AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1350680

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 22 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAATCAGATTCAACAAAA+AGG 0.337028 tig0011794:+975 None:intergenic
TAACTGCAGAAGCTTGGTTC+TGG 0.371129 tig0011794:-688 Msa1350680:intron
CATGATCAAACGTGTGTTTG+TGG 0.422325 tig0011794:+638 None:intergenic
CACAAACACACGTTTGATCA+TGG 0.456727 tig0011794:-637 Msa1350680:CDS
ATGGAAATACGCTACCAAAC+AGG 0.473396 tig0011794:-618 Msa1350680:intron
TTTGTTGAATCTGATTGTGC+AGG 0.486427 tig0011794:-971 Msa1350680:CDS
ATTCAAGGAATGGGTCGGTT+GGG 0.489585 tig0011794:-941 Msa1350680:CDS
ACGCTGGGAGATGGTGGATC+AGG 0.490895 tig0011794:-908 Msa1350680:CDS
GATGGTGGATCAGGACTTAG+AGG 0.492687 tig0011794:-899 Msa1350680:intron
GAAGGAACAACGCTGGGAGA+TGG 0.499001 tig0011794:-917 Msa1350680:CDS
AAACAAAGGACATACCTGTT+TGG 0.500908 tig0011794:+604 None:intergenic
CCATGTTAACTGCAGAAGCT+TGG 0.501911 tig0011794:-694 Msa1350680:intron
TGTGCAGGTTGTCAGATTCA+AGG 0.512612 tig0011794:-956 Msa1350680:CDS
GATTCAAGGAATGGGTCGGT+TGG 0.520448 tig0011794:-942 Msa1350680:CDS
GGTTGTCAGATTCAAGGAAT+GGG 0.533310 tig0011794:-950 Msa1350680:CDS
AGGTTGTCAGATTCAAGGAA+TGG 0.541574 tig0011794:-951 Msa1350680:CDS
GGAATGGGTCGGTTGGGAGA+AGG 0.541805 tig0011794:-935 Msa1350680:CDS
ATCAAACGTGTGTTTGTGGA+TGG 0.552470 tig0011794:+642 None:intergenic
GGAACAACGCTGGGAGATGG+TGG 0.563155 tig0011794:-914 Msa1350680:CDS
TTGGGAGAAGGAACAACGCT+GGG 0.568199 tig0011794:-923 Msa1350680:CDS
GTCAGATTCAAGGAATGGGT+CGG 0.597985 tig0011794:-946 Msa1350680:CDS
GTTGGGAGAAGGAACAACGC+TGG 0.636641 tig0011794:-924 Msa1350680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGCATTTAAAAATAAATAT+GGG + tig0011794:719-738 None:intergenic 10.0%
!! TTTGCATTTAAAAATAAATA+TGG + tig0011794:720-739 None:intergenic 10.0%
!! TTGCATTTAAAAATAAATAT+GGG + tig0011794:719-738 None:intergenic 10.0%
!! TTTGCATTTAAAAATAAATA+TGG + tig0011794:720-739 None:intergenic 10.0%
!!! TTTCAATTTATTTTTCTCTT+TGG - tig0011794:742-761 Msa1350680:intron 15.0%
!! AAGTTTGTATTCTAATTATT+TGG - tig0011794:980-999 Msa1350680:CDS 15.0%
!!! TTTCAATTTATTTTTCTCTT+TGG - tig0011794:742-761 Msa1350680:intron 15.0%
!! AAGTTTGTATTCTAATTATT+TGG - tig0011794:980-999 Msa1350680:CDS 15.0%
!!! TTGGATACGTTTTTTATTTT+GGG + tig0011794:167-186 None:intergenic 20.0%
!!! TTGGATACGTTTTTTATTTT+GGG + tig0011794:167-186 None:intergenic 20.0%
!!! ACGTTTTTTATTTTGGGAAA+AGG + tig0011794:161-180 None:intergenic 25.0%
!!! CTTGGATACGTTTTTTATTT+TGG + tig0011794:168-187 None:intergenic 25.0%
!!! ACATTTTGATACAGAAACAA+AGG + tig0011794:415-434 None:intergenic 25.0%
!!! AACTTTTTCCAAAACTTTGA+AGG + tig0011794:505-524 None:intergenic 25.0%
