AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG009600

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009600 MtrunA17_Chr2g0315201 98.418 316 5 0 1 316 1 316 0.0 635
MsaG009600 MtrunA17_Chr2g0315211 73.684 323 78 1 1 316 1 323 1.20e-152 430
MsaG009600 MtrunA17_Chr1g0154651 37.143 315 114 11 6 316 14 248 1.18e-38 137
MsaG009600 MtrunA17_Chr3g0141401 41.846 325 152 11 3 314 12 312 1.95e-35 130
MsaG009600 MtrunA17_Chr5g0403631 41.618 346 139 11 3 314 6 322 7.84e-33 123
MsaG009600 MtrunA17_Chr5g0408851 52.941 85 34 3 17 101 61 139 2.10e-15 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG009600 AT1G78700.1 67.365 334 82 8 1 316 1 325 1.11e-123 357
MsaG009600 AT4G18890.1 60.372 323 82 9 1 316 1 284 7.18e-100 295
MsaG009600 AT4G18890.2 51.012 247 75 9 77 316 1 208 1.44e-60 192
MsaG009600 AT1G19350.3 42.090 354 117 14 6 314 44 354 8.53e-48 164
MsaG009600 AT1G19350.5 42.090 354 117 14 6 314 22 332 1.16e-47 163
MsaG009600 AT1G19350.1 42.090 354 117 14 6 314 22 332 1.16e-47 163
MsaG009600 AT1G19350.6 42.090 354 117 14 6 314 22 332 1.16e-47 163
MsaG009600 AT1G19350.4 42.090 354 117 14 6 314 22 332 1.16e-47 163
MsaG009600 AT1G75080.2 39.326 356 128 13 6 316 23 335 1.29e-42 150
MsaG009600 AT1G75080.1 39.326 356 128 13 6 316 23 335 1.29e-42 150
MsaG009600 AT3G50750.1 46.275 255 75 9 6 229 14 237 5.27e-39 139
MsaG009600 AT4G36780.1 55.491 173 57 4 6 166 16 180 5.16e-30 115
MsaG009600 AT5G45300.2 58.333 60 25 0 17 76 97 156 4.02e-16 79.3
MsaG009600 AT5G45300.3 58.333 60 25 0 17 76 111 170 4.03e-16 79.3
MsaG009600 AT5G45300.1 58.333 60 25 0 17 76 97 156 4.03e-16 79.3
MsaG009600 AT2G45880.1 52.174 69 30 1 11 76 74 142 2.07e-14 74.3

Find 101 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATCCCAGCAAACCATTC+AGG 0.319016 2:+62213462 None:intergenic
ATAGAGCCACTATGAAAATA+AGG 0.322284 2:+62213645 None:intergenic
TACTCCTTCCTGCCTTCTTC+CGG 0.325671 2:-62213516 MsaT009600.1:CDS
AAGGAAGACGAGCCGGGGCT+TGG 0.330367 2:+62213789 None:intergenic
TCGAAGCCCATTTGCCTTCA+AGG 0.331246 2:-62213394 MsaT009600.1:CDS
CATTTGGAAGCAACACATTT+GGG 0.336623 2:-62213239 MsaT009600.1:CDS
CTCTCCACAGCTTCATCTTC+AGG 0.340264 2:-62213690 MsaT009600.1:CDS
TCATTGTTATCACAATGTTT+AGG 0.355738 2:+62217027 None:intergenic
GCATTTGGAAGCAACACATT+TGG 0.360050 2:-62213240 MsaT009600.1:CDS
GCATCTTCCTTGAAGGCAAA+TGG 0.365893 2:+62213387 None:intergenic
ATGTGGACCCCTGGACAGTC+AGG 0.369643 2:-62213342 MsaT009600.1:CDS
GCCTTTAGAGAACATGGATA+TGG 0.373174 2:-62213853 MsaT009600.1:CDS
