AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0128660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0128660 MtrunA17_Chr1g0195381 95.062 162 8 0 1 162 1 162 6.40e-102 289
Msa0128660 MtrunA17_Chr1g0195361 49.624 133 62 2 21 153 30 157 1.23e-45 147
Msa0128660 MtrunA17_Chr7g0269431 35.915 142 59 3 6 145 11 122 3.01e-24 92.0
Msa0128660 MtrunA17_Chr6g0485071 36.364 143 80 4 5 136 7 149 6.25e-23 89.0
Msa0128660 MtrunA17_Chr8g0378491 32.520 123 77 3 17 136 23 142 1.84e-15 69.7
Msa0128660 MtrunA17_Chr7g0249501 28.226 124 84 2 23 143 40 161 5.44e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0128660 AT1G02816.1 60.284 141 52 1 22 162 30 166 6.88e-60 183
Msa0128660 AT4G02370.1 52.830 159 68 2 8 162 12 167 1.99e-55 172
Msa0128660 AT4G02360.1 54.930 142 63 1 2 143 7 147 7.13e-54 167
Msa0128660 AT1G02813.1 45.070 142 75 2 3 142 2 142 1.22e-40 134
Msa0128660 AT5G19590.1 33.871 124 75 2 24 146 31 148 2.17e-17 74.7
Msa0128660 AT5G19590.2 33.871 124 75 2 24 146 31 148 2.17e-17 74.7
Msa0128660 AT3G07470.1 30.464 151 91 6 8 152 13 155 4.18e-15 69.3
Msa0128660 AT3G07470.3 29.861 144 88 5 8 146 13 148 1.33e-14 67.8
Msa0128660 AT3G07470.2 29.861 144 88 5 8 146 13 148 1.54e-14 67.4
Msa0128660 AT5G16380.1 28.767 146 92 4 5 144 12 151 2.25e-14 67.8
Msa0128660 AT5G19860.1 34.234 111 67 3 23 130 35 142 1.75e-13 65.1
Msa0128660 AT1G55265.1 34.711 121 71 4 25 141 55 171 1.80e-11 59.7

Find 50 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGTAGGCAGTTGGGTTTC+CGG 0.215272 1_3:-58488586 None:intergenic
GCGTCAAAGTGATGTTCTTC+TGG 0.264271 1_3:+58488811 Msa0128660:CDS
AAAATAGACTTACCGATCTA+AGG 0.267447 1_3:+58488781 Msa0128660:CDS
TGATTTGTCTAATTCGTAAC+TGG 0.313925 1_3:-58488658 None:intergenic
TGAATATTCTTGAAGTTGTT+AGG 0.334073 1_3:+58488835 Msa0128660:CDS
ACTCCTATCGGGAGAATTCC+CGG 0.413850 1_3:-58488633 None:intergenic
CGGTTAGCGCCGTCGCCGTC+AGG 0.414867 1_3:-58488560 None:intergenic
TCGTGTAGTTTCTCGTTACA+AGG 0.427526 1_3:+58488711 Msa0128660:CDS
CGCAAGGCCTCGTAGGCAGT+TGG 0.436838 1_3:-58488594 None:intergenic
AGGAGGAGGAGGAGAACGAC+GGG 0.447449 1_3:-58488540 None:intergenic
GGCAGTTGGGTTTCCGGTGA+CGG 0.448621 1_3:-58488580 None:intergenic
CGTCAAAGTGATGTTCTTCT+GGG 0.456544 1_3:+58488812 Msa0128660:CDS
CTCTGTTGGTGTTGCTTCTG+CGG 0.459033 1_3:+58488878 Msa0128660:CDS
TTTAAGCAGAAGAAAGAGAA+GGG 0.461680 1_3:-58488998 None:intergenic
TCGTAACTGGTTACTCCTAT+CGG 0.463432 1_3:-58488645 None:intergenic
