-14 65.1
Msa1283980 AT2G01520.1 28.777 139 96 3 1 138 1 137 5.36e-13 62.4
Msa1283980 AT1G30990.1 31.298 131 87 3 1 130 1 129 1.59e-12 61.2
Msa1283980 AT1G14940.1 29.496 139 95 3 1 138 1 137 4.40e-12 60.1
Msa1283980 AT1G35310.1 28.205 117 81 3 13 128 12 126 9.48e-11 56.6

Find 30 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCACTGCTGCTGCTAAA+TGG 0.310932 8_3:-25845175 Msa1283980:CDS
AAAGGTACTTACAAGCTCTT+TGG 0.360361 8_3:-25845260 Msa1283980:CDS
CACCCTTATCAATTACTTCA+AGG 0.382574 8_3:+25845198 None:intergenic
GGTAAACTTATTACTGAACT+TGG 0.415223 8_3:-25846058 Msa1283980:CDS
CATCCTTGAAGTAATTGATA+AGG 0.438738 8_3:-25845201 Msa1283980:CDS
ATCTTCACCCTCATGCAGCT+TGG 0.445602 8_3:+25845949 None:intergenic
AAGTAGTCCATCCAGCCATT+TGG 0.456227 8_3:+25845113 None:intergenic
AGATATTGATGAGCACTATA+AGG 0.456652 8_3:-25845234 Msa1283980:CDS
AAACACTGGACTTATGTCAT+AGG 0.470664 8_3:-25845905 Msa1283980:intron
ATCCTTGAAGTAATTGATAA+GGG 0.486541 8_3:-25845200 Msa1283980:CDS
TGAAATAACAACAGATGGTA+AGG 0.489687 8_3:-25845330 Msa1283980:intron
AGCTGCATGAGGGTGAAGAT+TGG 0.493681 8_3:-25845946 Msa1283980:CDS
GGTACTTACAAGCTCTTTGG+TGG 0.496480 8_3:-25845257 Msa1283980:CDS
ATATTGACCCTCCAAATGGC+TGG 0.527845 8_3:-25845124 Msa1283980:CDS
GAGGATATTGACCCTCCAAA+TGG 0.539495 8_3:-25845128 Msa1283980:CDS
GTAAACTTATTACTGAACTT+GGG 0.542207 8_3:-25846057 Msa1283980:CDS
ATTGATGAACAACACAAGAA+AGG 0.543540 8_3:-25845278 Msa1283980:CDS
AGATTGGCATCACACTGATT+CGG 0.545548 8_3:-25845930 Msa1283980:CDS
GAAGTAATTGATAAGGGTGA+TGG 0.549119 8_3:-25845194 Msa1283980:CDS
TAGTCCATCCAGCCATTTGG+AGG 0.551025 8_3:+25845116 None:intergenic
ACACTGATTCGGTCAAACAC+TGG 0.556043 8_3:-25845919 Msa1283980:CDS
TGACCCTCCAAATGGCTGGA+TGG 0.557517 8_3:-25845120 Msa1283980:CDS
GGATCAAAACACCCGCTGAA+AGG 0.578575 8_3:-25846036 Msa1283980:CDS
TCATGAAACCAAGCTGCATG+AGG 0.602712 8_3:-25845957 Msa1283980:CDS
CATGAAACCAAGCTGCATGA+GGG 0.630684 8_3:-25845956 Msa1283980:CDS
AGTTTGAAGAACCTTTCAGC+GGG 0.631322 8_3:+25846025 None:intergenic
GGTACACACATGTCATGAGA+AGG 0.648648 8_3:-25845309 Msa1283980:CDS
AGTCCATCCAGCCATTTGGA+GGG 0.649199 8_3:+25845117 None:intergenic
TAGTTTGAAGAACCTTTCAG+CGG 0.662028 8_3:+25846024 None:intergenic
TGAATATGAGAAGATCAATG+AGG 0.699788 8_3:-25845147 Msa1283980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATAATATTTGTCTAATA+TGG - chr8_3:25845660-25845679 Msa1283980:intron 10.0%
!! ATAATAATATTTGTCTAATA+TGG - chr8_3:25845660-25845679 Msa1283980:intron 10.0%
!!! TATTTTATTGAAAATAGCAA+CGG + chr8_3:25845443-25845462 None:intergenic 15.0%
!! TAGACAAATATTATTATTGA+TGG + chr8_3:25845657-25845676 None:intergenic 15.0%
!! AATCTTACTAAAAAATGTTA+AGG + chr8_3:25845783-25845802 None:intergenic 15.0%
