AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480021166.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480021166.01.T01 MTR_4g068190 96.622 148 5 0 1 148 1 148 6.75e-103 295
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480021166.01.T01 AT2G43560 60.993 141 49 2 8 148 8 142 2.37e-47 153
MsG0480021166.01.T01 AT2G43560 79.762 84 17 0 65 148 3 86 3.81e-41 136

Find 43 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGTTTCATCACATAATTT+TGG 0.254636 4:+54599779 None:intergenic
CATTCATTTGATGCTGCTAA+TGG 0.284118 4:-54599827 MsG0480021166.01.T01:CDS
CAAACTAGACAAACTAGATT+TGG 0.295021 4:-54600236 MsG0480021166.01.T01:five_prime_UTR
AATTCACGTAGAGACTTTCT+TGG 0.312447 4:-54599881 MsG0480021166.01.T01:CDS
TAGTCCACCAGTTGGATATC+AGG 0.360762 4:-54599139 MsG0480021166.01.T01:intron
AAGAAAGTCTCTACGTGAAT+TGG 0.368565 4:+54599883 None:intergenic
GACTTTCTTGGATTAGCATT+AGG 0.374464 4:-54599869 MsG0480021166.01.T01:CDS
CAATACAAGGATATTAAAGT+TGG 0.375129 4:-54599171 MsG0480021166.01.T01:CDS
CATCTGGACAAATATTTGAT+AGG 0.389186 4:-54598594 MsG0480021166.01.T01:CDS
TTCTCAACAGAAATGCTTTG+AGG 0.406961 4:+54599977 None:intergenic
GATTGACAGAAATTTGTAAT+CGG 0.436281 4:+54598565 None:intergenic
ATGATGTTATTGTTTGCAAA+TGG 0.440480 4:+54600203 None:intergenic
CCTATGGTAACTACTGAATC+AGG 0.444760 4:-54599198 MsG0480021166.01.T01:CDS
TATGTTGCAATGGTTCCATC+TGG 0.446081 4:-54598610 MsG0480021166.01.T01:CDS
TTTGATGCTGCTAATGGAGC+TGG 0.447449 4:-54599821 MsG0480021166.01.T01:CDS
ATGACACAATATTACATCCT+TGG 0.447775 4:-54600174 MsG0480021166.01.T01:five_prime_UTR
TGATATCCAACTGGTGGACT+AGG 0.460176 4:+54599141 None:intergenic
TTACACACCTGATATCCAAC+TGG 0.497134 4:+54599132 None:intergenic
TTTATGCATGAAGGTACCTA+TGG 0.499177 4:-54599214 MsG0480021166.01.T01:intron
AATACAAGGATATTAAAGTT+GGG 0.500943 4:-54599170 MsG0480021166.01.T01:CDS
CATTAGCAGCATCAAATGAA+TGG 0.505775 4:+54599828 None:intergenic
GTTATTGTTTGCAAATGGAA+TGG 0.514203 4:+54600208 None:intergenic
CTATCAAATATTTGTCCAGA+TGG 0.522457 4:+54598595 None:intergenic
TGAATCAGGTTTGCAATACA+AGG 0.531477 4:-54599184 MsG0480021166.01.T01:CDS
AGGACTTACAAAGTGGAAGC+AGG 0.541635 4:+54600126 None:intergenic
ATCCTTGGATATGCCTAGCA+TGG 0.544626 4:-54600159 MsG0480021166.01.T01:exon
TACAAAGTGGAAGCAGGAGA+GGG 0.573806 4:+54600132 None:intergenic
GGCTGCTAATTATGTTGCAA+TGG 0.576500 4:-54598620 MsG0480021166.01.T01:CDS
GATATCCAACTGGTGGACTA+GGG 0.580308 4:+54599142 None:intergenic
AGGAGAGGGGAAGCCATGCT+AGG 0.580475 4:+54600146 None:intergenic
