AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0011010


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0011010 MtrunA17_Chr1g0159601 93.365 211 13 1 1 211 46 255 6.64e-146 406
Msa0011010 MtrunA17_Chr1g0159611 78.676 136 29 0 1 136 46 181 4.52e-75 236
Msa0011010 MtrunA17_Chr8g0380681 45.536 224 102 6 4 209 2 223 8.86e-53 182
Msa0011010 MtrunA17_Chr8g0380681 39.000 200 109 6 18 205 691 889 8.50e-37 136
Msa0011010 MtrunA17_Chr2g0277731 43.750 208 108 4 9 209 12 217 4.70e-51 174
Msa0011010 MtrunA17_Chr4g0039131 42.969 128 70 2 86 211 1 127 6.56e-31 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0011010 AT1G11050.1 42.708 192 103 4 25 210 26 216 2.39e-38 140

Find 36 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCTCTTCTTAGTCTCTT+TGG 0.194083 1_1:+16680776 Msa0011010:CDS
GTTGGTATTGTGAATCATTT+TGG 0.240330 1_1:+16681175 Msa0011010:CDS
GAAAGAGTGAAGTTTCTTTC+AGG 0.244676 1_1:-16680817 None:intergenic
CAGAAGGAGTAGCTATGATA+AGG 0.380662 1_1:-16680655 None:intergenic
TTGTAAAGGTGATTTGAAAT+CGG 0.388227 1_1:+16681042 Msa0011010:CDS
CAACAATGTTGTGTGTCAAT+TGG 0.393976 1_1:-16680752 None:intergenic
TGTGTCAATTGGGTCTCTGC+AGG 0.430262 1_1:-16680741 None:intergenic
CTTCTTAGTCTCTTTGGCAT+AGG 0.437265 1_1:+16680782 Msa0011010:CDS
CTTTACAAGAAGTGTCTAAA+GGG 0.447705 1_1:-16681027 None:intergenic
TAAGGGTGAAGAGGAGGAGA+AGG 0.460180 1_1:-16680637 None:intergenic
CCTTTAGACACTTCTTGTAA+AGG 0.468879 1_1:+16681028 Msa0011010:CDS
AACAATGTTGTGTGTCAATT+GGG 0.477153 1_1:-16680751 None:intergenic
TGCAGCACGTGCACTAATGC+TGG 0.478276 1_1:+16681073 Msa0011010:CDS
GTATCACAAACATCAAAGAT+TGG 0.490764 1_1:+16680981 Msa0011010:CDS
CTATGATAAGGGTGAAGAGG+AGG 0.492847 1_1:-16680643 None:intergenic
CCTTTACAAGAAGTGTCTAA+AGG 0.505136 1_1:-16681028 None:intergenic
TAGCTATGATAAGGGTGAAG+AGG 0.511716 1_1:-16680646 None:intergenic
GCTACAGCTAGTTGTATACT+TGG 0.511927 1_1:+16681211 Msa0011010:CDS
AGAAGGAGTAGCTATGATAA+GGG 0.514017 1_1:-16680654 None:intergenic
TTATTTCTCATCTTCTAAGC+GGG 0.515185 1_1:-16681237 None:intergenic
ATTGAGTTGTGGAAACAAGA+AGG 0.531475 1_1:-16680926 None:intergenic
TGACAAATTGAATTGAGTTG+TGG 0.533475 1_1:-16680937 None:intergenic
TTCTGCAGTATCATGTCCTA+TGG 0.534711 1_1:+16680679 Msa0011010:CDS
AAGAAGGGACTAACGAAGGT+TGG 0.536160 1_1:-16680910 None:intergenic
TCAACATAGCTGAGATCCAT+AGG 0.544235 1_1:-16680695 None:intergenic
ACAAACAACTCAAGCTGCGC+AGG 0.551790 1_1:+16680959 Msa0011010:CDS
AGTATACAACTAGCTGTAGC+AGG 0.563837 1_1:-16681208 None:intergenic
CTAGCTGTAGCAGGATCTGT+AGG 0.582604 1_1:-16681199 None:intergenic
TTGAGTTGTGGAAACAAGAA+GGG 0.597711 1_1:-16680925 None:intergenic
CTATGTTGAGACCTTTCCAT+GGG 0.598491 1_1:+16680709 Msa0011010:CDS
CTGCAGGTTGATGTGTCCCA+TGG 0.599274 1_1:-16680725 None:intergenic
CATGATACTGCAGAAGCAGA+AGG 0.601540 1_1:-16680671 None:intergenic
GGTTGATGTGTCCCATGGAA+AGG 0.611152 1_1:-16680720 None:intergenic
GCTATGTTGAGACCTTTCCA+TGG 0.614762 1_1:+16680708 Msa0011010:CDS
TTTATTTCTCATCTTCTAAG+CGG 0.636465 1_1:-16681238 None:intergenic
AAACAAGAAGGGACTAACGA+AGG 0.740560 1_1:-16680914 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAAAGTGTTTTTATTA+GGG - chr1_1:16680847-16680866 None:intergenic 10.0%
!!! GATTTTAAAGTGTTTTTATT+AGG - chr1_1:16680848-16680867 None:intergenic 15.0%
