AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG023961

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG023961 MtrunA17_Chr8g0383991 95.738 305 11 1 1 305 1 303 0.0 587
MsaG023961 MtrunA17_Chr3g0142891 30.660 212 93 3 139 302 52 257 6.82e-23 95.1
MsaG023961 MtrunA17_Chr3g0142871 30.702 228 98 4 132 302 428 652 1.07e-22 98.2
MsaG023961 MtrunA17_Chr7g0269901 31.140 228 97 4 132 302 428 652 1.47e-22 97.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG023961 AT5G45420.2 51.553 322 119 10 1 301 1 306 1.59e-82 251
MsaG023961 AT5G45420.1 51.553 322 119 10 1 301 1 306 1.59e-82 251
MsaG023961 AT5G45420.3 51.553 322 119 10 1 301 1 306 1.59e-82 251
MsaG023961 AT3G11450.1 34.615 182 80 3 159 302 466 646 6.90e-22 96.3
MsaG023961 AT5G06110.1 30.732 205 97 4 140 300 457 660 7.68e-19 87.4
MsaG023961 AT5G06110.2 30.732 205 97 4 140 300 457 660 7.68e-19 87.4

Find 96 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACGATTTCGTTGGTTTC+TGG 0.174909 4:+94118285 None:intergenic
AAAGTTGCTGCTGCTGTTCC+TGG 0.293700 4:-94117552 MsaT023961.1:CDS
TCGGTTGAGGTTTCCTGATC+GGG 0.354119 4:+94118083 None:intergenic
GTGAGAAAGTTGAAAGTGTT+TGG 0.354834 4:-94117647 MsaT023961.1:CDS
CAGAATTGAAGAAAGGGTTT+CGG 0.376978 4:-94117497 MsaT023961.1:CDS
TGCATTGTCGGCGGCGGTGG+TGG 0.384974 4:-94117931 MsaT023961.1:CDS
GGGTTTCGGACTGCAAAATC+TGG 0.390024 4:-94117483 MsaT023961.1:CDS
TTTGCATTCTCTCTCCTCCT+TGG 0.398248 4:-94118173 MsaT023961.1:CDS
TCGCCGCCGGTGATGGAGAT+TGG 0.407288 4:+94118140 None:intergenic
TTGAAGAATCGAAATGGAAA+TGG 0.409406 4:-94117963 MsaT023961.1:CDS
ATCGTCCGATCTGCGTTGCT+TGG 0.410728 4:+94118022 None:intergenic
CATCTCATAGCAACATCTTT+CGG 0.412166 4:+94117579 None:intergenic
AAAGGAGTTGGGAGAGAAGA+AGG 0.421544 4:-94117760 MsaT023961.1:CDS
AGAGAAGAAGGTTGATGATT+CGG 0.423910 4:-94117748 MsaT023961.1:CDS
GATAAGAGACTTGTTGAAGA+AGG 0.424391 4:-94117687 MsaT023961.1:CDS
GTCGGCGGCGGTGGTGGAGG+AGG 0.424999 4:-94117925 MsaT023961.1:CDS
TGTTGCATTGTCGGCGGCGG+TGG 0.428265 4:-94117934 MsaT023961.1:CDS
CGGGTGCACCGGACTGATAC+AGG 0.433545 4:+94118330 None:intergenic
ATTGTCGGCGGCGGTGGTGG+AGG 0.433697 4:-94117928 MsaT023961.1:CDS
