AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0033630


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0033630 MtrunA17_Chr4g0023901 96.364 55 2 0 1 55 1 55 1.09e-32 107
Msa0033630 MtrunA17_Chr2g0281741 64.835 91 16 3 1 84 1 82 3.98e-29 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 54 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGTAGCCATAACTGTAAT+AGG 0.226353 1_1:-61230505 None:intergenic
TTGTTTGTTTGGTGGAAGTT+GGG 0.310395 1_1:-61230297 None:intergenic
CCTCACCCCGACCGTCCTCC+TGG 0.346667 1_1:+61230459 Msa0033630:CDS
ATTGTTTGTTTGGTGGAAGT+TGG 0.347178 1_1:-61230298 None:intergenic
TTCGGTCATGATTGTTTGTT+TGG 0.366531 1_1:-61230308 None:intergenic
CCAGGAGGACGGTCGGGGTG+AGG 0.369145 1_1:-61230459 None:intergenic
TAAGGGTTAGGGTGAAGAGG+TGG 0.375340 1_1:-61230419 None:intergenic
TCGGATCCAGGAGGACGGTC+GGG 0.380838 1_1:-61230465 None:intergenic
GGGGCGGAGGGGTCGGATCC+AGG 0.386026 1_1:-61230477 None:intergenic
ACCGATCTGGAGTGAATTCA+TGG 0.400497 1_1:-61230247 None:intergenic
GGATTTGAGTTTGCCGTGTT+CGG 0.412366 1_1:-61230326 None:intergenic
GGTGAGGGAAACCGATGGCG+GGG 0.413789 1_1:-61230443 None:intergenic
GATTGCGGCGACGGCGGAGG+AGG 0.416666 1_1:-61230361 None:intergenic
AGGGTGAAGAGGTGGGAAAT+TGG 0.418104 1_1:-61230411 None:intergenic
GGGTGAGGGAAACCGATGGC+GGG 0.424253 1_1:-61230444 None:intergenic
TGTTTGTTTGGTGGAAGTTG+GGG 0.425035 1_1:-61230296 None:intergenic
CGGATCCAGGAGGACGGTCG+GGG 0.433438 1_1:-61230464 None:intergenic
GTAATAGGGAGGAGGGGCGG+AGG 0.435218 1_1:-61230490 None:intergenic
CCTCCTCCCTATTACAGTTA+TGG 0.441098 1_1:+61230498 Msa0033630:CDS
AACGAAGCCACTCACCGATC+TGG 0.446314 1_1:-61230260 None:intergenic
GGGGTGAGGGAAACCGATGG+CGG 0.446566 1_1:-61230445 None:intergenic
GGGTAAGGGTTAGGGTGAAG+AGG 0.448412 1_1:-61230422 None:intergenic
GGGAGGAGGGGCGGAGGGGT+CGG 0.470296 1_1:-61230484 None:intergenic
TAGTAGCCATAACTGTAATA+GGG 0.470585 1_1:-61230504 None:intergenic
GTGAGGGAAACCGATGGCGG+GGG 0.471021 1_1:-61230442 None:intergenic
CAGGAGGACGGTCGGGGTGA+GGG 0.471785 1_1:-61230458 None:intergenic
CGGAGGAGGGTGGCCGAAGT+AGG 0.477759 1_1:-61230347 None:intergenic
AATAGGGAGGAGGGGCGGAG+GGG 0.479253 1_1:-61230488 None:intergenic
GGTTGAAAGGATTGCGGCGA+CGG 0.493819 1_1:-61230370 None:intergenic
GTCGGATCCAGGAGGACGGT+CGG 0.498258 1_1:-61230466 None:intergenic
