AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0129590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0129590 MtrunA17_Chr5g0399781 56.604 53 22 1 4 56 13 64 2.27e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 134 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCGCGATCTA+TGG 0.184009 1_3:+59632986 Msa0129590:CDS
GGAGTTTGGTTTGAAAGCTT+TGG 0.278312 1_3:-59632258 None:intergenic
GAGTTTGGTTTGAAAGCTTT+GGG 0.293757 1_3:-59632257 None:intergenic
AAGACAAATGTTACTTCTAC+TGG 0.334161 1_3:+59633117 Msa0129590:CDS
CACAAGATTGGCTTCTCATA+TGG 0.357972 1_3:-59632120 None:intergenic
TTTCAACAGAAACTAAAGTT+TGG 0.373286 1_3:+59632088 Msa0129590:CDS
AAGTAACATTTGTCTTTAGA+AGG 0.383538 1_3:-59633110 None:intergenic
AAACTAAAGTTTGGCGTAAA+GGG 0.384790 1_3:+59632097 Msa0129590:CDS
CCAAGTAATGAGATAGGCCT+TGG 0.399836 1_3:+59633081 Msa0129590:CDS
CGCTTGTGGATTGCATTTCA+AGG 0.400895 1_3:+59632146 Msa0129590:CDS
GAAACTAAAGTTTGGCGTAA+AGG 0.437706 1_3:+59632096 Msa0129590:CDS
CCACAAGCGTTACACAAGAT+TGG 0.443944 1_3:-59632132 None:intergenic
CCAAGGCCTATCTCATTACT+TGG 0.465533 1_3:-59633081 None:intergenic
ATTGGTGTCGGCGTCTCCAT+TGG 0.465624 1_3:-59632952 None:intergenic
TTTATACCAAGTAATGAGAT+AGG 0.465649 1_3:+59633075 Msa0129590:CDS
GGATTGCATTTCAAGGCTAA+AGG 0.471066 1_3:+59632153 Msa0129590:CDS
CCAATCTTGTGTAACGCTTG+TGG 0.501436 1_3:+59632132 Msa0129590:CDS
ACAAAAGCTTCGCGATCTAT+GGG 0.510066 1_3:+59632987 Msa0129590:CDS
TCTTTAGAAGGCTGCACCCA+AGG 0.517338 1_3:-59633098 None:intergenic
TGTAGAGAGGTTGACACCAA+TGG 0.540998 1_3:+59632936 Msa0129590:intron
TGAAACTCCTCCATTGGTGT+CGG 0.552179 1_3:-59632964 None:intergenic
CAAGTAATGAGATAGGCCTT+GGG 0.567827 1_3:+59633082 Msa0129590:CDS
AATGGAGACGCCGACACCAA+TGG 0.570703 1_3:+59632954 Msa0129590:CDS
AAGCTTTCAAACCAAACTCC+AGG 0.583403 1_3:+59632261 Msa0129590:CDS
AGACAAATGTTACTTCTACT+GGG 0.600449 1_3:+59633118 Msa0129590:CDS
GGAGACGCCGACACCAATGG+AGG 0.674631 1_3:+59632957 Msa0129590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATATACTCAAATTAAT+GGG + chr1_3:59632450-59632469 Msa0129590:intron 10.0%
!! AAAAATATATACATCATATA+CGG - chr1_3:59632895-59632914 None:intergenic 10.0%
!! AAATATATACTCAAATTAAT+GGG + chr1_3:59632450-59632469 Msa0129590:intron 10.0%
!! AAAAATATATACATCATATA+CGG - chr1_3:59632895-59632914 None:intergenic 10.0%
!! TAAAAATAGATGATATAGTA+TGG - chr1_3:59632365-59632384 None:intergenic 15.0%
!! ATATATTTCAAAAACTTTAG+CGG - chr1_3:59632438-59632457 None:intergenic 15.0%
!! GAAATATATACTCAAATTAA+TGG + chr1_3:59632449-59632468 Msa0129590:intron 15.0%
!! ATAATTATCTCAAAAAATGT+AGG - chr1_3:59632746-59632765 None:intergenic 15.0%
!! TAAAAATAGATGATATAGTA+TGG - chr1_3:59632365-59632384 None:intergenic 15.0%
