AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0052150

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0052150 MtrunA17_Chr1g0152901 86.301 146 13 1 1 146 1 139 4.57e-86 248
Msa0052150 MtrunA17_Chr3g0134391 60.909 110 41 2 11 119 13 121 2.19e-39 130
Msa0052150 MtrunA17_Chr1g0185561 35.417 96 60 1 24 117 6 101 2.29e-15 72.0
Msa0052150 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
Msa0052150 AT1G47200.1 49.624 133 55 3 1 131 28 150 1.28e-36 124
Msa0052150 AT5G43070.1 51.969 127 55 3 18 139 27 152 2.51e-35 120
Msa0052150 AT5G27940.1 43.878 98 51 2 33 130 51 144 2.57e-21 84.3
Msa0052150 AT3G63130.1 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0052150 AT3G63130.2 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0052150 AT5G19320.1 34.118 85 54 1 35 117 16 100 1.00e-11 61.6
Msa0052150 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 1_2:+6339551 None:intergenic
TCTTGTTCGGGTTTGGCTTC+CGG 0.236651 1_2:+6339550 None:intergenic
GAGTAGTTACCGGTGAAATT+TGG 0.322650 1_2:+6339481 None:intergenic
GGAGGAGTCTTGTTCGGGTT+TGG 0.340745 1_2:+6339543 None:intergenic
AGCGAGGGAGGAGTCTTGTT+CGG 0.384493 1_2:+6339537 None:intergenic
GCGAGGGAGGAGTCTTGTTC+GGG 0.389014 1_2:+6339538 None:intergenic
GCGTTGTGCGGGAGGCCATA+TGG 0.389468 1_2:+6339459 None:intergenic
GCTATCGTTGCCCGTGGAAG+TGG 0.401756 1_2:+6339291 None:intergenic
CTCGATCTGGCTAGCGGCGG+CGG 0.404744 1_2:+6339342 None:intergenic
GAGACGAGATTTAGCTTTAA+CGG 0.420770 1_2:+6339216 None:intergenic
AGAAAGCTTCGTCCTCGATC+TGG 0.425698 1_2:+6339329 None:intergenic
GGACATTGTGCCGTAGCGTT+TGG 0.463221 1_2:+6339378 None:intergenic
GGAGCCTCCGTAGAGGGAGG+TGG 0.466455 1_2:+6339514 None:intergenic
CAATCAAGATTCAAAACAGC+GGG 0.470125 1_2:+6339142 None:intergenic
CCTCGCTCCACCTCCCTCTA+CGG 0.475624 1_2:-6339521 Msa0052150:CDS
TGGAAAGTGTTTCGATCAAA+CGG 0.476905 1_2:+6339416 None:intergenic
GGGGAATCAGCGGCAGAGGA+AGG 0.480076 1_2:+6339163 None:intergenic
GCGTCGCGAGTGCGTTGTGC+GGG 0.482089 1_2:+6339448 None:intergenic
AGAGGGAGGTGGAGCGAGGG+AGG 0.486555 1_2:+6339525 None:intergenic
CGCCGATGCTTCCACTTCCA+CGG 0.489244 1_2:-6339302 Msa0052150:CDS
CGTAGAGGGAGGTGGAGCGA+GGG 0.494922 1_2:+6339522 None:intergenic
TTCGGGTTTGGCTTCCGGGT+CGG 0.497869 1_2:+6339555 None:intergenic
AGGCCATATGGAGTAGTTAC+CGG 0.501206 1_2:+6339471 None:intergenic
TCACCGGTAACTACTCCATA+TGG 0.503114 1_2:-6339474 Msa0052150:CDS
GGCAGAGGAAGGAGCTCCGA+CGG 0.510995 1_2:+6339174 None:intergenic
TTTGGTGAGGACTGAGGGAG+TGG 0.512643 1_2:+6339396 None:intergenic
