AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580025552.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580025552.01.T01 MTR_5g030310 100.000 58 0 0 12 69 63 120 3.72e-36 117
MsG0580025552.01.T01 MTR_5g430440 100.000 58 0 0 12 69 63 120 4.24e-36 117
MsG0580025552.01.T01 MTR_5g430430 79.310 58 12 0 12 69 63 120 1.16e-28 99.0
MsG0580025552.01.T01 MTR_5g030290 79.310 58 12 0 12 69 63 120 1.16e-28 99.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATATCATTCTAAGAATA+TGG 0.288449 5:-20360266 MsG0580025552.01.T01:exon
TTACAGACCAATAGCATAGT+AGG 0.341240 5:+20359254 None:intergenic
AGGGCCTTCAGTCTTGAAAA+TGG 0.356723 5:+20359362 None:intergenic
AATTGACCCTACTATGCTAT+TGG 0.392442 5:-20359261 MsG0580025552.01.T01:three_prime_UTR
TTATGCAGTGATGGTGGAGC+TGG 0.397441 5:-20359459 MsG0580025552.01.T01:intron
CTTGCTCTTGAGTGAAGCTC+TGG 0.411535 5:+20360239 None:intergenic
TCACTGCTACTCTCAATAAC+TGG 0.438274 5:+20359432 None:intergenic
CCCTTGCCAGAGTTTACACC+AGG 0.459349 5:+20359342 None:intergenic
AATAGCATAGTAGGGTCAAT+TGG 0.465116 5:+20359263 None:intergenic
TGTGCCATCAGTTATGAAGT+TGG 0.489271 5:-20359193 MsG0580025552.01.T01:three_prime_UTR
TTAAGCAGCAGTGTGATGTT+TGG 0.514503 5:-20359151 MsG0580025552.01.T01:three_prime_UTR
TACAGACCAATAGCATAGTA+GGG 0.519482 5:+20359255 None:intergenic
CCCTGGTGTAAACTCTGGCA+AGG 0.541663 5:-20359343 MsG0580025552.01.T01:CDS
TATGCAGTGATGGTGGAGCT+GGG 0.557903 5:-20359458 MsG0580025552.01.T01:intron
ACATTCTGCAAGTGTGGTGA+AGG 0.561546 5:-20359396 MsG0580025552.01.T01:CDS
ATTGAGAGTAGCAGTGACAA+TGG 0.563224 5:-20359426 MsG0580025552.01.T01:CDS
CAGAGCTTCACTCAAGAGCA+AGG 0.567749 5:-20360238 MsG0580025552.01.T01:CDS
TTGCTCTTGAGTGAAGCTCT+GGG 0.573531 5:+20360240 None:intergenic
CAAACCAACTTCATAACTGA+TGG 0.577062 5:+20359189 None:intergenic
AAACTCTTATGCAGTGATGG+TGG 0.602169 5:-20359465 MsG0580025552.01.T01:intron
GAAGGCCCTGGTGTAAACTC+TGG 0.603912 5:-20359348 MsG0580025552.01.T01:CDS
CCTGGTGTAAACTCTGGCAA+GGG 0.620143 5:-20359342 MsG0580025552.01.T01:CDS
AGAGCTTCACTCAAGAGCAA+GGG 0.651871 5:-20360237 MsG0580025552.01.T01:intron
TCTGCAAGTGTGGTGAAGGG+TGG 0.652623 5:-20359392 MsG0580025552.01.T01:CDS
AGTGAAACATTCTGCAAGTG+TGG 0.671634 5:-20359402 MsG0580025552.01.T01:CDS
CATTCTGCAAGTGTGGTGAA+GGG 0.681189 5:-20359395 MsG0580025552.01.T01:CDS
CCTTGCCAGAGTTTACACCA+GGG 0.773669 5:+20359343 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAATTGTACTAAATAA+AGG - Chr5:20360174-20360193 MsG0580025552.01.T01:intron 10.0%
!! AAAAAATTGTACTAAATAAA+GGG - Chr5:20360175-20360194 MsG0580025552.01.T01:intron 10.0%
!! TTAATTATTTGTTTGTAATA+TGG - Chr5:20359643-20359662 MsG0580025552.01.T01:intron 10.0%
!! TAATATGAAATTGAGATTTA+AGG + Chr5:20359765-20359784 None:intergenic 15.0%
!! TGATCGAAAAATAAATAAAT+TGG - Chr5:20360284-20360303 MsG0580025552.01.T01:five_prime_UTR 15.0%
!!! AATATATCATTCTAAGAATA+TGG - Chr5:20359141-20359160 MsG0580025552.01.T01:three_prime_UTR 15.0%
