AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016545.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016545.01.T01 MTR_3g491830 100.000 124 0 0 37 160 267 390 4.04e-83 250
MsG0380016545.01.T01 MTR_4g123080 39.560 91 53 1 44 132 156 246 1.38e-14 69.3
MsG0380016545.01.T01 MTR_4g123080 39.560 91 53 1 44 132 269 359 3.43e-14 69.3
MsG0380016545.01.T01 MTR_4g123080 39.560 91 53 1 44 132 251 341 3.84e-14 68.9
MsG0380016545.01.T01 MTR_2g033000 42.466 73 42 0 44 116 256 328 7.80e-14 68.2
MsG0380016545.01.T01 MTR_1g086350 38.750 80 49 0 44 123 172 251 2.74e-12 63.2
MsG0380016545.01.T01 MTR_1g086350 38.750 80 49 0 44 123 274 353 7.16e-12 62.4
MsG0380016545.01.T01 MTR_1g086350 38.750 80 49 0 44 123 258 337 7.69e-12 62.4
MsG0380016545.01.T01 MTR_1g050520 37.975 79 43 2 41 116 566 641 1.02e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016545.01.T01 AT4G27800 72.358 123 34 0 37 159 266 388 1.46e-61 194
MsG0380016545.01.T01 AT4G27800 77.941 68 15 0 37 104 266 333 4.13e-31 114
MsG0380016545.01.T01 AT4G27800 73.333 60 16 0 37 96 266 325 3.25e-25 99.0
MsG0380016545.01.T01 AT1G48040 38.356 73 45 0 44 116 274 346 3.56e-12 63.5
MsG0380016545.01.T01 AT3G17250 36.986 73 46 0 44 116 318 390 3.71e-12 63.5
MsG0380016545.01.T01 AT3G62260 31.522 92 60 1 44 132 184 275 7.26e-12 62.4
MsG0380016545.01.T01 AT3G62260 31.522 92 60 1 44 132 273 364 8.50e-12 62.4
MsG0380016545.01.T01 AT3G62260 31.522 92 60 1 44 132 274 365 8.85e-12 62.4

Find 40 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTAGCATCCGATGGCTTA+TGG 0.271564 3:+84976322 MsG0380016542.01.T01:CDS
AGAGTTACTTGATAAATATC+AGG 0.343230 3:-84976276 None:intergenic
GAATTGTGTCTATTGGAATC+TGG 0.357830 3:+84977161 MsG0380016542.01.T01:exon
ACCGTTGGAATTGTGTCTAT+TGG 0.358693 3:+84977154 MsG0380016542.01.T01:exon
ATCCCTTGCACAAGTCGTTT+TGG 0.370646 3:+84976605 MsG0380016542.01.T01:CDS
AGCATTATAATTGCCGATCT+AGG 0.371221 3:+84976730 MsG0380016542.01.T01:CDS
AACATTTAAAAGAAAATATC+AGG 0.379728 3:-84977324 None:intergenic
GTTAGCATCCGATGGCTTAT+GGG 0.389003 3:+84976323 MsG0380016542.01.T01:CDS
GTGAAAAGGATGCTACAAAA+AGG 0.413005 3:+84976067 MsG0380016542.01.T01:intron
GATATTTATCAAGTAACTCT+TGG 0.438968 3:+84976279 MsG0380016542.01.T01:CDS
GGACAGAAAAGTTCATTTCC+CGG 0.447424 3:+84976107 MsG0380016542.01.T01:CDS
TTCCAACGGTGGCTAGGGCT+TGG 0.460560 3:-84977141 None:intergenic
CACAATTCCAACGGTGGCTA+GGG 0.467000 3:-84977146 None:intergenic
GAAGTAAAGAAGTATGCATC+TGG 0.475549 3:-84977235 None:intergenic
