AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0664210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0664210 MtrunA17_Chr4g0002211 93.145 248 17 0 1 248 3 250 5.32e-161 446
Msa0664210 MtrunA17_Chr4g0024021 50.000 66 33 0 6 71 36 101 1.53e-15 71.2
Msa0664210 MtrunA17_Chr2g0322971 50.820 61 30 0 4 64 29 89 2.46e-15 70.5
Msa0664210 MtrunA17_Chr2g0323271 50.000 66 33 0 4 69 3 68 2.47e-12 64.7
Msa0664210 MtrunA17_Chr2g0280901 48.276 58 30 0 4 61 3 60 3.29e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0664210 AT3G21150.1 31.624 234 130 3 6 239 5 208 8.54e-26 101
Msa0664210 AT4G27310.1 47.500 80 41 1 4 83 3 81 2.15e-15 73.2
Msa0664210 AT3G21890.1 51.613 62 30 0 5 66 30 91 4.88e-15 69.7
Msa0664210 AT5G54470.1 52.000 75 35 1 1 75 1 74 6.83e-15 71.6
Msa0664210 AT4G15248.1 44.156 77 43 0 6 82 32 108 1.45e-14 68.6

Find 62 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAGGTTGGAGAAAATATC+AGG 0.281886 4_4:+3246601 Msa0664210:CDS
TTCGGTGAAACCGTCGCATT+TGG 0.282536 4_4:-3246116 None:intergenic
CGCACCCTTCTTGCAATTCA+AGG 0.341656 4_4:-3246684 None:intergenic
CCGATTCCGCCTTTCTCTGC+CGG 0.365012 4_4:+3246026 Msa0664210:CDS
TTGTTATTGTTCTCCGGTGC+CGG 0.383054 4_4:-3246340 None:intergenic
TGGCTGCTGCGACGTCGTTT+TGG 0.398824 4_4:+3246527 Msa0664210:CDS
TTCCTCTTGTTATTGTTCTC+CGG 0.408628 4_4:-3246346 None:intergenic
AACAAGAGGAAGAAGATGAT+TGG 0.414945 4_4:+3246358 Msa0664210:CDS
AGCTGCGACGACGCCGTTCA+CGG 0.441391 4_4:+3246049 Msa0664210:CDS
CGGAGGAGATATTTGCGAAA+TGG 0.441862 4_4:+3246404 Msa0664210:CDS
ACAAGAGGAAGAAGATGATT+GGG 0.446433 4_4:+3246359 Msa0664210:CDS
CCGGCAGAGAAAGGCGGAAT+CGG 0.453844 4_4:-3246026 None:intergenic
TTCCGGTGAGCAAGAGCGGC+AGG 0.464761 4_4:-3246182 None:intergenic
GAACGGCGTCGTCGCAGCTC+CGG 0.476153 4_4:-3246045 None:intergenic
GTCGCAGCAGCCACCTTCAC+CGG 0.482296 4_4:-3246517 None:intergenic
AGTGCCGGAGATATGAATTT+CGG 0.485587 4_4:-3246134 None:intergenic
GAGAACGTGGAAGTTACTTC+CGG 0.494776 4_4:+3246498 Msa0664210:CDS
GTGGCTAAAATAAGCTTAGC+TGG 0.495492 4_4:-3246628 None:intergenic
GTCGCAGCTCCGGCAGAGAA+AGG 0.496029 4_4:-3246035 None:intergenic
TTCACCGAAATTCATATCTC+CGG 0.509514 4_4:+3246130 Msa0664210:CDS
GTGTCGTAATTTGATGAGGT+TGG 0.531412 4_4:+3246588 Msa0664210:CDS
GCCACACGATCACCGTTCAC+CGG 0.535889 4_4:-3246451 None:intergenic