!! ATATATTTCAAAAACTTTAG+CGG - chr1_3:59632438-59632457 None:intergenic 15.0%
!! GAAATATATACTCAAATTAA+TGG + chr1_3:59632449-59632468 Msa0129590:intron 15.0%
!! ATAATTATCTCAAAAAATGT+AGG - chr1_3:59632746-59632765 None:intergenic 15.0%
!!! TTATTGCAATTTTTATTACC+TGG - chr1_3:59632282-59632301 None:intergenic 20.0%
!!! AATAACTTCAGCTTTAAATT+TGG - chr1_3:59632332-59632351 None:intergenic 20.0%
!!! ATAATGCATTGATTTTATTG+TGG + chr1_3:59632390-59632409 Msa0129590:intron 20.0%
!! ATTGCAAGAATATTCTTAAA+GGG + chr1_3:59632552-59632571 Msa0129590:intron 20.0%
!! CAACTCATACATAAATATTA+CGG - chr1_3:59632608-59632627 None:intergenic 20.0%
!!! TAATATCTTATTTTGTAGAG+AGG + chr1_3:59632923-59632942 Msa0129590:intron 20.0%
!!! TTATTGCAATTTTTATTACC+TGG - chr1_3:59632282-59632301 None:intergenic 20.0%
!!! AATAACTTCAGCTTTAAATT+TGG - chr1_3:59632332-59632351 None:intergenic 20.0%
!!! ATAATGCATTGATTTTATTG+TGG + chr1_3:59632390-59632409 Msa0129590:intron 20.0%
!! ATTGCAAGAATATTCTTAAA+GGG + chr1_3:59632552-59632571 Msa0129590:intron 20.0%
!! CAACTCATACATAAATATTA+CGG - chr1_3:59632608-59632627 None:intergenic 20.0%
!!! TAATATCTTATTTTGTAGAG+AGG + chr1_3:59632923-59632942 Msa0129590:intron 20.0%
! TTTCAACAGAAACTAAAGTT+TGG + chr1_3:59632088-59632107 Msa0129590:CDS 25.0%
!! AATTTTTATTACCTGGAGTT+TGG - chr1_3:59632275-59632294 None:intergenic 25.0%
! AATAGATGATATAGTATGGA+GGG - chr1_3:59632361-59632380 None:intergenic 25.0%
! AAATAGATGATATAGTATGG+AGG - chr1_3:59632362-59632381 None:intergenic 25.0%
! CATTGCAAGAATATTCTTAA+AGG + chr1_3:59632551-59632570 Msa0129590:intron 25.0%
!!! TATTGATAGTGAAGCAAATT+AGG - chr1_3:59632643-59632662 None:intergenic 25.0%
! TCTCAAAAAATGTAGGAATA+TGG - chr1_3:59632739-59632758 None:intergenic 25.0%
! TTTATACCAAGTAATGAGAT+AGG + chr1_3:59633075-59633094 Msa0129590:CDS 25.0%
! AAGTAACATTTGTCTTTAGA+AGG - chr1_3:59633113-59633132 None:intergenic 25.0%
! TTTCAACAGAAACTAAAGTT+TGG + chr1_3:59632088-59632107 Msa0129590:CDS 25.0%
!! AATTTTTATTACCTGGAGTT+TGG - chr1_3:59632275-59632294 None:intergenic 25.0%
! AATAGATGATATAGTATGGA+GGG - chr1_3:59632361-59632380 None:intergenic 25.0%
! AAATAGATGATATAGTATGG+AGG - chr1_3:59632362-59632381 None:intergenic 25.0%
! CATTGCAAGAATATTCTTAA+AGG + chr1_3:59632551-59632570 Msa0129590:intron 25.0%
!!! TATTGATAGTGAAGCAAATT+AGG - chr1_3:59632643-59632662 None:intergenic 25.0%
! TCTCAAAAAATGTAGGAATA+TGG - chr1_3:59632739-59632758 None:intergenic 25.0%
! TTTATACCAAGTAATGAGAT+AGG + chr1_3:59633075-59633094 Msa0129590:CDS 25.0%
! AAGTAACATTTGTCTTTAGA+AGG - chr1_3:59633113-59633132 None:intergenic 25.0%
AAACTAAAGTTTGGCGTAAA+GGG + chr1_3:59632097-59632116 Msa0129590:CDS 30.0%
! GTCTAATAACAGATTTTGCT+GGG - chr1_3:59632208-59632227 None:intergenic 30.0%
