AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0056220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0056220 MtrunA17_Chr1g0148121 91.463 82 7 0 1 82 1 82 8.70e-46 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 152 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCGAGTGCGAATTTCGAATT+TGG 0.238449 1_2:+11750684 Msa0056220:CDS
CTATTTCGCCGGGAAGTAAT+CGG 0.364776 1_2:+11750650 Msa0056220:CDS
TCGAATTTGGCGTCGACGAC+GGG 0.372561 1_2:+11750697 Msa0056220:CDS
ACATTCTTCCGATTACTTCC+CGG 0.401889 1_2:-11750658 None:intergenic
TTATTCAGCATCTCTAGAAC+CGG 0.421788 1_2:-11752013 None:intergenic
TTGGCGTCGACGACGGGAAA+CGG 0.455624 1_2:+11750703 Msa0056220:CDS
TCCTCAATTGACTATTTCGC+CGG 0.488550 1_2:+11750639 Msa0056220:CDS
TTCGAATTTGGCGTCGACGA+CGG 0.501571 1_2:+11750696 Msa0056220:CDS
CCTCAATTGACTATTTCGCC+GGG 0.561696 1_2:+11750640 Msa0056220:CDS
CAATCTCAGGTGAGTACTTG+CGG 0.570802 1_2:-11750822 None:intergenic
GAAGTAATCGGAAGAATGTA+CGG 0.573623 1_2:+11750662 Msa0056220:CDS
GTTGACGCAGAAGGATTCCA+TGG 0.577555 1_2:-11750599 None:intergenic
GAATTACTCGGCAGCTGCAA+CGG 0.582790 1_2:-11750739 None:intergenic
TTATTCGACTTTGAATTACT+CGG 0.586429 1_2:-11750751 None:intergenic
AAAGTCGAATAATAGTGCGT+TGG 0.608667 1_2:+11750762 Msa0056220:CDS
TCAGGTGAGTACTTGCGGAA+AGG 0.614975 1_2:-11750817 None:intergenic
CGGGAAACGGTGCTGTTGTG+AGG 0.619284 1_2:+11750716 Msa0056220:CDS
CCCGGCGAAATAGTCAATTG+AGG 0.628438 1_2:-11750640 None:intergenic
GTACAAAGAGTTGACGCAGA+AGG 0.631834 1_2:-11750608 None:intergenic
GAGCAGCTTGATATTGAGCG+TGG 0.673845 1_2:+11750784 Msa0056220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTACTTTTGAATTTT+AGG + chr1_2:11751450-11751469 Msa0056220:intron 10.0%
!!! TTTTATTACTTTTGAATTTT+AGG + chr1_2:11751450-11751469 Msa0056220:intron 10.0%
!!! CACTTGATATTTTAGAATTT+TGG + chr1_2:11751643-11751662 Msa0056220:intron 20.0%
!!! TTCTAAAAAGAAATTAAGTG+TGG - chr1_2:11751739-11751758 None:intergenic 20.0%
!!! TATGTTTGGATAGATAATTT+TGG - chr1_2:11751819-11751838 None:intergenic 20.0%
!! CAGTCAACTTATTTATTTAT+TGG + chr1_2:11751968-11751987 Msa0056220:intron 20.0%
!!! CACTTGATATTTTAGAATTT+TGG + chr1_2:11751643-11751662 Msa0056220:intron 20.0%
!!! TTCTAAAAAGAAATTAAGTG+TGG - chr1_2:11751739-11751758 None:intergenic 20.0%
!!! TATGTTTGGATAGATAATTT+TGG - chr1_2:11751819-11751838 None:intergenic 20.0%
!! CAGTCAACTTATTTATTTAT+TGG + chr1_2:11751968-11751987 Msa0056220:intron 20.0%
