AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG040441


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040441 MtrunA17_Chr7g0270251 99.307 433 3 0 1 433 1 433 0.0 893
MsaG040441 MtrunA17_Chr1g0194351 69.340 424 102 4 1 412 1 408 0.0 583
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040441 AT2G47210.3 69.841 441 120 6 2 433 5 441 0.0 607
MsaG040441 AT2G47210.1 69.841 441 120 6 2 433 5 441 0.0 607
MsaG040441 AT2G47210.2 69.841 441 120 6 2 433 5 441 0.0 607

Find 100 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATACCAATATACCTGTTTC+TGG 0.156332 7:+100220070 None:intergenic
ATTCCCGATTCGTTGAATTT+TGG 0.213340 7:-100219648 MsaT040441.1:CDS
CTTGCCAGGGCTGCATCTTC+CGG 0.253582 7:-100222211 MsaT040441.1:CDS
TTTCTCTTGTTGTCTTGTTT+GGG 0.260220 7:+100221952 None:intergenic
ATTTCTTGTGAAACATTATA+TGG 0.283878 7:+100222007 None:intergenic
TCGGACTGTAGAGGAGTTAA+AGG 0.299488 7:-100222450 MsaT040441.1:CDS
TTTGACTTCACCTTAATGAT+AGG 0.315672 7:+100222172 None:intergenic
TTGCCAGGGCTGCATCTTCC+GGG 0.316334 7:-100222210 MsaT040441.1:CDS
AGGCGAAAGGGTTGGCAAAA+AGG 0.324610 7:-100219521 MsaT040441.1:CDS
TGCAACACATCCTATCATTA+AGG 0.347399 7:-100222182 MsaT040441.1:intron
ATGGACGCGAAGGATATTCT+TGG 0.347443 7:-100223777 MsaT040441.1:CDS
ATCATCTTTACGAGCAGAAT+TGG 0.368961 7:+100223298 None:intergenic
CACAAGAAATGGAGCGAAAA+CGG 0.373448 7:-100221994 MsaT040441.1:CDS
ATATAATGTTTCACAAGAAA+TGG 0.380297 7:-100222005 MsaT040441.1:CDS
TTTAGCTACCTTGTTGTACT+TGG 0.384441 7:+100223127 None:intergenic
TCCCTGTCATGTAGTGTTGC+GGG 0.387723 7:-100222242 MsaT040441.1:intron
CGAGTTACGGATGGCTTCTA+AGG 0.391035 7:-100221788 MsaT040441.1:intron
AATTGAGAAGCATCAATTGA+TGG 0.396902 7:+100223530 None:intergenic
ACCTCCAAAATTCAACGAAT+CGG 0.405812 7:+100219644 None:intergenic
CTTGTTGTCTTGTTTGGGAG+AGG 0.408483 7:+100221957 None:intergenic
TTTCCGACCTTTGGTGTGCC+TGG 0.419064 7:+100219778 None:intergenic
TTCAGCTTCGTGTATATTTG+AGG 0.419331 7:-100220503 MsaT040441.1:intron
TCCTCTACAGTCCGAGATGA+TGG 0.419890 7:+100222458 None:intergenic
AGCAAACATTGCAAGATCTC+GGG 0.423802 7:-100220410 MsaT040441.1:CDS
TGCGGGCTATATTACTTGCC+AGG 0.427836 7:-100222225 MsaT040441.1:CDS
ATGATCTTCATCTTTACCAT+TGG 0.430773 7:-100223280 MsaT040441.1:CDS
TGATCTTCATCTTTACCATT+GGG 0.431644 7:-100223279 MsaT040441.1:intron
ACAAGAAATGGAGCGAAAAC+GGG 0.436669 7:-100221993 MsaT040441.1:CDS
GGTTACTGAACAGTCTCAAT+TGG 0.436817 7:-100221088 MsaT040441.1:CDS
GTCAATGGTGTTCTACCTAC+TGG 0.449074 7:-100223164 MsaT040441.1:CDS
ATGGCTGAATCTCCAGAAAC+AGG 0.450187 7:-100220082 MsaT040441.1:intron
GCAGAAGGCACAACCATTTG+TGG 0.456839 7:+100220985 None:intergenic
TAATTCATTTGTCTCCTCCT+TGG 0.460992 7:+100222535 None:intergenic
AACTGTTGTTTCAGGCGAAA+GGG 0.463388 7:-100219533 MsaT040441.1:intron
CCTCCAAAATTCAACGAATC+GGG 0.465713 7:+100219645 None:intergenic
CAAGCTTCAAACTCAACTGC+TGG 0.466195 7:-100220456 MsaT040441.1:CDS
CTGGAGTTCGGACTATCAAA+CGG 0.471345 7:-100220437 MsaT040441.1:CDS
GACATATGCACTCGAGCAAA+TGG 0.476593 7:-100220481 MsaT040441.1:CDS
GAATGTGCAACTTCCACAAA+TGG 0.479963 7:-100220998 MsaT040441.1:CDS
GAGCAAACATTGCAAGATCT+CGG 0.481522 7:-100220411 MsaT040441.1:CDS
GCATCAATTGATGGCATAAG+AGG 0.485257 7:+100223539 None:intergenic
TAAAAGACCTAGAAAACAAA+AGG 0.485836 7:-100219335 MsaT040441.1:CDS
