AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG006549


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006549 MtrunA17_Chr2g0282581 93.675 664 28 4 14 672 237 891 0.0 1240
MsaG006549 MtrunA17_Chr3g0129941 45.455 88 48 0 581 668 879 966 3.82e-17 85.9
MsaG006549 MtrunA17_Chr8g0384131 40.964 83 49 0 586 668 693 775 5.85e-15 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006549 AT2G33835.1 30.192 520 265 19 221 671 96 586 4.56e-42 161
MsaG006549 AT3G18640.3 44.578 83 46 0 586 668 590 672 1.83e-16 84.0
MsaG006549 AT3G18640.1 44.578 83 46 0 586 668 590 672 1.83e-16 84.0
MsaG006549 AT3G18640.2 44.578 83 46 0 586 668 590 672 1.83e-16 84.0
MsaG006549 AT3G26850.2 42.353 85 49 0 588 672 181 265 2.03e-16 80.5
MsaG006549 AT3G26850.1 42.353 85 49 0 588 672 181 265 2.03e-16 80.5
MsaG006549 AT2G10553.1 42.683 82 47 0 591 672 1 82 1.88e-15 72.4

Find 136 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTGAAAACCCGTTCTAAT+TGG 0.146947 2:-6800971 MsaT006549.1:CDS
AACGTTGATGTTGAAAATTC+TGG 0.195896 2:-6802144 MsaT006549.1:CDS
AGAGACCCATCTCCAATATT+TGG 0.208217 2:+6800849 None:intergenic
AAGAGTTGCTAAAACCATTT+TGG 0.214650 2:-6800353 MsaT006549.1:CDS
CTGAAGAGAAAGAGGATTTA+TGG 0.227339 2:+6801054 None:intergenic
TAATGTGATGGCCGTACTTC+AGG 0.259079 2:+6802330 None:intergenic
CCACACCTATGTCACCATTT+TGG 0.265214 2:+6800595 None:intergenic
ACCTTTAGGTGCAAGTGCTT+TGG 0.308934 2:-6801087 MsaT006549.1:CDS
TATCTTCAGTGGTCGGAATT+TGG 0.312793 2:+6800247 None:intergenic
AGAGAATTGGAATTGGAAAA+AGG 0.326337 2:-6801525 MsaT006549.1:intron
TCCTGATGTTATCTCTGCTT+TGG 0.335129 2:+6800632 None:intergenic
TCTGCATCGGGCAGAGAATC+TGG 0.335633 2:+6803553 None:intergenic
AGTACGGCCATCACATTATA+TGG 0.337928 2:-6802325 MsaT006549.1:CDS
TTAAATGCAGATTTATTCTC+TGG 0.353007 2:+6801230 None:intergenic
AAAGCTTCCCTTCTAATTAG+AGG 0.355973 2:-6800825 MsaT006549.1:CDS
AATTAGAGGGTCATCCGTTC+AGG 0.358517 2:-6800811 MsaT006549.1:CDS
ATGCCTTTGGTGTTGAAGAT+AGG 0.361609 2:-6800566 MsaT006549.1:CDS
AGACGACCCTCATGCCAAAA+TGG 0.368470 2:+6800339 None:intergenic
AGCATTGAGATACCAAATAT+TGG 0.373167 2:-6800861 MsaT006549.1:CDS
GGATAATAAATTTCATGAAA+TGG 0.373961 2:-6800460 MsaT006549.1:CDS
TGGCCGTACTTCAGGGTTCT+CGG 0.379969 2:+6802338 None:intergenic
