AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0731900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0731900 MtrunA17_Chr5g0426441 96.463 311 11 0 6 316 648 958 0.0 617
Msa0731900 MtrunA17_Chr5g0426441 92.405 316 23 1 1 316 25 339 0.0 598
Msa0731900 MtrunA17_Chr5g0426441 93.248 311 20 1 6 316 339 648 0.0 594
Msa0731900 MtrunA17_Chr3g0116001 78.788 297 50 3 20 316 21 304 3.64e-171 476
Msa0731900 MtrunA17_Chr3g0116011 78.451 297 51 4 20 316 21 304 1.10e-169 473
Msa0731900 MtrunA17_Chr3g0115951 70.740 311 87 3 9 316 8 317 2.26e-154 434
Msa0731900 MtrunA17_Chr4g0050321 61.053 285 97 3 32 316 30 300 3.31e-122 352
Msa0731900 MtrunA17_Chr2g0279311 53.145 318 132 7 1 316 2 304 1.19e-118 343
Msa0731900 MtrunA17_Chr4g0018171 36.458 288 161 8 25 301 53 329 1.69e-47 162
Msa0731900 MtrunA17_Chr1g0188071 35.179 307 178 7 6 301 33 329 6.37e-47 161
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0731900 AT4G08950.1 71.237 299 76 6 24 316 20 314 5.02e-147 416
Msa0731900 AT1G35140.1 64.444 315 105 3 1 315 1 308 5.82e-142 403
Msa0731900 AT5G64260.1 57.468 308 121 4 10 316 7 305 1.71e-121 351
Msa0731900 AT5G09440.1 55.482 301 100 7 18 316 10 278 2.07e-102 301
Msa0731900 AT5G51550.1 35.410 305 175 7 20 313 38 331 5.14e-49 167
Msa0731900 AT3G02970.1 31.000 300 169 7 47 314 37 330 2.25e-43 152
Msa0731900 AT2G35150.1 33.538 325 189 10 6 312 1 316 1.64e-41 147
Msa0731900 AT2G17230.1 32.237 304 184 8 22 313 64 357 1.01e-40 145

Find 69 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATTTCACCAACCAATTTA+TGG 0.182864 5_1:+43496260 Msa0731900:CDS
TCAAGACCCACATCGTTATT+TGG 0.213136 5_1:-43496308 None:intergenic
TCTTATGGTGCACGCGTAAA+TGG 0.225421 5_1:+43496167 Msa0731900:CDS
AATCAGTTATGATGACTCTT+TGG 0.275197 5_1:-43495839 None:intergenic
GAAACAAATTTGCGTACATT+TGG 0.281754 5_1:+43496195 Msa0731900:CDS
GGAACCCATGGTTCTTCTTA+TGG 0.283880 5_1:+43496152 Msa0731900:CDS
CTCAATGAGAATTACTCTTT+AGG 0.291101 5_1:+43496008 Msa0731900:CDS
TGGTTATGCTGGGGACCTTT+TGG 0.299405 5_1:+43496472 Msa0731900:CDS
GCACTTTGTGGACCATAAAT+TGG 0.307975 5_1:-43496272 None:intergenic
GCTTCCAAAGGAGCTTCTTT+TGG 0.308698 5_1:-43496407 None:intergenic
TTGATGCGAGTTTAAGGATT+TGG 0.323024 5_1:-43496049 None:intergenic
AAACAAATTTGCGTACATTT+GGG 0.353432 5_1:+43496196 Msa0731900:CDS
GTACTGGTGTTTATGCTAAA+GGG 0.358568 5_1:+43496441 Msa0731900:CDS
