AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1377000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377000 MtrunA17_Chr1g0153881 90.090 111 10 1 8 118 33 142 1.73e-64 203
Msa1377000 MtrunA17_Chr1g0153941 78.632 117 23 2 3 118 15 130 8.23e-59 189
Msa1377000 MtrunA17_Chr1g0153931 78.070 114 23 2 6 118 16 128 3.01e-58 181
Msa1377000 MtrunA17_Chr3g0118831 58.182 110 43 3 10 118 23 130 1.19e-33 121
Msa1377000 MtrunA17_Chr3g0118841 56.190 105 44 2 15 118 28 131 2.10e-31 115
Msa1377000 MtrunA17_Chr3g0118851 57.143 105 43 2 15 118 27 130 4.18e-31 114
Msa1377000 MtrunA17_Chr3g0118861 55.769 104 44 2 15 118 27 128 2.30e-30 112
Msa1377000 MtrunA17_Chr3g0118891 53.846 104 48 0 15 118 27 130 3.99e-30 112
Msa1377000 MtrunA17_Chr3g0118881 51.376 109 43 3 15 118 27 130 2.89e-28 107
Msa1377000 MtrunA17_Chr1g0199991 52.055 73 29 2 48 118 19 87 2.44e-20 84.7
Msa1377000 MtrunA17_Chr3g0131731 60.714 56 22 0 63 118 28 83 7.25e-19 80.5
Msa1377000 MtrunA17_Chr1g0199971 52.055 73 29 2 48 118 19 87 9.81e-19 80.1
Msa1377000 MtrunA17_Chr2g0304931 63.158 57 20 1 62 118 35 90 1.25e-18 80.1
Msa1377000 MtrunA17_Chr1g0165811 53.448 58 26 1 61 118 26 82 2.25e-17 75.1
Msa1377000 MtrunA17_Chr5g0431301 65.455 55 18 1 64 118 28 81 3.21e-17 75.9
Msa1377000 MtrunA17_Chr3g0094811 57.627 59 24 1 60 118 25 82 3.26e-17 75.9
Msa1377000 MtrunA17_Chr3g0090331 44.318 88 41 2 38 118 40 126 5.83e-17 75.5
Msa1377000 MtrunA17_Chr8g0385871 60.714 56 21 1 63 118 31 85 9.26e-17 74.7
Msa1377000 MtrunA17_Chr3g0126051 60.000 55 21 1 64 118 32 85 3.25e-16 73.2
Msa1377000 MtrunA17_Chr4g0020241 36.975 119 57 3 6 118 19 125 5.09e-16 72.8
Msa1377000 MtrunA17_Chr4g0038311 57.895 57 23 1 62 118 31 86 1.61e-15 71.2
Msa1377000 MtrunA17_Chr2g0281631 54.386 57 25 1 62 118 42 97 1.89e-15 67.0
Msa1377000 MtrunA17_Chr3g0126031 65.455 55 18 1 64 118 27 80 2.83e-15 70.5
Msa1377000 MtrunA17_Chr4g0047861 58.929 56 22 1 63 118 51 105 5.93e-15 69.7
Msa1377000 MtrunA17_Chr7g0219051 56.140 57 24 1 62 118 32 87 6.86e-15 69.3
Msa1377000 MtrunA17_Chr7g0221551 54.545 55 24 1 64 118 29 82 1.38e-14 68.6
Msa1377000 MtrunA17_Chr7g0229631 54.545 55 23 2 64 118 32 84 2.22e-14 65.1
Msa1377000 MtrunA17_Chr2g0318911 47.458 59 29 2 62 118 36 94 5.00e-14 67.0
Msa1377000 MtrunA17_Chr1g0204191 54.386 57 25 1 62 118 88 143 5.19e-14 67.0
Msa1377000 MtrunA17_Chr2g0309521 47.458 59 29 2 62 118 35 93 7.16e-14 66.6
Msa1377000 MtrunA17_Chr7g0234041 58.491 53 22 0 66 118 27 79 9.11e-14 66.2
Msa1377000 MtrunA17_Chr4g0068841 47.368 57 30 0 62 118 35 91 1.47e-13 65.5
Msa1377000 MtrunA17_Chr2g0281621 58.182 55 22 1 64 118 34 87 1.63e-13 65.5
Msa1377000 MtrunA17_Chr4g0068861 47.368 57 30 0 62 118 81 137 2.76e-13 64.7
