AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0463040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0463040 MtrunA17_Chr3g0113121 93.229 192 13 0 1 192 25 216 1.66e-123 347
Msa0463040 MtrunA17_Chr5g0436501 45.238 126 61 3 24 147 77 196 4.80e-21 87.4
Msa0463040 MtrunA17_Chr3g0104071 37.415 147 75 3 9 147 79 216 2.42e-17 78.2
Msa0463040 MtrunA17_Chr5g0440731 57.143 77 27 4 68 143 102 173 2.43e-17 77.8
Msa0463040 MtrunA17_Chr5g0429521 37.209 129 68 2 25 147 80 201 3.41e-17 77.8
Msa0463040 MtrunA17_Chr5g0409841 36.567 134 75 3 14 143 32 159 2.40e-16 74.3
Msa0463040 MtrunA17_Chr7g0241761 40.708 113 53 3 35 147 111 209 3.03e-16 75.1
Msa0463040 MtrunA17_Chr5g0440741 58.904 73 24 4 72 143 101 168 3.65e-16 74.7
Msa0463040 MtrunA17_Chr5g0409831 43.023 86 43 2 37 116 37 122 2.24e-15 71.6
Msa0463040 MtrunA17_Chr3g0135671 38.136 118 57 2 25 142 57 158 2.41e-15 71.6
Msa0463040 MtrunA17_Chr1g0210471 49.367 79 33 2 68 146 121 192 1.05e-13 67.4
Msa0463040 MtrunA17_Chr4g0059701 33.913 115 64 2 2 116 27 129 1.06e-13 67.8
Msa0463040 MtrunA17_Chr1g0162081 45.570 79 36 2 68 146 119 190 4.24e-13 66.2
Msa0463040 MtrunA17_Chr2g0331031 37.079 89 49 1 56 144 94 175 7.68e-13 65.9
Msa0463040 MtrunA17_Chr8g0365011 35.948 153 64 6 8 146 42 174 1.40e-12 64.7
Msa0463040 MtrunA17_Chr6g0488471 38.843 121 52 5 68 188 94 192 1.60e-12 64.7
Msa0463040 MtrunA17_Chr4g0055931 36.607 112 52 2 35 146 71 163 1.79e-12 64.7
Msa0463040 MtrunA17_Chr4g0062741 44.304 79 37 2 68 146 135 206 2.11e-12 64.3
Msa0463040 MtrunA17_Chr5g0415191 55.102 49 22 0 68 116 99 147 3.15e-12 63.9
Msa0463040 MtrunA17_Chr8g0389241 44.000 75 34 1 68 142 102 168 6.20e-12 62.8
Msa0463040 MtrunA17_Chr5g0432921 45.833 96 43 5 40 134 85 172 7.59e-12 62.0
Msa0463040 MtrunA17_Chr8g0364731 50.794 63 26 1 81 143 11 68 5.65e-11 58.9
Msa0463040 MtrunA17_Chr6g0452791 56.522 46 20 0 71 116 80 125 7.33e-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
Msa0463040 AT5G05790.2 40.602 133 67 3 25 153 82 206 1.86e-20 86.7
Msa0463040 AT5G05790.1 40.602 133 67 3 25 153 82 206 1.86e-20 86.7
Msa0463040 AT3G11280.2 39.844 128 65 3 25 151 84 200 4.81e-19 82.4
Msa0463040 AT3G11280.1 39.844 128 65 3 25 151 84 200 4.81e-19 82.4
Msa0463040 AT5G01200.1 45.299 117 50 4 32 147 112 215 1.99e-18 80.9
Msa0463040 AT2G38090.1 37.069 116 63 2 35 147 102 210 1.01e-16 76.6