TACAATGCAAATGGTGATAA+TGG 0.362381 5_1:+43496518 Msa0731900:CDS
AGGACCAAAAGAAGCTCCTT+TGG 0.376105 5_1:+43496403 Msa0731900:CDS
GGGGCTTATCCTGGTTATGC+TGG 0.376447 5_1:+43496461 Msa0731900:CDS
CCATAAATTGGTTGGTGAAA+TGG 0.381983 5_1:-43496260 None:intergenic
AAATCTCAATCAACCTCATT+TGG 0.382865 5_1:+43495796 Msa0731900:CDS
AATAACGATGTGGGTCTTGA+TGG 0.390121 5_1:+43496311 Msa0731900:CDS
ATCAGTTATGATGACTCTTT+GGG 0.405878 5_1:-43495838 None:intergenic
CAGTGAGAAGAGGGCCTTTG+TGG 0.411734 5_1:-43495770 None:intergenic
TGTACTGGTGTTTATGCTAA+AGG 0.430957 5_1:+43496440 Msa0731900:CDS
GAAGCTGCTTCAGCTTGTAC+TGG 0.441264 5_1:+43496425 Msa0731900:CDS
GGTATTGAAATTTAAGTTGT+TGG 0.450783 5_1:-43495749 None:intergenic
CTAACACATCAGCAGCTGTT+AGG 0.451358 5_1:-43496103 None:intergenic
GGAACCGTAACGAATCCTTT+TGG 0.451430 5_1:+43496365 Msa0731900:CDS
TTTAAGTTGTTGGTCCGATT+CGG 0.453958 5_1:-43495739 None:intergenic
TGAAAATATCCATTACCAAA+AGG 0.461381 5_1:-43496380 None:intergenic
GCAACCAATGGTGCACTTTG+TGG 0.466845 5_1:-43496284 None:intergenic
TATGCTAAAGGGGCTTATCC+TGG 0.476402 5_1:+43496452 Msa0731900:CDS
GGGCTTATCCTGGTTATGCT+GGG 0.476504 5_1:+43496462 Msa0731900:CDS
AAATTTGCGTACATTTGGGT+TGG 0.481339 5_1:+43496200 Msa0731900:CDS
AGCTGTTAGGACAACGTTGA+TGG 0.491013 5_1:-43496090 None:intergenic
TCAATCAACCTCATTTGGTA+TGG 0.491730 5_1:+43495801 Msa0731900:CDS
GACGTGGTTGTTCCTCGTTT+AGG 0.494909 5_1:-43495882 None:intergenic
TGCAAGAAAACTCACCGAAT+CGG 0.499245 5_1:+43495725 Msa0731900:CDS
TGGTCCACAAAGTGCACCAT+TGG 0.507521 5_1:+43496280 Msa0731900:CDS
GCTGCTGATGTGTTAGTTGA+CGG 0.512705 5_1:+43496110 Msa0731900:CDS
TACTGGTGTTTATGCTAAAG+GGG 0.514152 5_1:+43496442 Msa0731900:CDS
TCGTTATTTGGTGCAACCAA+TGG 0.521248 5_1:-43496296 None:intergenic
TCCTCGTTTAGGAGAAGAGA+GGG 0.533776 5_1:-43495871 None:intergenic
ATTACCAAAAGGATTCGTTA+CGG 0.540975 5_1:-43496369 None:intergenic
GCTAAACTAGCTCTCTCACT+AGG 0.543046 5_1:+43495975 Msa0731900:CDS
CACAAAGGCCCTCTTCTCAC+TGG 0.547348 5_1:+43495771 Msa0731900:CDS
CGATGTGGGTCTTGATGGAA+TGG 0.552866 5_1:+43496316 Msa0731900:CDS
ATGCAAATGGTGATAATGGA+AGG 0.560708 5_1:+43496522 Msa0731900:CDS
TCAAGTAGGTGTGGAACCCA+TGG 0.564282 5_1:+43496140 Msa0731900:CDS
AAAAGGTCCCCAGCATAACC+AGG 0.566674 5_1:-43496470 None:intergenic
AACCTCAGTTTGTTCTACGT+TGG 0.567385 5_1:+43496577 Msa0731900:CDS
TTCCACCACGTGGCAACTGA+TGG 0.582258 5_1:-43495909 None:intergenic
