AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0765500

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0765500 MtrunA17_Chr6g0460951 74.302 179 6 2 3 141 34 212 7.11e-88 255
Msa0765500 MtrunA17_Chr1g0184271 44.915 118 32 2 9 95 12 127 2.23e-27 101
Msa0765500 MtrunA17_Chr5g0435641 41.176 119 39 1 8 95 6 124 9.72e-27 99.0
Msa0765500 MtrunA17_Chr7g0261031 44.355 124 35 2 8 100 7 127 2.52e-26 98.6
Msa0765500 MtrunA17_Chr7g0260971 48.544 103 22 1 8 79 13 115 8.41e-26 97.1
Msa0765500 MtrunA17_Chr8g0351701 47.059 102 23 1 9 79 23 124 3.56e-25 95.9
Msa0765500 MtrunA17_Chr8g0351721 43.200 125 39 2 3 95 12 136 8.20e-25 94.4
Msa0765500 MtrunA17_Chr7g0245871 44.118 102 26 1 9 79 27 128 1.01e-24 95.1
Msa0765500 MtrunA17_Chr1g0184281 46.535 101 23 1 9 78 15 115 9.15e-24 91.7
Msa0765500 MtrunA17_Chr4g0030001 32.919 161 72 4 6 130 21 181 5.85e-20 81.3
Msa0765500 MtrunA17_Chr3g0129071 36.036 111 41 1 7 87 45 155 5.18e-19 79.7
Msa0765500 MtrunA17_Chr5g0402611 39.216 102 32 1 8 79 7 108 1.45e-18 79.7
Msa0765500 MtrunA17_Chr5g0438091 33.333 111 44 1 8 88 38 148 1.20e-16 72.8
Msa0765500 MtrunA17_Chr3g0097221 35.345 116 42 2 8 93 6 118 1.22e-16 74.3
Msa0765500 MtrunA17_Chr7g0245861 43.956 91 18 2 8 65 11 101 3.12e-16 70.5
Msa0765500 MtrunA17_Chr1g0200201 34.513 113 44 2 10 92 73 185 1.23e-15 70.9
Msa0765500 MtrunA17_Chr8g0353981 41.975 81 17 1 8 58 6 86 3.01e-13 64.3
Msa0765500 MtrunA17_Chr5g0432451 36.190 105 37 1 7 81 41 145 1.09e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0765500 AT3G03760.1 55.556 144 29 2 8 116 50 193 4.89e-42 140
Msa0765500 AT2G42430.1 40.789 152 40 3 8 109 14 165 9.57e-29 105
Msa0765500 AT3G58190.1 44.915 118 33 2 9 95 11 127 8.48e-28 102
Msa0765500 AT5G06080.1 35.294 153 59 2 8 129 6 149 2.92e-25 95.1
Msa0765500 AT2G31310.1 43.137 102 27 1 8 78 6 107 6.94e-24 91.7
Msa0765500 AT2G42440.1 38.931 131 46 2 8 107 6 133 1.99e-23 92.0
Msa0765500 AT2G45420.1 46.154 104 25 1 12 84 40 143 2.88e-23 92.0
Msa0765500 AT4G00210.1 47.059 102 23 2 9 79 11 112 2.90e-23 90.9
Msa0765500 AT4G00220.1 44.231 104 27 1 12 84 20 123 5.22e-23 90.5
Msa0765500 AT2G45410.1 36.429 140 49 4 12 118 19 151 1.37e-19 80.9
Msa0765500 AT1G07900.1 37.168 113 41 2 6 88 30 142 1.78e-19 80.5
Msa0765500 AT2G28500.1 38.532 109 37 2 6 84 52 160 3.05e-18 78.2
Msa0765500 AT2G30130.1 34.146 123 49 2 5 97 4 124 1.63e-17 75.5
Msa0765500 AT2G30340.2 33.621 116 45 3 7 92 51 164 1.87e-17 76.6
Msa0765500 AT2G30340.1 33.621 116 45 3 7 92 50 163 1.92e-17 76.6
Msa0765500 AT1G16530.1 34.259 108 40 2 7 83 12 119 9.10e-17 72.8
Msa0765500 AT2G23660.2 34.615 104 38 2 8 81 4 107 4.80e-14 67.8
Msa0765500 AT2G23660.3 34.615 104 38 2 8 81 4 107 4.80e-14 67.8
Msa0765500 AT2G23660.1 34.615 104 38 2 8 81 4 107 4.80e-14 67.8
