AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0439940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0439940 MtrunA17_Chr2g0286251 99.020 102 1 0 1 102 1 102 9.53e-72 208
Msa0439940 MtrunA17_Chr4g0066791 78.641 103 21 1 1 102 1 103 6.53e-56 168
Msa0439940 MtrunA17_Chr4g0066801 78.641 103 21 1 1 102 1 103 6.53e-56 168
Msa0439940 MtrunA17_Chr4g0066811 78.641 103 21 1 1 102 1 103 6.53e-56 168
Msa0439940 MtrunA17_Chr2g0286271 63.725 102 37 0 1 102 1 102 7.70e-45 140
Msa0439940 MtrunA17_Chr7g0268751 52.941 102 48 0 1 102 1 102 4.69e-40 128
Msa0439940 MtrunA17_Chr1g0195951 53.922 102 47 0 1 102 1 102 5.29e-40 128
Msa0439940 MtrunA17_Chr1g0195971 58.416 101 42 0 1 101 1 101 3.09e-39 126
Msa0439940 MtrunA17_Chr1g0195981 58.947 95 39 0 1 95 1 95 4.94e-39 125
Msa0439940 MtrunA17_Chr1g0195991 56.842 95 41 0 1 95 1 95 5.82e-39 125
Msa0439940 MtrunA17_Chr7g0224091 57.282 103 43 1 1 102 22 124 2.29e-38 124
Msa0439940 MtrunA17_Chr7g0268711 55.789 95 42 0 1 95 1 95 1.74e-37 122
Msa0439940 MtrunA17_Chr7g0222551 53.398 103 47 1 1 102 30 132 1.19e-36 120
Msa0439940 MtrunA17_Chr7g0268731 55.882 102 44 1 1 101 1 102 2.11e-36 119
Msa0439940 MtrunA17_Chr7g0222541 52.427 103 48 1 1 102 30 132 1.04e-35 118
Msa0439940 MtrunA17_Chr7g0268721 54.902 102 45 1 1 101 1 102 1.30e-35 117
Msa0439940 MtrunA17_Chr7g0222491 51.456 103 49 1 1 102 30 132 4.36e-35 116
Msa0439940 MtrunA17_Chr1g0195931 50.000 102 51 0 1 102 1 102 3.74e-31 105
Msa0439940 MtrunA17_Chr7g0268761 44.554 101 56 0 1 101 1 101 6.38e-29 100
Msa0439940 MtrunA17_Chr2g0303741 46.667 105 52 1 2 102 40 144 2.84e-25 92.4
Msa0439940 MtrunA17_Chr2g0282951 41.346 104 51 3 4 102 29 127 3.18e-23 86.7
Msa0439940 MtrunA17_Chr2g0325001 37.864 103 57 2 4 102 41 140 9.76e-23 85.5
Msa0439940 MtrunA17_Chr4g0040601 39.000 100 56 2 6 102 58 155 3.85e-21 82.0
Msa0439940 MtrunA17_Chr1g0151231 43.137 102 56 1 3 102 48 149 5.14e-21 81.6
Msa0439940 MtrunA17_Chr7g0228311 40.000 100 60 0 1 100 3 102 1.81e-20 79.0
Msa0439940 MtrunA17_Chr3g0117411 38.000 100 62 0 1 100 18 117 2.28e-19 76.6
Msa0439940 MtrunA17_Chr3g0117391 37.000 100 63 0 1 100 21 120 1.59e-18 74.7
Msa0439940 MtrunA17_Chr3g0135811 39.604 101 53 3 3 101 23 117 1.19e-17 72.0
Msa0439940 MtrunA17_Chr5g0434201 40.777 103 59 1 2 102 21 123 1.97e-16 68.9
Msa0439940 MtrunA17_Chr1g0182971 36.364 99 62 1 2 99 84 182 3.04e-15 67.4
Msa0439940 MtrunA17_Chr8g0376641 38.835 103 61 1 2 102 21 123 6.10e-14 62.8
Msa0439940 MtrunA17_Chr2g0299021 33.333 84 56 0 2 85 84 167 2.98e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0439940 AT5G18600.1 76.471 102 24 0 1 102 1 102 4.89e-55 166
Msa0439940 AT4G15690.1 72.549 102 28 0 1 102 1 102 1.04e-54 166
Msa0439940 AT4G15680.1 69.608 102 31 0 1 102 1 102 8.20e-54 163
Msa0439940 AT4G15670.1 69.608 102 31 0 1 102 1 102 2.23e-53 162
Msa0439940 AT4G15700.1 70.588 102 30 0 1 102 1 102 3.61e-53 161
Msa0439940 AT4G15660.1 68.627 102 32 0 1 102 1 102 8.23e-52 158
Msa0439940 AT1G03020.1 59.804 102 41 0 1 102 1 102 3.40e-43 136
Msa0439940 AT3G62930.1 58.824 102 42 0 1 102 1 102 3.29e-42 134
Msa0439940 AT3G21460.1 59.804 102 41 0 1 102 1 102 2.21e-41 132
Msa0439940 AT2G47870.1 57.282 103 43 1 1 102 1 103 3.61e-40 129
Msa0439940 AT1G06830.1 55.789 95 42 0 1 95 1 95 6.74e-39 125
Msa0439940 AT2G47880.1 54.000 100 46 0 1 100 1 100 1.59e-38 124
Msa0439940 AT3G62950.1 53.398 103 47 1 1 102 1 103 2.65e-38 124
Msa0439940 AT2G30540.1 55.789 95 42 0 1 95 1 95 3.65e-38 124
Msa0439940 AT3G62960.1 52.632 95 45 0 1 95 1 95 9.22e-36 117
Msa0439940 AT5G14070.1 49.091 110 48 2 1 102 31 140 7.20e-33 111
Msa0439940 AT3G02000.1 52.830 106 44 1 3 102 31 136 1.43e-31 108
Msa0439940 AT4G33040.1 42.478 113 43 3 3 102 41 144 5.22e-21 81.6
Msa0439940 AT1G28480.1 35.238 105 64 1 2 102 33 137 1.58e-20 80.1
Msa0439940 AT5G63030.1 39.796 98 59 0 3 100 21 118 1.63e-19 77.4
Msa0439940 AT5G11930.1 43.000 100 47 3 3 101 57 147 4.31e-19 77.0
Msa0439940 AT5G40370.1 37.000 100 63 0 1 100 3 102 8.07e-19 75.1
Msa0439940 AT1G03850.2 37.634 93 54 1 10 102 62 150 4.66e-16 69.3
Msa0439940 AT4G28730.1 37.113 97 60 1 2 97 71 167 1.78e-14 65.5
Msa0439940 AT5G40370.2 38.372 86 53 0 15 100 42 127 1.24e-13 62.4
Msa0439940 AT2G20270.1 35.052 97 62 1 2 97 76 172 2.42e-13 62.8
Msa0439940 AT5G20500.1 34.737 95 62 0 4 98 35 129 1.42e-12 59.7

