AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1030060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTGAATGTTTGTGCTTC+AGG 0.226664 7_1:-63874686 Msa1030060:five_prime_UTR
TGATAGTATCAATCTTATAT+AGG 0.366162 7_1:-63874602 Msa1030060:five_prime_UTR
TCAGTCTCAGTTTGCACGAC+TGG 0.444944 7_1:-63874566 Msa1030060:five_prime_UTR
ACACTTGATTCCCTTGCGTT+GGG 0.449797 7_1:+63874091 None:intergenic
CACACTTGATTCCCTTGCGT+TGG 0.473753 7_1:+63874090 None:intergenic
AGGAAGCAATAAATTTAAGC+TGG 0.504728 7_1:-63874630 Msa1030060:five_prime_UTR
CGAGATACAACAATCTCATC+GGG 0.510114 7_1:-63873993 Msa1030060:CDS
AATGTTTGTGCTTCAGGTGT+GGG 0.510760 7_1:-63874680 Msa1030060:five_prime_UTR
GAGATCGGAAAGTTCTTCTC+AGG 0.511097 7_1:-63874143 Msa1030060:CDS
GAATGTTTGTGCTTCAGGTG+TGG 0.525033 7_1:-63874681 Msa1030060:five_prime_UTR
CAGGAAAGTAAAACACAAGA+TGG 0.533616 7_1:-63874124 Msa1030060:CDS
GTTCCTCTGTTCCCAACGCA+AGG 0.538012 7_1:-63874102 Msa1030060:CDS
AGCAGCAACAAAAGTAGTGA+AGG 0.542395 7_1:-63874656 Msa1030060:five_prime_UTR
ATTGTGTTAGGATGGGAGAT+CGG 0.543831 7_1:-63874158 Msa1030060:intron
TCGAGATACAACAATCTCAT+CGG 0.561426 7_1:-63873994 Msa1030060:CDS
AACAAAAGTAGTGAAGGAAG+AGG 0.570751 7_1:-63874650 Msa1030060:five_prime_UTR
CAGCCGCGAGTGTTAAAAGT+GGG 0.578565 7_1:-63874063 Msa1030060:CDS
CAACGCAAGGGAATCAAGTG+TGG 0.588672 7_1:-63874089 Msa1030060:CDS
TTCCCTTGCGTTGGGAACAG+AGG 0.594506 7_1:+63874099 None:intergenic
TTCCTCTGTTCCCAACGCAA+GGG 0.617747 7_1:-63874101 Msa1030060:CDS
GCCGCGAGTGTTAAAAGTGG+GGG 0.633082 7_1:-63874061 Msa1030060:CDS
AACGCAAGGGAATCAAGTGT+GGG 0.637961 7_1:-63874088 Msa1030060:CDS
TCAGCCGCGAGTGTTAAAAG+TGG 0.638737 7_1:-63874064 Msa1030060:CDS
AGCCGCGAGTGTTAAAAGTG+GGG 0.663832 7_1:-63874062 Msa1030060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATATCAGTTATTTTTTATA+AGG + chr7_1:63874018-63874037 None:intergenic 15.0%
!!! GATATCAGTTATTTTTTATA+AGG + chr7_1:63874018-63874037 None:intergenic 15.0%
!! TGATAGTATCAATCTTATAT+AGG - chr7_1:63874119-63874138 Msa1030060:CDS 20.0%
!! TATACAATAGAATACTTAAG+TGG + chr7_1:63874403-63874422 None:intergenic 20.0%
!! TGATAGTATCAATCTTATAT+AGG - chr7_1:63874119-63874138 Msa1030060:CDS 20.0%
!! TATACAATAGAATACTTAAG+TGG + chr7_1:63874403-63874422 None:intergenic 20.0%
! TATTACATCTGTATAGTTAC+TGG - chr7_1:63874236-63874255 Msa1030060:intron 25.0%
! GAAACATGTATAGGTATAAT+TGG + chr7_1:63874491-63874510 None:intergenic 25.0%
! TATTACATCTGTATAGTTAC+TGG - chr7_1:63874236-63874255 Msa1030060:intron 25.0%
! GAAACATGTATAGGTATAAT+TGG + chr7_1:63874491-63874510 None:intergenic 25.0%
AGGAAGCAATAAATTTAAGC+TGG - chr7_1:63874091-63874110 Msa1030060:CDS 30.0%
! TCAATCGTGTCAAATTTTCT+TGG - chr7_1:63874441-63874460 Msa1030060:intron 30.0%
! CAATCGTGTCAAATTTTCTT+GGG - chr7_1:63874442-63874461 Msa1030060:intron 30.0%
