AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG000209

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000209 MtrunA17_Chr1g0154641 87.413 286 33 2 29 311 111 396 2.40e-176 504
MsaG000209 MtrunA17_Chr1g0154651 91.393 244 21 0 305 548 6 249 1.24e-162 462
MsaG000209 MtrunA17_Chr3g0141401 45.130 308 104 6 304 546 6 313 3.23e-53 183
MsaG000209 MtrunA17_Chr5g0403631 36.562 320 110 8 313 545 9 322 6.24e-27 111
MsaG000209 MtrunA17_Chr2g0315211 38.245 319 108 13 313 545 6 321 4.24e-23 100
MsaG000209 MtrunA17_Chr2g0315201 62.500 88 32 1 313 400 6 92 8.64e-16 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG000209 AT1G19340.1 50.694 288 128 6 29 309 93 373 2.95e-81 260
MsaG000209 AT1G75080.2 45.541 314 93 8 312 547 22 335 6.33e-59 199
MsaG000209 AT1G75080.1 45.541 314 93 8 312 547 22 335 6.33e-59 199
MsaG000209 AT1G19350.3 44.089 313 97 8 312 546 43 355 6.69e-57 194
MsaG000209 AT1G19350.5 44.089 313 97 8 312 546 21 333 1.12e-56 193
MsaG000209 AT1G19350.1 44.089 313 97 8 312 546 21 333 1.12e-56 193
MsaG000209 AT1G19350.6 44.089 313 97 8 312 546 21 333 1.12e-56 193
MsaG000209 AT1G19350.4 44.089 313 97 8 312 546 21 333 1.12e-56 193
MsaG000209 AT4G36780.1 50.000 164 46 2 313 440 16 179 2.73e-31 122
MsaG000209 AT3G50750.1 42.254 284 94 10 307 542 8 269 1.35e-30 120
MsaG000209 AT4G18890.1 36.093 302 103 12 313 547 6 284 5.48e-20 90.9
MsaG000209 AT1G78700.1 33.233 331 104 10 313 542 6 320 8.03e-19 88.2
MsaG000209 AT2G45880.1 51.515 66 32 0 312 377 68 133 1.66e-12 70.9
MsaG000209 AT5G45300.2 54.237 59 27 0 325 383 98 156 6.42e-12 68.9
MsaG000209 AT5G45300.1 54.237 59 27 0 325 383 98 156 6.55e-12 68.9
MsaG000209 AT5G45300.3 54.237 59 27 0 325 383 112 170 6.69e-12 68.9

Find 132 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAAATGGGACATGGATTT+TGG 0.099494 1:+2773490 None:intergenic
GCCATATGAAAGCCTAATTT+TGG 0.141787 1:-2776792 MsaT000209.1:CDS
GTGTGAGTAAGTTGCTTAAT+AGG 0.264589 1:+2777069 None:intergenic
ATCGAATATCTTTGATGTTA+TGG 0.271986 1:+2774268 None:intergenic
TGCTCACAGTATTGCACATT+TGG 0.276460 1:+2778268 None:intergenic
CAGGACTGTATCCCAAAATT+AGG 0.282275 1:+2776780 None:intergenic
TGATGAGGGATTGGATGATT+TGG 0.284092 1:-2773088 MsaT000209.1:CDS
AGATGCAGCAAAAGGGTAAT+TGG 0.291581 1:+2773299 None:intergenic
GTTGAAATCGAATGAACTTT+TGG 0.299746 1:-2779135 MsaT000209.1:CDS
