AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0186670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0186670 MtrunA17_Chr1g0152901 86.301 146 13 1 1 146 1 139 4.57e-86 248
Msa0186670 MtrunA17_Chr3g0134391 60.909 110 41 2 11 119 13 121 2.19e-39 130
Msa0186670 MtrunA17_Chr1g0185561 35.417 96 60 1 24 117 6 101 2.29e-15 72.0
Msa0186670 MtrunA17_Chr1g0205881 32.941 85 55 1 35 117 20 104 1.16e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0186670 AT1G47200.1 49.624 133 55 3 1 131 28 150 1.28e-36 124
Msa0186670 AT5G43070.1 51.969 127 55 3 18 139 27 152 2.51e-35 120
Msa0186670 AT5G27940.1 43.878 98 51 2 33 130 51 144 2.57e-21 84.3
Msa0186670 AT3G63130.1 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0186670 AT3G63130.2 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0186670 AT5G19320.1 34.118 85 54 1 35 117 16 100 1.00e-11 61.6
Msa0186670 AT5G19320.2 34.118 85 54 1 35 117 16 100 1.00e-11 61.6

Find 57 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGTTCGGGTTTGGCTTCC+GGG 0.228499 2_1:+1455532 None:intergenic
TCTTGTTCGGGTTTGGCTTC+CGG 0.236651 2_1:+1455531 None:intergenic
GAGTAGTTTCCGGTGAAATT+TGG 0.305396 2_1:+1455462 None:intergenic
GGAGGAGTCTTGTTCGGGTT+TGG 0.340745 2_1:+1455524 None:intergenic
AGCGAGGGAGGAGTCTTGTT+CGG 0.384493 2_1:+1455518 None:intergenic
GCGAGGGAGGAGTCTTGTTC+GGG 0.389014 2_1:+1455519 None:intergenic
GCGTTGTGCGGGAGGCCATA+TGG 0.389468 2_1:+1455440 None:intergenic
GCTATCGTTGCCCGTGGAAG+TGG 0.401756 2_1:+1455272 None:intergenic
CTCGATCTGGCTAGCGGCGG+CGG 0.404744 2_1:+1455323 None:intergenic
AGGCCATATGGAGTAGTTTC+CGG 0.410196 2_1:+1455452 None:intergenic
GAGACGAGATTTAGCTTTAA+CGG 0.420770 2_1:+1455197 None:intergenic
AGAAAGCTTCGTCCTCGATC+TGG 0.425698 2_1:+1455310 None:intergenic
GGACATTGTGCCGTAGCGTT+TGG 0.463221 2_1:+1455359 None:intergenic
GGAGCCTCCGTAGAGGGAGG+TGG 0.466455 2_1:+1455495 None:intergenic
CAATCAAGATTCAAAACAGC+GGG 0.470125 2_1:+1455123 None:intergenic
CCTCGCTCCACCTCCCTCTA+CGG 0.475624 2_1:-1455502 Msa0186670:CDS
TGGAAAGTGTTTCGATCAAA+CGG 0.476905 2_1:+1455397 None:intergenic
GGGGAATCAGCGGCAGAGGA+AGG 0.480076 2_1:+1455144 None:intergenic
TCACCGGAAACTACTCCATA+TGG 0.480969 2_1:-1455455 Msa0186670:CDS
GCGTCGCGAGTGCGTTGTGC+GGG 0.482089 2_1:+1455429 None:intergenic
AGAGGGAGGTGGAGCGAGGG+AGG 0.486555 2_1:+1455506 None:intergenic
CGCCGATGCTTCCACTTCCA+CGG 0.489244 2_1:-1455283 Msa0186670:CDS
CGTAGAGGGAGGTGGAGCGA+GGG 0.494922 2_1:+1455503 None:intergenic
TTCGGGTTTGGCTTCCGGGT+CGG 0.497869 2_1:+1455536 None:intergenic
