AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG029222

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG029222 MtrunA17_Chr5g0441991 95.221 544 12 1 1 530 1 544 0.0 1067
MsaG029222 MtrunA17_Chr3g0094681 56.134 538 195 9 1 529 1 506 0.0 530
MsaG029222 MtrunA17_Chr4g0046591 53.571 56 26 0 20 75 33 88 3.37e-13 72.8
MsaG029222 MtrunA17_Chr2g0282771 51.724 58 28 0 20 77 42 99 1.21e-12 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG029222 AT4G03250.1 39.964 548 265 15 3 530 4 507 7.49e-85 272
MsaG029222 AT1G28420.1 55.357 56 25 0 20 75 41 96 1.87e-14 77.4

Find 117 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACTCCTTTGCACATTCTT+TGG 0.238382 5:-74687432 None:intergenic
TTGACAGAAAAGCAAGTTTC+TGG 0.248103 5:+74683654 MsaT029222.1:CDS
TCACTCCTTTGCGCTTTCTT+TGG 0.251232 5:-74687495 None:intergenic
GATTGCACCTTTCGGATTTA+AGG 0.253961 5:-74684051 None:intergenic
CCATTGCTCTCAACCTCTTT+AGG 0.268733 5:-74683840 None:intergenic
AAGAAAGAGGGCTATCTTCT+AGG 0.323284 5:+74687535 MsaT029222.1:CDS
GTGCAGGATGAATTGTTTAA+AGG 0.329048 5:+74687657 MsaT029222.1:intron
GTTGCATGATGTTCATGTTC+AGG 0.329068 5:+74687134 MsaT029222.1:CDS
CAAAACGCCTGCACAGCTTA+AGG 0.338384 5:+74683479 MsaT029222.1:CDS
CTGAAAAGTTTGTCTATGTT+TGG 0.340704 5:-74687187 None:intergenic
CAGGATCGTGGCAGTGGACT+TGG 0.340987 5:+74683768 MsaT029222.1:CDS
ACTGCTGTTAAGAAGCAATT+AGG 0.344355 5:+74684137 MsaT029222.1:CDS
ACATGGTGATTATAAGTATC+TGG 0.364601 5:+74683815 MsaT029222.1:CDS
CCCATGTTGATTGCACCTTT+CGG 0.370330 5:-74684059 None:intergenic
CTCCTTCCATATGAGTATCT+TGG 0.372564 5:-74687098 None:intergenic
GGAACCTGTTTCATATTGTA+TGG 0.374331 5:-74687901 None:intergenic
CCTTTGCACATTCTTTGGAT+TGG 0.379454 5:-74687427 None:intergenic
GAATTTGATCCACTTCCTCC+TGG 0.387621 5:+74684197 MsaT029222.1:CDS
CATGAACTGCGTCTTCAGTT+TGG 0.394238 5:-74684232 None:intergenic
GCAATTAGGAAGGAATTATC+AGG 0.404766 5:+74684151 MsaT029222.1:CDS
CAATCAATCCAGTGAGGAAC+TGG 0.405732 5:-74688687 None:intergenic
TGCAGGATGAATTGTTTAAA+GGG 0.406045 5:+74687658 MsaT029222.1:intron
TCCTTCCATATGAGTATCTT+GGG 0.407012 5:-74687097 None:intergenic
GCTAATTTCAATTCCTCTGT+TGG 0.408111 5:-74683612 None:intergenic
ACAACATTGCTAAGAATCAT+AGG 0.408486 5:+74687283 MsaT029222.1:CDS
CAAACTGAAGACGCAGTTCA+TGG 0.411080 5:+74684233 MsaT029222.1:CDS
CTAGAAGGCTCCATCTCATA+TGG 0.414116 5:-74684008 None:intergenic
