AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0227120

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0227120 MtrunA17_Chr2g0333541 90.244 164 13 1 2 165 1 161 3.69e-94 274
Msa0227120 MtrunA17_Chr8g0368371 78.723 141 15 1 2 127 1 141 1.20e-73 217
Msa0227120 MtrunA17_Chr2g0333641 41.279 172 74 6 5 152 23 191 1.61e-25 99.4
Msa0227120 MtrunA17_Chr2g0333621 39.153 189 81 6 2 162 20 202 5.37e-25 98.2
Msa0227120 MtrunA17_Chr8g0336681 59.155 71 29 0 87 157 145 215 3.21e-21 88.6
Msa0227120 MtrunA17_Chr2g0333611 47.115 104 52 3 65 167 13 114 6.79e-21 85.5
Msa0227120 MtrunA17_Chr4g0002801 47.959 98 46 1 60 152 109 206 6.28e-20 84.7
Msa0227120 MtrunA17_Chr7g0249811 59.091 66 26 1 87 151 153 218 2.49e-19 83.2
Msa0227120 MtrunA17_Chr4g0002781 54.795 73 33 0 80 152 156 228 1.05e-18 81.6
Msa0227120 MtrunA17_Chr5g0400621 47.619 84 42 1 83 166 144 225 7.55e-17 76.3
Msa0227120 MtrunA17_Chr5g0400661 38.583 127 63 3 54 165 90 216 1.47e-16 75.5
Msa0227120 MtrunA17_Chr4g0054581 40.708 113 63 1 54 162 150 262 5.16e-16 74.3
Msa0227120 MtrunA17_Chr5g0400671 44.706 85 43 2 78 161 137 218 6.10e-16 73.6
Msa0227120 MtrunA17_Chr2g0280161 47.826 69 36 0 89 157 168 236 1.58e-15 72.8
Msa0227120 MtrunA17_Chr4g0033291 50.000 68 32 1 85 152 144 209 2.77e-15 72.0
Msa0227120 MtrunA17_Chr7g0225901 45.455 77 42 0 76 152 66 142 2.88e-15 70.9
Msa0227120 MtrunA17_Chr4g0033281 40.171 117 60 3 44 152 93 207 4.92e-15 71.2
Msa0227120 MtrunA17_Chr4g0033391 47.222 72 36 1 85 156 136 205 1.67e-14 69.7
Msa0227120 MtrunA17_Chr6g0468461 33.742 163 88 4 23 165 78 240 1.70e-14 69.7
Msa0227120 MtrunA17_Chr4g0049331 44.444 81 41 1 77 153 110 190 2.83e-14 68.9
Msa0227120 MtrunA17_Chr4g0054561 43.284 67 38 0 91 157 148 214 7.60e-14 67.8
Msa0227120 MtrunA17_Chr4g0054551 43.662 71 40 0 91 161 148 218 8.55e-14 67.8
Msa0227120 MtrunA17_Chr2g0307131 47.222 72 37 1 85 156 167 237 3.56e-13 66.2
Msa0227120 MtrunA17_Chr6g0468491 44.872 78 42 1 76 152 114 191 1.01e-12 64.7
Msa0227120 MtrunA17_Chr2g0307141 50.847 59 29 0 98 156 183 241 1.04e-12 64.7
Msa0227120 MtrunA17_Chr5g0400641 55.769 52 23 0 101 152 1 52 1.41e-12 62.4
Msa0227120 MtrunA17_Chr4g0054571 53.333 60 28 0 96 155 148 207 2.13e-12 63.9
Msa0227120 MtrunA17_Chr4g0054621 38.947 95 53 1 63 152 132 226 1.12e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0227120 AT4G37850.2 37.391 115 68 2 55 165 105 219 5.66e-17 77.0
Msa0227120 AT4G37850.1 37.391 115 68 2 55 165 105 219 5.66e-17 77.0
Msa0227120 AT2G22770.1 51.786 56 27 0 98 153 132 187 3.81e-13 66.2
Msa0227120 AT2G22750.1 52.727 55 26 0 91 145 119 173 6.12e-13 65.5
Msa0227120 AT2G22750.2 52.727 55 26 0 91 145 119 173 6.47e-13 65.5
Msa0227120 AT2G22750.4 52.727 55 26 0 91 145 147 201 7.41e-13 65.5
Msa0227120 AT2G22750.5 52.727 55 26 0 91 145 143 197 7.53e-13 65.5
Msa0227120 AT2G22750.3 52.727 55 26 0 91 145 147 201 7.66e-13 65.5
Msa0227120 AT2G22760.2 46.032 63 34 0 91 153 112 174 8.73e-12 62.0
Msa0227120 AT2G22760.1 46.032 63 34 0 91 153 112 174 9.32e-12 62.0
Msa0227120 AT4G09820.1 42.424 66 38 0 86 151 351 416 8.28e-11 60.1