GGCTTATCCTGGTTATGCTG+GGG 0.583253 5_1:+43496463 Msa0731900:CDS
GGTGCTAGCTACAATGCAAA+TGG 0.590428 5_1:+43496509 Msa0731900:CDS
CAAGCTGAAGCAGCTTCCAA+AGG 0.594382 5_1:-43496419 None:intergenic
AATTCAGAGACACAATGTGC+TGG 0.594460 5_1:+43496224 Msa0731900:CDS
AACCATCAGTTGCCACGTGG+TGG 0.610757 5_1:+43495907 Msa0731900:CDS
TTTGTGGACCATAAATTGGT+TGG 0.611426 5_1:-43496268 None:intergenic
CTTAAATTTCAATACCACAA+AGG 0.623830 5_1:+43495756 Msa0731900:CDS
GTGCACCATAAGAAGAACCA+TGG 0.625761 5_1:-43496157 None:intergenic
GGTTGCACCAAATAACGATG+TGG 0.628110 5_1:+43496301 Msa0731900:CDS
TTCCTCGTTTAGGAGAAGAG+AGG 0.628736 5_1:-43495872 None:intergenic
TCGTTTAGGAGAAGAGAGGG+AGG 0.643573 5_1:-43495868 None:intergenic
TTCAGTTGATTTCCACCACG+TGG 0.645033 5_1:-43495919 None:intergenic
TGCACCATAAGAAGAACCAT+GGG 0.655555 5_1:-43496156 None:intergenic
GTTGCACCAAATAACGATGT+GGG 0.661869 5_1:+43496302 Msa0731900:CDS
GGCAACTGATGGTTGTGACG+TGG 0.693973 5_1:-43495898 None:intergenic
CACAACCATCAGTTGCCACG+TGG 0.702852 5_1:+43495904 Msa0731900:CDS
TACCAACGTAGAACAAACTG+AGG 0.704895 5_1:-43496579 None:intergenic
TCCCTCTCTTCTCCTAAACG+AGG 0.714038 5_1:+43495870 Msa0731900:CDS
AATGTGCTGGTCAATGCGCG+TGG 0.729505 5_1:+43496237 Msa0731900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GGTATTGAAATTTAAGTTGT+TGG - chr5_1:43495752-43495771 None:intergenic 25.0%
! CTTAAATTTCAATACCACAA+AGG + chr5_1:43495756-43495775 Msa0731900:CDS 25.0%
!!! TTTAGCTGACTTTTTATTGT+TGG - chr5_1:43495961-43495980 None:intergenic 25.0%
! AAACAAATTTGCGTACATTT+GGG + chr5_1:43496196-43496215 Msa0731900:CDS 25.0%
! TGAAAATATCCATTACCAAA+AGG - chr5_1:43496383-43496402 None:intergenic 25.0%
!!! TTTGGTAATGGATATTTTCA+AGG + chr5_1:43496383-43496402 Msa0731900:CDS 25.0%
AAATCTCAATCAACCTCATT+TGG + chr5_1:43495796-43495815 Msa0731900:CDS 30.0%
! TGAATTTTCCATACCAAATG+AGG - chr5_1:43495812-43495831 None:intergenic 30.0%
ATCAGTTATGATGACTCTTT+GGG - chr5_1:43495841-43495860 None:intergenic 30.0%
AATCAGTTATGATGACTCTT+TGG - chr5_1:43495842-43495861 None:intergenic 30.0%
!! ACTTTTTATTGTTGGTGAGT+TGG - chr5_1:43495953-43495972 None:intergenic 30.0%
CTCAATGAGAATTACTCTTT+AGG + chr5_1:43496008-43496027 Msa0731900:CDS 30.0%
GAAACAAATTTGCGTACATT+TGG + chr5_1:43496195-43496214 Msa0731900:CDS 30.0%
ATTACCAAAAGGATTCGTTA+CGG - chr5_1:43496372-43496391 None:intergenic 30.0%