!!! TTTTGGAAAAAGTTCTTGAT+GGG - tig0011794:511-530 Msa1350680:exon 25.0%
! ATTCAAAAACTTAGCTACAA+TGG + tig0011794:643-662 None:intergenic 25.0%
! CTTTGAGTAAAATAAACTCT+CGG + tig0011794:879-898 None:intergenic 25.0%
! TCAATAACAATCTCAACTAA+AGG + tig0011794:929-948 None:intergenic 25.0%
!!! ACGTTTTTTATTTTGGGAAA+AGG + tig0011794:161-180 None:intergenic 25.0%
!!! CTTGGATACGTTTTTTATTT+TGG + tig0011794:168-187 None:intergenic 25.0%
!!! ACATTTTGATACAGAAACAA+AGG + tig0011794:415-434 None:intergenic 25.0%
!!! AACTTTTTCCAAAACTTTGA+AGG + tig0011794:505-524 None:intergenic 25.0%
!!! TTTTGGAAAAAGTTCTTGAT+GGG - tig0011794:511-530 Msa1350680:exon 25.0%
! ATTCAAAAACTTAGCTACAA+TGG + tig0011794:643-662 None:intergenic 25.0%
! CTTTGAGTAAAATAAACTCT+CGG + tig0011794:879-898 None:intergenic 25.0%
! TCAATAACAATCTCAACTAA+AGG + tig0011794:929-948 None:intergenic 25.0%
CACAATCAGATTCAACAAAA+AGG + tig0011794:30-49 None:intergenic 30.0%
!! AGATTTAAAACAGAAGTGCT+TGG + tig0011794:186-205 None:intergenic 30.0%
! CAAAATGTGTTTTGCAGATT+CGG - tig0011794:427-446 Msa1350680:three_prime_UTR 30.0%
!!! GTTTTGGAAAAAGTTCTTGA+TGG - tig0011794:510-529 Msa1350680:exon 30.0%
TGCAAAAGAGAAAAATCACA+GGG + tig0011794:840-859 None:intergenic 30.0%
TTGCAAAAGAGAAAAATCAC+AGG + tig0011794:841-860 None:intergenic 30.0%
AGTAAAATAAACTCTCGGAA+TGG + tig0011794:874-893 None:intergenic 30.0%
CACAATCAGATTCAACAAAA+AGG + tig0011794:30-49 None:intergenic 30.0%
!! AGATTTAAAACAGAAGTGCT+TGG + tig0011794:186-205 None:intergenic 30.0%
! CAAAATGTGTTTTGCAGATT+CGG - tig0011794:427-446 Msa1350680:three_prime_UTR 30.0%
!!! GTTTTGGAAAAAGTTCTTGA+TGG - tig0011794:510-529 Msa1350680:exon 30.0%
TGCAAAAGAGAAAAATCACA+GGG + tig0011794:840-859 None:intergenic 30.0%
TTGCAAAAGAGAAAAATCAC+AGG + tig0011794:841-860 None:intergenic 30.0%
AGTAAAATAAACTCTCGGAA+TGG + tig0011794:874-893 None:intergenic 30.0%
TTTGTTGAATCTGATTGTGC+AGG - tig0011794:31-50 Msa1350680:three_prime_UTR 35.0%
CAGTGTGTTTATCAATTCTG+TGG - tig0011794:278-297 Msa1350680:three_prime_UTR 35.0%
AAACAAAGGACATACCTGTT+TGG + tig0011794:401-420 None:intergenic 35.0%
! GAAGTTCTCCTTCAAAGTTT+TGG - tig0011794:494-513 Msa1350680:three_prime_UTR 35.0%
! TTTTTCTCTTTGGCAGAAGT+TGG - tig0011794:752-771 Msa1350680:intron 35.0%
! CAGAATAGACAGAAGTACAT+TGG + tig0011794:802-821 None:intergenic 35.0%
ATGTACTTCTGTCTATTCTG+AGG - tig0011794:802-821 Msa1350680:intron 35.0%
AGAGAAAAATCACAGGGTAA+AGG + tig0011794:834-853 None:intergenic 35.0%
TTTGTTGAATCTGATTGTGC+AGG - tig0011794:31-50 Msa1350680:three_prime_UTR 35.0%
CAGTGTGTTTATCAATTCTG+TGG - tig0011794:278-297 Msa1350680:three_prime_UTR 35.0%
AAACAAAGGACATACCTGTT+TGG + tig0011794:401-420 None:intergenic 35.0%
