AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0416440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0416440 MtrunA17_Chr3g0113121 93.229 192 13 0 1 192 25 216 1.26e-123 347
Msa0416440 MtrunA17_Chr5g0436501 40.288 139 68 4 9 147 73 196 2.68e-20 85.5
Msa0416440 MtrunA17_Chr5g0429521 37.209 129 68 2 25 147 80 201 1.23e-17 79.0
Msa0416440 MtrunA17_Chr5g0440731 57.143 77 27 4 68 143 102 173 2.89e-17 77.8
Msa0416440 MtrunA17_Chr3g0104071 37.415 147 75 3 9 147 79 216 7.73e-17 77.0
Msa0416440 MtrunA17_Chr5g0409841 36.567 134 75 3 14 143 32 159 9.22e-17 75.5
Msa0416440 MtrunA17_Chr7g0241761 40.708 113 53 3 35 147 111 209 4.34e-16 74.7
Msa0416440 MtrunA17_Chr5g0440741 58.904 73 24 4 72 143 101 168 4.37e-16 74.3
Msa0416440 MtrunA17_Chr5g0409831 43.023 86 43 2 37 116 37 122 8.02e-16 72.8
Msa0416440 MtrunA17_Chr3g0135671 38.136 118 57 2 25 142 57 158 1.87e-15 72.0
Msa0416440 MtrunA17_Chr4g0059701 33.913 115 64 2 2 116 27 129 1.04e-13 67.8
Msa0416440 MtrunA17_Chr1g0210471 49.367 79 33 2 68 146 121 192 1.04e-13 67.4
Msa0416440 MtrunA17_Chr1g0162081 45.570 79 36 2 68 146 119 190 4.68e-13 66.2
Msa0416440 MtrunA17_Chr2g0331031 39.759 83 43 1 62 144 100 175 8.88e-13 65.5
Msa0416440 MtrunA17_Chr6g0488471 51.724 58 26 1 59 116 87 142 1.87e-12 64.3
Msa0416440 MtrunA17_Chr4g0055931 36.607 112 52 2 35 146 71 163 1.89e-12 64.7
Msa0416440 MtrunA17_Chr4g0062741 44.304 79 37 2 68 146 135 206 2.26e-12 64.3
Msa0416440 MtrunA17_Chr5g0415191 55.102 49 22 0 68 116 99 147 3.27e-12 63.9
Msa0416440 MtrunA17_Chr8g0365011 35.948 153 64 7 8 146 42 174 4.38e-12 63.2
Msa0416440 MtrunA17_Chr8g0389241 44.000 75 34 1 68 142 102 168 6.39e-12 62.8
Msa0416440 MtrunA17_Chr5g0432921 45.833 96 43 5 40 134 85 172 7.37e-12 62.0
Msa0416440 MtrunA17_Chr8g0364731 50.794 63 26 1 81 143 11 68 5.48e-11 58.9
Msa0416440 MtrunA17_Chr6g0452791 56.522 46 20 0 71 116 80 125 7.26e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0416440 AT5G05790.2 40.602 133 67 3 25 153 82 206 3.80e-20 85.5
Msa0416440 AT5G05790.1 40.602 133 67 3 25 153 82 206 3.80e-20 85.5
Msa0416440 AT3G11280.2 41.406 128 63 4 25 151 84 200 6.90e-19 82.0
Msa0416440 AT3G11280.1 41.406 128 63 4 25 151 84 200 6.90e-19 82.0
Msa0416440 AT5G01200.1 45.299 117 50 4 32 147 112 215 1.93e-18 80.9
