AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1116260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1116260 MtrunA17_Chr1g0184031 71.429 119 9 1 1 94 78 196 2.24e-50 158
Msa1116260 MtrunA17_Chr1g0184011 70.000 120 10 2 1 94 78 197 8.56e-49 154
Msa1116260 MtrunA17_Chr1g0183981 65.833 120 14 3 1 94 70 188 2.55e-43 140
Msa1116260 MtrunA17_Chr1g0184071 63.636 99 11 1 3 76 65 163 7.85e-34 115
Msa1116260 MtrunA17_Chr1g0184061 60.606 99 13 2 1 74 72 169 1.81e-29 105
Msa1116260 MtrunA17_Chr4g0026881 43.636 110 33 2 9 90 99 207 4.72e-21 84.0
Msa1116260 MtrunA17_Chr2g0283171 69.231 52 16 0 4 55 60 111 2.91e-20 79.7
Msa1116260 MtrunA17_Chr4g0046161 64.151 53 19 0 3 55 53 105 1.10e-19 77.4
Msa1116260 MtrunA17_Chr4g0026931 77.273 44 10 0 9 52 133 176 6.74e-19 78.6
Msa1116260 MtrunA17_Chr8g0335311 71.429 49 14 0 7 55 96 144 7.95e-19 77.0
Msa1116260 MtrunA17_Chr1g0196871 75.510 49 12 0 7 55 16 64 1.17e-18 74.3
Msa1116260 MtrunA17_Chr1g0186671 64.151 53 19 0 7 59 19 71 1.49e-18 75.1
Msa1116260 MtrunA17_Chr2g0283181 69.388 49 15 0 7 55 149 197 3.28e-18 77.0
Msa1116260 MtrunA17_Chr7g0261151 55.882 68 29 1 1 68 14 80 3.78e-18 73.9
Msa1116260 MtrunA17_Chr1g0184081 71.429 49 14 0 7 55 21 69 4.65e-18 73.9
Msa1116260 MtrunA17_Chr8g0335331 69.388 49 15 0 7 55 125 173 6.45e-18 74.7
Msa1116260 MtrunA17_Chr7g0221501 59.375 64 24 2 4 67 48 109 9.73e-18 73.9
Msa1116260 MtrunA17_Chr4g0055761 69.388 49 15 0 7 55 145 193 9.88e-18 75.5
Msa1116260 MtrunA17_Chr7g0261101 57.353 68 28 1 1 68 14 80 1.28e-17 72.8
Msa1116260 MtrunA17_Chr1g0186731 68.085 47 15 0 9 55 23 69 2.52e-17 72.0
Msa1116260 MtrunA17_Chr4g0055801 64.151 53 19 0 3 55 150 202 5.78e-17 73.9
Msa1116260 MtrunA17_Chr4g0055781 62.264 53 20 0 3 55 98 150 8.14e-17 72.8
Msa1116260 MtrunA17_Chr7g0221471 59.375 64 24 2 4 67 48 109 8.52e-17 71.2
Msa1116260 MtrunA17_Chr1g0170531 67.347 49 16 0 7 55 89 137 1.12e-16 72.0
Msa1116260 MtrunA17_Chr7g0250721 67.347 49 16 0 7 55 61 109 1.35e-16 71.6
Msa1116260 MtrunA17_Chr7g0250731 67.347 49 16 0 7 55 61 109 1.36e-16 71.6
Msa1116260 MtrunA17_Chr1g0186681 55.556 63 26 2 7 68 19 80 1.05e-15 67.4
Msa1116260 MtrunA17_Chr1g0186741 46.218 119 34 2 3 94 69 184 1.05e-15 69.3
Msa1116260 MtrunA17_Chr8g0335321 61.224 49 19 0 7 55 96 144 1.54e-15 68.9
Msa1116260 MtrunA17_Chr7g0250711 63.265 49 18 0 7 55 60 108 1.72e-15 68.6
