AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0628970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0628970 MtrunA17_Chr4g0005041 84.865 185 22 4 16 197 17 198 4.40e-114 323
Msa0628970 MtrunA17_Chr4g0005081 77.273 198 43 2 1 197 1 197 2.01e-107 306
Msa0628970 MtrunA17_Chr4g0005031 77.387 199 43 2 1 197 23 221 2.20e-106 304
Msa0628970 MtrunA17_Chr4g0005071 76.263 198 44 2 1 197 1 196 3.27e-104 298
Msa0628970 MtrunA17_Chr4g0005011 69.849 199 56 3 1 197 1 197 5.29e-93 270
Msa0628970 MtrunA17_Chr7g0243501 68.254 189 57 2 11 197 5 192 2.47e-83 245
Msa0628970 MtrunA17_Chr4g0005111 57.672 189 74 3 9 197 8 190 2.56e-76 227
Msa0628970 MtrunA17_Chr4g0005131 61.538 169 63 2 30 197 24 191 5.12e-69 208
Msa0628970 MtrunA17_Chr1g0175911 60.000 165 63 2 34 197 30 192 4.87e-67 203
Msa0628970 MtrunA17_Chr7g0259121 53.049 164 72 2 39 197 30 193 3.96e-59 184
Msa0628970 MtrunA17_Chr7g0259091 49.462 186 91 3 13 197 11 194 7.32e-58 180
Msa0628970 MtrunA17_Chr4g0037481 52.597 154 72 1 45 197 39 192 2.87e-57 179
Msa0628970 MtrunA17_Chr7g0259071 48.171 164 84 1 35 197 28 191 5.12e-57 178
Msa0628970 MtrunA17_Chr4g0005091 49.206 189 77 3 9 197 6 175 1.41e-56 176
Msa0628970 MtrunA17_Chr7g0259101 46.073 191 90 3 13 197 11 194 2.40e-55 180
Msa0628970 MtrunA17_Chr7g0259101 49.390 164 82 1 35 197 230 393 2.64e-54 177
Msa0628970 MtrunA17_Chr1g0177051 46.497 157 79 3 44 196 30 185 7.58e-48 154
Msa0628970 MtrunA17_Chr3g0085311 50.336 149 70 3 49 196 43 188 6.47e-46 150
Msa0628970 MtrunA17_Chr3g0136641 47.368 152 78 2 48 197 37 188 1.27e-45 149
Msa0628970 MtrunA17_Chr4g0040551 44.737 152 82 1 46 197 36 185 6.89e-45 147
Msa0628970 MtrunA17_Chr3g0085291 49.664 149 69 3 49 196 43 186 1.29e-44 146
Msa0628970 MtrunA17_Chr3g0090231 45.395 152 81 1 46 197 36 185 1.31e-44 146
Msa0628970 MtrunA17_Chr5g0446751 43.137 204 90 6 4 197 2 189 1.62e-43 144
Msa0628970 MtrunA17_Chr3g0136631 40.933 193 103 4 8 197 5 189 5.18e-43 142
Msa0628970 MtrunA17_Chr3g0085321 38.947 190 108 4 8 196 6 188 6.43e-43 142
Msa0628970 MtrunA17_Chr3g0085301 40.625 192 103 5 6 196 12 193 3.70e-42 140
Msa0628970 MtrunA17_Chr4g0068381 38.028 142 88 0 56 197 39 180 7.70e-28 103
Msa0628970 MtrunA17_Chr4g0068391 37.931 145 84 2 56 197 39 180 9.42e-26 97.8