GATGACCTTGATTTCTCTGT+TGG 0.467199 1_3:+58488864 Msa0128660:CDS
GCGCCGTCGCCGTCAGGAGG+AGG 0.477696 1_3:-58488554 None:intergenic
AAATAGACTTACCGATCTAA+GGG 0.481492 1_3:+58488782 Msa0128660:CDS
GAATCTCCGCAGTGTGGTTG+TGG 0.488470 1_3:+58488924 Msa0128660:CDS
GCAAGGCCTCGTAGGCAGTT+GGG 0.489260 1_3:-58488593 None:intergenic
TCCGCAGTGTGGTTGTGGAT+TGG 0.495192 1_3:+58488929 Msa0128660:CDS
CGTAACTGGTTACTCCTATC+GGG 0.502559 1_3:-58488644 None:intergenic
AACGATCACCGGTAAAATAA+CGG 0.509312 1_3:+58488758 Msa0128660:CDS
CCGTCGCCGTCAGGAGGAGG+AGG 0.512636 1_3:-58488551 None:intergenic
AATTCCCGGTGGGAAATTGT+AGG 0.515251 1_3:-58488619 None:intergenic
CAACACCAACAGAGAAATCA+AGG 0.526235 1_3:-58488869 None:intergenic
GCGACGGCGCTAACCGTCAC+CGG 0.534133 1_3:+58488567 Msa0128660:CDS
GACGCTTATACCCCTTAGAT+CGG 0.549482 1_3:-58488793 None:intergenic
CGTACCTACAATTTCCCACC+GGG 0.555651 1_3:+58488615 Msa0128660:CDS
CCTCCTCCTCCTGACGGCGA+CGG 0.559285 1_3:+58488551 Msa0128660:CDS
AGAACGACGGGGCTAGTCAT+CGG 0.573947 1_3:-58488528 None:intergenic
TTAGCGCCGTCGCCGTCAGG+AGG 0.577589 1_3:-58488557 None:intergenic
GCGTACCTACAATTTCCCAC+CGG 0.578143 1_3:+58488614 Msa0128660:CDS
CAGGAGGAGGAGGAGAACGA+CGG 0.578931 1_3:-58488541 None:intergenic
CCACCGGGAATTCTCCCGAT+AGG 0.583587 1_3:+58488630 Msa0128660:CDS
AGTTACAAATCAACGATCAC+CGG 0.584572 1_3:+58488747 Msa0128660:CDS
TGGGAAATTGTAGGTACGCA+AGG 0.589209 1_3:-58488610 None:intergenic
CGTTCTCCTCCTCCTCCTGA+CGG 0.595497 1_3:+58488545 Msa0128660:CDS
TACGAATTAGACAAATCAAG+TGG 0.598160 1_3:+58488663 Msa0128660:CDS
CGGAAACCCAACTGCCTACG+AGG 0.623801 1_3:+58488587 Msa0128660:CDS
TTCTTTGAATCTCCGCAGTG+TGG 0.624219 1_3:+58488918 Msa0128660:CDS
GTAACGAGAAACTACACGAA+CGG 0.631098 1_3:-58488707 None:intergenic
GTAGGTACGCAAGGCCTCGT+AGG 0.643114 1_3:-58488601 None:intergenic
GATTCAAAGAAATTATCCAA+AGG 0.666602 1_3:-58488906 None:intergenic
CTATCGGGAGAATTCCCGGT+GGG 0.669781 1_3:-58488629 None:intergenic
AATAGACTTACCGATCTAAG+GGG 0.686558 1_3:+58488783 Msa0128660:CDS
GGAGGAGGAGGAGAACGACG+GGG 0.724686 1_3:-58488539 None:intergenic
TCCAATCCACAACCACACTG+CGG 0.744486 1_3:-58488930 None:intergenic
CCTATCGGGAGAATTCCCGG+TGG 0.777816 1_3:-58488630 None:intergenic
ACGAACGGTTTAGATCAGCG+CGG 0.852399 1_3:-58488692 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAGTTTTCTAATTCTCAA+AGG - chr1_3:58488963-58488982 None:intergenic 20.0%
!!! TCTATTTTCCGTTATTTTAC+CGG - chr1_3:58488769-58488788 None:intergenic 25.0%