Msa0765500 AT3G50510.1 28.302 106 46 1 4 79 7 112 1.36e-12 62.4
Msa0765500 AT3G50510.2 28.302 106 46 1 4 79 7 112 1.36e-12 62.4
Msa0765500 AT2G40470.2 35.345 116 45 1 7 92 18 133 1.63e-11 59.7
Msa0765500 AT2G40470.1 35.345 116 45 1 7 92 43 158 1.95e-11 59.7

Find 39 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTGAAACGGCGGCTGATA+TGG 0.240934 5_2:-26548853 None:intergenic
AGGCTAGCTGATCCGGTTTA+TGG 0.264632 5_2:+26548593 Msa0765500:CDS
AACAACTTCAACCCTGGTTT+TGG 0.284974 5_2:+26548934 Msa0765500:CDS
CATTCTTGCTTTGCAGCAAC+AGG 0.339538 5_2:+26548628 Msa0765500:CDS
TGCATCTTTGCACCCTACTT+TGG 0.399115 5_2:+26548434 Msa0765500:CDS
TAGCCTAGCTTGAGCCTCAT+AGG 0.409914 5_2:-26548576 None:intergenic
CGCATCATTGATAGATGAAC+CGG 0.418650 5_2:+26548358 None:intergenic
ATTGAAACGGCGGCTGATAT+GGG 0.422968 5_2:-26548852 None:intergenic
TGAAGTTGTTCATATTCATA+AGG 0.429426 5_2:-26548921 None:intergenic
AAACTCAATTGATGAATAAG+AGG 0.436075 5_2:+26548797 Msa0765500:CDS
TCAAGCTAGGCTAGCTGATC+CGG 0.442761 5_2:+26548586 Msa0765500:CDS
GTTGTTCATATTCATAAGGT+TGG 0.472998 5_2:-26548917 None:intergenic
TTGAGGAGGAAGTGTAGTAG+TGG 0.488789 5_2:+26548410 Msa0765500:CDS
GGCTACAAGCTCTGTGATGA+AGG 0.499636 5_2:-26548976 None:intergenic
GTGGACACACAACCATAAAC+CGG 0.504022 5_2:-26548605 None:intergenic
TCCATTGTGAGGCCAAAACC+AGG 0.513069 5_2:-26548946 None:intergenic
GGTGGAAGCAGATGAGTTGT+TGG 0.513070 5_2:-26548893 None:intergenic
GTTCATATTCATAAGGTTGG+TGG 0.513150 5_2:-26548914 None:intergenic
GCACCACACGGAGATATAAC+CGG 0.519771 5_2:-26548377 None:intergenic
CATATTCATAAGGTTGGTGG+TGG 0.528819 5_2:-26548911 None:intergenic
CTGTTGCTGCAAAGCAAGAA+TGG 0.532688 5_2:-26548627 None:intergenic
AATATGAACAACTTCAACCC+TGG 0.543651 5_2:+26548928 Msa0765500:CDS
ACCTTGGTCAGTACCAAAGT+AGG 0.553693 5_2:-26548447 None:intergenic
GCTGGCTGCACAAATTGAAA+CGG 0.572987 5_2:-26548865 None:intergenic
TTTCCTATGAGGCTCAAGCT+AGG 0.592261 5_2:+26548573 Msa0765500:CDS
TGCGGCGACTATTTCCTATG+AGG 0.598387 5_2:+26548562 Msa0765500:CDS
CCTTGGTCAGTACCAAAGTA+GGG 0.599955 5_2:-26548446 None:intergenic
TTGAAACGGCGGCTGATATG+GGG 0.604833 5_2:-26548851 None:intergenic
GATGAGTTGTTGGAATATGC+TGG 0.605347 5_2:-26548883 None:intergenic
CCCTACTTTGGTACTGACCA+AGG 0.613176 5_2:+26548446 Msa0765500:CDS
GTGGTGCTTGCAAGTTCTTG+AGG 0.646814 5_2:+26548393 Msa0765500:CDS
GGCTGCACAAATTGAAACGG+CGG 0.671846 5_2:-26548862 None:intergenic
GGTGGCAGCTATGCAAGCAG+AGG 0.672106 5_2:+26548762 Msa0765500:intron
GTGCTTGCAAGTTCTTGAGG+AGG 0.680170 5_2:+26548396 Msa0765500:CDS
AAGAACTTGCAAGCACCACA+CGG 0.685626 5_2:-26548389 None:intergenic
CCATTGTGAGGCCAAAACCA+GGG 0.697828 5_2:-26548945 None:intergenic
AAGGTGTTGTCTCCATTGTG+AGG 0.699953 5_2:-26548957 None:intergenic
TTGCTGCAAAGCAAGAATGG+TGG 0.702855 5_2:-26548624 None:intergenic
