AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0643470

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0643470 MtrunA17_Chr4g0029791 97.872 94 2 0 1 94 1 94 6.33e-65 190
Msa0643470 MtrunA17_Chr2g0326261 45.361 97 27 4 1 94 1 74 1.80e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0643470 AT5G60400.3 40.449 89 51 1 6 94 5 91 9.26e-12 56.2

Find 25 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGTACTGTTCTTTCTTTC+TGG 0.038179 4_3:-46461639 None:intergenic
GGAGTTCCTCTCTGTCTTTC+TGG 0.075036 4_3:+46461768 Msa0643470:CDS
GTTTAACATGGACTGCATTT+TGG 0.222924 4_3:-46461730 None:intergenic
AAAATCAAATATGCATCTTT+TGG 0.233478 4_3:+46462385 Msa0643470:three_prime_UTR
ACTTACTAGAATGTTAATTT+AGG 0.250075 4_3:-46462281 None:intergenic
AAAAGCTGCTTAGTTAGATT+TGG 0.304540 4_3:+46462148 Msa0643470:exon
CGAAGTTTCACCCTATTCAT+TGG 0.395651 4_3:-46462328 None:intergenic
TGATGATGATCTTGAAGATC+TGG 0.442771 4_3:+46462076 Msa0643470:CDS
TTCGTACGGACATATTTGTA+TGG 0.453259 4_3:+46462347 Msa0643470:three_prime_UTR
AGTGCATGCAAATCAAGAAA+AGG 0.472454 4_3:+46462010 Msa0643470:CDS
GACTGATGTGACCAATGAAT+AGG 0.482367 4_3:+46462317 Msa0643470:three_prime_UTR
TTAAACCTTCGTGCTACTCA+TGG 0.498021 4_3:+46461747 Msa0643470:CDS
ACTGATGTGACCAATGAATA+GGG 0.501250 4_3:+46462318 Msa0643470:three_prime_UTR
ACCGAAGAAGAAAAGATATG+AGG 0.524381 4_3:+46461976 Msa0643470:CDS
GTGCATGCAAATCAAGAAAA+GGG 0.524986 4_3:+46462011 Msa0643470:CDS
CTGTCTCTTACTTATCTCAC+AGG 0.529035 4_3:+46462116 Msa0643470:CDS
TACTCTTTGGAAAGAGCAAG+AGG 0.575505 4_3:-46461801 None:intergenic
AACATTCTAGTAAGTTCAGA+CGG 0.600784 4_3:+46462289 Msa0643470:three_prime_UTR
TTTGGAAAGAGCAAGAGGGT+TGG 0.601098 4_3:-46461796 None:intergenic
AAAAGGATGGGAAATAAAGG+AGG 0.624688 4_3:-46461679 None:intergenic
GAATAGGGTGAAACTTCGTA+CGG 0.636390 4_3:+46462333 Msa0643470:three_prime_UTR
ACTCTTTGGAAAGAGCAAGA+GGG 0.667434 4_3:-46461800 None:intergenic
AGTAGCACGAAGGTTTAACA+TGG 0.672060 4_3:-46461742 None:intergenic
GTGATTCCAGAAAGACAGAG+AGG 0.712435 4_3:-46461774 None:intergenic
GAACTCCATGAGTAGCACGA+AGG 0.732005 4_3:-46461752 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTAATTAATTTACTCTT+TGG - chr4_3:46461817-46461836 None:intergenic 10.0%
!! AAATTAATTAATTTACTCTT+TGG - chr4_3:46461817-46461836 None:intergenic 10.0%
!! TGATATATGTTTGAATTTGA+TGG + chr4_3:46461934-46461953 Msa0643470:intron 20.0%
!! ACTTACTAGAATGTTAATTT+AGG - chr4_3:46462284-46462303 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG - chr4_3:46462381-46462400 None:intergenic 20.0%
!!! AAAATCAAATATGCATCTTT+TGG + chr4_3:46462385-46462404 Msa0643470:three_prime_UTR 20.0%
!! TGATATATGTTTGAATTTGA+TGG + chr4_3:46461934-46461953 Msa0643470:intron 20.0%
!! ACTTACTAGAATGTTAATTT+AGG - chr4_3:46462284-46462303 None:intergenic 20.0%
!!! ATGCATATTTGATTTTGATT+TGG - chr4_3:46462381-46462400 None:intergenic 20.0%
!!! AAAATCAAATATGCATCTTT+TGG + chr4_3:46462385-46462404 Msa0643470:three_prime_UTR 20.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG - chr4_3:46461699-46461718 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG - chr4_3:46461707-46461726 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG - chr4_3:46461713-46461732 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG + chr4_3:46462043-46462062 Msa0643470:CDS 25.0%
!! TTTTCTAGGTAAAGGAAAAA+AGG - chr4_3:46461699-46461718 None:intergenic 25.0%
