AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0101210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0101210 MtrunA17_Chr1g0149481 74.390 164 29 1 1 151 1 164 1.63e-73 217
Msa0101210 MtrunA17_Chr1g0149491 96.026 151 6 0 1 151 1 151 7.01e-69 205
Msa0101210 MtrunA17_Chr1g0149471 54.630 216 27 4 1 151 1 210 2.37e-55 172
Msa0101210 MtrunA17_Chr3g0137521 61.589 151 35 3 1 150 1 129 1.82e-46 147
Msa0101210 MtrunA17_Chr4g0056411 46.429 168 72 3 1 150 1 168 1.02e-37 126
Msa0101210 MtrunA17_Chr3g0137531 57.792 154 37 3 1 151 1 129 4.96e-36 121
Msa0101210 MtrunA17_Chr4g0060391 55.556 108 40 2 47 151 21 123 1.62e-34 117
Msa0101210 MtrunA17_Chr4g0056371 63.855 83 30 0 69 151 50 132 3.65e-33 114
Msa0101210 MtrunA17_Chr4g0056391 63.636 88 31 1 65 151 56 143 4.75e-32 111
Msa0101210 MtrunA17_Chr4g0056401 59.091 88 35 1 65 151 47 134 2.05e-31 109
Msa0101210 MtrunA17_Chr2g0290521 55.556 90 39 1 62 151 39 127 6.75e-27 97.8
Msa0101210 MtrunA17_Chr5g0399081 50.575 87 41 2 65 150 91 176 1.10e-25 96.3
Msa0101210 MtrunA17_Chr5g0399091 49.425 87 42 2 65 150 84 169 3.70e-25 94.7
Msa0101210 MtrunA17_Chr4g0056381 52.941 85 38 2 67 150 103 186 1.87e-23 90.9
Msa0101210 MtrunA17_Chr2g0290571 44.706 85 43 2 67 151 119 199 6.99e-20 81.6
Msa0101210 MtrunA17_Chr2g0290561 43.529 85 44 2 67 151 115 195 2.53e-18 77.4
Msa0101210 MtrunA17_Chr3g0120411 52.326 86 39 2 66 150 251 335 9.48e-18 78.2
Msa0101210 MtrunA17_Chr2g0290531 42.529 87 43 3 67 151 179 260 3.32e-16 73.2
Msa0101210 MtrunA17_Chr4g0064361 53.571 84 37 2 69 151 151 233 3.45e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0101210 AT4G12490.1 45.055 182 69 3 1 151 1 182 4.80e-42 138
Msa0101210 AT2G45180.1 75.904 83 20 0 69 151 52 134 2.02e-39 130
Msa0101210 AT4G12470.1 66.292 89 29 1 64 151 73 161 1.55e-36 123
Msa0101210 AT4G12480.1 67.045 88 28 1 65 151 81 168 1.14e-35 121
Msa0101210 AT4G12500.1 64.773 88 30 1 65 151 90 177 6.21e-35 120
Msa0101210 AT1G62510.1 66.667 84 27 1 68 150 66 149 5.42e-33 114
Msa0101210 AT4G00165.1 49.533 107 48 2 45 150 27 128 3.23e-31 109
Msa0101210 AT4G00165.2 49.533 107 48 2 45 150 27 128 3.23e-31 109
Msa0101210 AT4G12520.1 47.059 153 55 4 1 151 1 129 1.20e-30 107
Msa0101210 AT4G12510.1 47.059 153 55 4 1 151 1 129 1.20e-30 107
Msa0101210 AT1G12100.1 43.151 146 60 4 7 151 9 132 1.52e-30 107
Msa0101210 AT5G46890.1 61.957 92 32 2 60 151 39 127 3.32e-30 106