ACATCTTAGTAGAATCTACT+TGG 0.485502 3:+84977289 MsG0380016542.01.T01:exon
ACACAATTCCAACGGTGGCT+AGG 0.491960 3:-84977147 None:intergenic
GCTTATGGGATTACATGAGC+AGG 0.519531 3:+84976337 MsG0380016542.01.T01:CDS
ATGTACACTAAATATTATAC+AGG 0.519730 3:-84977261 None:intergenic
AAGGAGCTCAGGAAGGAAGA+TGG 0.526606 3:+84976086 MsG0380016542.01.T01:CDS
GCATTATAATTGCCGATCTA+GGG 0.535217 3:+84976731 MsG0380016542.01.T01:CDS
TTTATAGTGTTAGCATCCGA+TGG 0.544491 3:+84976315 MsG0380016542.01.T01:CDS
GTGCTTGCAGGAAGACAGAC+TGG 0.546345 3:+84977074 MsG0380016542.01.T01:intron
GTCCAAGCCCTAGCCACCGT+TGG 0.555090 3:+84977139 MsG0380016542.01.T01:exon
ACAAAATACATACCCTAGAT+CGG 0.557827 3:-84976743 None:intergenic
TGTACAGTTCAAAGATGACT+TGG 0.565147 3:+84976242 MsG0380016542.01.T01:CDS
TACCAAAACGACTTGTGCAA+GGG 0.580364 3:-84976607 None:intergenic
TTACCAAAACGACTTGTGCA+AGG 0.581838 3:-84976608 None:intergenic
ACACTAAATATTATACAGGC+AGG 0.583996 3:-84977257 None:intergenic
CATACATAAGATTACCTACC+GGG 0.587235 3:-84976125 None:intergenic
GAGTTACTTGATAAATATCA+GGG 0.596312 3:-84976275 None:intergenic
AGAAAAGTTCATTTCCCGGT+AGG 0.604812 3:+84976111 MsG0380016542.01.T01:CDS
GCAAAAGGTAGATAACACTT+AGG 0.605615 3:-84976042 None:intergenic
CATGTAATCCCATAAGCCAT+CGG 0.609703 3:-84976331 None:intergenic
TCTGCAGGACCAACGTACAC+AGG 0.646615 3:+84976699 MsG0380016542.01.T01:intron
AGGGATCAACTACGAAAACA+TGG 0.647059 3:+84976470 MsG0380016542.01.T01:CDS
TCCAATAGACACAATTCCAA+CGG 0.647966 3:-84977155 None:intergenic
ACATACATAAGATTACCTAC+CGG 0.655727 3:-84976126 None:intergenic
ACGAAAACATGGAAACACAC+AGG 0.687122 3:+84976481 MsG0380016542.01.T01:CDS
AATAGACACAATTCCAACGG+TGG 0.712558 3:-84977152 None:intergenic
TGACATTATCCTGTGTACGT+TGG 0.736320 3:-84976708 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACATTTAAAAGAAAATATC+AGG - Chr3:84977327-84977346 None:intergenic 15.0%
!! ATTTAATAAAACTCATATTC+TGG + Chr3:84976857-84976876 MsG0380016542.01.T01:intron 15.0%
!!! TTTTTTTTTTCTTTTCACAA+AGG - Chr3:84976826-84976845 None:intergenic 15.0%
!! ATGTACACTAAATATTATAC+AGG - Chr3:84977264-84977283 None:intergenic 20.0%
! AGAGTTACTTGATAAATATC+AGG - Chr3:84976279-84976298 None:intergenic 25.0%
! GAGTTACTTGATAAATATCA+GGG - Chr3:84976278-84976297 None:intergenic 25.0%
! GATATTTATCAAGTAACTCT+TGG + Chr3:84976279-84976298 MsG0380016542.01.T01:CDS 25.0%
! TGCCAAAAACTTTATATTTG+AGG + Chr3:84976506-84976525 MsG0380016542.01.T01:intron 25.0%
! TTGTCATGTATATATGACTT+TGG + Chr3:84976762-84976781 MsG0380016542.01.T01:intron 25.0%
