AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0363690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0363690 MtrunA17_Chr5g0446491 44.681 94 51 1 28 120 18 111 2.73e-22 89.7
Msa0363690 MtrunA17_Chr3g0102351 45.000 100 52 1 37 136 32 128 6.63e-22 89.0
Msa0363690 MtrunA17_Chr2g0290491 41.000 100 58 1 22 120 6 105 1.64e-21 87.4
Msa0363690 MtrunA17_Chr1g0191981 42.529 87 50 0 36 122 8 94 1.77e-21 85.9
Msa0363690 MtrunA17_Chr7g0263601 41.053 95 55 1 27 120 20 114 2.71e-21 86.7
Msa0363690 MtrunA17_Chr8g0382931 38.261 115 69 2 8 120 2 116 4.01e-21 87.0
Msa0363690 MtrunA17_Chr8g0384451 46.429 84 45 0 37 120 45 128 1.01e-20 86.3
Msa0363690 MtrunA17_Chr1g0185911 38.710 93 57 0 37 129 34 126 1.25e-20 85.1
Msa0363690 MtrunA17_Chr1g0165041 35.433 127 79 3 30 153 3 129 1.30e-20 85.5
Msa0363690 MtrunA17_Chr1g0195851 42.857 84 48 0 37 120 41 124 3.06e-20 84.7
Msa0363690 MtrunA17_Chr4g0076381 37.500 112 69 1 10 120 35 146 3.25e-20 85.5
Msa0363690 MtrunA17_Chr4g0076321 42.857 84 48 0 37 120 24 107 7.97e-19 79.3
Msa0363690 MtrunA17_Chr4g0067091 34.906 106 65 1 15 120 9 110 4.22e-18 79.3
Msa0363690 MtrunA17_Chr2g0296321 40.476 84 50 0 37 120 71 154 1.23e-17 79.0
Msa0363690 MtrunA17_Chr5g0446601 34.066 91 60 0 36 126 28 118 1.39e-16 74.7
Msa0363690 MtrunA17_Chr1g0159291 35.802 81 52 0 37 117 7 87 2.48e-12 60.8
Msa0363690 MtrunA17_Chr3g0104021 51.786 56 27 0 143 198 45 100 1.46e-11 59.7
Msa0363690 MtrunA17_Chr1g0159271 34.667 75 49 0 46 120 1 75 2.48e-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
Msa0363690 AT2G38880.7 36.607 112 70 1 19 129 7 118 7.98e-23 90.1
Msa0363690 AT2G38880.2 37.864 103 63 1 19 120 7 109 2.92e-22 89.0
Msa0363690 AT2G38880.1 37.864 103 63 1 19 120 7 109 2.92e-22 89.0
Msa0363690 AT2G38880.5 37.864 103 63 1 19 120 7 109 2.92e-22 89.0
Msa0363690 AT2G38880.3 37.864 103 63 1 19 120 7 109 3.60e-22 88.6
Msa0363690 AT2G38880.11 37.864 103 63 1 19 120 7 109 5.51e-22 89.0
Msa0363690 AT2G38880.8 37.864 103 63 1 19 120 7 109 5.51e-22 89.0
Msa0363690 AT4G14540.1 46.429 84 45 0 37 120 26 109 6.26e-22 88.6
Msa0363690 AT2G38880.4 37.864 103 63 1 19 120 7 109 9.68e-22 86.7
Msa0363690 AT2G37060.2 41.935 93 53 1 29 120 26 118 6.57e-21 86.3
Msa0363690 AT2G37060.3 41.935 93 53 1 29 120 26 118 6.57e-21 86.3
Msa0363690 AT2G37060.1 41.935 93 53 1 29 120 26 118 6.57e-21 86.3
Msa0363690 AT5G47640.1 46.429 84 45 0 37 120 32 115 8.90e-21 86.3
Msa0363690 AT1G21970.1 35.570 149 85 3 21 158 43 191 1.10e-20 87.0
