AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0772930

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0772930 MtrunA17_Chr5g0426441 95.177 311 15 0 6 316 648 958 0.0 609
Msa0772930 MtrunA17_Chr5g0426441 92.089 316 24 1 1 316 25 339 0.0 595
Msa0772930 MtrunA17_Chr5g0426441 92.926 311 21 1 6 316 339 648 0.0 591
Msa0772930 MtrunA17_Chr3g0116001 78.788 297 50 3 20 316 21 304 1.24e-170 475
Msa0772930 MtrunA17_Chr3g0116011 78.451 297 51 4 20 316 21 304 2.47e-169 472
Msa0772930 MtrunA17_Chr3g0115951 71.061 311 86 3 9 316 8 317 1.09e-154 435
Msa0772930 MtrunA17_Chr4g0050321 60.702 285 98 3 32 316 30 300 3.21e-121 350
Msa0772930 MtrunA17_Chr2g0279311 52.830 318 133 7 1 316 2 304 7.52e-118 342
Msa0772930 MtrunA17_Chr4g0018171 36.458 288 161 8 25 301 53 329 2.81e-47 162
Msa0772930 MtrunA17_Chr1g0188071 34.169 319 189 7 6 313 33 341 2.00e-46 160
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0772930 AT4G08950.1 71.572 299 75 6 24 316 20 314 3.24e-147 417
Msa0772930 AT1G35140.1 64.762 315 104 3 1 315 1 308 5.67e-143 405
Msa0772930 AT5G64260.1 57.792 308 120 4 10 316 7 305 3.07e-122 353
Msa0772930 AT5G09440.1 55.482 301 100 7 18 316 10 278 1.28e-102 302
Msa0772930 AT5G51550.1 36.066 305 173 8 20 313 38 331 4.40e-50 169
Msa0772930 AT3G02970.1 31.208 298 167 7 49 314 39 330 3.29e-45 157
Msa0772930 AT2G35150.1 33.746 323 186 11 9 312 3 316 6.96e-43 150
Msa0772930 AT2G17230.1 32.566 304 183 9 22 313 64 357 1.32e-41 148

Find 65 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAACAAGTTCGCGTATATT+TGG 0.180098 5_2:+47384045 Msa0772930:CDS
CCATTTCACCAACCAATTTA+TGG 0.182864 5_2:+47384110 Msa0772930:CDS
TCTTATGGTGCACGTGTAAA+TGG 0.207934 5_2:+47384017 Msa0772930:CDS
TCAAGACCTACATCGTTATT+TGG 0.256091 5_2:-47384158 None:intergenic
TTGATGCAAGTTTAAGGATT+TGG 0.266389 5_2:-47383899 None:intergenic
GAGGTTGATTGAGATATTTC+TGG 0.268346 5_2:-47383640 None:intergenic
GGAACCCATGGTTCTTCTTA+TGG 0.283880 5_2:+47384002 Msa0772930:CDS
TGGTTATGCTGGGGCCCTTT+TGG 0.286824 5_2:+47384322 Msa0772930:CDS
CTCGATGAGAATTACTCTTT+AGG 0.297921 5_2:+47383858 Msa0772930:CDS
GCACTTTGTGGACCATAAAT+TGG 0.307975 5_2:-47384122 None:intergenic
GCTTCCAAAGGAGCTTCTTT+TGG 0.308698 5_2:-47384257 None:intergenic
AGCTCCTTTGGAAGCTGCTT+CGG 0.362716 5_2:+47384265 Msa0772930:CDS