! TTATTCGACTTTGAATTACT+CGG - chr1_2:11750754-11750773 None:intergenic 25.0%
! TAAAAAAAACGTACAATCTC+AGG - chr1_2:11750838-11750857 None:intergenic 25.0%
!! ATTGTTCTCTTAGTCTATTT+TGG + chr1_2:11750976-11750995 Msa0056220:intron 25.0%
! TTCATAAGTTCTTCCAAATA+CGG + chr1_2:11751046-11751065 Msa0056220:intron 25.0%
! AGAAATAAGTCAATCCAAAT+GGG - chr1_2:11751072-11751091 None:intergenic 25.0%
!!! TAGATAATTTTGGAGTTGAA+GGG - chr1_2:11751809-11751828 None:intergenic 25.0%
!!! ATAGATAATTTTGGAGTTGA+AGG - chr1_2:11751810-11751829 None:intergenic 25.0%
!! ATGTTAATTGATGGTATGTT+TGG - chr1_2:11751833-11751852 None:intergenic 25.0%
! ATCAATTAACATGTAGGAAT+GGG + chr1_2:11751841-11751860 Msa0056220:intron 25.0%
! TTATTCGACTTTGAATTACT+CGG - chr1_2:11750754-11750773 None:intergenic 25.0%
! TAAAAAAAACGTACAATCTC+AGG - chr1_2:11750838-11750857 None:intergenic 25.0%
!! ATTGTTCTCTTAGTCTATTT+TGG + chr1_2:11750976-11750995 Msa0056220:intron 25.0%
! TTCATAAGTTCTTCCAAATA+CGG + chr1_2:11751046-11751065 Msa0056220:intron 25.0%
! AGAAATAAGTCAATCCAAAT+GGG - chr1_2:11751072-11751091 None:intergenic 25.0%
!!! TAGATAATTTTGGAGTTGAA+GGG - chr1_2:11751809-11751828 None:intergenic 25.0%
!!! ATAGATAATTTTGGAGTTGA+AGG - chr1_2:11751810-11751829 None:intergenic 25.0%
!! ATGTTAATTGATGGTATGTT+TGG - chr1_2:11751833-11751852 None:intergenic 25.0%
! ATCAATTAACATGTAGGAAT+GGG + chr1_2:11751841-11751860 Msa0056220:intron 25.0%
CAGAAATAAGTCAATCCAAA+TGG - chr1_2:11751073-11751092 None:intergenic 30.0%
! AGAATTTTGGATTGTCTTGA+AGG + chr1_2:11751656-11751675 Msa0056220:intron 30.0%
! GAATTTTGGATTGTCTTGAA+GGG + chr1_2:11751657-11751676 Msa0056220:intron 30.0%
CATACCATCAATTAACATGT+AGG + chr1_2:11751835-11751854 Msa0056220:intron 30.0%
CATTCCTACATGTTAATTGA+TGG - chr1_2:11751842-11751861 None:intergenic 30.0%
CATCAATTAACATGTAGGAA+TGG + chr1_2:11751840-11751859 Msa0056220:intron 30.0%
! TCTCTTTGGGAAAACAAAAT+TGG + chr1_2:11751935-11751954 Msa0056220:intron 30.0%
! CTCTTTGGGAAAACAAAATT+GGG + chr1_2:11751936-11751955 Msa0056220:intron 30.0%
!! ATTGGATACTAGTTCTAAGT+TGG + chr1_2:11751986-11752005 Msa0056220:intron 30.0%
CAGAAATAAGTCAATCCAAA+TGG - chr1_2:11751073-11751092 None:intergenic 30.0%
! AGAATTTTGGATTGTCTTGA+AGG + chr1_2:11751656-11751675 Msa0056220:intron 30.0%
! GAATTTTGGATTGTCTTGAA+GGG + chr1_2:11751657-11751676 Msa0056220:intron 30.0%
CATACCATCAATTAACATGT+AGG + chr1_2:11751835-11751854 Msa0056220:intron 30.0%