ACGGGAAAAGATGTGGTTAC+TGG 0.386220 2:-6802021 MsaT006549.1:CDS
TCAGAAGAGAGAATTGGAAT+TGG 0.391834 2:-6801532 MsaT006549.1:CDS
CGAGGAACAGAACTTCTGTT+TGG 0.394825 2:+6800675 None:intergenic
CGGATGACCCTCTAATTAGA+AGG 0.396020 2:+6800817 None:intergenic
GAAGCTTTGCTATTGCAATC+TGG 0.406483 2:+6802084 None:intergenic
TGAAGAGAAAGAGGATTTAT+GGG 0.410865 2:+6801055 None:intergenic
AAGAGGGTCATAAAGATCTC+TGG 0.414544 2:+6800890 None:intergenic
ACTGAAAACCCGTTCTAATT+GGG 0.418464 2:-6800970 MsaT006549.1:CDS
AGTTGTGCAAACTACCAAAA+TGG 0.421565 2:-6800609 MsaT006549.1:CDS
CTACCATGACCAGACCTTGA+TGG 0.426349 2:+6801892 None:intergenic
TTTCCCTGTAACAGGTGTTA+AGG 0.435675 2:-6801435 MsaT006549.1:intron
TGTAGATTCAAGCCAACATA+TGG 0.439592 2:-6802406 MsaT006549.1:intron
TCCATCTTTAATCTCAGCAC+TGG 0.439675 2:+6801692 None:intergenic
AGGGTTGCACCACATGCTAA+TGG 0.439793 2:-6800999 MsaT006549.1:CDS
TGCACATCAGAAGAGAGAAT+TGG 0.443524 2:-6801538 MsaT006549.1:CDS
ATCCTCTTTCTCTTCAGATC+GGG 0.443545 2:-6801048 MsaT006549.1:CDS
AACTTGATTTCTGCTGAAGA+TGG 0.446098 2:-6802183 MsaT006549.1:CDS
AGCAATATGTTTCTTTATGT+CGG 0.448405 2:-6800218 MsaT006549.1:CDS
TTCATCTAGTTGGTTCATCT+AGG 0.451325 2:-6801019 MsaT006549.1:CDS
TCATCTAGTTGGTTCATCTA+GGG 0.454338 2:-6801018 MsaT006549.1:CDS
TGATTGCATAACTTTCTCCT+TGG 0.455572 2:+6801948 None:intergenic
TCATGAGATGGATGCCAACT+TGG 0.456645 2:+6801287 None:intergenic
TTGCTACGTTTATCTGCATC+GGG 0.457556 2:+6803541 None:intergenic
GGCCGTACTTCAGGGTTCTC+GGG 0.459568 2:+6802339 None:intergenic
AGAAGGTTCCCAATTAGAAC+GGG 0.465289 2:+6800962 None:intergenic
GGTGTGGGACATTATGCCTT+TGG 0.465758 2:-6800579 MsaT006549.1:CDS
CACCAAGTCATCTAGTGATA+CGG 0.475093 2:-6802040 MsaT006549.1:CDS
TGATGTGAAAGAGGAGAACT+TGG 0.477135 2:-6802379 MsaT006549.1:CDS
CCCAGTGCTGAGATTAAAGA+TGG 0.477210 2:-6801693 MsaT006549.1:CDS
CTCTGCACGGGATGAATATG+AGG 0.483485 2:+6801175 None:intergenic
TTTGCTACGTTTATCTGCAT+CGG 0.483721 2:+6803540 None:intergenic
GAGATACCAAATATTGGAGA+TGG 0.486987 2:-6800855 MsaT006549.1:CDS
AATGTGATGGCCGTACTTCA+GGG 0.491889 2:+6802331 None:intergenic
TGGTTCACTGCATCCTTCAG+TGG 0.492124 2:+6802104 None:intergenic
TTCCCGATCTGAAGAGAAAG+AGG 0.494946 2:+6801046 None:intergenic