CTTGGTTCTATCTCAGCAAC+AGG 0.414880 5:-74687922 None:intergenic
AAAACGCCTGCACAGCTTAA+GGG 0.415864 5:+74683480 MsaT029222.1:CDS
TATCGCGATGCAGGTGGAGC+AGG 0.417846 5:+74687702 MsaT029222.1:CDS
ATTGCACCTTTCGGATTTAA+GGG 0.420903 5:-74684050 None:intergenic
AGAGTCTTCGTACAAATCTA+AGG 0.421428 5:-74687244 None:intergenic
TCAACCATACAATATGAAAC+AGG 0.427437 5:+74687897 MsaT029222.1:CDS
CAAGTCCACTGCCACGATCC+TGG 0.429748 5:-74683767 None:intergenic
GATGCTTTCAAATGAGACTA+TGG 0.432046 5:+74687725 MsaT029222.1:CDS
ATGAAATCTACTGAAGAAAG+AGG 0.433865 5:+74687522 MsaT029222.1:CDS
GAAGAGCAGGATCAGCAATA+TGG 0.436376 5:-74686584 None:intergenic
AAAGAAGAAGCAAATGCTAA+TGG 0.457102 5:+74683717 MsaT029222.1:CDS
TCCAATCCCTTAAGCTGTGC+AGG 0.458833 5:-74683486 None:intergenic
CAGGAAGATGGTCCACTACT+TGG 0.459717 5:+74684170 MsaT029222.1:CDS
GCTCCATCTCATATGGATCT+TGG 0.461565 5:-74684001 None:intergenic
CATATGGAAGGAGTTGACTT+TGG 0.462273 5:+74687108 MsaT029222.1:CDS
TTTGTCTATGTTTGGTACCA+TGG 0.463442 5:-74687179 None:intergenic
GGATTCCAAGCGTGGTGTTG+AGG 0.467670 5:+74687308 MsaT029222.1:CDS
TTTCTTCATAGCGATCACTA+TGG 0.468844 5:-74687356 None:intergenic
GATTCCAAGCGTGGTGTTGA+GGG 0.471960 5:+74687309 MsaT029222.1:CDS
ATGAATTGTTTAAAGGGGAC+AGG 0.473398 5:+74687664 MsaT029222.1:CDS
AGAGCTTTACTATATCTAGA+AGG 0.474291 5:-74684023 None:intergenic
GGGAAGTCTGAATGTTTGAC+TGG 0.478673 5:-74687384 None:intergenic
TCAAATGCCCCAGGAGGAAG+TGG 0.480809 5:-74684206 None:intergenic
TCTGGAGAATTCAGAAGAGC+AGG 0.481510 5:-74686597 None:intergenic
CATACCCTCAACACCACGCT+TGG 0.482706 5:-74687313 None:intergenic
GTCATCCAGGATCGTGGCAG+TGG 0.484263 5:+74683762 MsaT029222.1:CDS
GCCTGCACAGCTTAAGGGAT+TGG 0.485122 5:+74683485 MsaT029222.1:CDS
GATTTGTACGAAGACTCTAC+TGG 0.489485 5:+74687249 MsaT029222.1:CDS
TGCTGATACCAGTTCCTCAC+TGG 0.497663 5:+74688679 MsaT029222.1:CDS
CAGAAAAGCAAGTTTCTGGA+TGG 0.513041 5:+74683658 MsaT029222.1:CDS
TGGTTCCCAAGATACTCATA+TGG 0.513127 5:+74687092 MsaT029222.1:CDS
AACATGGGATATAAGCCATC+GGG 0.524849 5:+74684074 MsaT029222.1:CDS
TCTAAGGAAGAGTTCCTGCC+AGG 0.525417 5:-74687228 None:intergenic
AATTTGATCCACTTCCTCCT+GGG 0.526950 5:+74684198 MsaT029222.1:CDS
TCGTTCAAGCGGTGTCATCC+AGG 0.527070 5:+74683749 MsaT029222.1:CDS
TTCTGAAAATGTCAGTGGAA+TGG 0.528577 5:+74683920 MsaT029222.1:CDS
GTTTGGCATTCAAATGCCCC+AGG 0.531719 5:-74684215 None:intergenic
