AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0798070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0798070 MtrunA17_Chr5g0402331 97.938 97 2 0 1 97 93 189 3.78e-63 189
Msa0798070 MtrunA17_Chr5g0402361 97.938 97 2 0 1 97 265 361 3.94e-61 189
Msa0798070 MtrunA17_Chr5g0402361 97.895 95 2 0 1 95 92 186 4.38e-59 184
Msa0798070 MtrunA17_Chr4g0044961 53.333 90 41 1 1 90 101 189 1.86e-27 99.0
Msa0798070 MtrunA17_Chr1g0161211 50.538 93 43 2 1 91 90 181 1.39e-23 89.4
Msa0798070 MtrunA17_Chr1g0161211 43.548 62 35 0 28 89 45 106 9.48e-12 58.2
Msa0798070 MtrunA17_Chr3g0111371 45.556 90 46 1 1 90 49 135 1.94e-23 87.0
Msa0798070 MtrunA17_Chr5g0434951 44.565 92 51 0 1 92 48 139 1.76e-22 84.7
Msa0798070 MtrunA17_Chr8g0391691 50.515 97 45 2 1 95 80 175 1.79e-22 86.3
Msa0798070 MtrunA17_Chr8g0391691 47.692 65 34 0 29 93 36 100 4.37e-13 61.6
Msa0798070 MtrunA17_Chr1g0169581 40.860 93 52 1 1 90 48 140 3.15e-20 79.0
Msa0798070 MtrunA17_Chr1g0169581 40.909 66 39 0 27 92 2 67 2.87e-11 55.8
Msa0798070 MtrunA17_Chr7g0245911 42.157 102 51 2 1 94 93 194 1.41e-19 78.6
Msa0798070 MtrunA17_Chr8g0392951 39.362 94 57 0 1 94 68 161 4.46e-19 76.6
Msa0798070 MtrunA17_Chr8g0351681 43.137 102 51 2 1 95 95 196 2.96e-18 75.5
Msa0798070 MtrunA17_Chr7g0256701 51.515 66 31 1 26 90 147 212 6.51e-18 74.7
Msa0798070 MtrunA17_Chr3g0121191 44.444 90 45 2 9 95 135 222 6.96e-18 75.1
Msa0798070 MtrunA17_Chr6g0482731 37.778 90 56 0 1 90 71 160 1.95e-17 72.8
Msa0798070 MtrunA17_Chr1g0169621 50.769 65 32 0 26 90 101 165 3.35e-17 72.0
Msa0798070 MtrunA17_Chr1g0188171 41.667 96 49 2 1 92 56 148 7.45e-17 70.5
Msa0798070 MtrunA17_Chr3g0116141 37.778 90 56 0 1 90 49 138 3.45e-16 68.6
Msa0798070 MtrunA17_Chr3g0116151 37.778 90 56 0 1 90 50 139 3.46e-16 68.6
Msa0798070 MtrunA17_Chr4g0033601 40.625 96 54 2 1 93 49 144 4.03e-16 68.9
Msa0798070 MtrunA17_Chr1g0185001 37.778 90 56 0 2 91 57 146 5.00e-16 68.6
Msa0798070 MtrunA17_Chr7g0254731 41.053 95 49 2 1 91 56 147 5.22e-16 68.6
Msa0798070 MtrunA17_Chr7g0254731 40.323 62 37 0 29 90 12 73 3.02e-11 56.2
Msa0798070 MtrunA17_Chr7g0256171 45.000 100 52 2 1 97 49 148 6.07e-16 68.2
Msa0798070 MtrunA17_Chr5g0440931 41.053 95 49 2 1 91 56 147 1.07e-15 67.8
Msa0798070 MtrunA17_Chr6g0460211 41.053 95 49 2 1 91 56 147 1.10e-15 67.8
Msa0798070 MtrunA17_Chr3g0093271 41.053 95 49 2 1 91 107 198 2.16e-15 67.8
