AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0031030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031030 MtrunA17_Chr1g0188911 59.809 209 45 4 1 187 1 192 2.36e-73 219
Msa0031030 MtrunA17_Chr1g0188901 69.149 188 53 2 1 187 1 184 1.14e-70 212
Msa0031030 MtrunA17_Chr1g0197281 50.595 168 57 7 43 187 135 299 9.31e-38 133
Msa0031030 MtrunA17_Chr2g0320311 37.013 154 71 4 57 187 126 276 3.98e-19 82.8
Msa0031030 MtrunA17_Chr7g0263121 38.346 133 54 5 60 188 44 152 6.51e-19 79.7
Msa0031030 MtrunA17_Chr1g0182161 35.338 133 61 3 60 188 39 150 1.56e-18 78.6
Msa0031030 MtrunA17_Chr1g0180311 34.483 174 71 5 44 187 104 264 2.76e-18 80.5
Msa0031030 MtrunA17_Chr1g0212561 43.333 90 36 1 59 148 44 118 3.46e-18 78.6
Msa0031030 MtrunA17_Chr7g0263131 37.121 132 58 5 60 188 34 143 3.02e-17 75.1
Msa0031030 MtrunA17_Chr1g0182181 36.842 133 58 6 60 188 35 145 6.24e-16 71.6
Msa0031030 MtrunA17_Chr7g0222831 42.391 92 33 1 59 150 39 110 1.43e-15 71.2
Msa0031030 MtrunA17_Chr4g0012791 29.891 184 100 4 28 187 200 378 5.12e-15 72.4
Msa0031030 MtrunA17_Chr4g0012691 40.449 89 45 1 60 148 220 300 3.09e-14 69.7
Msa0031030 MtrunA17_Chr1g0207451 37.079 89 38 2 60 148 83 153 5.88e-12 62.4
Msa0031030 MtrunA17_Chr1g0169561 30.303 99 60 1 59 148 40 138 1.04e-11 62.4
Msa0031030 MtrunA17_Chr7g0231181 30.075 133 62 3 55 187 235 336 4.91e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031030 AT3G10470.1 39.766 171 65 6 55 187 177 347 1.56e-26 104
Msa0031030 AT5G04390.1 40.437 183 71 8 40 187 136 315 4.47e-26 102
Msa0031030 AT2G28200.1 39.130 161 63 5 53 187 108 259 6.80e-26 100
Msa0031030 AT5G03510.1 35.915 142 80 3 58 188 116 257 2.70e-18 80.9
Msa0031030 AT2G37430.1 37.589 141 58 6 53 188 40 155 9.58e-18 77.0
Msa0031030 AT3G53600.1 32.576 132 62 3 58 188 47 152 7.18e-16 72.0
Msa0031030 AT3G46090.1 35.338 133 60 3 58 185 38 149 3.71e-14 67.4
Msa0031030 AT5G59820.1 30.337 178 81 6 14 186 8 147 1.48e-13 65.9
Msa0031030 AT3G49930.1 45.556 90 36 3 60 148 94 171 3.21e-13 65.9
Msa0031030 AT2G45120.1 33.333 129 64 3 60 188 194 300 6.53e-13 66.2
Msa0031030 AT4G35280.1 35.714 140 63 4 50 189 152 264 6.65e-13 65.9
Msa0031030 AT3G46080.1 38.298 94 34 2 58 148 35 107 2.04e-12 62.8
Msa0031030 AT5G67450.1 37.778 90 55 1 60 148 97 186 2.78e-12 63.5
Msa0031030 AT5G56200.1 37.624 101 51 3 60 152 342 438 4.79e-12 63.9
Msa0031030 AT5G43170.1 31.034 116 52 4 36 148 50 140 2.49e-11 60.5
Msa0031030 AT5G04340.1 35.556 90 51 2 59 148 88 170 4.31e-11 60.5
Msa0031030 AT3G60580.1 39.130 92 35 3 60 148 173 246 8.62e-11 60.1

Find 49 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAACAAATCCAAGGTTTA+TGG 0.208425 1_1:+57597866 Msa0031030:CDS
ATTCACTTTGGTGACATTAA+TGG 0.242417 1_1:-57597555 None:intergenic
AATGAACGTCTCTTTGGATT+TGG 0.242721 1_1:+57598033 Msa0031030:CDS