Msa1377000 MtrunA17_Chr2g0309541 47.170 53 27 1 67 118 40 92 3.69e-13 64.3
Msa1377000 MtrunA17_Chr2g0309511 45.763 59 30 2 62 118 35 93 3.80e-13 64.3
Msa1377000 MtrunA17_Chr7g0229611 51.852 54 24 2 65 118 25 76 2.44e-12 58.5
Msa1377000 MtrunA17_Chr8g0338461 50.877 57 28 0 62 118 27 83 4.82e-12 61.2
Msa1377000 MtrunA17_Chr7g0234051 52.830 53 25 0 66 118 30 82 6.58e-12 60.8
Msa1377000 MtrunA17_Chr7g0229621 50.909 55 25 2 64 118 24 76 9.32e-12 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377000 AT3G07990.1 58.209 67 22 2 54 118 26 88 3.21e-19 82.0
Msa1377000 AT2G35770.1 52.113 71 30 1 48 118 24 90 4.16e-19 81.6
Msa1377000 AT3G63470.1 41.441 111 62 2 8 118 26 133 1.18e-18 80.5
Msa1377000 AT2G24010.1 60.656 61 23 1 58 118 23 82 2.18e-18 79.7
Msa1377000 AT1G28110.1 64.286 56 19 1 63 118 29 83 4.12e-18 79.0
Msa1377000 AT1G28110.2 64.286 56 19 1 63 118 29 83 4.12e-18 79.0
Msa1377000 AT3G56540.1 50.685 73 31 2 46 118 64 131 1.18e-17 76.3
Msa1377000 AT2G24010.2 60.000 60 23 1 58 117 23 81 1.21e-17 77.8
Msa1377000 AT5G23210.3 60.656 61 23 1 58 118 44 103 3.43e-17 76.3
Msa1377000 AT5G23210.1 60.656 61 23 1 58 118 44 103 3.66e-17 76.3
Msa1377000 AT2G05850.1 44.330 97 50 3 23 118 23 116 7.47e-17 75.5
Msa1377000 AT5G42230.1 64.912 57 19 1 62 118 25 80 7.80e-17 75.5
Msa1377000 AT5G42230.2 64.912 57 19 1 62 118 25 80 7.80e-17 75.5
Msa1377000 AT3G52020.1 50.685 73 31 2 46 118 64 131 2.67e-16 73.9
Msa1377000 AT2G33530.1 55.932 59 25 1 60 118 28 85 3.23e-16 73.6
Msa1377000 AT3G52010.1 45.714 70 38 0 49 118 48 117 3.83e-16 73.2
Msa1377000 AT5G42240.1 64.912 57 19 1 62 118 29 84 3.98e-16 73.2
Msa1377000 AT2G12480.2 61.404 57 21 1 62 118 28 83 8.29e-16 72.4
Msa1377000 AT2G12480.1 61.404 57 21 1 62 118 28 83 8.53e-16 72.4
Msa1377000 AT2G24010.4 61.538 52 19 1 66 117 2 52 1.07e-15 71.6
Msa1377000 AT1G43780.1 63.636 55 19 1 64 118 36 89 1.18e-15 72.0
Msa1377000 AT2G35780.1 52.542 59 26 1 62 118 26 84 1.22e-15 72.0
Msa1377000 AT4G30610.1 59.016 61 23 2 59 118 26 85 1.38e-15 71.6
Msa1377000 AT2G24000.2 60.345 58 21 2 62 118 27 83 1.38e-15 71.6
Msa1377000 AT2G24010.3 61.538 52 19 1 66 117 2 52 1.56e-15 71.6
Msa1377000 AT2G24000.1 60.345 58 21 2 62 118 27 83 1.67e-15 71.6
Msa1377000 AT3G02110.1 54.386 57 25 1 62 118 34 89 2.06e-15 71.2
Msa1377000 AT2G12480.3 61.404 57 21 1 62 118 28 83 2.73e-15 70.9
Msa1377000 AT2G12480.4 61.404 57 21 1 62 118 28 83 2.84e-15 70.9
Msa1377000 AT4G30810.1 43.662 71 40 0 48 118 20 90 6.52e-15 69.7
Msa1377000 AT3G52000.1 50.877 57 28 0 62 118 60 116 1.02e-14 69.3
Msa1377000 AT4G15100.1 48.684 76 38 1 43 118 22 96 2.48e-14 68.2
Msa1377000 AT1G61130.1 58.182 55 22 1 64 118 30 83 3.51e-14 67.8
Msa1377000 AT1G11080.1 56.140 57 24 1 62 118 47 102 1.37e-13 66.2