Msa0798070 MtrunA17_Chr5g0396261 37.634 93 53 2 1 89 21 112 2.18e-15 65.9
Msa0798070 MtrunA17_Chr7g0225921 36.264 91 58 0 1 91 51 141 4.21e-15 65.9
Msa0798070 MtrunA17_Chr1g0166281 39.583 96 51 2 1 92 56 148 8.71e-15 65.5
Msa0798070 MtrunA17_Chr4g0057641 35.556 90 58 0 1 90 50 139 1.96e-14 64.3
Msa0798070 MtrunA17_Chr2g0329371 42.857 98 51 2 1 93 108 205 3.13e-14 65.1
Msa0798070 MtrunA17_Chr4g0057661 35.556 90 58 0 1 90 50 139 3.18e-14 63.5
Msa0798070 MtrunA17_Chr4g0057651 35.556 90 58 0 1 90 50 139 1.04e-13 62.4
Msa0798070 MtrunA17_Chr6g0459231 34.066 91 60 0 1 91 52 142 1.28e-13 62.0
Msa0798070 MtrunA17_Chr8g0366401 32.292 96 61 1 2 93 62 157 1.36e-13 62.4
Msa0798070 MtrunA17_Chr7g0274101 40.860 93 54 1 1 92 56 148 1.49e-13 62.0
Msa0798070 MtrunA17_Chr4g0064231 49.275 69 33 1 27 93 151 219 2.28e-13 63.2
Msa0798070 MtrunA17_Chr8g0373691 32.967 91 60 1 1 90 97 187 1.09e-12 60.5
Msa0798070 MtrunA17_Chr8g0373691 42.188 64 37 0 27 90 51 114 3.98e-12 59.3
Msa0798070 MtrunA17_Chr7g0217621 43.373 83 43 2 12 92 119 199 3.13e-11 57.0
Msa0798070 MtrunA17_Chr8g0368681 30.108 93 62 1 1 90 56 148 3.71e-11 56.2
Msa0798070 MtrunA17_Chr7g0245231 41.176 68 40 0 23 90 24 91 4.72e-11 55.8
Msa0798070 MtrunA17_Chr7g0245231 36.559 93 57 2 1 92 74 165 6.68e-11 55.5
Msa0798070 MtrunA17_Chr6g0450921 43.077 65 37 0 26 90 26 90 5.62e-11 55.8
Msa0798070 MtrunA17_Chr4g0042491 43.750 80 40 2 12 90 100 175 7.21e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0798070 AT2G15680.1 51.111 90 43 1 1 90 94 182 2.17e-28 101
Msa0798070 AT1G24620.1 47.423 97 48 2 1 95 81 176 8.63e-24 89.7
Msa0798070 AT5G37770.1 43.299 97 50 1 2 93 62 158 7.36e-22 84.0
Msa0798070 AT5G37770.1 45.161 62 34 0 28 89 16 77 4.01e-11 56.2
Msa0798070 AT5G37770.2 43.299 97 50 1 2 93 62 158 7.36e-22 84.0
Msa0798070 AT5G37770.2 45.161 62 34 0 28 89 16 77 4.01e-11 56.2
Msa0798070 AT1G66400.1 43.158 95 47 2 2 91 60 152 4.84e-21 82.0
Msa0798070 AT1G18210.2 42.222 90 49 1 1 90 67 153 3.72e-20 80.1
Msa0798070 AT1G18210.2 40.845 71 42 0 27 97 21 91 3.34e-11 56.6
Msa0798070 AT1G18210.1 42.222 90 49 1 1 90 67 153 3.72e-20 80.1
Msa0798070 AT1G18210.1 40.845 71 42 0 27 97 21 91 3.34e-11 56.6
Msa0798070 AT5G17470.1 46.465 99 49 3 1 95 46 144 5.05e-20 79.0
Msa0798070 AT2G36180.1 47.475 99 47 3 1 95 44 141 7.59e-20 78.6
Msa0798070 AT5G42380.1 41.758 91 51 1 2 90 94 184 1.34e-18 76.3