Find 27 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGAAGAGCAGGAGCTATT+TGG 0.243476 3_3:-6399016 Msa0439940:CDS
TCATCAAGTTCATGAACTTC+TGG 0.278380 3_3:+6399185 None:intergenic
TTGGAATCAAAGACCTATTA+AGG 0.291286 3_3:+6399042 None:intergenic
TTATGAGCCTTCACCTTAAT+AGG 0.313253 3_3:-6399055 Msa0439940:CDS
TAGAAGAGCAGGAGCTATTT+GGG 0.338414 3_3:-6399015 Msa0439940:CDS
TCTGTGCCTGCTGTGTTCAT+TGG 0.345825 3_3:-6399107 Msa0439940:CDS
CACTCCAAAGTCATTGAAAA+GGG 0.415156 3_3:+6399211 None:intergenic
TCACTCCAAAGTCATTGAAA+AGG 0.427326 3_3:+6399210 None:intergenic
TTCATTGGTGGTGAGCTTGT+TGG 0.448261 3_3:-6399092 Msa0439940:CDS
GTGCCTGCTGTGTTCATTGG+TGG 0.469372 3_3:-6399104 Msa0439940:CDS
ATTCCAATGCTTAGAAGAGC+AGG 0.473528 3_3:-6399026 Msa0439940:CDS
GCTCCTGCTCTTCTAAGCAT+TGG 0.494845 3_3:+6399023 None:intergenic
ATTGGTGGTGAGCTTGTTGG+TGG 0.505118 3_3:-6399089 Msa0439940:CDS
ATGAACACAGCAGGCACAGA+AGG 0.552108 3_3:+6399110 None:intergenic
TCACCACCAATGAACACAGC+AGG 0.561831 3_3:+6399101 None:intergenic
TCAAAGACCTATTAAGGTGA+AGG 0.569141 3_3:+6399048 None:intergenic
CAACCTTACATTAATGGAGA+GGG 0.591764 3_3:-6399309 None:intergenic
AATGGAGAGGGTGACACAGT+TGG 0.593802 3_3:-6399297 Msa0439940:CDS
ATGAACTTGATGAAATGAGT+GGG 0.613266 3_3:-6399175 Msa0439940:CDS
TCAACCTTACATTAATGGAG+AGG 0.626935 3_3:-6399310 None:intergenic
TGAACACAGCAGGCACAGAA+GGG 0.649613 3_3:+6399111 None:intergenic
CATGAACTTGATGAAATGAG+TGG 0.682020 3_3:-6399176 Msa0439940:CDS
GAACTTGATGAAATGAGTGG+GGG 0.688177 3_3:-6399173 Msa0439940:CDS
TGAACTTGATGAAATGAGTG+GGG 0.691196 3_3:-6399174 Msa0439940:CDS
GTTGGCATCAGAGAGGTCAG+TGG 0.695839 3_3:-6399279 Msa0439940:CDS
AACTTGATGAAATGAGTGGG+GGG 0.697784 3_3:-6399172 Msa0439940:CDS
TGACACAGTTGGCATCAGAG+AGG 0.724593 3_3:-6399286 Msa0439940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAACCCTTTTCAATGACTT+TGG - chr3_3:6399091-6399110 Msa0439940:CDS 30.0%
ATGAACTTGATGAAATGAGT+GGG - chr3_3:6399131-6399150 Msa0439940:CDS 30.0%
! ACATTGAACAAGCACTTTTA+AGG - chr3_3:6399161-6399180 Msa0439940:CDS 30.0%
TTGGAATCAAAGACCTATTA+AGG + chr3_3:6399267-6399286 None:intergenic 30.0%
CACTCCAAAGTCATTGAAAA+GGG + chr3_3:6399098-6399117 None:intergenic 35.0%
TCACTCCAAAGTCATTGAAA+AGG + chr3_3:6399099-6399118 None:intergenic 35.0%
TCATCAAGTTCATGAACTTC+TGG + chr3_3:6399124-6399143 None:intergenic 35.0%