GCGAAAACGGGCACTGTCCA+TGG 0.488734 7:-100221981 MsaT040441.1:CDS
TTTCAGGTTCGAGTAGTCAA+TGG 0.491064 7:-100223179 MsaT040441.1:intron
ACCTAGAAAACAAAAGGCCT+CGG 0.494235 7:-100219329 MsaT040441.1:CDS
TACTCTAGCTTCTCTTCGCA+TGG 0.494649 7:-100220950 MsaT040441.1:intron
GTCCCCGGAAGATGCAGCCC+TGG 0.501841 7:+100222207 None:intergenic
AAACTGTTGTTTCAGGCGAA+AGG 0.502998 7:-100219534 MsaT040441.1:intron
ACAAGAGAAAAGAGATGAAG+AGG 0.510309 7:-100221939 MsaT040441.1:intron
CAAACTCAACTGCTGGAGTT+CGG 0.511526 7:-100220449 MsaT040441.1:CDS
ATCACGGAAAGATGAACCTT+CGG 0.512389 7:+100219819 None:intergenic
ACCTCGCGTGAAATGCCATC+AGG 0.515608 7:+100223681 None:intergenic
GTCCCTGTCATGTAGTGTTG+CGG 0.515697 7:-100222243 MsaT040441.1:intron
ACTTTATTTGTATAGGGGCA+TGG 0.516874 7:-100219379 MsaT040441.1:intron
AAAGCCTCCTACTCACGAAA+AGG 0.530448 7:-100223501 MsaT040441.1:intron
TGGAGTTCGGACTATCAAAC+GGG 0.542516 7:-100220436 MsaT040441.1:CDS
TCTTTCCGTGATGGATCCTA+CGG 0.547451 7:-100219808 MsaT040441.1:CDS
TTAAAGGATCGATATTATAG+TGG 0.547811 7:-100222434 MsaT040441.1:intron
GAAGGTTCATCTTTCCGTGA+TGG 0.548182 7:-100219817 MsaT040441.1:CDS
CTTAGAAGCCATCCGTAACT+CGG 0.558886 7:+100221789 None:intergenic
GTTGCAGAGAGGGCTGTCCC+TGG 0.559311 7:-100221039 MsaT040441.1:CDS
TGTGGAAGTTGCACATTCGA+AGG 0.559456 7:+100221003 None:intergenic
TATCAGCTATAACAACAAAA+CGG 0.560637 7:+100222486 None:intergenic
GTTGTTTCAGGCGAAAGGGT+TGG 0.562497 7:-100219529 MsaT040441.1:intron
TTTCTCTGAGATTCTTTGGG+AGG 0.563303 7:+100223705 None:intergenic
TAGGTTTATGCACTTACTGG+TGG 0.564499 7:-100223569 MsaT040441.1:CDS
TGCCAGGGCTGCATCTTCCG+GGG 0.572929 7:-100222209 MsaT040441.1:CDS
GTAGAAGCATTATCTGCAGA+AGG 0.577553 7:+100220970 None:intergenic
TCCAGGTAAATTTGAAACCG+AGG 0.579026 7:-100220161 MsaT040441.1:intron
CCAGGTAAATTTGAAACCGA+GGG 0.579215 7:-100220160 MsaT040441.1:intron
CTGATAGGTTCCCATCATCT+CGG 0.582805 7:-100222469 MsaT040441.1:CDS
TCTTGTTTGGGAGAGGACCA+TGG 0.585148 7:+100221964 None:intergenic
TTACGAGCAGAATTGGTGAA+AGG 0.585208 7:+100223305 None:intergenic
ACCTGATGGCATTTCACGCG+AGG 0.587818 7:-100223682 MsaT040441.1:intron
GCGGGCTATATTACTTGCCA+GGG 0.590495 7:-100222224 MsaT040441.1:CDS
CCTCTACAGTCCGAGATGAT+GGG 0.592270 7:+100222459 None:intergenic
TGTGCCTGGTGTTTCACCGT+AGG 0.598536 7:+100219792 None:intergenic
GGATCCTACGGTGAAACACC+AGG 0.600080 7:-100219796 MsaT040441.1:CDS
GTGGCAGGTGCAATATAAAG+AGG 0.604781 7:-100219842 MsaT040441.1:intron
GAAACCCTAAATGGACGCGA+AGG 0.605606 7:-100223787 None:intergenic
CCCATCATCTCGGACTGTAG+AGG 0.606561 7:-100222459 MsaT040441.1:CDS
TGATGCAGAAGTTGCAGAGA+GGG 0.607610 7:-100221049 MsaT040441.1:CDS
GAAGGAGATACAGTTTCACC+AGG 0.611694 7:+100221021 None:intergenic
AAGAATAGCCGAGTTACGGA+TGG 0.620429 7:-100221797 MsaT040441.1:CDS
GCAAAAGAATAGTCTCCAGT+AGG 0.625902 7:+100223149 None:intergenic
TCAATTGATGGCATAAGAGG+TGG 0.628674 7:+100223542 None:intergenic
AATTATTTGATTTGTGTGAG+AGG 0.630139 7:-100222517 MsaT040441.1:CDS
GAATCTCAGAGAAAACCTGA+TGG 0.650054 7:-100223696 MsaT040441.1:CDS
GCAAACATTGCAAGATCTCG+GGG 0.655130 7:-100220409 MsaT040441.1:intron
AGGATGTGTTGCAATGTCCC+CGG 0.656289 7:+100222192 None:intergenic
TGAAACACCAGGCACACCAA+AGG 0.660161 7:-100219785 MsaT040441.1:intron
CCGGAGGAATTAAAGATCCG+AGG 0.665879 7:+100219312 None:intergenic
GTGCAATATAAAGAGGCCGA+AGG 0.666909 7:-100219835 MsaT040441.1:CDS