!! AAACTGTAAAGATGAAATAA+AGG + Chr5:20359212-20359231 None:intergenic 20.0%
!! AATTTATCGTTCAACTTATT+AGG + Chr5:20359727-20359746 None:intergenic 20.0%
!! ATAATTAATAATAAGAGGAG+TGG + Chr5:20359519-20359538 None:intergenic 20.0%
!! TATCGTGGAAAAAAAATATA+AGG - Chr5:20359573-20359592 MsG0580025552.01.T01:intron 20.0%
!! TTATTAGGTAAAAGTTCAAT+AGG + Chr5:20359712-20359731 None:intergenic 20.0%
!! TTCTATAAGCATAAAATTAG+TGG + Chr5:20359837-20359856 None:intergenic 20.0%
!!! ACGAAAATAGAGCATTATTT+TGG + Chr5:20359298-20359317 None:intergenic 25.0%
!!! TTAACCAATAAGTTTTGTGT+AGG - Chr5:20359334-20359353 MsG0580025552.01.T01:CDS 25.0%
CAAAGTCAAGATAAAAACTC+AGG - Chr5:20359360-20359379 MsG0580025552.01.T01:CDS 30.0%
! CTGAGTTTTTATCTTGACTT+TGG + Chr5:20359362-20359381 None:intergenic 30.0%
!! TGGTGCAATCATTTTAACAA+TGG + Chr5:20359673-20359692 None:intergenic 30.0%
AATAGCATAGTAGGGTCAAT+TGG + Chr5:20360147-20360166 None:intergenic 35.0%
AATTGACCCTACTATGCTAT+TGG - Chr5:20360146-20360165 MsG0580025552.01.T01:intron 35.0%
ATCAAACTCTTATGCAGTGA+TGG - Chr5:20359939-20359958 MsG0580025552.01.T01:intron 35.0%
ATTTGACAAGAAAGCTATCG+TGG - Chr5:20359558-20359577 MsG0580025552.01.T01:intron 35.0%
CAAACCAACTTCATAACTGA+TGG + Chr5:20360221-20360240 None:intergenic 35.0%
GGTTCCTACACAAAACTTAT+TGG + Chr5:20359341-20359360 None:intergenic 35.0%
GTTGGACATGTGTTATAACT+AGG - Chr5:20359421-20359440 MsG0580025552.01.T01:CDS 35.0%
TACAGACCAATAGCATAGTA+GGG + Chr5:20360155-20360174 None:intergenic 35.0%
TAGGTAAGATCTTCATGTCA+TGG + Chr5:20359693-20359712 None:intergenic 35.0%
TGTGTTATAACTAGGACTGA+AGG - Chr5:20359429-20359448 MsG0580025552.01.T01:CDS 35.0%
TTACAGACCAATAGCATAGT+AGG + Chr5:20360156-20360175 None:intergenic 35.0%
! GGCAAAGTTTTTGCTAAATG+TGG - Chr5:20359460-20359479 MsG0580025552.01.T01:intron 35.0%
!! TGTTCCATTTTCAAGACTGA+AGG - Chr5:20360041-20360060 MsG0580025552.01.T01:intron 35.0%
AAACTCTTATGCAGTGATGG+TGG - Chr5:20359942-20359961 MsG0580025552.01.T01:intron 40.0%
AGTGAAACATTCTGCAAGTG+TGG - Chr5:20360005-20360024 MsG0580025552.01.T01:intron 40.0%
ATTGAGAGTAGCAGTGACAA+TGG - Chr5:20359981-20360000 MsG0580025552.01.T01:intron 40.0%
CAAGATAAAAACTCAGGCCA+GGG - Chr5:20359366-20359385 MsG0580025552.01.T01:CDS 40.0%
TAGCAAAAACTTTGCCCATC+AGG + Chr5:20359456-20359475 None:intergenic 40.0%
TCAAGATAAAAACTCAGGCC+AGG - Chr5:20359365-20359384 MsG0580025552.01.T01:CDS 40.0%
TCACTGCTACTCTCAATAAC+TGG + Chr5:20359978-20359997 None:intergenic 40.0%
TGTGCCATCAGTTATGAAGT+TGG - Chr5:20360214-20360233 MsG0580025552.01.T01:intron 40.0%
TTAAGCAGCAGTGTGATGTT+TGG - Chr5:20360256-20360275 MsG0580025552.01.T01:exon 40.0%
ACATTCTGCAAGTGTGGTGA+AGG - Chr5:20360011-20360030 MsG0580025552.01.T01:intron 45.0%
AGAGCTTCACTCAAGAGCAA+GGG - Chr5:20359170-20359189 MsG0580025552.01.T01:three_prime_UTR 45.0%
AGGGCCTTCAGTCTTGAAAA+TGG + Chr5:20360048-20360067 None:intergenic 45.0%
CATTCTGCAAGTGTGGTGAA+GGG - Chr5:20360012-20360031 MsG0580025552.01.T01:intron 45.0%