!!! TAGATGCTTTTTCAATGTCA+TGG - chr1_3:59632230-59632249 None:intergenic 30.0%
!!! TGCATTGATTTTATTGTGGT+AGG + chr1_3:59632394-59632413 Msa0129590:intron 30.0%
TATTTCAAAAACTTTAGCGG+CGG - chr1_3:59632435-59632454 None:intergenic 30.0%
TACTCATAAGCAGTGTAAAA+TGG + chr1_3:59632496-59632515 Msa0129590:intron 30.0%
ACTCATAAGCAGTGTAAAAT+GGG + chr1_3:59632497-59632516 Msa0129590:intron 30.0%
! ATTCTTAAAGGGTACAATTC+AGG + chr1_3:59632563-59632582 Msa0129590:intron 30.0%
! TTCTTAAAGGGTACAATTCA+GGG + chr1_3:59632564-59632583 Msa0129590:intron 30.0%
TTGCTTCACTATCAATAAGA+TGG + chr1_3:59632646-59632665 Msa0129590:intron 30.0%
TGTATGTGTGTTACAAAGTT+TGG - chr1_3:59632713-59632732 None:intergenic 30.0%
AAAGACAACTAAAGAAGAGT+CGG + chr1_3:59632774-59632793 Msa0129590:intron 30.0%
! AAGACAAATGTTACTTCTAC+TGG + chr1_3:59633117-59633136 Msa0129590:CDS 30.0%
! AGACAAATGTTACTTCTACT+GGG + chr1_3:59633118-59633137 Msa0129590:CDS 30.0%
!! AACATTTGTCTTTTGAAGAG+TGG - chr1_3:59633145-59633164 None:intergenic 30.0%
AAACTAAAGTTTGGCGTAAA+GGG + chr1_3:59632097-59632116 Msa0129590:CDS 30.0%
! GTCTAATAACAGATTTTGCT+GGG - chr1_3:59632208-59632227 None:intergenic 30.0%
!!! TAGATGCTTTTTCAATGTCA+TGG - chr1_3:59632230-59632249 None:intergenic 30.0%
!!! TGCATTGATTTTATTGTGGT+AGG + chr1_3:59632394-59632413 Msa0129590:intron 30.0%
TATTTCAAAAACTTTAGCGG+CGG - chr1_3:59632435-59632454 None:intergenic 30.0%
TACTCATAAGCAGTGTAAAA+TGG + chr1_3:59632496-59632515 Msa0129590:intron 30.0%
ACTCATAAGCAGTGTAAAAT+GGG + chr1_3:59632497-59632516 Msa0129590:intron 30.0%
! ATTCTTAAAGGGTACAATTC+AGG + chr1_3:59632563-59632582 Msa0129590:intron 30.0%
! TTCTTAAAGGGTACAATTCA+GGG + chr1_3:59632564-59632583 Msa0129590:intron 30.0%
TTGCTTCACTATCAATAAGA+TGG + chr1_3:59632646-59632665 Msa0129590:intron 30.0%
TGTATGTGTGTTACAAAGTT+TGG - chr1_3:59632713-59632732 None:intergenic 30.0%
AAAGACAACTAAAGAAGAGT+CGG + chr1_3:59632774-59632793 Msa0129590:intron 30.0%
! AAGACAAATGTTACTTCTAC+TGG + chr1_3:59633117-59633136 Msa0129590:CDS 30.0%
! AGACAAATGTTACTTCTACT+GGG + chr1_3:59633118-59633137 Msa0129590:CDS 30.0%
!! AACATTTGTCTTTTGAAGAG+TGG - chr1_3:59633145-59633164 None:intergenic 30.0%
GAAACTAAAGTTTGGCGTAA+AGG + chr1_3:59632096-59632115 Msa0129590:CDS 35.0%
! GGTCTAATAACAGATTTTGC+TGG - chr1_3:59632209-59632228 None:intergenic 35.0%
!! GAGTTTGGTTTGAAAGCTTT+GGG - chr1_3:59632260-59632279 None:intergenic 35.0%
! TGGGTTGAGAATGAAAATGT+TGG + chr1_3:59632469-59632488 Msa0129590:intron 35.0%
GGGTTGAGAATGAAAATGTT+GGG + chr1_3:59632470-59632489 Msa0129590:intron 35.0%
! TCTTAAAGGGTACAATTCAG+GGG + chr1_3:59632565-59632584 Msa0129590:intron 35.0%
! TTTTGTTGAAACTCCTCCAT+TGG - chr1_3:59632973-59632992 None:intergenic 35.0%
GAAACTAAAGTTTGGCGTAA+AGG + chr1_3:59632096-59632115 Msa0129590:CDS 35.0%
