AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0586560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0586560 MtrunA17_Chr8g0384141 93.878 245 13 1 1 243 21 265 1.05e-148 415
Msa0586560 MtrunA17_Chr3g0134001 73.958 96 25 0 60 155 139 234 4.44e-47 157
Msa0586560 MtrunA17_Chr8g0375121 68.571 105 33 0 60 164 100 204 4.53e-38 133
Msa0586560 MtrunA17_Chr5g0402161 64.545 110 39 0 60 169 105 214 1.01e-37 132
Msa0586560 MtrunA17_Chr8g0341421 60.577 104 36 2 58 156 289 392 5.51e-29 113
Msa0586560 MtrunA17_Chr2g0330641 62.105 95 35 1 63 156 260 354 6.39e-27 107
Msa0586560 MtrunA17_Chr7g0243041 67.857 56 18 0 98 153 32 87 9.73e-21 85.5
Msa0586560 MtrunA17_Chr5g0435021 45.455 99 52 2 58 154 182 280 1.39e-19 85.9
Msa0586560 MtrunA17_Chr1g0152651 66.071 56 19 0 101 156 283 338 5.78e-19 84.7
Msa0586560 MtrunA17_Chr5g0393721 66.071 56 19 0 101 156 233 288 5.99e-19 84.3
Msa0586560 MtrunA17_Chr1g0207301 41.176 102 59 1 56 156 251 352 1.23e-18 84.0
Msa0586560 MtrunA17_Chr1g0207311 66.071 56 19 0 101 156 205 260 2.05e-18 82.0
Msa0586560 MtrunA17_Chr3g0134741 60.606 66 25 1 92 156 228 293 5.10e-18 81.6
Msa0586560 MtrunA17_Chr4g0074161 50.667 75 37 0 80 154 194 268 1.43e-15 75.1
Msa0586560 MtrunA17_Chr1g0179061 59.259 54 22 0 102 155 180 233 2.01e-14 70.5
Msa0586560 MtrunA17_Chr1g0190731 50.000 70 35 0 85 154 186 255 1.33e-13 69.3
Msa0586560 MtrunA17_Chr2g0311101 44.737 76 40 1 82 155 157 232 1.79e-13 68.6
Msa0586560 MtrunA17_Chr2g0323091 52.632 57 27 0 102 158 146 202 2.24e-13 68.2
Msa0586560 MtrunA17_Chr4g0014771 59.259 54 21 1 102 154 128 181 2.12e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0586560 AT5G09750.1 81.651 109 13 1 65 166 92 200 1.25e-46 155
Msa0586560 AT4G00120.1 82.022 89 16 0 67 155 87 175 2.16e-46 153
Msa0586560 AT3G21330.1 52.632 133 56 1 56 188 233 358 7.68e-38 136
Msa0586560 AT5G67060.2 75.824 91 22 0 65 155 83 173 4.25e-36 128
Msa0586560 AT5G67060.1 75.824 91 22 0 65 155 95 185 6.44e-36 127
Msa0586560 AT3G50330.1 74.725 91 23 0 65 155 92 182 2.04e-35 126
Msa0586560 AT5G01305.1 64.179 67 24 0 90 156 35 101 3.75e-21 87.4
Msa0586560 AT2G14760.1 67.857 56 18 0 101 156 246 301 6.19e-19 84.7
Msa0586560 AT5G43175.1 47.500 80 42 0 77 156 117 196 6.65e-19 82.8
Msa0586560 AT4G33880.1 67.857 56 18 0 101 156 275 330 7.04e-19 84.7
Msa0586560 AT1G27740.1 50.704 71 35 0 86 156 161 231 1.13e-17 80.1
