AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005150.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005150.01.T01 MTR_1g093980 97.059 68 1 1 1 68 1 67 1.02e-35 115
MsG0180005150.01.T01 MTR_3g073005 69.118 68 6 1 1 68 1 53 1.31e-19 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAAACATGCACCATATTA+TGG 0.203774 1:+87635974 None:intergenic
ACTTACACACTACTCTTCTA+AGG 0.295265 1:+87636363 None:intergenic
TATTTATGTACCTTCCTCTT+AGG 0.298377 1:+87636179 None:intergenic
ACCTTGGAGGCTCTAGCTTT+AGG 0.324474 1:+87636233 None:intergenic
AGTAGTGTGTAAGTGTAAAA+TGG 0.327048 1:-87636354 MsG0180005150.01.T01:exon
AATATGAAGAATCCATAATA+TGG 0.340279 1:-87635986 MsG0180005150.01.T01:three_prime_UTR
AGGAGTAGTCCCACTAGTTT+TGG 0.346620 1:+87636253 None:intergenic
CATGTAAATCCTTGCCAGTT+TGG 0.348500 1:-87635890 MsG0180005150.01.T01:three_prime_UTR
TCTTTCTTGACTTGCCCTGA+TGG 0.433141 1:+87636284 None:intergenic
TCTGGTAGCTCTCAACCATC+AGG 0.435394 1:-87636299 MsG0180005150.01.T01:CDS
TTTCTTTGGTGCTACCTTGG+AGG 0.439933 1:+87636220 None:intergenic
TATCAGTAGTACTATCTGTA+TGG 0.447641 1:-87635945 MsG0180005150.01.T01:three_prime_UTR
GAGAAACCAACTGAGAAATC+TGG 0.453123 1:-87636317 MsG0180005150.01.T01:CDS
GAGCTACCAGATTTCTCAGT+TGG 0.466377 1:+87636311 None:intergenic
AGCAGAAATCTCAGCCTAAG+AGG 0.534590 1:-87636193 MsG0180005150.01.T01:CDS
TCCTAAAGCTAGAGCCTCCA+AGG 0.550929 1:-87636234 MsG0180005150.01.T01:CDS
TTTAAAAGGCCAAACTGGCA+AGG 0.553496 1:+87635881 None:intergenic
GAAATCTCAGCCTAAGAGGA+AGG 0.560994 1:-87636189 MsG0180005150.01.T01:intron
CAAACTGGCAAGGATTTACA+TGG 0.573072 1:+87635891 None:intergenic
GAGCCTGCTGCCAAAACTAG+TGG 0.582011 1:-87636263 MsG0180005150.01.T01:CDS
AGCCTGCTGCCAAAACTAGT+GGG 0.610029 1:-87636262 MsG0180005150.01.T01:CDS
AATGAGACAACATAAGCAAG+TGG 0.629024 1:+87635920 None:intergenic
CTGGTAGCTCTCAACCATCA+GGG 0.637266 1:-87636298 MsG0180005150.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTTGAAAAAATAATTGT+TGG - Chr1:87636202-87636221 MsG0180005150.01.T01:CDS 15.0%
!! AATATGAAGAATCCATAATA+TGG - Chr1:87636247-87636266 MsG0180005150.01.T01:CDS 20.0%
!!! ATCTTTTGATTACTTGTTTC+AGG - Chr1:87636140-87636159 MsG0180005150.01.T01:intron 25.0%
!!! TTTTATTTAAAAGGCCAAAC+TGG + Chr1:87636360-87636379 None:intergenic 25.0%
AGTAGTGTGTAAGTGTAAAA+TGG - Chr1:87635879-87635898 MsG0180005150.01.T01:three_prime_UTR 30.0%
ATGAAACATGCACCATATTA+TGG + Chr1:87636262-87636281 None:intergenic 30.0%
TATCAGTAGTACTATCTGTA+TGG - Chr1:87636288-87636307 MsG0180005150.01.T01:CDS 30.0%
TATTTATGTACCTTCCTCTT+AGG + Chr1:87636057-87636076 None:intergenic 30.0%
AATGAGACAACATAAGCAAG+TGG + Chr1:87636316-87636335 None:intergenic 35.0%
ACTTACACACTACTCTTCTA+AGG + Chr1:87635873-87635892 None:intergenic 35.0%
! GATTTCTGCTCAGTTTTCTT+TGG + Chr1:87636030-87636049 None:intergenic 35.0%