CTTTGAGGAGCAGTAAGAGA+AGG 0.581278 4:+54599992 None:intergenic
AAGTGAAGTCCACAGAGACA+AGG 0.592596 4:-54599934 MsG0480021166.01.T01:CDS
AGTGCATTCCCTTGTCTCTG+TGG 0.600039 4:+54599925 None:intergenic
CAAGGCCCTAGTCCACCAGT+TGG 0.601514 4:-54599147 MsG0480021166.01.T01:CDS
CCTGATTCAGTAGTTACCAT+AGG 0.608091 4:+54599198 None:intergenic
TGACAGAAATTTGTAATCGG+CGG 0.608098 4:+54598568 None:intergenic
CACACCTGATATCCAACTGG+TGG 0.614939 4:+54599135 None:intergenic
AAGGATATTAAAGTTGGGCA+AGG 0.616109 4:-54599165 MsG0480021166.01.T01:CDS
TTACAAAGTGGAAGCAGGAG+AGG 0.616382 4:+54600131 None:intergenic
AGTGAAGTCCACAGAGACAA+GGG 0.625615 4:-54599933 MsG0480021166.01.T01:CDS
AGCCATGCTAGGCATATCCA+AGG 0.638646 4:+54600157 None:intergenic
ACAAAGTGGAAGCAGGAGAG+GGG 0.648340 4:+54600133 None:intergenic
GGATGTAATATTGTGTCATG+TGG 0.676551 4:+54600178 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATATTAATCATTTGATA+AGG + Chr4:54600021-54600040 None:intergenic 10.0%
!! AATATTTATCTACTAAAATT+AGG - Chr4:54599165-54599184 MsG0480021166.01.T01:CDS 10.0%
!!! ATATAAATTTAGAGTATCAT+AGG + Chr4:54599820-54599839 None:intergenic 15.0%
!!! TTTTAGTAGATAAATATTGA+AGG + Chr4:54599163-54599182 None:intergenic 15.0%
!! AAGATACAAATCAAGTATTT+AGG + Chr4:54599769-54599788 None:intergenic 20.0%
!! AATACAAGGATATTAAAGTT+GGG - Chr4:54599618-54599637 MsG0480021166.01.T01:intron 20.0%
!! TCATTAACTATCGATATTAA+TGG + Chr4:54599540-54599559 None:intergenic 20.0%
!!! AAATACTTGATTTGTATCTT+AGG - Chr4:54599769-54599788 MsG0480021166.01.T01:CDS 20.0%
!!! ATGTTTTCGGTTAAAAAAAT+TGG - Chr4:54599225-54599244 MsG0480021166.01.T01:intron 20.0%
!!! TATGTGACTAAAAATGTTTT+CGG - Chr4:54599212-54599231 MsG0480021166.01.T01:intron 20.0%
!!! TGTTTTCGGTTAAAAAAATT+GGG - Chr4:54599226-54599245 MsG0480021166.01.T01:intron 20.0%
!!! TTTTATATAGATTCTACTTG+TGG - Chr4:54598766-54598785 MsG0480021166.01.T01:intron 20.0%
! AGTAATCCTATATCATTATC+AGG + Chr4:54599896-54599915 None:intergenic 25.0%
! ATGATGTTATTGTTTGCAAA+TGG + Chr4:54598588-54598607 None:intergenic 25.0%
! ATTTGTGAAGAACCTTATAA+TGG + Chr4:54599337-54599356 None:intergenic 25.0%
! CAATACAAGGATATTAAAGT+TGG - Chr4:54599617-54599636 MsG0480021166.01.T01:intron 25.0%
! CAGTATTATTTATGCATTGT+TGG + Chr4:54598712-54598731 None:intergenic 25.0%
! GATTGACAGAAATTTGTAAT+CGG + Chr4:54600226-54600245 None:intergenic 25.0%
!! CAAGTTTCATCACATAATTT+TGG + Chr4:54599012-54599031 None:intergenic 25.0%
!!! CATAATTTTGGTTTTTCTTC+TGG + Chr4:54599000-54599019 None:intergenic 25.0%
