AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0588830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0588830 MtrunA17_Chr4g0005041 85.405 185 21 4 16 197 17 198 4.07e-115 325
Msa0588830 MtrunA17_Chr4g0005081 77.273 198 43 2 1 197 1 197 2.42e-107 306
Msa0588830 MtrunA17_Chr4g0005031 77.889 199 42 2 1 197 23 221 1.02e-106 305
Msa0588830 MtrunA17_Chr4g0005071 76.263 198 44 2 1 197 1 196 3.98e-104 298
Msa0588830 MtrunA17_Chr4g0005011 69.849 199 56 3 1 197 1 197 9.56e-93 269
Msa0588830 MtrunA17_Chr7g0243501 67.725 189 58 2 11 197 5 192 2.01e-82 243
Msa0588830 MtrunA17_Chr4g0005111 57.672 189 74 3 9 197 8 190 3.68e-76 226
Msa0588830 MtrunA17_Chr4g0005131 60.947 169 64 2 30 197 24 191 1.61e-68 207
Msa0588830 MtrunA17_Chr1g0175911 60.000 165 63 2 34 197 30 192 6.61e-67 203
Msa0588830 MtrunA17_Chr7g0259121 53.049 164 72 2 39 197 30 193 7.29e-59 184
Msa0588830 MtrunA17_Chr7g0259091 49.462 186 91 3 13 197 11 194 1.93e-57 179
Msa0588830 MtrunA17_Chr4g0037481 52.632 152 71 1 47 197 41 192 7.16e-57 177
Msa0588830 MtrunA17_Chr7g0259071 48.171 164 84 1 35 197 28 191 1.36e-56 177
Msa0588830 MtrunA17_Chr4g0005091 49.206 189 77 3 9 197 6 175 4.01e-56 175
Msa0588830 MtrunA17_Chr7g0259101 46.073 191 90 3 13 197 11 194 6.29e-55 179
Msa0588830 MtrunA17_Chr7g0259101 47.312 186 95 3 13 197 210 393 7.31e-54 176
Msa0588830 MtrunA17_Chr1g0177051 47.134 157 78 3 44 196 30 185 5.47e-48 155
Msa0588830 MtrunA17_Chr3g0136641 46.584 161 83 3 40 197 28 188 8.99e-46 149
Msa0588830 MtrunA17_Chr3g0085311 49.664 149 71 3 49 196 43 188 4.28e-45 147
Msa0588830 MtrunA17_Chr4g0040551 44.737 152 82 1 46 197 36 185 7.68e-45 147
Msa0588830 MtrunA17_Chr3g0090231 45.395 152 81 1 46 197 36 185 1.35e-44 146
Msa0588830 MtrunA17_Chr3g0085321 39.474 190 107 4 8 196 6 188 5.54e-44 145
Msa0588830 MtrunA17_Chr3g0085291 48.993 149 70 3 49 196 43 186 7.40e-44 144
Msa0588830 MtrunA17_Chr5g0446751 42.647 204 91 5 4 197 2 189 2.61e-43 143
Msa0588830 MtrunA17_Chr3g0136631 40.933 193 103 4 8 197 5 189 1.44e-42 141
Msa0588830 MtrunA17_Chr3g0085301 40.625 192 103 5 6 196 12 193 8.16e-42 139
Msa0588830 MtrunA17_Chr4g0068381 38.028 142 88 0 56 197 39 180 1.81e-28 105
Msa0588830 MtrunA17_Chr4g0068391 34.595 185 111 2 17 197 2 180 1.06e-26 100
Msa0588830 MtrunA17_Chr4g0024951 29.655 145 102 0 48 192 29 173 1.97e-19 81.6