Msa0463040 AT5G58900.1 36.424 151 72 5 10 147 71 210 1.07e-16 76.6
Msa0463040 AT5G08520.1 39.073 151 68 7 8 145 46 185 1.71e-16 75.9
Msa0463040 AT4G09450.1 39.837 123 61 4 46 162 66 181 2.24e-14 68.9
Msa0463040 AT5G04760.1 49.367 79 33 2 68 146 96 167 1.11e-13 67.0
Msa0463040 AT1G19000.2 50.877 57 28 0 60 116 91 147 3.37e-13 66.6
Msa0463040 AT1G19000.1 50.877 57 28 0 60 116 91 147 3.37e-13 66.6
Msa0463040 AT5G47390.1 33.588 131 69 2 62 192 87 199 4.03e-13 67.0
Msa0463040 AT1G49010.1 45.570 79 36 2 68 146 131 202 1.44e-12 65.1
Msa0463040 AT3G10580.2 46.835 79 33 1 68 146 92 161 1.45e-12 64.7
Msa0463040 AT3G10580.1 46.835 79 33 1 68 146 92 161 1.50e-12 65.1
Msa0463040 AT1G70000.1 41.096 73 41 1 46 116 71 143 3.95e-12 63.5
Msa0463040 AT1G70000.2 41.096 73 41 1 46 116 71 143 3.95e-12 63.5
Msa0463040 AT5G56840.1 52.632 57 27 0 68 124 88 144 1.38e-11 61.6
Msa0463040 AT5G61620.1 45.570 79 36 1 68 146 105 176 2.28e-11 62.0
Msa0463040 AT1G74840.2 55.102 49 22 0 68 116 93 141 4.06e-11 60.5
Msa0463040 AT1G74840.1 55.102 49 22 0 68 116 93 141 4.47e-11 60.5
Msa0463040 AT3G16350.1 53.061 49 23 0 68 116 134 182 5.59e-11 60.8

Find 27 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGATCTTGATCACATTCT+TGG 0.190525 3_3:-62278731 None:intergenic
GACTCATATGCGTGGTTATT+TGG 0.243758 3_3:+62278648 Msa0463040:CDS
ATAACTACTCTTGATCTTCT+TGG 0.251399 3_3:+62278618 Msa0463040:CDS
AGTTCTATTGTTATTATTAT+CGG 0.281602 3_3:-62278228 None:intergenic
TTTGAGCATGGCTTGCTACT+TGG 0.356659 3_3:-62278515 None:intergenic
AAAATATCAAAAGGAAACTT+AGG 0.373972 3_3:+62278580 Msa0463040:CDS
CATTCAAGAAAGTGGTTCAT+TGG 0.387227 3_3:+62278279 Msa0463040:CDS
TTGAGCATGGCTTGCTACTT+GGG 0.417939 3_3:-62278514 None:intergenic
TATTTGTAGGCGTTTCTTGA+AGG 0.450413 3_3:+62278422 Msa0463040:intron
AAATATCAAAAGGAAACTTA+GGG 0.461487 3_3:+62278581 Msa0463040:CDS
AAAGTGGAAAGAAATCTCTA+AGG 0.472931 3_3:+62278467 Msa0463040:CDS
AAAGAAATCATTCAAGAAAG+TGG 0.476326 3_3:+62278271 Msa0463040:CDS
ATTTGTAGGCGTTTCTTGAA+GGG 0.494586 3_3:+62278423 Msa0463040:intron
GATCAAGAGTAGTTATATCA+TGG 0.499404 3_3:-62278611 None:intergenic
TACACGGCAAAGACGGAAAG+TGG 0.504210 3_3:+62278451 Msa0463040:CDS
GCATGGCTTGCTACTTGGGA+TGG 0.505418 3_3:-62278510 None:intergenic
TGTTGTCGTCTTCAATCACT+TGG 0.511632 3_3:-62278674 None:intergenic
GGACTTCTACACGGCAAAGA+CGG 0.559413 3_3:+62278444 Msa0463040:CDS