ATCGGGATATTTGAAAGTGA+AGG 0.542663 5:+74684091 MsaT029222.1:CDS
GCAGGATCAGCAATATGGTA+TGG 0.543728 5:-74686579 None:intergenic
GCTATCTTCTAGGATGACTA+AGG 0.550617 5:+74687545 MsaT029222.1:CDS
CAAGAACGTTTGTATCCTCA+AGG 0.550906 5:+74683978 MsaT029222.1:CDS
AAATTCTTCACAACAATGGA+AGG 0.554885 5:+74682687 None:intergenic
TAAGTATCTGGATCCTAAAG+AGG 0.555927 5:+74683827 MsaT029222.1:CDS
GGAAGGAATTATCAGGAAGA+TGG 0.556235 5:+74684158 MsaT029222.1:CDS
TTCACTTTCAAATATCCCGA+TGG 0.557109 5:-74684089 None:intergenic
TCATATGGATCTTGGCCTTG+AGG 0.561124 5:-74683993 None:intergenic
ATCGCGATGCAGGTGGAGCA+GGG 0.572378 5:+74687703 MsaT029222.1:CDS
AAGCAATATCGCGATGCAGG+TGG 0.577401 5:+74687696 MsaT029222.1:CDS
CAGATATGACGTACGGACGC+AGG 0.578687 5:+74683889 MsaT029222.1:CDS
AGGCCAAGATCCATATGAGA+TGG 0.579497 5:+74683998 MsaT029222.1:CDS
TCCGAAAGGTGCAATCAACA+TGG 0.580879 5:+74684058 MsaT029222.1:CDS
GATTCATATTATACTAAACA+TGG 0.583805 5:+74687072 MsaT029222.1:CDS
CTACTTACAGAGCTAAGACC+AGG 0.590912 5:-74686642 None:intergenic
TCCCAAGATACTCATATGGA+AGG 0.591524 5:+74687096 MsaT029222.1:CDS
CAAGATAAGAAAGCTTTCCA+TGG 0.592693 5:+74687162 MsaT029222.1:CDS
CAACATGGGATATAAGCCAT+CGG 0.596722 5:+74684073 MsaT029222.1:CDS
ATTTGATCCACTTCCTCCTG+GGG 0.597335 5:+74684199 MsaT029222.1:CDS
ATTGTTTAAAGGGGACAGGA+AGG 0.604577 5:+74687668 MsaT029222.1:CDS
AGTCTGAATGTTTGACTGGG+AGG 0.604885 5:-74687380 None:intergenic
TCGGGATATTTGAAAGTGAA+GGG 0.606990 5:+74684092 MsaT029222.1:CDS
CCTAAAGAGGTTGAGAGCAA+TGG 0.608573 5:+74683840 MsaT029222.1:CDS
TCATCCTCGCTAAAGCTAGA+CGG 0.613881 5:-74688653 None:intergenic
TCCACAGTGAAAAGTCGACC+TGG 0.615507 5:+74686624 MsaT029222.1:CDS
CAGACAAATCGCGATTGTAG+AGG 0.616427 5:-74683863 None:intergenic
GTTCCTGCCAGGAAAACGAC+TGG 0.617478 5:-74687217 None:intergenic
TGAAATCTACTGAAGAAAGA+GGG 0.619272 5:+74687523 MsaT029222.1:CDS
TCAAATTCTACACCAAGTAG+TGG 0.621557 5:-74684182 None:intergenic
CATAGGAAGGATTCCAAGCG+TGG 0.623253 5:+74687300 MsaT029222.1:CDS
CATTGCTAAGAATCATAGGA+AGG 0.626755 5:+74687287 MsaT029222.1:CDS
ATTGAAATTAGCAATTGCTG+AGG 0.629418 5:+74683623 MsaT029222.1:CDS
TCTGTTGCAGATATGACGTA+CGG 0.637863 5:+74683882 MsaT029222.1:CDS
CTTCCACCCTTAAATCCGAA+AGG 0.637927 5:+74684044 MsaT029222.1:CDS
AGCGGTGTCATCCAGGATCG+TGG 0.640192 5:+74683756 MsaT029222.1:CDS
GCAGGATGAATTGTTTAAAG+GGG 0.640528 5:+74687659 MsaT029222.1:intron