Msa0588830 MtrunA17_Chr4g0024961 29.371 143 101 0 50 192 31 173 6.23e-19 80.1
Msa0588830 MtrunA17_Chr4g0005061 57.353 68 23 2 132 197 163 226 4.00e-18 79.0
Msa0588830 MtrunA17_Chr4g0005061 75.000 44 11 0 77 120 1 44 7.98e-17 75.5
Msa0588830 MtrunA17_Chr8g0387701 33.571 140 84 3 49 180 34 172 6.49e-16 72.4
Msa0588830 MtrunA17_Chr8g0387711 32.836 134 79 4 56 180 37 168 1.13e-13 66.2
Msa0588830 MtrunA17_Chr1g0169281 37.778 90 55 1 84 173 141 229 1.31e-13 67.4
Msa0588830 MtrunA17_Chr1g0169511 41.111 90 52 1 84 173 135 223 1.57e-13 67.0
Msa0588830 MtrunA17_Chr1g0169291 41.111 90 52 1 84 173 135 223 2.23e-13 66.6
Msa0588830 MtrunA17_Chr1g0212861 35.537 121 67 4 85 196 235 353 7.93e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0588830 AT1G58170.1 59.677 186 68 1 12 197 7 185 8.29e-80 236
Msa0588830 AT5G49040.1 55.851 188 82 1 11 197 4 191 3.58e-76 227
Msa0588830 AT1G55210.1 55.789 190 77 3 9 197 4 187 1.57e-74 223
Msa0588830 AT1G55210.2 55.789 190 77 3 9 197 4 187 1.57e-74 223
Msa0588830 AT3G13650.1 53.763 186 83 1 12 197 4 186 9.58e-70 211
Msa0588830 AT5G49030.3 55.172 174 77 1 11 183 4 177 2.38e-59 200
Msa0588830 AT1G65870.1 56.000 150 66 0 47 196 40 189 8.55e-58 180
Msa0588830 AT3G13662.1 49.714 175 81 3 11 184 4 172 3.71e-55 173
Msa0588830 AT2G21100.1 50.323 155 77 0 42 196 33 187 6.83e-55 173
Msa0588830 AT2G21100.2 50.323 155 77 0 42 196 33 187 6.83e-55 173
Msa0588830 AT3G13660.1 66.102 118 40 0 80 197 8 125 1.19e-53 167
Msa0588830 AT5G42500.1 48.667 150 75 1 47 196 38 185 1.02e-48 157
Msa0588830 AT1G22900.1 50.000 150 73 1 47 196 46 193 1.11e-48 157
Msa0588830 AT5G42510.1 48.667 150 75 1 47 196 35 182 6.77e-48 155
Msa0588830 AT4G38700.1 43.827 162 85 3 42 197 29 190 2.63e-44 146
Msa0588830 AT3G58090.1 54.128 109 50 0 88 196 163 271 1.40e-39 136
Msa0588830 AT2G21110.1 38.462 169 95 2 33 197 23 186 2.27e-39 133
Msa0588830 AT4G23690.1 33.766 154 89 4 30 179 25 169 5.21e-17 75.5
Msa0588830 AT1G64160.1 31.944 144 91 3 41 180 25 165 4.60e-16 73.2
Msa0588830 AT4G11190.1 29.651 172 98 6 5 172 6 158 1.05e-14 69.3
Msa0588830 AT4G11210.1 29.834 181 101 7 7 180 5 166 1.69e-14 68.9
Msa0588830 AT4G13580.1 34.951 103 60 2 84 180 129 230 3.43e-11 60.8
Msa0588830 AT3G24020.1 37.778 90 55 1 84 173 128 216 3.50e-11 60.8