!!! TATTTTATTGAAAATAGCAA+CGG + chr8_3:25845443-25845462 None:intergenic 15.0%
!! TAGACAAATATTATTATTGA+TGG + chr8_3:25845657-25845676 None:intergenic 15.0%
!! AATCTTACTAAAAAATGTTA+AGG + chr8_3:25845783-25845802 None:intergenic 15.0%
!! ACAAATATTATTATTGATGG+TGG + chr8_3:25845654-25845673 None:intergenic 20.0%
!! AATTAAAGAGATGTACAAAA+AGG - chr8_3:25845752-25845771 Msa1283980:intron 20.0%
!!! AAAACTGCTGTTATTTTTTT+TGG - chr8_3:25845810-25845829 Msa1283980:intron 20.0%
!! ACAAATATTATTATTGATGG+TGG + chr8_3:25845654-25845673 None:intergenic 20.0%
!! AATTAAAGAGATGTACAAAA+AGG - chr8_3:25845752-25845771 Msa1283980:intron 20.0%
!!! AAAACTGCTGTTATTTTTTT+TGG - chr8_3:25845810-25845829 Msa1283980:intron 20.0%
! GTAAACTTATTACTGAACTT+GGG - chr8_3:25845119-25845138 Msa1283980:CDS 25.0%
!!! GATCCTTTCCATTTTTAATA+AGG - chr8_3:25845590-25845609 Msa1283980:intron 25.0%
! GATCCTTATTAAAAATGGAA+AGG + chr8_3:25845596-25845615 None:intergenic 25.0%
! TACTGGATCCTTATTAAAAA+TGG + chr8_3:25845601-25845620 None:intergenic 25.0%
! AGCAAAAAATTGTACAATAC+TGG + chr8_3:25845618-25845637 None:intergenic 25.0%
! TGTTGTACTACAAATGATAA+CGG + chr8_3:25845712-25845731 None:intergenic 25.0%
! ATCCTTGAAGTAATTGATAA+GGG - chr8_3:25845976-25845995 Msa1283980:CDS 25.0%
! GTAAACTTATTACTGAACTT+GGG - chr8_3:25845119-25845138 Msa1283980:CDS 25.0%
!!! GATCCTTTCCATTTTTAATA+AGG - chr8_3:25845590-25845609 Msa1283980:intron 25.0%
! GATCCTTATTAAAAATGGAA+AGG + chr8_3:25845596-25845615 None:intergenic 25.0%
! TACTGGATCCTTATTAAAAA+TGG + chr8_3:25845601-25845620 None:intergenic 25.0%
! AGCAAAAAATTGTACAATAC+TGG + chr8_3:25845618-25845637 None:intergenic 25.0%
! TGTTGTACTACAAATGATAA+CGG + chr8_3:25845712-25845731 None:intergenic 25.0%
! ATCCTTGAAGTAATTGATAA+GGG - chr8_3:25845976-25845995 Msa1283980:CDS 25.0%
GGTAAACTTATTACTGAACT+TGG - chr8_3:25845118-25845137 Msa1283980:CDS 30.0%
!! ACCATCTGTTGTTATTTCAT+GGG + chr8_3:25845845-25845864 None:intergenic 30.0%
!! TACCATCTGTTGTTATTTCA+TGG + chr8_3:25845846-25845865 None:intergenic 30.0%
TGAAATAACAACAGATGGTA+AGG - chr8_3:25845846-25845865 Msa1283980:intron 30.0%
ATTGATGAACAACACAAGAA+AGG - chr8_3:25845898-25845917 Msa1283980:intron 30.0%
AGATATTGATGAGCACTATA+AGG - chr8_3:25845942-25845961 Msa1283980:CDS 30.0%
CATCCTTGAAGTAATTGATA+AGG - chr8_3:25845975-25845994 Msa1283980:CDS 30.0%
TGAATATGAGAAGATCAATG+AGG - chr8_3:25846029-25846048 Msa1283980:CDS 30.0%
GGTAAACTTATTACTGAACT+TGG - chr8_3:25845118-25845137 Msa1283980:CDS 30.0%
!! ACCATCTGTTGTTATTTCAT+GGG + chr8_3:25845845-25845864 None:intergenic 30.0%
!! TACCATCTGTTGTTATTTCA+TGG + chr8_3:25845846-25845865 None:intergenic 30.0%
TGAAATAACAACAGATGGTA+AGG - chr8_3:25845846-25845865 Msa1283980:intron 30.0%