Msa1116260 MtrunA17_Chr4g0062551 59.184 49 19 1 7 55 53 100 2.78e-15 66.6
Msa1116260 MtrunA17_Chr2g0282621 62.963 54 19 1 2 55 10 62 3.20e-15 67.4
Msa1116260 MtrunA17_Chr7g0253424 53.704 54 24 1 2 55 34 86 8.70e-15 67.8
Msa1116260 MtrunA17_Chr4g0062161 59.184 49 19 1 7 55 53 100 9.49e-15 66.6
Msa1116260 MtrunA17_Chr8g0378811 54.545 55 24 1 1 55 49 102 1.20e-14 67.4
Msa1116260 MtrunA17_Chr1g0167781 80.000 50 10 0 6 55 81 130 1.61e-14 66.2
Msa1116260 MtrunA17_Chr6g0453661 59.184 49 19 1 7 55 38 85 1.79e-14 67.4
Msa1116260 MtrunA17_Chr6g0461271 59.184 49 19 1 7 55 33 80 1.91e-14 67.0
Msa1116260 MtrunA17_Chr7g0252381 65.306 49 16 1 7 55 42 89 1.93e-14 66.6
Msa1116260 MtrunA17_Chr1g0170471 71.429 42 12 0 14 55 90 131 1.97e-14 65.1
Msa1116260 MtrunA17_Chr8g0367911 65.306 49 16 1 7 55 44 91 2.64e-14 66.6
Msa1116260 MtrunA17_Chr7g0217991 57.143 49 20 1 7 55 42 89 4.51e-14 66.2
Msa1116260 MtrunA17_Chr7g0261171 50.000 96 41 2 3 98 81 169 7.32e-14 64.7
Msa1116260 MtrunA17_Chr2g0297331 61.224 49 19 0 7 55 14 62 1.10e-13 62.4
Msa1116260 MtrunA17_Chr4g0066931 55.556 54 23 1 2 55 48 100 1.11e-13 65.1
Msa1116260 MtrunA17_Chr7g0261201 46.465 99 25 1 3 73 94 192 1.55e-13 63.9
Msa1116260 MtrunA17_Chr5g0396911 63.265 49 17 1 7 55 112 159 1.62e-13 64.3
Msa1116260 MtrunA17_Chr8g0383591 61.538 52 19 1 4 55 142 192 2.00e-13 64.3
Msa1116260 MtrunA17_Chr2g0316931 68.889 45 13 1 7 51 31 74 2.03e-13 63.2
Msa1116260 MtrunA17_Chr4g0044871 65.306 49 16 1 7 55 96 143 2.12e-13 63.5
Msa1116260 MtrunA17_Chr1g0184041 80.488 41 7 1 55 94 27 67 2.15e-13 62.8
Msa1116260 MtrunA17_Chr5g0412641 65.306 49 16 1 7 55 46 93 2.56e-13 64.3
Msa1116260 MtrunA17_Chr5g0438831 63.265 49 17 1 7 55 46 93 2.90e-13 63.5
Msa1116260 MtrunA17_Chr4g0044911 65.306 49 16 1 7 55 96 143 3.08e-13 63.2
Msa1116260 MtrunA17_Chr3g0126321 54.545 55 24 1 1 55 107 160 3.19e-13 63.9
Msa1116260 MtrunA17_Chr5g0438801 63.265 49 17 1 7 55 51 98 4.01e-13 63.2
Msa1116260 MtrunA17_Chr1g0183931 33.333 126 56 2 4 101 98 223 4.02e-13 62.8
Msa1116260 MtrunA17_Chr4g0044881 60.377 53 20 1 3 55 110 161 4.29e-13 62.8
Msa1116260 MtrunA17_Chr4g0044901 65.306 49 16 1 7 55 96 143 5.32e-13 62.4
Msa1116260 MtrunA17_Chr2g0282651 61.224 49 18 1 3 51 66 113 5.97e-13 62.4
Msa1116260 MtrunA17_Chr2g0286161 55.102 49 21 1 7 55 50 97 6.97e-13 62.8
Msa1116260 MtrunA17_Chr1g0195151 59.615 52 20 1 4 55 74 124 7.97e-13 62.4