TGCGGTGGAGCCTCCGTAGA+GGG 0.519645 1_2:+6339508 None:intergenic
GTGAAATTTGGTTGTTGCGG+TGG 0.524980 1_2:+6339493 None:intergenic
TCGCGAGTGCGTTGTGCGGG+AGG 0.530415 1_2:+6339451 None:intergenic
GCCGATGCTTCCACTTCCAC+GGG 0.537590 1_2:-6339301 Msa0052150:CDS
TAGCGTTTGGTGAGGACTGA+GGG 0.560021 1_2:+6339391 None:intergenic
CCGTAGAGGGAGGTGGAGCG+AGG 0.564877 1_2:+6339521 None:intergenic
AAATCTCGTCTCGCTGATGA+CGG 0.565498 1_2:-6339205 Msa0052150:CDS
GCCCGTGGAAGTGGAAGCAT+CGG 0.569170 1_2:+6339300 None:intergenic
CGCTCCACCTCCCTCTACGG+AGG 0.572005 1_2:-6339518 Msa0052150:CDS
GGCGTCGCGAGTGCGTTGTG+CGG 0.572105 1_2:+6339447 None:intergenic
CGATAGCGTTACGATTCTTG+AGG 0.579942 1_2:-6339275 Msa0052150:CDS
GATTCTTGAGGTTTACTCGA+AGG 0.581915 1_2:-6339263 Msa0052150:CDS
CGCCGCCGCTAGCCAGATCG+AGG 0.588312 1_2:-6339341 Msa0052150:CDS
CCGCAACAACCAAATTTCAC+CGG 0.592190 1_2:-6339490 Msa0052150:CDS
CCGGTGAAATTTGGTTGTTG+CGG 0.597792 1_2:+6339490 None:intergenic
GGAAGTGGAAGCATCGGCGA+CGG 0.598077 1_2:+6339306 None:intergenic
GTAGCGTTTGGTGAGGACTG+AGG 0.608047 1_2:+6339390 None:intergenic
AGAGGAAGGAGCTCCGACGG+AGG 0.609670 1_2:+6339177 None:intergenic
GATGACGGTAACGCCTCCGT+CGG 0.613328 1_2:-6339190 Msa0052150:CDS
TTGCGGTGGAGCCTCCGTAG+AGG 0.615033 1_2:+6339507 None:intergenic
TTGTGCCGTAGCGTTTGGTG+AGG 0.632497 1_2:+6339383 None:intergenic
GGCGGCGGAAGCTTCGTCAG+CGG 0.636492 1_2:+6339357 None:intergenic
ATTCCTCACAATGTCCGACC+CGG 0.637935 1_2:-6339569 None:intergenic
GGTGGAGCCTCCGTAGAGGG+AGG 0.638102 1_2:+6339511 None:intergenic
TCAGTCCTCACCAAACGCTA+CGG 0.644599 1_2:-6339388 Msa0052150:CDS
CGTAACGCTATCGTTGCCCG+TGG 0.647560 1_2:+6339285 None:intergenic
TTCGTCCTCGATCTGGCTAG+CGG 0.649591 1_2:+6339336 None:intergenic
ATCAAGATTCAAAACAGCGG+GGG 0.654507 1_2:+6339144 None:intergenic
GTCCTCGATCTGGCTAGCGG+CGG 0.689668 1_2:+6339339 None:intergenic
TCAATCAAGATTCAAAACAG+CGG 0.702532 1_2:+6339141 None:intergenic
AATCAAGATTCAAAACAGCG+GGG 0.726201 1_2:+6339143 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAATCAAGATTCAAAACAG+CGG + chr1_2:6339562-6339581 None:intergenic 30.0%
! TTCGATCAAACGGTTTTTGA+CGG + chr1_2:6339277-6339296 None:intergenic 35.0%
!! TGGAAAGTGTTTCGATCAAA+CGG + chr1_2:6339287-6339306 None:intergenic 35.0%
!! GAGACGAGATTTAGCTTTAA+CGG + chr1_2:6339487-6339506 None:intergenic 35.0%
AATCAAGATTCAAAACAGCG+GGG + chr1_2:6339560-6339579 None:intergenic 35.0%
CAATCAAGATTCAAAACAGC+GGG + chr1_2:6339561-6339580 None:intergenic 35.0%