! TGAATATTCTTGAAGTTGTT+AGG + chr1_3:58488835-58488854 Msa0128660:CDS 25.0%
! GATTCAAAGAAATTATCCAA+AGG - chr1_3:58488909-58488928 None:intergenic 25.0%
! TGATTTGTCTAATTCGTAAC+TGG - chr1_3:58488661-58488680 None:intergenic 30.0%
TACGAATTAGACAAATCAAG+TGG + chr1_3:58488663-58488682 Msa0128660:CDS 30.0%
AAAATAGACTTACCGATCTA+AGG + chr1_3:58488781-58488800 Msa0128660:CDS 30.0%
AAATAGACTTACCGATCTAA+GGG + chr1_3:58488782-58488801 Msa0128660:CDS 30.0%
AGTTACAAATCAACGATCAC+CGG + chr1_3:58488747-58488766 Msa0128660:CDS 35.0%
AACGATCACCGGTAAAATAA+CGG + chr1_3:58488758-58488777 Msa0128660:CDS 35.0%
AATAGACTTACCGATCTAAG+GGG + chr1_3:58488783-58488802 Msa0128660:CDS 35.0%
TCGTAACTGGTTACTCCTAT+CGG - chr1_3:58488648-58488667 None:intergenic 40.0%
GTAACGAGAAACTACACGAA+CGG - chr1_3:58488710-58488729 None:intergenic 40.0%
TCGTGTAGTTTCTCGTTACA+AGG + chr1_3:58488711-58488730 Msa0128660:CDS 40.0%
CGTCAAAGTGATGTTCTTCT+GGG + chr1_3:58488812-58488831 Msa0128660:CDS 40.0%
GATGACCTTGATTTCTCTGT+TGG + chr1_3:58488864-58488883 Msa0128660:CDS 40.0%
CAACACCAACAGAGAAATCA+AGG - chr1_3:58488872-58488891 None:intergenic 40.0%
TGGGAAATTGTAGGTACGCA+AGG - chr1_3:58488613-58488632 None:intergenic 45.0%
AATTCCCGGTGGGAAATTGT+AGG - chr1_3:58488622-58488641 None:intergenic 45.0%
CGTAACTGGTTACTCCTATC+GGG - chr1_3:58488647-58488666 None:intergenic 45.0%
GACGCTTATACCCCTTAGAT+CGG - chr1_3:58488796-58488815 None:intergenic 45.0%
GCGTCAAAGTGATGTTCTTC+TGG + chr1_3:58488811-58488830 Msa0128660:CDS 45.0%
TTCTTTGAATCTCCGCAGTG+TGG + chr1_3:58488918-58488937 Msa0128660:CDS 45.0%
GCGTACCTACAATTTCCCAC+CGG + chr1_3:58488614-58488633 Msa0128660:CDS 50.0%
CGTACCTACAATTTCCCACC+GGG + chr1_3:58488615-58488634 Msa0128660:CDS 50.0%
ACTCCTATCGGGAGAATTCC+CGG - chr1_3:58488636-58488655 None:intergenic 50.0%
ACGAACGGTTTAGATCAGCG+CGG - chr1_3:58488695-58488714 None:intergenic 50.0%
!! CTCTGTTGGTGTTGCTTCTG+CGG + chr1_3:58488878-58488897 Msa0128660:CDS 50.0%
! TGCTTCTGCGGCTTTTCCTT+TGG + chr1_3:58488890-58488909 Msa0128660:CDS 50.0%
TCCAATCCACAACCACACTG+CGG - chr1_3:58488933-58488952 None:intergenic 50.0%
CTCGTAGGCAGTTGGGTTTC+CGG - chr1_3:58488589-58488608 None:intergenic 55.0%
CTATCGGGAGAATTCCCGGT+GGG - chr1_3:58488632-58488651 None:intergenic 55.0%
GAATCTCCGCAGTGTGGTTG+TGG + chr1_3:58488924-58488943 Msa0128660:CDS 55.0%
TCCGCAGTGTGGTTGTGGAT+TGG + chr1_3:58488929-58488948 Msa0128660:CDS 55.0%