TCCCGTATCACTAGATGACT+TGG 0.504697 2:+6802038 None:intergenic
CCATCTTTAATCTCAGCACT+GGG 0.507231 2:+6801693 None:intergenic
TATATCCTCTGTACATATGT+TGG 0.511338 2:+6801132 None:intergenic
AGAGGGTCATAAAGATCTCT+GGG 0.511884 2:+6800891 None:intergenic
ACTTGATTTCTGCTGAAGAT+GGG 0.513950 2:-6802182 MsaT006549.1:CDS
TCCAAAGCACTTGCACCTAA+AGG 0.515626 2:+6801086 None:intergenic
AATCCTCTTTCTCTTCAGAT+CGG 0.517995 2:-6801049 MsaT006549.1:CDS
GAAAGTTATGCAATCAGAGA+TGG 0.522327 2:-6801941 MsaT006549.1:CDS
CAAAATAAATAGAGTAGCAA+AGG 0.523624 2:-6800481 MsaT006549.1:CDS
TCCTCAACAAAATTATCTCT+CGG 0.531272 2:+6801991 None:intergenic
TCACATCAAGCTCCATATGT+TGG 0.531391 2:+6802394 None:intergenic
ATGTGAAACAAAAGCCATCA+AGG 0.533118 2:-6801906 MsaT006549.1:intron
ACCAAGTCATCTAGTGATAC+GGG 0.535354 2:-6802039 MsaT006549.1:CDS
ACCAAAGCAGAGATAACATC+AGG 0.539299 2:-6800633 MsaT006549.1:CDS
ATAGTGTGAATAATACTGAC+CGG 0.541166 2:-6801584 MsaT006549.1:CDS
TATGGAGCTTGATGTGAAAG+AGG 0.541245 2:-6802388 MsaT006549.1:CDS
TGCCCGAGAACCCTGAAGTA+CGG 0.541918 2:-6802341 MsaT006549.1:CDS
GCTGAAGATGGGATAAATCA+AGG 0.542823 2:-6802171 MsaT006549.1:CDS
AGCTTCTTTATCTGATGTCA+AGG 0.546038 2:-6802067 MsaT006549.1:CDS
AGCAATCATTTCCTCTGCAC+GGG 0.546220 2:+6801163 None:intergenic
AGAACAAGAAACAGTTGTAG+AGG 0.548644 2:-6803602 MsaT006549.1:CDS
GGAAACAAGCTGTCCCTCAT+CGG 0.553716 2:+6801251 None:intergenic
TATGATGATTCTGCTGCAGT+TGG 0.555386 2:-6800768 MsaT006549.1:CDS
AAGCTTCCCTTCTAATTAGA+GGG 0.556317 2:-6800824 MsaT006549.1:CDS
TTCTCTTCCATATAATGTGA+TGG 0.556995 2:+6802318 None:intergenic
CGTATCACTAGATGACTTGG+TGG 0.557776 2:+6802041 None:intergenic
TAGCAATCATTTCCTCTGCA+CGG 0.558599 2:+6801162 None:intergenic
GAGGTTGACTTTCAGACAGA+TGG 0.560149 2:-6800438 MsaT006549.1:CDS
TAATAAATTTCATGAAATGG+AGG 0.564842 2:-6800457 MsaT006549.1:CDS
CAGAAGGTTCCCAATTAGAA+CGG 0.565372 2:+6800961 None:intergenic
AGATGCTTTACTCATGCTCA+TGG 0.570346 2:+6802290 None:intergenic
CTCATATTCATCCCGTGCAG+AGG 0.570912 2:-6801174 MsaT006549.1:CDS
AGCAATAGACATGGAAGTGG+AGG 0.572253 2:-6803626 None:intergenic
AAAAGAGAAGTTTCCGATGA+GGG 0.572557 2:-6801264 MsaT006549.1:CDS
GATGGTCGAAATGGAACAGA+AGG 0.573242 2:+6800945 None:intergenic
AGAAGCAATAGACATGGAAG+TGG 0.577567 2:-6803629 None:intergenic