Msa0628970 MtrunA17_Chr4g0024951 29.655 145 102 0 48 192 29 173 2.46e-19 81.3
Msa0628970 MtrunA17_Chr4g0024961 29.371 143 101 0 50 192 31 173 5.72e-19 80.1
Msa0628970 MtrunA17_Chr4g0005061 57.353 68 23 2 132 197 163 226 3.53e-18 79.3
Msa0628970 MtrunA17_Chr4g0005061 75.000 44 11 0 77 120 1 44 8.49e-17 75.5
Msa0628970 MtrunA17_Chr8g0387701 31.788 151 94 3 38 180 23 172 4.65e-16 72.8
Msa0628970 MtrunA17_Chr8g0387711 33.083 133 78 4 57 180 38 168 9.08e-14 66.6
Msa0628970 MtrunA17_Chr1g0169281 37.778 90 55 1 84 173 141 229 9.63e-14 67.8
Msa0628970 MtrunA17_Chr1g0169511 41.111 90 52 1 84 173 135 223 1.11e-13 67.4
Msa0628970 MtrunA17_Chr1g0169291 41.111 90 52 1 84 173 135 223 1.72e-13 67.0
Msa0628970 MtrunA17_Chr1g0212861 35.537 121 67 4 85 196 235 353 7.07e-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
Msa0628970 AT1G58170.1 59.677 186 68 1 12 197 7 185 3.57e-80 237
Msa0628970 AT5G49040.1 55.851 188 82 1 11 197 4 191 4.17e-76 227
Msa0628970 AT1G55210.1 55.789 190 77 3 9 197 4 187 1.52e-74 223
Msa0628970 AT1G55210.2 55.789 190 77 3 9 197 4 187 1.52e-74 223
Msa0628970 AT3G13650.1 53.763 186 83 1 12 197 4 186 1.10e-69 210
Msa0628970 AT5G49030.3 55.172 174 77 1 11 183 4 177 2.40e-59 200
Msa0628970 AT1G65870.1 56.000 150 66 0 47 196 40 189 4.49e-58 181
Msa0628970 AT3G13662.1 49.714 175 81 3 11 184 4 172 1.83e-55 174
Msa0628970 AT2G21100.1 50.323 155 77 0 42 196 33 187 5.68e-55 173
Msa0628970 AT2G21100.2 50.323 155 77 0 42 196 33 187 5.68e-55 173
Msa0628970 AT3G13660.1 66.102 118 40 0 80 197 8 125 4.71e-54 169
Msa0628970 AT5G42500.1 48.667 150 75 1 47 196 38 185 4.48e-49 158
Msa0628970 AT1G22900.1 50.000 150 73 1 47 196 46 193 1.04e-48 157
Msa0628970 AT5G42510.1 48.667 150 75 1 47 196 35 182 3.06e-48 155
Msa0628970 AT4G38700.1 43.827 162 85 3 42 197 29 190 1.88e-44 146
Msa0628970 AT3G58090.1 54.128 109 50 0 88 196 163 271 6.97e-40 137
Msa0628970 AT2G21110.1 38.462 169 95 2 33 197 23 186 2.20e-39 133
Msa0628970 AT4G23690.1 35.664 143 84 4 41 179 31 169 3.25e-17 76.3
Msa0628970 AT1G64160.1 31.944 144 91 3 41 180 25 165 3.29e-16 73.6
Msa0628970 AT4G11190.1 33.824 136 82 5 41 172 27 158 1.58e-15 71.6
Msa0628970 AT4G11210.1 29.834 181 101 7 7 180 5 166 6.86e-15 70.1
Msa0628970 AT4G13580.1 34.951 103 60 2 84 180 129 230 3.07e-11 60.8