!!! GTTTTGTTTTTTCTAGGTAA+AGG - chr4_3:46461707-46461726 None:intergenic 25.0%
!!! TGGTTTGTTTTGTTTTTTCT+AGG - chr4_3:46461713-46461732 None:intergenic 25.0%
!! TCAAAGAAACAATGATTTTG+TGG + chr4_3:46462043-46462062 Msa0643470:CDS 25.0%
ATAGTACTGTTCTTTCTTTC+TGG - chr4_3:46461642-46461661 None:intergenic 30.0%
GAAAAAAGGATGGGAAATAA+AGG - chr4_3:46461685-46461704 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG - chr4_3:46461694-46461713 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG - chr4_3:46461980-46461999 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG + chr4_3:46462053-46462072 Msa0643470:CDS 30.0%
AAAAGCTGCTTAGTTAGATT+TGG + chr4_3:46462148-46462167 Msa0643470:exon 30.0%
! TCTAGATCACTTTCATTTTC+TGG + chr4_3:46462185-46462204 Msa0643470:three_prime_UTR 30.0%
AACATTCTAGTAAGTTCAGA+CGG + chr4_3:46462289-46462308 Msa0643470:three_prime_UTR 30.0%
ATAGTACTGTTCTTTCTTTC+TGG - chr4_3:46461642-46461661 None:intergenic 30.0%
GAAAAAAGGATGGGAAATAA+AGG - chr4_3:46461685-46461704 None:intergenic 30.0%
TAGGTAAAGGAAAAAAGGAT+GGG - chr4_3:46461694-46461713 None:intergenic 30.0%
! TCCTCATATCTTTTCTTCTT+CGG - chr4_3:46461980-46461999 None:intergenic 30.0%
! AATGATTTTGTGGAGATGAA+AGG + chr4_3:46462053-46462072 Msa0643470:CDS 30.0%
AAAAGCTGCTTAGTTAGATT+TGG + chr4_3:46462148-46462167 Msa0643470:exon 30.0%
! TCTAGATCACTTTCATTTTC+TGG + chr4_3:46462185-46462204 Msa0643470:three_prime_UTR 30.0%
AACATTCTAGTAAGTTCAGA+CGG + chr4_3:46462289-46462308 Msa0643470:three_prime_UTR 30.0%
AAAAGGATGGGAAATAAAGG+AGG - chr4_3:46461682-46461701 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG - chr4_3:46461695-46461714 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG - chr4_3:46461733-46461752 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG - chr4_3:46461875-46461894 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG + chr4_3:46461940-46461959 Msa0643470:intron 35.0%
ACCGAAGAAGAAAAGATATG+AGG + chr4_3:46461976-46461995 Msa0643470:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG + chr4_3:46462010-46462029 Msa0643470:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG + chr4_3:46462011-46462030 Msa0643470:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG + chr4_3:46462076-46462095 Msa0643470:CDS 35.0%
ACTGATGTGACCAATGAATA+GGG + chr4_3:46462318-46462337 Msa0643470:three_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG + chr4_3:46462347-46462366 Msa0643470:three_prime_UTR 35.0%
AAAAGGATGGGAAATAAAGG+AGG - chr4_3:46461682-46461701 None:intergenic 35.0%
CTAGGTAAAGGAAAAAAGGA+TGG - chr4_3:46461695-46461714 None:intergenic 35.0%
!! GTTTAACATGGACTGCATTT+TGG - chr4_3:46461733-46461752 None:intergenic 35.0%
GTGAGATCATAGATCAAAAG+AGG - chr4_3:46461875-46461894 None:intergenic 35.0%
!! ATGTTTGAATTTGATGGTGC+AGG + chr4_3:46461940-46461959 Msa0643470:intron 35.0%
ACCGAAGAAGAAAAGATATG+AGG + chr4_3:46461976-46461995 Msa0643470:CDS 35.0%
AGTGCATGCAAATCAAGAAA+AGG + chr4_3:46462010-46462029 Msa0643470:CDS 35.0%
GTGCATGCAAATCAAGAAAA+GGG + chr4_3:46462011-46462030 Msa0643470:CDS 35.0%
! TGATGATGATCTTGAAGATC+TGG + chr4_3:46462076-46462095 Msa0643470:CDS 35.0%
ACTGATGTGACCAATGAATA+GGG + chr4_3:46462318-46462337 Msa0643470:three_prime_UTR 35.0%
TTCGTACGGACATATTTGTA+TGG + chr4_3:46462347-46462366 Msa0643470:three_prime_UTR 35.0%