CAAACTGGCAAGGATTTACA+TGG + Chr1:87636345-87636364 None:intergenic 40.0%
CATGTAAATCCTTGCCAGTT+TGG - Chr1:87636343-87636362 MsG0180005150.01.T01:exon 40.0%
GAGAAACCAACTGAGAAATC+TGG - Chr1:87635916-87635935 MsG0180005150.01.T01:three_prime_UTR 40.0%
TTTAAAAGGCCAAACTGGCA+AGG + Chr1:87636355-87636374 None:intergenic 40.0%
!!! AGTTTTCTTTGGTGCTACCT+TGG + Chr1:87636019-87636038 None:intergenic 40.0%
AGCAGAAATCTCAGCCTAAG+AGG - Chr1:87636040-87636059 MsG0180005150.01.T01:exon 45.0%
GAAATCTCAGCCTAAGAGGA+AGG - Chr1:87636044-87636063 MsG0180005150.01.T01:exon 45.0%
GAGCTACCAGATTTCTCAGT+TGG + Chr1:87635925-87635944 None:intergenic 45.0%
!! AGGAGTAGTCCCACTAGTTT+TGG + Chr1:87635983-87636002 None:intergenic 45.0%
!! TCTTTCTTGACTTGCCCTGA+TGG + Chr1:87635952-87635971 None:intergenic 45.0%
!! TTTCTTTGGTGCTACCTTGG+AGG + Chr1:87636016-87636035 None:intergenic 45.0%
!!! ATAAGTATATTTTATTTAAA+AGG + Chr1:87636369-87636388 None:intergenic 5.0%
AGCCTGCTGCCAAAACTAGT+GGG - Chr1:87635971-87635990 MsG0180005150.01.T01:three_prime_UTR 50.0%
CTGGTAGCTCTCAACCATCA+GGG - Chr1:87635935-87635954 MsG0180005150.01.T01:three_prime_UTR 50.0%
TCCTAAAGCTAGAGCCTCCA+AGG - Chr1:87635999-87636018 MsG0180005150.01.T01:three_prime_UTR 50.0%
TCTGGTAGCTCTCAACCATC+AGG - Chr1:87635934-87635953 MsG0180005150.01.T01:three_prime_UTR 50.0%
!! ACCTTGGAGGCTCTAGCTTT+AGG + Chr1:87636003-87636022 None:intergenic 50.0%
GAGCCTGCTGCCAAAACTAG+TGG - Chr1:87635970-87635989 MsG0180005150.01.T01:three_prime_UTR 55.0%
!!! GTCCCACTAGTTTTGGCAGC+AGG + Chr1:87635976-87635995 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
Chr1 gene 87635855 87636400 87635855 ID=MsG0180005150.01;Name=MsG0180005150.01
Chr1 mRNA 87635855 87636400 87635855 ID=MsG0180005150.01.T01;Parent=MsG0180005150.01;Name=MsG0180005150.01.T01;_AED=0.49;_eAED=0.49;_QI=43|1|1|1|1|1|2|200|68
Chr1 exon 87635855 87636093 87635855 ID=MsG0180005150.01.T01:exon:47709;Parent=MsG0180005150.01.T01
Chr1 exon 87636190 87636400 87636190 ID=MsG0180005150.01.T01:exon:47708;Parent=MsG0180005150.01.T01
Chr1 five_prime_UTR 87636358 87636400 87636358 ID=MsG0180005150.01.T01:five_prime_utr;Parent=MsG0180005150.01.T01
Chr1 CDS 87636190 87636357 87636190 ID=MsG0180005150.01.T01:cds;Parent=MsG0180005150.01.T01
Chr1 CDS 87636055 87636093 87636055 ID=MsG0180005150.01.T01:cds;Parent=MsG0180005150.01.T01
Chr1 three_prime_UTR 87635855 87636054 87635855 ID=MsG0180005150.01.T01:three_prime_utr;Parent=MsG0180005150.01.T01
Gene Sequence

>MsG0180005150.01.T01

ATGGCATCACTCAAAGCTGAGAAACCAACTGAGAAATCTGGTAGCTCTCAACCATCAGGGCAAGTCAAGAAAGAGCCTGCTGCCAAAACTAGTGGGACTACTCCTAAAGCTAGAGCCTCCAAGGTAGCACCAAAGAAAACTGAGCAGAAATCTCAGCCTAAGAGGAAGGCTAGCAGCATTAAGCAGAAGATAACAAGTGAAACTTAA

Protein sequence

>MsG0180005150.01.T01

MASLKAEKPTEKSGSSQPSGQVKKEPAAKTSGTTPKARASKVAPKKTEQKSQPKRKASSIKQKITSET*