AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0006580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0006580 MtrunA17_Chr1g0149491 95.425 153 5 1 1 153 1 151 2.09e-95 272
Msa0006580 MtrunA17_Chr1g0149481 75.000 164 30 1 1 153 1 164 6.16e-74 218
Msa0006580 MtrunA17_Chr1g0149471 55.556 216 27 4 1 153 1 210 6.92e-56 174
Msa0006580 MtrunA17_Chr3g0137521 61.438 153 34 3 1 152 1 129 1.03e-46 148
Msa0006580 MtrunA17_Chr4g0056411 45.833 168 75 3 1 152 1 168 1.71e-37 126
Msa0006580 MtrunA17_Chr3g0137531 57.692 156 36 3 1 153 1 129 2.80e-36 121
Msa0006580 MtrunA17_Chr4g0060391 55.556 108 40 2 49 153 21 123 1.81e-34 117
Msa0006580 MtrunA17_Chr4g0056371 63.855 83 30 0 71 153 50 132 3.79e-33 114
Msa0006580 MtrunA17_Chr4g0056391 63.636 88 31 1 67 153 56 143 5.55e-32 111
Msa0006580 MtrunA17_Chr4g0056401 59.091 88 35 1 67 153 47 134 2.27e-31 109
Msa0006580 MtrunA17_Chr2g0290521 55.556 90 39 1 64 153 39 127 6.54e-27 97.8
Msa0006580 MtrunA17_Chr5g0399081 50.575 87 41 2 67 152 91 176 1.28e-25 96.3
Msa0006580 MtrunA17_Chr5g0399091 49.425 87 42 2 67 152 84 169 3.59e-25 94.7
Msa0006580 MtrunA17_Chr4g0056381 52.941 85 38 2 69 152 103 186 2.42e-23 90.5
Msa0006580 MtrunA17_Chr2g0290571 44.706 85 43 2 69 153 119 199 6.90e-20 81.6
Msa0006580 MtrunA17_Chr2g0290561 44.048 84 43 2 69 152 115 194 2.49e-18 77.8
Msa0006580 MtrunA17_Chr3g0120411 52.326 86 39 2 68 152 251 335 9.48e-18 78.2
Msa0006580 MtrunA17_Chr2g0290531 42.529 87 43 3 69 153 179 260 2.90e-16 73.2
Msa0006580 MtrunA17_Chr4g0064361 53.571 84 37 2 71 153 151 233 3.83e-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
Msa0006580 AT4G12490.1 45.355 183 69 3 1 153 1 182 1.56e-42 139
Msa0006580 AT2G45180.1 75.904 83 20 0 71 153 52 134 2.22e-39 130
Msa0006580 AT4G12470.1 66.292 89 29 1 66 153 73 161 1.42e-36 124
Msa0006580 AT4G12480.1 67.045 88 28 1 67 153 81 168 1.29e-35 121
Msa0006580 AT4G12500.1 43.820 178 74 4 1 153 1 177 1.87e-35 121
Msa0006580 AT1G62510.1 66.667 84 27 1 70 152 66 149 6.27e-33 114
Msa0006580 AT4G00165.1 49.533 107 48 2 47 152 27 128 3.31e-31 109
Msa0006580 AT4G00165.2 49.533 107 48 2 47 152 27 128 3.31e-31 109
Msa0006580 AT4G12520.1 62.376 101 36 2 54 153 30 129 2.21e-30 107
Msa0006580 AT4G12510.1 62.376 101 36 2 54 153 30 129 2.21e-30 107
Msa0006580 AT5G46890.1 61.957 92 32 2 62 153 39 127 4.14e-30 106
Msa0006580 AT1G12100.1 41.892 148 61 4 7 153 9 132 5.50e-30 106
Msa0006580 AT1G12090.1 65.000 80 27 1 74 152 58 137 1.70e-29 105
