AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0097120

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097120 MtrunA17_Chr1g0152901 86.301 146 13 1 1 146 1 139 4.57e-86 248
Msa0097120 MtrunA17_Chr3g0134391 60.909 110 41 2 11 119 13 121 2.19e-39 130
Msa0097120 MtrunA17_Chr1g0185561 35.417 96 60 1 24 117 6 101 2.29e-15 72.0
Msa0097120 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
Msa0097120 AT1G47200.1 49.624 133 55 3 1 131 28 150 1.28e-36 124
Msa0097120 AT5G43070.1 51.969 127 55 3 18 139 27 152 2.51e-35 120
Msa0097120 AT5G27940.1 43.878 98 51 2 33 130 51 144 2.57e-21 84.3
Msa0097120 AT3G63130.1 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0097120 AT3G63130.2 35.294 85 53 1 35 117 17 101 2.69e-13 66.2
Msa0097120 AT5G19320.1 34.118 85 54 1 35 117 16 100 1.00e-11 61.6
Msa0097120 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_3:+2956648 None:intergenic
TCTTGTTCGGGTTTGGCTTC+CGG 0.236651 1_3:+2956647 None:intergenic
GAGTAGTTTCCGGTGAAATT+TGG 0.305396 1_3:+2956578 None:intergenic
GGAGGAGTCTTGTTCGGGTT+TGG 0.340745 1_3:+2956640 None:intergenic
AGCGAGGGAGGAGTCTTGTT+CGG 0.384493 1_3:+2956634 None:intergenic
GCGAGGGAGGAGTCTTGTTC+GGG 0.389014 1_3:+2956635 None:intergenic
GCGTTGTGCGGGAGGCCATA+TGG 0.389468 1_3:+2956556 None:intergenic
GCTATCGTTGCCCGTGGAAG+TGG 0.401756 1_3:+2956388 None:intergenic
CTCGATCTGGCTAGCGGCGG+CGG 0.404744 1_3:+2956439 None:intergenic
AGGCCATATGGAGTAGTTTC+CGG 0.410196 1_3:+2956568 None:intergenic
GAGACGAGATTTAGCTTTAA+CGG 0.420770 1_3:+2956313 None:intergenic
AGAAAGCTTCGTCCTCGATC+TGG 0.425698 1_3:+2956426 None:intergenic
GGACATTGTGCCGTAGCGTT+TGG 0.463221 1_3:+2956475 None:intergenic
GGAGCCTCCGTAGAGGGAGG+TGG 0.466455 1_3:+2956611 None:intergenic
CAATCAAGATTCAAAACAGC+GGG 0.470125 1_3:+2956239 None:intergenic
CCTCGCTCCACCTCCCTCTA+CGG 0.475624 1_3:-2956618 Msa0097120:CDS
TGGAAAGTGTTTCGATCAAA+CGG 0.476905 1_3:+2956513 None:intergenic
GGGGAATCAGCGGCAGAGGA+AGG 0.480076 1_3:+2956260 None:intergenic
TCACCGGAAACTACTCCATA+TGG 0.480969 1_3:-2956571 Msa0097120:CDS
GCGTCGCGAGTGCGTTGTGC+GGG 0.482089 1_3:+2956545 None:intergenic
AGAGGGAGGTGGAGCGAGGG+AGG 0.486555 1_3:+2956622 None:intergenic
CGCCGATGCTTCCACTTCCA+CGG 0.489244 1_3:-2956399 Msa0097120:CDS
CGTAGAGGGAGGTGGAGCGA+GGG 0.494922 1_3:+2956619 None:intergenic
TTCGGGTTTGGCTTCCGGGT+CGG 0.497869 1_3:+2956652 None:intergenic
GGCAGAGGAAGGAGCTCCGA+CGG 0.510995 1_3:+2956271 None:intergenic
TTTGGTGAGGACTGAGGGAG+TGG 0.512643 1_3:+2956493 None:intergenic