AACTACCAAAATGGTGACAT+AGG 0.578382 2:-6800600 MsaT006549.1:CDS
TATCCTATCTTCAACACCAA+AGG 0.584215 2:+6800563 None:intergenic
CAGGGATATGTCAATAAACA+TGG 0.586684 2:-6800063 MsaT006549.1:CDS
AATGTCAATTCCTCATGCAA+CGG 0.586889 2:+6802264 None:intergenic
AAAATTCTGGACATCTTCAG+AGG 0.589780 2:-6802131 MsaT006549.1:CDS
CAAGATCAACAAGGACTGCA+TGG 0.589786 2:+6800379 None:intergenic
TGCAATCAGAGATGGAGTCA+AGG 0.591805 2:-6801933 MsaT006549.1:CDS
AGATACCAAATATTGGAGAT+GGG 0.592018 2:-6800854 MsaT006549.1:CDS
GCAATCAGAGATGGAGTCAA+GGG 0.592070 2:-6801932 MsaT006549.1:CDS
GTGTTAAGGAAAATGTTGAC+AGG 0.595611 2:-6801421 MsaT006549.1:CDS
ATGATGATTCTGCTGCAGTT+GGG 0.600513 2:-6800767 MsaT006549.1:CDS
TGGAAGAAGCAAGTCCAAGT+TGG 0.600753 2:-6801301 MsaT006549.1:CDS
TAGTGTGAATAATACTGACC+GGG 0.602372 2:-6801583 MsaT006549.1:CDS
CCAAAATGGTGACATAGGTG+TGG 0.606094 2:-6800595 MsaT006549.1:CDS
TTAGCAGTATCTTCAGTGGT+CGG 0.606678 2:+6800240 None:intergenic
AACTTGTGATGAAGCCTGAA+CGG 0.612804 2:+6800797 None:intergenic
AACGGACTGAGCATGATGCT+AGG 0.615927 2:-6800527 MsaT006549.1:CDS
CTTCAGAGGAAAACCACTGA+AGG 0.618372 2:-6802117 MsaT006549.1:CDS
GGATGACCCTCTAATTAGAA+GGG 0.619254 2:+6800818 None:intergenic
AAATGTTGACAGGTCAAGAA+CGG 0.621080 2:-6801411 MsaT006549.1:intron
GATGTGAAAGAGGAGAACTT+GGG 0.624477 2:-6802378 MsaT006549.1:CDS
GCTAAAGGTTGGTGCATCCG+AGG 0.627168 2:-6801636 MsaT006549.1:CDS
AGCATCTGTTCCGTTGCATG+AGG 0.628622 2:-6802274 MsaT006549.1:CDS
TAGTGATACGGGAAAAGATG+TGG 0.628779 2:-6802028 MsaT006549.1:CDS
ATCTCAATGCTATCACGAAG+AGG 0.632520 2:+6800873 None:intergenic
AGTGTATATCCATTAGCATG+TGG 0.634510 2:+6800990 None:intergenic
TTGCTTAGCAGTATCTTCAG+TGG 0.635718 2:+6800236 None:intergenic
GATGCAGATAAACGTAGCAA+AGG 0.640040 2:-6803538 MsaT006549.1:intron
TCTCAATGCTATCACGAAGA+GGG 0.642743 2:+6800874 None:intergenic
GCATGAGGGTCGTCTCAGCA+AGG 0.648486 2:-6800331 MsaT006549.1:CDS
TCAGTGGTCGGAATTTGGCG+TGG 0.649706 2:+6800252 None:intergenic
GGAAGCTACAAGAACTACCT+CGG 0.649982 2:+6801619 None:intergenic
ATGTGAAAGAGGAGAACTTG+GGG 0.650828 2:-6802377 MsaT006549.1:CDS
CAAAATGGTGACATAGGTGT+GGG 0.653939 2:-6800594 MsaT006549.1:CDS
TTTGTTGAGGATGCTGATGG+TGG 0.658081 2:-6801979 MsaT006549.1:CDS
AGTGTGAATAATACTGACCG+GGG 0.665731 2:-6801582 MsaT006549.1:CDS