TCGTGTGGAAGCAGTAAACA+TGG 0.646504 5:+74683798 MsaT029222.1:CDS
CTGTTAAGAAGCAATTAGGA+AGG 0.648535 5:+74684141 MsaT029222.1:CDS
CCGAAAGGTGCAATCAACAT+GGG 0.662695 5:+74684059 MsaT029222.1:CDS
CCAATCCAAAGAATGTGCAA+AGG 0.663942 5:+74687427 MsaT029222.1:CDS
GGACTTGGACAAGATTCGTG+TGG 0.667990 5:+74683783 MsaT029222.1:CDS
GGAAGTCTGAATGTTTGACT+GGG 0.668574 5:-74687383 None:intergenic
GCACCTTTCGGATTTAAGGG+TGG 0.674376 5:-74684047 None:intergenic
GGACGACAAGATCGTTCAAG+CGG 0.685566 5:+74683738 MsaT029222.1:CDS
TGGCATTCAAATGCCCCAGG+AGG 0.687115 5:-74684212 None:intergenic
TCAATCCAAAGAAAGCGCAA+AGG 0.687671 5:+74687490 MsaT029222.1:CDS
AGAGCACAAATATCCAACAG+AGG 0.705663 5:+74683599 MsaT029222.1:intron
AGAAGAAAATAAAGTCTCTG+CGG 0.706177 5:+74683434 MsaT029222.1:CDS
TAGAACCAAGGAAAACTCAG+AGG 0.706448 5:+74687935 MsaT029222.1:CDS
GATGCCGTCTAGCTTTAGCG+AGG 0.724075 5:+74688649 MsaT029222.1:CDS
ACAAAACAATCAATCCAGTG+AGG 0.737591 5:-74688693 None:intergenic
CTGTTGCTGAGATAGAACCA+AGG 0.743299 5:+74687923 MsaT029222.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 74682702 74688706 74682702 ID=MsaG029222
Chr5 mRNA 74682702 74688706 74682702 ID=MsaT029222.1;Parent=MsaG029222
Chr5 exon 74682702 74682708 74682702 ID=MsaT029222.1.exon1;Parent=MsaT029222.1
Chr5 CDS 74682702 74682708 74682702 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74683415 74683522 74683415 ID=MsaT029222.1.exon2;Parent=MsaT029222.1
Chr5 CDS 74683415 74683522 74683415 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74683601 74684254 74683601 ID=MsaT029222.1.exon3;Parent=MsaT029222.1
Chr5 CDS 74683601 74684254 74683601 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74686577 74686656 74686577 ID=MsaT029222.1.exon4;Parent=MsaT029222.1
Chr5 CDS 74686577 74686656 74686577 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74687066 74687566 74687066 ID=MsaT029222.1.exon5;Parent=MsaT029222.1
Chr5 CDS 74687066 74687566 74687066 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74687663 74687746 74687663 ID=MsaT029222.1.exon6;Parent=MsaT029222.1
Chr5 CDS 74687663 74687746 74687663 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74687868 74687956 74687868 ID=MsaT029222.1.exon7;Parent=MsaT029222.1
Chr5 CDS 74687868 74687956 74687868 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Chr5 exon 74688637 74688706 74688637 ID=MsaT029222.1.exon8;Parent=MsaT029222.1