Msa0006580 AT5G46900.1 66.250 80 25 1 74 153 50 127 4.99e-29 103
Msa0006580 AT3G22142.1 56.701 97 39 3 57 152 1384 1478 2.37e-27 107
Msa0006580 AT4G12550.1 49.451 91 45 1 64 153 21 111 6.73e-27 97.8
Msa0006580 AT4G22460.1 44.444 126 47 2 27 151 28 131 5.02e-26 96.3
Msa0006580 AT4G12530.1 50.588 85 42 0 68 152 31 115 1.28e-25 94.7
Msa0006580 AT4G12545.1 50.549 91 41 2 64 153 21 108 1.60e-24 91.7
Msa0006580 AT2G10940.2 57.143 84 34 2 71 153 208 290 4.57e-23 92.4
Msa0006580 AT2G10940.1 57.143 84 34 2 71 153 208 290 4.57e-23 92.4
Msa0006580 AT3G22120.2 56.977 86 34 3 69 152 265 349 2.92e-21 88.2
Msa0006580 AT3G22120.1 56.977 86 34 3 69 152 248 332 4.54e-21 87.8
Msa0006580 AT4G15160.2 52.326 86 39 2 69 152 97 182 3.11e-19 80.1
Msa0006580 AT4G15160.1 52.326 86 39 2 69 152 179 264 5.52e-19 81.3
Msa0006580 AT1G62500.1 48.193 83 41 2 71 152 212 293 8.39e-19 80.9
Msa0006580 AT4G22490.1 38.710 93 50 3 63 152 28 116 3.40e-15 67.8

Find 35 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAGAGAAAATAATATAATT+AGG 0.201862 1_1:-9537753 None:intergenic
TTGCCTTTGTACTGCTATTA+AGG 0.221337 1_1:+9538071 Msa0006580:CDS
CTAGGCTTTGGCTTTGGCTT+TGG 0.279961 1_1:-9537841 None:intergenic
GCTATTAAGGCTAATGTTCT+TGG 0.285703 1_1:+9538084 Msa0006580:CDS
GCTTCAAGGTTTGGTTGATT+TGG 0.319262 1_1:+9538038 Msa0006580:CDS
TTTGGCTTTGGCTTTGGCTT+AGG 0.340034 1_1:-9537835 None:intergenic
TTTGGCTTTGGCTTAGGCTT+AGG 0.360992 1_1:-9537829 None:intergenic
GGAGGACTAGGCTTTGGCTT+TGG 0.385876 1_1:-9537847 None:intergenic
GCTGGTGGAGGACTAGGCTT+TGG 0.388141 1_1:-9537853 None:intergenic
GGTGTGTGTGCTGATGTTCT+AGG 0.388503 1_1:+9537964 Msa0006580:CDS
GAGAGAAAATAATATAATTA+GGG 0.389348 1_1:-9537752 None:intergenic
GGACTTGTTAATATTATTGT+TGG 0.394838 1_1:+9537985 Msa0006580:CDS
AAGTGTTGTGCATTGCTTCA+AGG 0.409572 1_1:+9538024 Msa0006580:CDS
TTGTGCATTGCTTCAAGGTT+TGG 0.410333 1_1:+9538029 Msa0006580:CDS
AATTAGGGCACTAAGCTTGT+TGG 0.421182 1_1:-9537737 None:intergenic
GGTGAAGCTGGTGGAGGACT+AGG 0.427892 1_1:-9537859 None:intergenic
GGACATGGTGTTGGTGAAGC+TGG 0.438461 1_1:-9537871 None:intergenic
AGTAGGAGACTGAGTGTGAT+AGG 0.453246 1_1:-9538123 None:intergenic
GGAGGTGTTGCTGAAGGTGT+TGG 0.497717 1_1:-9537895 None:intergenic
TTAGGCTTAGGTGATGGAGT+TGG 0.509676 1_1:-9537817 None:intergenic
GCTGAAGGTGTTGGAGGACA+TGG 0.512621 1_1:-9537886 None:intergenic
ACAAGAAAGTCTATGAACAT+TGG 0.516294 1_1:-9538179 None:intergenic
TTTGGCTTAGGCTTAGGTGA+TGG 0.525931 1_1:-9537823 None:intergenic