Msa0363690 AT2G38880.9 37.864 103 63 1 19 120 7 109 1.52e-20 84.7
Msa0363690 AT2G38880.10 37.864 103 63 1 19 120 7 109 1.52e-20 84.7
Msa0363690 AT2G38880.6 37.864 103 63 1 19 120 7 109 1.52e-20 84.7
Msa0363690 AT2G13570.1 46.429 84 45 0 37 120 41 124 6.11e-20 84.7
Msa0363690 AT1G09030.1 40.476 84 50 0 37 120 8 91 1.95e-19 81.3
Msa0363690 AT3G53340.5 39.785 93 55 1 29 120 25 117 5.48e-19 81.3
Msa0363690 AT3G53340.1 39.785 93 55 1 29 120 25 117 5.48e-19 81.3
Msa0363690 AT2G47810.1 40.476 84 50 0 37 120 56 139 7.77e-19 80.5
Msa0363690 AT3G53340.4 39.785 93 55 1 29 120 25 117 1.31e-18 79.0
Msa0363690 AT5G47670.2 38.298 94 57 1 28 120 24 117 2.02e-18 80.5
Msa0363690 AT5G47670.1 38.298 94 57 1 28 120 53 146 2.80e-18 80.5
Msa0363690 AT5G47670.3 38.298 94 57 1 28 120 53 146 2.80e-18 80.5
Msa0363690 AT3G53340.3 39.785 93 55 1 29 120 25 117 4.26e-18 78.2
Msa0363690 AT3G53340.2 39.785 93 55 1 29 120 25 117 4.26e-18 78.2

Find 50 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGAATGAATTAGATAATT+TGG 0.119818 3_1:+56321911 Msa0363690:CDS
CAGGGAATGCAGGAAAATTT+TGG 0.155460 3_1:+56321623 Msa0363690:CDS
CTCAAACTCATTTATTGATT+TGG 0.201982 3_1:+56321863 Msa0363690:CDS
ATTAAGGGTCATAAAGTCTA+TGG 0.242488 3_1:+56321659 Msa0363690:CDS
TTTCGTTATAGTAATGAAAT+TGG 0.264459 3_1:+56321726 Msa0363690:CDS
TCATCTATGTTGCATCAAAT+TGG 0.269641 3_1:+56321366 None:intergenic
CCACCGCCACCCATTGCAAT+TGG 0.289759 3_1:+56321822 Msa0363690:CDS
TGGAATGAATTAGATAATTT+GGG 0.310908 3_1:+56321912 Msa0363690:CDS
CTTGGATTCATTATACTTGT+TGG 0.316399 3_1:-56321411 None:intergenic
GGTACAAGGGCATCATTTCT+TGG 0.339623 3_1:-56321429 None:intergenic
GGGTGGCGGTGGTGGTAAGG+TGG 0.341905 3_1:-56321811 None:intergenic
TAGACTTTATGACCCTTAAT+AGG 0.346002 3_1:-56321656 None:intergenic
TTTGTCTCGAATTGCTAGTT+GGG 0.369014 3_1:-56321451 None:intergenic
GATGATAAAATGAATGATTA+AGG 0.370091 3_1:+56322014 Msa0363690:CDS
TGGGTGCAGATGACCTATTA+AGG 0.383571 3_1:+56321643 Msa0363690:CDS
TACATATCTTATAAACTTTG+AGG 0.420260 3_1:-56321574 None:intergenic
CCACCCATTGCAATTGGGCC+AGG 0.425492 3_1:+56321828 Msa0363690:CDS
GGGTGCAGATGACCTATTAA+GGG 0.425849 3_1:+56321644 Msa0363690:CDS
GAATTAGATAATTTGGGTGC+TGG 0.432438 3_1:+56321918 Msa0363690:CDS
TTCCCTGTGACAACGTTCAA+TGG 0.434461 3_1:-56321607 None:intergenic
ATTGGATATTTGAAACTTGT+TGG 0.437848 3_1:+56321744 Msa0363690:CDS
CAATGGGCATGAATGAGGTT+TGG 0.438089 3_1:+56321892 Msa0363690:CDS
GGTGGCGGTGGTGGTAAGGT+GGG 0.449680 3_1:-56321810 None:intergenic
CACCGCCACCCATTGCAATT+GGG 0.452773 3_1:+56321823 Msa0363690:CDS