AACCTGCCGCTCTTGCTCAC+CGG 0.536391 4_4:+3246180 Msa0664210:CDS
CGATGATACATCTCCGGCAC+CGG 0.539008 4_4:+3246327 Msa0664210:CDS
GAACGGTGATCGTGTGGCGG+TGG 0.541705 4_4:+3246456 Msa0664210:CDS
TGAGGTTGGAGAAAATATCA+GGG 0.543347 4_4:+3246602 Msa0664210:CDS
TCGTGTGGCGGTGGAAGCTA+TGG 0.543504 4_4:+3246465 Msa0664210:CDS
CAGAGAAAGGCGGAATCGGA+AGG 0.554491 4_4:-3246022 None:intergenic
ACGGTGGTGTAGTGTAGTGC+CGG 0.554858 4_4:-3246149 None:intergenic
AACACCTTGAATTGCAAGAA+GGG 0.556767 4_4:+3246680 Msa0664210:CDS
TCACCGGAAAATCATTCCTC+CGG 0.557681 4_4:+3246196 Msa0664210:CDS
TGAAAGTGTTGGATCGGTGG+CGG 0.559970 4_4:+3246384 Msa0664210:CDS
AAGTGTTGGATCGGTGGCGG+AGG 0.560614 4_4:+3246387 Msa0664210:CDS
AGATTGAGAACTCGCCTCAC+CGG 0.561454 4_4:-3246215 None:intergenic
GACTGAAAGTGTTGGATCGG+TGG 0.563595 4_4:+3246381 Msa0664210:CDS
TCCGGTGAACGGTGATCGTG+TGG 0.570131 4_4:+3246450 Msa0664210:CDS
CAACACCTTGAATTGCAAGA+AGG 0.572050 4_4:+3246679 Msa0664210:CDS
GTGGAAGTTACTTCCGGTGA+AGG 0.577957 4_4:+3246504 Msa0664210:CDS
ATGATTGGGACTGAAAGTGT+TGG 0.593930 4_4:+3246373 Msa0664210:CDS
GAAGTTACTTCCGGTGAAGG+TGG 0.596707 4_4:+3246507 Msa0664210:CDS
CCACGTGTCGTAATTTGATG+AGG 0.597307 4_4:+3246584 Msa0664210:CDS
GAGGAAGTTAGCGCCGTGAA+CGG 0.601829 4_4:-3246062 None:intergenic
ATCTTGTGCTCCAAATGCGA+CGG 0.602290 4_4:+3246106 Msa0664210:CDS
AGCGGCAGGTTGATGAGAGA+CGG 0.602586 4_4:-3246168 None:intergenic
CGGAGATGTATCATCGGTAA+CGG 0.606238 4_4:-3246320 None:intergenic
CGTTACCGATGATACATCTC+CGG 0.613031 4_4:+3246321 Msa0664210:CDS
CACCGGAGAACAATAACAAG+AGG 0.613856 4_4:+3246344 Msa0664210:CDS
CCTCATCAAATTACGACACG+TGG 0.625412 4_4:-3246584 None:intergenic
TGGGACTGAAAGTGTTGGAT+CGG 0.630097 4_4:+3246378 Msa0664210:CDS
ATTTGGAGCACAAGATGTGA+CGG 0.631824 4_4:-3246099 None:intergenic
GCAGCTCCGGCAGAGAAAGG+CGG 0.638220 4_4:-3246032 None:intergenic
TGTGGCGGTGGAAGCTATGG+CGG 0.643579 4_4:+3246468 Msa0664210:CDS
TTGAGAACTCGCCTCACCGG+AGG 0.643923 4_4:-3246212 None:intergenic
CGGTGCCGGAGATGTATCAT+CGG 0.645343 4_4:-3246326 None:intergenic
GGTGAACGGTGATCGTGTGG+CGG 0.678941 4_4:+3246453 Msa0664210:CDS
GGAAAATCATTCCTCCGGTG+AGG 0.685941 4_4:+3246201 Msa0664210:CDS
ACGTGCGAGTTTCACATGTG+TGG 0.691088 4_4:-3246647 None:intergenic
GGCAGGTTGATGAGAGACGG+TGG 0.691500 4_4:-3246165 None:intergenic
TGGCGGTGTGTATGAGAACG+TGG 0.692845 4_4:+3246485 Msa0664210:CDS