CTCCATTTCCAATGAATCTA+TGG 0.308568 1:-2773328 MsaT000209.1:CDS
TTGGAACTCACTCTTGGAAC+TGG 0.334633 1:-2773069 MsaT000209.1:CDS
AACTACGAGCTTCTCTCTAT+TGG 0.336295 1:+2777017 None:intergenic
GCTCACAGTATTGCACATTT+GGG 0.341446 1:+2778269 None:intergenic
GAGTAGAGAGGAGGTGTAAC+AGG 0.350527 1:+2773390 None:intergenic
GGAAAATGCCATAGATTCAT+TGG 0.351258 1:+2773320 None:intergenic
ATTTAGATCTCTTCCATCAT+AGG 0.352718 1:-2776814 MsaT000209.1:CDS
ACAACAAAATTATTGAATAC+TGG 0.361221 1:+2778232 None:intergenic
TGCCATAGATTCATTGGAAA+TGG 0.364323 1:+2773326 None:intergenic
CTTGGGTTCGTTGGACTAGC+AGG 0.366375 1:+2773270 None:intergenic
ATCAAAATTTAAGCCTTTGA+AGG 0.371609 1:-2776625 MsaT000209.1:CDS
GGTATTCAACCTTGCCCAAT+AGG 0.371952 1:-2777107 MsaT000209.1:CDS
GATGAAAACTGTGTTTGAAT+TGG 0.375593 1:+2779686 None:intergenic
AACTGGGAAAGGAAAGATTT+AGG 0.375942 1:-2773052 None:intergenic
TTGTGGTTTCAACCTTATAA+TGG 0.379434 1:-2777605 MsaT000209.1:CDS
TCATTTATGGAAGTCAGATC+TGG 0.383012 1:-2778024 MsaT000209.1:intron
AAGGCGGATCCACCATTATA+AGG 0.384797 1:+2777593 None:intergenic
TCAAGAAAACCTCCAATTGC+AGG 0.390111 1:-2776567 MsaT000209.1:intron
GGAATTGAAGTTGGAAAAGA+TGG 0.394254 1:+2773468 None:intergenic
GATGATTTGGAACTCACTCT+TGG 0.402192 1:-2773075 MsaT000209.1:CDS
CCCAAAATTAGGCTTTCATA+TGG 0.405670 1:+2776791 None:intergenic
AAGGTGCCCTTGTAGCATTA+TGG 0.408636 1:-2777044 MsaT000209.1:CDS
GAAGAGGTTGGCACTGCAAA+TGG 0.411998 1:+2773207 None:intergenic
CTGTGTTTGAATTGGAGAAT+TGG 0.415353 1:+2779694 None:intergenic
CATGTGATTATGAGCATTCC+TGG 0.421682 1:-2776597 MsaT000209.1:CDS
AGGTGCCCTTGTAGCATTAT+GGG 0.424361 1:-2777043 MsaT000209.1:CDS
CTATTGCAGCTGAAAGCAAA+TGG 0.439050 1:-2776851 MsaT000209.1:intron
TTGATTGGAGTATGAAGGCT+TGG 0.439266 1:+2773252 None:intergenic
CAGATTCGCAATCTCATTCC+CGG 0.441058 1:-2777999 MsaT000209.1:intron
GGCTTTCATATGGCCTATGA+TGG 0.441407 1:+2776801 None:intergenic
CTCTTCATCTTTCAATGCTG+TGG 0.445261 1:-2773190 MsaT000209.1:CDS
AGTTGGAAAAGATGGACAAA+TGG 0.453995 1:+2773476 None:intergenic
GCAAAAGGATGGAACTTGAT+TGG 0.457115 1:+2773237 None:intergenic
CTATCGTTATTCCACAAATC+AGG 0.459548 1:-2779723 MsaT000209.1:CDS
TAATGCTACAAGGGCACCTT+CGG 0.461852 1:+2777047 None:intergenic
GGGGTAGAAGATGCAGCAAA+AGG 0.462613 1:+2773291 None:intergenic
TGGTATGAAGGAATTGAAGT+TGG 0.464795 1:+2773459 None:intergenic