TGGAAACGGTGTTGCATTGT+CGG 0.435353 4:-94117943 MsaT023961.1:CDS
TGCCGTCAATTTCCCCGATC+AGG 0.438106 4:-94118096 MsaT023961.1:CDS
GGCGGCGGTGGTGGAGGAGG+AGG 0.446195 4:-94117922 MsaT023961.1:CDS
AGAATTGCAGAATTGAAGAA+AGG 0.450045 4:-94117504 MsaT023961.1:CDS
ATCGGTTGAGGTTTCCTGAT+CGG 0.454293 4:+94118082 None:intergenic
GAGGCGATAGCGGAGGCATT+CGG 0.458797 4:-94117819 MsaT023961.1:CDS
GATTTCGTTGGTTTCTGGTA+AGG 0.461575 4:+94118290 None:intergenic
TTCAGTGGCCGCGGGTGCAC+CGG 0.461986 4:+94118319 None:intergenic
CGAAAGATGTTGCTATGAGA+TGG 0.463082 4:-94117578 MsaT023961.1:CDS
TGGAGGAGGAGGAGAAGGAA+TGG 0.463216 4:-94117911 MsaT023961.1:CDS
GTTTCGTTGAAGAATCGAAA+TGG 0.464225 4:-94117969 MsaT023961.1:CDS
CAACCGATGAGGATGATTCC+AGG 0.465520 4:-94118067 MsaT023961.1:CDS
GGCGATTCCCGTGTCGGCCG+TGG 0.468929 4:-94118122 MsaT023961.1:CDS
GGAATCATCCTCATCGGTTG+AGG 0.470477 4:+94118070 None:intergenic
TCGATTTGAGCGGTTCAGAT+TGG 0.470526 4:+94118207 None:intergenic
AGGCTGTGATTCAGTGGCCG+CGG 0.476901 4:+94118310 None:intergenic
CGGCATGACCACGGCCGACA+CGG 0.478990 4:+94118114 None:intergenic
TTCAACGAAACCACCGGCGC+TGG 0.480043 4:+94117981 None:intergenic
GGCATGACCACGGCCGACAC+GGG 0.485981 4:+94118115 None:intergenic
ACGGGAATCGCCGCCGGTGA+TGG 0.488045 4:+94118133 None:intergenic
GGTGGTGGAGGAGGAGGAGA+AGG 0.492408 4:-94117916 MsaT023961.1:CDS
AAGAGACTTGTTGAAGAAGG+AGG 0.496476 4:-94117684 MsaT023961.1:CDS
TCCCACCGTCCTGGTTTCCC+CGG 0.499822 4:+94117840 None:intergenic
GAAGATTGAAGAGATTGAAA+CGG 0.500067 4:+94118253 None:intergenic
GGCTGTGATTCAGTGGCCGC+GGG 0.502205 4:+94118311 None:intergenic
GAATTGCAGAATTGAAGAAA+GGG 0.503367 4:-94117503 MsaT023961.1:CDS
CAAGCTGCTTTCGATTTCCC+AGG 0.506123 4:+94117534 None:intergenic
GCCGACACGGGAATCGCCGC+CGG 0.510103 4:+94118127 None:intergenic
CACCGTCCTGGTTTCCCCGG+TGG 0.513685 4:+94117843 None:intergenic
GGTGAAGAAATCAAAGGAGT+TGG 0.518193 4:-94117772 MsaT023961.1:CDS
CGGTGTTGCATTGTCGGCGG+CGG 0.518420 4:-94117937 MsaT023961.1:CDS
GTGAAGAAATCAAAGGAGTT+GGG 0.518866 4:-94117771 MsaT023961.1:CDS
CGATTCTTCAACGAAACCAC+CGG 0.522401 4:+94117975 None:intergenic
GAAGGAGGAGATTTAGCGAC+GGG 0.533839 4:-94117669 MsaT023961.1:CDS