ATTGATGAACAACACAAGAA+AGG - chr8_3:25845898-25845917 Msa1283980:intron 30.0%
AGATATTGATGAGCACTATA+AGG - chr8_3:25845942-25845961 Msa1283980:CDS 30.0%
CATCCTTGAAGTAATTGATA+AGG - chr8_3:25845975-25845994 Msa1283980:CDS 30.0%
TGAATATGAGAAGATCAATG+AGG - chr8_3:25846029-25846048 Msa1283980:CDS 30.0%
TAGTTTGAAGAACCTTTCAG+CGG + chr8_3:25845155-25845174 None:intergenic 35.0%
AAACACTGGACTTATGTCAT+AGG - chr8_3:25845271-25845290 Msa1283980:CDS 35.0%
TGCCAACAAAATCATCTTGT+TGG - chr8_3:25845320-25845339 Msa1283980:intron 35.0%
! GTCCAACAAGATGATTTTGT+TGG + chr8_3:25845325-25845344 None:intergenic 35.0%
CAAAATCATCTTGTTGGACT+TGG - chr8_3:25845326-25845345 Msa1283980:intron 35.0%
!! AAAGGTACTTACAAGCTCTT+TGG - chr8_3:25845916-25845935 Msa1283980:CDS 35.0%
CACCCTTATCAATTACTTCA+AGG + chr8_3:25845981-25846000 None:intergenic 35.0%
GAAGTAATTGATAAGGGTGA+TGG - chr8_3:25845982-25846001 Msa1283980:CDS 35.0%
TAGTTTGAAGAACCTTTCAG+CGG + chr8_3:25845155-25845174 None:intergenic 35.0%
AAACACTGGACTTATGTCAT+AGG - chr8_3:25845271-25845290 Msa1283980:CDS 35.0%
TGCCAACAAAATCATCTTGT+TGG - chr8_3:25845320-25845339 Msa1283980:intron 35.0%
! GTCCAACAAGATGATTTTGT+TGG + chr8_3:25845325-25845344 None:intergenic 35.0%
CAAAATCATCTTGTTGGACT+TGG - chr8_3:25845326-25845345 Msa1283980:intron 35.0%
!! AAAGGTACTTACAAGCTCTT+TGG - chr8_3:25845916-25845935 Msa1283980:CDS 35.0%
CACCCTTATCAATTACTTCA+AGG + chr8_3:25845981-25846000 None:intergenic 35.0%
GAAGTAATTGATAAGGGTGA+TGG - chr8_3:25845982-25846001 Msa1283980:CDS 35.0%
AGTTTGAAGAACCTTTCAGC+GGG + chr8_3:25845154-25845173 None:intergenic 40.0%
! AGATTGGCATCACACTGATT+CGG - chr8_3:25845246-25845265 Msa1283980:CDS 40.0%
GCCCATGAAATAACAACAGA+TGG - chr8_3:25845841-25845860 Msa1283980:intron 40.0%
AGTTTGAAGAACCTTTCAGC+GGG + chr8_3:25845154-25845173 None:intergenic 40.0%
! AGATTGGCATCACACTGATT+CGG - chr8_3:25845246-25845265 Msa1283980:CDS 40.0%
GCCCATGAAATAACAACAGA+TGG - chr8_3:25845841-25845860 Msa1283980:intron 40.0%
TCATGAAACCAAGCTGCATG+AGG - chr8_3:25845219-25845238 Msa1283980:CDS 45.0%
CATGAAACCAAGCTGCATGA+GGG - chr8_3:25845220-25845239 Msa1283980:CDS 45.0%
!! ACACTGATTCGGTCAAACAC+TGG - chr8_3:25845257-25845276 Msa1283980:CDS 45.0%
GGTACACACATGTCATGAGA+AGG - chr8_3:25845867-25845886 Msa1283980:intron 45.0%
GGTACTTACAAGCTCTTTGG+TGG - chr8_3:25845919-25845938 Msa1283980:CDS 45.0%
GAGGATATTGACCCTCCAAA+TGG - chr8_3:25846048-25846067 Msa1283980:CDS 45.0%
ATATTGACCCTCCAAATGGC+TGG - chr8_3:25846052-25846071 Msa1283980:CDS 45.0%
AAGTAGTCCATCCAGCCATT+TGG + chr8_3:25846066-25846085 None:intergenic 45.0%
TCATGAAACCAAGCTGCATG+AGG - chr8_3:25845219-25845238 Msa1283980:CDS 45.0%
CATGAAACCAAGCTGCATGA+GGG - chr8_3:25845220-25845239 Msa1283980:CDS 45.0%