! GGTCTAATAACAGATTTTGC+TGG - chr1_3:59632209-59632228 None:intergenic 35.0%
!! GAGTTTGGTTTGAAAGCTTT+GGG - chr1_3:59632260-59632279 None:intergenic 35.0%
! TGGGTTGAGAATGAAAATGT+TGG + chr1_3:59632469-59632488 Msa0129590:intron 35.0%
GGGTTGAGAATGAAAATGTT+GGG + chr1_3:59632470-59632489 Msa0129590:intron 35.0%
! TCTTAAAGGGTACAATTCAG+GGG + chr1_3:59632565-59632584 Msa0129590:intron 35.0%
! TTTTGTTGAAACTCCTCCAT+TGG - chr1_3:59632973-59632992 None:intergenic 35.0%
!! CACAAGATTGGCTTCTCATA+TGG - chr1_3:59632123-59632142 None:intergenic 40.0%
GGATTGCATTTCAAGGCTAA+AGG + chr1_3:59632153-59632172 Msa0129590:CDS 40.0%
! CTTCGGGAGATAGTTTTCAA+GGG - chr1_3:59632181-59632200 None:intergenic 40.0%
! TCTTCGGGAGATAGTTTTCA+AGG - chr1_3:59632182-59632201 None:intergenic 40.0%
! AGATTTTGCTGGGCTATCTT+CGG - chr1_3:59632198-59632217 None:intergenic 40.0%
!! GGAGTTTGGTTTGAAAGCTT+TGG - chr1_3:59632261-59632280 None:intergenic 40.0%
AAGCTTTCAAACCAAACTCC+AGG + chr1_3:59632261-59632280 Msa0129590:CDS 40.0%
CATAAGCAGTGTAAAATGGG+CGG + chr1_3:59632500-59632519 Msa0129590:intron 40.0%
ATAAGCAGTGTAAAATGGGC+GGG + chr1_3:59632501-59632520 Msa0129590:intron 40.0%
AACAAAAGCTTCGCGATCTA+TGG + chr1_3:59632986-59633005 Msa0129590:CDS 40.0%
ACAAAAGCTTCGCGATCTAT+GGG + chr1_3:59632987-59633006 Msa0129590:CDS 40.0%
CAAGTAATGAGATAGGCCTT+GGG + chr1_3:59633082-59633101 Msa0129590:CDS 40.0%
!! CACAAGATTGGCTTCTCATA+TGG - chr1_3:59632123-59632142 None:intergenic 40.0%
GGATTGCATTTCAAGGCTAA+AGG + chr1_3:59632153-59632172 Msa0129590:CDS 40.0%
! CTTCGGGAGATAGTTTTCAA+GGG - chr1_3:59632181-59632200 None:intergenic 40.0%
! TCTTCGGGAGATAGTTTTCA+AGG - chr1_3:59632182-59632201 None:intergenic 40.0%
! AGATTTTGCTGGGCTATCTT+CGG - chr1_3:59632198-59632217 None:intergenic 40.0%
!! GGAGTTTGGTTTGAAAGCTT+TGG - chr1_3:59632261-59632280 None:intergenic 40.0%
AAGCTTTCAAACCAAACTCC+AGG + chr1_3:59632261-59632280 Msa0129590:CDS 40.0%
CATAAGCAGTGTAAAATGGG+CGG + chr1_3:59632500-59632519 Msa0129590:intron 40.0%
ATAAGCAGTGTAAAATGGGC+GGG + chr1_3:59632501-59632520 Msa0129590:intron 40.0%
AACAAAAGCTTCGCGATCTA+TGG + chr1_3:59632986-59633005 Msa0129590:CDS 40.0%
ACAAAAGCTTCGCGATCTAT+GGG + chr1_3:59632987-59633006 Msa0129590:CDS 40.0%
CAAGTAATGAGATAGGCCTT+GGG + chr1_3:59633082-59633101 Msa0129590:CDS 40.0%
CCACAAGCGTTACACAAGAT+TGG - chr1_3:59632135-59632154 None:intergenic 45.0%
CCAATCTTGTGTAACGCTTG+TGG + chr1_3:59632132-59632151 Msa0129590:CDS 45.0%
! CGCTTGTGGATTGCATTTCA+AGG + chr1_3:59632146-59632165 Msa0129590:CDS 45.0%
! GATTTTGCTGGGCTATCTTC+GGG - chr1_3:59632197-59632216 None:intergenic 45.0%
TGTAGAGAGGTTGACACCAA+TGG + chr1_3:59632936-59632955 Msa0129590:intron 45.0%