Msa0416440 AT2G38090.1 37.069 116 63 2 35 147 102 210 1.44e-16 76.3
Msa0416440 AT5G58900.1 44.681 94 45 1 54 147 124 210 3.01e-16 75.1
Msa0416440 AT5G08520.1 39.073 151 68 7 8 145 46 185 5.39e-16 74.7
Msa0416440 AT4G09450.1 39.837 123 61 4 46 162 66 181 3.12e-14 68.6
Msa0416440 AT5G04760.1 49.367 79 33 2 68 146 96 167 1.26e-13 67.0
Msa0416440 AT1G19000.2 50.877 57 28 0 60 116 91 147 3.41e-13 66.6
Msa0416440 AT1G19000.1 50.877 57 28 0 60 116 91 147 3.41e-13 66.6
Msa0416440 AT5G47390.1 33.588 131 69 2 62 192 87 199 3.92e-13 67.0
Msa0416440 AT1G70000.1 41.096 73 41 1 46 116 71 143 1.07e-12 65.1
Msa0416440 AT1G70000.2 41.096 73 41 1 46 116 71 143 1.07e-12 65.1
Msa0416440 AT3G10580.2 46.835 79 33 1 68 146 92 161 1.46e-12 64.7
Msa0416440 AT1G49010.1 45.570 79 36 2 68 146 131 202 1.58e-12 65.1
Msa0416440 AT3G10580.1 46.835 79 33 1 68 146 92 161 1.62e-12 65.1
Msa0416440 AT5G56840.1 52.632 57 27 0 68 124 88 144 1.35e-11 61.6
Msa0416440 AT5G61620.1 45.570 79 36 1 68 146 105 176 2.41e-11 61.6
Msa0416440 AT1G74840.2 55.102 49 22 0 68 116 93 141 4.18e-11 60.5
Msa0416440 AT1G74840.1 55.102 49 22 0 68 116 93 141 4.61e-11 60.5
Msa0416440 AT3G16350.1 53.061 49 23 0 68 116 134 182 5.53e-11 60.8

Find 26 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGATCTTTATCACATTCT+TGG 0.225450 3_2:-63220471 None:intergenic
GACTCATATGCGTGGTTATT+TGG 0.243758 3_2:+63220388 Msa0416440:CDS
ATAACTACTCTTGATCTTCT+TGG 0.251399 3_2:+63220358 Msa0416440:CDS
AGTTCTATTGTTATTATTAT+CGG 0.281602 3_2:-63219971 None:intergenic
TTTGAGCATGGCTTGCTACT+TGG 0.356659 3_2:-63220255 None:intergenic
AAAATATCAAAAGGAAACTT+AGG 0.373972 3_2:+63220320 Msa0416440:CDS
CATTCAAGAAAGTGGTTCAT+TGG 0.387227 3_2:+63220022 Msa0416440:CDS
TTGAGCATGGCTTGCTACTT+GGG 0.417939 3_2:-63220254 None:intergenic
TATTTGTAGGCGTTTCTTGA+AGG 0.450413 3_2:+63220162 Msa0416440:intron
AAATATCAAAAGGAAACTTA+GGG 0.461487 3_2:+63220321 Msa0416440:CDS
AAAGTGGAAAGAAATCTCTA+AGG 0.472931 3_2:+63220207 Msa0416440:CDS
AAAGAAATCATTCAAGAAAG+TGG 0.476326 3_2:+63220014 Msa0416440:CDS
ATTTGTAGGCGTTTCTTGAA+GGG 0.494586 3_2:+63220163 Msa0416440:intron
GATCAAGAGTAGTTATATCA+TGG 0.499404 3_2:-63220351 None:intergenic
TACACGGCAAAGACGGAAAG+TGG 0.504210 3_2:+63220191 Msa0416440:CDS
GCATGGCTTGCTACTTGGGA+TGG 0.505418 3_2:-63220250 None:intergenic
TGTTGTCGTCTTCAATCACT+TGG 0.511632 3_2:-63220414 None:intergenic