GGTTCTTCATCTTCTTTGTT+TGG 0.288377 1_1:-57597998 None:intergenic
CTCATTAACACCAATGGCTT+TGG 0.300691 1_1:+57597973 Msa0031030:CDS
GGTGGTGGTGGTGTTGGTGT+TGG 0.356632 1_1:-57597798 None:intergenic
AGTGGTGATGGTGGTGGTGG+TGG 0.359856 1_1:-57597813 None:intergenic
GTTTATGGGTGCTCTATTTG+TGG 0.395805 1_1:+57597881 Msa0031030:CDS
GAGGTCGCCTCCACCGGTGC+AGG 0.405277 1_1:-57597953 None:intergenic
TGGATTTGATCTTCTTAAGT+TGG 0.408226 1_1:-57598070 None:intergenic
TGTGGTTCTAAATTGACATC+TGG 0.409768 1_1:+57597899 Msa0031030:CDS
GGTAGTGGTGATGGTGGTGG+TGG 0.409982 1_1:-57597816 None:intergenic
ACAACAAATCCAAGGTTTAT+GGG 0.411833 1_1:+57597867 Msa0031030:CDS
GAATAAGCAATGATGGAGAA+AGG 0.431980 1_1:-57597617 None:intergenic
TTCACTTCATTTCAAGCACT+TGG 0.432350 1_1:+57597713 Msa0031030:CDS
GTTAATGAGGTCGCCTCCAC+CGG 0.455728 1_1:-57597959 None:intergenic
GTTGTTGTTGGTAGTGGTGA+TGG 0.460433 1_1:-57597825 None:intergenic
GTTGGTAGTGGTGATGGTGG+TGG 0.472547 1_1:-57597819 None:intergenic
CCTAGAAAAGTTCATAGAAA+AGG 0.473509 1_1:+57597761 Msa0031030:CDS
TTGTTTGGTTCCAAAGCCAT+TGG 0.473981 1_1:-57597983 None:intergenic
CAAAGTGAATATAACTCAAA+AGG 0.474354 1_1:+57597568 Msa0031030:CDS
AGTAGAAGAATAAGCAATGA+TGG 0.477070 1_1:-57597624 None:intergenic
TTCTAAATTGACATCTGGCC+AGG 0.487074 1_1:+57597904 Msa0031030:CDS
TTGACATCTGGCCAGGCACT+TGG 0.490879 1_1:+57597911 Msa0031030:CDS
GTGCAGGGTGGAAGTTCATA+TGG 0.495014 1_1:-57597937 None:intergenic
TCATATGGCCACCAAGTGCC+TGG 0.495422 1_1:-57597922 None:intergenic
CTTCCACCCTGCACCGGTGG+AGG 0.496858 1_1:+57597946 Msa0031030:CDS
AATAAGCAATGATGGAGAAA+GGG 0.498901 1_1:-57597616 None:intergenic
ACATCTGGCCAGGCACTTGG+TGG 0.509591 1_1:+57597914 Msa0031030:CDS
ATTTGATCTTCTTAAGTTGG+AGG 0.515985 1_1:-57598067 None:intergenic
AGAAAGGGATAGGAGATTGT+GGG 0.519333 1_1:-57597601 None:intergenic
ACTTCATTTCAAGCACTTGG+AGG 0.520190 1_1:+57597716 Msa0031030:CDS
GCTTATTCTTCTACTAGAGA+AGG 0.521996 1_1:+57597632 Msa0031030:CDS
GCAATGATGGAGAAAGGGAT+AGG 0.524368 1_1:-57597611 None:intergenic
CAAAGCCATTGGTGTTAATG+AGG 0.530269 1_1:-57597972 None:intergenic
GAGAAAGGGATAGGAGATTG+TGG 0.535781 1_1:-57597602 None:intergenic
AAAGGGATAGGAGATTGTGG+GGG 0.541180 1_1:-57597599 None:intergenic
GATCTTCTTAAGTTGGAGGA+AGG 0.550154 1_1:-57598063 None:intergenic
AATAGAGCACCCATAAACCT+TGG 0.557739 1_1:-57597876 None:intergenic
AGGTCGCCTCCACCGGTGCA+GGG 0.559156 1_1:-57597952 None:intergenic
GAAAGGGATAGGAGATTGTG+GGG 0.561722 1_1:-57597600 None:intergenic
GAACTTCCACCCTGCACCGG+TGG 0.571423 1_1:+57597943 Msa0031030:CDS
TATGAACTTCCACCCTGCAC+CGG 0.571843 1_1:+57597940 Msa0031030:CDS
GTTGTTGGTAGTGGTGATGG+TGG 0.572411 1_1:-57597822 None:intergenic
GGCGACCTCATTAACACCAA+TGG 0.589385 1_1:+57597967 Msa0031030:CDS
AAGGGATAGGAGATTGTGGG+GGG 0.595859 1_1:-57597598 None:intergenic
CTACAACAACAACAAATCCA+AGG 0.624442 1_1:+57597859 Msa0031030:CDS