TACAATGCAAATGGTGATAA+TGG + chr5_1:43496518-43496537 Msa0731900:CDS 30.0%
!! TTTAAGTTGTTGGTCCGATT+CGG - chr5_1:43495742-43495761 None:intergenic 35.0%
TCAATCAACCTCATTTGGTA+TGG + chr5_1:43495801-43495820 Msa0731900:CDS 35.0%
TTGATGCGAGTTTAAGGATT+TGG - chr5_1:43496052-43496071 None:intergenic 35.0%
! TTGACGGTTTTTGTTCAAGT+AGG + chr5_1:43496126-43496145 Msa0731900:CDS 35.0%
AAATTTGCGTACATTTGGGT+TGG + chr5_1:43496200-43496219 Msa0731900:CDS 35.0%
!! CCATAAATTGGTTGGTGAAA+TGG - chr5_1:43496263-43496282 None:intergenic 35.0%
CCATTTCACCAACCAATTTA+TGG + chr5_1:43496260-43496279 Msa0731900:CDS 35.0%
TTTGTGGACCATAAATTGGT+TGG - chr5_1:43496271-43496290 None:intergenic 35.0%
!!! AATGTTGCTAGTCTTTTAGC+TGG + chr5_1:43496344-43496363 Msa0731900:CDS 35.0%
! GTAACGAATCCTTTTGGTAA+TGG + chr5_1:43496371-43496390 Msa0731900:CDS 35.0%
! TGTACTGGTGTTTATGCTAA+AGG + chr5_1:43496440-43496459 Msa0731900:CDS 35.0%
! GTACTGGTGTTTATGCTAAA+GGG + chr5_1:43496441-43496460 Msa0731900:CDS 35.0%
TACTGGTGTTTATGCTAAAG+GGG + chr5_1:43496442-43496461 Msa0731900:CDS 35.0%
!! ATGCAAATGGTGATAATGGA+AGG + chr5_1:43496522-43496541 Msa0731900:CDS 35.0%
! GTAGAACAAACTGAGGTTTT+TGG - chr5_1:43496575-43496594 None:intergenic 35.0%
TGCAAGAAAACTCACCGAAT+CGG + chr5_1:43495725-43495744 Msa0731900:CDS 40.0%
! AGATTTTGCCAGTGAGAAGA+GGG - chr5_1:43495782-43495801 None:intergenic 40.0%
! GTGCTTTTGATGCGAGTTTA+AGG - chr5_1:43496058-43496077 None:intergenic 40.0%
! GGTTTTTGTTCAAGTAGGTG+TGG + chr5_1:43496131-43496150 Msa0731900:CDS 40.0%
TGCACCATAAGAAGAACCAT+GGG - chr5_1:43496159-43496178 None:intergenic 40.0%
AATTCAGAGACACAATGTGC+TGG + chr5_1:43496224-43496243 Msa0731900:CDS 40.0%
GCACTTTGTGGACCATAAAT+TGG - chr5_1:43496275-43496294 None:intergenic 40.0%
!! TCGTTATTTGGTGCAACCAA+TGG - chr5_1:43496299-43496318 None:intergenic 40.0%
GTTGCACCAAATAACGATGT+GGG + chr5_1:43496302-43496321 Msa0731900:CDS 40.0%
TCAAGACCCACATCGTTATT+TGG - chr5_1:43496311-43496330 None:intergenic 40.0%
AATAACGATGTGGGTCTTGA+TGG + chr5_1:43496311-43496330 Msa0731900:CDS 40.0%
!!! CACTTGTTTTGTCCACCAAA+AGG - chr5_1:43496490-43496509 None:intergenic 40.0%
!! CTTTTGGTGGACAAAACAAG+TGG + chr5_1:43496488-43496507 Msa0731900:CDS 40.0%
!! GTTTTTGGATCAACAATCGC+AGG - chr5_1:43496560-43496579 None:intergenic 40.0%
! AACCTCAGTTTGTTCTACGT+TGG + chr5_1:43496577-43496596 Msa0731900:CDS 40.0%
TACCAACGTAGAACAAACTG+AGG - chr5_1:43496582-43496601 None:intergenic 40.0%