Msa0628970 AT3G24020.1 37.778 90 55 1 84 173 128 216 3.10e-11 60.8
Msa0628970 AT4G11180.1 32.331 133 84 4 48 176 34 164 4.70e-11 59.7

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_3:-9797057 Msa0628970:CDS
AGTTCTGGTCCTAATGTTAA+AGG 0.200219 4_3:+9797188 None:intergenic
CTAAACACGACAACTGCTTT+TGG 0.250268 4_3:-9797233 Msa0628970:CDS
ATTGATAACCCTTTAACATT+AGG 0.316470 4_3:-9797197 Msa0628970:CDS
TTTAATAATTTGCGGTCTAT+AGG 0.343916 4_3:+9797356 None:intergenic
AGATGAAGTTGATTTGCTTA+TGG 0.369472 4_3:-9797114 Msa0628970:CDS
CATTGGTTTGATATCAAAAC+CGG 0.379656 4_3:-9796939 Msa0628970:CDS
TTTACTGAAGGAAAATATAA+TGG 0.380359 4_3:-9797077 Msa0628970:CDS
AGGACCAGAACTGAGTTCTA+AGG 0.395502 4_3:-9797177 Msa0628970:CDS
AAGTGATGGTGTTGCAAGAT+AGG 0.403929 4_3:+9797426 None:intergenic
TCTTTAGGTTTAATAATTTG+CGG 0.414614 4_3:+9797348 None:intergenic
GTTCTGGTCCTAATGTTAAA+GGG 0.423463 4_3:+9797189 None:intergenic
ATGCTGAAGCTAATACTCAT+TGG 0.445682 4_3:-9796956 Msa0628970:CDS
GAACTGAGTTCTAAGGTTGT+TGG 0.452309 4_3:-9797170 Msa0628970:CDS
GTTGTCGTGTTTAGTTTCAA+TGG 0.464443 4_3:+9797242 None:intergenic
GGAACAACTGCAACTGAAGT+AGG 0.473877 4_3:+9797269 None:intergenic
ACAACCTTAGAACTCAGTTC+TGG 0.474628 4_3:+9797173 None:intergenic
AGAACAAAGTGATGAAGTGT+TGG 0.478622 4_3:+9797459 None:intergenic
GAACAAAGTGATGAAGTGTT+GGG 0.498072 4_3:+9797460 None:intergenic
GTGTTTAGTTTCAATGGTGG+TGG 0.501953 4_3:+9797248 None:intergenic
TAAGTCATTTCAGATTCTAC+TGG 0.503837 4_3:-9797316 Msa0628970:CDS
AAGGTTGTTGGAAAAGCTCA+AGG 0.511935 4_3:-9797158 Msa0628970:CDS
ATGCCTGTGATTGGTGGAAG+TGG 0.514663 4_3:-9797002 Msa0628970:CDS
CAAATTATTAAACCTAAAGA+AGG 0.527897 4_3:-9797345 Msa0628970:CDS
TGGTGTTGCAAGATAGGAGA+AGG 0.539243 4_3:+9797432 None:intergenic
ATACTCAACAATAGCATCCC+CGG 0.565003 4_3:+9796920 None:intergenic
GTTAGAGAGATGCCTGTGAT+TGG 0.567283 4_3:-9797011 Msa0628970:CDS
ACTCCACTTCCACCAATCAC+AGG 0.589329 4_3:+9796999 None:intergenic
GAACAACTGCAACTGAAGTA+GGG 0.596771 4_3:+9797270 None:intergenic
AGAGAGATGCCTGTGATTGG+TGG 0.606895 4_3:-9797008 Msa0628970:CDS
TGATGATGATGTTAAAGTGA+TGG 0.638584 4_3:+9797412 None:intergenic
TACTGGCACGACATAGTGAG+TGG 0.639000 4_3:-9797299 Msa0628970:CDS
AGGTTGTTGGAAAAGCTCAA+GGG 0.639795 4_3:-9797157 Msa0628970:CDS
ATTGGTTTGATATCAAAACC+GGG 0.644981 4_3:-9796938 Msa0628970:CDS