!! TTGTAAAGGTGATTTGAAAT+CGG + chr1_1:16681042-16681061 Msa0011010:CDS 25.0%
!!! TTTTCAGTTTTATATGCTGT+TGG + chr1_1:16681157-16681176 Msa0011010:CDS 25.0%
AACAATGTTGTGTGTCAATT+GGG - chr1_1:16680754-16680773 None:intergenic 30.0%
! TGACAAATTGAATTGAGTTG+TGG - chr1_1:16680940-16680959 None:intergenic 30.0%
GTATCACAAACATCAAAGAT+TGG + chr1_1:16680981-16681000 Msa0011010:CDS 30.0%
AAAGATTGGAAGCAAAAAGT+TGG + chr1_1:16680995-16681014 Msa0011010:CDS 30.0%
!! CTTTACAAGAAGTGTCTAAA+GGG - chr1_1:16681030-16681049 None:intergenic 30.0%
!!! AAGCACTTAGTTGCATTTTT+TGG - chr1_1:16681133-16681152 None:intergenic 30.0%
! GTTGGTATTGTGAATCATTT+TGG + chr1_1:16681175-16681194 Msa0011010:CDS 30.0%
AGAAGGAGTAGCTATGATAA+GGG - chr1_1:16680657-16680676 None:intergenic 35.0%
CAACAATGTTGTGTGTCAAT+TGG - chr1_1:16680755-16680774 None:intergenic 35.0%
CAATCTCTTCTTAGTCTCTT+TGG + chr1_1:16680776-16680795 Msa0011010:CDS 35.0%
GAAAGAGTGAAGTTTCTTTC+AGG - chr1_1:16680820-16680839 None:intergenic 35.0%
! TTGAGTTGTGGAAACAAGAA+GGG - chr1_1:16680928-16680947 None:intergenic 35.0%
! ATTGAGTTGTGGAAACAAGA+AGG - chr1_1:16680929-16680948 None:intergenic 35.0%
!! CCTTTACAAGAAGTGTCTAA+AGG - chr1_1:16681031-16681050 None:intergenic 35.0%
CCTTTAGACACTTCTTGTAA+AGG + chr1_1:16681028-16681047 Msa0011010:CDS 35.0%
TAGCTATGATAAGGGTGAAG+AGG - chr1_1:16680649-16680668 None:intergenic 40.0%
CAGAAGGAGTAGCTATGATA+AGG - chr1_1:16680658-16680677 None:intergenic 40.0%
TTCTGCAGTATCATGTCCTA+TGG + chr1_1:16680679-16680698 Msa0011010:CDS 40.0%
TCAACATAGCTGAGATCCAT+AGG - chr1_1:16680698-16680717 None:intergenic 40.0%
CTATGTTGAGACCTTTCCAT+GGG + chr1_1:16680709-16680728 Msa0011010:CDS 40.0%
CTTCTTAGTCTCTTTGGCAT+AGG + chr1_1:16680782-16680801 Msa0011010:CDS 40.0%
AAACAAGAAGGGACTAACGA+AGG - chr1_1:16680917-16680936 None:intergenic 40.0%
AGTATACAACTAGCTGTAGC+AGG - chr1_1:16681211-16681230 None:intergenic 40.0%
GCTACAGCTAGTTGTATACT+TGG + chr1_1:16681211-16681230 Msa0011010:CDS 40.0%
CTATGATAAGGGTGAAGAGG+AGG - chr1_1:16680646-16680665 None:intergenic 45.0%
CATGATACTGCAGAAGCAGA+AGG - chr1_1:16680674-16680693 None:intergenic 45.0%
GCTATGTTGAGACCTTTCCA+TGG + chr1_1:16680708-16680727 Msa0011010:CDS 45.0%
AAGAAGGGACTAACGAAGGT+TGG - chr1_1:16680913-16680932 None:intergenic 45.0%
TAAGGGTGAAGAGGAGGAGA+AGG - chr1_1:16680640-16680659 None:intergenic 50.0%
! GGTTGATGTGTCCCATGGAA+AGG - chr1_1:16680723-16680742 None:intergenic 50.0%
TGTGTCAATTGGGTCTCTGC+AGG - chr1_1:16680744-16680763 None:intergenic 50.0%
ACAAACAACTCAAGCTGCGC+AGG + chr1_1:16680959-16680978 Msa0011010:CDS 50.0%
CTAGCTGTAGCAGGATCTGT+AGG - chr1_1:16681202-16681221 None:intergenic 50.0%
!! CTGCAGGTTGATGTGTCCCA+TGG - chr1_1:16680728-16680747 None:intergenic 55.0%
TGCAGCACGTGCACTAATGC+TGG + chr1_1:16681073-16681092 Msa0011010:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 16680617 16681252 16680617 ID=Msa0011010;Name=Msa0011010
chr1_1 mRNA 16680617 16681252 16680617 ID=Msa0011010-mRNA-1;Parent=Msa0011010;Name=Msa0011010-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|211
chr1_1 exon 16680617 16681252 16680617 ID=Msa0011010-mRNA-1:exon:6055;Parent=Msa0011010-mRNA-1
chr1_1 CDS 16680617 16681252 16680617 ID=Msa0011010-mRNA-1:cds;Parent=Msa0011010-mRNA-1
Gene Sequence