GAGTAGTTACCGGTGAAATT+TGG + chr1_2:6339222-6339241 None:intergenic 40.0%
GATTCTTGAGGTTTACTCGA+AGG - chr1_2:6339437-6339456 Msa0052150:CDS 40.0%
ATCAAGATTCAAAACAGCGG+GGG + chr1_2:6339559-6339578 None:intergenic 40.0%
GTGAAATTTGGTTGTTGCGG+TGG + chr1_2:6339210-6339229 None:intergenic 45.0%
CCGGTGAAATTTGGTTGTTG+CGG + chr1_2:6339213-6339232 None:intergenic 45.0%
CCGCAACAACCAAATTTCAC+CGG - chr1_2:6339210-6339229 Msa0052150:CDS 45.0%
TCACCGGTAACTACTCCATA+TGG - chr1_2:6339226-6339245 Msa0052150:CDS 45.0%
AGGCCATATGGAGTAGTTAC+CGG + chr1_2:6339232-6339251 None:intergenic 45.0%
CGATAGCGTTACGATTCTTG+AGG - chr1_2:6339425-6339444 Msa0052150:CDS 45.0%
AAATCTCGTCTCGCTGATGA+CGG - chr1_2:6339495-6339514 Msa0052150:CDS 45.0%
! TCTTGTTCGGGTTTGGCTTC+CGG + chr1_2:6339153-6339172 None:intergenic 50.0%
! TAGCGTTTGGTGAGGACTGA+GGG + chr1_2:6339312-6339331 None:intergenic 50.0%
TCAGTCCTCACCAAACGCTA+CGG - chr1_2:6339312-6339331 Msa0052150:CDS 50.0%
AGAAAGCTTCGTCCTCGATC+TGG + chr1_2:6339374-6339393 None:intergenic 50.0%
! CTTGTTCGGGTTTGGCTTCC+GGG + chr1_2:6339152-6339171 None:intergenic 55.0%
!! GGAGGAGTCTTGTTCGGGTT+TGG + chr1_2:6339160-6339179 None:intergenic 55.0%
!! AGCGAGGGAGGAGTCTTGTT+CGG + chr1_2:6339166-6339185 None:intergenic 55.0%
TTTGGTGAGGACTGAGGGAG+TGG + chr1_2:6339307-6339326 None:intergenic 55.0%
! GTAGCGTTTGGTGAGGACTG+AGG + chr1_2:6339313-6339332 None:intergenic 55.0%
! TTGTGCCGTAGCGTTTGGTG+AGG + chr1_2:6339320-6339339 None:intergenic 55.0%
GGACATTGTGCCGTAGCGTT+TGG + chr1_2:6339325-6339344 None:intergenic 55.0%
TTCGTCCTCGATCTGGCTAG+CGG + chr1_2:6339367-6339386 None:intergenic 55.0%
CAAAACAGCGGGGGAATCAG+CGG + chr1_2:6339550-6339569 None:intergenic 55.0%
! TTCGGGTTTGGCTTCCGGGT+CGG + chr1_2:6339148-6339167 None:intergenic 60.0%
!! GCGAGGGAGGAGTCTTGTTC+GGG + chr1_2:6339165-6339184 None:intergenic 60.0%
!! GGAAGTGGAAGCATCGGCGA+CGG + chr1_2:6339397-6339416 None:intergenic 60.0%
CGCCGATGCTTCCACTTCCA+CGG - chr1_2:6339398-6339417 Msa0052150:CDS 60.0%
GCCGATGCTTCCACTTCCAC+GGG - chr1_2:6339399-6339418 Msa0052150:CDS 60.0%
! GCCCGTGGAAGTGGAAGCAT+CGG + chr1_2:6339403-6339422 None:intergenic 60.0%
GCTATCGTTGCCCGTGGAAG+TGG + chr1_2:6339412-6339431 None:intergenic 60.0%
CGTAACGCTATCGTTGCCCG+TGG + chr1_2:6339418-6339437 None:intergenic 60.0%
! GATGACGGTAACGCCTCCGT+CGG - chr1_2:6339510-6339529 Msa0052150:CDS 60.0%
CGTAGAGGGAGGTGGAGCGA+GGG + chr1_2:6339181-6339200 None:intergenic 65.0%
CCTCGCTCCACCTCCCTCTA+CGG - chr1_2:6339179-6339198 Msa0052150:CDS 65.0%