CCAATTGCAATGGGTGGCGG+TGG 0.456974 3_1:-56321822 None:intergenic
GGCCCAATTGCAATGGGTGG+CGG 0.468146 3_1:-56321825 None:intergenic
TATTGATTTGGATGAAGCAA+TGG 0.481286 3_1:+56321875 Msa0363690:CDS
AATGGGTGGCGGTGGTGGTA+AGG 0.484109 3_1:-56321814 None:intergenic
ATTGATTTGGATGAAGCAAT+GGG 0.487540 3_1:+56321876 Msa0363690:CDS
ATTGCAATGGGTGGCGGTGG+TGG 0.491572 3_1:-56321819 None:intergenic
GAATTGCTAGTTGGGGTACA+AGG 0.493363 3_1:-56321443 None:intergenic
TGATGATATCTTTCAAGAGA+TGG 0.493769 3_1:+56321992 Msa0363690:CDS
AAGCCATTGAACGTTGTCAC+AGG 0.498720 3_1:+56321604 Msa0363690:CDS
AACGTTGTCACAGGGAATGC+AGG 0.505564 3_1:+56321613 Msa0363690:CDS
ATCTGAAAAGCTGGTAAGGT+GGG 0.524201 3_1:-56321780 None:intergenic
CTCTCGTGGAGCAAAGGAGA+TGG 0.534626 3_1:+56321539 Msa0363690:CDS
AAGCCTGGCCCAATTGCAAT+GGG 0.536639 3_1:-56321831 None:intergenic
AAAGCTGGTAAGGTGGGCTT+AGG 0.541538 3_1:-56321774 None:intergenic
TAAGCCTGGCCCAATTGCAA+TGG 0.545356 3_1:-56321832 None:intergenic
TTTGAGTTCAAAGATAAGCC+TGG 0.560916 3_1:-56321846 None:intergenic
TTGTCTCGAATTGCTAGTTG+GGG 0.568122 3_1:-56321450 None:intergenic
TTAAGGGTCATAAAGTCTAT+GGG 0.580731 3_1:+56321660 Msa0363690:CDS
AGCGATCTGAAAAGCTGGTA+AGG 0.583971 3_1:-56321784 None:intergenic
GGAGAAGCGATCTGAAAAGC+TGG 0.592152 3_1:-56321789 None:intergenic
TGGAGCTCTTGTATCTGCAG+AGG 0.594098 3_1:-56321391 None:intergenic
CCTGGCCCAATTGCAATGGG+TGG 0.610784 3_1:-56321828 None:intergenic
TGAAGCAATGGGCATGAATG+AGG 0.611051 3_1:+56321887 Msa0363690:CDS
AGCCATTGAACGTTGTCACA+GGG 0.613629 3_1:+56321605 Msa0363690:CDS
GATCTGAAAAGCTGGTAAGG+TGG 0.629020 3_1:-56321781 None:intergenic
AATTGCTAGTTGGGGTACAA+GGG 0.641551 3_1:-56321442 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACATATCTTATAAACTTTG+AGG - chr3_1:56321577-56321596 None:intergenic 20.0%
!! TTTCGTTATAGTAATGAAAT+TGG + chr3_1:56321726-56321745 Msa0363690:CDS 20.0%
!! TTGGAATGAATTAGATAATT+TGG + chr3_1:56321911-56321930 Msa0363690:CDS 20.0%
!! TGGAATGAATTAGATAATTT+GGG + chr3_1:56321912-56321931 Msa0363690:CDS 20.0%
!!! ATTGTAGCCACATTTTTTAT+TGG - chr3_1:56321486-56321505 None:intergenic 25.0%
!! ATTGGATATTTGAAACTTGT+TGG + chr3_1:56321744-56321763 Msa0363690:CDS 25.0%
!! CTCAAACTCATTTATTGATT+TGG + chr3_1:56321863-56321882 Msa0363690:CDS 25.0%
CTTGGATTCATTATACTTGT+TGG - chr3_1:56321414-56321433 None:intergenic 30.0%
TACCTTGCCAATAAAAAATG+TGG + chr3_1:56321476-56321495 Msa0363690:CDS 30.0%
TAGACTTTATGACCCTTAAT+AGG - chr3_1:56321659-56321678 None:intergenic 30.0%