GATATCCACAAAGGAGGAAA+AGG 0.466792 1:+2773423 None:intergenic
TATAATGGTGGATCCGCCTT+GGG 0.469513 1:-2777590 MsaT000209.1:CDS
ATTGGTATATACCTGATTTG+TGG 0.470959 1:+2779712 None:intergenic
GAGATCTAAATCACCAATCA+AGG 0.471124 1:+2776826 None:intergenic
ATGGAGTCCCATGCTGGAAT+TGG 0.471276 1:+2773345 None:intergenic
GAAAAGGCTGAGGAGTGAAT+TGG 0.472490 1:+2773439 None:intergenic
CAGACAACAATACCTGCAAT+TGG 0.472946 1:+2776555 None:intergenic
CTTCTGCACAAAGAGCTTTG+AGG 0.474572 1:+2774189 None:intergenic
TTGGGTTCGTTGGACTAGCA+GGG 0.477261 1:+2773271 None:intergenic
GGTGTAAGGCTTATTGATGT+TGG 0.478866 1:+2773366 None:intergenic
AAAGCTCTTTGTGCAGAAGC+TGG 0.483728 1:-2774185 MsaT000209.1:CDS
TTGGGGTGCAAGTAAAGCCT+TGG 0.488933 1:-2773128 MsaT000209.1:CDS
AAAGCAAATGGGTCCTTGAT+TGG 0.492572 1:-2776839 MsaT000209.1:CDS
CATTTATGGAAGTCAGATCT+GGG 0.495680 1:-2778023 MsaT000209.1:intron
ATTGATGTTGGTGAGTAGAG+AGG 0.496798 1:+2773378 None:intergenic
GCAAATGGAGATTGTGCAAA+AGG 0.501672 1:+2773222 None:intergenic
GTATGAAGGCTTGGGTTCGT+TGG 0.502888 1:+2773261 None:intergenic
ATTTAGCGTAACAACAAGAT+CGG 0.503776 1:+2779013 None:intergenic
TTATAATGGTGGATCCGCCT+TGG 0.504708 1:-2777591 MsaT000209.1:CDS
GGAACTTGATTGGAGTATGA+AGG 0.505849 1:+2773247 None:intergenic
GTTGGAAAAGATGGACAAAT+GGG 0.506046 1:+2773477 None:intergenic
TGGGGTGCAAGTAAAGCCTT+GGG 0.507029 1:-2773127 MsaT000209.1:CDS
CTCACTCTTGGAACTGGGAA+AGG 0.507498 1:-2773063 MsaT000209.1:CDS
ACGTATCCGTGACACTGATA+AGG 0.508783 1:-2778988 MsaT000209.1:CDS
TGATTGGAGTATGAAGGCTT+GGG 0.509209 1:+2773253 None:intergenic
TTGGAAATGGAGTCCCATGC+TGG 0.515325 1:+2773339 None:intergenic
CTAGTGCTCATCAGAAATCA+AGG 0.516618 1:-2777561 MsaT000209.1:intron
CCCATGCTGGAATTGGTGTA+AGG 0.517184 1:+2773352 None:intergenic
GAGTAAGTTGCTTAATAGGA+AGG 0.517447 1:+2777073 None:intergenic
CCGTGACACTGATAAGGACT+TGG 0.518122 1:-2778982 MsaT000209.1:CDS
ATATGATGAGAGAAAGAAGA+AGG 0.521014 1:-2774295 MsaT000209.1:CDS
GTGCCTGCATCATTGTTTAG+TGG 0.523421 1:+2773528 None:intergenic
CTCTTTGTGCAGAAGCTGGT+TGG 0.523500 1:-2774181 MsaT000209.1:CDS
ATGGAGATTGTGCAAAAGGA+TGG 0.524930 1:+2773226 None:intergenic
TGTGTTTAGTGTAGGAATTG+AGG 0.526558 1:-2779187 MsaT000209.1:intron
TTTAGCGTAACAACAAGATC+GGG 0.528985 1:+2779014 None:intergenic
CCTGCATCATTGTTTAGTGG+AGG 0.531453 1:+2773531 None:intergenic
TTGTGCAGAAGCTGGTTGGT+CGG 0.532073 1:-2774177 MsaT000209.1:CDS