Msa1116260 MtrunA17_Chr4g0042761 59.184 49 19 1 7 55 48 95 9.08e-13 62.4
Msa1116260 MtrunA17_Chr2g0334031 59.615 52 20 1 4 55 114 164 9.27e-13 62.4
Msa1116260 MtrunA17_Chr8g0375031 43.529 85 44 2 4 85 122 205 9.65e-13 61.6
Msa1116260 MtrunA17_Chr3g0099871 42.593 108 44 5 7 97 27 133 9.84e-13 61.6
Msa1116260 MtrunA17_Chr7g0261181 61.111 54 21 0 2 55 8 61 1.15e-12 59.7
Msa1116260 MtrunA17_Chr8g0344961 62.500 48 17 1 4 51 121 167 1.23e-12 62.4
Msa1116260 MtrunA17_Chr2g0295421 59.615 52 20 1 4 55 93 143 1.98e-12 61.2
Msa1116260 MtrunA17_Chr1g0200931 64.286 42 14 1 7 48 23 63 2.24e-12 59.3
Msa1116260 MtrunA17_Chr1g0183961 67.347 49 16 0 7 55 27 75 2.40e-12 59.3
Msa1116260 MtrunA17_Chr5g0437371 54.717 53 23 1 2 54 61 112 2.90e-12 61.2
Msa1116260 MtrunA17_Chr2g0324131 61.224 49 18 1 7 55 218 265 3.66e-12 60.8
Msa1116260 MtrunA17_Chr5g0432821 56.000 50 21 1 5 54 122 170 4.21e-12 60.5
Msa1116260 MtrunA17_Chr1g0196781 57.143 49 20 1 7 55 152 199 5.30e-12 60.5
Msa1116260 MtrunA17_Chr8g0350701 53.061 49 22 1 7 55 27 74 7.23e-12 59.7
Msa1116260 MtrunA17_Chr5g0425561 56.604 53 22 1 7 59 173 224 8.37e-12 59.7
Msa1116260 MtrunA17_Chr3g0115631 56.604 53 22 1 7 59 150 201 8.90e-12 59.7
Msa1116260 MtrunA17_Chr8g0382491 56.604 53 22 1 7 59 113 164 1.38e-11 58.9
Msa1116260 MtrunA17_Chr4g0063751 53.704 54 24 1 1 54 1 53 2.53e-11 57.8
Msa1116260 MtrunA17_Chr4g0023411 54.717 53 23 1 2 54 60 111 3.79e-11 57.0
Msa1116260 MtrunA17_Chr1g0189941 54.000 50 22 1 2 51 19 67 7.78e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1116260 AT3G23240.1 49.505 101 26 1 6 81 81 181 4.24e-24 91.7
Msa1116260 AT2G31230.1 47.872 94 23 1 1 68 80 173 7.67e-21 83.6
Msa1116260 AT5G43410.1 66.038 53 18 0 3 55 11 63 4.64e-19 76.6
Msa1116260 AT4G17500.1 71.429 49 14 0 7 55 148 196 4.26e-18 77.0
Msa1116260 AT5G47220.1 71.429 49 14 0 7 55 117 165 6.63e-18 75.9
Msa1116260 AT5G47230.1 64.151 53 19 0 3 55 152 204 2.39e-17 75.1
Msa1116260 AT4G18450.1 69.388 49 15 0 7 55 110 158 4.05e-17 74.7
Msa1116260 AT5G51190.1 61.111 54 21 0 2 55 67 120 7.46e-17 72.8
Msa1116260 AT2G44840.1 65.306 49 17 0 7 55 92 140 7.65e-17 72.8
Msa1116260 AT3G23230.1 57.407 54 23 0 2 55 15 68 2.39e-16 69.7
Msa1116260 AT4G17490.1 64.151 53 19 0 3 55 133 185 2.48e-16 72.4
Msa1116260 AT5G61600.1 63.265 49 18 0 7 55 88 136 5.11e-16 70.9
Msa1116260 AT1G28360.1 45.977 87 41 2 7 88 12 97 5.51e-16 70.1
