AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0455470

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0455470 MtrunA17_Chr5g0446491 44.681 94 51 1 28 120 18 111 5.43e-22 89.0
Msa0455470 MtrunA17_Chr2g0290491 42.000 100 57 1 22 120 6 105 1.01e-21 87.8
Msa0455470 MtrunA17_Chr3g0102351 47.619 84 44 0 37 120 32 115 1.69e-21 87.8
Msa0455470 MtrunA17_Chr1g0185911 34.375 128 70 2 3 129 12 126 2.01e-21 87.4
Msa0455470 MtrunA17_Chr1g0191981 42.529 87 50 0 36 122 8 94 4.31e-21 85.1
Msa0455470 MtrunA17_Chr7g0263601 41.053 95 55 1 27 120 20 114 5.15e-21 86.3
Msa0455470 MtrunA17_Chr8g0382931 38.261 115 69 2 8 120 2 116 1.03e-20 86.3
Msa0455470 MtrunA17_Chr1g0165041 35.433 127 79 3 30 153 3 129 3.08e-20 84.3
Msa0455470 MtrunA17_Chr4g0076381 37.500 112 69 1 10 120 35 146 4.34e-20 85.1
Msa0455470 MtrunA17_Chr1g0195851 42.857 84 48 0 37 120 41 124 5.86e-20 84.0
Msa0455470 MtrunA17_Chr8g0384451 44.048 84 47 0 37 120 45 128 2.89e-19 82.4
Msa0455470 MtrunA17_Chr4g0076321 44.048 84 47 0 37 120 24 107 4.46e-19 80.1
Msa0455470 MtrunA17_Chr4g0067091 34.259 108 67 1 13 120 7 110 7.92e-18 78.6
Msa0455470 MtrunA17_Chr2g0296321 40.476 84 50 0 37 120 71 154 2.20e-17 78.2
Msa0455470 MtrunA17_Chr5g0446601 35.165 91 59 0 36 126 28 118 1.12e-16 75.1
Msa0455470 MtrunA17_Chr1g0159291 37.037 81 51 0 37 117 7 87 4.80e-13 62.8
Msa0455470 MtrunA17_Chr1g0159271 36.000 75 48 0 46 120 1 75 6.89e-12 60.1
Msa0455470 MtrunA17_Chr3g0104021 50.000 56 28 0 143 198 45 100 9.54e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0455470 AT2G38880.7 37.500 112 69 1 19 129 7 118 2.75e-23 91.7
Msa0455470 AT2G38880.11 38.983 118 66 2 9 125 2 114 1.32e-22 90.5
Msa0455470 AT2G38880.8 38.983 118 66 2 9 125 2 114 1.32e-22 90.5
Msa0455470 AT2G38880.2 38.835 103 62 1 19 120 7 109 1.64e-22 89.4
Msa0455470 AT2G38880.1 38.835 103 62 1 19 120 7 109 1.64e-22 89.4
Msa0455470 AT2G38880.5 38.835 103 62 1 19 120 7 109 1.64e-22 89.4
Msa0455470 AT2G38880.3 38.835 103 62 1 19 120 7 109 1.94e-22 89.4
Msa0455470 AT2G38880.4 38.835 103 62 1 19 120 7 109 4.40e-22 87.4
Msa0455470 AT4G14540.1 46.429 84 45 0 37 120 26 109 1.43e-21 87.8
Msa0455470 AT5G47640.1 47.619 84 44 0 37 120 32 115 3.68e-21 87.4
Msa0455470 AT2G38880.9 38.835 103 62 1 19 120 7 109 8.59e-21 85.5
Msa0455470 AT2G38880.10 38.835 103 62 1 19 120 7 109 8.59e-21 85.5
Msa0455470 AT2G38880.6 38.835 103 62 1 19 120 7 109 8.59e-21 85.5
