AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1016570

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1016570 MtrunA17_Chr7g0231891 90.000 70 7 0 67 136 1 70 2.67e-39 129
Msa1016570 MtrunA17_Chr7g0231901 87.500 40 5 0 15 54 9 48 1.21e-17 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1016570 AT4G00030.1 68.182 110 35 0 27 136 30 139 3.99e-47 151

Find 36 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGCTTGGTGGGGTTGTTT+TGG 0.185547 7_1:+33513548 None:intergenic
GTTTGAGAGGTGAATGGGTT+GGG 0.302248 7_1:+33513643 None:intergenic
ATTGAGAAGGCTGGATTGTT+TGG 0.319900 7_1:-33513403 Msa1016570:CDS
GGAAGTGGTGGTGGCGGTGG+TGG 0.334577 7_1:+33513675 None:intergenic
GGTGATTGAGTTGAGTTTCA+TGG 0.349798 7_1:+33513699 None:intergenic
GAATGGGTTGGGGAAGAAAA+AGG 0.357353 7_1:+33513654 None:intergenic
AGTGGTGGTGGCGGTGGTGG+TGG 0.362361 7_1:+33513678 None:intergenic
GGGTCTTGAGGCCACGGTCT+TGG 0.384643 7_1:+33513569 None:intergenic
TTGGTGGTTTGAGAGGTGAA+TGG 0.418869 7_1:+33513637 None:intergenic
CGACAACTTGGCGATTGCTC+TGG 0.431797 7_1:-33513453 Msa1016570:CDS
AAAGGAAGTGGTGGTGGCGG+TGG 0.444699 7_1:+33513672 None:intergenic
TTGTTCATCATTGAGAAGGC+TGG 0.454495 7_1:-33513412 Msa1016570:CDS
GGATTGTTTGGAACTAAAGC+TGG 0.458772 7_1:-33513391 Msa1016570:CDS
GGTTTGAGAGGTGAATGGGT+TGG 0.461814 7_1:+33513642 None:intergenic
TGGTGGTTTGAGAGGTGAAT+GGG 0.462983 7_1:+33513638 None:intergenic
TTTGAGAGGTGAATGGGTTG+GGG 0.476901 7_1:+33513644 None:intergenic
CGTTACCGTGATCGATTCAA+TGG 0.505248 7_1:-33513518 Msa1016570:CDS
ACGATCGACACTAGCTTGGT+GGG 0.505817 7_1:+33513538 None:intergenic
ATCGATTCAATGGTCAAGCT+TGG 0.520360 7_1:-33513508 Msa1016570:CDS
AACGATCGACACTAGCTTGG+TGG 0.521234 7_1:+33513537 None:intergenic
GTGATTCCCTATCGACAACT+TGG 0.524705 7_1:-33513465 Msa1016570:CDS
GGTAACGATCGACACTAGCT+TGG 0.536165 7_1:+33513534 None:intergenic
CACGGTCTTGGTCAGAGATG+AGG 0.542439 7_1:+33513581 None:intergenic
GCAATCGCCAAGTTGTCGAT+AGG 0.562831 7_1:+33513458 None:intergenic
CAATCGCCAAGTTGTCGATA+GGG 0.568619 7_1:+33513459 None:intergenic
ACGGTCTTGGTCAGAGATGA+GGG 0.570760 7_1:+33513582 None:intergenic
GCAGTTGTTCATCATTGAGA+AGG 0.573282 7_1:-33513416 Msa1016570:CDS
TCAATGGTCAAGCTTGGCAT+CGG 0.588669 7_1:-33513502 Msa1016570:CDS
GGCATCGGTACAGTAACCAC+TGG 0.604053 7_1:-33513487 Msa1016570:CDS
CTTGGTCAGAGATGAGGGTG+AGG 0.611807 7_1:+33513587 None:intergenic
ATTGCTCTGGACTACTGAGA+AGG 0.631356 7_1:-33513440 Msa1016570:CDS
GGTCAGAGATGAGGGTGAGG+AGG 0.635921 7_1:+33513590 None:intergenic
CGATCGACACTAGCTTGGTG+GGG 0.639447 7_1:+33513539 None:intergenic
CTTGACCATTGAATCGATCA+CGG 0.654095 7_1:+33513513 None:intergenic
CTCATCTCTGACCAAGACCG+TGG 0.686718 7_1:-33513580 Msa1016570:CDS
TGTCGATAGGGAATCACCAG+TGG 0.698896 7_1:+33513471 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAAAAAAAAAACCATCAGG+AGG + chr7_1:33513699-33513718 None:intergenic 30.0%
! TAAAGCTGGAGATGTTTTAC+AGG - chr7_1:33513629-33513648 Msa1016570:CDS 35.0%
!! GTTATTACTTTTCCTCCTGA+TGG - chr7_1:33513684-33513703 Msa1016570:CDS 35.0%
!!! TCTTTTGTTGGTGGTTTGAG+AGG + chr7_1:33513379-33513398 None:intergenic 40.0%
!!! TTTGGCGGTTAGTCTTTTGT+TGG + chr7_1:33513391-33513410 None:intergenic 40.0%
CTTGACCATTGAATCGATCA+CGG + chr7_1:33513496-33513515 None:intergenic 40.0%