Msa1116260 AT5G07580.1 65.306 49 17 0 7 55 110 158 1.72e-15 68.9
Msa1116260 AT2G33710.1 66.000 50 16 1 6 55 69 117 1.72e-15 69.3
Msa1116260 AT2G33710.2 66.000 50 16 1 6 55 69 117 2.37e-15 68.9
Msa1116260 AT5G19790.1 57.692 52 21 1 4 55 19 69 3.91e-15 68.6
Msa1116260 AT5G13910.1 65.306 49 16 1 7 55 20 67 5.77e-15 67.8
Msa1116260 AT3G16770.1 63.462 52 18 1 4 55 76 126 1.31e-14 67.4
Msa1116260 AT5G18560.1 63.265 49 17 1 7 55 55 102 1.41e-14 68.2
Msa1116260 AT1G28160.1 63.265 49 17 1 7 55 39 86 2.30e-14 66.6
Msa1116260 AT4G11140.1 49.351 77 33 3 9 81 89 163 6.88e-14 65.9
Msa1116260 AT5G13330.1 55.738 61 25 2 7 67 39 97 8.22e-14 64.7
Msa1116260 AT5G61890.1 57.377 61 24 2 7 67 90 148 1.46e-13 64.3
Msa1116260 AT4G27950.1 61.111 54 19 2 2 55 114 165 1.56e-13 65.1
Msa1116260 AT1G06160.1 50.562 89 18 1 6 68 81 169 2.25e-13 63.9
Msa1116260 AT3G15210.1 68.889 45 13 1 7 51 25 68 2.89e-13 63.2
Msa1116260 AT1G24590.1 65.306 49 16 1 7 55 58 105 3.68e-13 63.9
Msa1116260 AT1G12890.1 59.184 49 19 1 3 51 17 64 4.22e-13 62.8
Msa1116260 AT5G44210.1 60.784 51 19 1 1 51 27 76 4.97e-13 62.4
Msa1116260 AT5G53290.1 56.604 53 22 1 3 55 121 172 6.03e-13 63.5
Msa1116260 AT3G23220.1 75.510 49 12 0 7 55 14 62 6.56e-13 60.8
Msa1116260 AT1G22190.1 46.250 80 34 3 7 82 83 157 6.61e-13 62.8
Msa1116260 AT1G28370.1 63.265 49 17 1 7 55 20 67 7.09e-13 61.2
Msa1116260 AT1G72360.1 46.154 78 40 2 3 80 21 96 8.06e-13 62.0
Msa1116260 AT1G28370.2 63.265 49 17 1 7 55 58 105 8.68e-13 61.6
Msa1116260 AT2G47520.1 56.604 53 22 1 3 55 46 97 9.76e-13 61.2
Msa1116260 AT3G61630.1 59.184 49 19 1 7 55 105 152 1.09e-12 62.8
Msa1116260 AT3G20310.1 65.306 49 16 1 7 55 27 74 1.16e-12 62.0
Msa1116260 AT1G75490.1 52.381 63 26 2 2 64 37 95 1.79e-12 60.8
Msa1116260 AT1G72360.2 46.154 78 40 2 3 80 72 147 1.84e-12 61.6
Msa1116260 AT1G72360.3 46.154 78 40 2 3 80 70 145 1.85e-12 61.6
Msa1116260 AT1G12980.1 63.265 49 17 1 7 55 57 104 1.98e-12 62.0
Msa1116260 AT1G50640.1 66.667 45 14 1 7 51 28 71 3.55e-12 60.5
Msa1116260 AT1G03800.1 59.184 49 19 1 7 55 53 100 3.59e-12 60.8
Msa1116260 AT1G22985.1 55.556 54 22 1 3 54 71 124 3.93e-12 59.3
Msa1116260 AT1G04370.1 64.103 39 14 0 3 41 16 54 4.64e-12 58.5
Msa1116260 AT4G13620.1 42.500 80 41 2 7 82 232 310 4.65e-12 60.8
Msa1116260 AT2G22200.1 59.615 52 20 1 4 55 68 118 7.82e-12 60.1
Msa1116260 AT1G78080.1 56.604 53 22 1 7 59 152 203 1.06e-11 60.1