ATCTACCTAGATGTGGACCA+AGG 0.676327 7:-100222552 MsaT040441.1:intron
CATCATCAAATACACAGACG+AGG 0.685360 7:-100223012 MsaT040441.1:CDS
TAAGAAGAGAAATACTAACA+TGG 0.691447 7:-100220101 MsaT040441.1:CDS
CTGATGCAGAAGTTGCAGAG+AGG 0.692246 7:-100221050 MsaT040441.1:CDS
TTTCACCGTAGGATCCATCA+CGG 0.706383 7:+100219803 None:intergenic
AAGGAGATACAGTTTCACCA+GGG 0.739390 7:+100221022 None:intergenic
TACCTAGATGTGGACCAAGG+AGG 0.740553 7:-100222549 MsaT040441.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 100219321 100223799 100219321 ID=MsaG040441
Chr7 mRNA 100219321 100223799 100219321 ID=MsaT040441.1;Parent=MsaG040441
Chr7 exon 100219321 100219386 100219321 ID=MsaT040441.1.exon16;Parent=MsaT040441.1
Chr7 CDS 100219321 100219386 100219321 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100219507 100219541 100219507 ID=MsaT040441.1.exon15;Parent=MsaT040441.1
Chr7 CDS 100219507 100219541 100219507 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100219646 100219682 100219646 ID=MsaT040441.1.exon14;Parent=MsaT040441.1
Chr7 CDS 100219646 100219682 100219646 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100219786 100219857 100219786 ID=MsaT040441.1.exon13;Parent=MsaT040441.1
Chr7 CDS 100219786 100219857 100219786 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100220083 100220178 100220083 ID=MsaT040441.1.exon12;Parent=MsaT040441.1
Chr7 CDS 100220083 100220178 100220083 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100220410 100220520 100220410 ID=MsaT040441.1.exon11;Parent=MsaT040441.1
Chr7 CDS 100220410 100220520 100220410 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100220951 100221109 100220951 ID=MsaT040441.1.exon10;Parent=MsaT040441.1
Chr7 CDS 100220951 100221109 100220951 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100221789 100221836 100221789 ID=MsaT040441.1.exon9;Parent=MsaT040441.1
Chr7 CDS 100221789 100221836 100221789 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100221940 100222032 100221940 ID=MsaT040441.1.exon8;Parent=MsaT040441.1
Chr7 CDS 100221940 100222032 100221940 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100222183 100222250 100222183 ID=MsaT040441.1.exon7;Parent=MsaT040441.1
Chr7 CDS 100222183 100222250 100222183 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100222435 100222564 100222435 ID=MsaT040441.1.exon6;Parent=MsaT040441.1
Chr7 CDS 100222435 100222564 100222435 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100222986 100223042 100222986 ID=MsaT040441.1.exon5;Parent=MsaT040441.1
Chr7 CDS 100222986 100223042 100222986 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100223136 100223195 100223136 ID=MsaT040441.1.exon4;Parent=MsaT040441.1
Chr7 CDS 100223136 100223195 100223136 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100223280 100223345 100223280 ID=MsaT040441.1.exon3;Parent=MsaT040441.1
Chr7 CDS 100223280 100223345 100223280 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100223502 100223588 100223502 ID=MsaT040441.1.exon2;Parent=MsaT040441.1
Chr7 CDS 100223502 100223588 100223502 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Chr7 exon 100223683 100223799 100223683 ID=MsaT040441.1.exon1;Parent=MsaT040441.1
Chr7 CDS 100223683 100223799 100223683 ID=cds.MsaT040441.1;Parent=MsaT040441.1
Gene Sequence

