AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0346410

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0346410 MtrunA17_Chr3g0077861 93.413 167 11 0 2 168 1 167 3.32e-110 311
Msa0346410 MtrunA17_Chr3g0077911 93.750 160 10 0 2 161 1 160 7.03e-106 300
Msa0346410 MtrunA17_Chr3g0077891 63.068 176 56 2 2 168 1 176 4.05e-66 200
Msa0346410 MtrunA17_Chr3g0077881 61.932 176 58 2 2 168 1 176 3.81e-65 197
Msa0346410 MtrunA17_Chr3g0077941 62.857 175 57 2 2 168 1 175 1.14e-63 193
Msa0346410 MtrunA17_Chr1g0205821 48.667 150 73 3 14 161 21 168 9.50e-36 122
Msa0346410 MtrunA17_Chr1g0205821 44.595 74 38 1 10 80 100 173 1.99e-12 62.4
Msa0346410 MtrunA17_Chr1g0206771 49.007 151 67 4 10 157 17 160 1.08e-33 117
Msa0346410 MtrunA17_Chr1g0206771 50.000 68 31 1 9 73 95 162 1.27e-11 60.1
Msa0346410 MtrunA17_Chr4g0075861 45.882 170 86 3 3 169 83 249 1.45e-32 119
Msa0346410 MtrunA17_Chr4g0075861 44.079 152 79 2 9 160 12 157 8.51e-31 114
Msa0346410 MtrunA17_Chr4g0075861 44.595 74 37 1 91 164 12 81 2.61e-12 63.9
Msa0346410 MtrunA17_Chr4g0075971 44.706 170 88 3 3 169 83 249 1.25e-29 114
Msa0346410 MtrunA17_Chr4g0075971 42.857 147 78 2 9 155 12 152 4.91e-28 109
Msa0346410 MtrunA17_Chr4g0075971 44.595 74 37 1 91 164 12 81 3.15e-12 63.9
Msa0346410 MtrunA17_Chr4g0075971 43.373 83 44 1 16 95 182 264 4.00e-12 63.5
Msa0346410 MtrunA17_Chr3g0077811 67.500 80 22 1 2 77 6 85 2.72e-29 104
Msa0346410 MtrunA17_Chr3g0077811 46.575 73 39 0 85 157 7 79 4.91e-12 60.1
Msa0346410 MtrunA17_Chr8g0364231 42.683 164 81 4 3 158 36 194 1.16e-28 111
Msa0346410 MtrunA17_Chr8g0364231 63.636 77 27 1 85 161 36 111 3.55e-24 98.6
Msa0346410 MtrunA17_Chr5g0415031 40.506 158 89 3 3 156 37 193 2.32e-25 102
Msa0346410 MtrunA17_Chr5g0415031 56.180 89 38 1 81 169 33 120 8.47e-24 97.4
Msa0346410 MtrunA17_Chr6g0452001 40.385 156 88 3 3 154 57 211 1.22e-23 97.1
Msa0346410 MtrunA17_Chr6g0452001 57.692 78 32 1 84 161 56 132 2.03e-20 87.8
Msa0346410 MtrunA17_Chr1g0205831 40.411 146 72 2 16 161 12 142 2.18e-23 91.3
Msa0346410 MtrunA17_Chr1g0205831 49.180 61 31 0 22 82 89 149 1.85e-13 65.1
Msa0346410 MtrunA17_Chr6g0452021 37.805 164 94 4 3 163 37 195 1.03e-22 94.0
Msa0346410 MtrunA17_Chr7g0218891 38.235 136 82 2 23 157 118 252 1.12e-22 91.7
Msa0346410 MtrunA17_Chr7g0218891 35.484 155 93 3 10 158 14 167 1.80e-20 85.5
Msa0346410 MtrunA17_Chr1g0209201 40.000 140 73 3 5 142 12 142 2.78e-21 84.7
Msa0346410 MtrunA17_Chr1g0209201 48.052 77 38 1 81 157 6 80 5.84e-15 68.2
Msa0346410 MtrunA17_Chr1g0205811 52.874 87 38 1 8 91 13 99 8.45e-21 82.8
Msa0346410 MtrunA17_Chr1g0205811 54.118 85 37 2 91 175 14 96 1.36e-18 77.0
Msa0346410 MtrunA17_Chr1g0206781 58.108 74 30 1 84 157 4 76 9.48e-21 82.8