! GAGATTTTGCCAGTGAGAAG+AGG - chr5_1:43495783-43495802 None:intergenic 45.0%
TCCTCGTTTAGGAGAAGAGA+GGG - chr5_1:43495874-43495893 None:intergenic 45.0%
TTCCTCGTTTAGGAGAAGAG+AGG - chr5_1:43495875-43495894 None:intergenic 45.0%
! TTCAGTTGATTTCCACCACG+TGG - chr5_1:43495922-43495941 None:intergenic 45.0%
! GCTAAACTAGCTCTCTCACT+AGG + chr5_1:43495975-43495994 Msa0731900:CDS 45.0%
AGCTGTTAGGACAACGTTGA+TGG - chr5_1:43496093-43496112 None:intergenic 45.0%
CTAACACATCAGCAGCTGTT+AGG - chr5_1:43496106-43496125 None:intergenic 45.0%
GCTGCTGATGTGTTAGTTGA+CGG + chr5_1:43496110-43496129 Msa0731900:CDS 45.0%
GGAACCCATGGTTCTTCTTA+TGG + chr5_1:43496152-43496171 Msa0731900:CDS 45.0%
GTGCACCATAAGAAGAACCA+TGG - chr5_1:43496160-43496179 None:intergenic 45.0%
TCTTATGGTGCACGCGTAAA+TGG + chr5_1:43496167-43496186 Msa0731900:CDS 45.0%
GGTTGCACCAAATAACGATG+TGG + chr5_1:43496301-43496320 Msa0731900:CDS 45.0%
! GGAACCGTAACGAATCCTTT+TGG + chr5_1:43496365-43496384 Msa0731900:CDS 45.0%
AGGACCAAAAGAAGCTCCTT+TGG + chr5_1:43496403-43496422 Msa0731900:CDS 45.0%
! GCTTCCAAAGGAGCTTCTTT+TGG - chr5_1:43496410-43496429 None:intergenic 45.0%
TATGCTAAAGGGGCTTATCC+TGG + chr5_1:43496452-43496471 Msa0731900:CDS 45.0%
GGTGCTAGCTACAATGCAAA+TGG + chr5_1:43496509-43496528 Msa0731900:CDS 45.0%
TCGTTTAGGAGAAGAGAGGG+AGG - chr5_1:43495871-43495890 None:intergenic 50.0%
TCCCTCTCTTCTCCTAAACG+AGG + chr5_1:43495870-43495889 Msa0731900:CDS 50.0%
GACGTGGTTGTTCCTCGTTT+AGG - chr5_1:43495885-43495904 None:intergenic 50.0%
TCAAGTAGGTGTGGAACCCA+TGG + chr5_1:43496140-43496159 Msa0731900:CDS 50.0%
TGGTCCACAAAGTGCACCAT+TGG + chr5_1:43496280-43496299 Msa0731900:CDS 50.0%
GCAACCAATGGTGCACTTTG+TGG - chr5_1:43496287-43496306 None:intergenic 50.0%
CGATGTGGGTCTTGATGGAA+TGG + chr5_1:43496316-43496335 Msa0731900:CDS 50.0%
CAAGCTGAAGCAGCTTCCAA+AGG - chr5_1:43496422-43496441 None:intergenic 50.0%
GAAGCTGCTTCAGCTTGTAC+TGG + chr5_1:43496425-43496444 Msa0731900:CDS 50.0%
GGGCTTATCCTGGTTATGCT+GGG + chr5_1:43496462-43496481 Msa0731900:CDS 50.0%
GGCTTATCCTGGTTATGCTG+GGG + chr5_1:43496463-43496482 Msa0731900:CDS 50.0%
AAAAGGTCCCCAGCATAACC+AGG - chr5_1:43496473-43496492 None:intergenic 50.0%
! TGGTTATGCTGGGGACCTTT+TGG + chr5_1:43496472-43496491 Msa0731900:CDS 50.0%
! TTATGCTGGGGACCTTTTGG+TGG + chr5_1:43496475-43496494 Msa0731900:CDS 50.0%