GTGTTGTGCAAGACAGGTAA+AGG - Chr5:20359399-20359418 MsG0580025552.01.T01:CDS 45.0%
TGTGCAAGACAGGTAAAGGT+TGG - Chr5:20359403-20359422 MsG0580025552.01.T01:CDS 45.0%
TTGCTCTTGAGTGAAGCTCT+GGG + Chr5:20359170-20359189 None:intergenic 45.0%
!! ATTTTCAAGACTGAAGGCCC+TGG - Chr5:20360047-20360066 MsG0580025552.01.T01:intron 45.0%
!! TTAAAATAATTAATAATAAG+AGG + Chr5:20359524-20359543 None:intergenic 5.0%
AAAAACTCAGGCCAGGGCTT+GGG - Chr5:20359372-20359391 MsG0580025552.01.T01:CDS 50.0%
ACTAGGACTGAAGGACCTGA+TGG - Chr5:20359438-20359457 MsG0580025552.01.T01:CDS 50.0%
CAGAGCTTCACTCAAGAGCA+AGG - Chr5:20359169-20359188 MsG0580025552.01.T01:three_prime_UTR 50.0%
CCTGGTGTAAACTCTGGCAA+GGG - Chr5:20360065-20360084 MsG0580025552.01.T01:intron 50.0%
CCTTGCCAGAGTTTACACCA+GGG + Chr5:20360067-20360086 None:intergenic 50.0%
CTAGGACTGAAGGACCTGAT+GGG - Chr5:20359439-20359458 MsG0580025552.01.T01:CDS 50.0%
CTTGCTCTTGAGTGAAGCTC+TGG + Chr5:20359171-20359190 None:intergenic 50.0%
GGCAATGTGTTGTGCAAGAC+AGG - Chr5:20359393-20359412 MsG0580025552.01.T01:CDS 50.0%
TAAAAACTCAGGCCAGGGCT+TGG - Chr5:20359371-20359390 MsG0580025552.01.T01:CDS 50.0%
!! TATGCAGTGATGGTGGAGCT+GGG - Chr5:20359949-20359968 MsG0580025552.01.T01:intron 50.0%
!! TTATGCAGTGATGGTGGAGC+TGG - Chr5:20359948-20359967 MsG0580025552.01.T01:intron 50.0%
ACAACACATTGCCCAAGCCC+TGG + Chr5:20359386-20359405 None:intergenic 55.0%
CCCTGGTGTAAACTCTGGCA+AGG - Chr5:20360064-20360083 MsG0580025552.01.T01:intron 55.0%
CCCTTGCCAGAGTTTACACC+AGG + Chr5:20360068-20360087 None:intergenic 55.0%
GAAGGCCCTGGTGTAAACTC+TGG - Chr5:20360059-20360078 MsG0580025552.01.T01:intron 55.0%
TCTGCAAGTGTGGTGAAGGG+TGG - Chr5:20360015-20360034 MsG0580025552.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr5 gene 20359095 20360334 20359095 ID=MsG0580025552.01;Name=MsG0580025552.01
Chr5 mRNA 20359095 20360334 20359095 ID=MsG0580025552.01.T01;Parent=MsG0580025552.01;Name=MsG0580025552.01.T01;_AED=0.49;_eAED=0.49;_QI=65|0|1|1|0|0|2|201|69
Chr5 exon 20359095 20359473 20359095 ID=MsG0580025552.01.T01:exon:8904;Parent=MsG0580025552.01.T01
Chr5 exon 20360238 20360334 20360238 ID=MsG0580025552.01.T01:exon:8903;Parent=MsG0580025552.01.T01
Chr5 five_prime_UTR 20360270 20360334 20360270 ID=MsG0580025552.01.T01:five_prime_utr;Parent=MsG0580025552.01.T01
Chr5 CDS 20360238 20360269 20360238 ID=MsG0580025552.01.T01:cds;Parent=MsG0580025552.01.T01
Chr5 CDS 20359296 20359473 20359296 ID=MsG0580025552.01.T01:cds;Parent=MsG0580025552.01.T01
Chr5 three_prime_UTR 20359095 20359295 20359095 ID=MsG0580025552.01.T01:three_prime_utr;Parent=MsG0580025552.01.T01
Gene Sequence

>MsG0580025552.01.T01

ATGGAGTCCCAGAGCTTCACTCAAGAGCAAGGTGATGGTGGAGCTGGGTCACCAGTTATTGAGAGTAGCAGTGACAATGGCAGTGAAACATTCTGCAAGTGTGGTGAAGGGTGGAGTTGTTCCATTTTCAAGACTGAAGGCCCTGGTGTAAACTCTGGCAAGGGCTTTGCTGAATGCACTCAACAGTATAACTGTGCTTGTAACTGTTGA

Protein sequence

>MsG0580025552.01.T01

MESQSFTQEQGDGGAGSPVIESSSDNGSETFCKCGEGWSCSIFKTEGPGVNSGKGFAECTQQYNCACNC*