TAATAGGGAGGAGGGGCGGA+GGG 0.504583 1_1:-61230489 None:intergenic
AAGGATTGCGGCGACGGCGG+AGG 0.507727 1_1:-61230364 None:intergenic
AAGGGTTAGGGTGAAGAGGT+GGG 0.523980 1_1:-61230418 None:intergenic
GCGGCGACGGCGGAGGAGGG+TGG 0.525558 1_1:-61230357 None:intergenic
GTTTGTTTGGTGGAAGTTGG+GGG 0.531733 1_1:-61230295 None:intergenic
GGTCATGATTGTTTGTTTGG+TGG 0.539968 1_1:-61230305 None:intergenic
CATAACTGTAATAGGGAGGA+GGG 0.545322 1_1:-61230497 None:intergenic
CTCGTACTGAGGAGGTTGAA+AGG 0.548056 1_1:-61230383 None:intergenic
ATTGCGGCGACGGCGGAGGA+GGG 0.550016 1_1:-61230360 None:intergenic
CCATAACTGTAATAGGGAGG+AGG 0.554457 1_1:-61230498 None:intergenic
CAAACAATCATGACCGAACA+CGG 0.568465 1_1:+61230313 Msa0033630:CDS
GGCAAACTCAAATCCTACTT+CGG 0.572114 1_1:+61230334 Msa0033630:CDS
GCGGAGGGGTCGGATCCAGG+AGG 0.575604 1_1:-61230474 None:intergenic
TGAAAGGATTGCGGCGACGG+CGG 0.584093 1_1:-61230367 None:intergenic
AGGGGTCGGATCCAGGAGGA+CGG 0.585435 1_1:-61230470 None:intergenic
AATTGGAAAGACTCGTACTG+AGG 0.630700 1_1:-61230394 None:intergenic
TCCATGAATTCACTCCAGAT+CGG 0.641820 1_1:+61230246 None:intergenic
GTCGGGGTGAGGGAAACCGA+TGG 0.644761 1_1:-61230448 None:intergenic
ACTGTAATAGGGAGGAGGGG+CGG 0.647217 1_1:-61230493 None:intergenic
TGGAAAGACTCGTACTGAGG+AGG 0.658466 1_1:-61230391 None:intergenic
TGAGGAGGTTGAAAGGATTG+CGG 0.659256 1_1:-61230376 None:intergenic
TAGCCATAACTGTAATAGGG+AGG 0.673963 1_1:-61230501 None:intergenic
ATTCACTCCAGATCGGTGAG+TGG 0.692086 1_1:+61230253 Msa0033630:CDS
ATAACTGTAATAGGGAGGAG+GGG 0.695524 1_1:-61230496 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TAGTAGCCATAACTGTAATA+GGG - chr1_1:61230507-61230526 None:intergenic 30.0%
TTAGTAGCCATAACTGTAAT+AGG - chr1_1:61230508-61230527 None:intergenic 30.0%
! TTGTTTGTTTGGTGGAAGTT+GGG - chr1_1:61230300-61230319 None:intergenic 35.0%
! ATTGTTTGTTTGGTGGAAGT+TGG - chr1_1:61230301-61230320 None:intergenic 35.0%
TTCGGTCATGATTGTTTGTT+TGG - chr1_1:61230311-61230330 None:intergenic 35.0%
! TGTTTGTTTGGTGGAAGTTG+GGG - chr1_1:61230299-61230318 None:intergenic 40.0%
GGTCATGATTGTTTGTTTGG+TGG - chr1_1:61230308-61230327 None:intergenic 40.0%
CAAACAATCATGACCGAACA+CGG + chr1_1:61230313-61230332 Msa0033630:CDS 40.0%
GGCAAACTCAAATCCTACTT+CGG + chr1_1:61230334-61230353 Msa0033630:CDS 40.0%
AATTGGAAAGACTCGTACTG+AGG - chr1_1:61230397-61230416 None:intergenic 40.0%