Msa0455470 AT2G37060.2 41.935 93 53 1 29 120 26 118 1.33e-20 85.5
Msa0455470 AT2G37060.3 41.935 93 53 1 29 120 26 118 1.33e-20 85.5
Msa0455470 AT2G37060.1 41.935 93 53 1 29 120 26 118 1.33e-20 85.5
Msa0455470 AT1G21970.1 35.570 149 85 3 21 158 43 191 1.72e-20 86.7
Msa0455470 AT2G47810.1 41.667 84 49 0 37 120 56 139 4.27e-19 81.3
Msa0455470 AT3G53340.5 38.679 106 62 2 29 133 25 128 7.83e-19 80.9
Msa0455470 AT3G53340.1 38.679 106 62 2 29 133 25 128 7.83e-19 80.9
Msa0455470 AT1G09030.1 39.286 84 51 0 37 120 8 91 1.88e-18 79.0
Msa0455470 AT2G13570.1 44.048 84 47 0 37 120 41 124 1.97e-18 80.9
Msa0455470 AT3G53340.4 39.785 93 55 1 29 120 25 117 2.19e-18 78.2
Msa0455470 AT5G47670.2 38.298 94 57 1 28 120 24 117 4.28e-18 79.7
Msa0455470 AT5G47670.1 38.298 94 57 1 28 120 53 146 6.51e-18 79.7
Msa0455470 AT5G47670.3 38.298 94 57 1 28 120 53 146 6.51e-18 79.7
Msa0455470 AT3G53340.3 39.785 93 55 1 29 120 25 117 7.76e-18 77.4
Msa0455470 AT3G53340.2 39.785 93 55 1 29 120 25 117 7.76e-18 77.4

Find 47 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGAATGAATTGGATAATT+TGG 0.149282 3_3:+48395421 Msa0455470:CDS
CAGCGAATGCAGGAAAATTT+TGG 0.155460 3_3:+48395133 Msa0455470:CDS
CTCAAACTCATTTATTGATT+TGG 0.201982 3_3:+48395373 Msa0455470:CDS
TCATCTATGTTGCATCAAAT+TGG 0.269641 3_3:+48394876 None:intergenic
CCACCGCCACCCATTGCAAT+TGG 0.296308 3_3:+48395332 Msa0455470:CDS
GGCACAAGGGCATCATTTCT+TGG 0.320738 3_3:-48394939 None:intergenic
GGGTGGCGGTGGTGGTAAGG+TGG 0.341905 3_3:-48395321 None:intergenic
TGGAATGAATTGGATAATTT+GGG 0.348468 3_3:+48395422 Msa0455470:CDS
GATGATAAAATGAATGATTA+AGG 0.370091 3_3:+48395524 Msa0455470:CDS
TTTGTCTCGAATTGCTAGTT+GGG 0.382494 3_3:-48394961 None:intergenic
GAATGAGGTTTGGAATGAAT+TGG 0.382994 3_3:+48395412 Msa0455470:CDS
TGGGTGCAGATGACCTATTA+AGG 0.383571 3_3:+48395153 Msa0455470:CDS
TAGACTCCATGACCCTTAAT+AGG 0.389610 3_3:-48395166 None:intergenic
TTTCGTTATAGTAATGAAAC+TGG 0.406421 3_3:+48395236 Msa0455470:CDS
CCACCCATTGCAATTGGGTC+AGG 0.408457 3_3:+48395338 Msa0455470:CDS
TACATATCTTATAAACTTTG+AGG 0.420260 3_3:-48395084 None:intergenic
GGGTGCAGATGACCTATTAA+GGG 0.425849 3_3:+48395154 Msa0455470:CDS
TTCGCTGTGACAACGTTCAA+TGG 0.440976 3_3:-48395117 None:intergenic
ACTGGATATTTGAAACTTGT+TGG 0.444006 3_3:+48395254 Msa0455470:CDS
GGTGGCGGTGGTGGTAAGGT+GGG 0.449680 3_3:-48395320 None:intergenic
CACCGCCACCCATTGCAATT+GGG 0.468956 3_3:+48395333 Msa0455470:CDS