Msa0798070 AT4G14640.2 41.667 96 49 2 1 92 39 131 4.53e-18 73.6
Msa0798070 AT4G14640.1 41.667 96 49 2 1 92 57 149 1.40e-17 72.8
Msa0798070 AT1G73630.1 40.000 90 51 1 1 90 64 150 2.23e-17 72.8
Msa0798070 AT2G41410.1 44.737 76 40 2 19 93 136 210 4.48e-17 73.2
Msa0798070 AT3G22930.1 41.304 92 53 1 1 91 79 170 1.61e-16 70.9
Msa0798070 AT1G66410.4 41.053 95 49 2 1 91 20 111 1.87e-16 68.9
Msa0798070 AT1G66410.3 41.053 95 49 2 1 91 20 111 1.87e-16 68.9
Msa0798070 AT3G43810.4 41.053 95 49 2 1 91 20 111 3.43e-16 68.2
Msa0798070 AT3G43810.3 41.053 95 49 2 1 91 20 111 3.43e-16 68.2
Msa0798070 AT3G03400.1 42.353 85 44 2 1 81 49 132 4.46e-16 68.6
Msa0798070 AT5G37780.4 41.053 95 49 2 1 91 43 134 6.71e-16 68.2
Msa0798070 AT5G21274.1 42.105 95 48 2 1 91 56 147 7.44e-16 68.6
Msa0798070 AT1G66410.1 41.053 95 49 2 1 91 56 147 7.61e-16 68.6
Msa0798070 AT5G37780.1 41.053 95 49 2 1 91 56 147 7.61e-16 68.6
Msa0798070 AT2G27030.3 40.404 99 52 2 1 95 56 151 7.92e-16 68.9
Msa0798070 AT3G56800.1 42.105 95 48 2 1 91 56 147 8.20e-16 68.2
Msa0798070 AT2G41110.1 42.105 95 48 2 1 91 56 147 8.20e-16 68.2
Msa0798070 AT2G27030.1 42.105 95 48 2 1 91 56 147 8.20e-16 68.2
Msa0798070 AT2G41110.2 42.105 95 48 2 1 91 68 159 9.17e-16 68.6
Msa0798070 AT1G66410.2 41.053 95 49 2 1 91 66 157 9.59e-16 68.6
Msa0798070 AT3G50360.1 38.462 91 55 1 1 90 71 161 1.25e-15 68.2
Msa0798070 AT3G50360.1 44.615 65 36 0 26 90 24 88 2.11e-11 57.4
Msa0798070 AT3G10190.1 40.659 91 53 1 1 90 115 205 1.28e-15 68.9
Msa0798070 AT5G37780.2 41.053 95 49 2 1 91 71 162 1.31e-15 68.2
Msa0798070 AT3G43810.1 41.053 95 49 2 1 91 56 147 1.51e-15 67.8
Msa0798070 AT5G37780.3 41.053 95 49 2 1 91 82 173 1.58e-15 68.2
Msa0798070 AT3G43810.2 39.806 103 53 3 1 97 56 155 2.54e-15 68.6
Msa0798070 AT3G59440.1 40.816 98 50 3 1 93 95 189 2.64e-15 68.2
Msa0798070 AT2G43290.1 38.614 101 54 2 1 93 109 209 3.89e-15 67.8
Msa0798070 AT1G05990.1 42.268 97 52 2 1 93 49 145 3.29e-14 64.3
Msa0798070 AT1G32250.1 30.208 96 60 1 2 90 61 156 2.34e-13 62.4
Msa0798070 AT4G03290.1 39.000 100 55 2 1 94 49 148 3.16e-13 61.6
Msa0798070 AT4G12860.1 41.000 100 56 2 1 97 49 148 6.35e-13 60.8
Msa0798070 AT1G21550.1 36.735 98 48 3 9 92 57 154 7.72e-13 60.8
Msa0798070 AT1G76650.2 33.708 89 59 0 2 90 78 166 8.00e-13 60.8
Msa0798070 AT1G76650.1 33.708 89 59 0 2 90 88 176 9.66e-13 60.8
Msa0798070 AT1G76650.3 33.708 89 59 0 2 90 88 176 9.66e-13 60.8