GAACCGGTTATATCTCCGTG+TGG 0.743909 5_2:+26548374 Msa0765500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATCATTTGCAGAATATTTT+CGG + chr5_2:26548707-26548726 Msa0765500:intron 20.0%
! AAGATGAATAACTTACCTTA+TGG + chr5_2:26548731-26548750 Msa0765500:intron 25.0%
! AAACTCAATTGATGAATAAG+AGG + chr5_2:26548797-26548816 Msa0765500:CDS 25.0%
! TGAAGTTGTTCATATTCATA+AGG - chr5_2:26548924-26548943 None:intergenic 25.0%
GTTGTTCATATTCATAAGGT+TGG - chr5_2:26548920-26548939 None:intergenic 30.0%
GTTCATATTCATAAGGTTGG+TGG - chr5_2:26548917-26548936 None:intergenic 35.0%
AATATGAACAACTTCAACCC+TGG + chr5_2:26548928-26548947 Msa0765500:CDS 35.0%
! ACTTACCTTATGGCTGATTC+AGG + chr5_2:26548741-26548760 Msa0765500:intron 40.0%
GATGAGTTGTTGGAATATGC+TGG - chr5_2:26548886-26548905 None:intergenic 40.0%
!! CATATTCATAAGGTTGGTGG+TGG - chr5_2:26548914-26548933 None:intergenic 40.0%
! AACAACTTCAACCCTGGTTT+TGG + chr5_2:26548934-26548953 Msa0765500:CDS 40.0%
AAGAACTTGCAAGCACCACA+CGG - chr5_2:26548392-26548411 None:intergenic 45.0%
! TTGAGGAGGAAGTGTAGTAG+TGG + chr5_2:26548410-26548429 Msa0765500:CDS 45.0%
TGCATCTTTGCACCCTACTT+TGG + chr5_2:26548434-26548453 Msa0765500:CDS 45.0%
CCTTGGTCAGTACCAAAGTA+GGG - chr5_2:26548449-26548468 None:intergenic 45.0%
ACCTTGGTCAGTACCAAAGT+AGG - chr5_2:26548450-26548469 None:intergenic 45.0%
TTTCCTATGAGGCTCAAGCT+AGG + chr5_2:26548573-26548592 Msa0765500:CDS 45.0%
GTGGACACACAACCATAAAC+CGG - chr5_2:26548608-26548627 None:intergenic 45.0%
TTGCTGCAAAGCAAGAATGG+TGG - chr5_2:26548627-26548646 None:intergenic 45.0%
CTGTTGCTGCAAAGCAAGAA+TGG - chr5_2:26548630-26548649 None:intergenic 45.0%
CATTCTTGCTTTGCAGCAAC+AGG + chr5_2:26548628-26548647 Msa0765500:CDS 45.0%
! TACCTTATGGCTGATTCAGG+TGG + chr5_2:26548744-26548763 Msa0765500:intron 45.0%
ATTGAAACGGCGGCTGATAT+GGG - chr5_2:26548855-26548874 None:intergenic 45.0%
AATTGAAACGGCGGCTGATA+TGG - chr5_2:26548856-26548875 None:intergenic 45.0%
GCTGGCTGCACAAATTGAAA+CGG - chr5_2:26548868-26548887 None:intergenic 45.0%
!! AAGGTGTTGTCTCCATTGTG+AGG - chr5_2:26548960-26548979 None:intergenic 45.0%
GAACCGGTTATATCTCCGTG+TGG + chr5_2:26548374-26548393 Msa0765500:CDS 50.0%
GCACCACACGGAGATATAAC+CGG - chr5_2:26548380-26548399 None:intergenic 50.0%
GTGGTGCTTGCAAGTTCTTG+AGG + chr5_2:26548393-26548412 Msa0765500:CDS 50.0%
GTGCTTGCAAGTTCTTGAGG+AGG + chr5_2:26548396-26548415 Msa0765500:CDS 50.0%
!! CCCTACTTTGGTACTGACCA+AGG + chr5_2:26548446-26548465 Msa0765500:CDS 50.0%
!! CCAAGGTGCTGCTAAGTTTG+CGG + chr5_2:26548463-26548482 Msa0765500:intron 50.0%
TAAGTTTGCGGCTGTGCACA+AGG + chr5_2:26548475-26548494 Msa0765500:intron 50.0%
AGCTTCATGGCGATGGTTAG+CGG - chr5_2:26548543-26548562 None:intergenic 50.0%
TAACCATCGCCATGAAGCTG+CGG + chr5_2:26548544-26548563 Msa0765500:intron 50.0%