CCAATTGCAATGGGTGGCGG+TGG 0.473098 3_3:-48395332 None:intergenic
CAGTGGGCATGAATGAGGTT+TGG 0.475910 3_3:+48395402 Msa0455470:CDS
TTAAGGGTCATGGAGTCTAT+AGG 0.476992 3_3:+48395170 Msa0455470:CDS
AATGGGTGGCGGTGGTGGTA+AGG 0.484109 3_3:-48395324 None:intergenic
ATTGCAATGGGTGGCGGTGG+TGG 0.491572 3_3:-48395329 None:intergenic
GAATTGGATAATTTGGGTGC+TGG 0.493441 3_3:+48395428 Msa0455470:CDS
AACGTTGTCACAGCGAATGC+AGG 0.495853 3_3:+48395123 Msa0455470:CDS
TCACGATATCTTTCAAGAGA+TGG 0.505210 3_3:+48395502 Msa0455470:CDS
GACCCAATTGCAATGGGTGG+CGG 0.506575 3_3:-48395335 None:intergenic
ATCTGAAAAGCTGGTAAGGT+GGG 0.524201 3_3:-48395290 None:intergenic
CTCTCGTGGAGCAAAGGAGA+TGG 0.534626 3_3:+48395049 Msa0455470:CDS
AAGCCTGACCCAATTGCAAT+GGG 0.536639 3_3:-48395341 None:intergenic
AAAGCTGGTAAGGTGGGCTT+AGG 0.541538 3_3:-48395284 None:intergenic
TATTGATTTGGATGAAGCAG+TGG 0.556331 3_3:+48395385 Msa0455470:CDS
GAATTGCTAGTTGGGGCACA+AGG 0.564590 3_3:-48394953 None:intergenic
TTGTCTCGAATTGCTAGTTG+GGG 0.571725 3_3:-48394960 None:intergenic
ATTGATTTGGATGAAGCAGT+GGG 0.573123 3_3:+48395386 Msa0455470:CDS
TAAGCCTGACCCAATTGCAA+TGG 0.575839 3_3:-48395342 None:intergenic
AGCGATCTGAAAAGCTGGTA+AGG 0.583971 3_3:-48395294 None:intergenic
AGATGACCTATTAAGGGTCA+TGG 0.587003 3_3:+48395160 Msa0455470:CDS
GGAGAAGCGATCTGAAAAGC+TGG 0.592152 3_3:-48395299 None:intergenic
TGAAGCAGTGGGCATGAATG+AGG 0.622575 3_3:+48395397 Msa0455470:CDS
TGAAGCTCTTGTATCTGCAG+AGG 0.623936 3_3:-48394901 None:intergenic
GATCTGAAAAGCTGGTAAGG+TGG 0.629020 3_3:-48395291 None:intergenic
CCTGACCCAATTGCAATGGG+TGG 0.641990 3_3:-48395338 None:intergenic
AATTGCTAGTTGGGGCACAA+GGG 0.680281 3_3:-48394952 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACATATCTTATAAACTTTG+AGG - chr3_3:48395087-48395106 None:intergenic 20.0%
! TACCTTACCAATAAAAAATG+TGG + chr3_3:48394986-48395005 Msa0455470:CDS 25.0%
!!! ATTGTTGCCACATTTTTTAT+TGG - chr3_3:48394996-48395015 None:intergenic 25.0%
! TTTCGTTATAGTAATGAAAC+TGG + chr3_3:48395236-48395255 Msa0455470:CDS 25.0%
!! CTCAAACTCATTTATTGATT+TGG + chr3_3:48395373-48395392 Msa0455470:CDS 25.0%
! TTGGAATGAATTGGATAATT+TGG + chr3_3:48395421-48395440 Msa0455470:CDS 25.0%
! TGGAATGAATTGGATAATTT+GGG + chr3_3:48395422-48395441 Msa0455470:CDS 25.0%
!!! TGCCACATTTTTTATTGGTA+AGG - chr3_3:48394991-48395010 None:intergenic 30.0%
! ACTGGATATTTGAAACTTGT+TGG + chr3_3:48395254-48395273 Msa0455470:CDS 30.0%