GTCGTGTTTAGTTTCAATGG+TGG 0.656285 4_3:+9797245 None:intergenic
TTGGTTTGATATCAAAACCG+GGG 0.681345 4_3:-9796937 Msa0628970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTAGGTTTAATAATTTG+CGG + chr4_3:9797018-9797037 None:intergenic 20.0%
!! CAAATTATTAAACCTAAAGA+AGG - chr4_3:9797018-9797037 Msa0628970:CDS 20.0%
!!! ATTATATTTTCCTTCAGTAA+AGG + chr4_3:9797287-9797306 None:intergenic 20.0%
!! TTTACTGAAGGAAAATATAA+TGG - chr4_3:9797286-9797305 Msa0628970:CDS 20.0%
!! TTTAATAATTTGCGGTCTAT+AGG + chr4_3:9797010-9797029 None:intergenic 25.0%
!! ATTGATAACCCTTTAACATT+AGG - chr4_3:9797166-9797185 Msa0628970:CDS 25.0%
! TGATGATGATGTTAAAGTGA+TGG + chr4_3:9796954-9796973 None:intergenic 30.0%
!! GACTTAGTTTTTCCTTCTTT+AGG + chr4_3:9797033-9797052 None:intergenic 30.0%
TAAGTCATTTCAGATTCTAC+TGG - chr4_3:9797047-9797066 Msa0628970:CDS 30.0%
!! AGATGAAGTTGATTTGCTTA+TGG - chr4_3:9797249-9797268 Msa0628970:CDS 30.0%
! ATGAATTTTGCCTTTACTGA+AGG - chr4_3:9797274-9797293 Msa0628970:CDS 30.0%
!! TGGAAGTACACTTACTATTT+TGG - chr4_3:9797306-9797325 Msa0628970:CDS 30.0%
!! GGAAGTACACTTACTATTTT+GGG - chr4_3:9797307-9797326 Msa0628970:CDS 30.0%
!! CATTGGTTTGATATCAAAAC+CGG - chr4_3:9797424-9797443 Msa0628970:CDS 30.0%
!! ATTGGTTTGATATCAAAACC+GGG - chr4_3:9797425-9797444 Msa0628970:CDS 30.0%
! GAACAAAGTGATGAAGTGTT+GGG + chr4_3:9796906-9796925 None:intergenic 35.0%
AGAACAAAGTGATGAAGTGT+TGG + chr4_3:9796907-9796926 None:intergenic 35.0%
! GTTGTCGTGTTTAGTTTCAA+TGG + chr4_3:9797124-9797143 None:intergenic 35.0%
GTTCTGGTCCTAATGTTAAA+GGG + chr4_3:9797177-9797196 None:intergenic 35.0%
! AGTTCTGGTCCTAATGTTAA+AGG + chr4_3:9797178-9797197 None:intergenic 35.0%
!! GTACACTTACTATTTTGGGA+AGG - chr4_3:9797311-9797330 Msa0628970:CDS 35.0%
ATGCTGAAGCTAATACTCAT+TGG - chr4_3:9797407-9797426 Msa0628970:CDS 35.0%
! TTGGTTTGATATCAAAACCG+GGG - chr4_3:9797426-9797445 Msa0628970:CDS 35.0%
!! AAGTGATGGTGTTGCAAGAT+AGG + chr4_3:9796940-9796959 None:intergenic 40.0%
GAACAACTGCAACTGAAGTA+GGG + chr4_3:9797096-9797115 None:intergenic 40.0%
! GTGTTTAGTTTCAATGGTGG+TGG + chr4_3:9797118-9797137 None:intergenic 40.0%
! GTCGTGTTTAGTTTCAATGG+TGG + chr4_3:9797121-9797140 None:intergenic 40.0%
! CTAAACACGACAACTGCTTT+TGG - chr4_3:9797130-9797149 Msa0628970:CDS 40.0%