GCATAGTATGAAACATGTAT+AGG + chr7_1:63874500-63874519 None:intergenic 30.0%
!! CGCATGATTTTAACATTTAC+TGG + chr7_1:63874538-63874557 None:intergenic 30.0%
! AAGAACTTGTGTTTTACTTG+CGG + chr7_1:63874691-63874710 None:intergenic 30.0%
AGGAAGCAATAAATTTAAGC+TGG - chr7_1:63874091-63874110 Msa1030060:CDS 30.0%
! TCAATCGTGTCAAATTTTCT+TGG - chr7_1:63874441-63874460 Msa1030060:intron 30.0%
! CAATCGTGTCAAATTTTCTT+GGG - chr7_1:63874442-63874461 Msa1030060:intron 30.0%
GCATAGTATGAAACATGTAT+AGG + chr7_1:63874500-63874519 None:intergenic 30.0%
!! CGCATGATTTTAACATTTAC+TGG + chr7_1:63874538-63874557 None:intergenic 30.0%
! AAGAACTTGTGTTTTACTTG+CGG + chr7_1:63874691-63874710 None:intergenic 30.0%
ATCTTGAATGTTTGTGCTTC+AGG - chr7_1:63874035-63874054 Msa1030060:CDS 35.0%
AACAAAAGTAGTGAAGGAAG+AGG - chr7_1:63874071-63874090 Msa1030060:CDS 35.0%
TACATCTGTATAGTTACTGG+TGG - chr7_1:63874239-63874258 Msa1030060:intron 35.0%
CTACCTAAGCTTCATCTATA+AGG - chr7_1:63874351-63874370 Msa1030060:intron 35.0%
ATATCATCAGTTTCCTAGCT+GGG + chr7_1:63874379-63874398 None:intergenic 35.0%
AATATCATCAGTTTCCTAGC+TGG + chr7_1:63874380-63874399 None:intergenic 35.0%
CAGGAAAGTAAAACACAAGA+TGG - chr7_1:63874597-63874616 Msa1030060:five_prime_UTR 35.0%
TCGAGATACAACAATCTCAT+CGG - chr7_1:63874727-63874746 Msa1030060:five_prime_UTR 35.0%
ATCTTGAATGTTTGTGCTTC+AGG - chr7_1:63874035-63874054 Msa1030060:CDS 35.0%
AACAAAAGTAGTGAAGGAAG+AGG - chr7_1:63874071-63874090 Msa1030060:CDS 35.0%
TACATCTGTATAGTTACTGG+TGG - chr7_1:63874239-63874258 Msa1030060:intron 35.0%
CTACCTAAGCTTCATCTATA+AGG - chr7_1:63874351-63874370 Msa1030060:intron 35.0%
ATATCATCAGTTTCCTAGCT+GGG + chr7_1:63874379-63874398 None:intergenic 35.0%
AATATCATCAGTTTCCTAGC+TGG + chr7_1:63874380-63874399 None:intergenic 35.0%
CAGGAAAGTAAAACACAAGA+TGG - chr7_1:63874597-63874616 Msa1030060:five_prime_UTR 35.0%
TCGAGATACAACAATCTCAT+CGG - chr7_1:63874727-63874746 Msa1030060:five_prime_UTR 35.0%
AATGTTTGTGCTTCAGGTGT+GGG - chr7_1:63874041-63874060 Msa1030060:CDS 40.0%
AGCAGCAACAAAAGTAGTGA+AGG - chr7_1:63874065-63874084 Msa1030060:CDS 40.0%
! TCTAAGATGCGCACCTAATT+TGG - chr7_1:63874264-63874283 Msa1030060:intron 40.0%
CTAAGATGCGCACCTAATTT+GGG - chr7_1:63874265-63874284 Msa1030060:intron 40.0%
TAAGATGCGCACCTAATTTG+GGG - chr7_1:63874266-63874285 Msa1030060:intron 40.0%
AAGTTTCCAGTGGCCAATAA+GGG + chr7_1:63874305-63874324 None:intergenic 40.0%
GTGCCTTATAGATGAAGCTT+AGG + chr7_1:63874357-63874376 None:intergenic 40.0%
TCATGCGCTTGAATTGTGTT+AGG - chr7_1:63874551-63874570 Msa1030060:five_prime_UTR 40.0%
CGCTTGAATTGTGTTAGGAT+GGG - chr7_1:63874556-63874575 Msa1030060:five_prime_UTR 40.0%
ATTGTGTTAGGATGGGAGAT+CGG - chr7_1:63874563-63874582 Msa1030060:five_prime_UTR 40.0%
CGAGATACAACAATCTCATC+GGG - chr7_1:63874728-63874747 Msa1030060:five_prime_UTR 40.0%