TTTGTCTCGAATTGCTAGTT+GGG - chr3_3:48394964-48394983 None:intergenic 35.0%
! TTTTGTCTCGAATTGCTAGT+TGG - chr3_3:48394965-48394984 None:intergenic 35.0%
!!! ACAACGTTCAATGGCTTTTT+TGG - chr3_3:48395111-48395130 None:intergenic 35.0%
! AGCGAATGCAGGAAAATTTT+GGG + chr3_3:48395134-48395153 Msa0455470:CDS 35.0%
!! TATTGATTTGGATGAAGCAG+TGG + chr3_3:48395385-48395404 Msa0455470:CDS 35.0%
!! ATTGATTTGGATGAAGCAGT+GGG + chr3_3:48395386-48395405 Msa0455470:CDS 35.0%
! GAATGAGGTTTGGAATGAAT+TGG + chr3_3:48395412-48395431 Msa0455470:CDS 35.0%
TCACGATATCTTTCAAGAGA+TGG + chr3_3:48395502-48395521 Msa0455470:CDS 35.0%
TTGTCTCGAATTGCTAGTTG+GGG - chr3_3:48394963-48394982 None:intergenic 40.0%
! CGAGAGATTTTTGTGTTTGG+TGG - chr3_3:48395035-48395054 None:intergenic 40.0%
! CCACGAGAGATTTTTGTGTT+TGG - chr3_3:48395038-48395057 None:intergenic 40.0%
CCAAACACAAAAATCTCTCG+TGG + chr3_3:48395035-48395054 Msa0455470:CDS 40.0%
AAAAATCTCTCGTGGAGCAA+AGG + chr3_3:48395043-48395062 Msa0455470:CDS 40.0%
! CAGCGAATGCAGGAAAATTT+TGG + chr3_3:48395133-48395152 Msa0455470:CDS 40.0%
AGATGACCTATTAAGGGTCA+TGG + chr3_3:48395160-48395179 Msa0455470:CDS 40.0%
TAGACTCCATGACCCTTAAT+AGG - chr3_3:48395169-48395188 None:intergenic 40.0%
TTAAGGGTCATGGAGTCTAT+AGG + chr3_3:48395170-48395189 Msa0455470:CDS 40.0%
ATCTGAAAAGCTGGTAAGGT+GGG - chr3_3:48395293-48395312 None:intergenic 40.0%
GAATTGGATAATTTGGGTGC+TGG + chr3_3:48395428-48395447 Msa0455470:CDS 40.0%
TGAAGCTCTTGTATCTGCAG+AGG - chr3_3:48394904-48394923 None:intergenic 45.0%
AATTGCTAGTTGGGGCACAA+GGG - chr3_3:48394955-48394974 None:intergenic 45.0%
TTCGCTGTGACAACGTTCAA+TGG - chr3_3:48395120-48395139 None:intergenic 45.0%
TGGGTGCAGATGACCTATTA+AGG + chr3_3:48395153-48395172 Msa0455470:CDS 45.0%
GGGTGCAGATGACCTATTAA+GGG + chr3_3:48395154-48395173 Msa0455470:CDS 45.0%
GATCTGAAAAGCTGGTAAGG+TGG - chr3_3:48395294-48395313 None:intergenic 45.0%
AGCGATCTGAAAAGCTGGTA+AGG - chr3_3:48395297-48395316 None:intergenic 45.0%
AAGCCTGACCCAATTGCAAT+GGG - chr3_3:48395344-48395363 None:intergenic 45.0%
TAAGCCTGACCCAATTGCAA+TGG - chr3_3:48395345-48395364 None:intergenic 45.0%
!! GGCACAAGGGCATCATTTCT+TGG - chr3_3:48394942-48394961 None:intergenic 50.0%
GAATTGCTAGTTGGGGCACA+AGG - chr3_3:48394956-48394975 None:intergenic 50.0%
AACGTTGTCACAGCGAATGC+AGG + chr3_3:48395123-48395142 Msa0455470:CDS 50.0%
! AAAGCTGGTAAGGTGGGCTT+AGG - chr3_3:48395287-48395306 None:intergenic 50.0%
GGAGAAGCGATCTGAAAAGC+TGG - chr3_3:48395302-48395321 None:intergenic 50.0%