ATACATATGAACATATCAAG+TGG 0.590413 3_3:-62278766 None:intergenic
TTCTTGAAGGGACTTCTACA+CGG 0.594579 3_3:+62278435 Msa0463040:CDS
GAAGACGACAACAATAACAA+TGG 0.605151 3_3:+62278684 Msa0463040:CDS
TCAGCACAACATCGATGAAG+TGG 0.609150 3_3:+62278121 Msa0463040:CDS
TTATTATTATCGGTTGCATG+AGG 0.632701 3_3:-62278218 None:intergenic
GCACAACATCGATGAAGTGG+TGG 0.668571 3_3:+62278124 Msa0463040:CDS
AATATCAAAAGGAAACTTAG+GGG 0.670754 3_3:+62278582 Msa0463040:CDS
CAATAGAACTACGAATACCG+TGG 0.681495 3_3:+62278241 Msa0463040:CDS
GAAGTGATGACTCATATGCG+TGG 0.764866 3_3:+62278640 Msa0463040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTCTATTGTTATTATTAT+CGG - chr3_3:62278231-62278250 None:intergenic 15.0%
!!! TTTCTTGAATGATTTCTTTT+TGG - chr3_3:62278270-62278289 None:intergenic 20.0%
!! ACAATAATAAACGATGAAAA+AGG - chr3_3:62278328-62278347 None:intergenic 20.0%
!! ATGATAGCAAAAATATCAAA+AGG + chr3_3:62278571-62278590 Msa0463040:CDS 20.0%
!! AAAATATCAAAAGGAAACTT+AGG + chr3_3:62278580-62278599 Msa0463040:CDS 20.0%
!! AAATATCAAAAGGAAACTTA+GGG + chr3_3:62278581-62278600 Msa0463040:CDS 20.0%
! AAAGAAATCATTCAAGAAAG+TGG + chr3_3:62278271-62278290 Msa0463040:CDS 25.0%
!!! GACATGGATTTTTTATTTGT+AGG + chr3_3:62278409-62278428 Msa0463040:intron 25.0%
! AATATCAAAAGGAAACTTAG+GGG + chr3_3:62278582-62278601 Msa0463040:CDS 25.0%
! TTATTATTATCGGTTGCATG+AGG - chr3_3:62278221-62278240 None:intergenic 30.0%
! TGATTTCTTTTTGGATTCCA+CGG - chr3_3:62278261-62278280 None:intergenic 30.0%
AAAGTGGAAAGAAATCTCTA+AGG + chr3_3:62278467-62278486 Msa0463040:CDS 30.0%
!!! TTTTTTCGTACTTTTGAGCA+TGG - chr3_3:62278530-62278549 None:intergenic 30.0%
! ATGCTCAAAAGTACGAAAAA+AGG + chr3_3:62278529-62278548 Msa0463040:CDS 30.0%
GATCAAGAGTAGTTATATCA+TGG - chr3_3:62278614-62278633 None:intergenic 30.0%
ATAACTACTCTTGATCTTCT+TGG + chr3_3:62278618-62278637 Msa0463040:CDS 30.0%
CATTCAAGAAAGTGGTTCAT+TGG + chr3_3:62278279-62278298 Msa0463040:CDS 35.0%
TATTTGTAGGCGTTTCTTGA+AGG + chr3_3:62278422-62278441 Msa0463040:intron 35.0%
ATTTGTAGGCGTTTCTTGAA+GGG + chr3_3:62278423-62278442 Msa0463040:intron 35.0%
GAAGACGACAACAATAACAA+TGG + chr3_3:62278684-62278703 Msa0463040:CDS 35.0%
CATGATCTTGATCACATTCT+TGG - chr3_3:62278734-62278753 None:intergenic 35.0%
CAATAGAACTACGAATACCG+TGG + chr3_3:62278241-62278260 Msa0463040:CDS 40.0%
TTCTTGAAGGGACTTCTACA+CGG + chr3_3:62278435-62278454 Msa0463040:CDS 40.0%