AAATAGTCGCCGCAGCTTCA+TGG - chr5_2:26548556-26548575 None:intergenic 50.0%
TGCGGCGACTATTTCCTATG+AGG + chr5_2:26548562-26548581 Msa0765500:CDS 50.0%
TAGCCTAGCTTGAGCCTCAT+AGG - chr5_2:26548579-26548598 None:intergenic 50.0%
! TCAAGCTAGGCTAGCTGATC+CGG + chr5_2:26548586-26548605 Msa0765500:CDS 50.0%
! AGGCTAGCTGATCCGGTTTA+TGG + chr5_2:26548593-26548612 Msa0765500:CDS 50.0%
TCTTGCTTTGCAGCAACAGG+TGG + chr5_2:26548631-26548650 Msa0765500:intron 50.0%
TGCCACCTGAATCAGCCATA+AGG - chr5_2:26548749-26548768 None:intergenic 50.0%
TTGAAACGGCGGCTGATATG+GGG - chr5_2:26548854-26548873 None:intergenic 50.0%
GGCTGCACAAATTGAAACGG+CGG - chr5_2:26548865-26548884 None:intergenic 50.0%
GGTGGAAGCAGATGAGTTGT+TGG - chr5_2:26548896-26548915 None:intergenic 50.0%
CCATTGTGAGGCCAAAACCA+GGG - chr5_2:26548948-26548967 None:intergenic 50.0%
TCCATTGTGAGGCCAAAACC+AGG - chr5_2:26548949-26548968 None:intergenic 50.0%
CCGCAAACTTAGCAGCACCT+TGG - chr5_2:26548466-26548485 None:intergenic 55.0%
GCTTCATGGCGATGGTTAGC+GGG - chr5_2:26548542-26548561 None:intergenic 55.0%
!!! CCCTGGTTTTGGCCTCACAA+TGG + chr5_2:26548945-26548964 Msa0765500:CDS 55.0%
! GCGGCTGTGCACAAGGTGTT+TGG + chr5_2:26548482-26548501 Msa0765500:intron 60.0%
GGTGGCAGCTATGCAAGCAG+AGG + chr5_2:26548762-26548781 Msa0765500:intron 60.0%
TCGCCGCAGCTTCATGGCGA+TGG - chr5_2:26548550-26548569 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 26548365 26548996 26548365 ID=Msa0765500;Name=Msa0765500
chr5_2 mRNA 26548365 26548996 26548365 ID=Msa0765500-mRNA-1;Parent=Msa0765500;Name=Msa0765500-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|3|0|141
chr5_2 exon 26548365 26548467 26548365 ID=Msa0765500-mRNA-1:exon:10498;Parent=Msa0765500-mRNA-1
chr5_2 exon 26548561 26548649 26548561 ID=Msa0765500-mRNA-1:exon:10499;Parent=Msa0765500-mRNA-1
chr5_2 exon 26548763 26548996 26548763 ID=Msa0765500-mRNA-1:exon:10500;Parent=Msa0765500-mRNA-1
chr5_2 CDS 26548365 26548467 26548365 ID=Msa0765500-mRNA-1:cds;Parent=Msa0765500-mRNA-1
chr5_2 CDS 26548561 26548649 26548561 ID=Msa0765500-mRNA-1:cds;Parent=Msa0765500-mRNA-1
chr5_2 CDS 26548763 26548996 26548763 ID=Msa0765500-mRNA-1:cds;Parent=Msa0765500-mRNA-1
Gene Sequence

>Msa0765500

TTGATAGATGAACCGGTTATATCTCCGTGTGGTGCTTGCAAGTTCTTGAGGAGGAAGTGTAGTAGTGGATGCATCTTTGCACCCTACTTTGGTACTGACCAAGCTGCGGCGACTATTTCCTATGAGGCTCAAGCTAGGCTAGCTGATCCGGTTTATGGTTGTGTGTCCACCATTCTTGCTTTGCAGCAACAGGTGGCAGCTATGCAAGCAGAGGTCTCAATGATGCAAACTCAATTGATGAATAAGAGGCTTGCATATGCAAATGCAAGTACTCTTCAAACCCCATATCAGCCGCCGTTTCAATTTGTGCAGCCAGCATATTCCAACAACTCATCTGCTTCCACCACCAACCTTATGAATATGAACAACTTCAACCCTGGTTTTGGCCTCACAATGGAGACAACACCTTCATCACAGAGCTTGTAG
Protein sequence

>Msa0765500

LIDEPVISPCGACKFLRRKCSSGCIFAPYFGTDQAAATISYEAQARLADPVYGCVSTILALQQQVAAMQAEVSMMQTQLMNKRLAYANASTLQTPYQPPFQFVQPAYSNNSSASTTNLMNMNNFNPGFGLTMETTPSSQSL*