Msa0798070 AT3G07490.1 38.000 100 59 2 1 97 49 148 1.41e-12 60.1
Msa0798070 AT3G03000.1 30.851 94 63 1 2 93 65 158 3.60e-12 59.3
Msa0798070 AT4G37010.1 35.165 91 58 1 1 90 71 161 6.95e-12 58.5
Msa0798070 AT4G37010.2 35.165 91 58 1 1 90 75 165 7.66e-12 58.5
Msa0798070 AT3G50770.1 34.375 96 57 2 1 90 108 203 7.72e-12 58.9
Msa0798070 AT2G41100.2 33.929 112 55 3 1 94 20 130 9.29e-12 58.5
Msa0798070 AT2G41100.7 33.929 112 55 3 1 94 110 220 2.16e-11 58.5
Msa0798070 AT2G41100.6 33.929 112 55 3 1 94 110 220 2.16e-11 58.5
Msa0798070 AT2G41100.3 33.929 112 55 3 1 94 110 220 2.16e-11 58.5
Msa0798070 AT2G41100.4 33.929 112 55 3 1 94 145 255 2.63e-11 58.5
Msa0798070 AT2G41100.1 33.929 112 55 3 1 94 145 255 2.63e-11 58.5
Msa0798070 AT1G76640.1 44.615 65 36 0 26 90 19 83 3.08e-11 56.6
Msa0798070 AT5G19360.1 38.043 92 56 1 2 93 418 508 5.41e-11 57.8
Msa0798070 AT5G12180.1 38.043 92 56 1 2 93 423 513 5.91e-11 57.8
Msa0798070 AT5G44460.1 43.590 78 39 2 18 90 97 174 9.67e-11 55.8

Find 20 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAGACTTTAAAGAGTTTA+TGG 0.095878 5_3:+10632117 Msa0798070:CDS
TTTCAAGTATTTGATATAAA+TGG 0.216373 5_3:+10632193 Msa0798070:CDS
CCTTAGTGCTTGTAAGAAAA+TGG 0.341545 5_3:+10632279 Msa0798070:CDS
AATTGTCTCAAATATTTAAG+AGG 0.413219 5_3:+10632239 Msa0798070:CDS
TCTCAAATATTTAAGAGGTT+AGG 0.421604 5_3:+10632244 Msa0798070:CDS
GAGTTTATGGAAATGTTCAA+TGG 0.480442 5_3:+10632130 Msa0798070:CDS
TAGATTTGAATGAGTTTACA+AGG 0.501078 5_3:+10632335 Msa0798070:CDS
GCCATCTTTGTCAGAGTCCA+TGG 0.508786 5_3:-10632092 None:intergenic
AAAATGGTGAAAGGTGTTGA+TGG 0.531030 5_3:+10632295 Msa0798070:CDS
GTATTTGATATAAATGGTGA+TGG 0.547891 5_3:+10632199 Msa0798070:CDS
ATGGAAATGTTCAATGGAGA+GGG 0.552020 5_3:+10632136 Msa0798070:CDS
GGGTAGTAAGATAAAAGAAG+AGG 0.559838 5_3:+10632156 Msa0798070:CDS
TATGGAAATGTTCAATGGAG+AGG 0.569106 5_3:+10632135 Msa0798070:CDS
GGTGTTGATGGTGATGGAGA+TGG 0.571699 5_3:+10632307 Msa0798070:CDS
GTGAAAGGTGTTGATGGTGA+TGG 0.580268 5_3:+10632301 Msa0798070:CDS
TTTACAAGGATGATGATGAA+TGG 0.601621 5_3:+10632349 Msa0798070:CDS
TATTTGATATAAATGGTGAT+GGG 0.605312 5_3:+10632200 Msa0798070:CDS
GCCATGGACTCTGACAAAGA+TGG 0.639323 5_3:+10632091 None:intergenic
GCTTGTAAGAAAATGGTGAA+AGG 0.660596 5_3:+10632286 Msa0798070:CDS