CATTCCTACATGTTAATTGA+TGG - chr1_2:11751842-11751861 None:intergenic 30.0%
CATCAATTAACATGTAGGAA+TGG + chr1_2:11751840-11751859 Msa0056220:intron 30.0%
! TCTCTTTGGGAAAACAAAAT+TGG + chr1_2:11751935-11751954 Msa0056220:intron 30.0%
! CTCTTTGGGAAAACAAAATT+GGG + chr1_2:11751936-11751955 Msa0056220:intron 30.0%
!! ATTGGATACTAGTTCTAAGT+TGG + chr1_2:11751986-11752005 Msa0056220:intron 30.0%
GAAGTAATCGGAAGAATGTA+CGG + chr1_2:11750662-11750681 Msa0056220:CDS 35.0%
AAAGTCGAATAATAGTGCGT+TGG + chr1_2:11750762-11750781 Msa0056220:CDS 35.0%
CATTATTCGTAAGCTTGTCA+AGG + chr1_2:11751135-11751154 Msa0056220:intron 35.0%
CGTTAGCCAAACACAATTAA+GGG - chr1_2:11751368-11751387 None:intergenic 35.0%
CTAGTCACACTCAACTTATT+TGG + chr1_2:11751475-11751494 Msa0056220:intron 35.0%
CAACAACCAAACTAACTAGT+TGG - chr1_2:11751516-11751535 None:intergenic 35.0%
!!! TAATTTTGGAGTTGAAGGGT+GGG - chr1_2:11751805-11751824 None:intergenic 35.0%
!!! ATAATTTTGGAGTTGAAGGG+TGG - chr1_2:11751806-11751825 None:intergenic 35.0%
! TTAACATGTAGGAATGGGTT+TGG + chr1_2:11751846-11751865 Msa0056220:intron 35.0%
! TAACATGTAGGAATGGGTTT+GGG + chr1_2:11751847-11751866 Msa0056220:intron 35.0%
AGTGAGGATCTCATTGTTAA+GGG - chr1_2:11751874-11751893 None:intergenic 35.0%
AAGTGAGGATCTCATTGTTA+AGG - chr1_2:11751875-11751894 None:intergenic 35.0%
AGATCCTCACTTTATGTGTA+TGG + chr1_2:11751883-11751902 Msa0056220:intron 35.0%
GATCCTCACTTTATGTGTAT+GGG + chr1_2:11751884-11751903 Msa0056220:intron 35.0%
TATCCCATACACATAAAGTG+AGG - chr1_2:11751890-11751909 None:intergenic 35.0%
!! TTATTCAGCATCTCTAGAAC+CGG - chr1_2:11752016-11752035 None:intergenic 35.0%
GAAGTAATCGGAAGAATGTA+CGG + chr1_2:11750662-11750681 Msa0056220:CDS 35.0%
AAAGTCGAATAATAGTGCGT+TGG + chr1_2:11750762-11750781 Msa0056220:CDS 35.0%
CATTATTCGTAAGCTTGTCA+AGG + chr1_2:11751135-11751154 Msa0056220:intron 35.0%
CGTTAGCCAAACACAATTAA+GGG - chr1_2:11751368-11751387 None:intergenic 35.0%
CTAGTCACACTCAACTTATT+TGG + chr1_2:11751475-11751494 Msa0056220:intron 35.0%
CAACAACCAAACTAACTAGT+TGG - chr1_2:11751516-11751535 None:intergenic 35.0%
!!! TAATTTTGGAGTTGAAGGGT+GGG - chr1_2:11751805-11751824 None:intergenic 35.0%
!!! ATAATTTTGGAGTTGAAGGG+TGG - chr1_2:11751806-11751825 None:intergenic 35.0%
! TTAACATGTAGGAATGGGTT+TGG + chr1_2:11751846-11751865 Msa0056220:intron 35.0%
! TAACATGTAGGAATGGGTTT+GGG + chr1_2:11751847-11751866 Msa0056220:intron 35.0%
AGTGAGGATCTCATTGTTAA+GGG - chr1_2:11751874-11751893 None:intergenic 35.0%