Msa0588830 AT4G11180.1 32.331 133 84 4 48 176 34 164 6.32e-11 59.3

Find 36 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGAAGTACACTTACTATTT+TGG 0.090168 4_2:-11297945 Msa0588830:CDS
AGTTCTGGTCCTAATGTTAA+AGG 0.200219 4_2:+11298076 None:intergenic
CTAAACACGACAACTGCTTT+TGG 0.250268 4_2:-11298121 Msa0588830:CDS
ATTGATAACCCTTTAACATT+AGG 0.316470 4_2:-11298085 Msa0588830:CDS
CTTAATAATTTGCGGTCTAT+AGG 0.353141 4_2:+11298244 None:intergenic
AGATGAAGTTGATTTGCTTA+TGG 0.369472 4_2:-11298002 Msa0588830:CDS
CATTGGTTTGATATCAAAAC+CGG 0.379656 4_2:-11297827 Msa0588830:CDS
TTTACTGAAGGAAAATATAA+TGG 0.380359 4_2:-11297965 Msa0588830:CDS
AGGACCAGAACTGAGTTCTA+AGG 0.395502 4_2:-11298065 Msa0588830:CDS
AAGTGATGGTGTTGCAAGAT+AGG 0.403929 4_2:+11298314 None:intergenic
TCTTTAGGCTTAATAATTTG+CGG 0.414614 4_2:+11298236 None:intergenic
GTTCTGGTCCTAATGTTAAA+GGG 0.423463 4_2:+11298077 None:intergenic
ATGCTGAAGCTAATACTCAT+TGG 0.445682 4_2:-11297844 Msa0588830:CDS
GAACTGAGTTCTAAGGTTGT+TGG 0.452309 4_2:-11298058 Msa0588830:CDS
GTTGTCGTGTTTAGTTTCAA+TGG 0.464443 4_2:+11298130 None:intergenic
GGAACAACTGCAACTGAAGT+AGG 0.473877 4_2:+11298157 None:intergenic
ACAACCTTAGAACTCAGTTC+TGG 0.474628 4_2:+11298061 None:intergenic
AGAACAAAGTGATGAAGTGT+TGG 0.478622 4_2:+11298347 None:intergenic
GAACAAAGTGATGAAGTGTT+GGG 0.498072 4_2:+11298348 None:intergenic
GTGTTTAGTTTCAATGGTGG+TGG 0.501953 4_2:+11298136 None:intergenic
TAAGTCATTTCAGATTCTAC+TGG 0.503837 4_2:-11298204 Msa0588830:CDS
CAAATTATTAAGCCTAAAGA+AGG 0.508677 4_2:-11298233 Msa0588830:CDS
AAGGTTGTTGGAAAAGCTCA+AGG 0.511935 4_2:-11298046 Msa0588830:CDS
TGGTGTTGCAAGATAGGAGA+AGG 0.539243 4_2:+11298320 None:intergenic
ATGCCTGTGATTGGTGGCAG+TGG 0.540114 4_2:-11297890 Msa0588830:CDS
ATACTCAACAATAGCATCCC+CGG 0.565003 4_2:+11297808 None:intergenic
GTTAGAGAGATGCCTGTGAT+TGG 0.567283 4_2:-11297899 Msa0588830:CDS
GAACAACTGCAACTGAAGTA+GGG 0.596771 4_2:+11298158 None:intergenic
AATCCACTGCCACCAATCAC+AGG 0.619144 4_2:+11297887 None:intergenic
AGAGAGATGCCTGTGATTGG+TGG 0.622674 4_2:-11297896 Msa0588830:CDS
TGATGATGATGTTAAAGTGA+TGG 0.638584 4_2:+11298300 None:intergenic
TACTGGCACGACATAGTGAG+TGG 0.639000 4_2:-11298187 Msa0588830:CDS
AGGTTGTTGGAAAAGCTCAA+GGG 0.639795 4_2:-11298045 Msa0588830:CDS
ATTGGTTTGATATCAAAACC+GGG 0.644981 4_2:-11297826 Msa0588830:CDS