ACAACCTTAGAACTCAGTTC+TGG + chr4_3:9797193-9797212 None:intergenic 40.0%
!! GAACTGAGTTCTAAGGTTGT+TGG - chr4_3:9797193-9797212 Msa0628970:CDS 40.0%
AAGGTTGTTGGAAAAGCTCA+AGG - chr4_3:9797205-9797224 Msa0628970:CDS 40.0%
AGGTTGTTGGAAAAGCTCAA+GGG - chr4_3:9797206-9797225 Msa0628970:CDS 40.0%
!!! GGAGTTTTCAGATTTGCTAG+AGG - chr4_3:9797382-9797401 Msa0628970:CDS 40.0%
ATACTCAACAATAGCATCCC+CGG + chr4_3:9797446-9797465 None:intergenic 40.0%
!! TGGTGTTGCAAGATAGGAGA+AGG + chr4_3:9796934-9796953 None:intergenic 45.0%
GGAACAACTGCAACTGAAGT+AGG + chr4_3:9797097-9797116 None:intergenic 45.0%
AGGACCAGAACTGAGTTCTA+AGG - chr4_3:9797186-9797205 Msa0628970:CDS 45.0%
GTTAGAGAGATGCCTGTGAT+TGG - chr4_3:9797352-9797371 Msa0628970:CDS 45.0%
TACTGGCACGACATAGTGAG+TGG - chr4_3:9797064-9797083 Msa0628970:CDS 50.0%
AGAGAGATGCCTGTGATTGG+TGG - chr4_3:9797355-9797374 Msa0628970:CDS 50.0%
ATGCCTGTGATTGGTGGAAG+TGG - chr4_3:9797361-9797380 Msa0628970:CDS 50.0%
ACTCCACTTCCACCAATCAC+AGG + chr4_3:9797367-9797386 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 9796896 9797489 9796896 ID=Msa0628970;Name=Msa0628970
chr4_3 mRNA 9796896 9797489 9796896 ID=Msa0628970-mRNA-1;Parent=Msa0628970;Name=Msa0628970-mRNA-1;_AED=0.34;_eAED=0.34;_QI=0|-1|0|1|-1|1|1|0|197
chr4_3 exon 9796896 9797489 9796896 ID=Msa0628970-mRNA-1:exon:2975;Parent=Msa0628970-mRNA-1
chr4_3 CDS 9796896 9797489 9796896 ID=Msa0628970-mRNA-1:cds;Parent=Msa0628970-mRNA-1
Gene Sequence

>Msa0628970

ATGCAAACCCAACACTTCATCACTTTGTTCTTCTTCCTTCTCCTATCTTGCAACACCATCACTTTAACATCATCATCATCAGAAAATGATGACACTTTTGAATTTGTTCGTCCTATAGACCGCAAATTATTAAACCTAAAGAAGGAAAAACTAAGTCATTTCAGATTCTACTGGCACGACATAGTGAGTGGAAAAAACCCTACTTCAGTTGCAGTTGTTCCACCACCATTGAAACTAAACACGACAACTGCTTTTGGAACAGTTCGCATGATTGATAACCCTTTAACATTAGGACCAGAACTGAGTTCTAAGGTTGTTGGAAAAGCTCAAGGGTTCTATGCATCTGCATGCAAAGATGAAGTTGATTTGCTTATGGCTATGAATTTTGCCTTTACTGAAGGAAAATATAATGGAAGTACACTTACTATTTTGGGAAGGAATGCTGTTTTTCATAAAGTTAGAGAGATGCCTGTGATTGGTGGAAGTGGAGTTTTCAGATTTGCTAGAGGATATGCTGAAGCTAATACTCATTGGTTTGATATCAAAACCGGGGATGCTATTGTTGAGTATAATGTTTATGTTTTTCACTATTGA
Protein sequence

>Msa0628970

MQTQHFITLFFFLLLSCNTITLTSSSSENDDTFEFVRPIDRKLLNLKKEKLSHFRFYWHDIVSGKNPTSVAVVPPPLKLNTTTAFGTVRMIDNPLTLGPELSSKVVGKAQGFYASACKDEVDLLMAMNFAFTEGKYNGSTLTILGRNAVFHKVREMPVIGGSGVFRFARGYAEANTHWFDIKTGDAIVEYNVYVFHY*