AAAACTTGCAATGAAATGAC+AGG + Chr4:54599402-54599421 None:intergenic 30.0%
AGAAAGAGCTTGAAAATGTA+TGG - Chr4:54599034-54599053 MsG0480021166.01.T01:intron 30.0%
ATGACACAATATTACATCCT+TGG - Chr4:54598614-54598633 MsG0480021166.01.T01:CDS 30.0%
CAAACTAGACAAACTAGATT+TGG - Chr4:54598552-54598571 MsG0480021166.01.T01:CDS 30.0%
CATCTGGACAAATATTTGAT+AGG - Chr4:54600194-54600213 MsG0480021166.01.T01:five_prime_UTR 30.0%
CTATCAAATATTTGTCCAGA+TGG + Chr4:54600196-54600215 None:intergenic 30.0%
GTAGACATTAATCACAGTTA+AGG + Chr4:54599086-54599105 None:intergenic 30.0%
GTTATTGTTTGCAAATGGAA+TGG + Chr4:54598583-54598602 None:intergenic 30.0%
! ACTGAGTATTTTATGCATGA+AGG - Chr4:54599565-54599584 MsG0480021166.01.T01:intron 30.0%
! CTTTAGCTAGTTTAGATTGA+AGG + Chr4:54599988-54600007 None:intergenic 30.0%
! GGTACTGAAATCATCAATAT+TGG + Chr4:54599875-54599894 None:intergenic 30.0%
! TCAGTACCTGATAATGATAT+AGG - Chr4:54599887-54599906 MsG0480021166.01.T01:CDS 30.0%
! TTCAGTATTTTCTACGTAGA+AGG + Chr4:54599852-54599871 None:intergenic 30.0%
! TTTTCATGTGCTTATCTGAT+AGG - Chr4:54600144-54600163 MsG0480021166.01.T01:CDS 30.0%
!! CATTGACTGCATTTTTGAAA+TGG + Chr4:54599724-54599743 None:intergenic 30.0%
!!! AATTTTGGTTTTTCTTCTGG+TGG + Chr4:54598997-54599016 None:intergenic 30.0%
AAGAAAGTCTCTACGTGAAT+TGG + Chr4:54598908-54598927 None:intergenic 35.0%
AAGGATATTAAAGTTGGGCA+AGG - Chr4:54599623-54599642 MsG0480021166.01.T01:intron 35.0%
AAGTGAAAGGACTTACAAAG+TGG + Chr4:54598672-54598691 None:intergenic 35.0%
AATTCACGTAGAGACTTTCT+TGG - Chr4:54598907-54598926 MsG0480021166.01.T01:intron 35.0%
ACGAAAGGACTTCCATTATA+AGG - Chr4:54599322-54599341 MsG0480021166.01.T01:intron 35.0%
AGTTTAGATTGAAGGAAGCA+AGG + Chr4:54599980-54599999 None:intergenic 35.0%
ATCACAGTTAAGGCATAGAA+AGG + Chr4:54599076-54599095 None:intergenic 35.0%
CATTAGCAGCATCAAATGAA+TGG + Chr4:54598963-54598982 None:intergenic 35.0%
CATTCATTTGATGCTGCTAA+TGG - Chr4:54598961-54598980 MsG0480021166.01.T01:intron 35.0%
CTCTTAAAACGTTTGACGAA+AGG - Chr4:54599307-54599326 MsG0480021166.01.T01:intron 35.0%
GCATCAATCTCGTTCAAAAT+TGG + Chr4:54599747-54599766 None:intergenic 35.0%
GGATGTAATATTGTGTCATG+TGG + Chr4:54598613-54598632 None:intergenic 35.0%
TCACAGTTAAGGCATAGAAA+GGG + Chr4:54599075-54599094 None:intergenic 35.0%
TGAATCAGGTTTGCAATACA+AGG - Chr4:54599604-54599623 MsG0480021166.01.T01:intron 35.0%
TGACAGAAATTTGTAATCGG+CGG + Chr4:54600223-54600242 None:intergenic 35.0%