!! ACACTGATTCGGTCAAACAC+TGG - chr8_3:25845257-25845276 Msa1283980:CDS 45.0%
GGTACACACATGTCATGAGA+AGG - chr8_3:25845867-25845886 Msa1283980:intron 45.0%
GGTACTTACAAGCTCTTTGG+TGG - chr8_3:25845919-25845938 Msa1283980:CDS 45.0%
GAGGATATTGACCCTCCAAA+TGG - chr8_3:25846048-25846067 Msa1283980:CDS 45.0%
ATATTGACCCTCCAAATGGC+TGG - chr8_3:25846052-25846071 Msa1283980:CDS 45.0%
AAGTAGTCCATCCAGCCATT+TGG + chr8_3:25846066-25846085 None:intergenic 45.0%
GGATCAAAACACCCGCTGAA+AGG - chr8_3:25845140-25845159 Msa1283980:CDS 50.0%
ATCTTCACCCTCATGCAGCT+TGG + chr8_3:25845230-25845249 None:intergenic 50.0%
AGCTGCATGAGGGTGAAGAT+TGG - chr8_3:25845230-25845249 Msa1283980:CDS 50.0%
ATGGCACTGCTGCTGCTAAA+TGG - chr8_3:25846001-25846020 Msa1283980:CDS 50.0%
AGTCCATCCAGCCATTTGGA+GGG + chr8_3:25846062-25846081 None:intergenic 50.0%
TAGTCCATCCAGCCATTTGG+AGG + chr8_3:25846063-25846082 None:intergenic 50.0%
GGATCAAAACACCCGCTGAA+AGG - chr8_3:25845140-25845159 Msa1283980:CDS 50.0%
ATCTTCACCCTCATGCAGCT+TGG + chr8_3:25845230-25845249 None:intergenic 50.0%
AGCTGCATGAGGGTGAAGAT+TGG - chr8_3:25845230-25845249 Msa1283980:CDS 50.0%
ATGGCACTGCTGCTGCTAAA+TGG - chr8_3:25846001-25846020 Msa1283980:CDS 50.0%
AGTCCATCCAGCCATTTGGA+GGG + chr8_3:25846062-25846081 None:intergenic 50.0%
TAGTCCATCCAGCCATTTGG+AGG + chr8_3:25846063-25846082 None:intergenic 50.0%
TGACCCTCCAAATGGCTGGA+TGG - chr8_3:25846056-25846075 Msa1283980:CDS 55.0%
TGACCCTCCAAATGGCTGGA+TGG - chr8_3:25846056-25846075 Msa1283980:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 25845106 25846092 25845106 ID=Msa1283980;Name=Msa1283980
chr8_3 mRNA 25845106 25846092 25845106 ID=Msa1283980-mRNA-1;Parent=Msa1283980;Name=Msa1283980-mRNA-1;_AED=0.06;_eAED=0.07;_QI=0|0|0|1|1|0.5|2|0|140
chr8_3 exon 25845906 25846092 25845906 ID=Msa1283980-mRNA-1:exon:9068;Parent=Msa1283980-mRNA-1
chr8_3 exon 25845106 25845338 25845106 ID=Msa1283980-mRNA-1:exon:9067;Parent=Msa1283980-mRNA-1
chr8_3 CDS 25845906 25846092 25845906 ID=Msa1283980-mRNA-1:cds;Parent=Msa1283980-mRNA-1
chr8_3 CDS 25845106 25845338 25845106 ID=Msa1283980-mRNA-1:cds;Parent=Msa1283980-mRNA-1
Gene Sequence

>Msa1283980

ATGGTGCTTGCTGGTAAACTTATTACTGAACTTGGGATCAAAACACCCGCTGAAAGGTTCTTCAAACTATTTGCATCAGAACTTCATGAAGTGCAAAAACACTGTGAAAGAGTTCATGAAACCAAGCTGCATGAGGGTGAAGATTGGCATCACACTGATTCGGTCAAACACTGGACTTATGTCATAGATGGTAAGGTACACACATGTCATGAGAAGGTTGAAGAAATTGATGAACAACACAAGAAAGGTACTTACAAGCTCTTTGGTGGAGATATTGATGAGCACTATAAGGACTTTAAGCTCATCCTTGAAGTAATTGATAAGGGTGATGGCACTGCTGCTGCTAAATGGACAGTTGAATATGAGAAGATCAATGAGGATATTGACCCTCCAAATGGCTGGATGGACTACTTATGCAAA

Protein sequence

>Msa1283980

MVLAGKLITELGIKTPAERFFKLFASELHEVQKHCERVHETKLHEGEDWHHTDSVKHWTYVIDGKVHTCHEKVEEIDEQHKKGTYKLFGGDIDEHYKDFKLILEVIDKGDGTAAAKWTVEYEKINEDIDPPNGWMDYLCK