GACTCATATGCGTGGTTATT+TGG + chr3_3:62278648-62278667 Msa0463040:CDS 40.0%
TGTTGTCGTCTTCAATCACT+TGG - chr3_3:62278677-62278696 None:intergenic 40.0%
TCAGCACAACATCGATGAAG+TGG + chr3_3:62278121-62278140 Msa0463040:CDS 45.0%
!! TCGACGAGCGTTTCACTTTT+TGG + chr3_3:62278164-62278183 Msa0463040:CDS 45.0%
GTGCACACATGTGTTTGACA+TGG + chr3_3:62278393-62278412 Msa0463040:intron 45.0%
!! TTGAGCATGGCTTGCTACTT+GGG - chr3_3:62278517-62278536 None:intergenic 45.0%
!! TTTGAGCATGGCTTGCTACT+TGG - chr3_3:62278518-62278537 None:intergenic 45.0%
GAAGTGATGACTCATATGCG+TGG + chr3_3:62278640-62278659 Msa0463040:CDS 45.0%
GCACAACATCGATGAAGTGG+TGG + chr3_3:62278124-62278143 Msa0463040:CDS 50.0%
GGACTTCTACACGGCAAAGA+CGG + chr3_3:62278444-62278463 Msa0463040:CDS 50.0%
TACACGGCAAAGACGGAAAG+TGG + chr3_3:62278451-62278470 Msa0463040:CDS 50.0%
!! GCATGGCTTGCTACTTGGGA+TGG - chr3_3:62278513-62278532 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 62278083 62278773 62278083 ID=Msa0463040;Name=Msa0463040
chr3_3 mRNA 62278083 62278773 62278083 ID=Msa0463040-mRNA-1;Parent=Msa0463040;Name=Msa0463040-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|192
chr3_3 exon 62278083 62278318 62278083 ID=Msa0463040-mRNA-1:exon:13256;Parent=Msa0463040-mRNA-1
chr3_3 exon 62278431 62278773 62278431 ID=Msa0463040-mRNA-1:exon:13257;Parent=Msa0463040-mRNA-1
chr3_3 CDS 62278083 62278318 62278083 ID=Msa0463040-mRNA-1:cds;Parent=Msa0463040-mRNA-1
chr3_3 CDS 62278431 62278773 62278431 ID=Msa0463040-mRNA-1:cds;Parent=Msa0463040-mRNA-1
Gene Sequence

>Msa0463040

ATGAAGGAAACTATGCTATGTAGTGTTGATCAAATCAATCAGCACAACATCGATGAAGTGGTGGTAGAAAATAATATTGCATCGACGAGCGTTTCACTTTTTGGATATGATTCAGTTGATTCTTTCAACTTCTCTCCTCATGCAACCGATAATAATAACAATAGAACTACGAATACCGTGGAATCCAAAAAGAAATCATTCAAGAAAGTGGTTCATTGGTCACGTGATGAACACATGCGTTTCTTGAAGGGACTTCTACACGGCAAAGACGGAAAGTGGAAAGAAATCTCTAAGGACTATGTAAAAACAAAGACTCCATCCCAAGTAGCAAGCCATGCTCAAAAGTACGAAAAAAGGCAAAAGCAAAGACTTGATGATGATAGCAAAAATATCAAAAGGAAACTTAGGGGTAGCATCCATGATATAACTACTCTTGATCTTCTTGGAAGTGATGACTCATATGCGTGGTTATTTGGTGACCAAGTGATTGAAGACGACAACAATAACAATGGATCACTCTCAGTCACAACTTTCAACCAAGAATGTGATCAAGATCATGAAGTTGTTGCTTCCACTTGA
Protein sequence

>Msa0463040

MKETMLCSVDQINQHNIDEVVVENNIASTSVSLFGYDSVDSFNFSPHATDNNNNRTTNTVESKKKSFKKVVHWSRDEHMRFLKGLLHGKDGKWKEISKDYVKTKTPSQVASHAQKYEKRQKQRLDDDSKNIKRKLRGSIHDITTLDLLGSDDSYAWLFGDQVIEDDNNNNGSLSVTTFNQECDQDHEVVAST*