AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1269800

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269800 MtrunA17_Chr3g0085321 93.651 189 12 0 1 189 1 189 2.52e-128 358
Msa1269800 MtrunA17_Chr3g0085301 81.481 189 35 0 1 189 6 194 1.77e-112 318
Msa1269800 MtrunA17_Chr3g0090231 73.262 187 44 2 1 186 1 182 3.16e-98 282
Msa1269800 MtrunA17_Chr4g0040551 72.727 187 45 2 1 186 1 182 1.26e-97 280
Msa1269800 MtrunA17_Chr3g0085311 65.079 189 66 0 1 189 1 189 1.43e-88 258
Msa1269800 MtrunA17_Chr3g0085291 64.021 189 66 2 1 189 1 187 1.79e-84 247
Msa1269800 MtrunA17_Chr1g0177051 51.572 159 73 3 30 186 27 183 5.09e-48 154
Msa1269800 MtrunA17_Chr1g0175911 50.000 148 70 3 41 186 44 189 8.28e-45 147
Msa1269800 MtrunA17_Chr4g0005081 47.973 148 75 1 41 186 47 194 5.85e-43 142
Msa1269800 MtrunA17_Chr4g0005031 46.622 148 77 1 41 186 71 218 1.34e-41 139
Msa1269800 MtrunA17_Chr4g0005071 45.270 148 79 1 41 186 46 193 1.33e-40 136
Msa1269800 MtrunA17_Chr4g0005041 43.243 148 82 1 41 186 48 195 2.47e-39 133
Msa1269800 MtrunA17_Chr7g0259071 40.909 176 88 4 17 184 19 186 3.73e-38 129
Msa1269800 MtrunA17_Chr4g0005011 43.836 146 78 2 43 186 51 194 3.87e-38 130
Msa1269800 MtrunA17_Chr7g0259091 40.722 194 104 5 1 186 1 191 3.85e-37 127
Msa1269800 MtrunA17_Chr7g0243501 38.421 190 112 3 1 186 1 189 8.28e-37 126
Msa1269800 MtrunA17_Chr4g0005111 37.234 188 117 1 1 187 1 188 1.64e-36 125
Msa1269800 MtrunA17_Chr7g0259101 42.784 194 100 5 1 186 1 191 4.20e-36 129
Msa1269800 MtrunA17_Chr7g0259101 41.436 181 97 4 10 184 211 388 6.52e-35 126
Msa1269800 MtrunA17_Chr7g0259121 45.161 155 74 4 41 186 38 190 9.36e-36 124
Msa1269800 MtrunA17_Chr4g0037481 37.500 152 92 1 38 186 38 189 1.69e-33 118
Msa1269800 MtrunA17_Chr5g0446751 39.153 189 96 7 7 186 8 186 1.69e-32 115
Msa1269800 MtrunA17_Chr3g0136631 42.000 150 80 4 43 186 38 186 1.27e-30 110
Msa1269800 MtrunA17_Chr4g0005131 36.709 158 95 2 34 187 33 189 9.17e-30 108
Msa1269800 MtrunA17_Chr3g0136641 42.282 149 80 4 43 186 38 185 1.05e-28 105
Msa1269800 MtrunA17_Chr4g0068391 34.503 171 92 3 4 170 9 163 3.58e-23 90.9
Msa1269800 MtrunA17_Chr4g0024951 31.690 142 95 1 50 189 37 178 9.29e-22 87.4
Msa1269800 MtrunA17_Chr4g0024961 33.803 142 92 1 50 189 37 178 1.83e-21 86.7