>MsaT040441.1

ATGGACGCGAAGGATATTCTTGGTTTGCACAAAAACTCATTTCCATCTTCTCTTGATAATAAAAAATCTCGACCTCCCAAAGAATCTCAGAGAAAACCTGATGGCATTTCACGCGAGGTTTATGCACTTACTGGTGGAATGCCACCTCTTATGCCATCAATTGATGCTTCTCAATTGAAGAAAAAGCCTCCTACTCACGAAAAGGTTACTTGGCAATGGCTTCCTTTCACCAATTCTGCTCGTAAAGATGATCTTCATCTTTACCATTGGGTTCGAGTAGTCAATGGTGTTCTACCTACTGGAGACTATTCTTTTGCCAAGTACAACAAGTCTGTTGACATCATCAAATACACAGACGAGGAATACGAAAAGTATTTGACAGATCCTATGTGGACCAAGGAGGAGACAAATGAATTATTTGATTTGTGTGAGAGGTTCGATCTCCGTTTTGTTGTTATAGCTGATAGGTTCCCATCATCTCGGACTGTAGAGGAGTTAAAGGATCGATATTATAGTGTGTTGCGGGCTATATTACTTGCCAGGGCTGCATCTTCCGGGGACATTGCAACACATCCTATCATTAAGGAACCATATAATGTTTCACAAGAAATGGAGCGAAAACGGGCACTGTCCATGGTCCTCTCCCAAACAAGACAACAAGAGAAAAGAGATGAAGAGGTTCTTATTGAAGCAAAAAGAATAGCCGAGTTACGGATGGCTTCTAAGGTTACTGAACAGTCTCAATTGGCTGTTGCTTCAAATGCTGATGCAGAAGTTGCAGAGAGGGCTGTCCCTGGTGAAACTGTATCTCCTTCGAATGTGCAACTTCCACAAATGGTTGTGCCTTCTGCAGATAATGCTTCTACTCTAGCTTCTCTTCGCATGCTTCGTGTATATTTGAGGACATATGCACTCGAGCAAATGGTGCAAGCTTCAAACTCAACTGCTGGAGTTCGGACTATCAAACGGGTTGAGCAAACATTGCAAGATCTCGGGGTAAATTTGAAACCGAGGGTTCCAACAAAAGCTGTTTGTGCAGAGCATCTTGAACTAAGAAGAGAAATACTAACATGGCTGAATCTCCAGAAACAGGTGCAATATAAAGAGGCCGAAGGTTCATCTTTCCGTGATGGATCCTACGGTGAAACACCAGGCACACCAAAGGATCGTACATTTATTCCCGATTCGTTGAATTTTGGAGGCGAAAGGGTTGGCAAAAAGGACCAAAAACGCAAGGGGCATGGAGCTCCACCTACAGCAGCTCATAAAAGACCTAGAAAACAAAAGGCCTCGGATCTTTAA

Protein sequence

>MsaT040441.1

MDAKDILGLHKNSFPSSLDNKKSRPPKESQRKPDGISREVYALTGGMPPLMPSIDASQLKKKPPTHEKVTWQWLPFTNSARKDDLHLYHWVRVVNGVLPTGDYSFAKYNKSVDIIKYTDEEYEKYLTDPMWTKEETNELFDLCERFDLRFVVIADRFPSSRTVEELKDRYYSVLRAILLARAASSGDIATHPIIKEPYNVSQEMERKRALSMVLSQTRQQEKRDEEVLIEAKRIAELRMASKVTEQSQLAVASNADAEVAERAVPGETVSPSNVQLPQMVVPSADNASTLASLRMLRVYLRTYALEQMVQASNSTAGVRTIKRVEQTLQDLGVNLKPRVPTKAVCAEHLELRREILTWLNLQKQVQYKEAEGSSFRDGSYGETPGTPKDRTFIPDSLNFGGERVGKKDQKRKGHGAPPTAAHKRPRKQKASDL*