AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0830500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0830500 MtrunA17_Chr1g0169581 66.901 142 44 2 1 139 1 142 5.86e-57 174
Msa0830500 MtrunA17_Chr5g0396261 73.913 115 28 1 27 139 1 115 1.43e-53 164
Msa0830500 MtrunA17_Chr5g0434951 64.748 139 43 3 1 136 1 136 2.14e-51 159
Msa0830500 MtrunA17_Chr1g0169621 56.098 164 44 2 1 136 1 164 1.49e-50 158
Msa0830500 MtrunA17_Chr3g0111371 53.957 139 59 2 2 139 3 137 2.69e-45 144
Msa0830500 MtrunA17_Chr8g0392951 46.667 135 70 2 3 136 23 156 4.53e-31 108
Msa0830500 MtrunA17_Chr6g0482731 45.652 138 72 3 3 138 25 161 2.22e-29 105
Msa0830500 MtrunA17_Chr1g0161211 37.692 130 80 1 8 136 50 179 1.09e-22 88.6
Msa0830500 MtrunA17_Chr8g0351681 43.165 139 68 5 8 136 53 190 1.93e-19 80.1
Msa0830500 MtrunA17_Chr8g0391691 32.812 128 85 1 8 134 40 167 2.01e-19 79.7
Msa0830500 MtrunA17_Chr7g0245911 37.671 146 81 5 1 136 44 189 1.94e-17 74.7
Msa0830500 MtrunA17_Chr4g0033601 34.091 132 84 2 8 136 9 140 3.28e-17 73.2
Msa0830500 MtrunA17_Chr7g0256171 35.507 138 86 2 2 136 3 140 3.54e-17 73.2
Msa0830500 MtrunA17_Chr6g0459231 34.615 130 83 2 8 136 12 140 9.85e-16 68.9
Msa0830500 MtrunA17_Chr1g0166281 33.094 139 89 2 2 136 7 145 1.80e-15 68.6
Msa0830500 MtrunA17_Chr5g0440931 30.233 129 89 1 9 136 17 145 1.74e-14 65.9
Msa0830500 MtrunA17_Chr6g0460211 30.233 129 89 1 9 136 17 145 1.87e-14 65.9
Msa0830500 MtrunA17_Chr7g0245371 33.562 146 84 4 4 136 24 169 2.69e-14 66.2
Msa0830500 MtrunA17_Chr5g0402331 31.429 140 87 4 2 136 46 181 3.33e-14 66.2
Msa0830500 MtrunA17_Chr7g0254731 29.457 129 90 1 9 136 17 145 3.74e-14 65.1
Msa0830500 MtrunA17_Chr3g0093271 30.088 113 79 0 24 136 84 196 7.78e-14 65.5
Msa0830500 MtrunA17_Chr5g0402361 31.429 140 87 4 2 136 218 353 1.05e-13 66.6
Msa0830500 MtrunA17_Chr5g0402361 30.435 138 90 3 2 136 46 180 6.76e-12 61.6
Msa0830500 MtrunA17_Chr7g0225921 31.298 131 87 3 8 136 10 139 2.62e-13 62.8
Msa0830500 MtrunA17_Chr3g0121191 32.927 82 55 0 55 136 135 216 4.22e-13 63.9
Msa0830500 MtrunA17_Chr4g0044961 31.884 138 91 2 3 139 56 191 5.82e-13 63.2
Msa0830500 MtrunA17_Chr1g0188171 30.233 129 89 1 9 136 17 145 1.10e-12 61.2
Msa0830500 MtrunA17_Chr3g0116151 30.328 122 84 1 15 136 18 138 4.00e-12 59.7
Msa0830500 MtrunA17_Chr3g0116141 30.328 122 84 1 15 136 17 137 4.05e-12 59.7