Msa0346410 MtrunA17_Chr1g0206781 40.650 123 44 2 10 129 12 108 4.84e-18 75.5
Msa0346410 MtrunA17_Chr2g0328701 44.660 103 52 1 9 111 29 126 5.44e-20 80.9
Msa0346410 MtrunA17_Chr2g0328701 43.421 76 39 1 91 166 29 100 6.23e-13 62.4
Msa0346410 MtrunA17_Chr8g0364021 52.703 74 34 1 84 157 37 109 2.14e-17 76.6
Msa0346410 MtrunA17_Chr8g0364021 46.914 81 38 2 3 80 38 116 3.99e-13 65.1
Msa0346410 MtrunA17_Chr1g0205861 45.783 83 43 2 77 158 1 82 2.40e-16 71.2
Msa0346410 MtrunA17_Chr1g0205861 38.095 84 49 1 6 86 13 96 8.64e-11 56.6
Msa0346410 MtrunA17_Chr1g0205801 42.857 91 43 2 8 95 11 95 3.73e-14 65.5
Msa0346410 MtrunA17_Chr1g0205801 50.000 64 31 1 91 154 12 74 1.44e-12 61.2
Msa0346410 MtrunA17_Chr7g0218911 44.286 70 38 1 95 164 2 70 1.65e-13 63.9
Msa0346410 MtrunA17_Chr1g0156171 63.043 46 17 0 116 161 11 56 6.96e-12 59.7
Msa0346410 MtrunA17_Chr5g0431721 45.570 79 42 1 82 159 2 80 1.70e-11 58.5
Msa0346410 MtrunA17_Chr7g0256011 47.222 72 33 2 79 150 8 74 6.67e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0346410 AT1G24190.2 39.412 170 98 3 3 168 8 176 1.98e-28 111
Msa0346410 AT1G24190.2 56.790 81 34 1 84 164 7 86 7.54e-23 95.1
Msa0346410 AT1G24190.3 39.412 170 98 3 3 168 8 176 2.18e-28 110
Msa0346410 AT1G24190.3 56.790 81 34 1 84 164 7 86 7.77e-23 95.1
Msa0346410 AT1G24190.1 39.412 170 98 3 3 168 8 176 2.27e-28 110
Msa0346410 AT1G24190.1 56.790 81 34 1 84 164 7 86 8.31e-23 95.1
Msa0346410 AT1G70060.2 40.881 159 88 3 3 156 8 165 3.34e-25 102
Msa0346410 AT1G70060.2 60.241 83 32 1 84 166 7 88 1.60e-23 97.1
Msa0346410 AT1G70060.1 40.881 159 88 3 3 156 8 165 3.34e-25 102
Msa0346410 AT1G70060.1 60.241 83 32 1 84 166 7 88 1.60e-23 97.1
Msa0346410 AT1G10450.3 42.953 149 80 3 9 154 84 230 1.64e-24 99.8
Msa0346410 AT1G10450.3 62.162 74 27 1 91 164 84 156 5.32e-21 89.7
Msa0346410 AT1G10450.2 42.953 149 80 3 9 154 33 179 1.85e-24 99.8
Msa0346410 AT1G10450.2 62.162 74 27 1 91 164 33 105 4.41e-21 90.1
Msa0346410 AT1G10450.1 42.953 149 80 3 9 154 33 179 1.85e-24 99.8
Msa0346410 AT1G10450.1 62.162 74 27 1 91 164 33 105 4.41e-21 90.1
Msa0346410 AT3G01320.1 36.313 179 110 2 1 176 49 226 3.46e-24 99.0
Msa0346410 AT3G01320.2 36.313 179 110 2 1 176 49 226 3.52e-24 99.0
Msa0346410 AT5G15020.1 37.288 177 106 3 3 176 46 220 8.00e-24 97.8
Msa0346410 AT5G15020.1 55.696 79 34 1 83 161 44 121 6.72e-20 86.7
Msa0346410 AT5G15020.2 37.288 177 106 3 3 176 46 220 8.23e-24 97.8
Msa0346410 AT5G15020.2 55.696 79 34 1 83 161 44 121 6.98e-20 86.7
Msa0346410 AT1G70030.1 38.994 159 91 3 3 158 5 160 3.55e-23 90.5
Msa0346410 AT1G70030.1 46.154 78 41 1 84 161 4 80 4.49e-14 66.6
Msa0346410 AT1G59890.3 63.514 74 26 1 91 164 45 117 6.02e-23 95.5
Msa0346410 AT1G59890.3 38.312 154 90 3 9 159 45 196 4.68e-21 90.1