CTAAGTTACCTTGCGATAGG+TGG 0.533179 1:+2774139 None:intergenic
TTCTCTTTCTCCTTCCACGA+TGG 0.536162 1:+2774320 None:intergenic
ATGTGATTATGAGCATTCCT+GGG 0.539415 1:-2776596 MsaT000209.1:CDS
TATGCAGCTCACACTGATTG+TGG 0.541945 1:-2777622 MsaT000209.1:intron
TGGTTTCAACCTTATAATGG+TGG 0.547761 1:-2777602 MsaT000209.1:CDS
ATTCTAAGTTACCTTGCGAT+AGG 0.550407 1:+2774136 None:intergenic
TTACAAGGCCTAACCTTCCC+AGG 0.551312 1:+2776761 None:intergenic
TCGGAGGAAGCCATCGTGGA+AGG 0.554225 1:-2774330 MsaT000209.1:CDS
TATTGCAGCTGAAAGCAAAT+GGG 0.554271 1:-2776850 MsaT000209.1:intron
TGGAACTCACTCTTGGAACT+GGG 0.557403 1:-2773068 MsaT000209.1:CDS
TGAGGAGTGAATTGGTATGA+AGG 0.559547 1:+2773447 None:intergenic
CACAGCATTGAAAGATGAAG+AGG 0.562677 1:+2773191 None:intergenic
CACAAAGGAGGAAAAGGCTG+AGG 0.574609 1:+2773429 None:intergenic
TGGTTACCCATAATGCTACA+AGG 0.574789 1:+2777037 None:intergenic
ACAACAATACCTGCAATTGG+AGG 0.578994 1:+2776558 None:intergenic
ATAACATCAAAGATATTCGA+TGG 0.589300 1:-2774266 MsaT000209.1:CDS
GGGTAGAAGATGCAGCAAAA+GGG 0.593286 1:+2773292 None:intergenic
CCTCCACTAAACAATGATGC+AGG 0.594195 1:-2773531 MsaT000209.1:CDS
CTCACAGTATTGCACATTTG+GGG 0.595476 1:+2778270 None:intergenic
ATCACATGATCATCCTTCAA+AGG 0.596842 1:+2776612 None:intergenic
GCCTTACACCAATTCCAGCA+TGG 0.599458 1:-2773353 MsaT000209.1:CDS
AGTAAGTTGCTTAATAGGAA+GGG 0.601313 1:+2777074 None:intergenic
TTTGGGATACAGTCCTGGGA+AGG 0.602187 1:-2776774 MsaT000209.1:intron
CCTTACACCAATTCCAGCAT+GGG 0.605296 1:-2773352 MsaT000209.1:CDS
ATGTAAAAGCAGCTCTCTCG+AGG 0.609778 1:+2778154 None:intergenic
CCAAGTCCTTATCAGTGTCA+CGG 0.613168 1:+2778982 None:intergenic
GGTTGGTCGGTCGAAGAAGA+CGG 0.613610 1:-2774164 MsaT000209.1:CDS
ATGTGCAATACTGTGAGCAA+AGG 0.621542 1:-2778264 MsaT000209.1:CDS
AAAGATGGACAAATGGGACA+TGG 0.629842 1:+2773483 None:intergenic
GACACTGATAAGGACTTGGA+AGG 0.629938 1:-2778978 MsaT000209.1:intron
GATGTTGGTGAGTAGAGAGG+AGG 0.631246 1:+2773381 None:intergenic
TTGAAAGAGAAGTGTGAGGG+TGG 0.631283 1:-2779071 MsaT000209.1:CDS
TGGGTTCGTTGGACTAGCAG+GGG 0.631509 1:+2773272 None:intergenic
GAATTCGGAGGAAGCCATCG+TGG 0.640888 1:-2774334 MsaT000209.1:CDS
TGCTTGAAAGAGAAGTGTGA+GGG 0.641507 1:-2779074 MsaT000209.1:CDS
GGTTACCCATAATGCTACAA+GGG 0.647091 1:+2777038 None:intergenic
AGACGGAACCACCTATCGCA+AGG 0.647720 1:-2774147 MsaT000209.1:intron