Msa0830500 MtrunA17_Chr8g0387671 32.174 115 72 3 24 136 392 502 6.18e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0830500 AT1G18210.2 46.212 132 66 2 8 138 27 154 6.03e-32 112
Msa0830500 AT1G18210.1 46.212 132 66 2 8 138 27 154 6.03e-32 112
Msa0830500 AT1G66400.1 42.958 142 71 4 1 136 13 150 9.03e-28 100
Msa0830500 AT1G73630.1 42.308 130 70 2 8 136 24 149 5.86e-26 96.3
Msa0830500 AT5G37770.1 41.844 141 77 3 3 138 16 156 1.85e-25 95.1
Msa0830500 AT5G37770.2 41.844 141 77 3 3 138 16 156 1.85e-25 95.1
Msa0830500 AT5G17470.1 39.568 139 77 3 5 138 3 139 2.04e-22 86.7
Msa0830500 AT1G24620.1 35.606 132 84 1 8 138 41 172 1.41e-21 85.9
Msa0830500 AT2G36180.1 39.855 138 75 3 5 136 1 136 2.68e-20 81.3
Msa0830500 AT3G07490.1 37.500 136 82 2 4 136 5 140 5.56e-19 78.2
Msa0830500 AT2G15680.1 36.842 133 79 3 8 138 54 183 1.01e-18 78.2
Msa0830500 AT1G66410.4 30.275 109 76 0 28 136 1 109 2.90e-15 67.4
Msa0830500 AT1G66410.3 30.275 109 76 0 28 136 1 109 2.90e-15 67.4
Msa0830500 AT3G03400.1 33.333 129 83 2 5 130 6 134 3.62e-15 67.8
Msa0830500 AT1G05990.1 35.338 133 82 3 8 136 9 141 3.65e-15 68.2
Msa0830500 AT5G37780.4 30.088 113 79 0 24 136 20 132 5.72e-15 67.4
Msa0830500 AT1G66410.1 30.233 129 89 1 9 136 17 145 7.13e-15 67.4
Msa0830500 AT5G37780.1 30.233 129 89 1 9 136 17 145 7.13e-15 67.4
Msa0830500 AT1G66410.2 30.000 110 77 0 27 136 46 155 9.87e-15 67.4
Msa0830500 AT3G43810.4 30.275 109 76 0 28 136 1 109 1.01e-14 66.2
Msa0830500 AT3G43810.3 30.275 109 76 0 28 136 1 109 1.01e-14 66.2
Msa0830500 AT5G37780.2 30.088 113 79 0 24 136 48 160 1.35e-14 67.0
Msa0830500 AT5G37780.3 30.000 110 77 0 27 136 62 171 1.60e-14 67.0
Msa0830500 AT4G37010.1 32.143 112 76 0 28 139 52 163 2.05e-14 66.6
Msa0830500 AT4G37010.2 32.143 112 76 0 28 139 56 167 2.05e-14 66.6
Msa0830500 AT3G56800.1 30.233 129 89 1 9 136 17 145 2.48e-14 65.9
Msa0830500 AT2G41110.1 30.233 129 89 1 9 136 17 145 2.48e-14 65.9
Msa0830500 AT2G27030.1 30.233 129 89 1 9 136 17 145 2.48e-14 65.9
Msa0830500 AT3G43810.1 30.233 129 89 1 9 136 17 145 2.58e-14 65.9
Msa0830500 AT5G21274.1 30.233 129 89 1 9 136 17 145 2.61e-14 65.9
Msa0830500 AT2G41110.2 30.088 113 79 0 24 136 45 157 3.51e-14 65.9
Msa0830500 AT2G27030.3 30.233 129 89 1 9 136 17 145 5.21e-14 65.9
Msa0830500 AT4G12860.1 33.088 136 88 2 4 136 5 140 1.10e-13 64.3