! TTTGTTTAAATCCTAACCTT+TGG - Chr3:84976934-84976953 None:intergenic 25.0%
!! TGCCTCAAATATAAAGTTTT+TGG - Chr3:84976511-84976530 None:intergenic 25.0%
ACAAAATACATACCCTAGAT+CGG - Chr3:84976746-84976765 None:intergenic 30.0%
ACACTAAATATTATACAGGC+AGG - Chr3:84977260-84977279 None:intergenic 30.0%
ACATACATAAGATTACCTAC+CGG - Chr3:84976129-84976148 None:intergenic 30.0%
ACATCTTAGTAGAATCTACT+TGG + Chr3:84977289-84977308 MsG0380016542.01.T01:exon 30.0%
CAGCAATTACGTTCTATAAT+TGG + Chr3:84976789-84976808 MsG0380016542.01.T01:intron 30.0%
GAACAAGCAGAATATTATTG+CGG - Chr3:84976565-84976584 None:intergenic 30.0%
TAAAACTCATATTCTGGTCA+TGG + Chr3:84976863-84976882 MsG0380016542.01.T01:intron 30.0%
! ATATCACTAGAGCATTAATG+TGG + Chr3:84976907-84976926 MsG0380016542.01.T01:intron 30.0%
AAGCACTCATATAAAACGCA+TGG - Chr3:84977060-84977079 None:intergenic 35.0%
AAGGGTAGCAGAAATGATTT+GGG - Chr3:84976377-84976396 None:intergenic 35.0%
AGCATTATAATTGCCGATCT+AGG + Chr3:84976730-84976749 MsG0380016542.01.T01:CDS 35.0%
ATTAATGTGGTCCAAAGGTT+AGG + Chr3:84976920-84976939 MsG0380016542.01.T01:intron 35.0%
ATTGTGAAGGTAATTCTCTG+CGG - Chr3:84976412-84976431 None:intergenic 35.0%
CATACATAAGATTACCTACC+GGG - Chr3:84976128-84976147 None:intergenic 35.0%
GAATTGTGTCTATTGGAATC+TGG + Chr3:84977161-84977180 MsG0380016542.01.T01:exon 35.0%
GCAAAAGGTAGATAACACTT+AGG - Chr3:84976045-84976064 None:intergenic 35.0%
GCATTATAATTGCCGATCTA+GGG + Chr3:84976731-84976750 MsG0380016542.01.T01:CDS 35.0%
GTGAAAAGGATGCTACAAAA+AGG + Chr3:84976067-84976086 MsG0380016542.01.T01:intron 35.0%
TCCAATAGACACAATTCCAA+CGG - Chr3:84977158-84977177 None:intergenic 35.0%
TGTACAGTTCAAAGATGACT+TGG + Chr3:84976242-84976261 MsG0380016542.01.T01:CDS 35.0%
TTTATAGTGTTAGCATCCGA+TGG + Chr3:84976315-84976334 MsG0380016542.01.T01:CDS 35.0%
! GAAGTAAAGAAGTATGCATC+TGG - Chr3:84977238-84977257 None:intergenic 35.0%
!! TTCTTTTCACAAAGGCATAG+CGG - Chr3:84976818-84976837 None:intergenic 35.0%
!!! TTCTGCTACCCTTCTTTTTT+TGG + Chr3:84976384-84976403 MsG0380016542.01.T01:intron 35.0%
AATAGACACAATTCCAACGG+TGG - Chr3:84977155-84977174 None:intergenic 40.0%
ACCGTTGGAATTGTGTCTAT+TGG + Chr3:84977154-84977173 MsG0380016542.01.T01:exon 40.0%
ACGAAAACATGGAAACACAC+AGG + Chr3:84976481-84976500 MsG0380016542.01.T01:CDS 40.0%
AGAAAAGTTCATTTCCCGGT+AGG + Chr3:84976111-84976130 MsG0380016542.01.T01:CDS 40.0%
AGGGATCAACTACGAAAACA+TGG + Chr3:84976470-84976489 MsG0380016542.01.T01:CDS 40.0%
AGGGTAGCAGAAATGATTTG+GGG - Chr3:84976376-84976395 None:intergenic 40.0%