AATGTTTGTGCTTCAGGTGT+GGG - chr7_1:63874041-63874060 Msa1030060:CDS 40.0%
AGCAGCAACAAAAGTAGTGA+AGG - chr7_1:63874065-63874084 Msa1030060:CDS 40.0%
! TCTAAGATGCGCACCTAATT+TGG - chr7_1:63874264-63874283 Msa1030060:intron 40.0%
CTAAGATGCGCACCTAATTT+GGG - chr7_1:63874265-63874284 Msa1030060:intron 40.0%
TAAGATGCGCACCTAATTTG+GGG - chr7_1:63874266-63874285 Msa1030060:intron 40.0%
AAGTTTCCAGTGGCCAATAA+GGG + chr7_1:63874305-63874324 None:intergenic 40.0%
GTGCCTTATAGATGAAGCTT+AGG + chr7_1:63874357-63874376 None:intergenic 40.0%
TCATGCGCTTGAATTGTGTT+AGG - chr7_1:63874551-63874570 Msa1030060:five_prime_UTR 40.0%
CGCTTGAATTGTGTTAGGAT+GGG - chr7_1:63874556-63874575 Msa1030060:five_prime_UTR 40.0%
ATTGTGTTAGGATGGGAGAT+CGG - chr7_1:63874563-63874582 Msa1030060:five_prime_UTR 40.0%
CGAGATACAACAATCTCATC+GGG - chr7_1:63874728-63874747 Msa1030060:five_prime_UTR 40.0%
GAATGTTTGTGCTTCAGGTG+TGG - chr7_1:63874040-63874059 Msa1030060:CDS 45.0%
! TGTACGCTTGCTACCCTTAT+TGG - chr7_1:63874289-63874308 Msa1030060:intron 45.0%
CAAGTTTCCAGTGGCCAATA+AGG + chr7_1:63874306-63874325 None:intergenic 45.0%
TTCCTCTGACAAGTTTCCAG+TGG + chr7_1:63874315-63874334 None:intergenic 45.0%
GCGCTTGAATTGTGTTAGGA+TGG - chr7_1:63874555-63874574 Msa1030060:five_prime_UTR 45.0%
GAGATCGGAAAGTTCTTCTC+AGG - chr7_1:63874578-63874597 Msa1030060:five_prime_UTR 45.0%
ACACTTGATTCCCTTGCGTT+GGG + chr7_1:63874633-63874652 None:intergenic 45.0%
AACGCAAGGGAATCAAGTGT+GGG - chr7_1:63874633-63874652 Msa1030060:five_prime_UTR 45.0%
GAATGTTTGTGCTTCAGGTG+TGG - chr7_1:63874040-63874059 Msa1030060:CDS 45.0%
! TGTACGCTTGCTACCCTTAT+TGG - chr7_1:63874289-63874308 Msa1030060:intron 45.0%
CAAGTTTCCAGTGGCCAATA+AGG + chr7_1:63874306-63874325 None:intergenic 45.0%
TTCCTCTGACAAGTTTCCAG+TGG + chr7_1:63874315-63874334 None:intergenic 45.0%
GCGCTTGAATTGTGTTAGGA+TGG - chr7_1:63874555-63874574 Msa1030060:five_prime_UTR 45.0%
GAGATCGGAAAGTTCTTCTC+AGG - chr7_1:63874578-63874597 Msa1030060:five_prime_UTR 45.0%
ACACTTGATTCCCTTGCGTT+GGG + chr7_1:63874633-63874652 None:intergenic 45.0%
AACGCAAGGGAATCAAGTGT+GGG - chr7_1:63874633-63874652 Msa1030060:five_prime_UTR 45.0%
TCAGTCTCAGTTTGCACGAC+TGG - chr7_1:63874155-63874174 Msa1030060:intron 50.0%
GCAAGCGTACACCCCAAATT+AGG + chr7_1:63874280-63874299 None:intergenic 50.0%
TTGCTACCCTTATTGGCCAC+TGG - chr7_1:63874296-63874315 Msa1030060:intron 50.0%
! CATCTATAAGGCACCCAGCT+AGG - chr7_1:63874363-63874382 Msa1030060:intron 50.0%
TTCCTCTGTTCCCAACGCAA+GGG - chr7_1:63874620-63874639 Msa1030060:five_prime_UTR 50.0%
CACACTTGATTCCCTTGCGT+TGG + chr7_1:63874634-63874653 None:intergenic 50.0%
CAACGCAAGGGAATCAAGTG+TGG - chr7_1:63874632-63874651 Msa1030060:five_prime_UTR 50.0%
TCAGCCGCGAGTGTTAAAAG+TGG - chr7_1:63874657-63874676 Msa1030060:five_prime_UTR 50.0%