GAGGTTGGAGAAAATATCAG+GGG 0.723090 4_4:+3246603 Msa0664210:CDS
TGGAGCACAAGATGTGACGG+AGG 0.724489 4_4:-3246096 None:intergenic
GACGGAGGTGACGAGCGACG+AGG 0.727759 4_4:-3246081 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAGTTAGAGTTAGATTTTC+CGG + chr4_4:3246432-3246451 Msa0664210:CDS 30.0%
TTCACCGAAATTCATATCTC+CGG + chr4_4:3246130-3246149 Msa0664210:CDS 35.0%
!! TTCCTCTTGTTATTGTTCTC+CGG - chr4_4:3246349-3246368 None:intergenic 35.0%
AACAAGAGGAAGAAGATGAT+TGG + chr4_4:3246358-3246377 Msa0664210:CDS 35.0%
ACAAGAGGAAGAAGATGATT+GGG + chr4_4:3246359-3246378 Msa0664210:CDS 35.0%
ATGAGGTTGGAGAAAATATC+AGG + chr4_4:3246601-3246620 Msa0664210:CDS 35.0%
TGAGGTTGGAGAAAATATCA+GGG + chr4_4:3246602-3246621 Msa0664210:CDS 35.0%
AACACCTTGAATTGCAAGAA+GGG + chr4_4:3246680-3246699 Msa0664210:CDS 35.0%
! ATTTGGAGCACAAGATGTGA+CGG - chr4_4:3246102-3246121 None:intergenic 40.0%
! AGTGCCGGAGATATGAATTT+CGG - chr4_4:3246137-3246156 None:intergenic 40.0%
! ATGATTGGGACTGAAAGTGT+TGG + chr4_4:3246373-3246392 Msa0664210:CDS 40.0%
! GAGTTAGATTTTCCGGTGAA+CGG + chr4_4:3246439-3246458 Msa0664210:CDS 40.0%
! TGGTTGGGGTTAAGATTTTG+TGG + chr4_4:3246547-3246566 Msa0664210:CDS 40.0%
! GGTTGGGGTTAAGATTTTGT+GGG + chr4_4:3246548-3246567 Msa0664210:CDS 40.0%
! GTTGGGGTTAAGATTTTGTG+GGG + chr4_4:3246549-3246568 Msa0664210:CDS 40.0%
GTGTCGTAATTTGATGAGGT+TGG + chr4_4:3246588-3246607 Msa0664210:CDS 40.0%
GAGGTTGGAGAAAATATCAG+GGG + chr4_4:3246603-3246622 Msa0664210:CDS 40.0%
GTGGCTAAAATAAGCTTAGC+TGG - chr4_4:3246631-3246650 None:intergenic 40.0%
CAACACCTTGAATTGCAAGA+AGG + chr4_4:3246679-3246698 Msa0664210:CDS 40.0%
ATCTTGTGCTCCAAATGCGA+CGG + chr4_4:3246106-3246125 Msa0664210:CDS 45.0%
TCACCGGAAAATCATTCCTC+CGG + chr4_4:3246196-3246215 Msa0664210:CDS 45.0%
! TCACCGGAGGAATGATTTTC+CGG - chr4_4:3246202-3246221 None:intergenic 45.0%
CGGAGATGTATCATCGGTAA+CGG - chr4_4:3246323-3246342 None:intergenic 45.0%
CGTTACCGATGATACATCTC+CGG + chr4_4:3246321-3246340 Msa0664210:CDS 45.0%
! TTGTTATTGTTCTCCGGTGC+CGG - chr4_4:3246343-3246362 None:intergenic 45.0%
CACCGGAGAACAATAACAAG+AGG + chr4_4:3246344-3246363 Msa0664210:CDS 45.0%
!! TGGGACTGAAAGTGTTGGAT+CGG + chr4_4:3246378-3246397 Msa0664210:CDS 45.0%
CGGAGGAGATATTTGCGAAA+TGG + chr4_4:3246404-3246423 Msa0664210:CDS 45.0%
GAGAACGTGGAAGTTACTTC+CGG + chr4_4:3246498-3246517 Msa0664210:CDS 45.0%