GTCGTGTTTAGTTTCAATGG+TGG 0.656285 4_2:+11298133 None:intergenic
TTGGTTTGATATCAAAACCG+GGG 0.681345 4_2:-11297825 Msa0588830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTATATTTTCCTTCAGTAA+AGG + chr4_2:11298175-11298194 None:intergenic 20.0%
!! TTTACTGAAGGAAAATATAA+TGG - chr4_2:11298174-11298193 Msa0588830:CDS 20.0%
! TCTTTAGGCTTAATAATTTG+CGG + chr4_2:11297906-11297925 None:intergenic 25.0%
! CAAATTATTAAGCCTAAAGA+AGG - chr4_2:11297906-11297925 Msa0588830:CDS 25.0%
!! ATTGATAACCCTTTAACATT+AGG - chr4_2:11298054-11298073 Msa0588830:CDS 25.0%
! TGATGATGATGTTAAAGTGA+TGG + chr4_2:11297842-11297861 None:intergenic 30.0%
! CTTAATAATTTGCGGTCTAT+AGG + chr4_2:11297898-11297917 None:intergenic 30.0%
!! GACTTAGTTTTTCCTTCTTT+AGG + chr4_2:11297921-11297940 None:intergenic 30.0%
TAAGTCATTTCAGATTCTAC+TGG - chr4_2:11297935-11297954 Msa0588830:CDS 30.0%
!! AGATGAAGTTGATTTGCTTA+TGG - chr4_2:11298137-11298156 Msa0588830:CDS 30.0%
! ATGAATTTTGCCTTTACTGA+AGG - chr4_2:11298162-11298181 Msa0588830:CDS 30.0%
!! TGGAAGTACACTTACTATTT+TGG - chr4_2:11298194-11298213 Msa0588830:CDS 30.0%
!! GGAAGTACACTTACTATTTT+GGG - chr4_2:11298195-11298214 Msa0588830:CDS 30.0%
!! CATTGGTTTGATATCAAAAC+CGG - chr4_2:11298312-11298331 Msa0588830:CDS 30.0%
!! ATTGGTTTGATATCAAAACC+GGG - chr4_2:11298313-11298332 Msa0588830:CDS 30.0%
! GAACAAAGTGATGAAGTGTT+GGG + chr4_2:11297794-11297813 None:intergenic 35.0%
AGAACAAAGTGATGAAGTGT+TGG + chr4_2:11297795-11297814 None:intergenic 35.0%
! GTTGTCGTGTTTAGTTTCAA+TGG + chr4_2:11298012-11298031 None:intergenic 35.0%
GTTCTGGTCCTAATGTTAAA+GGG + chr4_2:11298065-11298084 None:intergenic 35.0%
! AGTTCTGGTCCTAATGTTAA+AGG + chr4_2:11298066-11298085 None:intergenic 35.0%
!! GTACACTTACTATTTTGGGA+AGG - chr4_2:11298199-11298218 Msa0588830:CDS 35.0%
!!! GGATTTTTCAGATTTGCTAG+AGG - chr4_2:11298270-11298289 Msa0588830:CDS 35.0%
ATGCTGAAGCTAATACTCAT+TGG - chr4_2:11298295-11298314 Msa0588830:CDS 35.0%
! TTGGTTTGATATCAAAACCG+GGG - chr4_2:11298314-11298333 Msa0588830:CDS 35.0%
!! AAGTGATGGTGTTGCAAGAT+AGG + chr4_2:11297828-11297847 None:intergenic 40.0%
GAACAACTGCAACTGAAGTA+GGG + chr4_2:11297984-11298003 None:intergenic 40.0%
! GTGTTTAGTTTCAATGGTGG+TGG + chr4_2:11298006-11298025 None:intergenic 40.0%
! GTCGTGTTTAGTTTCAATGG+TGG + chr4_2:11298009-11298028 None:intergenic 40.0%