CAGCCGCGAGTGTTAAAAGT+GGG - chr7_1:63874658-63874677 Msa1030060:five_prime_UTR 50.0%
AGCCGCGAGTGTTAAAAGTG+GGG - chr7_1:63874659-63874678 Msa1030060:five_prime_UTR 50.0%
!! TCCCCCACTTTTAACACTCG+CGG + chr7_1:63874664-63874683 None:intergenic 50.0%
TCAGTCTCAGTTTGCACGAC+TGG - chr7_1:63874155-63874174 Msa1030060:intron 50.0%
GCAAGCGTACACCCCAAATT+AGG + chr7_1:63874280-63874299 None:intergenic 50.0%
TTGCTACCCTTATTGGCCAC+TGG - chr7_1:63874296-63874315 Msa1030060:intron 50.0%
! CATCTATAAGGCACCCAGCT+AGG - chr7_1:63874363-63874382 Msa1030060:intron 50.0%
TTCCTCTGTTCCCAACGCAA+GGG - chr7_1:63874620-63874639 Msa1030060:five_prime_UTR 50.0%
CACACTTGATTCCCTTGCGT+TGG + chr7_1:63874634-63874653 None:intergenic 50.0%
CAACGCAAGGGAATCAAGTG+TGG - chr7_1:63874632-63874651 Msa1030060:five_prime_UTR 50.0%
TCAGCCGCGAGTGTTAAAAG+TGG - chr7_1:63874657-63874676 Msa1030060:five_prime_UTR 50.0%
CAGCCGCGAGTGTTAAAAGT+GGG - chr7_1:63874658-63874677 Msa1030060:five_prime_UTR 50.0%
AGCCGCGAGTGTTAAAAGTG+GGG - chr7_1:63874659-63874678 Msa1030060:five_prime_UTR 50.0%
!! TCCCCCACTTTTAACACTCG+CGG + chr7_1:63874664-63874683 None:intergenic 50.0%
GGCCACTGGAAACTTGTCAG+AGG - chr7_1:63874310-63874329 Msa1030060:intron 55.0%
GTTCCTCTGTTCCCAACGCA+AGG - chr7_1:63874619-63874638 Msa1030060:five_prime_UTR 55.0%
TTCCCTTGCGTTGGGAACAG+AGG + chr7_1:63874625-63874644 None:intergenic 55.0%
GCCGCGAGTGTTAAAAGTGG+GGG - chr7_1:63874660-63874679 Msa1030060:five_prime_UTR 55.0%
GGCCACTGGAAACTTGTCAG+AGG - chr7_1:63874310-63874329 Msa1030060:intron 55.0%
GTTCCTCTGTTCCCAACGCA+AGG - chr7_1:63874619-63874638 Msa1030060:five_prime_UTR 55.0%
TTCCCTTGCGTTGGGAACAG+AGG + chr7_1:63874625-63874644 None:intergenic 55.0%
GCCGCGAGTGTTAAAAGTGG+GGG - chr7_1:63874660-63874679 Msa1030060:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 63873990 63874753 63873990 ID=Msa1030060;Name=Msa1030060
chr7_1 mRNA 63873990 63874753 63873990 ID=Msa1030060-mRNA-1;Parent=Msa1030060;Name=Msa1030060-mRNA-1;_AED=0.00;_eAED=0.00;_QI=208|1|0.5|1|0|0|2|0|64
chr7_1 exon 63873990 63874170 63873990 ID=Msa1030060-mRNA-1:exon:13940;Parent=Msa1030060-mRNA-1
chr7_1 exon 63874535 63874753 63874535 ID=Msa1030060-mRNA-1:exon:13939;Parent=Msa1030060-mRNA-1
chr7_1 five_prime_UTR 63874546 63874753 63874546 ID=Msa1030060-mRNA-1:five_prime_utr;Parent=Msa1030060-mRNA-1
chr7_1 CDS 63874535 63874545 63874535 ID=Msa1030060-mRNA-1:cds;Parent=Msa1030060-mRNA-1
chr7_1 CDS 63873990 63874170 63873990 ID=Msa1030060-mRNA-1:cds;Parent=Msa1030060-mRNA-1
Gene Sequence

>Msa1030060

ATGCTAATCATGATGGGAGATCGGAAAGTTCTTCTCAGGAAAGTAAAACACAAGATGGTTCCTCTGTTCCCAACGCAAGGGAATCAAGTGTGGGATCAGCCGCGAGTGTTAAAAGTGGGGGATCAGCCGCAAGTAAAACACAAGTTCTTCAGTGCTGTTAAAAGCTCGAGATACAACAATCTCATCGGGTAT
Protein sequence

>Msa1030060

MLIMMGDRKVLLRKVKHKMVPLFPTQGNQVWDQPRVLKVGDQPQVKHKFFSAVKSSRYNNLIGY