CCTCATCAAATTACGACACG+TGG - chr4_4:3246587-3246606 None:intergenic 45.0%
CCACGTGTCGTAATTTGATG+AGG + chr4_4:3246584-3246603 Msa0664210:CDS 45.0%
TTCGGTGAAACCGTCGCATT+TGG - chr4_4:3246119-3246138 None:intergenic 50.0%
! GATTTTCCGGTGAGCAAGAG+CGG - chr4_4:3246189-3246208 None:intergenic 50.0%
GGAAAATCATTCCTCCGGTG+AGG + chr4_4:3246201-3246220 Msa0664210:CDS 50.0%
AGATTGAGAACTCGCCTCAC+CGG - chr4_4:3246218-3246237 None:intergenic 50.0%
!! GACTGAAAGTGTTGGATCGG+TGG + chr4_4:3246381-3246400 Msa0664210:CDS 50.0%
!! TGAAAGTGTTGGATCGGTGG+CGG + chr4_4:3246384-3246403 Msa0664210:CDS 50.0%
GTGGAAGTTACTTCCGGTGA+AGG + chr4_4:3246504-3246523 Msa0664210:CDS 50.0%
GAAGTTACTTCCGGTGAAGG+TGG + chr4_4:3246507-3246526 Msa0664210:CDS 50.0%
ACGTGCGAGTTTCACATGTG+TGG - chr4_4:3246650-3246669 None:intergenic 50.0%
CGCACCCTTCTTGCAATTCA+AGG - chr4_4:3246687-3246706 None:intergenic 50.0%
CAGAGAAAGGCGGAATCGGA+AGG - chr4_4:3246025-3246044 None:intergenic 55.0%
GAGGAAGTTAGCGCCGTGAA+CGG - chr4_4:3246065-3246084 None:intergenic 55.0%
TGGAGCACAAGATGTGACGG+AGG - chr4_4:3246099-3246118 None:intergenic 55.0%
ACGGTGGTGTAGTGTAGTGC+CGG - chr4_4:3246152-3246171 None:intergenic 55.0%
!! AGCGGCAGGTTGATGAGAGA+CGG - chr4_4:3246171-3246190 None:intergenic 55.0%
! CGGTGCCGGAGATGTATCAT+CGG - chr4_4:3246329-3246348 None:intergenic 55.0%
CGATGATACATCTCCGGCAC+CGG + chr4_4:3246327-3246346 Msa0664210:CDS 55.0%
TGGCGGTGTGTATGAGAACG+TGG + chr4_4:3246485-3246504 Msa0664210:CDS 55.0%
!! TGCTGCGACGTCGTTTTGGT+TGG + chr4_4:3246531-3246550 Msa0664210:CDS 55.0%
!!! GCTGCGACGTCGTTTTGGTT+GGG + chr4_4:3246532-3246551 Msa0664210:CDS 55.0%
!!! CTGCGACGTCGTTTTGGTTG+GGG + chr4_4:3246533-3246552 Msa0664210:CDS 55.0%
CCGGCAGAGAAAGGCGGAAT+CGG - chr4_4:3246029-3246048 None:intergenic 60.0%
CCGATTCCGCCTTTCTCTGC+CGG + chr4_4:3246026-3246045 Msa0664210:CDS 60.0%
!! GGCAGGTTGATGAGAGACGG+TGG - chr4_4:3246168-3246187 None:intergenic 60.0%
AACCTGCCGCTCTTGCTCAC+CGG + chr4_4:3246180-3246199 Msa0664210:CDS 60.0%
TTGAGAACTCGCCTCACCGG+AGG - chr4_4:3246215-3246234 None:intergenic 60.0%
!! AAGTGTTGGATCGGTGGCGG+AGG + chr4_4:3246387-3246406 Msa0664210:CDS 60.0%
TCCGGTGAACGGTGATCGTG+TGG + chr4_4:3246450-3246469 Msa0664210:CDS 60.0%
GCCACACGATCACCGTTCAC+CGG - chr4_4:3246454-3246473 None:intergenic 60.0%