AAGTGAGGATCTCATTGTTA+AGG - chr1_2:11751875-11751894 None:intergenic 35.0%
AGATCCTCACTTTATGTGTA+TGG + chr1_2:11751883-11751902 Msa0056220:intron 35.0%
GATCCTCACTTTATGTGTAT+GGG + chr1_2:11751884-11751903 Msa0056220:intron 35.0%
TATCCCATACACATAAAGTG+AGG - chr1_2:11751890-11751909 None:intergenic 35.0%
!! TTATTCAGCATCTCTAGAAC+CGG - chr1_2:11752016-11752035 None:intergenic 35.0%
TCCTCAATTGACTATTTCGC+CGG + chr1_2:11750639-11750658 Msa0056220:CDS 40.0%
ACATTCTTCCGATTACTTCC+CGG - chr1_2:11750661-11750680 None:intergenic 40.0%
AAGGGTCTGCTTAGATTGTT+TGG - chr1_2:11751350-11751369 None:intergenic 40.0%
AGCAGACCCTTAATTGTGTT+TGG + chr1_2:11751359-11751378 Msa0056220:intron 40.0%
GCGTTAGCCAAACACAATTA+AGG - chr1_2:11751369-11751388 None:intergenic 40.0%
CTTATTTGGCACTTGAGTGA+TGG + chr1_2:11751489-11751508 Msa0056220:intron 40.0%
GATGGTCCAACTAGTTAGTT+TGG + chr1_2:11751507-11751526 Msa0056220:intron 40.0%
AAGAGACACAAGTGTCAAGT+AGG + chr1_2:11751540-11751559 Msa0056220:intron 40.0%
TGTCAAGTAGGTAGCTAGAT+TGG + chr1_2:11751552-11751571 Msa0056220:intron 40.0%
!! ACGTCGGAGAAGTTTTAACA+AGG + chr1_2:11751586-11751605 Msa0056220:intron 40.0%
!! TCGGAGAAGTTTTAACAAGG+AGG + chr1_2:11751589-11751608 Msa0056220:intron 40.0%
!!! AATTTTGGAGTTGAAGGGTG+GGG - chr1_2:11751804-11751823 None:intergenic 40.0%
!! CTAGTTCTAAGTTGGTAGTC+CGG + chr1_2:11751994-11752013 Msa0056220:intron 40.0%
TCCTCAATTGACTATTTCGC+CGG + chr1_2:11750639-11750658 Msa0056220:CDS 40.0%
ACATTCTTCCGATTACTTCC+CGG - chr1_2:11750661-11750680 None:intergenic 40.0%
AAGGGTCTGCTTAGATTGTT+TGG - chr1_2:11751350-11751369 None:intergenic 40.0%
AGCAGACCCTTAATTGTGTT+TGG + chr1_2:11751359-11751378 Msa0056220:intron 40.0%
GCGTTAGCCAAACACAATTA+AGG - chr1_2:11751369-11751388 None:intergenic 40.0%
CTTATTTGGCACTTGAGTGA+TGG + chr1_2:11751489-11751508 Msa0056220:intron 40.0%
GATGGTCCAACTAGTTAGTT+TGG + chr1_2:11751507-11751526 Msa0056220:intron 40.0%
AAGAGACACAAGTGTCAAGT+AGG + chr1_2:11751540-11751559 Msa0056220:intron 40.0%
TGTCAAGTAGGTAGCTAGAT+TGG + chr1_2:11751552-11751571 Msa0056220:intron 40.0%
!! ACGTCGGAGAAGTTTTAACA+AGG + chr1_2:11751586-11751605 Msa0056220:intron 40.0%
!! TCGGAGAAGTTTTAACAAGG+AGG + chr1_2:11751589-11751608 Msa0056220:intron 40.0%
!!! AATTTTGGAGTTGAAGGGTG+GGG - chr1_2:11751804-11751823 None:intergenic 40.0%
!! CTAGTTCTAAGTTGGTAGTC+CGG + chr1_2:11751994-11752013 Msa0056220:intron 40.0%