Msa0101210 AT1G12090.1 65.000 80 27 1 72 150 58 137 1.47e-29 105
Msa0101210 AT5G46900.1 66.250 80 25 1 72 151 50 127 4.18e-29 103
Msa0101210 AT3G22142.1 56.701 97 39 3 55 150 1384 1478 2.76e-27 106
Msa0101210 AT4G12550.1 49.451 91 45 1 62 151 21 111 6.37e-27 97.8
Msa0101210 AT4G22460.1 47.059 119 44 2 32 149 31 131 3.18e-26 96.7
Msa0101210 AT4G12530.1 50.588 85 42 0 66 150 31 115 1.11e-25 94.7
Msa0101210 AT4G12545.1 50.549 91 41 2 62 151 21 108 1.59e-24 91.7
Msa0101210 AT2G10940.2 57.143 84 34 2 69 151 208 290 3.70e-23 92.4
Msa0101210 AT2G10940.1 57.143 84 34 2 69 151 208 290 3.70e-23 92.4
Msa0101210 AT3G22120.2 56.977 86 34 3 67 150 265 349 3.29e-21 88.2
Msa0101210 AT3G22120.1 56.977 86 34 3 67 150 248 332 5.29e-21 87.4
Msa0101210 AT4G15160.2 52.326 86 39 2 67 150 97 182 2.99e-19 80.1
Msa0101210 AT4G15160.1 52.326 86 39 2 67 150 179 264 5.14e-19 81.3
Msa0101210 AT1G62500.1 48.193 83 41 2 69 150 212 293 8.66e-19 80.9
Msa0101210 AT4G22490.1 38.710 93 50 3 61 150 28 116 3.25e-15 67.8

Find 34 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGAGAAAATAATATAATT+AGG 0.201862 1_3:+7780131 None:intergenic
TTGCCTTTGTACTGCTATTA+AGG 0.221337 1_3:-7779819 Msa0101210:CDS
CTAGGCTTTGGCTTTGGCTT+TGG 0.279961 1_3:+7780049 None:intergenic
GCTATTAAGGCTAATGTTCT+TGG 0.285703 1_3:-7779806 Msa0101210:CDS
GCTTCAAGGTTTGGTTGATT+TGG 0.319262 1_3:-7779852 Msa0101210:CDS
TTTGGCTTTGGCTTTGGCTT+AGG 0.346021 1_3:+7780055 None:intergenic
GGAGGACTAGGCTTTGGCTT+TGG 0.385876 1_3:+7780043 None:intergenic
GCTGGTGGAGGACTAGGCTT+TGG 0.388141 1_3:+7780037 None:intergenic
GGTGTGTGTGCTGATGTTCT+AGG 0.388503 1_3:-7779926 Msa0101210:CDS
GAGAGAAAATAATATAATTA+GGG 0.389348 1_3:+7780132 None:intergenic
GGACTTGTTAATATTATTGT+TGG 0.394838 1_3:-7779905 Msa0101210:CDS
AAGTGTTGTGCATTGCTTCA+AGG 0.409572 1_3:-7779866 Msa0101210:CDS
TTGTGCATTGCTTCAAGGTT+TGG 0.410333 1_3:-7779861 Msa0101210:CDS
AATTAGGGCACTAAGCTTGT+TGG 0.421182 1_3:+7780147 None:intergenic
GGTGAAGCTGGTGGAGGACT+AGG 0.427892 1_3:+7780031 None:intergenic
GGACATGGTGTTGGTGAAGC+TGG 0.438461 1_3:+7780019 None:intergenic
AGTAGGAGACTGAGTGTGAT+AGG 0.453246 1_3:+7779767 None:intergenic
TTTGGCTTTGGCTTAGGTGA+TGG 0.478826 1_3:+7780061 None:intergenic
GGAGGTGTTGCTGAAGGTGT+TGG 0.497717 1_3:+7779995 None:intergenic
GCTGAAGGTGTTGGAGGACA+TGG 0.512621 1_3:+7780004 None:intergenic
ACAAGAAAGTCTATGAACAT+TGG 0.516294 1_3:+7779711 None:intergenic