Msa1269800 MtrunA17_Chr4g0068381 37.398 123 73 2 46 165 35 156 2.42e-20 83.6
Msa1269800 MtrunA17_Chr4g0005091 31.694 183 107 3 7 187 7 173 1.49e-19 81.6
Msa1269800 MtrunA17_Chr1g0169281 36.634 101 63 1 64 164 129 228 9.06e-13 64.7
Msa1269800 MtrunA17_Chr1g0169511 39.326 89 53 1 76 164 135 222 3.87e-12 63.2
Msa1269800 MtrunA17_Chr1g0169291 39.326 89 53 1 76 164 135 222 5.01e-12 62.8
Msa1269800 MtrunA17_Chr1g0212861 37.363 91 54 2 77 164 235 325 8.17e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269800 AT1G22900.1 41.808 177 95 3 10 184 19 189 1.72e-45 149
Msa1269800 AT1G65870.1 42.515 167 92 2 22 186 23 187 6.28e-44 145
Msa1269800 AT5G42500.1 41.509 159 89 3 28 184 25 181 8.94e-41 136
Msa1269800 AT5G42510.1 42.484 153 80 3 36 184 30 178 2.02e-40 135
Msa1269800 AT2G21100.1 43.421 152 82 2 38 186 35 185 3.83e-38 130
Msa1269800 AT2G21100.2 43.421 152 82 2 38 186 35 185 3.83e-38 130
Msa1269800 AT1G58170.1 37.569 181 105 3 6 184 6 180 4.09e-37 127
Msa1269800 AT3G13650.1 40.411 146 86 1 41 186 39 183 8.04e-35 121
Msa1269800 AT1G55210.1 37.349 166 99 3 6 168 3 166 2.26e-34 120
Msa1269800 AT1G55210.2 37.349 166 99 3 6 168 3 166 2.26e-34 120
Msa1269800 AT5G49040.1 38.750 160 92 4 13 168 13 170 4.04e-32 114
Msa1269800 AT3G58090.1 49.524 105 53 0 82 186 165 269 1.45e-30 112
Msa1269800 AT3G13662.1 39.844 128 76 1 41 168 38 164 7.30e-30 108
Msa1269800 AT5G49030.3 40.458 131 74 2 41 168 41 170 1.53e-29 114
Msa1269800 AT4G38700.1 38.562 153 84 4 43 186 36 187 4.33e-28 104
Msa1269800 AT2G21110.1 35.714 154 91 2 40 186 31 183 5.59e-26 99.0
Msa1269800 AT3G13660.1 40.000 115 69 0 72 186 8 122 2.67e-24 92.8
Msa1269800 AT4G11210.1 28.492 179 122 5 9 186 6 179 7.05e-14 67.0
Msa1269800 AT4G11190.1 26.994 163 111 5 30 186 19 179 1.52e-11 60.8
Msa1269800 AT1G64160.1 28.205 156 103 5 36 186 27 178 8.10e-11 58.9

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCCATTTGGTACATTTAT+TGG 0.153260 8_3:+3106066 None:intergenic
CTTTCTTCACTTCAAGATCT+TGG 0.247590 8_3:-3105955 Msa1269800:CDS
TACTCAACAACAAAATGTTC+AGG 0.343328 8_3:+3105751 None:intergenic
ATAAATGTACCAAATGGATT+TGG 0.359511 8_3:-3106063 Msa1269800:CDS
GGAAGAGCTCAAGGGTTGTT+TGG 0.380080 8_3:-3105979 Msa1269800:CDS
TAATGTCATGGTAGTAGAAA+TGG 0.395728 8_3:+3106130 None:intergenic
ATGCCTATTGTTGGTGGAAC+TGG 0.410474 8_3:-3105832 Msa1269800:CDS