Msa0586560 AT1G66470.1 64.815 54 19 0 101 154 204 257 1.33e-17 80.5
Msa0586560 AT5G37800.1 52.778 72 26 1 83 154 200 263 1.65e-17 80.5
Msa0586560 AT4G30980.1 59.091 66 26 1 90 154 127 192 1.94e-16 77.4
Msa0586560 AT4G30980.2 59.091 66 26 1 90 154 175 240 3.98e-16 77.0
Msa0586560 AT2G24260.2 62.963 54 20 0 101 154 44 97 4.55e-16 75.5
Msa0586560 AT2G24260.1 49.333 75 32 1 86 154 126 200 9.26e-16 75.9
Msa0586560 AT2G14760.3 55.072 69 18 1 101 156 246 314 1.46e-15 75.1
Msa0586560 AT5G58010.1 52.113 71 33 1 85 154 91 161 5.43e-15 73.2

Find 52 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATGAATTCTTCTGGAATT+TGG 0.166878 4_2:+7818651 Msa0586560:CDS
GGTTCACTCAGTGACATATT+AGG 0.250977 4_2:+7818725 Msa0586560:CDS
TTGTTATTGTCTCCTTCTTC+TGG 0.266342 4_2:+7819142 Msa0586560:CDS
TGTTCCTGGTGGAACTAAAA+TGG 0.289003 4_2:+7818967 Msa0586560:CDS
CAAGTTCCTATGAATTCTTC+TGG 0.298023 4_2:+7818644 Msa0586560:CDS
ATCATGCTGTTGTAGCTATT+TGG 0.316175 4_2:-7818677 None:intergenic
CTTCTTCTGGTTGTGACGTC+TGG 0.336110 4_2:+7819155 Msa0586560:CDS
GTGGAAGTGAGTAGTAAATT+TGG 0.351622 4_2:-7819187 None:intergenic
ATTCGAACGTTTCTTCGCTT+TGG 0.353088 4_2:-7818866 None:intergenic
TGTCTAGCTGCAACACTTTG+TGG 0.381712 4_2:-7818899 None:intergenic
ATCCTTCAAAGACTTGTTCC+TGG 0.399593 4_2:+7818953 Msa0586560:CDS
GAAGAACAAGAAGAAGAGTT+AGG 0.401481 4_2:+7818770 Msa0586560:CDS
AGAAGAGTTAGGAGCTATGA+AGG 0.405429 4_2:+7818781 Msa0586560:CDS
GTTCACTCAGTGACATATTA+GGG 0.414540 4_2:+7818726 Msa0586560:CDS
GATCTTGTTGGAGAATAATA+CGG 0.432514 4_2:-7818616 None:intergenic
AGTAGTAAATTTGGTGCAAA+AGG 0.442540 4_2:-7819178 None:intergenic
GTTCTTCTACATCTTCGATT+CGG 0.446833 4_2:-7818754 None:intergenic
TCCGGCGTCAAATTGAATTC+CGG 0.450878 4_2:-7819236 None:intergenic
CAAATTCCAGAAGAATTCAT+AGG 0.451806 4_2:-7818650 None:intergenic
CAGAAGAATTCATAGGAACT+TGG 0.471897 4_2:-7818643 None:intergenic
CACCAGGAACAAGTCTTTGA+AGG 0.481487 4_2:-7818955 None:intergenic
GAACTTGGTGGTGATCTTGT+TGG 0.483925 4_2:-7818628 None:intergenic
CTTCTACATCTTCGATTCGG+TGG 0.493447 4_2:-7818751 None:intergenic
CAAGATTGCAGCTATGCAAC+CGG 0.495861 4_2:+7818814 Msa0586560:CDS
GCACCACCACCACCTTCATC+AGG 0.499844 4_2:+7818704 Msa0586560:CDS
GTCCACTGTGGCAGCTGTTG+TGG 0.509617 4_2:-7819206 None:intergenic
CAGACGTCACAACCAGAAGA+AGG 0.532660 4_2:-7819154 None:intergenic
TAGCTACAACAGCATGATCA+TGG 0.539866 4_2:+7818682 Msa0586560:CDS
ATGCTGTTGTAGCTATTTGG+TGG 0.542016 4_2:-7818674 None:intergenic