AGGAGGAGGAGGAGAACGAC+GGG - chr1_3:58488543-58488562 None:intergenic 60.0%
CAGGAGGAGGAGGAGAACGA+CGG - chr1_3:58488544-58488563 None:intergenic 60.0%
CGTTCTCCTCCTCCTCCTGA+CGG + chr1_3:58488545-58488564 Msa0128660:CDS 60.0%
GGCAGTTGGGTTTCCGGTGA+CGG - chr1_3:58488583-58488602 None:intergenic 60.0%
CGGAAACCCAACTGCCTACG+AGG + chr1_3:58488587-58488606 Msa0128660:CDS 60.0%
GCAAGGCCTCGTAGGCAGTT+GGG - chr1_3:58488596-58488615 None:intergenic 60.0%
GTAGGTACGCAAGGCCTCGT+AGG - chr1_3:58488604-58488623 None:intergenic 60.0%
CCTATCGGGAGAATTCCCGG+TGG - chr1_3:58488633-58488652 None:intergenic 60.0%
CCACCGGGAATTCTCCCGAT+AGG + chr1_3:58488630-58488649 Msa0128660:CDS 60.0%
GGAGGAGGAGGAGAACGACG+GGG - chr1_3:58488542-58488561 None:intergenic 65.0%
CGCAAGGCCTCGTAGGCAGT+TGG - chr1_3:58488597-58488616 None:intergenic 65.0%
CCTCCTCCTCCTGACGGCGA+CGG + chr1_3:58488551-58488570 Msa0128660:CDS 70.0%
TTAGCGCCGTCGCCGTCAGG+AGG - chr1_3:58488560-58488579 None:intergenic 70.0%
GCGACGGCGCTAACCGTCAC+CGG + chr1_3:58488567-58488586 Msa0128660:CDS 70.0%
CCGTCGCCGTCAGGAGGAGG+AGG - chr1_3:58488554-58488573 None:intergenic 75.0%
CGGTTAGCGCCGTCGCCGTC+AGG - chr1_3:58488563-58488582 None:intergenic 75.0%
! GCGCCGTCGCCGTCAGGAGG+AGG - chr1_3:58488557-58488576 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 58488531 58489019 58488531 ID=Msa0128660;Name=Msa0128660
chr1_3 mRNA 58488531 58489019 58488531 ID=Msa0128660-mRNA-1;Parent=Msa0128660;Name=Msa0128660-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|162
chr1_3 exon 58488531 58489019 58488531 ID=Msa0128660-mRNA-1:exon:18778;Parent=Msa0128660-mRNA-1
chr1_3 CDS 58488531 58489019 58488531 ID=Msa0128660-mRNA-1:cds;Parent=Msa0128660-mRNA-1
Gene Sequence

>Msa0128660

ATGACTAGCCCCGTCGTTCTCCTCCTCCTCCTGACGGCGACGGCGCTAACCGTCACCGGAAACCCAACTGCCTACGAGGCCTTGCGTACCTACAATTTCCCACCGGGAATTCTCCCGATAGGAGTAACCAGTTACGAATTAGACAAATCAAGTGGCAATTTCCGCGCTGATCTAAACCGTTCGTGTAGTTTCTCGTTACAAGGTTCGTATCAATTGAGTTACAAATCAACGATCACCGGTAAAATAACGGAAAATAGACTTACCGATCTAAGGGGTATAAGCGTCAAAGTGATGTTCTTCTGGGTGAATATTCTTGAAGTTGTTAGGAAACATGATGACCTTGATTTCTCTGTTGGTGTTGCTTCTGCGGCTTTTCCTTTGGATAATTTCTTTGAATCTCCGCAGTGTGGTTGTGGATTGGATTGTGATCCTTTGAGAATTAGAAAACTTAAACTCAATACTAAAAACCCTTCTCTTTCTTCTGCTTAA
Protein sequence

>Msa0128660

MTSPVVLLLLLTATALTVTGNPTAYEALRTYNFPPGILPIGVTSYELDKSSGNFRADLNRSCSFSLQGSYQLSYKSTITGKITENRLTDLRGISVKVMFFWVNILEVVRKHDDLDFSVGVASAAFPLDNFFESPQCGCGLDCDPLRIRKLKLNTKNPSLSSA*