TCGTGTGCTTTCATCAACAA+AGG 0.649039 1:+2779164 None:intergenic
GCATTGAAAGATGAAGAGGT+TGG 0.651739 1:+2773195 None:intergenic
TGTGATTATGAGCATTCCTG+GGG 0.653506 1:-2776595 MsaT000209.1:CDS
TCGATGGACTTCGAGCTCAA+AGG 0.659335 1:-2774250 MsaT000209.1:CDS
CTGTTTGATATCCACAAAGG+AGG 0.659720 1:+2773417 None:intergenic
AAGCAACTTACTCACACCGA+AGG 0.671839 1:-2777063 MsaT000209.1:CDS
TTGCTTGAAAGAGAAGTGTG+AGG 0.696581 1:-2779075 MsaT000209.1:CDS
GCACTGTTTGATATCCACAA+AGG 0.716903 1:+2773414 None:intergenic
TGACATTGAAGATGACGCGG+TGG 0.746514 1:-2778206 MsaT000209.1:CDS
TAATGACATTGAAGATGACG+CGG 0.751021 1:-2778209 MsaT000209.1:CDS
GAAGCATTGTGACAACAACG+AGG 0.796257 1:-2774213 MsaT000209.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 2773053 2779763 2773053 ID=MsaG000209
Chr1 mRNA 2773053 2779763 2773053 ID=MsaT000209.1;Parent=MsaG000209
Chr1 exon 2773053 2773562 2773053 ID=MsaT000209.1.exon10;Parent=MsaT000209.1
Chr1 CDS 2773053 2773562 2773053 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2774148 2774371 2774148 ID=MsaT000209.1.exon9;Parent=MsaT000209.1
Chr1 CDS 2774148 2774371 2774148 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2776568 2776667 2776568 ID=MsaT000209.1.exon8;Parent=MsaT000209.1
Chr1 CDS 2776568 2776667 2776568 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2776775 2776864 2776775 ID=MsaT000209.1.exon7;Parent=MsaT000209.1
Chr1 CDS 2776775 2776864 2776775 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2776960 2777128 2776960 ID=MsaT000209.1.exon6;Parent=MsaT000209.1
Chr1 CDS 2776960 2777128 2776960 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2777562 2777637 2777562 ID=MsaT000209.1.exon5;Parent=MsaT000209.1
Chr1 CDS 2777562 2777637 2777562 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2778000 2778033 2778000 ID=MsaT000209.1.exon4;Parent=MsaT000209.1
Chr1 CDS 2778000 2778033 2778000 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2778153 2778295 2778153 ID=MsaT000209.1.exon3;Parent=MsaT000209.1
Chr1 CDS 2778153 2778295 2778153 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2778979 2779195 2778979 ID=MsaT000209.1.exon2;Parent=MsaT000209.1
Chr1 CDS 2778979 2779195 2778979 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Chr1 exon 2779680 2779763 2779680 ID=MsaT000209.1.exon1;Parent=MsaT000209.1