TGCGGTGGAGCCTCCGTAGA+GGG + chr1_2:6339195-6339214 None:intergenic 65.0%
TTGCGGTGGAGCCTCCGTAG+AGG + chr1_2:6339196-6339215 None:intergenic 65.0%
GCGTTGTGCGGGAGGCCATA+TGG + chr1_2:6339244-6339263 None:intergenic 65.0%
GTCCTCGATCTGGCTAGCGG+CGG + chr1_2:6339364-6339383 None:intergenic 65.0%
AGAGGAAGGAGCTCCGACGG+AGG + chr1_2:6339526-6339545 None:intergenic 65.0%
GGCAGAGGAAGGAGCTCCGA+CGG + chr1_2:6339529-6339548 None:intergenic 65.0%
GGGGAATCAGCGGCAGAGGA+AGG + chr1_2:6339540-6339559 None:intergenic 65.0%
AGAGGGAGGTGGAGCGAGGG+AGG + chr1_2:6339178-6339197 None:intergenic 70.0%
CCGTAGAGGGAGGTGGAGCG+AGG + chr1_2:6339182-6339201 None:intergenic 70.0%
CGCTCCACCTCCCTCTACGG+AGG - chr1_2:6339182-6339201 Msa0052150:CDS 70.0%
GGAGCCTCCGTAGAGGGAGG+TGG + chr1_2:6339189-6339208 None:intergenic 70.0%
GGTGGAGCCTCCGTAGAGGG+AGG + chr1_2:6339192-6339211 None:intergenic 70.0%
TCGCGAGTGCGTTGTGCGGG+AGG + chr1_2:6339252-6339271 None:intergenic 70.0%
GCGTCGCGAGTGCGTTGTGC+GGG + chr1_2:6339255-6339274 None:intergenic 70.0%
GGCGTCGCGAGTGCGTTGTG+CGG + chr1_2:6339256-6339275 None:intergenic 70.0%
GGCGGCGGAAGCTTCGTCAG+CGG + chr1_2:6339346-6339365 None:intergenic 70.0%
CTCGATCTGGCTAGCGGCGG+CGG + chr1_2:6339361-6339380 None:intergenic 70.0%
AGCGGGGGAATCAGCGGCAG+AGG + chr1_2:6339544-6339563 None:intergenic 70.0%
CGCCGCCGCTAGCCAGATCG+AGG - chr1_2:6339359-6339378 Msa0052150:CDS 75.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 6339141 6339581 6339141 ID=Msa0052150;Name=Msa0052150
chr1_2 mRNA 6339141 6339581 6339141 ID=Msa0052150-mRNA-1;Parent=Msa0052150;Name=Msa0052150-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|146
chr1_2 exon 6339141 6339581 6339141 ID=Msa0052150-mRNA-1:exon:2029;Parent=Msa0052150-mRNA-1
chr1_2 CDS 6339141 6339581 6339141 ID=Msa0052150-mRNA-1:cds;Parent=Msa0052150-mRNA-1
Gene Sequence

>Msa0052150

ATGTCCGACCCGGAAGCCAAACCCGAACAAGACTCCTCCCTCGCTCCACCTCCCTCTACGGAGGCTCCACCGCAACAACCAAATTTCACCGGTAACTACTCCATATGGCCTCCCGCACAACGCACTCGCGACGCCGTCAAAAACCGTTTGATCGAAACACTTTCCACTCCCTCAGTCCTCACCAAACGCTACGGCACAATGTCCGCTGACGAAGCTTCCGCCGCCGCTAGCCAGATCGAGGACGAAGCTTTCTCCGTCGCCGATGCTTCCACTTCCACGGGCAACGATAGCGTTACGATTCTTGAGGTTTACTCGAAGGAGATCAGTAAGCGCATGATCGAAACCGTTAAAGCTAAATCTCGTCTCGCTGATGACGGTAACGCCTCCGTCGGAGCTCCTTCCTCTGCCGCTGATTCCCCCGCTGTTTTGAATCTTGATTGA
Protein sequence

>Msa0052150

MSDPEAKPEQDSSLAPPPSTEAPPQQPNFTGNYSIWPPAQRTRDAVKNRLIETLSTPSVLTKRYGTMSADEASAAASQIEDEAFSVADASTSTGNDSVTILEVYSKEISKRMIETVKAKSRLADDGNASVGAPSSAADSPAVLNLD*