TGAGGAAAAGAGAAAGTGAA+AGG + Chr4:54598685-54598704 None:intergenic 35.0%
TTATGCATTGTTGGATAGTG+AGG + Chr4:54598703-54598722 None:intergenic 35.0%
TTCTCAACAGAAATGCTTTG+AGG + Chr4:54598814-54598833 None:intergenic 35.0%
!! GACTTTCTTGGATTAGCATT+AGG - Chr4:54598919-54598938 MsG0480021166.01.T01:intron 35.0%
!! TTTATGCATGAAGGTACCTA+TGG - Chr4:54599574-54599593 MsG0480021166.01.T01:intron 35.0%
!!! TGACTGCATTTTTGAAATGG+TGG + Chr4:54599721-54599740 None:intergenic 35.0%
AACAATACACATGCTGACAG+AGG + Chr4:54600100-54600119 None:intergenic 40.0%
ACTGAACAAAGCTTCTGTCA+GGG + Chr4:54599441-54599460 None:intergenic 40.0%
CCTATGGTAACTACTGAATC+AGG - Chr4:54599590-54599609 MsG0480021166.01.T01:intron 40.0%
CCTGATTCAGTAGTTACCAT+AGG + Chr4:54599593-54599612 None:intergenic 40.0%
GGCTGCTAATTATGTTGCAA+TGG - Chr4:54600168-54600187 MsG0480021166.01.T01:exon 40.0%
TAGATTGAAGGAAGCAAGGA+CGG + Chr4:54599976-54599995 None:intergenic 40.0%
TATGTTGCAATGGTTCCATC+TGG - Chr4:54600178-54600197 MsG0480021166.01.T01:five_prime_UTR 40.0%
TCATGTGCTTATCTGATAGG+TGG - Chr4:54600147-54600166 MsG0480021166.01.T01:CDS 40.0%
TTACACACCTGATATCCAAC+TGG + Chr4:54599659-54599678 None:intergenic 40.0%
! AGCTTCTGTCAGGGAATTTT+TGG + Chr4:54599432-54599451 None:intergenic 40.0%
AAGTGAAGTCCACAGAGACA+AGG - Chr4:54598854-54598873 MsG0480021166.01.T01:intron 45.0%
AGATTGAAGGAAGCAAGGAC+GGG + Chr4:54599975-54599994 None:intergenic 45.0%
AGGACTTACAAAGTGGAAGC+AGG + Chr4:54598665-54598684 None:intergenic 45.0%
AGTGAAGTCCACAGAGACAA+GGG - Chr4:54598855-54598874 MsG0480021166.01.T01:intron 45.0%
ATCCTTGGATATGCCTAGCA+TGG - Chr4:54598629-54598648 MsG0480021166.01.T01:intron 45.0%
CACTGAACAAAGCTTCTGTC+AGG + Chr4:54599442-54599461 None:intergenic 45.0%
TACAAAGTGGAAGCAGGAGA+GGG + Chr4:54598659-54598678 None:intergenic 45.0%
TAGTCCACCAGTTGGATATC+AGG - Chr4:54599649-54599668 MsG0480021166.01.T01:intron 45.0%
TTACAAAGTGGAAGCAGGAG+AGG + Chr4:54598660-54598679 None:intergenic 45.0%
TTGAAGGTGACACAACTGCA+TGG + Chr4:54599147-54599166 None:intergenic 45.0%
TTTGATGCTGCTAATGGAGC+TGG - Chr4:54598967-54598986 MsG0480021166.01.T01:intron 45.0%
! CTTTGAGGAGCAGTAAGAGA+AGG + Chr4:54598799-54598818 None:intergenic 45.0%
!! CTGACAGAAGCTTTGTTCAG+TGG - Chr4:54599440-54599459 MsG0480021166.01.T01:intron 45.0%
!! GATATCCAACTGGTGGACTA+GGG + Chr4:54599649-54599668 None:intergenic 45.0%
!! TGATATCCAACTGGTGGACT+AGG + Chr4:54599650-54599669 None:intergenic 45.0%
ACAAAGTGGAAGCAGGAGAG+GGG + Chr4:54598658-54598677 None:intergenic 50.0%