ATAACTGTAATAGGGAGGAG+GGG - chr1_1:61230499-61230518 None:intergenic 40.0%
CATAACTGTAATAGGGAGGA+GGG - chr1_1:61230500-61230519 None:intergenic 40.0%
TAGCCATAACTGTAATAGGG+AGG - chr1_1:61230504-61230523 None:intergenic 40.0%
! GTTTGTTTGGTGGAAGTTGG+GGG - chr1_1:61230298-61230317 None:intergenic 45.0%
! GGATTTGAGTTTGCCGTGTT+CGG - chr1_1:61230329-61230348 None:intergenic 45.0%
TGAGGAGGTTGAAAGGATTG+CGG - chr1_1:61230379-61230398 None:intergenic 45.0%
CCATAACTGTAATAGGGAGG+AGG - chr1_1:61230501-61230520 None:intergenic 45.0%
CCTCCTCCCTATTACAGTTA+TGG + chr1_1:61230498-61230517 Msa0033630:CDS 45.0%
ATTCACTCCAGATCGGTGAG+TGG + chr1_1:61230253-61230272 Msa0033630:CDS 50.0%
TTTGGTGGAAGTTGGGGGTT+AGG - chr1_1:61230293-61230312 None:intergenic 50.0%
CTCGTACTGAGGAGGTTGAA+AGG - chr1_1:61230386-61230405 None:intergenic 50.0%
TGGAAAGACTCGTACTGAGG+AGG - chr1_1:61230394-61230413 None:intergenic 50.0%
AGGGTGAAGAGGTGGGAAAT+TGG - chr1_1:61230414-61230433 None:intergenic 50.0%
AAGGGTTAGGGTGAAGAGGT+GGG - chr1_1:61230421-61230440 None:intergenic 50.0%
TAAGGGTTAGGGTGAAGAGG+TGG - chr1_1:61230422-61230441 None:intergenic 50.0%
AACGAAGCCACTCACCGATC+TGG - chr1_1:61230263-61230282 None:intergenic 55.0%
GTGGAAGTTGGGGGTTAGGA+GGG - chr1_1:61230289-61230308 None:intergenic 55.0%
GGTTGAAAGGATTGCGGCGA+CGG - chr1_1:61230373-61230392 None:intergenic 55.0%
GGGTAAGGGTTAGGGTGAAG+AGG - chr1_1:61230425-61230444 None:intergenic 55.0%
ACTGTAATAGGGAGGAGGGG+CGG - chr1_1:61230496-61230515 None:intergenic 55.0%
GGTGGAAGTTGGGGGTTAGG+AGG - chr1_1:61230290-61230309 None:intergenic 60.0%
TGAAAGGATTGCGGCGACGG+CGG - chr1_1:61230370-61230389 None:intergenic 60.0%
!! GATGGCGGGGGTAAGGGTTA+GGG - chr1_1:61230433-61230452 None:intergenic 60.0%
CTAACCCTTACCCCCGCCAT+CGG + chr1_1:61230432-61230451 Msa0033630:CDS 60.0%
!! GAAACCGATGGCGGGGGTAA+GGG - chr1_1:61230439-61230458 None:intergenic 60.0%
TAATAGGGAGGAGGGGCGGA+GGG - chr1_1:61230492-61230511 None:intergenic 60.0%
!! CGATGGCGGGGGTAAGGGTT+AGG - chr1_1:61230434-61230453 None:intergenic 65.0%
!! GGAAACCGATGGCGGGGGTA+AGG - chr1_1:61230440-61230459 None:intergenic 65.0%
! GTGAGGGAAACCGATGGCGG+GGG - chr1_1:61230445-61230464 None:intergenic 65.0%
GGTGAGGGAAACCGATGGCG+GGG - chr1_1:61230446-61230465 None:intergenic 65.0%
GGGTGAGGGAAACCGATGGC+GGG - chr1_1:61230447-61230466 None:intergenic 65.0%