ATTAAGGGTCATAAAGTCTA+TGG + chr3_1:56321659-56321678 Msa0363690:CDS 30.0%
TTAAGGGTCATAAAGTCTAT+GGG + chr3_1:56321660-56321679 Msa0363690:CDS 30.0%
!! TATTGATTTGGATGAAGCAA+TGG + chr3_1:56321875-56321894 Msa0363690:CDS 30.0%
!! ATTGATTTGGATGAAGCAAT+GGG + chr3_1:56321876-56321895 Msa0363690:CDS 30.0%
TGATGATATCTTTCAAGAGA+TGG + chr3_1:56321992-56322011 Msa0363690:CDS 30.0%
TTTGTCTCGAATTGCTAGTT+GGG - chr3_1:56321454-56321473 None:intergenic 35.0%
! TTTTGTCTCGAATTGCTAGT+TGG - chr3_1:56321455-56321474 None:intergenic 35.0%
!!! AGCCACATTTTTTATTGGCA+AGG - chr3_1:56321481-56321500 None:intergenic 35.0%
!!! ACAACGTTCAATGGCTTTTT+TGG - chr3_1:56321601-56321620 None:intergenic 35.0%
! AGGGAATGCAGGAAAATTTT+GGG + chr3_1:56321624-56321643 Msa0363690:CDS 35.0%
! TTTGAGTTCAAAGATAAGCC+TGG - chr3_1:56321849-56321868 None:intergenic 35.0%
GAATTAGATAATTTGGGTGC+TGG + chr3_1:56321918-56321937 Msa0363690:CDS 35.0%
AATTGCTAGTTGGGGTACAA+GGG - chr3_1:56321445-56321464 None:intergenic 40.0%
TTGTCTCGAATTGCTAGTTG+GGG - chr3_1:56321453-56321472 None:intergenic 40.0%
! CGAGAGATTTTTGTGTTTGG+TGG - chr3_1:56321525-56321544 None:intergenic 40.0%
! CCACGAGAGATTTTTGTGTT+TGG - chr3_1:56321528-56321547 None:intergenic 40.0%
CCAAACACAAAAATCTCTCG+TGG + chr3_1:56321525-56321544 Msa0363690:CDS 40.0%
AAAAATCTCTCGTGGAGCAA+AGG + chr3_1:56321533-56321552 Msa0363690:CDS 40.0%
! CAGGGAATGCAGGAAAATTT+TGG + chr3_1:56321623-56321642 Msa0363690:CDS 40.0%
ATCTGAAAAGCTGGTAAGGT+GGG - chr3_1:56321783-56321802 None:intergenic 40.0%
!! GGTACAAGGGCATCATTTCT+TGG - chr3_1:56321432-56321451 None:intergenic 45.0%
GAATTGCTAGTTGGGGTACA+AGG - chr3_1:56321446-56321465 None:intergenic 45.0%
AAGCCATTGAACGTTGTCAC+AGG + chr3_1:56321604-56321623 Msa0363690:CDS 45.0%
AGCCATTGAACGTTGTCACA+GGG + chr3_1:56321605-56321624 Msa0363690:CDS 45.0%
TTCCCTGTGACAACGTTCAA+TGG - chr3_1:56321610-56321629 None:intergenic 45.0%
TGGGTGCAGATGACCTATTA+AGG + chr3_1:56321643-56321662 Msa0363690:CDS 45.0%
GGGTGCAGATGACCTATTAA+GGG + chr3_1:56321644-56321663 Msa0363690:CDS 45.0%
GATCTGAAAAGCTGGTAAGG+TGG - chr3_1:56321784-56321803 None:intergenic 45.0%
AGCGATCTGAAAAGCTGGTA+AGG - chr3_1:56321787-56321806 None:intergenic 45.0%
TGAAGCAATGGGCATGAATG+AGG + chr3_1:56321887-56321906 Msa0363690:CDS 45.0%
CAATGGGCATGAATGAGGTT+TGG + chr3_1:56321892-56321911 Msa0363690:CDS 45.0%
TGGAGCTCTTGTATCTGCAG+AGG - chr3_1:56321394-56321413 None:intergenic 50.0%
AACGTTGTCACAGGGAATGC+AGG + chr3_1:56321613-56321632 Msa0363690:CDS 50.0%