AAACAAGTTCGCGTATATTT+GGG 0.369538 5_2:+47384046 Msa0772930:CDS
AGGACCAAAAGAAGCTCCTT+TGG 0.376105 5_2:+47384253 Msa0772930:CDS
CCATAAATTGGTTGGTGAAA+TGG 0.381983 5_2:-47384110 None:intergenic
TGGTGAGAAGAGGGCCTTTG+TGG 0.385274 5_2:-47383620 None:intergenic
ATATCTCAATCAACCTCATT+TGG 0.389685 5_2:+47383646 Msa0772930:CDS
GGAGCTTATCCTGGTTATGC+TGG 0.412712 5_2:+47384311 Msa0772930:CDS
TACAACGCTAATGGTGATAA+TGG 0.420824 5_2:+47384368 Msa0772930:CDS
ATCCTTAAACTTGCATCAAA+AGG 0.429930 5_2:+47383903 Msa0772930:CDS
GGAACGGTAACGAATCCTTT+TGG 0.438734 5_2:+47384215 Msa0772930:CDS
GATGTGGTTGTTCCTTGTTT+AGG 0.441091 5_2:-47383732 None:intergenic
GGTATTGAAATTTAAGTTGT+TGG 0.450783 5_2:-47383599 None:intergenic
AGCTGTTAGAACAACGTTGA+TGG 0.452654 5_2:-47383940 None:intergenic
TGAAAATATCCATTACCAAA+AGG 0.461381 5_2:-47384230 None:intergenic
CGCTAGAAAACTCACTGAAT+CGG 0.469442 5_2:+47383575 Msa0772930:CDS
TACGCTAAAGGAGCTTATCC+TGG 0.473884 5_2:+47384302 Msa0772930:CDS
GAAGCTGCTTCGGCTTGTAC+CGG 0.475241 5_2:+47384275 Msa0772930:CDS
TGTACCGGTGTTTACGCTAA+AGG 0.482677 5_2:+47384290 Msa0772930:CDS
GCAACCAACGGTGCACTTTG+TGG 0.494418 5_2:-47384134 None:intergenic
TCAATCAACCTCATTTGGTA+TGG 0.498550 5_2:+47383651 Msa0772930:CDS
AATAACGATGTAGGTCTTGA+CGG 0.500974 5_2:+47384161 Msa0772930:CDS
AACTTCAGCTTGTTCTACAT+TGG 0.507055 5_2:+47384427 Msa0772930:CDS
GGTGCTAGCTACAACGCTAA+TGG 0.508260 5_2:+47384359 Msa0772930:CDS
GCTGCTGATGTGTTAGTTGA+CGG 0.512705 5_2:+47383960 Msa0772930:CDS
GAGCTTATCCTGGTTATGCT+GGG 0.517406 5_2:+47384312 Msa0772930:CDS
AGATATTTCTGGTGAGAAGA+GGG 0.530673 5_2:-47383629 None:intergenic
GGTTATGAAATCAGTTATGA+TGG 0.539205 5_2:-47383697 None:intergenic
CGATGTAGGTCTTGACGGAA+TGG 0.541134 5_2:+47384166 Msa0772930:CDS
AAGTTCGCGTATATTTGGGT+TGG 0.543691 5_2:+47384050 Msa0772930:CDS
GAGATATTTCTGGTGAGAAG+AGG 0.546758 5_2:-47383630 None:intergenic
TCGTTATTTGGTGCAACCAA+CGG 0.547290 5_2:-47384146 None:intergenic
AATTCTGAAACTCAATGTGC+TGG 0.549654 5_2:+47384074 Msa0772930:CDS
GTTATGATGGCTCTTTGAGA+TGG 0.551294 5_2:-47383684 None:intergenic
TTCCACCACGTGGCAACAGA+TGG 0.552839 5_2:-47383759 None:intergenic
GCTAAACTAGCTCTCTCGCT+AGG 0.554999 5_2:+47383825 Msa0772930:CDS
TCAAGTAGGTGTGGAACCCA+TGG 0.564282 5_2:+47383990 Msa0772930:CDS
AAAAGGGCCCCAGCATAACC+AGG 0.566264 5_2:-47384320 None:intergenic