GGGGTGAGGGAAACCGATGG+CGG - chr1_1:61230448-61230467 None:intergenic 65.0%
GTCGGGGTGAGGGAAACCGA+TGG - chr1_1:61230451-61230470 None:intergenic 65.0%
TCGGATCCAGGAGGACGGTC+GGG - chr1_1:61230468-61230487 None:intergenic 65.0%
GTCGGATCCAGGAGGACGGT+CGG - chr1_1:61230469-61230488 None:intergenic 65.0%
AGGGGTCGGATCCAGGAGGA+CGG - chr1_1:61230473-61230492 None:intergenic 65.0%
AATAGGGAGGAGGGGCGGAG+GGG - chr1_1:61230491-61230510 None:intergenic 65.0%
GTAATAGGGAGGAGGGGCGG+AGG - chr1_1:61230493-61230512 None:intergenic 65.0%
CGGAGGAGGGTGGCCGAAGT+AGG - chr1_1:61230350-61230369 None:intergenic 70.0%
ATTGCGGCGACGGCGGAGGA+GGG - chr1_1:61230363-61230382 None:intergenic 70.0%
AAGGATTGCGGCGACGGCGG+AGG - chr1_1:61230367-61230386 None:intergenic 70.0%
CAGGAGGACGGTCGGGGTGA+GGG - chr1_1:61230461-61230480 None:intergenic 70.0%
CGGATCCAGGAGGACGGTCG+GGG - chr1_1:61230467-61230486 None:intergenic 70.0%
GATTGCGGCGACGGCGGAGG+AGG - chr1_1:61230364-61230383 None:intergenic 75.0%
CCAGGAGGACGGTCGGGGTG+AGG - chr1_1:61230462-61230481 None:intergenic 75.0%
CCTCACCCCGACCGTCCTCC+TGG + chr1_1:61230459-61230478 Msa0033630:CDS 75.0%
GCGGAGGGGTCGGATCCAGG+AGG - chr1_1:61230477-61230496 None:intergenic 75.0%
! GGGGCGGAGGGGTCGGATCC+AGG - chr1_1:61230480-61230499 None:intergenic 80.0%
! GGGAGGAGGGGCGGAGGGGT+CGG - chr1_1:61230487-61230506 None:intergenic 80.0%
! GCGGCGACGGCGGAGGAGGG+TGG - chr1_1:61230360-61230379 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 61230249 61230527 61230249 ID=Msa0033630;Name=Msa0033630
chr1_1 mRNA 61230249 61230527 61230249 ID=Msa0033630-mRNA-1;Parent=Msa0033630;Name=Msa0033630-mRNA-1;_AED=0.43;_eAED=0.50;_QI=0|-1|0|1|-1|1|1|0|92
chr1_1 exon 61230249 61230527 61230249 ID=Msa0033630-mRNA-1:exon:19218;Parent=Msa0033630-mRNA-1
chr1_1 CDS 61230249 61230527 61230249 ID=Msa0033630-mRNA-1:cds;Parent=Msa0033630-mRNA-1
Gene Sequence

>Msa0033630

ATGAATTCACTCCAGATCGGTGAGTGGCTTCGTTCTTCCCTCCTAACCCCCAACTTCCACCAAACAAACAATCATGACCGAACACGGCAAACTCAAATCCTACTTCGGCCACCCTCCTCCGCCGTCGCCGCAATCCTTTCAACCTCCTCAGTACGAGTCTTTCCAATTTCCCACCTCTTCACCCTAACCCTTACCCCCGCCATCGGTTTCCCTCACCCCGACCGTCCTCCTGGATCCGACCCCTCCGCCCCTCCTCCCTATTACAGTTATGGCTACTAA

Protein sequence

>Msa0033630

MNSLQIGEWLRSSLLTPNFHQTNNHDRTRQTQILLRPPSSAVAAILSTSSVRVFPISHLFTLTLTPAIGFPHPDRPPGSDPSAPPPYYSYGY*