GGCAGAGGAAGGAGCTCCGA+CGG 0.510995 2_1:+1455155 None:intergenic
TTTGGTGAGGACTGAGGGAG+TGG 0.512643 2_1:+1455377 None:intergenic
TGCGGTGGAGCCTCCGTAGA+GGG 0.519645 2_1:+1455489 None:intergenic
GTGAAATTTGGTTGTTGCGG+TGG 0.524980 2_1:+1455474 None:intergenic
TCGCGAGTGCGTTGTGCGGG+AGG 0.530415 2_1:+1455432 None:intergenic
GCCGATGCTTCCACTTCCAC+GGG 0.537590 2_1:-1455282 Msa0186670:CDS
TAGCGTTTGGTGAGGACTGA+GGG 0.560021 2_1:+1455372 None:intergenic
CCGTAGAGGGAGGTGGAGCG+AGG 0.564877 2_1:+1455502 None:intergenic
AAATCTCGTCTCGCTGATGA+CGG 0.565498 2_1:-1455186 Msa0186670:CDS
GCCCGTGGAAGTGGAAGCAT+CGG 0.569170 2_1:+1455281 None:intergenic
CGCTCCACCTCCCTCTACGG+AGG 0.572005 2_1:-1455499 Msa0186670:CDS
GGCGTCGCGAGTGCGTTGTG+CGG 0.572105 2_1:+1455428 None:intergenic
CCGCAACAACCAAATTTCAC+CGG 0.575174 2_1:-1455471 Msa0186670:CDS
CGATAGCGTTACGATTCTTG+AGG 0.579942 2_1:-1455256 Msa0186670:CDS
GATTCTTGAGGTTTACTCGA+AGG 0.581915 2_1:-1455244 Msa0186670:CDS
CCGGTGAAATTTGGTTGTTG+CGG 0.585855 2_1:+1455471 None:intergenic
CGCCGCCGCTAGCCAGATCG+AGG 0.588312 2_1:-1455322 Msa0186670:CDS
GGAAGTGGAAGCATCGGCGA+CGG 0.598077 2_1:+1455287 None:intergenic
GTAGCGTTTGGTGAGGACTG+AGG 0.608047 2_1:+1455371 None:intergenic
AGAGGAAGGAGCTCCGACGG+AGG 0.609670 2_1:+1455158 None:intergenic
GATGACGGTAACGCCTCCGT+CGG 0.613328 2_1:-1455171 Msa0186670:CDS
TTGCGGTGGAGCCTCCGTAG+AGG 0.615033 2_1:+1455488 None:intergenic
TTGTGCCGTAGCGTTTGGTG+AGG 0.632497 2_1:+1455364 None:intergenic
GGCGGCGGAAGCTTCGTCAG+CGG 0.636492 2_1:+1455338 None:intergenic
ATTCCTCACAATGTCCGACC+CGG 0.637935 2_1:-1455550 None:intergenic
GGTGGAGCCTCCGTAGAGGG+AGG 0.638102 2_1:+1455492 None:intergenic
TCAGTCCTCACCAAACGCTA+CGG 0.644599 2_1:-1455369 Msa0186670:CDS
CGTAACGCTATCGTTGCCCG+TGG 0.647560 2_1:+1455266 None:intergenic
TTCGTCCTCGATCTGGCTAG+CGG 0.649591 2_1:+1455317 None:intergenic
ATCAAGATTCAAAACAGCGG+GGG 0.654507 2_1:+1455125 None:intergenic
GTCCTCGATCTGGCTAGCGG+CGG 0.689668 2_1:+1455320 None:intergenic
TCAATCAAGATTCAAAACAG+CGG 0.702532 2_1:+1455122 None:intergenic
AATCAAGATTCAAAACAGCG+GGG 0.726201 2_1:+1455124 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAATCAAGATTCAAAACAG+CGG + chr2_1:1455543-1455562 None:intergenic 30.0%
! TTCGATCAAACGGTTTTTGA+CGG + chr2_1:1455258-1455277 None:intergenic 35.0%
!! TGGAAAGTGTTTCGATCAAA+CGG + chr2_1:1455268-1455287 None:intergenic 35.0%
!! GAGACGAGATTTAGCTTTAA+CGG + chr2_1:1455468-1455487 None:intergenic 35.0%
AATCAAGATTCAAAACAGCG+GGG + chr2_1:1455541-1455560 None:intergenic 35.0%