! AAAGCTGGTAAGGTGGGCTT+AGG - chr3_1:56321777-56321796 None:intergenic 50.0%
GGAGAAGCGATCTGAAAAGC+TGG - chr3_1:56321792-56321811 None:intergenic 50.0%
AAGCCTGGCCCAATTGCAAT+GGG - chr3_1:56321834-56321853 None:intergenic 50.0%
TAAGCCTGGCCCAATTGCAA+TGG - chr3_1:56321835-56321854 None:intergenic 50.0%
CTCTCGTGGAGCAAAGGAGA+TGG + chr3_1:56321539-56321558 Msa0363690:CDS 55.0%
CACCGCCACCCATTGCAATT+GGG + chr3_1:56321823-56321842 Msa0363690:CDS 55.0%
! AATGGGTGGCGGTGGTGGTA+AGG - chr3_1:56321817-56321836 None:intergenic 60.0%
! ATTGCAATGGGTGGCGGTGG+TGG - chr3_1:56321822-56321841 None:intergenic 60.0%
! CCAATTGCAATGGGTGGCGG+TGG - chr3_1:56321825-56321844 None:intergenic 60.0%
CCACCGCCACCCATTGCAAT+TGG + chr3_1:56321822-56321841 Msa0363690:CDS 60.0%
GGCCCAATTGCAATGGGTGG+CGG - chr3_1:56321828-56321847 None:intergenic 60.0%
CCTGGCCCAATTGCAATGGG+TGG - chr3_1:56321831-56321850 None:intergenic 60.0%
CCACCCATTGCAATTGGGCC+AGG + chr3_1:56321828-56321847 Msa0363690:CDS 60.0%
! GGTGGCGGTGGTGGTAAGGT+GGG - chr3_1:56321813-56321832 None:intergenic 65.0%
! GGGTGGCGGTGGTGGTAAGG+TGG - chr3_1:56321814-56321833 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 56321372 56322034 56321372 ID=Msa0363690;Name=Msa0363690
chr3_1 mRNA 56321372 56322034 56321372 ID=Msa0363690-mRNA-1;Parent=Msa0363690;Name=Msa0363690-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|-1|0|1|-1|1|1|0|220
chr3_1 exon 56321372 56322034 56321372 ID=Msa0363690-mRNA-1:exon:10335;Parent=Msa0363690-mRNA-1
chr3_1 CDS 56321372 56322034 56321372 ID=Msa0363690-mRNA-1:cds;Parent=Msa0363690-mRNA-1
Gene Sequence

>Msa0363690

ATGTTGCATCAAATTGGTGCCTCTGCAGATACAAGAGCTCCAACAAGTATAATGAATCCAAGAAATGATGCCCTTGTACCCCAACTAGCAATTCGAGACAAAAATACCTTGCCAATAAAAAATGTGGCTACAATCATGAGAAAAGTTCTTCCACCAAACACAAAAATCTCTCGTGGAGCAAAGGAGATGGTTGAACAAATCACCTCAAAGTTTATAAGATATGTAACCAAAAAAGCCATTGAACGTTGTCACAGGGAATGCAGGAAAATTTTGGGTGCAGATGACCTATTAAGGGTCATAAAGTCTATGGGTTATAATAATTATTATGAGTATCTCAATTTTTATCTCAAATGCTTTCGTTATAGTAATGAAATTGGATATTTGAAACTTGTTGGTGAGCTTCCTAAGCCCACCTTACCAGCTTTTCAGATCGCTTCTCCCACCTTACCACCACCGCCACCCATTGCAATTGGGCCAGGCTTATCTTTGAACTCAAACTCATTTATTGATTTGGATGAAGCAATGGGCATGAATGAGGTTTGGAATGAATTAGATAATTTGGGTGCTGGTTCTCTAGAGACTGCTTTAACAAACTTTGATCATTCAATTCAATTCAACTTTGATGATATCTTTCAAGAGATGGATGATAAAATGAATGATTAA

Protein sequence

>Msa0363690

MLHQIGASADTRAPTSIMNPRNDALVPQLAIRDKNTLPIKNVATIMRKVLPPNTKISRGAKEMVEQITSKFIRYVTKKAIERCHRECRKILGADDLLRVIKSMGYNNYYEYLNFYLKCFRYSNEIGYLKLVGELPKPTLPAFQIASPTLPPPPPIAIGPGLSLNSNSFIDLDEAMGMNEVWNELDNLGAGSLETALTNFDHSIQFNFDDIFQEMDDKMND*