TCTGAAGAAGAGAAAAGCGT+TGG 0.535242 4:-94117709 MsaT023961.1:CDS
GCTATCGCCTCCCACCGTCC+TGG 0.536007 4:+94117831 None:intergenic
ACCGGCGGCGATTCCCGTGT+CGG 0.539059 4:-94118128 MsaT023961.1:CDS
CTCTGTAGTAGCTCCAGCGC+CGG 0.539400 4:-94117994 MsaT023961.1:CDS
AATCGAAATGGAAATGGAAA+CGG 0.539438 4:-94117957 MsaT023961.1:CDS
TTTCCTGGAATCATCCTCAT+CGG 0.539989 4:+94118064 None:intergenic
AGGACGGTGGGAGGCGATAG+CGG 0.545275 4:-94117829 MsaT023961.1:CDS
GGGGAAACCAGGACGGTGGG+AGG 0.546154 4:-94117838 MsaT023961.1:CDS
CAGATCCAAGCAACGCAGAT+CGG 0.552256 4:-94118027 MsaT023961.1:CDS
AAGTTGCTGCTGCTGTTCCT+GGG 0.554829 4:-94117551 MsaT023961.1:CDS
ACCGGGGAAACCAGGACGGT+GGG 0.559178 4:-94117841 MsaT023961.1:CDS
CCGAAGTTCCTGTATCAGTC+CGG 0.563162 4:-94118338 MsaT023961.1:CDS
GGCATTCGGAGGGCGTCACA+AGG 0.566101 4:-94117805 MsaT023961.1:CDS
GAAAGATGTTGCTATGAGAT+GGG 0.567305 4:-94117577 MsaT023961.1:CDS
CTGGTAAGGCTGTGATTCAG+TGG 0.573589 4:+94118304 None:intergenic
CCGGACTGATACAGGAACTT+CGG 0.574834 4:+94118338 None:intergenic
TGTAGTAGCTCCAGCGCCGG+TGG 0.575392 4:-94117991 MsaT023961.1:CDS
CACCGGGGAAACCAGGACGG+TGG 0.578167 4:-94117842 MsaT023961.1:CDS
TTCCTGATCGGGGAAATTGA+CGG 0.583685 4:+94118094 None:intergenic
GCGATAGCGGAGGCATTCGG+AGG 0.585439 4:-94117816 MsaT023961.1:CDS
GGAAATTGACGGCATGACCA+CGG 0.588936 4:+94118105 None:intergenic
TTCGCTCCAATCTCCATCAC+CGG 0.592700 4:-94118146 MsaT023961.1:CDS
GTATCAGTCCGGTGCACCCG+CGG 0.599158 4:-94118327 MsaT023961.1:CDS
GCGTCACAAGGTGGAAAGCG+TGG 0.605173 4:-94117793 MsaT023961.1:CDS
GTGATGGAGATTGGAGCGAA+AGG 0.606633 4:+94118149 None:intergenic
ACAGCGATGAACGATTTCGT+TGG 0.617295 4:+94118278 None:intergenic
TGAGATTCTGAAGAAACAGA+TGG 0.629866 4:-94117874 MsaT023961.1:CDS
CGGTTGAGGTTTCCTGATCG+GGG 0.631525 4:+94118084 None:intergenic
ATCCACCGGGGAAACCAGGA+CGG 0.634948 4:-94117845 MsaT023961.1:CDS
AAGTGTTTGGAGTTCAAACG+AGG 0.645478 4:-94117634 MsaT023961.1:CDS
AGAAGGAGGAGATTTAGCGA+CGG 0.648578 4:-94117670 MsaT023961.1:CDS
CGGCGCTGGAGCTACTACAG+AGG 0.650195 4:+94117995 None:intergenic
CGATAGCGGAGGCATTCGGA+GGG 0.653736 4:-94117815 MsaT023961.1:CDS
ACGGTGGGAGGCGATAGCGG+AGG 0.665574 4:-94117826 MsaT023961.1:CDS
GCTCCAATCTCCATCACCGG+CGG 0.666192 4:-94118143 MsaT023961.1:CDS