TGTGATGTTGAAGGAGTAGG+AGG 0.527946 1_3:+7779977 None:intergenic
TTTGGCTTAGGTGATGGAGT+TGG 0.542252 1_3:+7780067 None:intergenic
GCACAACACTTGCTAGAAGC+AGG 0.549118 1_3:+7779878 None:intergenic
GTGAAAATGTTGCATAAGCA+AGG 0.554272 1_3:+7780110 None:intergenic
CCTACTGACACATTAAAGCT+AGG 0.564359 1_3:-7779947 Msa0101210:CDS
CATGGTGTTGGTGAAGCTGG+TGG 0.586112 1_3:+7780022 None:intergenic
GGAGTAGGAGGTGTTGCTGA+AGG 0.590328 1_3:+7779989 None:intergenic
GGTGTTGGAGGACATGGTGT+TGG 0.594079 1_3:+7780010 None:intergenic
GGTGTTGGTGAAGCTGGTGG+AGG 0.615450 1_3:+7780025 None:intergenic
CCTAGCTTTAATGTGTCAGT+AGG 0.615781 1_3:+7779947 None:intergenic
GGTGTTGCTGAAGGTGTTGG+AGG 0.621506 1_3:+7779998 None:intergenic
TAGCCTTAATAGCAGTACAA+AGG 0.655083 1_3:+7779816 None:intergenic
TATGAACATTGGAAACCCGA+AGG 0.685560 1_3:+7779722 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAGAGAAAATAATATAATTA+GGG + chr1_3:7779746-7779765 None:intergenic 15.0%
!! GGAGAGAAAATAATATAATT+AGG + chr1_3:7779747-7779766 None:intergenic 20.0%
!!! GGACTTGTTAATATTATTGT+TGG - chr1_3:7779970-7779989 Msa0101210:CDS 25.0%
! ATTTTTCACAAGCACTAAGT+AGG + chr1_3:7780128-7780147 None:intergenic 30.0%
TTGTGAAAAATCTGTTCCTT+CGG - chr1_3:7780137-7780156 Msa0101210:CDS 30.0%
GTGAAAATGTTGCATAAGCA+AGG + chr1_3:7779768-7779787 None:intergenic 35.0%
! TTTTGTGATGTTGAAGGAGT+AGG + chr1_3:7779904-7779923 None:intergenic 35.0%
! GGACATTTTTGTGATGTTGA+AGG + chr1_3:7779910-7779929 None:intergenic 35.0%
TTGCCTTTGTACTGCTATTA+AGG - chr1_3:7780056-7780075 Msa0101210:CDS 35.0%
! TAGCCTTAATAGCAGTACAA+AGG + chr1_3:7780062-7780081 None:intergenic 35.0%
GCTATTAAGGCTAATGTTCT+TGG - chr1_3:7780069-7780088 Msa0101210:CDS 35.0%
TGTGAAAAATCTGTTCCTTC+GGG - chr1_3:7780138-7780157 Msa0101210:CDS 35.0%
! AATTAGGGCACTAAGCTTGT+TGG + chr1_3:7779731-7779750 None:intergenic 40.0%
! GCAACATTTTCACATGCTTG+TGG - chr1_3:7779775-7779794 Msa0101210:CDS 40.0%
!! CCTAGCTTTAATGTGTCAGT+AGG + chr1_3:7779931-7779950 None:intergenic 40.0%
CCTACTGACACATTAAAGCT+AGG - chr1_3:7779928-7779947 Msa0101210:CDS 40.0%
! AAGTGTTGTGCATTGCTTCA+AGG - chr1_3:7780009-7780028 Msa0101210:CDS 40.0%
TTGTGCATTGCTTCAAGGTT+TGG - chr1_3:7780014-7780033 Msa0101210:CDS 40.0%
! GCTTCAAGGTTTGGTTGATT+TGG - chr1_3:7780023-7780042 Msa0101210:CDS 40.0%
TATGAACATTGGAAACCCGA+AGG + chr1_3:7780156-7780175 None:intergenic 40.0%
!! TTTGGCTTAGGTGATGGAGT+TGG + chr1_3:7779811-7779830 None:intergenic 45.0%