GGACTTCTACACGGCAAAGA+CGG 0.559413 3_2:+63220184 Msa0416440:CDS
ATACATATGAACATATCAAG+TGG 0.590413 3_2:-63220506 None:intergenic
TTCTTGAAGGGACTTCTACA+CGG 0.594579 3_2:+63220175 Msa0416440:CDS
GAAGACGACAACAATAACAA+TGG 0.605151 3_2:+63220424 Msa0416440:CDS
TCAGCACAACATCGATGAAG+TGG 0.609150 3_2:+63219864 Msa0416440:CDS
TTATTATTATCGGTTGCATG+AGG 0.632701 3_2:-63219961 None:intergenic
GCACAACATCGATGAAGTGG+TGG 0.668571 3_2:+63219867 Msa0416440:CDS
AATATCAAAAGGAAACTTAG+GGG 0.670754 3_2:+63220322 Msa0416440:CDS
GAAGTGATGACTCATATGCG+TGG 0.764866 3_2:+63220380 Msa0416440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTCTATTGTTATTATTAT+CGG - chr3_2:63219974-63219993 None:intergenic 15.0%
!!! TTTCTTGAATGATTTCTTTT+TGG - chr3_2:63220013-63220032 None:intergenic 20.0%
!! ATGATAGCAAAAATATCAAA+AGG + chr3_2:63220311-63220330 Msa0416440:CDS 20.0%
!! AAAATATCAAAAGGAAACTT+AGG + chr3_2:63220320-63220339 Msa0416440:CDS 20.0%
!! AAATATCAAAAGGAAACTTA+GGG + chr3_2:63220321-63220340 Msa0416440:CDS 20.0%
! AAAGAAATCATTCAAGAAAG+TGG + chr3_2:63220014-63220033 Msa0416440:CDS 25.0%
! GAAACAATAAACGATGAAAA+AGG - chr3_2:63220071-63220090 None:intergenic 25.0%
!!! GACATGGATTTTTTATTTGT+AGG + chr3_2:63220149-63220168 Msa0416440:intron 25.0%
! AATATCAAAAGGAAACTTAG+GGG + chr3_2:63220322-63220341 Msa0416440:CDS 25.0%
! TTATTATTATCGGTTGCATG+AGG - chr3_2:63219964-63219983 None:intergenic 30.0%
AAAGTGGAAAGAAATCTCTA+AGG + chr3_2:63220207-63220226 Msa0416440:CDS 30.0%
!!! TTTTTTCGTACTTTTGAGCA+TGG - chr3_2:63220270-63220289 None:intergenic 30.0%
! ATGCTCAAAAGTACGAAAAA+AGG + chr3_2:63220269-63220288 Msa0416440:CDS 30.0%
GATCAAGAGTAGTTATATCA+TGG - chr3_2:63220354-63220373 None:intergenic 30.0%
ATAACTACTCTTGATCTTCT+TGG + chr3_2:63220358-63220377 Msa0416440:CDS 30.0%
CATGATCTTTATCACATTCT+TGG - chr3_2:63220474-63220493 None:intergenic 30.0%
CATTCAAGAAAGTGGTTCAT+TGG + chr3_2:63220022-63220041 Msa0416440:CDS 35.0%
TATTTGTAGGCGTTTCTTGA+AGG + chr3_2:63220162-63220181 Msa0416440:intron 35.0%
ATTTGTAGGCGTTTCTTGAA+GGG + chr3_2:63220163-63220182 Msa0416440:intron 35.0%
GAAGACGACAACAATAACAA+TGG + chr3_2:63220424-63220443 Msa0416440:CDS 35.0%
TTCTTGAAGGGACTTCTACA+CGG + chr3_2:63220175-63220194 Msa0416440:CDS 40.0%
GACTCATATGCGTGGTTATT+TGG + chr3_2:63220388-63220407 Msa0416440:CDS 40.0%