CAGTGAGAAGAGGGCCTTTG+TGG - chr5_1:43495773-43495792 None:intergenic 55.0%
CACAAAGGCCCTCTTCTCAC+TGG + chr5_1:43495771-43495790 Msa0731900:CDS 55.0%
GGCAACTGATGGTTGTGACG+TGG - chr5_1:43495901-43495920 None:intergenic 55.0%
CACAACCATCAGTTGCCACG+TGG + chr5_1:43495904-43495923 Msa0731900:CDS 55.0%
AACCATCAGTTGCCACGTGG+TGG + chr5_1:43495907-43495926 Msa0731900:CDS 55.0%
TTCCACCACGTGGCAACTGA+TGG - chr5_1:43495912-43495931 None:intergenic 55.0%
! AATGTGCTGGTCAATGCGCG+TGG + chr5_1:43496237-43496256 Msa0731900:CDS 55.0%
GGGGCTTATCCTGGTTATGC+TGG + chr5_1:43496461-43496480 Msa0731900:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 43495654 43496604 43495654 ID=Msa0731900;Name=Msa0731900
chr5_1 mRNA 43495654 43496604 43495654 ID=Msa0731900-mRNA-1;Parent=Msa0731900;Name=Msa0731900-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|316
chr5_1 exon 43495654 43496604 43495654 ID=Msa0731900-mRNA-1:exon:12429;Parent=Msa0731900-mRNA-1
chr5_1 CDS 43495654 43496604 43495654 ID=Msa0731900-mRNA-1:cds;Parent=Msa0731900-mRNA-1
Gene Sequence

>Msa0731900

ATGGCATCTTTTAAGTTAAGTGTAATCTTCACTCTTTTTCTCACAATTTCACTGCTTCATTTAATCTCAGCTGCAAGAAAACTCACCGAATCGGACCAACAACTTAAATTTCAATACCACAAAGGCCCTCTTCTCACTGGCAAAATCTCAATCAACCTCATTTGGTATGGAAAATTCAAATCGTCCCAAAGAGTCATCATAACTGATTTCATAACCTCCCTCTCTTCTCCTAAACGAGGAACAACCACGTCACAACCATCAGTTGCCACGTGGTGGAAATCAACTGAAAAATATTACCAACTCACCAACAATAAAAAGTCAGCTAAACTAGCTCTCTCACTAGGTGCTCAAATTCTCAATGAGAATTACTCTTTAGGAAAATCTCTCACAACTAACCAAATCCTTAAACTCGCATCAAAAGCACAACAACAAAACGCCATCAACGTTGTCCTAACAGCTGCTGATGTGTTAGTTGACGGTTTTTGTTCAAGTAGGTGTGGAACCCATGGTTCTTCTTATGGTGCACGCGTAAATGGAAAAAGAAACAAATTTGCGTACATTTGGGTTGGAAATTCAGAGACACAATGTGCTGGTCAATGCGCGTGGCCATTTCACCAACCAATTTATGGTCCACAAAGTGCACCATTGGTTGCACCAAATAACGATGTGGGTCTTGATGGAATGGTTATAAATGTTGCTAGTCTTTTAGCTGGAACCGTAACGAATCCTTTTGGTAATGGATATTTTCAAGGACCAAAAGAAGCTCCTTTGGAAGCTGCTTCAGCTTGTACTGGTGTTTATGCTAAAGGGGCTTATCCTGGTTATGCTGGGGACCTTTTGGTGGACAAAACAAGTGGTGCTAGCTACAATGCAAATGGTGATAATGGAAGGAAGTATTTGTTGCCTGCGATTGTTGATCCAAAAACCTCAGTTTGTTCTACGTTGGTATGA
Protein sequence

>Msa0731900

MASFKLSVIFTLFLTISLLHLISAARKLTESDQQLKFQYHKGPLLTGKISINLIWYGKFKSSQRVIITDFITSLSSPKRGTTTSQPSVATWWKSTEKYYQLTNNKKSAKLALSLGAQILNENYSLGKSLTTNQILKLASKAQQQNAINVVLTAADVLVDGFCSSRCGTHGSSYGARVNGKRNKFAYIWVGNSETQCAGQCAWPFHQPIYGPQSAPLVAPNNDVGLDGMVINVASLLAGTVTNPFGNGYFQGPKEAPLEAASACTGVYAKGAYPGYAGDLLVDKTSGASYNANGDNGRKYLLPAIVDPKTSVCSTLV*