TGTGATGTTGAAGGAGTAGG+AGG 0.527946 1_1:-9537913 None:intergenic
GTGAAAATGTTGAATAAGCA+AGG 0.536879 1_1:-9537774 None:intergenic
GCACAACACTTGCTAGAAGC+AGG 0.549118 1_1:-9538012 None:intergenic
CCTACTGACACATTAAAGCT+AGG 0.564359 1_1:+9537943 Msa0006580:CDS
CATGGTGTTGGTGAAGCTGG+TGG 0.586112 1_1:-9537868 None:intergenic
GGAGTAGGAGGTGTTGCTGA+AGG 0.590328 1_1:-9537901 None:intergenic
GGTGTTGGAGGACATGGTGT+TGG 0.594079 1_1:-9537880 None:intergenic
GGTGTTGGTGAAGCTGGTGG+AGG 0.615450 1_1:-9537865 None:intergenic
CCTAGCTTTAATGTGTCAGT+AGG 0.615781 1_1:-9537943 None:intergenic
GGTGTTGCTGAAGGTGTTGG+AGG 0.621506 1_1:-9537892 None:intergenic
TAGCCTTAATAGCAGTACAA+AGG 0.655083 1_1:-9538074 None:intergenic
TATGAACATTGGAAACCCGA+AGG 0.685560 1_1:-9538168 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAGAGAAAATAATATAATTA+GGG - chr1_1:9537755-9537774 None:intergenic 15.0%
!! GGAGAGAAAATAATATAATT+AGG - chr1_1:9537756-9537775 None:intergenic 20.0%
!!! GGACTTGTTAATATTATTGT+TGG + chr1_1:9537985-9538004 Msa0006580:CDS 25.0%
GTGAAAATGTTGAATAAGCA+AGG - chr1_1:9537777-9537796 None:intergenic 30.0%
! ATTTTTCACAAGCACTAAGT+AGG - chr1_1:9538143-9538162 None:intergenic 30.0%
TTGTGAAAAATCTGTTCCTT+CGG + chr1_1:9538152-9538171 Msa0006580:CDS 30.0%
! TCAACATTTTCACATGCTTG+TGG + chr1_1:9537784-9537803 Msa0006580:CDS 35.0%
! TTTTGTGATGTTGAAGGAGT+AGG - chr1_1:9537919-9537938 None:intergenic 35.0%
! GGACATTTTTGTGATGTTGA+AGG - chr1_1:9537925-9537944 None:intergenic 35.0%
TTGCCTTTGTACTGCTATTA+AGG + chr1_1:9538071-9538090 Msa0006580:CDS 35.0%
! TAGCCTTAATAGCAGTACAA+AGG - chr1_1:9538077-9538096 None:intergenic 35.0%
GCTATTAAGGCTAATGTTCT+TGG + chr1_1:9538084-9538103 Msa0006580:CDS 35.0%
TGTGAAAAATCTGTTCCTTC+GGG + chr1_1:9538153-9538172 Msa0006580:CDS 35.0%
! AATTAGGGCACTAAGCTTGT+TGG - chr1_1:9537740-9537759 None:intergenic 40.0%
!! CCTAGCTTTAATGTGTCAGT+AGG - chr1_1:9537946-9537965 None:intergenic 40.0%
CCTACTGACACATTAAAGCT+AGG + chr1_1:9537943-9537962 Msa0006580:CDS 40.0%
! AAGTGTTGTGCATTGCTTCA+AGG + chr1_1:9538024-9538043 Msa0006580:CDS 40.0%
TTGTGCATTGCTTCAAGGTT+TGG + chr1_1:9538029-9538048 Msa0006580:CDS 40.0%
! GCTTCAAGGTTTGGTTGATT+TGG + chr1_1:9538038-9538057 Msa0006580:CDS 40.0%
TATGAACATTGGAAACCCGA+AGG - chr1_1:9538171-9538190 None:intergenic 40.0%
!! TTAGGCTTAGGTGATGGAGT+TGG - chr1_1:9537820-9537839 None:intergenic 45.0%
! TTTGGCTTAGGCTTAGGTGA+TGG - chr1_1:9537826-9537845 None:intergenic 45.0%