!! TTTGGCTTTGGCTTAGGTGA+TGG + chr1_3:7779817-7779836 None:intergenic 45.0%
!! TTTGGCTTTGGCTTTGGCTT+AGG + chr1_3:7779823-7779842 None:intergenic 45.0%
TGTGATGTTGAAGGAGTAGG+AGG + chr1_3:7779901-7779920 None:intergenic 45.0%
AGTAGGAGACTGAGTGTGAT+AGG + chr1_3:7780111-7780130 None:intergenic 45.0%
!! CTAGGCTTTGGCTTTGGCTT+TGG + chr1_3:7779829-7779848 None:intergenic 50.0%
! GGTGTGTGTGCTGATGTTCT+AGG - chr1_3:7779949-7779968 Msa0101210:CDS 50.0%
! GCACAACACTTGCTAGAAGC+AGG + chr1_3:7780000-7780019 None:intergenic 50.0%
! GGAGGACTAGGCTTTGGCTT+TGG + chr1_3:7779835-7779854 None:intergenic 55.0%
!! CATGGTGTTGGTGAAGCTGG+TGG + chr1_3:7779856-7779875 None:intergenic 55.0%
!! GGACATGGTGTTGGTGAAGC+TGG + chr1_3:7779859-7779878 None:intergenic 55.0%
! GGTGTTGGAGGACATGGTGT+TGG + chr1_3:7779868-7779887 None:intergenic 55.0%
!! GCTGAAGGTGTTGGAGGACA+TGG + chr1_3:7779874-7779893 None:intergenic 55.0%
!! GGTGTTGCTGAAGGTGTTGG+AGG + chr1_3:7779880-7779899 None:intergenic 55.0%
!! GGAGGTGTTGCTGAAGGTGT+TGG + chr1_3:7779883-7779902 None:intergenic 55.0%
!! GGAGTAGGAGGTGTTGCTGA+AGG + chr1_3:7779889-7779908 None:intergenic 55.0%
GCTGGTGGAGGACTAGGCTT+TGG + chr1_3:7779841-7779860 None:intergenic 60.0%
GGTGAAGCTGGTGGAGGACT+AGG + chr1_3:7779847-7779866 None:intergenic 60.0%
!! GGTGTTGGTGAAGCTGGTGG+AGG + chr1_3:7779853-7779872 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 7779721 7780176 7779721 ID=Msa0101210;Name=Msa0101210
chr1_3 mRNA 7779721 7780176 7779721 ID=Msa0101210-mRNA-1;Parent=Msa0101210;Name=Msa0101210-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|151
chr1_3 exon 7779721 7780176 7779721 ID=Msa0101210-mRNA-1:exon:3058;Parent=Msa0101210-mRNA-1
chr1_3 CDS 7779721 7780176 7779721 ID=Msa0101210-mRNA-1:cds;Parent=Msa0101210-mRNA-1
Gene Sequence

>Msa0101210

ATGGCTTCCAACAAGCTTAGTGCCCTAATTATATTATTTTCTCTCCTTGCTTATGCAACATTTTCACATGCTTGTGGTTCATGCAAACCAACTCCATCACCTAAGCCAAAGCCAAAGCCAAAGCCTAGTCCTCCACCAGCTTCACCAACACCATGTCCTCCAACACCTTCAGCAACACCTCCTACTCCTTCAACATCACAAAAATGTCCTACTGACACATTAAAGCTAGGTGTGTGTGCTGATGTTCTAGGACTTGTTAATATTATTGTTGGAAGTCCTGCTTCTAGCAAGTGTTGTGCATTGCTTCAAGGTTTGGTTGATTTGGATGCAGCAATTTGCCTTTGTACTGCTATTAAGGCTAATGTTCTTGGTATCAACTTGAATGTTCCTATCACACTCAGTCTCCTACTTAGTGCTTGTGAAAAATCTGTTCCTTCGGGTTTCCAATGTTCATAG
Protein sequence

>Msa0101210

MASNKLSALIILFSLLAYATFSHACGSCKPTPSPKPKPKPKPSPPPASPTPCPPTPSATPPTPSTSQKCPTDTLKLGVCADVLGLVNIIVGSPASSKCCALLQGLVDLDAAICLCTAIKANVLGINLNVPITLSLLLSACEKSVPSGFQCS*