TGTGTCAATGATTTGTACTA+TGG 0.414022 8_3:+3106089 None:intergenic
ACTCAATTAACAACCACAAA+TGG 0.417248 8_3:-3106222 Msa1269800:CDS
AAAGTTGAACCAAATCCATT+TGG 0.421388 8_3:+3106054 None:intergenic
AAAATGTTCAGGGGTAGAAA+TGG 0.424631 8_3:+3105762 None:intergenic
GGAAGTAGTCTTAGTATGTT+GGG 0.434106 8_3:-3105886 Msa1269800:CDS
ACACCAGTTCCACCAACAAT+AGG 0.442036 8_3:+3105829 None:intergenic
TGTGTTAGTTTCTCTGTTCG+TGG 0.453538 8_3:+3106156 None:intergenic
CTCTGTTCGTGGTTGTTCTG+AGG 0.455164 8_3:+3106167 None:intergenic
TCTGTTCGTGGTTGTTCTGA+GGG 0.458437 8_3:+3106168 None:intergenic
TGGAAGTAGTCTTAGTATGT+TGG 0.463038 8_3:-3105887 Msa1269800:CDS
ACACCAATAAATGTACCAAA+TGG 0.472256 8_3:-3106069 Msa1269800:CDS
AATAGAGAAATGCCTATTGT+TGG 0.476777 8_3:-3105841 Msa1269800:CDS
TTCTGAGGGTAATATGATGT+TGG 0.478821 8_3:+3106182 None:intergenic
TTGTGAGAAATCTCCATTTG+TGG 0.485204 8_3:+3106209 None:intergenic
AGAGAAATGCCTATTGTTGG+TGG 0.518085 8_3:-3105838 Msa1269800:CDS
ATGTGATTTGAACTTAACTC+TGG 0.531516 8_3:+3106003 None:intergenic
TCAATGATTTGTACTATGGT+GGG 0.533940 8_3:+3106093 None:intergenic
ACTCAACAACAAAATGTTCA+GGG 0.537652 8_3:+3105752 None:intergenic
AAATGAGTGTGAGGGAGAAG+AGG 0.539387 8_3:+3106247 None:intergenic
AATCACATTGGAAGAGCTCA+AGG 0.541975 8_3:-3105988 Msa1269800:CDS
GTCAATGATTTGTACTATGG+TGG 0.552285 8_3:+3106092 None:intergenic
TTTAAGGAAGGGGAATATGG+TGG 0.575067 8_3:-3105907 Msa1269800:CDS
CAATGATTTGTACTATGGTG+GGG 0.575820 8_3:+3106094 None:intergenic
GTAGTCTTAGTATGTTGGGA+AGG 0.607491 8_3:-3105882 Msa1269800:CDS
ATGGATGATGCAATGACTGA+AGG 0.615844 8_3:-3106027 Msa1269800:CDS
TGGATGATGCAATGACTGAA+GGG 0.619095 8_3:-3106026 Msa1269800:CDS
CTCAACAACAAAATGTTCAG+GGG 0.634579 8_3:+3105753 None:intergenic
ATTGAGTGAAAATGAGTGTG+AGG 0.635383 8_3:+3106238 None:intergenic
GAGTTAAGTTCAAATCACAT+TGG 0.654375 8_3:-3106000 Msa1269800:CDS
TTGAGTGAAAATGAGTGTGA+GGG 0.676577 8_3:+3106239 None:intergenic
ATCACATTGGAAGAGCTCAA+GGG 0.681788 8_3:-3105987 Msa1269800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTGACAAATTTTGTTTTTA+AGG - chr8_3:3106076-3106095 Msa1269800:CDS 20.0%
!!! ACAAATTTTGTTTTTAAGGA+AGG - chr8_3:3106080-3106099 Msa1269800:CDS 20.0%
!!! CAAATTTTGTTTTTAAGGAA+GGG - chr8_3:3106081-3106100 Msa1269800:CDS 20.0%