ACGCTAATGGTGATAATGGA+AGG 0.567526 5_2:+47384372 Msa0772930:CDS
AGCTTATCCTGGTTATGCTG+GGG 0.590478 5_2:+47384313 Msa0772930:CDS
TGGTCCACAAAGTGCACCGT+TGG 0.596808 5_2:+47384130 Msa0772930:CDS
GTTGCACCAAATAACGATGT+AGG 0.601769 5_2:+47384152 Msa0772930:CDS
AACCATCTGTTGCCACGTGG+TGG 0.604103 5_2:+47383757 Msa0772930:CDS
TTGTTTAGGAGAAGAGAGTG+AGG 0.609851 5_2:-47383718 None:intergenic
TTTGTGGACCATAAATTGGT+TGG 0.611426 5_2:-47384118 None:intergenic
CTTAAATTTCAATACCACAA+AGG 0.623830 5_2:+47383606 Msa0772930:CDS
GTGCACCATAAGAAGAACCA+TGG 0.635354 5_2:-47384007 None:intergenic
TTCAGTTGATTTCCACCACG+TGG 0.645033 5_2:-47383769 None:intergenic
CAAGCCGAAGCAGCTTCCAA+AGG 0.645366 5_2:-47384269 None:intergenic
TCACTCTCTTCTCCTAAACA+AGG 0.648969 5_2:+47383720 Msa0772930:CDS
TGCACCATAAGAAGAACCAT+GGG 0.667974 5_2:-47384006 None:intergenic
CACAACCATCTGTTGCCACG+TGG 0.682786 5_2:+47383754 Msa0772930:CDS
GGCAACAGATGGTTGTGATG+TGG 0.684003 5_2:-47383748 None:intergenic
AGCTCCTTTAGCGTAAACAC+CGG 0.692829 5_2:-47384294 None:intergenic
AATGTGCTGGTCAATGCACA+TGG 0.706563 5_2:+47384087 Msa0772930:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAGCTGATTTTTTATTGT+TGG - chr5_2:47383811-47383830 None:intergenic 20.0%
!!! GGTATTGAAATTTAAGTTGT+TGG - chr5_2:47383602-47383621 None:intergenic 25.0%
! CTTAAATTTCAATACCACAA+AGG + chr5_2:47383606-47383625 Msa0772930:CDS 25.0%
!!! ATTTTTTATTGTTGGTGAGT+TGG - chr5_2:47383803-47383822 None:intergenic 25.0%
! TGAAAATATCCATTACCAAA+AGG - chr5_2:47384233-47384252 None:intergenic 25.0%
!!! TTTGGTAATGGATATTTTCA+AGG + chr5_2:47384233-47384252 Msa0772930:CDS 25.0%
CAGTGAAATTGTGAGAAAAA+TGG - chr5_2:47383538-47383557 None:intergenic 30.0%
ATATCTCAATCAACCTCATT+TGG + chr5_2:47383646-47383665 Msa0772930:CDS 30.0%
! TGAATTTTCCATACCAAATG+AGG - chr5_2:47383662-47383681 None:intergenic 30.0%
GGTTATGAAATCAGTTATGA+TGG - chr5_2:47383700-47383719 None:intergenic 30.0%
TTGATGCAAGTTTAAGGATT+TGG - chr5_2:47383902-47383921 None:intergenic 30.0%
ATCCTTAAACTTGCATCAAA+AGG + chr5_2:47383903-47383922 Msa0772930:CDS 30.0%
AAACAAGTTCGCGTATATTT+GGG + chr5_2:47384046-47384065 Msa0772930:CDS 30.0%
!! AGATATTTCTGGTGAGAAGA+GGG - chr5_2:47383632-47383651 None:intergenic 35.0%
! GAGGTTGATTGAGATATTTC+TGG - chr5_2:47383643-47383662 None:intergenic 35.0%