Msa0346410 AT1G59890.1 63.514 74 26 1 91 164 45 117 6.02e-23 95.5
Msa0346410 AT1G59890.1 38.312 154 90 3 9 159 45 196 4.64e-21 90.1
Msa0346410 AT1G59890.2 63.514 74 26 1 91 164 45 117 6.02e-23 95.5
Msa0346410 AT1G59890.2 38.312 154 90 3 9 159 45 196 4.55e-21 90.1
Msa0346410 AT1G59890.4 63.514 74 26 1 91 164 45 117 6.19e-23 95.5
Msa0346410 AT1G59890.4 38.312 154 90 3 9 159 45 196 5.31e-21 89.7
Msa0346410 AT1G24200.1 36.709 158 90 4 4 156 9 161 1.02e-21 87.8
Msa0346410 AT1G24200.1 53.731 67 30 1 91 157 14 79 3.33e-15 70.5
Msa0346410 AT1G24230.1 32.886 149 81 3 9 153 14 147 1.83e-20 85.5
Msa0346410 AT1G24230.1 26.277 137 98 1 24 160 104 237 1.86e-13 66.6
Msa0346410 AT1G24230.1 42.188 64 37 0 91 154 14 77 5.31e-11 59.7
Msa0346410 AT1G24250.1 30.409 171 98 3 12 162 21 190 1.10e-18 80.9
Msa0346410 AT4G12020.4 52.632 76 34 1 91 166 308 381 9.76e-18 80.5
Msa0346410 AT4G12020.4 48.684 76 36 2 6 78 305 380 5.18e-14 69.7
Msa0346410 AT4G12020.2 52.632 76 34 1 91 166 308 381 9.85e-18 80.5
Msa0346410 AT4G12020.2 48.684 76 36 2 6 78 305 380 5.14e-14 69.7
Msa0346410 AT4G12020.11 52.632 76 34 1 91 166 308 381 1.01e-17 80.5
Msa0346410 AT4G12020.11 48.684 76 36 2 6 78 305 380 5.37e-14 69.7
Msa0346410 AT4G12020.7 52.632 76 34 1 91 166 308 381 1.04e-17 80.5
Msa0346410 AT4G12020.7 48.684 76 36 2 6 78 305 380 5.47e-14 69.7
Msa0346410 AT4G12020.1 52.632 76 34 1 91 166 308 381 1.04e-17 80.5
Msa0346410 AT4G12020.1 48.684 76 36 2 6 78 305 380 5.47e-14 69.7
Msa0346410 AT4G12020.9 52.632 76 34 1 91 166 308 381 1.04e-17 80.5
Msa0346410 AT4G12020.9 48.684 76 36 2 6 78 305 380 5.47e-14 69.7
Msa0346410 AT4G12020.5 52.632 76 34 1 91 166 241 314 1.04e-17 80.5
Msa0346410 AT4G12020.5 48.684 76 36 2 6 78 238 313 5.53e-14 69.7
Msa0346410 AT4G12020.10 52.632 76 34 1 91 166 308 381 1.04e-17 80.5
Msa0346410 AT4G12020.10 48.684 76 36 2 6 78 305 380 5.49e-14 69.7
Msa0346410 AT4G12020.3 52.632 76 34 1 91 166 308 381 1.04e-17 80.5
Msa0346410 AT4G12020.3 48.684 76 36 2 6 78 305 380 5.54e-14 69.7
Msa0346410 AT4G12020.6 52.632 76 34 1 91 166 308 381 1.25e-17 80.1
Msa0346410 AT4G12020.6 48.684 76 36 2 6 78 305 380 6.37e-14 69.3
Msa0346410 AT4G12020.8 52.632 76 34 1 91 166 308 381 1.25e-17 80.1
Msa0346410 AT4G12020.8 48.684 76 36 2 6 78 305 380 6.37e-14 69.3
Msa0346410 AT1G27260.1 33.553 152 92 4 10 153 4 154 1.98e-17 77.0
Msa0346410 AT5G15025.1 47.312 93 48 1 69 161 25 116 2.19e-17 74.3
Msa0346410 AT5G15025.1 47.945 73 35 1 6 75 44 116 2.42e-12 61.2
Msa0346410 AT1G23810.1 30.539 167 102 3 9 162 14 179 3.87e-17 76.6
Msa0346410 AT1G70030.2 35.220 159 65 3 3 158 16 139 7.75e-16 70.9
Msa0346410 AT1G70030.2 46.154 78 41 1 84 161 15 91 3.00e-14 66.6
Msa0346410 AT1G70030.3 46.154 78 41 1 84 161 15 91 2.12e-14 66.6