Chr5 CDS 74688637 74688706 74688637 ID=cds.MsaT029222.1;Parent=MsaT029222.1
Gene Sequence

>MsaT029222.1

ATGGAAGAATCAAGTGAGTTGCAACCAGAAGAAAATAAAGTCTCTGCGGAGAAGTTTCCGAAAAGAAAGCTCAAAACGCCTGCACAGCTTAAGGGATTGGAGAAATTTTATACGGAGCACAAATATCCAACAGAGGAATTGAAATTAGCAATTGCTGAGGAGTTAGAGTTGACAGAAAAGCAAGTTTCTGGATGGTTTTGTCACCGAAGGTTAAAGGATAAAAGATTGTTGAAAGAAGAAGCAAATGCTAATGGACGACAAGATCGTTCAAGCGGTGTCATCCAGGATCGTGGCAGTGGACTTGGACAAGATTCGTGTGGAAGCAGTAAACATGGTGATTATAAGTATCTGGATCCTAAAGAGGTTGAGAGCAATGGCCTCTACAATCGCGATTTGTCTGTTGCAGATATGACGTACGGACGCAGGAATCATTTTTCTGAAAATGTCAGTGGAATGGATGATGACACATCATCTGAGAGTAGCTCTTATTTGCAAGAACGTTTGTATCCTCAAGGCCAAGATCCATATGAGATGGAGCCTTCTAGATATAGTAAAGCTCTTCCACCCTTAAATCCGAAAGGTGCAATCAACATGGGATATAAGCCATCGGGATATTTGAAAGTGAAGGGTGAGATAGAACATGCTGCTATAACTGCTGTTAAGAAGCAATTAGGAAGGAATTATCAGGAAGATGGTCCACTACTTGGTGTAGAATTTGATCCACTTCCTCCTGGGGCATTTGAATGCCAAACTGAAGACGCAGTTCATGAACCATACCATATTGCTGATCCTGCTCTTCTGAATTCTCCAGAAATCTCCACAGTGAAAAGTCGACCTGGTCTTAGCTCTAGATATGATTCATATTATACTAAACATGGTTCCCAAGATACTCATATGGAAGGAGTTGACTTTGGTTCGTTGCATGATGTTCATGTTCAGGATAAACAAGATAAGAAAGCTTTCCATGGTACCAAACATAGACAAACTTTTCAGAGTAATGCCAGTCGTTTTCCTGGCAGGAACTCTTCCTTAGATTTGTACGAAGACTCTACTGGAGAAGCTGCTTACAACATTGCTAAGAATCATAGGAAGGATTCCAAGCGTGGTGTTGAGGGTATGAGATCTGATTCTACTTCTAACCATAGTGATCGCTATGAAGAAAACCTCCCAGTCAAACATTCAGACTTCCCACAGTATAACTATGAAAACACCAATCCAAAGAATGTGCAAAGGAGTGTTCATGCAGACATTCTTCAATATGACTATGATAATGTCAATCCAAAGAAAGCGCAAAGGAGTGAACACATGAAATCTACTGAAGAAAGAGGGCTATCTTCTAGGATGACTAAGGATGAATTGTTTAAAGGGGACAGGAAGGCAAAAAAGCAATATCGCGATGCAGGTGGAGCAGGGATGCTTTCAAATGAGACTATGGTTGCAAAACGACTTAAAGCAAATACGTTTCAACCATACAATATGAAACAGGTTCCTGTTGCTGAGATAGAACCAAGGAAAACTCAGAGATCTGCTGCAGAGATGCCGTCTAGCTTTAGCGAGGATGAAACTGCTGATACCAGTTCCTCACTGGATTGA
Protein sequence

>MsaT029222.1

MEESSELQPEENKVSAEKFPKRKLKTPAQLKGLEKFYTEHKYPTEELKLAIAEELELTEKQVSGWFCHRRLKDKRLLKEEANANGRQDRSSGVIQDRGSGLGQDSCGSSKHGDYKYLDPKEVESNGLYNRDLSVADMTYGRRNHFSENVSGMDDDTSSESSSYLQERLYPQGQDPYEMEPSRYSKALPPLNPKGAINMGYKPSGYLKVKGEIEHAAITAVKKQLGRNYQEDGPLLGVEFDPLPPGAFECQTEDAVHEPYHIADPALLNSPEISTVKSRPGLSSRYDSYYTKHGSQDTHMEGVDFGSLHDVHVQDKQDKKAFHGTKHRQTFQSNASRFPGRNSSLDLYEDSTGEAAYNIAKNHRKDSKRGVEGMRSDSTSNHSDRYEENLPVKHSDFPQYNYENTNPKNVQRSVHADILQYDYDNVNPKKAQRSEHMKSTEERGLSSRMTKDELFKGDRKAKKQYRDAGGAGMLSNETMVAKRLKANTFQPYNMKQVPVAEIEPRKTQRSAAEMPSSFSEDETADTSSSLD*