TCAATCAACCTCATTTGGTA+TGG + chr5_2:47383651-47383670 Msa0772930:CDS 35.0%
CTCGATGAGAATTACTCTTT+AGG + chr5_2:47383858-47383877 Msa0772930:CDS 35.0%
! GTCCTTTTGATGCAAGTTTA+AGG - chr5_2:47383908-47383927 None:intergenic 35.0%
! TTGACGGTTTTTGTTCAAGT+AGG + chr5_2:47383976-47383995 Msa0772930:CDS 35.0%
GAAACAAGTTCGCGTATATT+TGG + chr5_2:47384045-47384064 Msa0772930:CDS 35.0%
!! AATTCTGAAACTCAATGTGC+TGG + chr5_2:47384074-47384093 Msa0772930:CDS 35.0%
!! CCATAAATTGGTTGGTGAAA+TGG - chr5_2:47384113-47384132 None:intergenic 35.0%
CCATTTCACCAACCAATTTA+TGG + chr5_2:47384110-47384129 Msa0772930:CDS 35.0%
TTTGTGGACCATAAATTGGT+TGG - chr5_2:47384121-47384140 None:intergenic 35.0%
TCAAGACCTACATCGTTATT+TGG - chr5_2:47384161-47384180 None:intergenic 35.0%
AATAACGATGTAGGTCTTGA+CGG + chr5_2:47384161-47384180 Msa0772930:CDS 35.0%
!!! AATGTTGCTAGTCTTTTAGC+TGG + chr5_2:47384194-47384213 Msa0772930:CDS 35.0%
! GTAACGAATCCTTTTGGTAA+TGG + chr5_2:47384221-47384240 Msa0772930:CDS 35.0%
!!! ACTTGTTTTGTCCACCAAAA+GGG - chr5_2:47384339-47384358 None:intergenic 35.0%
TACAACGCTAATGGTGATAA+TGG + chr5_2:47384368-47384387 Msa0772930:CDS 35.0%
! GTAGAACAAGCTGAAGTTTT+AGG - chr5_2:47384425-47384444 None:intergenic 35.0%
! AACTTCAGCTTGTTCTACAT+TGG + chr5_2:47384427-47384446 Msa0772930:CDS 35.0%
! CGATTCAGTGAGTTTTCTAG+CGG - chr5_2:47383577-47383596 None:intergenic 40.0%
CGCTAGAAAACTCACTGAAT+CGG + chr5_2:47383575-47383594 Msa0772930:CDS 40.0%
!! GAGATATTTCTGGTGAGAAG+AGG - chr5_2:47383633-47383652 None:intergenic 40.0%
! GTTATGATGGCTCTTTGAGA+TGG - chr5_2:47383687-47383706 None:intergenic 40.0%
TTGTTTAGGAGAAGAGAGTG+AGG - chr5_2:47383721-47383740 None:intergenic 40.0%
TCACTCTCTTCTCCTAAACA+AGG + chr5_2:47383720-47383739 Msa0772930:CDS 40.0%
! GATGTGGTTGTTCCTTGTTT+AGG - chr5_2:47383735-47383754 None:intergenic 40.0%
AGCTGTTAGAACAACGTTGA+TGG - chr5_2:47383943-47383962 None:intergenic 40.0%
! GGTTTTTGTTCAAGTAGGTG+TGG + chr5_2:47383981-47384000 Msa0772930:CDS 40.0%
TGCACCATAAGAAGAACCAT+GGG - chr5_2:47384009-47384028 None:intergenic 40.0%
TCTTATGGTGCACGTGTAAA+TGG + chr5_2:47384017-47384036 Msa0772930:CDS 40.0%
AAGTTCGCGTATATTTGGGT+TGG + chr5_2:47384050-47384069 Msa0772930:CDS 40.0%
GCACTTTGTGGACCATAAAT+TGG - chr5_2:47384125-47384144 None:intergenic 40.0%
!! TCGTTATTTGGTGCAACCAA+CGG - chr5_2:47384149-47384168 None:intergenic 40.0%