GAACCTGATGAAGGTGGTGG+TGG 0.552409 4_2:-7818707 None:intergenic
ATGAACATGTGAATGTCCTC+CGG 0.556908 4_2:-7819254 None:intergenic
GGCGTCAAATTGAATTCCGG+TGG 0.574382 4_2:-7819233 None:intergenic
CAAGAACTTAACATAACGAA+TGG 0.583966 4_2:-7819014 None:intergenic
TCACATGTTCATGCTTGTGA+AGG 0.591006 4_2:+7819265 Msa0586560:CDS
GCCACAGTGGACTTACCCAC+CGG 0.591865 4_2:+7819217 Msa0586560:CDS
AAGAATTCATAGGAACTTGG+TGG 0.592411 4_2:-7818640 None:intergenic
ACTCACTAATTACCTCATGA+TGG 0.592814 4_2:-7819303 None:intergenic
GACAATAACAAAGCACTAGG+AGG 0.606861 4_2:-7819130 None:intergenic
GGAGACAATAACAAAGCACT+AGG 0.609214 4_2:-7819133 None:intergenic
GGAATTCAATTTGACGCCGG+AGG 0.622262 4_2:+7819238 Msa0586560:CDS
CTTCAAAGACTTGTTCCTGG+TGG 0.627271 4_2:+7818956 Msa0586560:CDS
GTTGCTGGGTCGATATCCAC+CGG 0.629556 4_2:-7818833 None:intergenic
ACCGGAATTCAATTTGACGC+CGG 0.643580 4_2:+7819235 Msa0586560:CDS
ATCAAGCTTTAACCATCATG+AGG 0.658321 4_2:+7819291 Msa0586560:CDS
TTAATGCATTGTGATGAAAG+TGG 0.662271 4_2:-7819100 None:intergenic
TCACTGAGTGAACCTGATGA+AGG 0.669394 4_2:-7818716 None:intergenic
GATTGCAGCTATGCAACCGG+TGG 0.671341 4_2:+7818817 Msa0586560:CDS
GCGTCAAATTGAATTCCGGT+GGG 0.674022 4_2:-7819232 None:intergenic
TTCCACAACAGCTGCCACAG+TGG 0.676021 4_2:+7819204 Msa0586560:CDS
AGTGAACCTGATGAAGGTGG+TGG 0.679836 4_2:-7818710 None:intergenic
CTGAGTGAACCTGATGAAGG+TGG 0.711599 4_2:-7818713 None:intergenic
TCCGGTGGGTAAGTCCACTG+TGG 0.759981 4_2:-7819218 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GATCTTGTTGGAGAATAATA+CGG - chr4_2:7818619-7818638 None:intergenic 30.0%
CAAATTCCAGAAGAATTCAT+AGG - chr4_2:7818653-7818672 None:intergenic 30.0%
!! CTATGAATTCTTCTGGAATT+TGG + chr4_2:7818651-7818670 Msa0586560:CDS 30.0%
CAAGAACTTAACATAACGAA+TGG - chr4_2:7819017-7819036 None:intergenic 30.0%
!!! TGTTGTTGTTGTTGATTTTG+AGG - chr4_2:7819070-7819089 None:intergenic 30.0%
TTAATGCATTGTGATGAAAG+TGG - chr4_2:7819103-7819122 None:intergenic 30.0%
!! AGTAGTAAATTTGGTGCAAA+AGG - chr4_2:7819181-7819200 None:intergenic 30.0%
AAGAATTCATAGGAACTTGG+TGG - chr4_2:7818643-7818662 None:intergenic 35.0%
CAGAAGAATTCATAGGAACT+TGG - chr4_2:7818646-7818665 None:intergenic 35.0%
CAAGTTCCTATGAATTCTTC+TGG + chr4_2:7818644-7818663 Msa0586560:CDS 35.0%
ATCATGCTGTTGTAGCTATT+TGG - chr4_2:7818680-7818699 None:intergenic 35.0%
GTTCACTCAGTGACATATTA+GGG + chr4_2:7818726-7818745 Msa0586560:CDS 35.0%