Msa0346410 AT1G70030.3 42.574 101 55 1 3 100 16 116 4.30e-14 65.9
Msa0346410 AT1G27220.1 50.000 66 32 1 91 156 14 78 6.37e-14 67.0
Msa0346410 AT1G27250.1 47.887 71 36 1 86 156 16 85 1.34e-13 65.1
Msa0346410 AT5G35610.1 38.043 92 54 2 84 175 3 91 1.16e-11 60.1
Msa0346410 AT1G24210.1 45.070 71 38 1 84 154 7 76 2.67e-11 59.3
Msa0346410 AT1G27270.1 30.909 165 96 4 9 156 14 177 8.27e-11 59.3

Find 25 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGGCATACAGATTTAATTT+TGG 0.178085 3_1:+6834530 Msa0346410:CDS
AGAGTGTATGAGTTGTTTAA+AGG 0.253520 3_1:+6834252 Msa0346410:CDS
AGAGTCAAGGATTTGTTTAA+AGG 0.255525 3_1:+6834510 Msa0346410:CDS
ATCTCAAAATTAAATCTTCA+TGG 0.296791 3_1:-6834275 None:intergenic
AGCAGTAAAACAAAAGATTA+TGG 0.348530 3_1:+6834155 Msa0346410:CDS
GAGTCAAGGATTTGTTTAAA+GGG 0.376970 3_1:+6834511 Msa0346410:CDS
ACAAATTGTATTGGATTTCA+AGG 0.384142 3_1:+6834197 Msa0346410:CDS
AAAACTTATGAAGGATTTCA+AGG 0.385249 3_1:+6834455 Msa0346410:CDS
AGGCTGAAAATATTGATACT+AGG 0.410413 3_1:+6834217 Msa0346410:CDS
AGTGTGTTTCCATATGTCTT+AGG 0.412686 3_1:-6834570 None:intergenic
ATCTTCTTGCCTAAGACATA+TGG 0.434139 3_1:+6834561 Msa0346410:CDS
ATATGAAATCAAACTTCCAT+TGG 0.495726 3_1:+6834320 Msa0346410:CDS
GGCTGAAAATATTGATACTA+GGG 0.509868 3_1:+6834218 Msa0346410:CDS
AAAGTAAAAGATACGTTTCG+AGG 0.529617 3_1:+6834402 Msa0346410:CDS
AGTTTGATTTCATATTCAGT+TGG 0.545841 3_1:-6834312 None:intergenic
AATTGATACAAGTGGTGTTG+CGG 0.577415 3_1:+6834485 Msa0346410:CDS
TTCATATTCAGTTGGCACGA+AGG 0.577696 3_1:-6834304 None:intergenic
CTTCGACCTCAGCTTGACAC+TGG 0.608719 3_1:+6834591 Msa0346410:CDS
TCGTTATTATCATGATCCAA+TGG 0.609457 3_1:-6834336 None:intergenic
TGGTGTTGCGGAAAGAGTCA+AGG 0.618099 3_1:+6834497 Msa0346410:CDS
TAACGCTAATGCATCACCAC+GGG 0.620032 3_1:-6834127 None:intergenic
TACTGACCAGTGTCAAGCTG+AGG 0.642089 3_1:-6834597 None:intergenic
GCTTGTAGAATTGATACAAG+TGG 0.651698 3_1:+6834477 Msa0346410:CDS
ATGATGAAGAAGCGCACCCG+TGG 0.703947 3_1:+6834111 Msa0346410:CDS
GTAACGCTAATGCATCACCA+CGG 0.738440 3_1:-6834128 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTTTTATACAAATTGTAT+TGG + chr3_1:6834188-6834207 Msa0346410:CDS 15.0%
!! ATCTCAAAATTAAATCTTCA+TGG - chr3_1:6834278-6834297 None:intergenic 20.0%
!!! CTTCATAAGTTTTAAAAACT+CGG - chr3_1:6834448-6834467 None:intergenic 20.0%
! AGCAGTAAAACAAAAGATTA+TGG + chr3_1:6834155-6834174 Msa0346410:CDS 25.0%
! ACAAATTGTATTGGATTTCA+AGG + chr3_1:6834197-6834216 Msa0346410:CDS 25.0%
!! AGTTTGATTTCATATTCAGT+TGG - chr3_1:6834315-6834334 None:intergenic 25.0%
! ATATGAAATCAAACTTCCAT+TGG + chr3_1:6834320-6834339 Msa0346410:CDS 25.0%
!!! CGAGTTTTTAAAACTTATGA+AGG + chr3_1:6834446-6834465 Msa0346410:CDS 25.0%