TGATGGTGGTCAGAACTCCA+AGG 0.667489 2:-6801965 MsaT006549.1:CDS
AACAGAAGTTCTGTTCCTCG+CGG 0.678826 2:-6800672 MsaT006549.1:CDS
GTGTGAATAATACTGACCGG+GGG 0.679900 2:-6801581 MsaT006549.1:CDS
CGAAACCAACATATGTACAG+AGG 0.688687 2:-6801137 MsaT006549.1:CDS
AGGGTCATAAAGATCTCTGG+GGG 0.694830 2:+6800893 None:intergenic
ACTCTTTCACAAGATCAACA+AGG 0.723096 2:+6800370 None:intergenic
GAGGGTCATAAAGATCTCTG+GGG 0.728908 2:+6800892 None:intergenic
TGTGAATAATACTGACCGGG+GGG 0.742273 2:-6801580 MsaT006549.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 6800053 6803638 6800053 ID=MsaG006549
Chr2 mRNA 6800053 6803638 6800053 ID=MsaT006549.1;Parent=MsaG006549
Chr2 exon 6800053 6800082 6800053 ID=MsaT006549.1.exon6;Parent=MsaT006549.1
Chr2 CDS 6800053 6800082 6800053 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Chr2 exon 6800194 6801327 6800194 ID=MsaT006549.1.exon5;Parent=MsaT006549.1
Chr2 CDS 6800194 6801327 6800194 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Chr2 exon 6801412 6801443 6801412 ID=MsaT006549.1.exon4;Parent=MsaT006549.1
Chr2 CDS 6801412 6801443 6801412 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Chr2 exon 6801526 6801731 6801526 ID=MsaT006549.1.exon3;Parent=MsaT006549.1
Chr2 CDS 6801526 6801731 6801526 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Chr2 exon 6801907 6802423 6801907 ID=MsaT006549.1.exon2;Parent=MsaT006549.1
Chr2 CDS 6801907 6802423 6801907 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Chr2 exon 6803539 6803638 6803539 ID=MsaT006549.1.exon1;Parent=MsaT006549.1
Chr2 CDS 6803539 6803638 6803539 ID=cds.MsaT006549.1;Parent=MsaT006549.1
Gene Sequence

>MsaT006549.1

ATGGAAGTGGAGGAAGAACAAGAAACAGTTGTAGAGGAGAAAGATAAAGAGAAAAATGAGGTTCCAGATTCTCTGCCCGATGCAGATAAACGTAGCAAAGATTCAAGCCAACATATGGAGCTTGATGTGAAAGAGGAGAACTTGGGGTCAGTTTCTTATGTGCCCGAGAACCCTGAAGTACGGCCATCACATTATATGGAAGAGAATGATACCATGAGCATGAGTAAAGCATCTGTTCCGTTGCATGAGGAATTGACATTGAAAAATGAAGATTATCCCCTGAAACAAAAAGTTTCTAGTCCTCCAAAACCAAGTGAAAACTTGATTTCTGCTGAAGATGGGATAAATCAAGGCCTAAACGTTGATGTTGAAAATTCTGGACATCTTCAGAGGAAAACCACTGAAGGATGCAGTGAACCAGATTGCAATAGCAAAGCTTCTTTATCTGATGTCAAGGATGCCACCAAGTCATCTAGTGATACGGGAAAAGATGTGGTTACTGGAATCATACCGAGAGATAATTTTGTTGAGGATGCTGATGGTGGTCAGAACTCCAAGGAGAAAGTTATGCAATCAGAGATGGAGTCAAGGGTTGATGTGAAACAAAAGCCATCAAGGACTAGAAGTCTGTCTCCCAGTGCTGAGATTAAAGATGGAAACAAAAGACCTGCAATTATATGTGCTTTTTTTGCTAAAGGTTGGTGCATCCGAGGTAGTTCTTGTAGCTTCCTTCATGTAAAAGATAGTGTGAATAATACTGACCGGGGGGATGAAGGAGACGTAGTTACTGCACATCAGAAGAGAGAATTGGAATTGGAAAAAGGTGTTAAGGAAAATGTTGACAGGTCAAGAACGAATGTGGAAGAAGCAAGTCCAAGTTGGCATCCATCTCATGAAAAAGAGAAGTTTCCGATGAGGGACAGCTTGTTTCCAGAGAATAAATCTGCATTTAATTCATCAAACAATTATTTCAGCTCAAATCTTTCCTCATATTCATCCCGTGCAGAGGAAATGATTGCTATTCGAAACCAACATATGTACAGAGGATATACATCGACAAAAGATTTTAGTTCACCTTTAGGTGCAAGTGCTTTGGACTCTCACGCCCATAAATCCTCTTTCTCTTCAGATCGGGAAGATTTTCATCTAGTTGGTTCATCTAGGGTTGCACCACATGCTAATGGATATACACTGAAAACCCGTTCTAATTGGGAACCTTCTGTTCCATTTCGACCATCCTTTTTTATCACTTCGATGAATGTATCATCCCCCAGAGATCTTTATGACCCTCTTCGTGATAGCATTGAGATACCAAATATTGGAGATGGGTCTCTGAAAGCTTCCCTTCTAATTAGAGGGTCATCCGTTCAGGCTTCATCACAAGTTCGAACATATGATGATTCTGCTGCAGTTGGGAAACACATGTCTGATGTTAATGATGATAAAAGTTCTGTATCTTCCCATCATAAGTTTTATGAAAATGAGCCAAACAGAAGTTCTGTTCCTCGCGGAAAAGATTGTCTTGCAACCAAAGCAGAGATAACATCAGGAAGTTGTGCAAACTACCAAAATGGTGACATAGGTGTGGGACATTATGCCTTTGGTGTTGAAGATAGGATAGAAACACTGAAAAAACGGACTGAGCATGATGCTAGGCATCATAGTGATGAATCAGAGCACAAAATAAATAGAGTAGCAAAGGATAATAAATTTCATGAAATGGAGGTTGACTTTCAGACAGATGGCAGTGTACTCAAAGAAACAAAGACGCTGAAAATTTTCCATGCAGTCCTTGTTGATCTTGTGAAAGAGTTGCTAAAACCATTTTGGCATGAGGGTCGTCTCAGCAAGGATGCACATATATTGATAGTTAAAAAATCAGTTGACAAGGTTATTAGCACTTTAGAGCCACGCCAAATTCCGACCACTGAAGATACTGCTAAGCAATATGTTTCTTTATGTCGGCCAAAAATTGCAAAGTTAGTCCATGGATATGTCAATAAACATGGCAAATCTTGA

Protein sequence

>MsaT006549.1

MEVEEEQETVVEEKDKEKNEVPDSLPDADKRSKDSSQHMELDVKEENLGSVSYVPENPEVRPSHYMEENDTMSMSKASVPLHEELTLKNEDYPLKQKVSSPPKPSENLISAEDGINQGLNVDVENSGHLQRKTTEGCSEPDCNSKASLSDVKDATKSSSDTGKDVVTGIIPRDNFVEDADGGQNSKEKVMQSEMESRVDVKQKPSRTRSLSPSAEIKDGNKRPAIICAFFAKGWCIRGSSCSFLHVKDSVNNTDRGDEGDVVTAHQKRELELEKGVKENVDRSRTNVEEASPSWHPSHEKEKFPMRDSLFPENKSAFNSSNNYFSSNLSSYSSRAEEMIAIRNQHMYRGYTSTKDFSSPLGASALDSHAHKSSFSSDREDFHLVGSSRVAPHANGYTLKTRSNWEPSVPFRPSFFITSMNVSSPRDLYDPLRDSIEIPNIGDGSLKASLLIRGSSVQASSQVRTYDDSAAVGKHMSDVNDDKSSVSSHHKFYENEPNRSSVPRGKDCLATKAEITSGSCANYQNGDIGVGHYAFGVEDRIETLKKRTEHDARHHSDESEHKINRVAKDNKFHEMEVDFQTDGSVLKETKTLKIFHAVLVDLVKELLKPFWHEGRLSKDAHILIVKKSVDKVISTLEPRQIPTTEDTAKQYVSLCRPKIAKLVHGYVNKHGKS*