GTACAAAGAGTTGACGCAGA+AGG - chr1_2:11750611-11750630 None:intergenic 45.0%
CCTCAATTGACTATTTCGCC+GGG + chr1_2:11750640-11750659 Msa0056220:CDS 45.0%
CTATTTCGCCGGGAAGTAAT+CGG + chr1_2:11750650-11750669 Msa0056220:CDS 45.0%
GCGAGTGCGAATTTCGAATT+TGG + chr1_2:11750684-11750703 Msa0056220:CDS 45.0%
CAATCTCAGGTGAGTACTTG+CGG - chr1_2:11750825-11750844 None:intergenic 45.0%
TCTTCCAAATACGGCCCATT+TGG + chr1_2:11751055-11751074 Msa0056220:intron 45.0%
CAATCCAAATGGGCCGTATT+TGG - chr1_2:11751062-11751081 None:intergenic 45.0%
!! AAGCACTTGTGAGAGTGTTC+GGG - chr1_2:11751297-11751316 None:intergenic 45.0%
!! CAAGCACTTGTGAGAGTGTT+CGG - chr1_2:11751298-11751317 None:intergenic 45.0%
! ATTGGTGATCTGAGAGACGT+CGG + chr1_2:11751570-11751589 Msa0056220:intron 45.0%
ACCTTGTTGAACTTGAGAGC+AGG + chr1_2:11751911-11751930 Msa0056220:intron 45.0%
CCTTGTTGAACTTGAGAGCA+GGG + chr1_2:11751912-11751931 Msa0056220:intron 45.0%
GGGAAAACAAAATTGGGTGC+TGG + chr1_2:11751942-11751961 Msa0056220:intron 45.0%
GTACAAAGAGTTGACGCAGA+AGG - chr1_2:11750611-11750630 None:intergenic 45.0%
CCTCAATTGACTATTTCGCC+GGG + chr1_2:11750640-11750659 Msa0056220:CDS 45.0%
CTATTTCGCCGGGAAGTAAT+CGG + chr1_2:11750650-11750669 Msa0056220:CDS 45.0%
GCGAGTGCGAATTTCGAATT+TGG + chr1_2:11750684-11750703 Msa0056220:CDS 45.0%
CAATCTCAGGTGAGTACTTG+CGG - chr1_2:11750825-11750844 None:intergenic 45.0%
TCTTCCAAATACGGCCCATT+TGG + chr1_2:11751055-11751074 Msa0056220:intron 45.0%
CAATCCAAATGGGCCGTATT+TGG - chr1_2:11751062-11751081 None:intergenic 45.0%
!! AAGCACTTGTGAGAGTGTTC+GGG - chr1_2:11751297-11751316 None:intergenic 45.0%
!! CAAGCACTTGTGAGAGTGTT+CGG - chr1_2:11751298-11751317 None:intergenic 45.0%
! ATTGGTGATCTGAGAGACGT+CGG + chr1_2:11751570-11751589 Msa0056220:intron 45.0%
ACCTTGTTGAACTTGAGAGC+AGG + chr1_2:11751911-11751930 Msa0056220:intron 45.0%
CCTTGTTGAACTTGAGAGCA+GGG + chr1_2:11751912-11751931 Msa0056220:intron 45.0%
GGGAAAACAAAATTGGGTGC+TGG + chr1_2:11751942-11751961 Msa0056220:intron 45.0%
CCCGGCGAAATAGTCAATTG+AGG - chr1_2:11750643-11750662 None:intergenic 50.0%
!! TTCGAATTTGGCGTCGACGA+CGG + chr1_2:11750696-11750715 Msa0056220:CDS 50.0%
GAATTACTCGGCAGCTGCAA+CGG - chr1_2:11750742-11750761 None:intergenic 50.0%
GAGCAGCTTGATATTGAGCG+TGG + chr1_2:11750784-11750803 Msa0056220:CDS 50.0%
TCAGGTGAGTACTTGCGGAA+AGG - chr1_2:11750820-11750839 None:intergenic 50.0%
CCCTGCTCTCAAGTTCAACA+AGG - chr1_2:11751915-11751934 None:intergenic 50.0%