GTTCTTCTACATCTTCGATT+CGG - chr4_2:7818757-7818776 None:intergenic 35.0%
GAAGAACAAGAAGAAGAGTT+AGG + chr4_2:7818770-7818789 Msa0586560:CDS 35.0%
!!! TTGTTGTTGATTTTGAGGAG+TGG - chr4_2:7819065-7819084 None:intergenic 35.0%
! TTGTTATTGTCTCCTTCTTC+TGG + chr4_2:7819142-7819161 Msa0586560:CDS 35.0%
GTGGAAGTGAGTAGTAAATT+TGG - chr4_2:7819190-7819209 None:intergenic 35.0%
! ATCAAGCTTTAACCATCATG+AGG + chr4_2:7819291-7819310 Msa0586560:CDS 35.0%
ACTCACTAATTACCTCATGA+TGG - chr4_2:7819306-7819325 None:intergenic 35.0%
ATGCTGTTGTAGCTATTTGG+TGG - chr4_2:7818677-7818696 None:intergenic 40.0%
TAGCTACAACAGCATGATCA+TGG + chr4_2:7818682-7818701 Msa0586560:CDS 40.0%
GGTTCACTCAGTGACATATT+AGG + chr4_2:7818725-7818744 Msa0586560:CDS 40.0%
AGAAGAGTTAGGAGCTATGA+AGG + chr4_2:7818781-7818800 Msa0586560:CDS 40.0%
!! TTGGTTTTCGAATCGTTGCT+GGG - chr4_2:7818850-7818869 None:intergenic 40.0%
!!! TTTGGTTTTCGAATCGTTGC+TGG - chr4_2:7818851-7818870 None:intergenic 40.0%
ATTCGAACGTTTCTTCGCTT+TGG - chr4_2:7818869-7818888 None:intergenic 40.0%
! ATCCTTCAAAGACTTGTTCC+TGG + chr4_2:7818953-7818972 Msa0586560:CDS 40.0%
TGTTCCTGGTGGAACTAAAA+TGG + chr4_2:7818967-7818986 Msa0586560:CDS 40.0%
!!! GTATCCATTTTAGTTCCACC+AGG - chr4_2:7818974-7818993 None:intergenic 40.0%
! GACAATAACAAAGCACTAGG+AGG - chr4_2:7819133-7819152 None:intergenic 40.0%
! GGAGACAATAACAAAGCACT+AGG - chr4_2:7819136-7819155 None:intergenic 40.0%
ATGAACATGTGAATGTCCTC+CGG - chr4_2:7819257-7819276 None:intergenic 40.0%
TCACATGTTCATGCTTGTGA+AGG + chr4_2:7819265-7819284 Msa0586560:CDS 40.0%
!! GAACTTGGTGGTGATCTTGT+TGG - chr4_2:7818631-7818650 None:intergenic 45.0%
TCACTGAGTGAACCTGATGA+AGG - chr4_2:7818719-7818738 None:intergenic 45.0%
!! CTTCTACATCTTCGATTCGG+TGG - chr4_2:7818754-7818773 None:intergenic 45.0%
CAAGATTGCAGCTATGCAAC+CGG + chr4_2:7818814-7818833 Msa0586560:CDS 45.0%
TGTCTAGCTGCAACACTTTG+TGG - chr4_2:7818902-7818921 None:intergenic 45.0%
CACCAGGAACAAGTCTTTGA+AGG - chr4_2:7818958-7818977 None:intergenic 45.0%
! CTTCAAAGACTTGTTCCTGG+TGG + chr4_2:7818956-7818975 Msa0586560:CDS 45.0%
GCGTCAAATTGAATTCCGGT+GGG - chr4_2:7819235-7819254 None:intergenic 45.0%
ACCGGAATTCAATTTGACGC+CGG + chr4_2:7819235-7819254 Msa0586560:CDS 45.0%
TCCGGCGTCAAATTGAATTC+CGG - chr4_2:7819239-7819258 None:intergenic 45.0%
AGTGAACCTGATGAAGGTGG+TGG - chr4_2:7818713-7818732 None:intergenic 50.0%