Find 32 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATTAGAACACGAGATTTA+TGG 0.199679 2_1:+77732636 None:intergenic
ACTAGGCCAGTTGTGGCAAT+AGG 0.327076 2_1:+77733140 None:intergenic
CTTCTTCAATCCAGGTATAA+AGG 0.361311 2_1:+77732881 None:intergenic
AAGTAAGATCATAGAACTTT+CGG 0.375512 2_1:-77732904 Msa0227120:CDS
ACATAATGTCGGAGAGGAAT+AGG 0.390434 2_1:-77732941 Msa0227120:CDS
GAACTTTCGGCCTTTATACC+TGG 0.434477 2_1:-77732891 Msa0227120:CDS
TGATGGATGAGTTGTTTACT+AGG 0.442805 2_1:+77733123 None:intergenic
CTAGGCCAGTTGTGGCAATA+GGG 0.443059 2_1:+77733141 None:intergenic
GATCTTGTGGAGTCTGATAC+AGG 0.452617 2_1:+77733174 None:intergenic
AGTTGAATGTGACACATTGA+TGG 0.456224 2_1:+77733106 None:intergenic
CTTTATACCTGGATTGAAGA+AGG 0.465281 2_1:-77732880 Msa0227120:intron
AATGGCTGTGTAGATTGATA+AGG 0.480377 2_1:-77732761 Msa0227120:intron
ATACTAACCTTCTTCAATCC+AGG 0.486683 2_1:+77732873 None:intergenic
AGTGTCCCTATTGCCACAAC+TGG 0.491296 2_1:-77733146 Msa0227120:CDS
GACATTAAGAAGAAAGATGC+AGG 0.492316 2_1:-77732670 Msa0227120:CDS
TCATGGTGTTGTTCAATTGT+TGG 0.495507 2_1:+77733044 None:intergenic
AATGTCTCAGAAGCGCTTCG+AGG 0.506140 2_1:+77732969 None:intergenic
GCTTCTTTGAATTCGACCCT+TGG 0.521451 2_1:+77732991 None:intergenic
ATGACAAAGGCAAAGAATCA+TGG 0.529186 2_1:+77733027 None:intergenic
GGTATTGATAATGAGTTGGT+TGG 0.541397 2_1:+77733065 None:intergenic
TTTGCCTTTGTCATCATCAA+CGG 0.545210 2_1:-77733018 Msa0227120:CDS
TGTTGGTATTGATAATGAGT+TGG 0.562767 2_1:+77733061 None:intergenic
TGATAAGGTTCATGTGGTAA+CGG 0.571985 2_1:-77732746 Msa0227120:CDS
GACATTAGATCACATAATGT+CGG 0.591474 2_1:-77732952 Msa0227120:CDS
GGGACACTGAATTGATCTTG+TGG 0.603401 2_1:+77733161 None:intergenic
GTTGTTTACTAGGCCAGTTG+TGG 0.626590 2_1:+77733133 None:intergenic
TCATCATCAACGGATAACCA+AGG 0.662866 2_1:-77733008 Msa0227120:CDS
CATCATCAACGGATAACCAA+GGG 0.664890 2_1:-77733007 Msa0227120:CDS
TTATCCGTTGATGATGACAA+AGG 0.681037 2_1:+77733014 None:intergenic
TAGATCACATAATGTCGGAG+AGG 0.685140 2_1:-77732947 Msa0227120:CDS
GTAGATTGATAAGGTTCATG+TGG 0.700450 2_1:-77732752 Msa0227120:intron
TCTGATACAGGATATCTCTG+AGG 0.706562 2_1:+77733186 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATATTATATTAAACC+TGG - chr2_1:77733027-77733046 Msa0227120:CDS 10.0%
!! AATAAAAATGATCTAATTAA+TGG - chr2_1:77733096-77733115 Msa0227120:CDS 10.0%
!!! ATTTTTATAGTCGTTATCAT+TGG - chr2_1:77733062-77733081 Msa0227120:CDS 20.0%
! AAGTAAGATCATAGAACTTT+CGG - chr2_1:77732971-77732990 Msa0227120:CDS 25.0%
! AAAAATTTACTCATTCATCC+AGG + chr2_1:77733048-77733067 None:intergenic 25.0%
!! TGTTGGTATTGATAATGAGT+TGG + chr2_1:77732817-77732836 None:intergenic 30.0%
GACATTAGATCACATAATGT+CGG - chr2_1:77732923-77732942 Msa0227120:CDS 30.0%
! TGATGGATGAGTTGTTTACT+AGG + chr2_1:77732755-77732774 None:intergenic 35.0%
AGTTGAATGTGACACATTGA+TGG + chr2_1:77732772-77732791 None:intergenic 35.0%
!! GGTATTGATAATGAGTTGGT+TGG + chr2_1:77732813-77732832 None:intergenic 35.0%
!! TCATGGTGTTGTTCAATTGT+TGG + chr2_1:77732834-77732853 None:intergenic 35.0%
ATGACAAAGGCAAAGAATCA+TGG + chr2_1:77732851-77732870 None:intergenic 35.0%
TTTGCCTTTGTCATCATCAA+CGG - chr2_1:77732857-77732876 Msa0227120:intron 35.0%
!! TTATCCGTTGATGATGACAA+AGG + chr2_1:77732864-77732883 None:intergenic 35.0%
CTTCTTCAATCCAGGTATAA+AGG + chr2_1:77732997-77733016 None:intergenic 35.0%
CTTTATACCTGGATTGAAGA+AGG - chr2_1:77732995-77733014 Msa0227120:CDS 35.0%
ATACTAACCTTCTTCAATCC+AGG + chr2_1:77733005-77733024 None:intergenic 35.0%
AATGGCTGTGTAGATTGATA+AGG - chr2_1:77733114-77733133 Msa0227120:CDS 35.0%
GTAGATTGATAAGGTTCATG+TGG - chr2_1:77733123-77733142 Msa0227120:CDS 35.0%
TGATAAGGTTCATGTGGTAA+CGG - chr2_1:77733129-77733148 Msa0227120:CDS 35.0%
GACATTAAGAAGAAAGATGC+AGG - chr2_1:77733205-77733224 Msa0227120:CDS 35.0%
TCTGATACAGGATATCTCTG+AGG + chr2_1:77732692-77732711 None:intergenic 40.0%
TCATCATCAACGGATAACCA+AGG - chr2_1:77732867-77732886 Msa0227120:intron 40.0%
CATCATCAACGGATAACCAA+GGG - chr2_1:77732868-77732887 Msa0227120:intron 40.0%
TAGATCACATAATGTCGGAG+AGG - chr2_1:77732928-77732947 Msa0227120:CDS 40.0%
ACATAATGTCGGAGAGGAAT+AGG - chr2_1:77732934-77732953 Msa0227120:CDS 40.0%
GATCTTGTGGAGTCTGATAC+AGG + chr2_1:77732704-77732723 None:intergenic 45.0%
GGGACACTGAATTGATCTTG+TGG + chr2_1:77732717-77732736 None:intergenic 45.0%
GTTGTTTACTAGGCCAGTTG+TGG + chr2_1:77732745-77732764 None:intergenic 45.0%
GCTTCTTTGAATTCGACCCT+TGG + chr2_1:77732887-77732906 None:intergenic 45.0%
GAACTTTCGGCCTTTATACC+TGG - chr2_1:77732984-77733003 Msa0227120:CDS 45.0%
AGTGTCCCTATTGCCACAAC+TGG - chr2_1:77732729-77732748 Msa0227120:CDS 50.0%
CTAGGCCAGTTGTGGCAATA+GGG + chr2_1:77732737-77732756 None:intergenic 50.0%
ACTAGGCCAGTTGTGGCAAT+AGG + chr2_1:77732738-77732757 None:intergenic 50.0%
!! AATGTCTCAGAAGCGCTTCG+AGG + chr2_1:77732909-77732928 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 77732639 77733258 77732639 ID=Msa0227120;Name=Msa0227120
chr2_1 mRNA 77732639 77733258 77732639 ID=Msa0227120-mRNA-1;Parent=Msa0227120;Name=Msa0227120-mRNA-1;_AED=0.12;_eAED=0.15;_QI=0|0|0|1|1|1|2|0|169
chr2_1 exon 77732881 77733258 77732881 ID=Msa0227120-mRNA-1:exon:23687;Parent=Msa0227120-mRNA-1
chr2_1 exon 77732639 77732770 77732639 ID=Msa0227120-mRNA-1:exon:23686;Parent=Msa0227120-mRNA-1
chr2_1 CDS 77732881 77733258 77732881 ID=Msa0227120-mRNA-1:cds;Parent=Msa0227120-mRNA-1
chr2_1 CDS 77732639 77732770 77732639 ID=Msa0227120-mRNA-1:cds;Parent=Msa0227120-mRNA-1
Gene Sequence