Msa1377000 AT1G11080.2 56.140 57 24 1 62 118 47 102 1.37e-13 66.2
Msa1377000 AT5G08260.1 53.448 58 25 2 62 118 36 92 8.61e-12 60.8
Msa1377000 AT4G12910.2 45.614 57 31 0 62 118 31 87 1.40e-11 60.5
Msa1377000 AT4G12910.1 45.614 57 31 0 62 118 31 87 1.56e-11 60.1

Find 26 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTTATTCTATGGCTAAA+TGG 0.278593 tig0019847:-51029 Msa1377000:CDS
ATGTTGTTGAACAACAATTA+AGG 0.297399 tig0019847:-51202 Msa1377000:CDS
CCGCAAAGCCTCTTATTCTA+TGG 0.298269 tig0019847:-51037 Msa1377000:CDS
TGATCAAAATCCACCCCTTT+TGG 0.306850 tig0019847:+51140 None:intergenic
TGAACAACAATTAAGGTTGA+TGG 0.361619 tig0019847:-51195 Msa1377000:CDS
GAGGTATTCACTTTGTTGAT+TGG 0.364702 tig0019847:+51322 None:intergenic
CCATTTAGCCATAGAATAAG+AGG 0.381266 tig0019847:+51029 None:intergenic
GGCTTTGCGGAAGAATTTAG+AGG 0.402787 tig0019847:+51050 None:intergenic
AAGGTTGATGGAAGCTGATA+AGG 0.422221 tig0019847:-51183 Msa1377000:CDS
GTAACTGTTGATTCAAAAGC+AGG 0.449053 tig0019847:-51104 Msa1377000:CDS
CCATAGAATAAGAGGCTTTG+CGG 0.464109 tig0019847:+51037 None:intergenic
GATAAGGTGAAGGCTTTGCC+TGG 0.468779 tig0019847:-51167 Msa1377000:CDS
GCTTTGCCTGGACAACCAAA+AGG 0.470820 tig0019847:-51155 Msa1377000:CDS
CTTTGCCTGGACAACCAAAA+GGG 0.504988 tig0019847:-51154 Msa1377000:CDS
TTGATTGAATAAACTTGTAG+AGG 0.519280 tig0019847:+51303 None:intergenic
ACAAGTTTATTCAATCAAAG+AGG 0.545775 tig0019847:-51298 Msa1377000:CDS
GCCTGGACAACCAAAAGGGG+TGG 0.584025 tig0019847:-51150 Msa1377000:CDS
TGTTGATGAACATGTTTCAA+AGG 0.590932 tig0019847:-51228 Msa1377000:CDS
TAATAAGATTCTCCATGTGA+AGG 0.601123 tig0019847:+51263 None:intergenic
TAACTGTTGATTCAAAAGCA+GGG 0.604168 tig0019847:-51103 Msa1377000:CDS
TCTCAACAAAAGCCTTCACA+TGG 0.616190 tig0019847:-51275 Msa1377000:CDS
GATGGAAGCTGATAAGGTGA+AGG 0.629148 tig0019847:-51177 Msa1377000:CDS
AATATAGCACAAAACATGAG+AGG 0.640407 tig0019847:-51464 None:intergenic
TTTGCCTGGACAACCAAAAG+GGG 0.643225 tig0019847:-51153 Msa1377000:CDS
CTTATTCTATGGCTAAATGG+AGG 0.653468 tig0019847:-51026 Msa1377000:CDS
CTTTGCATGAGATTGCAAAG+TGG 0.677863 tig0019847:+51345 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGATTGAATAAACTTGTAG+AGG + tig0019847:51168-51187 None:intergenic 25.0%
! ACAAGTTTATTCAATCAAAG+AGG - tig0019847:51170-51189 Msa1377000:CDS 25.0%
! ATGTTGTTGAACAACAATTA+AGG - tig0019847:51266-51285 Msa1377000:CDS 25.0%
!!! TGTCACAAAAAGTACTTTTG+TGG - tig0019847:51080-51099 Msa1377000:CDS 30.0%
TAATAAGATTCTCCATGTGA+AGG + tig0019847:51208-51227 None:intergenic 30.0%
! TGTTGATGAACATGTTTCAA+AGG - tig0019847:51240-51259 Msa1377000:CDS 30.0%
TGAACAACAATTAAGGTTGA+TGG - tig0019847:51273-51292 Msa1377000:CDS 30.0%
!! TAACTGTTGATTCAAAAGCA+GGG - tig0019847:51365-51384 Msa1377000:intron 30.0%