CTGAGTGAACCTGATGAAGG+TGG - chr4_2:7818716-7818735 None:intergenic 50.0%
CAGACGTCACAACCAGAAGA+AGG - chr4_2:7819157-7819176 None:intergenic 50.0%
! CTTCTTCTGGTTGTGACGTC+TGG + chr4_2:7819155-7819174 Msa0586560:CDS 50.0%
GGCGTCAAATTGAATTCCGG+TGG - chr4_2:7819236-7819255 None:intergenic 50.0%
GGAATTCAATTTGACGCCGG+AGG + chr4_2:7819238-7819257 Msa0586560:CDS 50.0%
! GAACCTGATGAAGGTGGTGG+TGG - chr4_2:7818710-7818729 None:intergenic 55.0%
GATTGCAGCTATGCAACCGG+TGG + chr4_2:7818817-7818836 Msa0586560:CDS 55.0%
GTTGCTGGGTCGATATCCAC+CGG - chr4_2:7818836-7818855 None:intergenic 55.0%
TTCCACAACAGCTGCCACAG+TGG + chr4_2:7819204-7819223 Msa0586560:CDS 55.0%
GCACCACCACCACCTTCATC+AGG + chr4_2:7818704-7818723 Msa0586560:CDS 60.0%
GTCCACTGTGGCAGCTGTTG+TGG - chr4_2:7819209-7819228 None:intergenic 60.0%
! GCCACAGTGGACTTACCCAC+CGG + chr4_2:7819217-7819236 Msa0586560:CDS 60.0%
TCCGGTGGGTAAGTCCACTG+TGG - chr4_2:7819221-7819240 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 7818596 7819327 7818596 ID=Msa0586560;Name=Msa0586560
chr4_2 mRNA 7818596 7819327 7818596 ID=Msa0586560-mRNA-1;Parent=Msa0586560;Name=Msa0586560-mRNA-1;_AED=0.09;_eAED=0.11;_QI=0|-1|0|1|-1|1|1|0|243
chr4_2 exon 7818596 7819327 7818596 ID=Msa0586560-mRNA-1:exon:2077;Parent=Msa0586560-mRNA-1
chr4_2 CDS 7818596 7819327 7818596 ID=Msa0586560-mRNA-1:cds;Parent=Msa0586560-mRNA-1
Gene Sequence

>Msa0586560

ATGGAAACAAATGAACAAAACCGTATTATTCTCCAACAAGATCACCACCAAGTTCCTATGAATTCTTCTGGAATTTGGCCACCAAATAGCTACAACAGCATGATCATGGCACCACCACCACCTTCATCAGGTTCACTCAGTGACATATTAGGGATCCACCGAATCGAAGATGTAGAAGAACAAGAAGAAGAGTTAGGAGCTATGAAGGAAATGATGTACAAGATTGCAGCTATGCAACCGGTGGATATCGACCCAGCAACGATTCGAAAACCAAAGCGAAGAAACGTTCGAATCAGCGACGATCCACAAAGTGTTGCAGCTAGACATAGAAGAGAAAGAATCAGTGAGAAGATTCGTATCCTTCAAAGACTTGTTCCTGGTGGAACTAAAATGGATACAGCTTCTATGCTTGATGAAGCCATTCGTTATGTTAAGTTCTTGAAGAGACAAATCAAGTTGCTTCAATCCACTCCTCAAAATCAACAACAACAACACATTCAATTGCCACTTTCATCACAATGCATTAATTCTACTCCTCCTAGTGCTTTGTTATTGTCTCCTTCTTCTGGTTGTGACGTCTGGCCTTTTGCACCAAATTTACTACTCACTTCCACAACAGCTGCCACAGTGGACTTACCCACCGGAATTCAATTTGACGCCGGAGGACATTCACATGTTCATGCTTGTGAAGGCTCATCAAGCTTTAACCATCATGAGGTAATTAGTGAGTGA
Protein sequence

>Msa0586560

METNEQNRIILQQDHHQVPMNSSGIWPPNSYNSMIMAPPPPSSGSLSDILGIHRIEDVEEQEEELGAMKEMMYKIAAMQPVDIDPATIRKPKRRNVRISDDPQSVAARHRRERISEKIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQIKLLQSTPQNQQQQHIQLPLSSQCINSTPPSALLLSPSSGCDVWPFAPNLLLTSTTAATVDLPTGIQFDAGGHSHVHACEGSSSFNHHEVISE*