! AAAACTTATGAAGGATTTCA+AGG + chr3_1:6834455-6834474 Msa0346410:CDS 25.0%
AGGCTGAAAATATTGATACT+AGG + chr3_1:6834217-6834236 Msa0346410:CDS 30.0%
GGCTGAAAATATTGATACTA+GGG + chr3_1:6834218-6834237 Msa0346410:CDS 30.0%
AGAGTGTATGAGTTGTTTAA+AGG + chr3_1:6834252-6834271 Msa0346410:CDS 30.0%
TCGTTATTATCATGATCCAA+TGG - chr3_1:6834339-6834358 None:intergenic 30.0%
AAAGTAAAAGATACGTTTCG+AGG + chr3_1:6834402-6834421 Msa0346410:CDS 30.0%
! AGAGTCAAGGATTTGTTTAA+AGG + chr3_1:6834510-6834529 Msa0346410:CDS 30.0%
! GAGTCAAGGATTTGTTTAAA+GGG + chr3_1:6834511-6834530 Msa0346410:CDS 30.0%
!! AGGGCATACAGATTTAATTT+TGG + chr3_1:6834530-6834549 Msa0346410:CDS 30.0%
!! GGGCATACAGATTTAATTTT+GGG + chr3_1:6834531-6834550 Msa0346410:CDS 30.0%
GCTTGTAGAATTGATACAAG+TGG + chr3_1:6834477-6834496 Msa0346410:CDS 35.0%
! AATTGATACAAGTGGTGTTG+CGG + chr3_1:6834485-6834504 Msa0346410:CDS 35.0%
ATCTTCTTGCCTAAGACATA+TGG + chr3_1:6834561-6834580 Msa0346410:CDS 35.0%
AGTGTGTTTCCATATGTCTT+AGG - chr3_1:6834573-6834592 None:intergenic 35.0%
TTCATATTCAGTTGGCACGA+AGG - chr3_1:6834307-6834326 None:intergenic 40.0%
TAACGCTAATGCATCACCAC+GGG - chr3_1:6834130-6834149 None:intergenic 45.0%
GTAACGCTAATGCATCACCA+CGG - chr3_1:6834131-6834150 None:intergenic 45.0%
!! TGGTGTTGCGGAAAGAGTCA+AGG + chr3_1:6834497-6834516 Msa0346410:CDS 50.0%
TACTGACCAGTGTCAAGCTG+AGG - chr3_1:6834600-6834619 None:intergenic 50.0%
! ATGATGAAGAAGCGCACCCG+TGG + chr3_1:6834111-6834130 Msa0346410:CDS 55.0%
CTTCGACCTCAGCTTGACAC+TGG + chr3_1:6834591-6834610 Msa0346410:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 6834111 6834644 6834111 ID=Msa0346410;Name=Msa0346410
chr3_1 mRNA 6834111 6834644 6834111 ID=Msa0346410-mRNA-1;Parent=Msa0346410;Name=Msa0346410-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|177
chr3_1 exon 6834111 6834644 6834111 ID=Msa0346410-mRNA-1:exon:1934;Parent=Msa0346410-mRNA-1
chr3_1 CDS 6834111 6834644 6834111 ID=Msa0346410-mRNA-1:cds;Parent=Msa0346410-mRNA-1
Gene Sequence

>Msa0346410

ATGATGAAGAAGCGCACCCGTGGTGATGCATTAGCGTTACTCGCAGCAGTAAAACAAAAGATTATGGAAAAGTATGAATCTTTTATACAAATTGTATTGGATTTCAAGGCTGAAAATATTGATACTAGGGTTGTCAAATTAAGAGTGTATGAGTTGTTTAAAGGCCATGAAGATTTAATTTTGAGATTCAACACCTTCGTGCCAACTGAATATGAAATCAAACTTCCATTGGATCATGATAATAACGATAGTCGTCGATTAGAGAAAAAAGATGCATTATCGTTTCTCAAGAAAGTAAAAGATACGTTTCGAGGTAAGAATAGAAAAAAGTATGCCGAGTTTTTAAAACTTATGAAGGATTTCAAGGCTTGTAGAATTGATACAAGTGGTGTTGCGGAAAGAGTCAAGGATTTGTTTAAAGGGCATACAGATTTAATTTTGGGATTCAACATCTTCTTGCCTAAGACATATGGAAACACACTTCGACCTCAGCTTGACACTGGTCAGTACTCGACATATCTTGATAAATTTTAA
Protein sequence

>Msa0346410

MMKKRTRGDALALLAAVKQKIMEKYESFIQIVLDFKAENIDTRVVKLRVYELFKGHEDLILRFNTFVPTEYEIKLPLDHDNNDSRRLEKKDALSFLKKVKDTFRGKNRKKYAEFLKLMKDFKACRIDTSGVAERVKDLFKGHTDLILGFNIFLPKTYGNTLRPQLDTGQYSTYLDKF*