CATGAACTTGATGAAATGAG+TGG - chr3_3:6399130-6399149 Msa0439940:CDS 35.0%
TGAACTTGATGAAATGAGTG+GGG - chr3_3:6399132-6399151 Msa0439940:CDS 35.0%
TTATGAGCCTTCACCTTAAT+AGG - chr3_3:6399251-6399270 Msa0439940:CDS 35.0%
TCAAAGACCTATTAAGGTGA+AGG + chr3_3:6399261-6399280 None:intergenic 35.0%
GAACTTGATGAAATGAGTGG+GGG - chr3_3:6399133-6399152 Msa0439940:CDS 40.0%
AACTTGATGAAATGAGTGGG+GGG - chr3_3:6399134-6399153 Msa0439940:CDS 40.0%
!!! GAACAAGCACTTTTAAGGCT+AGG - chr3_3:6399166-6399185 Msa0439940:CDS 40.0%
ATTCCAATGCTTAGAAGAGC+AGG - chr3_3:6399280-6399299 Msa0439940:CDS 40.0%
TTAGAAGAGCAGGAGCTATT+TGG - chr3_3:6399290-6399309 Msa0439940:CDS 40.0%
TAGAAGAGCAGGAGCTATTT+GGG - chr3_3:6399291-6399310 Msa0439940:CDS 40.0%
!! TTCATTGGTGGTGAGCTTGT+TGG - chr3_3:6399214-6399233 Msa0439940:CDS 45.0%
TGACACAGTTGGCATCAGAG+AGG - chr3_3:6399020-6399039 Msa0439940:CDS 50.0%
TGAACACAGCAGGCACAGAA+GGG + chr3_3:6399198-6399217 None:intergenic 50.0%
ATGAACACAGCAGGCACAGA+AGG + chr3_3:6399199-6399218 None:intergenic 50.0%
TCTGTGCCTGCTGTGTTCAT+TGG - chr3_3:6399199-6399218 Msa0439940:CDS 50.0%
TCACCACCAATGAACACAGC+AGG + chr3_3:6399208-6399227 None:intergenic 50.0%
!! ATTGGTGGTGAGCTTGTTGG+TGG - chr3_3:6399217-6399236 Msa0439940:CDS 50.0%
GCTCCTGCTCTTCTAAGCAT+TGG + chr3_3:6399286-6399305 None:intergenic 50.0%
GTTGGCATCAGAGAGGTCAG+TGG - chr3_3:6399027-6399046 Msa0439940:CDS 55.0%
GTGCCTGCTGTGTTCATTGG+TGG - chr3_3:6399202-6399221 Msa0439940:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 6399010 6399318 6399010 ID=Msa0439940;Name=Msa0439940
chr3_3 mRNA 6399010 6399318 6399010 ID=Msa0439940-mRNA-1;Parent=Msa0439940;Name=Msa0439940-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|-1|0|1|-1|1|1|0|102
chr3_3 exon 6399010 6399318 6399010 ID=Msa0439940-mRNA-1:exon:1343;Parent=Msa0439940-mRNA-1
chr3_3 CDS 6399010 6399318 6399010 ID=Msa0439940-mRNA-1:cds;Parent=Msa0439940-mRNA-1
Gene Sequence

>Msa0439940

ATGGAGAGGGTGACACAGTTGGCATCAGAGAGGTCAGTGGTGATATTCAGCAAGAGTAGTTGTTGCATGTGTCACACAATCAAAACCCTTTTCAATGACTTTGGAGTGAATCCAGAAGTTCATGAACTTGATGAAATGAGTGGGGGGAGAGACATTGAACAAGCACTTTTAAGGCTAGGATGTAACCCTTCTGTGCCTGCTGTGTTCATTGGTGGTGAGCTTGTTGGTGGAGCTAATGAAGTTATGAGCCTTCACCTTAATAGGTCTTTGATTCCAATGCTTAGAAGAGCAGGAGCTATTTGGGTTTGA

Protein sequence

>Msa0439940

MERVTQLASERSVVIFSKSSCCMCHTIKTLFNDFGVNPEVHELDEMSGGRDIEQALLRLGCNPSVPAVFIGGELVGGANEVMSLHLNRSLIPMLRRAGAIWV*