>Msa0011010

ATGGATAACAAAGCAGTGTTCCTTCTCCTCCTCTTCACCCTTATCATAGCTACTCCTTCTGCTTCTGCAGTATCATGTCCTATGGATCTCAGCTATGTTGAGACCTTTCCATGGGACACATCAACCTGCAGAGACCCAATTGACACACAACATTGTTGTCAATCTCTTCTTAGTCTCTTTGGCATAGGACTTGCAAAACACCTGAAAGAAACTTCACTCTTTCAACTCCCTAATAAAAACACTTTAAAATCTTGCTTACAAGATTTCAAACTCAAACTTTCATGCTTAAAGATCCAACCTTCGTTAGTCCCTTCTTGTTTCCACAACTCAATTCAATTTGTCACAAACAACTCAAGCTGCGCAGGTATCACAAACATCAAAGATTGGAAGCAAAAAGTTGGTAGAATTAGCCCTTTAGACACTTCTTGTAAAGGTGATTTGAAATCGGACACTAGTTGCAGCACGTGCACTAATGCTGGTTTCAAAGTCACTTCTCAGCTTACAAGTATTGATCCAAAAAATGCAACTAAGTGCTTTTTCTTTTCAGTTTTATATGCTGTTGGTATTGTGAATCATTTTGGTCCTACAGATCCTGCTACAGCTAGTTGTATACTTGGTATCCCGCTTAGAAGATGA

Protein sequence

>Msa0011010

MDNKAVFLLLLFTLIIATPSASAVSCPMDLSYVETFPWDTSTCRDPIDTQHCCQSLLSLFGIGLAKHLKETSLFQLPNKNTLKSCLQDFKLKLSCLKIQPSLVPSCFHNSIQFVTNNSSCAGITNIKDWKQKVGRISPLDTSCKGDLKSDTSCSTCTNAGFKVTSQLTSIDPKNATKCFFFSVLYAVGIVNHFGPTDPATASCILGIPLRR*