Msa1116260 AT1G36060.1 61.224 49 18 1 7 55 143 190 1.36e-11 59.7
Msa1116260 AT4G23750.2 51.923 52 24 1 4 55 119 169 1.45e-11 59.7
Msa1116260 AT4G23750.1 51.923 52 24 1 4 55 119 169 1.45e-11 59.7
Msa1116260 AT2G46310.1 57.143 49 20 1 7 55 99 146 1.51e-11 59.3
Msa1116260 AT4G28140.1 39.560 91 53 2 7 97 143 231 1.65e-11 59.3
Msa1116260 AT4G39780.1 50.847 59 28 1 1 59 87 144 5.98e-11 57.4

Find 15 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCCTTGAGTGCAAGTTC+AGG 0.358098 7_3:-63871242 None:intergenic
AATCAAAAGTCTTCATATAT+AGG 0.378865 7_3:+63870995 Msa1116260:CDS
TAGTGTTGAGGATGCTGCTT+TGG 0.421410 7_3:+63871105 Msa1116260:CDS
CAAGAAGAGGAAGAAGGGTT+TGG 0.446404 7_3:+63871068 Msa1116260:CDS
TTCACCTGAACTTGCACTCA+AGG 0.465842 7_3:+63871238 Msa1116260:CDS
CAGAGGGATCAAGTGTCACT+TGG 0.491015 7_3:+63871330 Msa1116260:CDS
ATCAGAGACACAACAAGAAG+AGG 0.520617 7_3:+63871055 Msa1116260:CDS
AGAGGAAGAAGGGTTTGGCT+TGG 0.531425 7_3:+63871073 Msa1116260:CDS
ACACAACAAGAAGAGGAAGA+AGG 0.533196 7_3:+63871062 Msa1116260:CDS
CACAACAAGAAGAGGAAGAA+GGG 0.536520 7_3:+63871063 Msa1116260:CDS
AGAGGGATCAAGTGTCACTT+GGG 0.601330 7_3:+63871331 Msa1116260:CDS
TGGAACATTTGATAGTGTTG+AGG 0.606632 7_3:+63871093 Msa1116260:CDS
CAAAGAAAGATGTTATCCAA+AGG 0.625682 7_3:+63871275 Msa1116260:CDS
GGGAAACAAGATCAATCAGA+GGG 0.639790 7_3:+63871314 Msa1116260:CDS
AGGGAAACAAGATCAATCAG+AGG 0.654836 7_3:+63871313 Msa1116260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAAAAGTCTTCATATAT+AGG + chr7_3:63870995-63871014 Msa1116260:CDS 20.0%
!!! TGCTTTATTTTTTACACCTT+TGG - chr7_3:63871294-63871313 None:intergenic 25.0%
!! AAAGGTGTAAAAAATAAAGC+AGG + chr7_3:63871293-63871312 Msa1116260:CDS 25.0%
! AAGGTGTAAAAAATAAAGCA+GGG + chr7_3:63871294-63871313 Msa1116260:CDS 25.0%
! TGCTCAATTTTTCTGTTCAA+AGG + chr7_3:63871170-63871189 Msa1116260:intron 30.0%
! GCTCAATTTTTCTGTTCAAA+GGG + chr7_3:63871171-63871190 Msa1116260:intron 30.0%
AGATTCAATATGATTGCAGA+GGG + chr7_3:63871212-63871231 Msa1116260:intron 30.0%
CAAAGAAAGATGTTATCCAA+AGG + chr7_3:63871275-63871294 Msa1116260:CDS 30.0%
!! TGGAACATTTGATAGTGTTG+AGG + chr7_3:63871093-63871112 Msa1116260:CDS 35.0%
! CAAGCTGCATTTTTAATGAG+AGG + chr7_3:63871136-63871155 Msa1116260:CDS 35.0%
! TTTTCTGTTCAAAGGGTCAA+AGG + chr7_3:63871178-63871197 Msa1116260:intron 35.0%
GAGATTCAATATGATTGCAG+AGG + chr7_3:63871211-63871230 Msa1116260:intron 35.0%