AGTAGCACGAAGGTTTAACA+TGG - chr4_3:46461745-46461764 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG + chr4_3:46461747-46461766 Msa0643470:CDS 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG - chr4_3:46461803-46461822 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG - chr4_3:46461804-46461823 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG + chr4_3:46461944-46461963 Msa0643470:intron 40.0%
CTGTCTCTTACTTATCTCAC+AGG + chr4_3:46462116-46462135 Msa0643470:CDS 40.0%
GACTGATGTGACCAATGAAT+AGG + chr4_3:46462317-46462336 Msa0643470:three_prime_UTR 40.0%
CGAAGTTTCACCCTATTCAT+TGG - chr4_3:46462331-46462350 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG + chr4_3:46462333-46462352 Msa0643470:three_prime_UTR 40.0%
AGTAGCACGAAGGTTTAACA+TGG - chr4_3:46461745-46461764 None:intergenic 40.0%
! TTAAACCTTCGTGCTACTCA+TGG + chr4_3:46461747-46461766 Msa0643470:CDS 40.0%
! ACTCTTTGGAAAGAGCAAGA+GGG - chr4_3:46461803-46461822 None:intergenic 40.0%
! TACTCTTTGGAAAGAGCAAG+AGG - chr4_3:46461804-46461823 None:intergenic 40.0%
!! TTGAATTTGATGGTGCAGGA+TGG + chr4_3:46461944-46461963 Msa0643470:intron 40.0%
CTGTCTCTTACTTATCTCAC+AGG + chr4_3:46462116-46462135 Msa0643470:CDS 40.0%
GACTGATGTGACCAATGAAT+AGG + chr4_3:46462317-46462336 Msa0643470:three_prime_UTR 40.0%
CGAAGTTTCACCCTATTCAT+TGG - chr4_3:46462331-46462350 None:intergenic 40.0%
GAATAGGGTGAAACTTCGTA+CGG + chr4_3:46462333-46462352 Msa0643470:three_prime_UTR 40.0%
GTGATTCCAGAAAGACAGAG+AGG - chr4_3:46461777-46461796 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG - chr4_3:46461799-46461818 None:intergenic 45.0%
GTGATTCCAGAAAGACAGAG+AGG - chr4_3:46461777-46461796 None:intergenic 45.0%
TTTGGAAAGAGCAAGAGGGT+TGG - chr4_3:46461799-46461818 None:intergenic 45.0%
GAACTCCATGAGTAGCACGA+AGG - chr4_3:46461755-46461774 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG + chr4_3:46461768-46461787 Msa0643470:CDS 50.0%
GAACTCCATGAGTAGCACGA+AGG - chr4_3:46461755-46461774 None:intergenic 50.0%
GGAGTTCCTCTCTGTCTTTC+TGG + chr4_3:46461768-46461787 Msa0643470:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 46461603 46462409 46461603 ID=Msa0643470;Name=Msa0643470
chr4_3 mRNA 46461603 46462409 46461603 ID=Msa0643470-mRNA-1;Parent=Msa0643470;Name=Msa0643470-mRNA-1;_AED=0.09;_eAED=0.09;_QI=132|1|1|1|1|1|2|249|94
chr4_3 exon 46461603 46461820 46461603 ID=Msa0643470-mRNA-1:exon:10793;Parent=Msa0643470-mRNA-1
chr4_3 exon 46461962 46462409 46461962 ID=Msa0643470-mRNA-1:exon:10794;Parent=Msa0643470-mRNA-1
chr4_3 five_prime_UTR 46461603 46461734 46461603 ID=Msa0643470-mRNA-1:five_prime_utr;Parent=Msa0643470-mRNA-1
chr4_3 CDS 46461735 46461820 46461735 ID=Msa0643470-mRNA-1:cds;Parent=Msa0643470-mRNA-1
chr4_3 CDS 46461962 46462160 46461962 ID=Msa0643470-mRNA-1:cds;Parent=Msa0643470-mRNA-1
chr4_3 three_prime_UTR 46462161 46462409 46462161 ID=Msa0643470-mRNA-1:three_prime_utr;Parent=Msa0643470-mRNA-1
Gene Sequence

>Msa0643470

ATGCAGTCCATGTTAAACCTTCGTGCTACTCATGGAGTTCCTCTCTGTCTTTCTGGAATCACCAACCCTCTTGCTCTTTCCAAAGAGATGGCAGATCACGACCGAAGAAGAAAAGATATGAGGAAGCAAAGATCAGTGCATGCAAATCAAGAAAAGGGTGCACAAAGTCAAAGAAACAATGATTTTGTGGAGATGAAAGGTGATGATGATCTTGAAGATCTGGATGAAATCTTGCATCAACTGTCTCTTACTTATCTCACAGGTTTATCAGCAAAAGCTGCTTAG
Protein sequence

>Msa0643470

MQSMLNLRATHGVPLCLSGITNPLALSKEMADHDRRRKDMRKQRSVHANQEKGAQSQRNNDFVEMKGDDDLEDLDEILHQLSLTYLTGLSAKAA*