Chr1 CDS 2779680 2779763 2779680 ID=cds.MsaT000209.1;Parent=MsaT000209.1
Gene Sequence

>MsaT000209.1

ATGGAAGACTCACAGAAGCTATCGTTATTCCACAAATCAGGTATATACCAATTCTCCAATTCAAACACAGTTTTCATCGATCCAGAATTGAGGCCTTTGTTGATGAAAGCACACGAGTGTTTGTTGAAATCGAATGAACTTTTGGGTGCTCTGAAAGATTTGAGAAGTGAAAGTGATTCTTGTTGCTTGAAAGAGAAGTGTGAGGGTGGTGAACAATGTTTTGTTGAACTGGGACAGCAAGTGCCCGATCTTGTTGTTACGCTAAATTTACGTATCCGTGACACTGATAAGGACTTGGAAGATTCCCCAAATGTGCAATACTGTGAGCAAAGGTCGATACTACCAGTATTCAATAATTTTGTTGTTAATGACATTGAAGATGACGCGGTGGCTGAGATTTTGAACAATCATTATATAATGCCTCGAGAGAGCTGCTTTTACATGTCAGATCTGGGACAGATTCGCAATCTCATTCCCGCTCACACTGATTGTGGTTTCAACCTTATAATGGTGGATCCGCCTTGGGAAAATGCTAGTGCTCATCAGAAATCAAGGTATTCAACCTTGCCCAATAGGTACTTTTTATCCCTTCCTATTAAGCAACTTACTCACACCGAAGGTGCCCTTGTAGCATTATGGGTAACCAATAGAGAGAAGCTCGTAGTTTTGTCGAGAAAGAGCTTTTTGCAGCGTGGGGGTCAGCTATGCTGCAAGTTTTCATTACTGAAAGCAAATGGGTCCTTGATTGGTGATTTAGATCTCTTCCATCATAGGCCATATGAAAGCCTAATTTTGGGATACAGTCCTGGGAAGGTAAAAAATTCTGATAACCAATCAAAATTTAAGCCTTTGAAGGATGATCATGTGATTATGAGCATTCCTGGGGATTGCTCAAGAAAACCTCCAATTGCAGAAACTTCAACAAAAAGAATTCGGAGGAAGCCATCGTGGAAGGAGAAAGAGAAAAATATGATGAGAGAAAGAAGAAGGAGAGCCATAACATCAAAGATATTCGATGGACTTCGAGCTCAAAGGAGCTACAATTTATCGAAGCATTGTGACAACAACGAGGTCCTCAAAGCTCTTTGTGCAGAAGCTGGTTGGTCGGTCGAAGAAGACGGAACCACCTATCGCAAGGGTTACAATCCTCCACTAAACAATGATGCAGGCACCTCTTTCTCTTATTCCCAAAATCCATGTCCCATTTGTCCATCTTTTCCAACTTCAATTCCTTCATACCAATTCACTCCTCAGCCTTTTCCTCCTTTGTGGATATCAAACAGTGCTCCTGTTACACCTCCTCTCTACTCACCAACATCAATAAGCCTTACACCAATTCCAGCATGGGACTCCATTTCCAATGAATCTATGGCATTTTCCAATTACCCTTTTGCTGCATCTTCTACCCCTGCTAGTCCAACGAACCCAAGCCTTCATACTCCAATCAAGTTCCATCCTTTTGCACAATCTCCATTTGCAGTGCCAACCTCTTCATCTTTCAATGCTGTGGCTGATAACTCAATCAGTGAGATGACAAGTTCAAAAATGCTTGGGGTGCAAGTAAAGCCTTGGGTTGATGAAAAAATTCATGATGAGGGATTGGATGATTTGGAACTCACTCTTGGAACTGGGAAAGGAAAGATTTAG
Protein sequence

>MsaT000209.1

MEDSQKLSLFHKSGIYQFSNSNTVFIDPELRPLLMKAHECLLKSNELLGALKDLRSESDSCCLKEKCEGGEQCFVELGQQVPDLVVTLNLRIRDTDKDLEDSPNVQYCEQRSILPVFNNFVVNDIEDDAVAEILNNHYIMPRESCFYMSDLGQIRNLIPAHTDCGFNLIMVDPPWENASAHQKSRYSTLPNRYFLSLPIKQLTHTEGALVALWVTNREKLVVLSRKSFLQRGGQLCCKFSLLKANGSLIGDLDLFHHRPYESLILGYSPGKVKNSDNQSKFKPLKDDHVIMSIPGDCSRKPPIAETSTKRIRRKPSWKEKEKNMMRERRRRAITSKIFDGLRAQRSYNLSKHCDNNEVLKALCAEAGWSVEEDGTTYRKGYNPPLNNDAGTSFSYSQNPCPICPSFPTSIPSYQFTPQPFPPLWISNSAPVTPPLYSPTSISLTPIPAWDSISNESMAFSNYPFAASSTPASPTNPSLHTPIKFHPFAQSPFAVPTSSSFNAVADNSISEMTSSKMLGVQVKPWVDEKIHDEGLDDLELTLGTGKGKI*