ATCTCAGATGAATTTGCATT+TGG 0.385434 2:-62213255 MsaT009600.1:CDS
CTTGGGAAGGAAGACGAGCC+GGG 0.389874 2:+62213783 None:intergenic
TTCTCTGGTTTGAGAATGTA+TGG 0.389954 2:-62217063 MsaT009600.1:CDS
TCTGCACGGCCCGGGTGGAC+TGG 0.392696 2:-62213546 MsaT009600.1:CDS
GTTGATCCTGAATGGTTTGC+TGG 0.393927 2:-62213468 MsaT009600.1:CDS
ACTATCTGACGGCCAGGGCT+TGG 0.399313 2:+62213489 None:intergenic
GAGCTCAGGGGAGGTGTGAC+AGG 0.403615 2:+62213615 None:intergenic
CATCTGCTACAAATTCTTCA+TGG 0.405598 2:+62213187 None:intergenic
AAATAAGGATGAGGAAGTTT+CGG 0.409483 2:+62213660 None:intergenic
CATTTGGGATTGTGAAGCCT+TGG 0.410546 2:-62213224 MsaT009600.1:CDS
ACGGCCAGGGCTTGGAGGAC+CGG 0.427775 2:+62213497 None:intergenic
AAATGTTACCTTACGATAAG+TGG 0.428703 2:+62216951 None:intergenic
TCAAAGCCTGCTGCAATAGC+TGG 0.436153 2:+62213309 None:intergenic
GAACATGCCCCTGACTGTCC+AGG 0.438349 2:+62213333 None:intergenic
TTCTAGCAGTCGGAGAGCTC+AGG 0.440476 2:+62213601 None:intergenic
CATCTTCCTTGAAGGCAAAT+GGG 0.441986 2:+62213388 None:intergenic
ATCCATGTTCTCTAAAGGCT+TGG 0.461558 2:+62213857 None:intergenic
TCTGAGATGGCTTCAGACAT+TGG 0.466820 2:+62213270 None:intergenic
AGATTGAATGTCGGAGAAGT+TGG 0.467632 2:+62213423 None:intergenic
TGTTCTCCAGCTATTGCAGC+AGG 0.468934 2:-62213315 MsaT009600.1:CDS
ATAGCTGCTAAGATCTTCTC+TGG 0.470421 2:-62217078 MsaT009600.1:CDS
AAAGCTCTTTGTAATGAAGC+TGG 0.472686 2:-62216997 MsaT009600.1:CDS
TTACGATAAGTGGTTCCATC+AGG 0.476237 2:+62216961 None:intergenic
GGGCTTGGAGGACCGGAAGA+AGG 0.476639 2:+62213504 None:intergenic
TGGATCCTTTCTCCTTCCCA+AGG 0.477640 2:+62213207 None:intergenic
CAGGCAGCGGTTCGCGCATG+TGG 0.479649 2:-62213359 MsaT009600.1:CDS
GCGTTACGATTTGCAGCGTA+AGG 0.480138 2:+62213747 None:intergenic
ATGATCAATCTGCACGGCCC+GGG 0.481435 2:-62213554 MsaT009600.1:CDS
ATCTGACGGCCAGGGCTTGG+AGG 0.481702 2:+62213492 None:intergenic
GTCAGATAGTTGATCCTGAA+TGG 0.488622 2:-62213476 MsaT009600.1:CDS
TAAGGGGATGATGATGGACT+TGG 0.490391 2:+62213765 None:intergenic
ATTTGGGATTGTGAAGCCTT+GGG 0.491602 2:-62213223 MsaT009600.1:CDS
ACTTGGGAAGGAAGACGAGC+CGG 0.496049 2:+62213782 None:intergenic
TCTTCCGGTCCTCCAAGCCC+TGG 0.498896 2:-62213501 MsaT009600.1:CDS
TTCTCTCTCTCCTTCCATGT+TGG 0.499958 2:+62217132 None:intergenic
AAATGCAAATTCATCTGAGA+TGG 0.501657 2:+62213257 None:intergenic
GATGATCAATCTGCACGGCC+CGG 0.503778 2:-62213555 MsaT009600.1:CDS
TTGGAGGACCGGAAGAAGGC+AGG 0.505728 2:+62213508 None:intergenic
CTCTTTGTAATGAAGCTGGT+TGG 0.506195 2:-62216993 MsaT009600.1:CDS
TGAAGCCTTGGGAAGGAGAA+AGG 0.506728 2:-62213212 MsaT009600.1:CDS