GGTGAACGGTGATCGTGTGG+CGG + chr4_4:3246453-3246472 Msa0664210:CDS 60.0%
TCGTGTGGCGGTGGAAGCTA+TGG + chr4_4:3246465-3246484 Msa0664210:CDS 60.0%
TGTGGCGGTGGAAGCTATGG+CGG + chr4_4:3246468-3246487 Msa0664210:CDS 60.0%
! TGGCTGCTGCGACGTCGTTT+TGG + chr4_4:3246527-3246546 Msa0664210:CDS 60.0%
GCAGCTCCGGCAGAGAAAGG+CGG - chr4_4:3246035-3246054 None:intergenic 65.0%
GTCGCAGCTCCGGCAGAGAA+AGG - chr4_4:3246038-3246057 None:intergenic 65.0%
AGCTGCGACGACGCCGTTCA+CGG + chr4_4:3246049-3246068 Msa0664210:CDS 65.0%
TTCCGGTGAGCAAGAGCGGC+AGG - chr4_4:3246185-3246204 None:intergenic 65.0%
GAACGGTGATCGTGTGGCGG+TGG + chr4_4:3246456-3246475 Msa0664210:CDS 65.0%
GTCGCAGCAGCCACCTTCAC+CGG - chr4_4:3246520-3246539 None:intergenic 65.0%
GAACGGCGTCGTCGCAGCTC+CGG - chr4_4:3246048-3246067 None:intergenic 70.0%
GACGGAGGTGACGAGCGACG+AGG - chr4_4:3246084-3246103 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 3245971 3246717 3245971 ID=Msa0664210;Name=Msa0664210
chr4_4 mRNA 3245971 3246717 3245971 ID=Msa0664210-mRNA-1;Parent=Msa0664210;Name=Msa0664210-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|248
chr4_4 exon 3245971 3246717 3245971 ID=Msa0664210-mRNA-1:exon:965;Parent=Msa0664210-mRNA-1
chr4_4 CDS 3245971 3246717 3245971 ID=Msa0664210-mRNA-1:cds;Parent=Msa0664210-mRNA-1
Gene Sequence

>Msa0664210

ATGAAGTGCAAACAATGCGAACTTTGTAATCAACAAGCTTCTTTCTATTGTCCTTCCGATTCCGCCTTTCTCTGCCGGAGCTGCGACGACGCCGTTCACGGCGCTAACTTCCTCGTCGCTCGTCACCTCCGTCACATCTTGTGCTCCAAATGCGACGGTTTCACCGAAATTCATATCTCCGGCACTACACTACACCACCGTCTCTCATCAACCTGCCGCTCTTGCTCACCGGAAAATCATTCCTCCGGTGAGGCGAGTTCTCAATCTTCTTCATCTTGCGAGTCTTGCGTTACAGAAAAGAAGAAAACAAAATCTCGAAAGATAATGAAGAGTTTTTCAGTTTCGAATTCCGTTACCGATGATACATCTCCGGCACCGGAGAACAATAACAAGAGGAAGAAGATGATTGGGACTGAAAGTGTTGGATCGGTGGCGGAGGAGATATTTGCGAAATGGAGAAGAGAGTTAGAGTTAGATTTTCCGGTGAACGGTGATCGTGTGGCGGTGGAAGCTATGGCGGTGTGTATGAGAACGTGGAAGTTACTTCCGGTGAAGGTGGCTGCTGCGACGTCGTTTTGGTTGGGGTTAAGATTTTGTGGGGACAATAGTTTTGCCACGTGTCGTAATTTGATGAGGTTGGAGAAAATATCAGGGGTGCCAGCTAAGCTTATTTTAGCCACACATGTGAAACTCGCACGTGTCTTTACTCAACACCTTGAATTGCAAGAAGGGTGCGATGAGTCCTAA
Protein sequence

>Msa0664210

MKCKQCELCNQQASFYCPSDSAFLCRSCDDAVHGANFLVARHLRHILCSKCDGFTEIHISGTTLHHRLSSTCRSCSPENHSSGEASSQSSSSCESCVTEKKKTKSRKIMKSFSVSNSVTDDTSPAPENNNKRKKMIGTESVGSVAEEIFAKWRRELELDFPVNGDRVAVEAMAVCMRTWKLLPVKVAAATSFWLGLRFCGDNSFATCRNLMRLEKISGVPAKLILATHVKLARVFTQHLELQEGCDES*