>Msa0227120

GAAATGGAAGAACATTTGTGTCACACAAACAGCACATTTGATGAAGAGTTCCTCAGAGATATCCTGTATCAGACTCCACAAGATCAATTCAGTGTCCCTATTGCCACAACTGGCCTAGTAAACAACTCATCCATCAATGTGTCACATTCAACTCAACATGCTGAAGAAAATCCAACCAACTCATTATCAATACCAACAATTGAACAACACCATGATTCTTTGCCTTTGTCATCATCAACGGATAACCAAGGGTCGAATTCAAAGAAGCCTCGAAGCGCTTCTGAGACATTAGATCACATAATGTCGGAGAGGAATAGGAGACAACTACTTACAAGTAAGATCATAGAACTTTCGGCCTTTATACCTGGATTGAAGAAGATTGATAAGGTTCATGTGGTAACGGAAGCTATCAATTACGTGAAACATCTTGAAGAACGTTTGAAAGAGCTAGAAGAAGACATTAAGAAGAAAGATGCAGGATCATTGAGCACCATAAATCTCGTGTTCTAA
Protein sequence

>Msa0227120

EMEEHLCHTNSTFDEEFLRDILYQTPQDQFSVPIATTGLVNNSSINVSHSTQHAEENPTNSLSIPTIEQHHDSLPLSSSTDNQGSNSKKPRSASETLDHIMSERNRRQLLTSKIIELSAFIPGLKKIDKVHVVTEAINYVKHLEERLKELEEDIKKKDAGSLSTINLVF*