GGATCAACTATCTGACGGCC+AGG 0.508622 2:+62213483 None:intergenic
GAGTTACTCTCAATGACATC+TGG 0.509973 2:-62217165 None:intergenic
ATGGTAATTCTCTCATTCCA+TGG 0.516736 2:-62213722 MsaT009600.1:CDS
ACCATATCCATGTTCTCTAA+AGG 0.525017 2:+62213852 None:intergenic
GAGAACATGGATATGGTTGG+TGG 0.530636 2:-62213846 MsaT009600.1:CDS
CGTTACGATTTGCAGCGTAA+GGG 0.534170 2:+62213748 None:intergenic
AAGACGAGCCGGGGCTTGGA+TGG 0.534291 2:+62213793 None:intergenic
GTTACGATTTGCAGCGTAAG+GGG 0.536907 2:+62213749 None:intergenic
GCTGCAAATCGTAACGCTGA+TGG 0.540162 2:-62213741 MsaT009600.1:CDS
TTGGGAAGGAAGACGAGCCG+GGG 0.553399 2:+62213784 None:intergenic
TCTAGCAGTCGGAGAGCTCA+GGG 0.554727 2:+62213602 None:intergenic
AACATGCCCCTGACTGTCCA+GGG 0.556233 2:+62213334 None:intergenic
CCACTATGAAAATAAGGATG+AGG 0.557357 2:+62213651 None:intergenic
GTAATGTTGTCCAGTCCACC+CGG 0.557358 2:+62213536 None:intergenic
GGTTCGCGCATGTGGACCCC+TGG 0.559214 2:-62213351 MsaT009600.1:CDS
ATCCAAGCCTTTAGAGAACA+TGG 0.559843 2:-62213859 MsaT009600.1:CDS
GGATGATGATGGACTTGGGA+AGG 0.561521 2:+62213770 None:intergenic
TCATCTTACCATCCAAGCCC+CGG 0.562153 2:-62213801 MsaT009600.1:CDS
GCAGCGTAAGGGGATGATGA+TGG 0.565277 2:+62213759 None:intergenic
GGTTGGACTGTTGAACCTGA+TGG 0.566068 2:-62216976 MsaT009600.1:CDS
ATCAATCTGCACGGCCCGGG+TGG 0.570226 2:-62213551 MsaT009600.1:CDS
TTGATCCTGAATGGTTTGCT+GGG 0.572973 2:-62213467 MsaT009600.1:CDS
TGTGGACCCCTGGACAGTCA+GGG 0.577345 2:-62213341 MsaT009600.1:CDS
GGGATTGTGAAGCCTTGGGA+AGG 0.580106 2:-62213219 MsaT009600.1:CDS
TTAGAGAACATGGATATGGT+TGG 0.590409 2:-62213849 MsaT009600.1:CDS
AGGACCGGAAGAAGGCAGGA+AGG 0.591677 2:+62213512 None:intergenic
TGATGGAACCACTTATCGTA+AGG 0.595024 2:-62216959 MsaT009600.1:intron
CTGGTACAAGACTACCAACA+TGG 0.603713 2:-62217146 MsaT009600.1:CDS
AGGAGAGAGAGAACAACAAG+AGG 0.604704 2:-62217122 MsaT009600.1:CDS
GTGGACCCCTGGACAGTCAG+GGG 0.607774 2:-62213340 MsaT009600.1:CDS
CGAGATACAAGATTGAATGT+CGG 0.609297 2:+62213414 None:intergenic
CTTGGATGGTAAGATGAACA+AGG 0.613106 2:+62213807 None:intergenic
GATCAACTATCTGACGGCCA+GGG 0.614613 2:+62213484 None:intergenic
AATCGCGGTGTTCTAGCAGT+CGG 0.621032 2:+62213591 None:intergenic
CACTTGGTAACTCAAAGACC+AGG 0.624367 2:-62213152 MsaT009600.1:intron
GATGATCTTGAACTCACACT+TGG 0.629133 2:-62213168 MsaT009600.1:CDS
AAGGGGATGATGATGGACTT+GGG 0.629431 2:+62213766 None:intergenic
CTGAAGATGAAGCTGTGGAG+AGG 0.631008 2:+62213691 None:intergenic
TACAAGACTACCAACATGGA+AGG 0.634618 2:-62217142 MsaT009600.1:CDS
GCAGTCGGAGAGCTCAGGGG+AGG 0.643740 2:+62213606 None:intergenic