!!! AAATTTTGTTTTTAAGGAAG+GGG - chr8_3:3106082-3106101 Msa1269800:CDS 20.0%
! AATCCATTTGGTACATTTAT+TGG + chr8_3:3105936-3105955 None:intergenic 25.0%
!! ATAAATGTACCAAATGGATT+TGG - chr8_3:3105936-3105955 Msa1269800:CDS 25.0%
!!! ATTTGGTTCAACTTTTATGA+TGG - chr8_3:3105953-3105972 Msa1269800:CDS 25.0%
!! TCTCTATTTTGTTCAGAAAT+AGG + chr8_3:3106146-3106165 None:intergenic 25.0%
ACTCAATTAACAACCACAAA+TGG - chr8_3:3105777-3105796 Msa1269800:CDS 30.0%
TAATGTCATGGTAGTAGAAA+TGG + chr8_3:3105872-3105891 None:intergenic 30.0%
!! TTTTGTTGTCTCTAATGTCA+TGG + chr8_3:3105884-3105903 None:intergenic 30.0%
! TCAATGATTTGTACTATGGT+GGG + chr8_3:3105909-3105928 None:intergenic 30.0%
! TGTGTCAATGATTTGTACTA+TGG + chr8_3:3105913-3105932 None:intergenic 30.0%
ACACCAATAAATGTACCAAA+TGG - chr8_3:3105930-3105949 Msa1269800:CDS 30.0%
AAAGTTGAACCAAATCCATT+TGG + chr8_3:3105948-3105967 None:intergenic 30.0%
ATGTGATTTGAACTTAACTC+TGG + chr8_3:3105999-3106018 None:intergenic 30.0%
GAGTTAAGTTCAAATCACAT+TGG - chr8_3:3105999-3106018 Msa1269800:CDS 30.0%
AATAGAGAAATGCCTATTGT+TGG - chr8_3:3106158-3106177 Msa1269800:CDS 30.0%
!!! GTGTTTTTAGATTTGCTAGA+GGG - chr8_3:3106189-3106208 Msa1269800:CDS 30.0%
ACTCAACAACAAAATGTTCA+GGG + chr8_3:3106250-3106269 None:intergenic 30.0%
TACTCAACAACAAAATGTTC+AGG + chr8_3:3106251-3106270 None:intergenic 30.0%
TTGAGTGAAAATGAGTGTGA+GGG + chr8_3:3105763-3105782 None:intergenic 35.0%
ATTGAGTGAAAATGAGTGTG+AGG + chr8_3:3105764-3105783 None:intergenic 35.0%
TTGTGAGAAATCTCCATTTG+TGG + chr8_3:3105793-3105812 None:intergenic 35.0%
! TTCTGAGGGTAATATGATGT+TGG + chr8_3:3105820-3105839 None:intergenic 35.0%
! CAATGATTTGTACTATGGTG+GGG + chr8_3:3105908-3105927 None:intergenic 35.0%
! GTCAATGATTTGTACTATGG+TGG + chr8_3:3105910-3105929 None:intergenic 35.0%
CTTTCTTCACTTCAAGATCT+TGG - chr8_3:3106044-3106063 Msa1269800:CDS 35.0%
!! GTTTTTAAGGAAGGGGAATA+TGG - chr8_3:3106089-3106108 Msa1269800:CDS 35.0%
! TGGAAGTAGTCTTAGTATGT+TGG - chr8_3:3106112-3106131 Msa1269800:CDS 35.0%
! GGAAGTAGTCTTAGTATGTT+GGG - chr8_3:3106113-3106132 Msa1269800:CDS 35.0%
!!! GGTGTTTTTAGATTTGCTAG+AGG - chr8_3:3106188-3106207 Msa1269800:CDS 35.0%
AAAATGTTCAGGGGTAGAAA+TGG + chr8_3:3106240-3106259 None:intergenic 35.0%
CTCAACAACAAAATGTTCAG+GGG + chr8_3:3106249-3106268 None:intergenic 35.0%