! AGAACTTTTCTACTACTTTG+TGG - tig0019847:51390-51409 Msa1377000:intron 30.0%
! GAGGTATTCACTTTGTTGAT+TGG + tig0019847:51149-51168 None:intergenic 35.0%
!! GTGGATTTTGATCAATATGC+TGG - tig0019847:51337-51356 Msa1377000:CDS 35.0%
!! GTAACTGTTGATTCAAAAGC+AGG - tig0019847:51364-51383 Msa1377000:intron 35.0%
CCATTTAGCCATAGAATAAG+AGG + tig0019847:51442-51461 None:intergenic 35.0%
CCTCTTATTCTATGGCTAAA+TGG - tig0019847:51439-51458 Msa1377000:intron 35.0%
CTTATTCTATGGCTAAATGG+AGG - tig0019847:51442-51461 Msa1377000:intron 35.0%
CTTTGCATGAGATTGCAAAG+TGG + tig0019847:51126-51145 None:intergenic 40.0%
TCTCAACAAAAGCCTTCACA+TGG - tig0019847:51193-51212 Msa1377000:CDS 40.0%
!! AAGGTTGATGGAAGCTGATA+AGG - tig0019847:51285-51304 Msa1377000:CDS 40.0%
! TGATCAAAATCCACCCCTTT+TGG + tig0019847:51331-51350 None:intergenic 40.0%
CCATAGAATAAGAGGCTTTG+CGG + tig0019847:51434-51453 None:intergenic 40.0%
GATGGAAGCTGATAAGGTGA+AGG - tig0019847:51291-51310 Msa1377000:CDS 45.0%
CTTTGCCTGGACAACCAAAA+GGG - tig0019847:51314-51333 Msa1377000:CDS 45.0%
TTTGCCTGGACAACCAAAAG+GGG - tig0019847:51315-51334 Msa1377000:CDS 45.0%
GGCTTTGCGGAAGAATTTAG+AGG + tig0019847:51421-51440 None:intergenic 45.0%
CCGCAAAGCCTCTTATTCTA+TGG - tig0019847:51431-51450 Msa1377000:intron 45.0%
GATAAGGTGAAGGCTTTGCC+TGG - tig0019847:51301-51320 Msa1377000:CDS 50.0%
GCTTTGCCTGGACAACCAAA+AGG - tig0019847:51313-51332 Msa1377000:CDS 50.0%
!! TCCACCCCTTTTGGTTGTCC+AGG + tig0019847:51322-51341 None:intergenic 55.0%
GCCTGGACAACCAAAAGGGG+TGG - tig0019847:51318-51337 Msa1377000:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0019847 gene 51019 51471 51019 ID=Msa1377000;Name=Msa1377000
tig0019847 mRNA 51019 51471 51019 ID=Msa1377000-mRNA-1;Parent=Msa1377000;Name=Msa1377000-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0|0|1|1|1|2|0|119
tig0019847 exon 51465 51471 51465 ID=Msa1377000-mRNA-1:exon:5485;Parent=Msa1377000-mRNA-1
tig0019847 exon 51019 51371 51019 ID=Msa1377000-mRNA-1:exon:5484;Parent=Msa1377000-mRNA-1
tig0019847 CDS 51465 51471 51465 ID=Msa1377000-mRNA-1:cds;Parent=Msa1377000-mRNA-1
tig0019847 CDS 51019 51371 51019 ID=Msa1377000-mRNA-1:cds;Parent=Msa1377000-mRNA-1
Gene Sequence

>Msa1377000

ATGAGAGTGTGCCACTTTGCAATCTCATGCAAAGCCAATCAACAAAGTGAATACCTCTACAAGTTTATTCAATCAAAGAGGTCTCAACAAAAGCCTTCACATGGAGAATCTTATTATTCAAATGATGTTGTTGATGAACATGTTTCAAAGGTACATGTTGTTGAACAACAATTAAGGTTGATGGAAGCTGATAAGGTGAAGGCTTTGCCTGGACAACCAAAAGGGGTGGATTTTGATCAATATGCTGGCTATGTAACTGTTGATTCAAAAGCAGGGAGAGAACTTTTCTACTACTTTGTGGAATCACCTCTAAATTCTTCCGCAAAGCCTCTTATTCTATGGCTAAATGGAGGTAATTAA
Protein sequence

>Msa1377000

MRVCHFAISCKANQQSEYLYKFIQSKRSQQKPSHGESYYSNDVVDEHVSKVHVVEQQLRLMEADKVKALPGQPKGVDFDQYAGYVTVDSKAGRELFYYFVESPLNSSAKPLILWLNGGN*