CAATCAAGATTCAAAACAGC+GGG + chr2_1:1455542-1455561 None:intergenic 35.0%
GAGTAGTTTCCGGTGAAATT+TGG + chr2_1:1455203-1455222 None:intergenic 40.0%
GATTCTTGAGGTTTACTCGA+AGG - chr2_1:1455418-1455437 Msa0186670:CDS 40.0%
ATCAAGATTCAAAACAGCGG+GGG + chr2_1:1455540-1455559 None:intergenic 40.0%
GTGAAATTTGGTTGTTGCGG+TGG + chr2_1:1455191-1455210 None:intergenic 45.0%
CCGGTGAAATTTGGTTGTTG+CGG + chr2_1:1455194-1455213 None:intergenic 45.0%
CCGCAACAACCAAATTTCAC+CGG - chr2_1:1455191-1455210 Msa0186670:CDS 45.0%
TCACCGGAAACTACTCCATA+TGG - chr2_1:1455207-1455226 Msa0186670:CDS 45.0%
AGGCCATATGGAGTAGTTTC+CGG + chr2_1:1455213-1455232 None:intergenic 45.0%
CGATAGCGTTACGATTCTTG+AGG - chr2_1:1455406-1455425 Msa0186670:CDS 45.0%
AAATCTCGTCTCGCTGATGA+CGG - chr2_1:1455476-1455495 Msa0186670:CDS 45.0%
! TCTTGTTCGGGTTTGGCTTC+CGG + chr2_1:1455134-1455153 None:intergenic 50.0%
! TAGCGTTTGGTGAGGACTGA+GGG + chr2_1:1455293-1455312 None:intergenic 50.0%
TCAGTCCTCACCAAACGCTA+CGG - chr2_1:1455293-1455312 Msa0186670:CDS 50.0%
AGAAAGCTTCGTCCTCGATC+TGG + chr2_1:1455355-1455374 None:intergenic 50.0%
! CTTGTTCGGGTTTGGCTTCC+GGG + chr2_1:1455133-1455152 None:intergenic 55.0%
!! GGAGGAGTCTTGTTCGGGTT+TGG + chr2_1:1455141-1455160 None:intergenic 55.0%
!! AGCGAGGGAGGAGTCTTGTT+CGG + chr2_1:1455147-1455166 None:intergenic 55.0%
TTTGGTGAGGACTGAGGGAG+TGG + chr2_1:1455288-1455307 None:intergenic 55.0%
! GTAGCGTTTGGTGAGGACTG+AGG + chr2_1:1455294-1455313 None:intergenic 55.0%
! TTGTGCCGTAGCGTTTGGTG+AGG + chr2_1:1455301-1455320 None:intergenic 55.0%
GGACATTGTGCCGTAGCGTT+TGG + chr2_1:1455306-1455325 None:intergenic 55.0%
TTCGTCCTCGATCTGGCTAG+CGG + chr2_1:1455348-1455367 None:intergenic 55.0%
CAAAACAGCGGGGGAATCAG+CGG + chr2_1:1455531-1455550 None:intergenic 55.0%
! TTCGGGTTTGGCTTCCGGGT+CGG + chr2_1:1455129-1455148 None:intergenic 60.0%
!! GCGAGGGAGGAGTCTTGTTC+GGG + chr2_1:1455146-1455165 None:intergenic 60.0%
!! GGAAGTGGAAGCATCGGCGA+CGG + chr2_1:1455378-1455397 None:intergenic 60.0%
CGCCGATGCTTCCACTTCCA+CGG - chr2_1:1455379-1455398 Msa0186670:CDS 60.0%
GCCGATGCTTCCACTTCCAC+GGG - chr2_1:1455380-1455399 Msa0186670:CDS 60.0%
! GCCCGTGGAAGTGGAAGCAT+CGG + chr2_1:1455384-1455403 None:intergenic 60.0%
GCTATCGTTGCCCGTGGAAG+TGG + chr2_1:1455393-1455412 None:intergenic 60.0%
CGTAACGCTATCGTTGCCCG+TGG + chr2_1:1455399-1455418 None:intergenic 60.0%
! GATGACGGTAACGCCTCCGT+CGG - chr2_1:1455491-1455510 Msa0186670:CDS 60.0%
CGTAGAGGGAGGTGGAGCGA+GGG + chr2_1:1455162-1455181 None:intergenic 65.0%