! CTAAACACGACAACTGCTTT+TGG - chr4_2:11298018-11298037 Msa0588830:CDS 40.0%
ACAACCTTAGAACTCAGTTC+TGG + chr4_2:11298081-11298100 None:intergenic 40.0%
!! GAACTGAGTTCTAAGGTTGT+TGG - chr4_2:11298081-11298100 Msa0588830:CDS 40.0%
AAGGTTGTTGGAAAAGCTCA+AGG - chr4_2:11298093-11298112 Msa0588830:CDS 40.0%
AGGTTGTTGGAAAAGCTCAA+GGG - chr4_2:11298094-11298113 Msa0588830:CDS 40.0%
ATACTCAACAATAGCATCCC+CGG + chr4_2:11298334-11298353 None:intergenic 40.0%
!! TGGTGTTGCAAGATAGGAGA+AGG + chr4_2:11297822-11297841 None:intergenic 45.0%
GGAACAACTGCAACTGAAGT+AGG + chr4_2:11297985-11298004 None:intergenic 45.0%
AGGACCAGAACTGAGTTCTA+AGG - chr4_2:11298074-11298093 Msa0588830:CDS 45.0%
GTTAGAGAGATGCCTGTGAT+TGG - chr4_2:11298240-11298259 Msa0588830:CDS 45.0%
TACTGGCACGACATAGTGAG+TGG - chr4_2:11297952-11297971 Msa0588830:CDS 50.0%
AGAGAGATGCCTGTGATTGG+TGG - chr4_2:11298243-11298262 Msa0588830:CDS 50.0%
AATCCACTGCCACCAATCAC+AGG + chr4_2:11298255-11298274 None:intergenic 50.0%
! ATGCCTGTGATTGGTGGCAG+TGG - chr4_2:11298249-11298268 Msa0588830:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 11297784 11298377 11297784 ID=Msa0588830;Name=Msa0588830
chr4_2 mRNA 11297784 11298377 11297784 ID=Msa0588830-mRNA-1;Parent=Msa0588830;Name=Msa0588830-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|197
chr4_2 exon 11297784 11298377 11297784 ID=Msa0588830-mRNA-1:exon:3304;Parent=Msa0588830-mRNA-1
chr4_2 CDS 11297784 11298377 11297784 ID=Msa0588830-mRNA-1:cds;Parent=Msa0588830-mRNA-1
Gene Sequence

>Msa0588830

ATGCAAACCCAACACTTCATCACTTTGTTCTTCTTCCTTCTCCTATCTTGCAACACCATCACTTTAACATCATCATCATCAGAAAATGATGACACTTTTGAATTTGTTCGTCCTATAGACCGCAAATTATTAAGCCTAAAGAAGGAAAAACTAAGTCATTTCAGATTCTACTGGCACGACATAGTGAGTGGAAAAAACCCTACTTCAGTTGCAGTTGTTCCACCACCATTGAAACTAAACACGACAACTGCTTTTGGAACAGTTCGCATGATTGATAACCCTTTAACATTAGGACCAGAACTGAGTTCTAAGGTTGTTGGAAAAGCTCAAGGGTTCTATGCATCTGCATGCAAAGATGAAGTTGATTTGCTTATGGCTATGAATTTTGCCTTTACTGAAGGAAAATATAATGGAAGTACACTTACTATTTTGGGAAGGAATGCTGTTTTTCATAAAGTTAGAGAGATGCCTGTGATTGGTGGCAGTGGATTTTTCAGATTTGCTAGAGGATATGCTGAAGCTAATACTCATTGGTTTGATATCAAAACCGGGGATGCTATTGTTGAGTATAATGTTTATGTTTTTCACTATTGA
Protein sequence

>Msa0588830

MQTQHFITLFFFLLLSCNTITLTSSSSENDDTFEFVRPIDRKLLSLKKEKLSHFRFYWHDIVSGKNPTSVAVVPPPLKLNTTTAFGTVRMIDNPLTLGPELSSKVVGKAQGFYASACKDEVDLLMAMNFAFTEGKYNGSTLTILGRNAVFHKVREMPVIGGSGFFRFARGYAEANTHWFDIKTGDAIVEYNVYVFHY*