TGCGGTGGAGCCTCCGTAGA+GGG 0.519645 1_3:+2956605 None:intergenic
GTGAAATTTGGTTGTTGCGG+TGG 0.524980 1_3:+2956590 None:intergenic
TCGCGAGTGCGTTGTGCGGG+AGG 0.530415 1_3:+2956548 None:intergenic
GCCGATGCTTCCACTTCCAC+GGG 0.537590 1_3:-2956398 Msa0097120:CDS
TAGCGTTTGGTGAGGACTGA+GGG 0.560021 1_3:+2956488 None:intergenic
CCGTAGAGGGAGGTGGAGCG+AGG 0.564877 1_3:+2956618 None:intergenic
AAATCTCGTCTCGCTGATGA+CGG 0.565498 1_3:-2956302 Msa0097120:CDS
GCCCGTGGAAGTGGAAGCAT+CGG 0.569170 1_3:+2956397 None:intergenic
CGCTCCACCTCCCTCTACGG+AGG 0.572005 1_3:-2956615 Msa0097120:CDS
GGCGTCGCGAGTGCGTTGTG+CGG 0.572105 1_3:+2956544 None:intergenic
CCGCAACAACCAAATTTCAC+CGG 0.575174 1_3:-2956587 Msa0097120:CDS
CGATAGCGTTACGATTCTTG+AGG 0.579942 1_3:-2956372 Msa0097120:CDS
GATTCTTGAGGTTTACTCGA+AGG 0.581915 1_3:-2956360 Msa0097120:CDS
CCGGTGAAATTTGGTTGTTG+CGG 0.585855 1_3:+2956587 None:intergenic
CGCCGCCGCTAGCCAGATCG+AGG 0.588312 1_3:-2956438 Msa0097120:CDS
GGAAGTGGAAGCATCGGCGA+CGG 0.598077 1_3:+2956403 None:intergenic
GTAGCGTTTGGTGAGGACTG+AGG 0.608047 1_3:+2956487 None:intergenic
AGAGGAAGGAGCTCCGACGG+AGG 0.609670 1_3:+2956274 None:intergenic
GATGACGGTAACGCCTCCGT+CGG 0.613328 1_3:-2956287 Msa0097120:CDS
TTGCGGTGGAGCCTCCGTAG+AGG 0.615033 1_3:+2956604 None:intergenic
TTGTGCCGTAGCGTTTGGTG+AGG 0.632497 1_3:+2956480 None:intergenic
GGCGGCGGAAGCTTCGTCAG+CGG 0.636492 1_3:+2956454 None:intergenic
ATTCCTCACAATGTCCGACC+CGG 0.637935 1_3:-2956666 None:intergenic
GGTGGAGCCTCCGTAGAGGG+AGG 0.638102 1_3:+2956608 None:intergenic
TCAGTCCTCACCAAACGCTA+CGG 0.644599 1_3:-2956485 Msa0097120:CDS
CGTAACGCTATCGTTGCCCG+TGG 0.647560 1_3:+2956382 None:intergenic
TTCGTCCTCGATCTGGCTAG+CGG 0.649591 1_3:+2956433 None:intergenic
ATCAAGATTCAAAACAGCGG+GGG 0.654507 1_3:+2956241 None:intergenic
GTCCTCGATCTGGCTAGCGG+CGG 0.689668 1_3:+2956436 None:intergenic
TCAATCAAGATTCAAAACAG+CGG 0.702532 1_3:+2956238 None:intergenic
AATCAAGATTCAAAACAGCG+GGG 0.726201 1_3:+2956240 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAATCAAGATTCAAAACAG+CGG + chr1_3:2956659-2956678 None:intergenic 30.0%
! TTCGATCAAACGGTTTTTGA+CGG + chr1_3:2956374-2956393 None:intergenic 35.0%
!! TGGAAAGTGTTTCGATCAAA+CGG + chr1_3:2956384-2956403 None:intergenic 35.0%
!! GAGACGAGATTTAGCTTTAA+CGG + chr1_3:2956584-2956603 None:intergenic 35.0%
AATCAAGATTCAAAACAGCG+GGG + chr1_3:2956657-2956676 None:intergenic 35.0%
CAATCAAGATTCAAAACAGC+GGG + chr1_3:2956658-2956677 None:intergenic 35.0%