TATTCTTCTACTAGAGAAGG+AGG 0.628197 1_1:+57597635 Msa0031030:CDS
TCGCCTCCACCGGTGCAGGG+TGG 0.663528 1_1:-57597949 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTGAGTTATATTCACTT+TGG - chr1_1:57597570-57597589 None:intergenic 25.0%
! CAAAGTGAATATAACTCAAA+AGG + chr1_1:57597568-57597587 Msa0031030:CDS 25.0%
! ATTCACTTTGGTGACATTAA+TGG - chr1_1:57597558-57597577 None:intergenic 30.0%
! AATAAGCAATGATGGAGAAA+GGG - chr1_1:57597619-57597638 None:intergenic 30.0%
AGTAGAAGAATAAGCAATGA+TGG - chr1_1:57597627-57597646 None:intergenic 30.0%
! CCTTTTCTATGAACTTTTCT+AGG - chr1_1:57597764-57597783 None:intergenic 30.0%
CCTAGAAAAGTTCATAGAAA+AGG + chr1_1:57597761-57597780 Msa0031030:CDS 30.0%
AACAACAAATCCAAGGTTTA+TGG + chr1_1:57597866-57597885 Msa0031030:CDS 30.0%
ACAACAAATCCAAGGTTTAT+GGG + chr1_1:57597867-57597886 Msa0031030:CDS 30.0%
AGAAAAAATGAACGTCTCTT+TGG + chr1_1:57598027-57598046 Msa0031030:CDS 30.0%
! GAATAAGCAATGATGGAGAA+AGG - chr1_1:57597620-57597639 None:intergenic 35.0%
GCTTATTCTTCTACTAGAGA+AGG + chr1_1:57597632-57597651 Msa0031030:CDS 35.0%
TATTCTTCTACTAGAGAAGG+AGG + chr1_1:57597635-57597654 Msa0031030:CDS 35.0%
TTCACTTCATTTCAAGCACT+TGG + chr1_1:57597713-57597732 Msa0031030:CDS 35.0%
! GCTTCTTGTGAACTTTTCTA+TGG - chr1_1:57597742-57597761 None:intergenic 35.0%
CTACAACAACAACAAATCCA+AGG + chr1_1:57597859-57597878 Msa0031030:CDS 35.0%
!! TGTGGTTCTAAATTGACATC+TGG + chr1_1:57597899-57597918 Msa0031030:CDS 35.0%
GGTTCTTCATCTTCTTTGTT+TGG - chr1_1:57598001-57598020 None:intergenic 35.0%
AATGAACGTCTCTTTGGATT+TGG + chr1_1:57598033-57598052 Msa0031030:CDS 35.0%
AGAAAGGGATAGGAGATTGT+GGG - chr1_1:57597604-57597623 None:intergenic 40.0%
ACTTCATTTCAAGCACTTGG+AGG + chr1_1:57597716-57597735 Msa0031030:CDS 40.0%
! GTTGTTGTTGTTGTTGGTAG+TGG - chr1_1:57597834-57597853 None:intergenic 40.0%
! GTTGCTGTTGTTGTTGTTGT+TGG - chr1_1:57597840-57597859 None:intergenic 40.0%
! AATAGAGCACCCATAAACCT+TGG - chr1_1:57597879-57597898 None:intergenic 40.0%
GTTTATGGGTGCTCTATTTG+TGG + chr1_1:57597881-57597900 Msa0031030:CDS 40.0%
TTCTAAATTGACATCTGGCC+AGG + chr1_1:57597904-57597923 Msa0031030:CDS 40.0%
!! CAAAGCCATTGGTGTTAATG+AGG - chr1_1:57597975-57597994 None:intergenic 40.0%
CTCATTAACACCAATGGCTT+TGG + chr1_1:57597973-57597992 Msa0031030:CDS 40.0%
! TTGTTTGGTTCCAAAGCCAT+TGG - chr1_1:57597986-57598005 None:intergenic 40.0%
!!! ACGTTCATTTTTTCTGCAGG+TGG - chr1_1:57598022-57598041 None:intergenic 40.0%
!!! GAGACGTTCATTTTTTCTGC+AGG - chr1_1:57598025-57598044 None:intergenic 40.0%
AAAGGGATAGGAGATTGTGG+GGG - chr1_1:57597602-57597621 None:intergenic 45.0%
GAAAGGGATAGGAGATTGTG+GGG - chr1_1:57597603-57597622 None:intergenic 45.0%
GAGAAAGGGATAGGAGATTG+TGG - chr1_1:57597605-57597624 None:intergenic 45.0%
! GCAATGATGGAGAAAGGGAT+AGG - chr1_1:57597614-57597633 None:intergenic 45.0%