AGCCATGCTAGGCATATCCA+AGG + Chr4:54598634-54598653 None:intergenic 50.0%
AGTGCATTCCCTTGTCTCTG+TGG + Chr4:54598866-54598885 None:intergenic 50.0%
CACACCTGATATCCAACTGG+TGG + Chr4:54599656-54599675 None:intergenic 50.0%
GCGTTCAAGGGAAACTGAAC+AGG + Chr4:54599692-54599711 None:intergenic 50.0%
TGGTGGAGACGAGCGTTCAA+GGG + Chr4:54599704-54599723 None:intergenic 55.0%
! ATGGTGGAGACGAGCGTTCA+AGG + Chr4:54599705-54599724 None:intergenic 55.0%
AGGAGAGGGGAAGCCATGCT+AGG + Chr4:54598645-54598664 None:intergenic 60.0%
CAAGGCCCTAGTCCACCAGT+TGG - Chr4:54599641-54599660 MsG0480021166.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr4 gene 54598549 54600261 54598549 ID=MsG0480021166.01;Name=MsG0480021166.01
Chr4 mRNA 54598549 54600261 54598549 ID=MsG0480021166.01.T01;Parent=MsG0480021166.01;Name=MsG0480021166.01.T01;_AED=0.49;_eAED=0.53;_QI=90|1|0.75|1|1|1|4|0|163
Chr4 exon 54598549 54598644 54598549 ID=MsG0480021166.01.T01:exon:20269;Parent=MsG0480021166.01.T01
Chr4 exon 54599140 54599223 54599140 ID=MsG0480021166.01.T01:exon:20268;Parent=MsG0480021166.01.T01
Chr4 exon 54599760 54600034 54599760 ID=MsG0480021166.01.T01:exon:20267;Parent=MsG0480021166.01.T01
Chr4 exon 54600135 54600261 54600135 ID=MsG0480021166.01.T01:exon:20266;Parent=MsG0480021166.01.T01
Chr4 five_prime_UTR 54600172 54600261 54600172 ID=MsG0480021166.01.T01:five_prime_utr;Parent=MsG0480021166.01.T01
Chr4 CDS 54600135 54600171 54600135 ID=MsG0480021166.01.T01:cds;Parent=MsG0480021166.01.T01
Chr4 CDS 54599760 54600034 54599760 ID=MsG0480021166.01.T01:cds;Parent=MsG0480021166.01.T01
Chr4 CDS 54599140 54599223 54599140 ID=MsG0480021166.01.T01:cds;Parent=MsG0480021166.01.T01
Chr4 CDS 54598549 54598644 54598549 ID=MsG0480021166.01.T01:cds;Parent=MsG0480021166.01.T01
Gene Sequence

>MsG0480021166.01.T01

ATGCCTAGCATGGCTTCCCCTCTCCTGCTTCCACTTTATTCTACTTGTGGTAAAATTCCTTCTCTTACTGCTCCTCAAAGCATTTCTGTTGAGAAACTTAGAAGATTTGCTCTTAAAGTGAAGTCCACAGAGACAAGGGAATGCACTGCTAATGATATGTTTAATGCCAATTCACGTAGAGACTTTCTTGGATTAGCATTAGGAGTCTCTACTCTATTCATCCATTCATTTGATGCTGCTAATGGAGCTGGTTTGCCACCAGAAGAAAAACCAAAATTATGTGATGAAACTTGTGAGAAAGAGCTTGAAAATGTACCTATGGTAACTACTGAATCAGGTTTGCAATACAAGGATATTAAAGTTGGGCAAGGCCCTAGTCCACCAGTTGGATATCAGGTGGCTGCTAATTATGTTGCAATGGTTCCATCTGGACAAATATTTGATAGGTATCCGCCGATTACAAATTTCTGTCAATCTTTTCGTAGCTCTTAA
Protein sequence

>MsG0480021166.01.T01

MPSMASPLLLPLYSTCGKIPSLTAPQSISVEKLRRFALKVKSTETRECTANDMFNANSRRDFLGLALGVSTLFIHSFDAANGAGLPPEEKPKLCDETCEKELENVPMVTTESGLQYKDIKVGQGPSPPVGYQVAANYVAMVPSGQIFDRYPPITNFCQSFRSS*