GAGTAGTTTCCGGTGAAATT+TGG + chr1_3:2956319-2956338 None:intergenic 40.0%
GATTCTTGAGGTTTACTCGA+AGG - chr1_3:2956534-2956553 Msa0097120:CDS 40.0%
ATCAAGATTCAAAACAGCGG+GGG + chr1_3:2956656-2956675 None:intergenic 40.0%
GTGAAATTTGGTTGTTGCGG+TGG + chr1_3:2956307-2956326 None:intergenic 45.0%
CCGGTGAAATTTGGTTGTTG+CGG + chr1_3:2956310-2956329 None:intergenic 45.0%
CCGCAACAACCAAATTTCAC+CGG - chr1_3:2956307-2956326 Msa0097120:CDS 45.0%
TCACCGGAAACTACTCCATA+TGG - chr1_3:2956323-2956342 Msa0097120:CDS 45.0%
AGGCCATATGGAGTAGTTTC+CGG + chr1_3:2956329-2956348 None:intergenic 45.0%
CGATAGCGTTACGATTCTTG+AGG - chr1_3:2956522-2956541 Msa0097120:CDS 45.0%
AAATCTCGTCTCGCTGATGA+CGG - chr1_3:2956592-2956611 Msa0097120:CDS 45.0%
! TCTTGTTCGGGTTTGGCTTC+CGG + chr1_3:2956250-2956269 None:intergenic 50.0%
! TAGCGTTTGGTGAGGACTGA+GGG + chr1_3:2956409-2956428 None:intergenic 50.0%
TCAGTCCTCACCAAACGCTA+CGG - chr1_3:2956409-2956428 Msa0097120:CDS 50.0%
AGAAAGCTTCGTCCTCGATC+TGG + chr1_3:2956471-2956490 None:intergenic 50.0%
! CTTGTTCGGGTTTGGCTTCC+GGG + chr1_3:2956249-2956268 None:intergenic 55.0%
!! GGAGGAGTCTTGTTCGGGTT+TGG + chr1_3:2956257-2956276 None:intergenic 55.0%
!! AGCGAGGGAGGAGTCTTGTT+CGG + chr1_3:2956263-2956282 None:intergenic 55.0%
TTTGGTGAGGACTGAGGGAG+TGG + chr1_3:2956404-2956423 None:intergenic 55.0%
! GTAGCGTTTGGTGAGGACTG+AGG + chr1_3:2956410-2956429 None:intergenic 55.0%
! TTGTGCCGTAGCGTTTGGTG+AGG + chr1_3:2956417-2956436 None:intergenic 55.0%
GGACATTGTGCCGTAGCGTT+TGG + chr1_3:2956422-2956441 None:intergenic 55.0%
TTCGTCCTCGATCTGGCTAG+CGG + chr1_3:2956464-2956483 None:intergenic 55.0%
CAAAACAGCGGGGGAATCAG+CGG + chr1_3:2956647-2956666 None:intergenic 55.0%
! TTCGGGTTTGGCTTCCGGGT+CGG + chr1_3:2956245-2956264 None:intergenic 60.0%
!! GCGAGGGAGGAGTCTTGTTC+GGG + chr1_3:2956262-2956281 None:intergenic 60.0%
!! GGAAGTGGAAGCATCGGCGA+CGG + chr1_3:2956494-2956513 None:intergenic 60.0%
CGCCGATGCTTCCACTTCCA+CGG - chr1_3:2956495-2956514 Msa0097120:CDS 60.0%
GCCGATGCTTCCACTTCCAC+GGG - chr1_3:2956496-2956515 Msa0097120:CDS 60.0%
! GCCCGTGGAAGTGGAAGCAT+CGG + chr1_3:2956500-2956519 None:intergenic 60.0%
GCTATCGTTGCCCGTGGAAG+TGG + chr1_3:2956509-2956528 None:intergenic 60.0%
CGTAACGCTATCGTTGCCCG+TGG + chr1_3:2956515-2956534 None:intergenic 60.0%
! GATGACGGTAACGCCTCCGT+CGG - chr1_3:2956607-2956626 Msa0097120:CDS 60.0%
CGTAGAGGGAGGTGGAGCGA+GGG + chr1_3:2956278-2956297 None:intergenic 65.0%
CCTCGCTCCACCTCCCTCTA+CGG - chr1_3:2956276-2956295 Msa0097120:CDS 65.0%