TGATGGGAAAATTAGTGCTG+AGG 0.690315 5_3:+10632216 Msa0798070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCAAGTATTTGATATAAA+TGG + chr5_3:10632193-10632212 Msa0798070:CDS 15.0%
!! TATTTGATATAAATGGTGAT+GGG + chr5_3:10632200-10632219 Msa0798070:CDS 20.0%
!! AATTGTCTCAAATATTTAAG+AGG + chr5_3:10632239-10632258 Msa0798070:CDS 20.0%
!! CATAGACTTTAAAGAGTTTA+TGG + chr5_3:10632117-10632136 Msa0798070:CDS 25.0%
! GTATTTGATATAAATGGTGA+TGG + chr5_3:10632199-10632218 Msa0798070:CDS 25.0%
! TCTCAAATATTTAAGAGGTT+AGG + chr5_3:10632244-10632263 Msa0798070:CDS 25.0%
! TAGATTTGAATGAGTTTACA+AGG + chr5_3:10632335-10632354 Msa0798070:CDS 25.0%
GAGTTTATGGAAATGTTCAA+TGG + chr5_3:10632130-10632149 Msa0798070:CDS 30.0%
! TTTACAAGGATGATGATGAA+TGG + chr5_3:10632349-10632368 Msa0798070:CDS 30.0%
TATGGAAATGTTCAATGGAG+AGG + chr5_3:10632135-10632154 Msa0798070:CDS 35.0%
ATGGAAATGTTCAATGGAGA+GGG + chr5_3:10632136-10632155 Msa0798070:CDS 35.0%
GGGTAGTAAGATAAAAGAAG+AGG + chr5_3:10632156-10632175 Msa0798070:CDS 35.0%
! CCATTTTCTTACAAGCACTA+AGG - chr5_3:10632282-10632301 None:intergenic 35.0%
CCTTAGTGCTTGTAAGAAAA+TGG + chr5_3:10632279-10632298 Msa0798070:CDS 35.0%
GCTTGTAAGAAAATGGTGAA+AGG + chr5_3:10632286-10632305 Msa0798070:CDS 35.0%
!! AAAATGGTGAAAGGTGTTGA+TGG + chr5_3:10632295-10632314 Msa0798070:CDS 35.0%
TGATGGGAAAATTAGTGCTG+AGG + chr5_3:10632216-10632235 Msa0798070:CDS 40.0%
!! GTGAAAGGTGTTGATGGTGA+TGG + chr5_3:10632301-10632320 Msa0798070:CDS 45.0%
!! GGTGTTGATGGTGATGGAGA+TGG + chr5_3:10632307-10632326 Msa0798070:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 10632094 10632387 10632094 ID=Msa0798070;Name=Msa0798070
chr5_3 mRNA 10632094 10632387 10632094 ID=Msa0798070-mRNA-1;Parent=Msa0798070;Name=Msa0798070-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|-1|0|1|-1|1|1|0|97
chr5_3 exon 10632094 10632387 10632094 ID=Msa0798070-mRNA-1:exon:4424;Parent=Msa0798070-mRNA-1
chr5_3 CDS 10632094 10632387 10632094 ID=Msa0798070-mRNA-1:cds;Parent=Msa0798070-mRNA-1
Gene Sequence

>Msa0798070

ATGGACTCTGACAAAGATGGCTTCATAGACTTTAAAGAGTTTATGGAAATGTTCAATGGAGAGGGTAGTAAGATAAAAGAAGAGGAGATTAAGAGTGCTTTTCAAGTATTTGATATAAATGGTGATGGGAAAATTAGTGCTGAGGAATTGTCTCAAATATTTAAGAGGTTAGGAGAGAGTTGTAGCCTTAGTGCTTGTAAGAAAATGGTGAAAGGTGTTGATGGTGATGGAGATGGTCTTATAGATTTGAATGAGTTTACAAGGATGATGATGAATGGCAAGAAATGTGCCTAA
Protein sequence

>Msa0798070

MDSDKDGFIDFKEFMEMFNGEGSKIKEEEIKSAFQVFDINGDGKISAEELSQIFKRLGESCSLSACKKMVKGVDGDGDGLIDLNEFTRMMMNGKKCA*