ACTTGAGAGCAGGGTCTCTT+TGG + chr1_2:11751921-11751940 Msa0056220:intron 50.0%
CTTGAGAGCAGGGTCTCTTT+GGG + chr1_2:11751922-11751941 Msa0056220:intron 50.0%
CCCGGCGAAATAGTCAATTG+AGG - chr1_2:11750643-11750662 None:intergenic 50.0%
!! TTCGAATTTGGCGTCGACGA+CGG + chr1_2:11750696-11750715 Msa0056220:CDS 50.0%
GAATTACTCGGCAGCTGCAA+CGG - chr1_2:11750742-11750761 None:intergenic 50.0%
GAGCAGCTTGATATTGAGCG+TGG + chr1_2:11750784-11750803 Msa0056220:CDS 50.0%
TCAGGTGAGTACTTGCGGAA+AGG - chr1_2:11750820-11750839 None:intergenic 50.0%
CCCTGCTCTCAAGTTCAACA+AGG - chr1_2:11751915-11751934 None:intergenic 50.0%
ACTTGAGAGCAGGGTCTCTT+TGG + chr1_2:11751921-11751940 Msa0056220:intron 50.0%
CTTGAGAGCAGGGTCTCTTT+GGG + chr1_2:11751922-11751941 Msa0056220:intron 50.0%
!! TCGAATTTGGCGTCGACGAC+GGG + chr1_2:11750697-11750716 Msa0056220:CDS 55.0%
!! TCGAATTTGGCGTCGACGAC+GGG + chr1_2:11750697-11750716 Msa0056220:CDS 55.0%
!! TTGGCGTCGACGACGGGAAA+CGG + chr1_2:11750703-11750722 Msa0056220:CDS 60.0%
!! CGGGAAACGGTGCTGTTGTG+AGG + chr1_2:11750716-11750735 Msa0056220:CDS 60.0%
!! TTGGCGTCGACGACGGGAAA+CGG + chr1_2:11750703-11750722 Msa0056220:CDS 60.0%
!! CGGGAAACGGTGCTGTTGTG+AGG + chr1_2:11750716-11750735 Msa0056220:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 11750601 11752035 11750601 ID=Msa0056220;Name=Msa0056220
chr1_2 mRNA 11750601 11752035 11750601 ID=Msa0056220-mRNA-1;Parent=Msa0056220;Name=Msa0056220-mRNA-1;_AED=0.52;_eAED=0.52;_QI=0|0|0|0.33|1|1|3|0|90
chr1_2 exon 11750601 11750843 11750601 ID=Msa0056220-mRNA-1:exon:4509;Parent=Msa0056220-mRNA-1
chr1_2 exon 11751472 11751477 11751472 ID=Msa0056220-mRNA-1:exon:4510;Parent=Msa0056220-mRNA-1
chr1_2 exon 11752012 11752035 11752012 ID=Msa0056220-mRNA-1:exon:4511;Parent=Msa0056220-mRNA-1
chr1_2 CDS 11750601 11750843 11750601 ID=Msa0056220-mRNA-1:cds;Parent=Msa0056220-mRNA-1
chr1_2 CDS 11751472 11751477 11751472 ID=Msa0056220-mRNA-1:cds;Parent=Msa0056220-mRNA-1
chr1_2 CDS 11752012 11752035 11752012 ID=Msa0056220-mRNA-1:cds;Parent=Msa0056220-mRNA-1
Gene Sequence

>Msa0056220

ATGGAATCCTTCTGCGTCAACTCTTTGTACACAGTTTCTCCTCAATTGACTATTTCGCCGGGAAGTAATCGGAAGAATGTACGGCGAGTGCGAATTTCGAATTTGGCGTCGACGACGGGAAACGGTGCTGTTGTGAGGCCGTTGCAGCTGCCGAGTAATTCAAAGTCGAATAATAGTGCGTTGGAGCAGCTTGATATTGAGCGTGGTGTTTGTATACCTTTCCGCAAGTACTCACCTGAGATTGTGCTATCCGGTTCTAGAGATGCTGAATAA

Protein sequence

>Msa0056220

MESFCVNSLYTVSPQLTISPGSNRKNVRRVRISNLASTTGNGAVVRPLQLPSNSKSNNSALEQLDIERGVCIPFRKYSPEIVLSGSRDAE*