Msa0830500 AT3G43810.2 30.233 129 89 1 9 136 17 145 1.32e-13 65.5
Msa0830500 AT3G59440.1 32.353 136 80 4 8 136 55 185 3.86e-13 63.9
Msa0830500 AT2G43290.1 32.117 137 85 3 8 136 69 205 4.49e-13 63.9
Msa0830500 AT3G22930.1 32.673 101 68 0 36 136 68 168 6.01e-13 62.8
Msa0830500 AT4G03290.1 31.159 138 89 3 8 139 9 146 5.33e-12 60.1
Msa0830500 AT3G50360.1 31.481 108 74 0 32 139 56 163 1.13e-11 59.3
Msa0830500 AT4G14640.2 30.693 101 70 0 36 136 28 128 5.18e-11 57.0
Msa0830500 AT4G20780.1 29.870 154 87 3 4 136 29 182 6.95e-11 57.8
Msa0830500 AT4G14640.1 29.457 129 90 1 9 136 18 146 8.02e-11 57.0
Msa0830500 AT4G23650.1 29.927 137 85 5 8 139 387 517 9.72e-11 58.5

Find 22 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCACCAGATGTCATTT+TGG 0.229870 5_4:+3566766 None:intergenic
AGAACGATGTGCAGCTCTTT+TGG 0.236543 5_4:+3566584 None:intergenic
CCATTCTCTGAAAGTCATTT+AGG 0.343643 5_4:+3566537 None:intergenic
TGACAGAAATGTTAACTTTG+AGG 0.402956 5_4:-3566492 Msa0830500:CDS
TGGAACAGATTGATCAGAAC+GGG 0.406577 5_4:-3566733 Msa0830500:CDS
CACATCGTTCTTAATAAACT+TGG 0.408468 5_4:-3566572 Msa0830500:CDS
CCTAAATGACTTTCAGAGAA+TGG 0.410572 5_4:-3566537 Msa0830500:CDS
AAAGATCTTTGTCTTAGTGC+TGG 0.471542 5_4:-3566813 Msa0830500:CDS
CGTCCTTGTCGAGGTTGTAA+AGG 0.474104 5_4:+3566618 None:intergenic
AGCATAAGTGCAGTGAAAAT+CGG 0.476853 5_4:+3566682 None:intergenic
CATGGATCCAAAATGACATC+TGG 0.486416 5_4:-3566773 Msa0830500:CDS
CAACTACGCCATGGAAGATA+AGG 0.490365 5_4:-3566873 None:intergenic
TGCACTTATGCTGCTGCTGT+CGG 0.530962 5_4:-3566671 Msa0830500:CDS
TGGTGAAGCAAAACGCATGA+TGG 0.544746 5_4:-3566753 Msa0830500:CDS
GAAGAAATGCTTTCAACGCA+TGG 0.563370 5_4:-3566791 Msa0830500:CDS
GTTACACACCTTATCTTCCA+TGG 0.568028 5_4:+3566865 None:intergenic
ATGGAACAGATTGATCAGAA+CGG 0.603193 5_4:-3566734 Msa0830500:CDS
CGACCTTTACAACCTCGACA+AGG 0.609704 5_4:-3566621 Msa0830500:CDS
CTTTACAACCTCGACAAGGA+CGG 0.615705 5_4:-3566617 Msa0830500:CDS
AGATGAGACCGTCCTTGTCG+AGG 0.627789 5_4:+3566609 None:intergenic
AAAGGTCGAAAGCATCGTGA+AGG 0.659870 5_4:+3566636 None:intergenic
GGAACAGATTGATCAGAACG+GGG 0.750470 5_4:-3566732 Msa0830500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CACATCGTTCTTAATAAACT+TGG - chr5_4:3566757-3566776 Msa0830500:CDS 30.0%
TGACAGAAATGTTAACTTTG+AGG - chr5_4:3566837-3566856 Msa0830500:CDS 30.0%