GTTGCACCAAATAACGATGT+AGG + chr5_2:47384152-47384171 Msa0772930:CDS 40.0%
!!! TGCTAGTCTTTTAGCTGGAA+CGG + chr5_2:47384199-47384218 Msa0772930:CDS 40.0%
!!! CACTTGTTTTGTCCACCAAA+AGG - chr5_2:47384340-47384359 None:intergenic 40.0%
!! CTTTTGGTGGACAAAACAAG+TGG + chr5_2:47384338-47384357 Msa0772930:CDS 40.0%
!! ACGCTAATGGTGATAATGGA+AGG + chr5_2:47384372-47384391 Msa0772930:CDS 40.0%
!!! GTTTTAGGATCAACAATCGC+AGG - chr5_2:47384410-47384429 None:intergenic 40.0%
! TTCAGTTGATTTCCACCACG+TGG - chr5_2:47383772-47383791 None:intergenic 45.0%
GCTGCTGATGTGTTAGTTGA+CGG + chr5_2:47383960-47383979 Msa0772930:CDS 45.0%
GGAACCCATGGTTCTTCTTA+TGG + chr5_2:47384002-47384021 Msa0772930:CDS 45.0%
GTGCACCATAAGAAGAACCA+TGG - chr5_2:47384010-47384029 None:intergenic 45.0%
! AATGTGCTGGTCAATGCACA+TGG + chr5_2:47384087-47384106 Msa0772930:CDS 45.0%
! GGAACGGTAACGAATCCTTT+TGG + chr5_2:47384215-47384234 Msa0772930:CDS 45.0%
AGGACCAAAAGAAGCTCCTT+TGG + chr5_2:47384253-47384272 Msa0772930:CDS 45.0%
! GCTTCCAAAGGAGCTTCTTT+TGG - chr5_2:47384260-47384279 None:intergenic 45.0%
! TGTACCGGTGTTTACGCTAA+AGG + chr5_2:47384290-47384309 Msa0772930:CDS 45.0%
AGCTCCTTTAGCGTAAACAC+CGG - chr5_2:47384297-47384316 None:intergenic 45.0%
TACGCTAAAGGAGCTTATCC+TGG + chr5_2:47384302-47384321 Msa0772930:CDS 45.0%
GAGCTTATCCTGGTTATGCT+GGG + chr5_2:47384312-47384331 Msa0772930:CDS 45.0%
AGCTTATCCTGGTTATGCTG+GGG + chr5_2:47384313-47384332 Msa0772930:CDS 45.0%
GGCAACAGATGGTTGTGATG+TGG - chr5_2:47383751-47383770 None:intergenic 50.0%
! GCTAAACTAGCTCTCTCGCT+AGG + chr5_2:47383825-47383844 Msa0772930:CDS 50.0%
TCAAGTAGGTGTGGAACCCA+TGG + chr5_2:47383990-47384009 Msa0772930:CDS 50.0%
CGATGTAGGTCTTGACGGAA+TGG + chr5_2:47384166-47384185 Msa0772930:CDS 50.0%
! AGCTCCTTTGGAAGCTGCTT+CGG + chr5_2:47384265-47384284 Msa0772930:CDS 50.0%
GGAGCTTATCCTGGTTATGC+TGG + chr5_2:47384311-47384330 Msa0772930:CDS 50.0%
GGTGCTAGCTACAACGCTAA+TGG + chr5_2:47384359-47384378 Msa0772930:CDS 50.0%
TGGTGAGAAGAGGGCCTTTG+TGG - chr5_2:47383623-47383642 None:intergenic 55.0%
CACAACCATCTGTTGCCACG+TGG + chr5_2:47383754-47383773 Msa0772930:CDS 55.0%
AACCATCTGTTGCCACGTGG+TGG + chr5_2:47383757-47383776 Msa0772930:CDS 55.0%
TTCCACCACGTGGCAACAGA+TGG - chr5_2:47383762-47383781 None:intergenic 55.0%