! GAAGTTCTCCTTCAAAGTTT+TGG - tig0011794:494-513 Msa1350680:three_prime_UTR 35.0%
! TTTTTCTCTTTGGCAGAAGT+TGG - tig0011794:752-771 Msa1350680:intron 35.0%
! CAGAATAGACAGAAGTACAT+TGG + tig0011794:802-821 None:intergenic 35.0%
ATGTACTTCTGTCTATTCTG+AGG - tig0011794:802-821 Msa1350680:intron 35.0%
AGAGAAAAATCACAGGGTAA+AGG + tig0011794:834-853 None:intergenic 35.0%
AGGTTGTCAGATTCAAGGAA+TGG - tig0011794:51-70 Msa1350680:three_prime_UTR 40.0%
GGTTGTCAGATTCAAGGAAT+GGG - tig0011794:52-71 Msa1350680:three_prime_UTR 40.0%
ATCAAACGTGTGTTTGTGGA+TGG + tig0011794:363-382 None:intergenic 40.0%
CATGATCAAACGTGTGTTTG+TGG + tig0011794:367-386 None:intergenic 40.0%
CACAAACACACGTTTGATCA+TGG - tig0011794:365-384 Msa1350680:three_prime_UTR 40.0%
ATGGAAATACGCTACCAAAC+AGG - tig0011794:384-403 Msa1350680:three_prime_UTR 40.0%
AGGTTGTCAGATTCAAGGAA+TGG - tig0011794:51-70 Msa1350680:three_prime_UTR 40.0%
GGTTGTCAGATTCAAGGAAT+GGG - tig0011794:52-71 Msa1350680:three_prime_UTR 40.0%
ATCAAACGTGTGTTTGTGGA+TGG + tig0011794:363-382 None:intergenic 40.0%
CATGATCAAACGTGTGTTTG+TGG + tig0011794:367-386 None:intergenic 40.0%
CACAAACACACGTTTGATCA+TGG - tig0011794:365-384 Msa1350680:three_prime_UTR 40.0%
ATGGAAATACGCTACCAAAC+AGG - tig0011794:384-403 Msa1350680:three_prime_UTR 40.0%
TGTGCAGGTTGTCAGATTCA+AGG - tig0011794:46-65 Msa1350680:three_prime_UTR 45.0%
GTCAGATTCAAGGAATGGGT+CGG - tig0011794:56-75 Msa1350680:three_prime_UTR 45.0%
ATTCAAGGAATGGGTCGGTT+GGG - tig0011794:61-80 Msa1350680:three_prime_UTR 45.0%
CCAAGCTTCTGCAGTTAACA+TGG + tig0011794:311-330 None:intergenic 45.0%
CCATGTTAACTGCAGAAGCT+TGG - tig0011794:308-327 Msa1350680:three_prime_UTR 45.0%
TAACTGCAGAAGCTTGGTTC+TGG - tig0011794:314-333 Msa1350680:three_prime_UTR 45.0%
!! TCTGGAGCTTTTGTAGATCG+CGG - tig0011794:332-351 Msa1350680:three_prime_UTR 45.0%
TTCTCTTTGGCAGAAGTTGG+TGG - tig0011794:755-774 Msa1350680:intron 45.0%
TGTGCAGGTTGTCAGATTCA+AGG - tig0011794:46-65 Msa1350680:three_prime_UTR 45.0%
GTCAGATTCAAGGAATGGGT+CGG - tig0011794:56-75 Msa1350680:three_prime_UTR 45.0%
ATTCAAGGAATGGGTCGGTT+GGG - tig0011794:61-80 Msa1350680:three_prime_UTR 45.0%
CCAAGCTTCTGCAGTTAACA+TGG + tig0011794:311-330 None:intergenic 45.0%
CCATGTTAACTGCAGAAGCT+TGG - tig0011794:308-327 Msa1350680:three_prime_UTR 45.0%
TAACTGCAGAAGCTTGGTTC+TGG - tig0011794:314-333 Msa1350680:three_prime_UTR 45.0%
!! TCTGGAGCTTTTGTAGATCG+CGG - tig0011794:332-351 Msa1350680:three_prime_UTR 45.0%
TTCTCTTTGGCAGAAGTTGG+TGG - tig0011794:755-774 Msa1350680:intron 45.0%
GATTCAAGGAATGGGTCGGT+TGG - tig0011794:60-79 Msa1350680:three_prime_UTR 50.0%
TTGGGAGAAGGAACAACGCT+GGG - tig0011794:79-98 Msa1350680:three_prime_UTR 50.0%
!! GATGGTGGATCAGGACTTAG+AGG - tig0011794:103-122 Msa1350680:three_prime_UTR 50.0%