!! TTTGGCTTTGGCTTAGGCTT+AGG - chr1_1:9537832-9537851 None:intergenic 45.0%
!! TTTGGCTTTGGCTTTGGCTT+AGG - chr1_1:9537838-9537857 None:intergenic 45.0%
TGTGATGTTGAAGGAGTAGG+AGG - chr1_1:9537916-9537935 None:intergenic 45.0%
AGTAGGAGACTGAGTGTGAT+AGG - chr1_1:9538126-9538145 None:intergenic 45.0%
!! CTAGGCTTTGGCTTTGGCTT+TGG - chr1_1:9537844-9537863 None:intergenic 50.0%
! GGTGTGTGTGCTGATGTTCT+AGG + chr1_1:9537964-9537983 Msa0006580:CDS 50.0%
! GCACAACACTTGCTAGAAGC+AGG - chr1_1:9538015-9538034 None:intergenic 50.0%
! GGAGGACTAGGCTTTGGCTT+TGG - chr1_1:9537850-9537869 None:intergenic 55.0%
!! CATGGTGTTGGTGAAGCTGG+TGG - chr1_1:9537871-9537890 None:intergenic 55.0%
!! GGACATGGTGTTGGTGAAGC+TGG - chr1_1:9537874-9537893 None:intergenic 55.0%
! GGTGTTGGAGGACATGGTGT+TGG - chr1_1:9537883-9537902 None:intergenic 55.0%
!! GCTGAAGGTGTTGGAGGACA+TGG - chr1_1:9537889-9537908 None:intergenic 55.0%
!! GGTGTTGCTGAAGGTGTTGG+AGG - chr1_1:9537895-9537914 None:intergenic 55.0%
!! GGAGGTGTTGCTGAAGGTGT+TGG - chr1_1:9537898-9537917 None:intergenic 55.0%
!! GGAGTAGGAGGTGTTGCTGA+AGG - chr1_1:9537904-9537923 None:intergenic 55.0%
GCTGGTGGAGGACTAGGCTT+TGG - chr1_1:9537856-9537875 None:intergenic 60.0%
GGTGAAGCTGGTGGAGGACT+AGG - chr1_1:9537862-9537881 None:intergenic 60.0%
!! GGTGTTGGTGAAGCTGGTGG+AGG - chr1_1:9537868-9537887 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 9537730 9538191 9537730 ID=Msa0006580;Name=Msa0006580
chr1_1 mRNA 9537730 9538191 9537730 ID=Msa0006580-mRNA-1;Parent=Msa0006580;Name=Msa0006580-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|153
chr1_1 exon 9537730 9538191 9537730 ID=Msa0006580-mRNA-1:exon:3408;Parent=Msa0006580-mRNA-1
chr1_1 CDS 9537730 9538191 9537730 ID=Msa0006580-mRNA-1:cds;Parent=Msa0006580-mRNA-1
Gene Sequence

>Msa0006580

ATGGCTTCCAACAAGCTTAGTGCCCTAATTATATTATTTTCTCTCCTTGCTTATTCAACATTTTCACATGCTTGTGGTTCATGCAAACCAACTCCATCACCTAAGCCTAAGCCAAAGCCAAAGCCAAAGCCTAGTCCTCCACCAGCTTCACCAACACCATGTCCTCCAACACCTTCAGCAACACCTCCTACTCCTTCAACATCACAAAAATGTCCTACTGACACATTAAAGCTAGGTGTGTGTGCTGATGTTCTAGGACTTGTTAATATTATTGTTGGAAGTCCTGCTTCTAGCAAGTGTTGTGCATTGCTTCAAGGTTTGGTTGATTTGGATGCAGCAATTTGCCTTTGTACTGCTATTAAGGCTAATGTTCTTGGTATCAACTTGAATGTTCCTATCACACTCAGTCTCCTACTTAGTGCTTGTGAAAAATCTGTTCCTTCGGGTTTCCAATGTTCATAG

Protein sequence

>Msa0006580

MASNKLSALIILFSLLAYSTFSHACGSCKPTPSPKPKPKPKPKPSPPPASPTPCPPTPSATPPTPSTSQKCPTDTLKLGVCADVLGLVNIIVGSPASSKCCALLQGLVDLDAAICLCTAIKANVLGINLNVPITLSLLLSACEKSVPSGFQCS*