GATTCAATATGATTGCAGAG+GGG + chr7_3:63871213-63871232 Msa1116260:intron 35.0%
TAGGTGTGAGAAAAAGACCT+AGG + chr7_3:63871014-63871033 Msa1116260:CDS 40.0%
AGGTGTGAGAAAAAGACCTA+GGG + chr7_3:63871015-63871034 Msa1116260:CDS 40.0%
ATCAGAGACACAACAAGAAG+AGG + chr7_3:63871055-63871074 Msa1116260:CDS 40.0%
ACACAACAAGAAGAGGAAGA+AGG + chr7_3:63871062-63871081 Msa1116260:CDS 40.0%
CACAACAAGAAGAGGAAGAA+GGG + chr7_3:63871063-63871082 Msa1116260:CDS 40.0%
AGGGAAACAAGATCAATCAG+AGG + chr7_3:63871313-63871332 Msa1116260:CDS 40.0%
GGGAAACAAGATCAATCAGA+GGG + chr7_3:63871314-63871333 Msa1116260:CDS 40.0%
GGTGTGAGAAAAAGACCTAG+GGG + chr7_3:63871016-63871035 Msa1116260:CDS 45.0%
! TCTGCTGCATATTTTCCCCT+AGG - chr7_3:63871034-63871053 None:intergenic 45.0%
CAAGAAGAGGAAGAAGGGTT+TGG + chr7_3:63871068-63871087 Msa1116260:CDS 45.0%
! TAGTGTTGAGGATGCTGCTT+TGG + chr7_3:63871105-63871124 Msa1116260:CDS 45.0%
TTCACCTGAACTTGCACTCA+AGG + chr7_3:63871238-63871257 Msa1116260:CDS 45.0%
!! AGAGGGATCAAGTGTCACTT+GGG + chr7_3:63871331-63871350 Msa1116260:CDS 45.0%
AGAGGAAGAAGGGTTTGGCT+TGG + chr7_3:63871073-63871092 Msa1116260:CDS 50.0%
CTCTCCTTGAGTGCAAGTTC+AGG - chr7_3:63871245-63871264 None:intergenic 50.0%
! CAGAGGGATCAAGTGTCACT+TGG + chr7_3:63871330-63871349 Msa1116260:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 63870992 63871379 63870992 ID=Msa1116260;Name=Msa1116260
chr7_3 mRNA 63870992 63871379 63870992 ID=Msa1116260-mRNA-1;Parent=Msa1116260;Name=Msa1116260-mRNA-1;_AED=0.43;_eAED=0.59;_QI=0|0|0|1|1|1|2|0|104
chr7_3 exon 63870992 63871157 63870992 ID=Msa1116260-mRNA-1:exon:15031;Parent=Msa1116260-mRNA-1
chr7_3 exon 63871231 63871379 63871231 ID=Msa1116260-mRNA-1:exon:15032;Parent=Msa1116260-mRNA-1
chr7_3 CDS 63870992 63871157 63870992 ID=Msa1116260-mRNA-1:cds;Parent=Msa1116260-mRNA-1
chr7_3 CDS 63871231 63871379 63871231 ID=Msa1116260-mRNA-1:cds;Parent=Msa1116260-mRNA-1
Gene Sequence

>Msa1116260

ATGAATCAAAAGTCTTCATATATAGGTGTGAGAAAAAGACCTAGGGGAAAATATGCAGCAGAGATCAGAGACACAACAAGAAGAGGAAGAAGGGTTTGGCTTGGAACATTTGATAGTGTTGAGGATGCTGCTTTGGCTTACGATCAAGCTGCATTTTTAATGAGAGAGGGGTTTTCACCTGAACTTGCACTCAAGGAGAGACACTGTGAACAAAGAAAGATGTTATCCAAAGGTGTAAAAAATAAAGCAGGGAAACAAGATCAATCAGAGGGATCAAGTGTCACTTGGGAGTTGAATATCTTGAGCAACTTCTAA
Protein sequence

>Msa1116260

MNQKSSYIGVRKRPRGKYAAEIRDTTRRGRRVWLGTFDSVEDAALAYDQAAFLMREGFSPELALKERHCEQRKMLSKGVKNKAGKQDQSEGSSVTWELNILSNF*