TGTTGTCGTCTTCAATCACT+TGG - chr3_2:63220417-63220436 None:intergenic 40.0%
TCAGCACAACATCGATGAAG+TGG + chr3_2:63219864-63219883 Msa0416440:CDS 45.0%
!! TCGACGAGCGTTTCACTTTT+TGG + chr3_2:63219907-63219926 Msa0416440:CDS 45.0%
!! TTGAGCATGGCTTGCTACTT+GGG - chr3_2:63220257-63220276 None:intergenic 45.0%
!! TTTGAGCATGGCTTGCTACT+TGG - chr3_2:63220258-63220277 None:intergenic 45.0%
GAAGTGATGACTCATATGCG+TGG + chr3_2:63220380-63220399 Msa0416440:CDS 45.0%
GCACAACATCGATGAAGTGG+TGG + chr3_2:63219867-63219886 Msa0416440:CDS 50.0%
GCGCACACATGTGTTTGACA+TGG + chr3_2:63220133-63220152 Msa0416440:intron 50.0%
GGACTTCTACACGGCAAAGA+CGG + chr3_2:63220184-63220203 Msa0416440:CDS 50.0%
TACACGGCAAAGACGGAAAG+TGG + chr3_2:63220191-63220210 Msa0416440:CDS 50.0%
!! GCATGGCTTGCTACTTGGGA+TGG - chr3_2:63220253-63220272 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 63219826 63220513 63219826 ID=Msa0416440;Name=Msa0416440
chr3_2 mRNA 63219826 63220513 63219826 ID=Msa0416440-mRNA-1;Parent=Msa0416440;Name=Msa0416440-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|192
chr3_2 exon 63219826 63220061 63219826 ID=Msa0416440-mRNA-1:exon:13725;Parent=Msa0416440-mRNA-1
chr3_2 exon 63220171 63220513 63220171 ID=Msa0416440-mRNA-1:exon:13726;Parent=Msa0416440-mRNA-1
chr3_2 CDS 63219826 63220061 63219826 ID=Msa0416440-mRNA-1:cds;Parent=Msa0416440-mRNA-1
chr3_2 CDS 63220171 63220513 63220171 ID=Msa0416440-mRNA-1:cds;Parent=Msa0416440-mRNA-1
Gene Sequence

>Msa0416440

ATGAAGGAAACTATGCTATGTAGTGTTGATCAAATCAATCAGCACAACATCGATGAAGTGGTGGTAGAAAATAATATTGCATCGACGAGCGTTTCACTTTTTGGATATGATTCAGTTGATTCTTTCAACTTCTCTCCTCATGCAACCGATAATAATAACAATAGAACTACGAATATCGTAGAATCCAAAAAGAAATCATTCAAGAAAGTGGTTCATTGGTCACGTGATGAACACATGCGTTTCTTGAAGGGACTTCTACACGGCAAAGACGGAAAGTGGAAAGAAATCTCTAAGGACTATGTAAAAACAAAGACTCCATCCCAAGTAGCAAGCCATGCTCAAAAGTACGAAAAAAGGCAAAAGCAAAGACTTGATGATGATAGCAAAAATATCAAAAGGAAACTTAGGGGTAGCATCCATGATATAACTACTCTTGATCTTCTTGGAAGTGATGACTCATATGCGTGGTTATTTGGTGACCAAGTGATTGAAGACGACAACAATAACAATGGATCACTCTCAGTCACAACTTTCAACCAAGAATGTGATAAAGATCATGAAGTTGTTGCTTCCACTTGA
Protein sequence

>Msa0416440

MKETMLCSVDQINQHNIDEVVVENNIASTSVSLFGYDSVDSFNFSPHATDNNNNRTTNIVESKKKSFKKVVHWSRDEHMRFLKGLLHGKDGKWKEISKDYVKTKTPSQVASHAQKYEKRQKQRLDDDSKNIKRKLRGSIHDITTLDLLGSDDSYAWLFGDQVIEDDNNNNGSLSVTTFNQECDKDHEVVAST*