!! TTTGGCAGAAGTTGGTGGTG+AGG - tig0011794:760-779 Msa1350680:intron 50.0%
GATTCAAGGAATGGGTCGGT+TGG - tig0011794:60-79 Msa1350680:three_prime_UTR 50.0%
TTGGGAGAAGGAACAACGCT+GGG - tig0011794:79-98 Msa1350680:three_prime_UTR 50.0%
!! GATGGTGGATCAGGACTTAG+AGG - tig0011794:103-122 Msa1350680:three_prime_UTR 50.0%
!! TTTGGCAGAAGTTGGTGGTG+AGG - tig0011794:760-779 Msa1350680:intron 50.0%
GTTGGGAGAAGGAACAACGC+TGG - tig0011794:78-97 Msa1350680:three_prime_UTR 55.0%
GAAGGAACAACGCTGGGAGA+TGG - tig0011794:85-104 Msa1350680:three_prime_UTR 55.0%
GGTGGATCAGGACTTAGAGG+TGG - tig0011794:106-125 Msa1350680:three_prime_UTR 55.0%
GAGGTGGCAACTGCAACAAC+TGG - tig0011794:122-141 Msa1350680:three_prime_UTR 55.0%
GTTGGGAGAAGGAACAACGC+TGG - tig0011794:78-97 Msa1350680:three_prime_UTR 55.0%
GAAGGAACAACGCTGGGAGA+TGG - tig0011794:85-104 Msa1350680:three_prime_UTR 55.0%
GGTGGATCAGGACTTAGAGG+TGG - tig0011794:106-125 Msa1350680:three_prime_UTR 55.0%
GAGGTGGCAACTGCAACAAC+TGG - tig0011794:122-141 Msa1350680:three_prime_UTR 55.0%
GGAATGGGTCGGTTGGGAGA+AGG - tig0011794:67-86 Msa1350680:three_prime_UTR 60.0%
GGAACAACGCTGGGAGATGG+TGG - tig0011794:88-107 Msa1350680:three_prime_UTR 60.0%
!! ACGCTGGGAGATGGTGGATC+AGG - tig0011794:94-113 Msa1350680:three_prime_UTR 60.0%
GGAATGGGTCGGTTGGGAGA+AGG - tig0011794:67-86 Msa1350680:three_prime_UTR 60.0%
GGAACAACGCTGGGAGATGG+TGG - tig0011794:88-107 Msa1350680:three_prime_UTR 60.0%
!! ACGCTGGGAGATGGTGGATC+AGG - tig0011794:94-113 Msa1350680:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
tig0011794 gene 2 1022 2 ID=Msa1350680;Name=Msa1350680
tig0011794 mRNA 2 1022 2 ID=Msa1350680-mRNA-1;Parent=Msa1350680;Name=Msa1350680-mRNA-1;_AED=0.22;_eAED=0.22;_QI=0|0.5|0.66|1|0.5|0.33|3|527|70
tig0011794 exon 2 535 2 ID=Msa1350680-mRNA-1:exon:7528;Parent=Msa1350680-mRNA-1
tig0011794 exon 619 701 619 ID=Msa1350680-mRNA-1:exon:7527;Parent=Msa1350680-mRNA-1
tig0011794 exon 900 1022 900 ID=Msa1350680-mRNA-1:exon:7526;Parent=Msa1350680-mRNA-1
tig0011794 CDS 900 1022 900 ID=Msa1350680-mRNA-1:cds;Parent=Msa1350680-mRNA-1
tig0011794 CDS 619 701 619 ID=Msa1350680-mRNA-1:cds;Parent=Msa1350680-mRNA-1
tig0011794 CDS 529 535 529 ID=Msa1350680-mRNA-1:cds;Parent=Msa1350680-mRNA-1
tig0011794 three_prime_UTR 2 528 2 ID=Msa1350680-mRNA-1:three_prime_utr;Parent=Msa1350680-mRNA-1
Gene Sequence

>Msa1350680

ATGTGCAAAATTGTTGAATCTTATACCTTTTTGTTGAATCTGATTGTGCAGGTTGTCAGATTCAAGGAATGGGTCGGTTGGGAGAAGGAACAACGCTGGGAGATGGTGGATCAGGACTTAGAGAAGCTTGGTTCTGGAGCTTTTGTAGATCGCGGTGAAACCATCCACAAACACACGTTTGATCATGGAAATACGCTACCAAACAGATATTGA
Protein sequence

>Msa1350680

MCKIVESYTFLLNLIVQVVRFKEWVGWEKEQRWEMVDQDLEKLGSGAFVDRGETIHKHTFDHGNTLPNRY*