TGAAACTCCTCCATTGGTGT+CGG - chr1_3:59632967-59632986 None:intergenic 45.0%
CCAAGGCCTATCTCATTACT+TGG - chr1_3:59633084-59633103 None:intergenic 45.0%
CCAAGTAATGAGATAGGCCT+TGG + chr1_3:59633081-59633100 Msa0129590:CDS 45.0%
CCACAAGCGTTACACAAGAT+TGG - chr1_3:59632135-59632154 None:intergenic 45.0%
CCAATCTTGTGTAACGCTTG+TGG + chr1_3:59632132-59632151 Msa0129590:CDS 45.0%
! CGCTTGTGGATTGCATTTCA+AGG + chr1_3:59632146-59632165 Msa0129590:CDS 45.0%
! GATTTTGCTGGGCTATCTTC+GGG - chr1_3:59632197-59632216 None:intergenic 45.0%
TGTAGAGAGGTTGACACCAA+TGG + chr1_3:59632936-59632955 Msa0129590:intron 45.0%
TGAAACTCCTCCATTGGTGT+CGG - chr1_3:59632967-59632986 None:intergenic 45.0%
CCAAGGCCTATCTCATTACT+TGG - chr1_3:59633084-59633103 None:intergenic 45.0%
CCAAGTAATGAGATAGGCCT+TGG + chr1_3:59633081-59633100 Msa0129590:CDS 45.0%
! TCTTTAGAAGGCTGCACCCA+AGG - chr1_3:59633101-59633120 None:intergenic 50.0%
! TCTTTAGAAGGCTGCACCCA+AGG - chr1_3:59633101-59633120 None:intergenic 50.0%
!! ATTGGTGTCGGCGTCTCCAT+TGG - chr1_3:59632955-59632974 None:intergenic 55.0%
AATGGAGACGCCGACACCAA+TGG + chr1_3:59632954-59632973 Msa0129590:CDS 55.0%
!! ATTGGTGTCGGCGTCTCCAT+TGG - chr1_3:59632955-59632974 None:intergenic 55.0%
AATGGAGACGCCGACACCAA+TGG + chr1_3:59632954-59632973 Msa0129590:CDS 55.0%
GGAGACGCCGACACCAATGG+AGG + chr1_3:59632957-59632976 Msa0129590:CDS 65.0%
GGAGACGCCGACACCAATGG+AGG + chr1_3:59632957-59632976 Msa0129590:CDS 65.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 59632084 59633197 59632084 ID=Msa0129590;Name=Msa0129590
chr1_3 mRNA 59632084 59633197 59632084 ID=Msa0129590-mRNA-1;Parent=Msa0129590;Name=Msa0129590-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0|0|1|1|1|2|0|151
chr1_3 exon 59632084 59632282 59632084 ID=Msa0129590-mRNA-1:exon:19437;Parent=Msa0129590-mRNA-1
chr1_3 exon 59632941 59633197 59632941 ID=Msa0129590-mRNA-1:exon:19438;Parent=Msa0129590-mRNA-1
chr1_3 CDS 59632084 59632282 59632084 ID=Msa0129590-mRNA-1:cds;Parent=Msa0129590-mRNA-1
chr1_3 CDS 59632941 59633197 59632941 ID=Msa0129590-mRNA-1:cds;Parent=Msa0129590-mRNA-1
Gene Sequence

>Msa0129590

ATGATTTCAACAGAAACTAAAGTTTGGCGTAAAGGGCCATATGAGAAGCCAATCTTGTGTAACGCTTGTGGATTGCATTTCAAGGCTAAAGGAACCCTTGAAAACTATCTCCCGAAGATAGCCCAGCAAAATCTGTTATTAGACCATGACATTGAAAAAGCATCTAGAAGTGACCCAAAGCTTTCAAACCAAACTCCAGAGAGGTTGACACCAATGGAGACGCCGACACCAATGGAGGAGTTTCAACAAAAGCTTCGCGATCTATGGGAATCTGAGAAAGAAGCAAATGATTCATCATCAGACAATATTTTGTTGTTTGATAATATGAACAACTTTATACCAAGTAATGAGATAGGCCTTGGGTGCAGCCTTCTAAAGACAAATGTTACTTCTACTGGGTCCACTCTTCAAAAGACAAATGTTACTTCTACAAATCAACATGATTCACATGCATAG

Protein sequence

>Msa0129590

MISTETKVWRKGPYEKPILCNACGLHFKAKGTLENYLPKIAQQNLLLDHDIEKASRSDPKLSNQTPERLTPMETPTPMEEFQQKLRDLWESEKEANDSSSDNILLFDNMNNFIPSNEIGLGCSLLKTNVTSTGSTLQKTNVTSTNQHDSHA*