AAAGATCTTTGTCTTAGTGC+TGG - chr5_4:3566516-3566535 Msa0830500:CDS 35.0%
ATGGAACAGATTGATCAGAA+CGG - chr5_4:3566595-3566614 Msa0830500:CDS 35.0%
AGCATAAGTGCAGTGAAAAT+CGG + chr5_4:3566650-3566669 None:intergenic 35.0%
! CCATTCTCTGAAAGTCATTT+AGG + chr5_4:3566795-3566814 None:intergenic 35.0%
CCTAAATGACTTTCAGAGAA+TGG - chr5_4:3566792-3566811 Msa0830500:CDS 35.0%
GAAGAAATGCTTTCAACGCA+TGG - chr5_4:3566538-3566557 Msa0830500:CDS 40.0%
CATGGATCCAAAATGACATC+TGG - chr5_4:3566556-3566575 Msa0830500:CDS 40.0%
!! TGCTTCACCAGATGTCATTT+TGG + chr5_4:3566566-3566585 None:intergenic 40.0%
TGGAACAGATTGATCAGAAC+GGG - chr5_4:3566596-3566615 Msa0830500:CDS 40.0%
TGGTGAAGCAAAACGCATGA+TGG - chr5_4:3566576-3566595 Msa0830500:CDS 45.0%
GGAACAGATTGATCAGAACG+GGG - chr5_4:3566597-3566616 Msa0830500:CDS 45.0%
!! AAAGGTCGAAAGCATCGTGA+AGG + chr5_4:3566696-3566715 None:intergenic 45.0%
CTTTACAACCTCGACAAGGA+CGG - chr5_4:3566712-3566731 Msa0830500:CDS 45.0%
! AGAACGATGTGCAGCTCTTT+TGG + chr5_4:3566748-3566767 None:intergenic 45.0%
TGCACTTATGCTGCTGCTGT+CGG - chr5_4:3566658-3566677 Msa0830500:CDS 50.0%
CGACCTTTACAACCTCGACA+AGG - chr5_4:3566708-3566727 Msa0830500:CDS 50.0%
CGTCCTTGTCGAGGTTGTAA+AGG + chr5_4:3566714-3566733 None:intergenic 50.0%
AGATGAGACCGTCCTTGTCG+AGG + chr5_4:3566723-3566742 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 3566466 3566885 3566466 ID=Msa0830500;Name=Msa0830500
chr5_4 mRNA 3566466 3566885 3566466 ID=Msa0830500-mRNA-1;Parent=Msa0830500;Name=Msa0830500-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|139
chr5_4 exon 3566466 3566885 3566466 ID=Msa0830500-mRNA-1:exon:1425;Parent=Msa0830500-mRNA-1
chr5_4 CDS 3566466 3566885 3566466 ID=Msa0830500-mRNA-1:cds;Parent=Msa0830500-mRNA-1
Gene Sequence

>Msa0830500

ATGGAAGATAAGGTGTGTAACATCTTCATCAAGTTCGACAAGAACAACAGAAAGATCTTTGTCTTAGTGCTGGAAGAAATGCTTTCAACGCATGGATCCAAAATGACATCTGGTGAAGCAAAACGCATGATGGAACAGATTGATCAGAACGGGGACTGTTACATTGATCTCAAAGAATTCACCGATTTTCACTGCACTTATGCTGCTGCTGTCGGAAAAGACGACGACCTTCACGATGCTTTCGACCTTTACAACCTCGACAAGGACGGTCTCATCTCTCCAAAAGAGCTGCACATCGTTCTTAATAAACTTGGTGAGAAGTGCTGCCTAAATGACTTTCAGAGAATGGTTAGCAGCGTCGATGCTGACTGTGACAGAAATGTTAACTTTGAGGAATTCAAGAAGATGACGACTCGTTGA

Protein sequence

>Msa0830500

MEDKVCNIFIKFDKNNRKIFVLVLEEMLSTHGSKMTSGEAKRMMEQIDQNGDCYIDLKEFTDFHCTYAAAVGKDDDLHDAFDLYNLDKDGLISPKELHIVLNKLGEKCCLNDFQRMVSSVDADCDRNVNFEEFKKMTTR*