TGGTCCACAAAGTGCACCGT+TGG + chr5_2:47384130-47384149 Msa0772930:CDS 55.0%
GCAACCAACGGTGCACTTTG+TGG - chr5_2:47384137-47384156 None:intergenic 55.0%
CAAGCCGAAGCAGCTTCCAA+AGG - chr5_2:47384272-47384291 None:intergenic 55.0%
! GAAGCTGCTTCGGCTTGTAC+CGG + chr5_2:47384275-47384294 Msa0772930:CDS 55.0%
AAAAGGGCCCCAGCATAACC+AGG - chr5_2:47384323-47384342 None:intergenic 55.0%
! TGGTTATGCTGGGGCCCTTT+TGG + chr5_2:47384322-47384341 Msa0772930:CDS 55.0%
! TTATGCTGGGGCCCTTTTGG+TGG + chr5_2:47384325-47384344 Msa0772930:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 47383504 47384454 47383504 ID=Msa0772930;Name=Msa0772930
chr5_2 mRNA 47383504 47384454 47383504 ID=Msa0772930-mRNA-1;Parent=Msa0772930;Name=Msa0772930-mRNA-1;_AED=0.36;_eAED=0.36;_QI=0|-1|0|1|-1|1|1|0|316
chr5_2 exon 47383504 47384454 47383504 ID=Msa0772930-mRNA-1:exon:14234;Parent=Msa0772930-mRNA-1
chr5_2 CDS 47383504 47384454 47383504 ID=Msa0772930-mRNA-1:cds;Parent=Msa0772930-mRNA-1
Gene Sequence

>Msa0772930

ATGGCATCTTTTAAGTTAAGTGTAATCTTCACCATTTTTCTCACAATTTCACTGCTTCATTTAATCTCAGCCGCTAGAAAACTCACTGAATCGGACCAACAACTTAAATTTCAATACCACAAAGGCCCTCTTCTCACCAGAAATATCTCAATCAACCTCATTTGGTATGGAAAATTCAAACCATCTCAAAGAGCCATCATAACTGATTTCATAACCTCACTCTCTTCTCCTAAACAAGGAACAACCACATCACAACCATCTGTTGCCACGTGGTGGAAATCAACTGAAAAATATTACCAACTCACCAACAATAAAAAATCAGCTAAACTAGCTCTCTCGCTAGGTGCTCAAATTCTCGATGAGAATTACTCTTTAGGAAAATCTCTCACAACTAACCAAATCCTTAAACTTGCATCAAAAGGACAACAAAAAAACGCCATCAACGTTGTTCTAACAGCTGCTGATGTGTTAGTTGACGGTTTTTGTTCAAGTAGGTGTGGAACCCATGGTTCTTCTTATGGTGCACGTGTAAATGGAAAGAGAAACAAGTTCGCGTATATTTGGGTTGGAAATTCTGAAACTCAATGTGCTGGTCAATGCACATGGCCATTTCACCAACCAATTTATGGTCCACAAAGTGCACCGTTGGTTGCACCAAATAACGATGTAGGTCTTGACGGAATGGTTATAAATGTTGCTAGTCTTTTAGCTGGAACGGTAACGAATCCTTTTGGTAATGGATATTTTCAAGGACCAAAAGAAGCTCCTTTGGAAGCTGCTTCGGCTTGTACCGGTGTTTACGCTAAAGGAGCTTATCCTGGTTATGCTGGGGCCCTTTTGGTGGACAAAACAAGTGGTGCTAGCTACAACGCTAATGGTGATAATGGAAGGAAGTATTTGCTGCCTGCGATTGTTGATCCTAAAACTTCAGCTTGTTCTACATTGGTATAA
Protein sequence

>Msa0772930

MASFKLSVIFTIFLTISLLHLISAARKLTESDQQLKFQYHKGPLLTRNISINLIWYGKFKPSQRAIITDFITSLSSPKQGTTTSQPSVATWWKSTEKYYQLTNNKKSAKLALSLGAQILDENYSLGKSLTTNQILKLASKGQQKNAINVVLTAADVLVDGFCSSRCGTHGSSYGARVNGKRNKFAYIWVGNSETQCAGQCTWPFHQPIYGPQSAPLVAPNNDVGLDGMVINVASLLAGTVTNPFGNGYFQGPKEAPLEAASACTGVYAKGAYPGYAGALLVDKTSGASYNANGDNGRKYLLPAIVDPKTSACSTLV*