CAAGGATAGCAAGATTGTGA+AGG - Chr3:84976425-84976444 None:intergenic 40.0%
CATGTAATCCCATAAGCCAT+CGG - Chr3:84976334-84976353 None:intergenic 40.0%
CTGCGGAACCAAAAAAAGAA+GGG - Chr3:84976395-84976414 None:intergenic 40.0%
GAAGGGTAGCAGAAATGATT+TGG - Chr3:84976378-84976397 None:intergenic 40.0%
GGACAGAAAAGTTCATTTCC+CGG + Chr3:84976107-84976126 MsG0380016542.01.T01:CDS 40.0%
GTCATCTTTGAACTGTACAC+TGG - Chr3:84976241-84976260 None:intergenic 40.0%
TACCAAAACGACTTGTGCAA+GGG - Chr3:84976610-84976629 None:intergenic 40.0%
TCCATTATGATACACTCTGC+AGG + Chr3:84976684-84976703 MsG0380016542.01.T01:intron 40.0%
TCCTGCAGAGTGTATCATAA+TGG - Chr3:84976688-84976707 None:intergenic 40.0%
TCTGCGGAACCAAAAAAAGA+AGG - Chr3:84976396-84976415 None:intergenic 40.0%
TGACATTATCCTGTGTACGT+TGG - Chr3:84976711-84976730 None:intergenic 40.0%
TTACCAAAACGACTTGTGCA+AGG - Chr3:84976611-84976630 None:intergenic 40.0%
! AGACGCAGTTTCTTTTGTGA+GGG + Chr3:84976451-84976470 MsG0380016542.01.T01:CDS 40.0%
! AGAGCATTAATGTGGTCCAA+AGG + Chr3:84976915-84976934 MsG0380016542.01.T01:intron 40.0%
! CGTTTTATATGAGTGCTTGC+AGG + Chr3:84977062-84977081 MsG0380016542.01.T01:intron 40.0%
! TCTACCTTTTGCGTGTGAAA+AGG + Chr3:84976053-84976072 MsG0380016542.01.T01:intron 40.0%
CTACAAAAAGGAGCTCAGGA+AGG + Chr3:84976079-84976098 MsG0380016542.01.T01:CDS 45.0%
GATGCTACAAAAAGGAGCTC+AGG + Chr3:84976075-84976094 MsG0380016542.01.T01:CDS 45.0%
GCTTATGGGATTACATGAGC+AGG + Chr3:84976337-84976356 MsG0380016542.01.T01:CDS 45.0%
GTTAGCATCCGATGGCTTAT+GGG + Chr3:84976323-84976342 MsG0380016542.01.T01:CDS 45.0%
TATTATTGCGGCTGCTTCGA+TGG - Chr3:84976553-84976572 None:intergenic 45.0%
TGTTAGCATCCGATGGCTTA+TGG + Chr3:84976322-84976341 MsG0380016542.01.T01:CDS 45.0%
! ATCCCTTGCACAAGTCGTTT+TGG + Chr3:84976605-84976624 MsG0380016542.01.T01:CDS 45.0%
! CAGACGCAGTTTCTTTTGTG+AGG + Chr3:84976450-84976469 MsG0380016542.01.T01:CDS 45.0%
! GCATCCTTTTCACACGCAAA+AGG - Chr3:84976060-84976079 None:intergenic 45.0%
! GTGACATTTTGTTGCTGCAG+TGG - Chr3:84977109-84977128 None:intergenic 45.0%
AAGGAGCTCAGGAAGGAAGA+TGG + Chr3:84976086-84976105 MsG0380016542.01.T01:CDS 50.0%
ACACAATTCCAACGGTGGCT+AGG - Chr3:84977150-84977169 None:intergenic 50.0%
CACAATTCCAACGGTGGCTA+GGG - Chr3:84977149-84977168 None:intergenic 50.0%
!! CATGTTGCACAGAAGTGCTC+TGG + Chr3:84976969-84976988 MsG0380016542.01.T01:intron 50.0%
GAAACTGCGTCTGAGCTGCA+AGG - Chr3:84976443-84976462 None:intergenic 55.0%
GTGCTTGCAGGAAGACAGAC+TGG + Chr3:84977074-84977093 MsG0380016542.01.T01:intron 55.0%