AAGCGTGGTGAAGAAATCAA+AGG 0.666488 4:-94117778 MsaT023961.1:CDS
AAACGGTGTTGCATTGTCGG+CGG 0.669146 4:-94117940 MsaT023961.1:CDS
TCAGGAAACCTCAACCGATG+AGG 0.671357 4:-94118078 MsaT023961.1:CDS
AGATTGGAGCGAAAGGACCA+AGG 0.675323 4:+94118156 None:intergenic
ATTCGGAGGGCGTCACAAGG+TGG 0.679939 4:-94117802 MsaT023961.1:CDS
CAGATGAAAATCGATTTGAG+CGG 0.706129 4:+94118197 None:intergenic
TTGGAGCGAAAGGACCAAGG+AGG 0.738797 4:+94118159 None:intergenic
GGAGAAGGAATGGAACGACG+AGG 0.745135 4:-94117901 MsaT023961.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr4 gene 94117470 94118387 94117470 ID=MsaG023961
Chr4 mRNA 94117470 94118387 94117470 ID=MsaT023961.1;Parent=MsaG023961
Chr4 exon 94117470 94118387 94117470 ID=MsaT023961.1.exon1;Parent=MsaT023961.1
Chr4 CDS 94117470 94118387 94117470 ID=cds.MsaT023961.1;Parent=MsaT023961.1
Gene Sequence

>MsaT023961.1

ATGGAATTCTTAGACGAAGACGCGAAACCGAAGTTCCTGTATCAGTCCGGTGCACCCGCGGCCACTGAATCACAGCCTTACCAGAAACCAACGAAATCGTTCATCGCTGTAACCGTTTCAATCTCTTCAATCTTCTTCGCTCTCGCTTTCTTCGTGTTCCAATCTGAACCGCTCAAATCGATTTTCATCTGGTTTGCATTCTCTCTCCTCCTTGGTCCTTTCGCTCCAATCTCCATCACCGGCGGCGATTCCCGTGTCGGCCGTGGTCATGCCGTCAATTTCCCCGATCAGGAAACCTCAACCGATGAGGATGATTCCAGGAAAAAATCTCAGCAGCGCAGATCCAAGCAACGCAGATCGGACGATGTCACCTCTGTAGTAGCTCCAGCGCCGGTGGTTTCGTTGAAGAATCGAAATGGAAATGGAAACGGTGTTGCATTGTCGGCGGCGGTGGTGGAGGAGGAGGAGAAGGAATGGAACGACGAGGACATTGAGATTCTGAAGAAACAGATGGTGAAAAATCCACCGGGGAAACCAGGACGGTGGGAGGCGATAGCGGAGGCATTCGGAGGGCGTCACAAGGTGGAAAGCGTGGTGAAGAAATCAAAGGAGTTGGGAGAGAAGAAGGTTGATGATTCGGATTCGTATGAGCAGTTTCTGAAGAAGAGAAAAGCGTTGGATAAGAGACTTGTTGAAGAAGGAGGAGATTTAGCGACGGGTGAGAAAGTTGAAAGTGTTTGGAGTTCAAACGAGGATATTGCTTTGTTGAATGCTTTGAAAGCATTTCCGAAAGATGTTGCTATGAGATGGGAGAAAGTTGCTGCTGCTGTTCCTGGGAAATCGAAAGCAGCTTGTATGAAAAGAATTGCAGAATTGAAGAAAGGGTTTCGGACTGCAAAATCTGGTTCTGAAGTTTAG
Protein sequence

>MsaT023961.1

MEFLDEDAKPKFLYQSGAPAATESQPYQKPTKSFIAVTVSISSIFFALAFFVFQSEPLKSIFIWFAFSLLLGPFAPISITGGDSRVGRGHAVNFPDQETSTDEDDSRKKSQQRRSKQRRSDDVTSVVAPAPVVSLKNRNGNGNGVALSAAVVEEEEKEWNDEDIEILKKQMVKNPPGKPGRWEAIAEAFGGRHKVESVVKKSKELGEKKVDDSDSYEQFLKKRKALDKRLVEEGGDLATGEKVESVWSSNEDIALLNALKAFPKDVAMRWEKVAAAVPGKSKAACMKRIAELKKGFRTAKSGSEV*