TGATCCTGAAGATGAAGCTG+TGG 0.648099 2:+62213686 None:intergenic
GGAGAAGTTGGACTAGCATG+TGG 0.648324 2:+62213435 None:intergenic
TAATGTTGTCCAGTCCACCC+GGG 0.661081 2:+62213537 None:intergenic
ACATGCCCCTGACTGTCCAG+GGG 0.666992 2:+62213335 None:intergenic
CTAGCAGTCGGAGAGCTCAG+GGG 0.684940 2:+62213603 None:intergenic
ATTCAGGATCAACTATCTGA+CGG 0.695991 2:+62213478 None:intergenic
TTGGATGGTAAGATGAACAA+GGG 0.701552 2:+62213808 None:intergenic
ACTTCGATGATCAATCTGCA+CGG 0.712290 2:-62213560 MsaT009600.1:CDS
TCGAAGTCAGCATTCAATCG+CGG 0.720698 2:+62213576 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 62212919 62217175 62212919 ID=MsaG009600
Chr2 mRNA 62212919 62217175 62212919 ID=MsaT009600.1;Parent=MsaG009600
Chr2 exon 62212919 62212922 62212919 ID=MsaT009600.1.exon3;Parent=MsaT009600.1
Chr2 CDS 62212919 62212922 62212919 ID=cds.MsaT009600.1;Parent=MsaT009600.1
Chr2 exon 62213153 62213883 62213153 ID=MsaT009600.1.exon2;Parent=MsaT009600.1
Chr2 CDS 62213153 62213883 62213153 ID=cds.MsaT009600.1;Parent=MsaT009600.1
Chr2 exon 62216960 62217175 62216960 ID=MsaT009600.1.exon1;Parent=MsaT009600.1
Chr2 CDS 62216960 62217175 62216960 ID=cds.MsaT009600.1;Parent=MsaT009600.1
Gene Sequence

>MsaT009600.1

ATGACATCTGGTACAAGACTACCAACATGGAAGGAGAGAGAGAACAACAAGAGGAGAGAGAGAAGAAGAAGAGCTATAGCTGCTAAGATCTTCTCTGGTTTGAGAATGTATGGTAACTTTAGATTACCTAAACATTGTGATAACAATGAAGTTCTTAAAGCTCTTTGTAATGAAGCTGGTTGGACTGTTGAACCTGATGGAACCACTTATCGTAAGGGATCCAAGCCTTTAGAGAACATGGATATGGTTGGTGGATCATCAGCTGCAAGCCCTTGTTCATCTTACCATCCAAGCCCCGGCTCGTCTTCCTTCCCAAGTCCATCATCATCCCCTTACGCTGCAAATCGTAACGCTGATGGTAATTCTCTCATTCCATGGCTCAAAAACCTCTCCACAGCTTCATCTTCAGGATCATCTCCGAAACTTCCTCATCCTTATTTTCATAGTGGCTCTATCAGTGCTCCTGTCACACCTCCCCTGAGCTCTCCGACTGCTAGAACACCGCGATTGAATGCTGACTTCGATGATCAATCTGCACGGCCCGGGTGGACTGGACAACATTACTCCTTCCTGCCTTCTTCCGGTCCTCCAAGCCCTGGCCGTCAGATAGTTGATCCTGAATGGTTTGCTGGGATCAAACTTCCACATGCTAGTCCAACTTCTCCGACATTCAATCTTGTATCTCGAAGCCCATTTGCCTTCAAGGAAGATGCTTTTTCAGGCAGCGGTTCGCGCATGTGGACCCCTGGACAGTCAGGGGCATGTTCTCCAGCTATTGCAGCAGGCTTTGATCAAACTGCTGACATTCCAATGTCTGAAGCCATCTCAGATGAATTTGCATTTGGAAGCAACACATTTGGGATTGTGAAGCCTTGGGAAGGAGAAAGGATCCATGAAGAATTTGTAGCAGATGATCTTGAACTCACACTTGGTAACTCAAAGACCAGGTGA
Protein sequence

>MsaT009600.1

MTSGTRLPTWKERENNKRRERRRRAIAAKIFSGLRMYGNFRLPKHCDNNEVLKALCNEAGWTVEPDGTTYRKGSKPLENMDMVGGSSAASPCSSYHPSPGSSSFPSPSSSPYAANRNADGNSLIPWLKNLSTASSSGSSPKLPHPYFHSGSISAPVTPPLSSPTARTPRLNADFDDQSARPGWTGQHYSFLPSSGPPSPGRQIVDPEWFAGIKLPHASPTSPTFNLVSRSPFAFKEDAFSGSGSRMWTPGQSGACSPAIAAGFDQTADIPMSEAISDEFAFGSNTFGIVKPWEGERIHEEFVADDLELTLGNSKTR*