CCTCGCTCCACCTCCCTCTA+CGG - chr2_1:1455160-1455179 Msa0186670:CDS 65.0%
TGCGGTGGAGCCTCCGTAGA+GGG + chr2_1:1455176-1455195 None:intergenic 65.0%
TTGCGGTGGAGCCTCCGTAG+AGG + chr2_1:1455177-1455196 None:intergenic 65.0%
GCGTTGTGCGGGAGGCCATA+TGG + chr2_1:1455225-1455244 None:intergenic 65.0%
GTCCTCGATCTGGCTAGCGG+CGG + chr2_1:1455345-1455364 None:intergenic 65.0%
AGAGGAAGGAGCTCCGACGG+AGG + chr2_1:1455507-1455526 None:intergenic 65.0%
GGCAGAGGAAGGAGCTCCGA+CGG + chr2_1:1455510-1455529 None:intergenic 65.0%
GGGGAATCAGCGGCAGAGGA+AGG + chr2_1:1455521-1455540 None:intergenic 65.0%
AGAGGGAGGTGGAGCGAGGG+AGG + chr2_1:1455159-1455178 None:intergenic 70.0%
CCGTAGAGGGAGGTGGAGCG+AGG + chr2_1:1455163-1455182 None:intergenic 70.0%
CGCTCCACCTCCCTCTACGG+AGG - chr2_1:1455163-1455182 Msa0186670:CDS 70.0%
GGAGCCTCCGTAGAGGGAGG+TGG + chr2_1:1455170-1455189 None:intergenic 70.0%
GGTGGAGCCTCCGTAGAGGG+AGG + chr2_1:1455173-1455192 None:intergenic 70.0%
TCGCGAGTGCGTTGTGCGGG+AGG + chr2_1:1455233-1455252 None:intergenic 70.0%
GCGTCGCGAGTGCGTTGTGC+GGG + chr2_1:1455236-1455255 None:intergenic 70.0%
GGCGTCGCGAGTGCGTTGTG+CGG + chr2_1:1455237-1455256 None:intergenic 70.0%
GGCGGCGGAAGCTTCGTCAG+CGG + chr2_1:1455327-1455346 None:intergenic 70.0%
CTCGATCTGGCTAGCGGCGG+CGG + chr2_1:1455342-1455361 None:intergenic 70.0%
AGCGGGGGAATCAGCGGCAG+AGG + chr2_1:1455525-1455544 None:intergenic 70.0%
CGCCGCCGCTAGCCAGATCG+AGG - chr2_1:1455340-1455359 Msa0186670:CDS 75.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 1455122 1455562 1455122 ID=Msa0186670;Name=Msa0186670
chr2_1 mRNA 1455122 1455562 1455122 ID=Msa0186670-mRNA-1;Parent=Msa0186670;Name=Msa0186670-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|146
chr2_1 exon 1455122 1455562 1455122 ID=Msa0186670-mRNA-1:exon:587;Parent=Msa0186670-mRNA-1
chr2_1 CDS 1455122 1455562 1455122 ID=Msa0186670-mRNA-1:cds;Parent=Msa0186670-mRNA-1
Gene Sequence

>Msa0186670

ATGTCCGACCCGGAAGCCAAACCCGAACAAGACTCCTCCCTCGCTCCACCTCCCTCTACGGAGGCTCCACCGCAACAACCAAATTTCACCGGAAACTACTCCATATGGCCTCCCGCACAACGCACTCGCGACGCCGTCAAAAACCGTTTGATCGAAACACTTTCCACTCCCTCAGTCCTCACCAAACGCTACGGCACAATGTCCGCTGACGAAGCTTCCGCCGCCGCTAGCCAGATCGAGGACGAAGCTTTCTCCGTCGCCGATGCTTCCACTTCCACGGGCAACGATAGCGTTACGATTCTTGAGGTTTACTCGAAGGAGATCAGTAAGCGCATGATCGAAACCGTTAAAGCTAAATCTCGTCTCGCTGATGACGGTAACGCCTCCGTCGGAGCTCCTTCCTCTGCCGCTGATTCCCCCGCTGTTTTGAATCTTGATTGA
Protein sequence

>Msa0186670

MSDPEAKPEQDSSLAPPPSTEAPPQQPNFTGNYSIWPPAQRTRDAVKNRLIETLSTPSVLTKRYGTMSADEASAAASQIEDEAFSVADASTSTGNDSVTILEVYSKEISKRMIETVKAKSRLADDGNASVGAPSSAADSPAVLNLD*