!! GTTGTTGTTGGTAGTGGTGA+TGG - chr1_1:57597828-57597847 None:intergenic 45.0%
AAGGGATAGGAGATTGTGGG+GGG - chr1_1:57597601-57597620 None:intergenic 50.0%
!! GTTGTTGGTAGTGGTGATGG+TGG - chr1_1:57597825-57597844 None:intergenic 50.0%
GTGCAGGGTGGAAGTTCATA+TGG - chr1_1:57597940-57597959 None:intergenic 50.0%
TATGAACTTCCACCCTGCAC+CGG + chr1_1:57597940-57597959 Msa0031030:CDS 50.0%
GGCGACCTCATTAACACCAA+TGG + chr1_1:57597967-57597986 Msa0031030:CDS 50.0%
!! GTTGGTAGTGGTGATGGTGG+TGG - chr1_1:57597822-57597841 None:intergenic 55.0%
TTGACATCTGGCCAGGCACT+TGG + chr1_1:57597911-57597930 Msa0031030:CDS 55.0%
TCATATGGCCACCAAGTGCC+TGG - chr1_1:57597925-57597944 None:intergenic 55.0%
GTTAATGAGGTCGCCTCCAC+CGG - chr1_1:57597962-57597981 None:intergenic 55.0%
!! GGTGGTGGTGGTGTTGGTGT+TGG - chr1_1:57597801-57597820 None:intergenic 60.0%
!! AGTGGTGATGGTGGTGGTGG+TGG - chr1_1:57597816-57597835 None:intergenic 60.0%
!! GGTAGTGGTGATGGTGGTGG+TGG - chr1_1:57597819-57597838 None:intergenic 60.0%
ACATCTGGCCAGGCACTTGG+TGG + chr1_1:57597914-57597933 Msa0031030:CDS 60.0%
!! GGTGGTGGTGGTGGTGGTGT+TGG - chr1_1:57597807-57597826 None:intergenic 65.0%
!! GGTGATGGTGGTGGTGGTGG+TGG - chr1_1:57597813-57597832 None:intergenic 65.0%
GAACTTCCACCCTGCACCGG+TGG + chr1_1:57597943-57597962 Msa0031030:CDS 65.0%
! CTTCCACCCTGCACCGGTGG+AGG + chr1_1:57597946-57597965 Msa0031030:CDS 70.0%
AGGTCGCCTCCACCGGTGCA+GGG - chr1_1:57597955-57597974 None:intergenic 70.0%
TCGCCTCCACCGGTGCAGGG+TGG - chr1_1:57597952-57597971 None:intergenic 75.0%
GAGGTCGCCTCCACCGGTGC+AGG - chr1_1:57597956-57597975 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 57597509 57598078 57597509 ID=Msa0031030;Name=Msa0031030
chr1_1 mRNA 57597509 57598078 57597509 ID=Msa0031030-mRNA-1;Parent=Msa0031030;Name=Msa0031030-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|189
chr1_1 exon 57597509 57598078 57597509 ID=Msa0031030-mRNA-1:exon:17430;Parent=Msa0031030-mRNA-1
chr1_1 CDS 57597509 57598078 57597509 ID=Msa0031030-mRNA-1:cds;Parent=Msa0031030-mRNA-1
Gene Sequence

>Msa0031030

ATGGAAGCATCTCATGAACAACAACTCTCATTAAACACAAAACACACCATTAATGTCACCAAAGTGAATATAACTCAAAAGGTTATAAACCCCCCACAATCTCCTATCCCTTTCTCCATCATTGCTTATTCTTCTACTAGAGAAGGAGGAACAAGAGAAAGTGCACGTTACAATGTGTATACTTGCAAAACATGCAACAAAACATTCACTTCATTTCAAGCACTTGGAGGCCATAGAAAAGTTCACAAGAAGCCTAGAAAAGTTCATAGAAAAGGTCACAACAACAACACCAACACCAACACCACCACCACCACCACCATCACCACTACCAACAACAACAACAACAGCAACTACAACAACAACAAATCCAAGGTTTATGGGTGCTCTATTTGTGGTTCTAAATTGACATCTGGCCAGGCACTTGGTGGCCATATGAACTTCCACCCTGCACCGGTGGAGGCGACCTCATTAACACCAATGGCTTTGGAACCAAACAAAGAAGATGAAGAACCACCTGCAGAAAAAATGAACGTCTCTTTGGATTTGGATCTCAACCTTCCTCCAACTTAA
Protein sequence

>Msa0031030

MEASHEQQLSLNTKHTINVTKVNITQKVINPPQSPIPFSIIAYSSTREGGTRESARYNVYTCKTCNKTFTSFQALGGHRKVHKKPRKVHRKGHNNNTNTNTTTTTTITTTNNNNNSNYNNNKSKVYGCSICGSKLTSGQALGGHMNFHPAPVEATSLTPMALEPNKEDEEPPAEKMNVSLDLDLNLPPT*