TGCGGTGGAGCCTCCGTAGA+GGG + chr1_3:2956292-2956311 None:intergenic 65.0%
TTGCGGTGGAGCCTCCGTAG+AGG + chr1_3:2956293-2956312 None:intergenic 65.0%
GCGTTGTGCGGGAGGCCATA+TGG + chr1_3:2956341-2956360 None:intergenic 65.0%
GTCCTCGATCTGGCTAGCGG+CGG + chr1_3:2956461-2956480 None:intergenic 65.0%
AGAGGAAGGAGCTCCGACGG+AGG + chr1_3:2956623-2956642 None:intergenic 65.0%
GGCAGAGGAAGGAGCTCCGA+CGG + chr1_3:2956626-2956645 None:intergenic 65.0%
GGGGAATCAGCGGCAGAGGA+AGG + chr1_3:2956637-2956656 None:intergenic 65.0%
AGAGGGAGGTGGAGCGAGGG+AGG + chr1_3:2956275-2956294 None:intergenic 70.0%
CCGTAGAGGGAGGTGGAGCG+AGG + chr1_3:2956279-2956298 None:intergenic 70.0%
CGCTCCACCTCCCTCTACGG+AGG - chr1_3:2956279-2956298 Msa0097120:CDS 70.0%
GGAGCCTCCGTAGAGGGAGG+TGG + chr1_3:2956286-2956305 None:intergenic 70.0%
GGTGGAGCCTCCGTAGAGGG+AGG + chr1_3:2956289-2956308 None:intergenic 70.0%
TCGCGAGTGCGTTGTGCGGG+AGG + chr1_3:2956349-2956368 None:intergenic 70.0%
GCGTCGCGAGTGCGTTGTGC+GGG + chr1_3:2956352-2956371 None:intergenic 70.0%
GGCGTCGCGAGTGCGTTGTG+CGG + chr1_3:2956353-2956372 None:intergenic 70.0%
GGCGGCGGAAGCTTCGTCAG+CGG + chr1_3:2956443-2956462 None:intergenic 70.0%
CTCGATCTGGCTAGCGGCGG+CGG + chr1_3:2956458-2956477 None:intergenic 70.0%
AGCGGGGGAATCAGCGGCAG+AGG + chr1_3:2956641-2956660 None:intergenic 70.0%
CGCCGCCGCTAGCCAGATCG+AGG - chr1_3:2956456-2956475 Msa0097120:CDS 75.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 2956238 2956678 2956238 ID=Msa0097120;Name=Msa0097120
chr1_3 mRNA 2956238 2956678 2956238 ID=Msa0097120-mRNA-1;Parent=Msa0097120;Name=Msa0097120-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|146
chr1_3 exon 2956238 2956678 2956238 ID=Msa0097120-mRNA-1:exon:818;Parent=Msa0097120-mRNA-1
chr1_3 CDS 2956238 2956678 2956238 ID=Msa0097120-mRNA-1:cds;Parent=Msa0097120-mRNA-1
Gene Sequence

>Msa0097120

ATGTCCGACCCGGAAGCCAAACCCGAACAAGACTCCTCCCTCGCTCCACCTCCCTCTACGGAGGCTCCACCGCAACAACCAAATTTCACCGGAAACTACTCCATATGGCCTCCCGCACAACGCACTCGCGACGCCGTCAAAAACCGTTTGATCGAAACACTTTCCACTCCCTCAGTCCTCACCAAACGCTACGGCACAATGTCCGCTGACGAAGCTTCCGCCGCCGCTAGCCAGATCGAGGACGAAGCTTTCTCCGTCGCCGATGCTTCCACTTCCACGGGCAACGATAGCGTTACGATTCTTGAGGTTTACTCGAAGGAGATCAGTAAGCGCATGATCGAAACCGTTAAAGCTAAATCTCGTCTCGCTGATGACGGTAACGCCTCCGTCGGAGCTCCTTCCTCTGCCGCTGATTCCCCCGCTGTTTTGAATCTTGATTGA
Protein sequence

>Msa0097120

MSDPEAKPEQDSSLAPPPSTEAPPQQPNFTGNYSIWPPAQRTRDAVKNRLIETLSTPSVLTKRYGTMSADEASAAASQIEDEAFSVADASTSTGNDSVTILEVYSKEISKRMIETVKAKSRLADDGNASVGAPSSAADSPAVLNLD*