TCTGCAGGACCAACGTACAC+AGG + Chr3:84976699-84976718 MsG0380016542.01.T01:intron 55.0%
TTCCAACGGTGGCTAGGGCT+TGG - Chr3:84977144-84977163 None:intergenic 60.0%
GTCCAAGCCCTAGCCACCGT+TGG + Chr3:84977139-84977158 MsG0380016542.01.T01:exon 65.0%
Chromosome Type Strat End Strand Name
Chr3 gene 84976036 84977399 84976036 ID=MsG0380016545.01;Name=MsG0380016545.01
Chr3 mRNA 84976036 84977399 84976036 ID=MsG0380016545.01.T01;Parent=MsG0380016545.01;Name=MsG0380016545.01.T01;_AED=0.46;_eAED=0.54;_QI=0|0.8|0.83|1|0.4|0.66|6|192|160
Chr3 exon 84976036 84976142 84976036 ID=MsG0380016545.01.T01:exon:14379;Parent=MsG0380016545.01.T01
Chr3 exon 84976242 84976358 84976242 ID=MsG0380016545.01.T01:exon:14380;Parent=MsG0380016545.01.T01
Chr3 exon 84976448 84976502 84976448 ID=MsG0380016545.01.T01:exon:14381;Parent=MsG0380016545.01.T01
Chr3 exon 84976594 84976626 84976594 ID=MsG0380016545.01.T01:exon:14382;Parent=MsG0380016545.01.T01
Chr3 exon 84976706 84976752 84976706 ID=MsG0380016545.01.T01:exon:14383;Parent=MsG0380016545.01.T01
Chr3 exon 84977084 84977399 84977084 ID=MsG0380016545.01.T01:exon:14384;Parent=MsG0380016545.01.T01
Chr3 CDS 84976036 84976142 84976036 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 CDS 84976242 84976358 84976242 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 CDS 84976448 84976502 84976448 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 CDS 84976594 84976626 84976594 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 CDS 84976706 84976752 84976706 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 CDS 84977084 84977207 84977084 ID=MsG0380016545.01.T01:cds;Parent=MsG0380016545.01.T01
Chr3 three_prime_UTR 84977208 84977399 84977208 ID=MsG0380016545.01.T01:three_prime_utr;Parent=MsG0380016545.01.T01
Gene Sequence

>MsG0380016545.01.T01

ATGCTTCCTAAGTGTTATCTACCTTTTGCGTGTGAAAAGGATGCTACAAAAAGGAGCTCAGGAAGGAAGATGGACAGAAAAGTTCATTTCCCGGTAGGTAATCTTATTGTACAGTTCAAAGATGACTTGGTTGTTGCACGCCCTGATATTTATCAAGTAACTCTTGGCTCAGATGCAGAATTTATAGTGTTAGCATCCGATGGCTTATGGGATTACATGAGCAGCTCAGACGCAGTTTCTTTTGTGAGGGATCAACTACGAAAACATGGAAACACACAGCTAGCTTGTGAATCCCTTGCACAAGTCGTTTTGGACCAACGTACACAGGATAATGTCAGCATTATAATTGCCGATCTAGGGAAGACAGACTGGAAGAGTGTACCACTGCAGCAACAAAATGTCACATTTGAGCTAGTCCAAGCCCTAGCCACCGTTGGAATTGTGTCTATTGGAATCTGGTTTTCATCACAGCTTTCTTTATAG

Protein sequence

>MsG0380016545.01.T01

MLPKCYLPFACEKDATKRSSGRKMDRKVHFPVGNLIVQFKDDLVVARPDIYQVTLGSDAEFIVLASDGLWDYMSSSDAVSFVRDQLRKHGNTQLACESLAQVVLDQRTQDNVSIIIADLGKTDWKSVPLQQQNVTFELVQALATVGIVSIGIWFSSQLSL*