! TGTGTTAGTTTCTCTGTTCG+TGG + chr8_3:3105846-3105865 None:intergenic 40.0%
ATGGATGATGCAATGACTGA+AGG - chr8_3:3105972-3105991 Msa1269800:CDS 40.0%
TGGATGATGCAATGACTGAA+GGG - chr8_3:3105973-3105992 Msa1269800:CDS 40.0%
AATCACATTGGAAGAGCTCA+AGG - chr8_3:3106011-3106030 Msa1269800:CDS 40.0%
ATCACATTGGAAGAGCTCAA+GGG - chr8_3:3106012-3106031 Msa1269800:CDS 40.0%
TTTAAGGAAGGGGAATATGG+TGG - chr8_3:3106092-3106111 Msa1269800:CDS 40.0%
! GTAGTCTTAGTATGTTGGGA+AGG - chr8_3:3106117-3106136 Msa1269800:CDS 40.0%
AGAGAAATGCCTATTGTTGG+TGG - chr8_3:3106161-3106180 Msa1269800:CDS 40.0%
AAATGAGTGTGAGGGAGAAG+AGG + chr8_3:3105755-3105774 None:intergenic 45.0%
TCTGTTCGTGGTTGTTCTGA+GGG + chr8_3:3105834-3105853 None:intergenic 45.0%
! ATGCCTATTGTTGGTGGAAC+TGG - chr8_3:3106167-3106186 Msa1269800:CDS 45.0%
ACACCAGTTCCACCAACAAT+AGG + chr8_3:3106173-3106192 None:intergenic 45.0%
CTCTGTTCGTGGTTGTTCTG+AGG + chr8_3:3105835-3105854 None:intergenic 50.0%
GGAAGAGCTCAAGGGTTGTT+TGG - chr8_3:3106020-3106039 Msa1269800:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 3105726 3106295 3105726 ID=Msa1269800;Name=Msa1269800
chr8_3 mRNA 3105726 3106295 3105726 ID=Msa1269800-mRNA-1;Parent=Msa1269800;Name=Msa1269800-mRNA-1;_AED=0.41;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|189
chr8_3 exon 3105726 3106295 3105726 ID=Msa1269800-mRNA-1:exon:1014;Parent=Msa1269800-mRNA-1
chr8_3 CDS 3105726 3106295 3105726 ID=Msa1269800-mRNA-1:cds;Parent=Msa1269800-mRNA-1
Gene Sequence

>Msa1269800

ATGGCACTTTCACATAGTTTCTTTTTCCTCTTCTCCCTCACACTCATTTTCACTCAATTAACAACCACAAATGGAGATTTCTCACAACAATCCAACATCATATTACCCTCAGAACAACCACGAACAGAGAAACTAACACATATCCATTTCTACTACCATGACATTAGAGACAACAAAAGCCCCACCATAGTACAAATCATTGACACACCAATAAATGTACCAAATGGATTTGGTTCAACTTTTATGATGGATGATGCAATGACTGAAGGGCCAGAGTTAAGTTCAAATCACATTGGAAGAGCTCAAGGGTTGTTTGGTCTTTCTTCACTTCAAGATCTTGGAATGTTTATGTTGACAAATTTTGTTTTTAAGGAAGGGGAATATGGTGGAAGTAGTCTTAGTATGTTGGGAAGGAATCCTATTTCTGAACAAAATAGAGAAATGCCTATTGTTGGTGGAACTGGTGTTTTTAGATTTGCTAGAGGGTATGCTATTGCAAATAGTGTTGATTCCATTTCTACCCCTGAACATTTTGTTGTTGAGTATAATATTACTGTTTCTCTTCCCTAA
Protein sequence

>Msa1269800

MALSHSFFFLFSLTLIFTQLTTTNGDFSQQSNIILPSEQPRTEKLTHIHFYYHDIRDNKSPTIVQIIDTPINVPNGFGSTFMMDDAMTEGPELSSNHIGRAQGLFGLSSLQDLGMFMLTNFVFKEGEYGGSSLSMLGRNPISEQNREMPIVGGTGVFRFARGYAIANSVDSISTPEHFVVEYNITVSLP*