TGAAGCAGTGGGCATGAATG+AGG + chr3_3:48395397-48395416 Msa0455470:CDS 50.0%
CAGTGGGCATGAATGAGGTT+TGG + chr3_3:48395402-48395421 Msa0455470:CDS 50.0%
CTCTCGTGGAGCAAAGGAGA+TGG + chr3_3:48395049-48395068 Msa0455470:CDS 55.0%
CACCGCCACCCATTGCAATT+GGG + chr3_3:48395333-48395352 Msa0455470:CDS 55.0%
GACCCAATTGCAATGGGTGG+CGG - chr3_3:48395338-48395357 None:intergenic 55.0%
CCTGACCCAATTGCAATGGG+TGG - chr3_3:48395341-48395360 None:intergenic 55.0%
CCACCCATTGCAATTGGGTC+AGG + chr3_3:48395338-48395357 Msa0455470:CDS 55.0%
! AATGGGTGGCGGTGGTGGTA+AGG - chr3_3:48395327-48395346 None:intergenic 60.0%
! ATTGCAATGGGTGGCGGTGG+TGG - chr3_3:48395332-48395351 None:intergenic 60.0%
! CCAATTGCAATGGGTGGCGG+TGG - chr3_3:48395335-48395354 None:intergenic 60.0%
CCACCGCCACCCATTGCAAT+TGG + chr3_3:48395332-48395351 Msa0455470:CDS 60.0%
! GGTGGCGGTGGTGGTAAGGT+GGG - chr3_3:48395323-48395342 None:intergenic 65.0%
! GGGTGGCGGTGGTGGTAAGG+TGG - chr3_3:48395324-48395343 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 48394882 48395544 48394882 ID=Msa0455470;Name=Msa0455470
chr3_3 mRNA 48394882 48395544 48394882 ID=Msa0455470-mRNA-1;Parent=Msa0455470;Name=Msa0455470-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|-1|0|1|-1|1|1|0|220
chr3_3 exon 48394882 48395544 48394882 ID=Msa0455470-mRNA-1:exon:8979;Parent=Msa0455470-mRNA-1
chr3_3 CDS 48394882 48395544 48394882 ID=Msa0455470-mRNA-1:cds;Parent=Msa0455470-mRNA-1
Gene Sequence

>Msa0455470

ATGTTGCATCAAATTGGTGCCTCTGCAGATACAAGAGCTTCAACAAGTATAATGAATCCAAGAAATGATGCCCTTGTGCCCCAACTAGCAATTCGAGACAAAAATACCTTACCAATAAAAAATGTGGCAACAATCATGAGAAAAGTTCTTCCACCAAACACAAAAATCTCTCGTGGAGCAAAGGAGATGGTTGAACAAATCACCTCAAAGTTTATAAGATATGTAACCAAAAAAGCCATTGAACGTTGTCACAGCGAATGCAGGAAAATTTTGGGTGCAGATGACCTATTAAGGGTCATGGAGTCTATAGGTTATAATAACTATTATGAGTATCTCAATTTTTATCTCAAATGCTTTCGTTATAGTAATGAAACTGGATATTTGAAACTTGTTGGTGAGCTTCCTAAGCCCACCTTACCAGCTTTTCAGATCGCTTCTCCCACCTTACCACCACCGCCACCCATTGCAATTGGGTCAGGCTTATCTTTGAACTCAAACTCATTTATTGATTTGGATGAAGCAGTGGGCATGAATGAGGTTTGGAATGAATTGGATAATTTGGGTGCTGGTTCTCTAGAGACTGCTTTAACAAACTTTGATCATTCAATTCAATTCAACTTTCACGATATCTTTCAAGAGATGGATGATAAAATGAATGATTAA
Protein sequence

>Msa0455470

MLHQIGASADTRASTSIMNPRNDALVPQLAIRDKNTLPIKNVATIMRKVLPPNTKISRGAKEMVEQITSKFIRYVTKKAIERCHSECRKILGADDLLRVMESIGYNNYYEYLNFYLKCFRYSNETGYLKLVGELPKPTLPAFQIASPTLPPPPPIAIGSGLSLNSNSFIDLDEAVGMNEVWNELDNLGAGSLETALTNFDHSIQFNFHDIFQEMDDKMND*