! ATCGATTCAATGGTCAAGCT+TGG - chr7_1:33513498-33513517 Msa1016570:CDS 40.0%
GCAGTTGTTCATCATTGAGA+AGG - chr7_1:33513590-33513609 Msa1016570:CDS 40.0%
TTGTTCATCATTGAGAAGGC+TGG - chr7_1:33513594-33513613 Msa1016570:CDS 40.0%
ATTGAGAAGGCTGGATTGTT+TGG - chr7_1:33513603-33513622 Msa1016570:CDS 40.0%
! GGATTGTTTGGAACTAAAGC+TGG - chr7_1:33513615-33513634 Msa1016570:CDS 40.0%
GAAGAAAAAGGAAGTGGTGG+TGG + chr7_1:33513343-33513362 None:intergenic 45.0%
GTTGGGGAAGAAAAAGGAAG+TGG + chr7_1:33513349-33513368 None:intergenic 45.0%
!! GAATGGGTTGGGGAAGAAAA+AGG + chr7_1:33513355-33513374 None:intergenic 45.0%
!! TTTGAGAGGTGAATGGGTTG+GGG + chr7_1:33513365-33513384 None:intergenic 45.0%
! GTTTGAGAGGTGAATGGGTT+GGG + chr7_1:33513366-33513385 None:intergenic 45.0%
TGGTGGTTTGAGAGGTGAAT+GGG + chr7_1:33513371-33513390 None:intergenic 45.0%
! TTGGTGGTTTGAGAGGTGAA+TGG + chr7_1:33513372-33513391 None:intergenic 45.0%
!! TAGCTTGGTGGGGTTGTTTT+GGG + chr7_1:33513460-33513479 None:intergenic 45.0%
! CGTTACCGTGATCGATTCAA+TGG - chr7_1:33513488-33513507 Msa1016570:CDS 45.0%
TCAATGGTCAAGCTTGGCAT+CGG - chr7_1:33513504-33513523 Msa1016570:CDS 45.0%
GTGATTCCCTATCGACAACT+TGG - chr7_1:33513541-33513560 Msa1016570:CDS 45.0%
CAATCGCCAAGTTGTCGATA+GGG + chr7_1:33513550-33513569 None:intergenic 45.0%
! ATTGCTCTGGACTACTGAGA+AGG - chr7_1:33513566-33513585 Msa1016570:CDS 45.0%
!! GAAAAAGGAAGTGGTGGTGG+CGG + chr7_1:33513340-33513359 None:intergenic 50.0%
GGGGAAGAAAAAGGAAGTGG+TGG + chr7_1:33513346-33513365 None:intergenic 50.0%
GGTTTGAGAGGTGAATGGGT+TGG + chr7_1:33513367-33513386 None:intergenic 50.0%
!!! GGCGGTTAGTCTTTTGTTGG+TGG + chr7_1:33513388-33513407 None:intergenic 50.0%
! GGTGAGGAGGTTCTTTTTGG+CGG + chr7_1:33513406-33513425 None:intergenic 50.0%
! GAGGGTGAGGAGGTTCTTTT+TGG + chr7_1:33513409-33513428 None:intergenic 50.0%
ACGGTCTTGGTCAGAGATGA+GGG + chr7_1:33513427-33513446 None:intergenic 50.0%
!! TGTTTTGGGTCTTGAGGCCA+CGG + chr7_1:33513446-33513465 None:intergenic 50.0%
!!! TGGGGTTGTTTTGGGTCTTG+AGG + chr7_1:33513452-33513471 None:intergenic 50.0%
!! CTAGCTTGGTGGGGTTGTTT+TGG + chr7_1:33513461-33513480 None:intergenic 50.0%
! ACGATCGACACTAGCTTGGT+GGG + chr7_1:33513471-33513490 None:intergenic 50.0%
! AACGATCGACACTAGCTTGG+TGG + chr7_1:33513472-33513491 None:intergenic 50.0%
GGTAACGATCGACACTAGCT+TGG + chr7_1:33513475-33513494 None:intergenic 50.0%
TGTCGATAGGGAATCACCAG+TGG + chr7_1:33513538-33513557 None:intergenic 50.0%
GCAATCGCCAAGTTGTCGAT+AGG + chr7_1:33513551-33513570 None:intergenic 50.0%
CTTGGTCAGAGATGAGGGTG+AGG + chr7_1:33513422-33513441 None:intergenic 55.0%
CACGGTCTTGGTCAGAGATG+AGG + chr7_1:33513428-33513447 None:intergenic 55.0%
CTCATCTCTGACCAAGACCG+TGG - chr7_1:33513426-33513445 Msa1016570:CDS 55.0%
! CGATCGACACTAGCTTGGTG+GGG + chr7_1:33513470-33513489 None:intergenic 55.0%
!! GGCATCGGTACAGTAACCAC+TGG - chr7_1:33513519-33513538 Msa1016570:CDS 55.0%
CGACAACTTGGCGATTGCTC+TGG - chr7_1:33513553-33513572 Msa1016570:CDS 55.0%
!! AAAGGAAGTGGTGGTGGCGG+TGG + chr7_1:33513337-33513356 None:intergenic 60.0%
GGTCAGAGATGAGGGTGAGG+AGG + chr7_1:33513419-33513438 None:intergenic 60.0%
GGGTCTTGAGGCCACGGTCT+TGG + chr7_1:33513440-33513459 None:intergenic 65.0%
!! AGTGGTGGTGGCGGTGGTGG+TGG + chr7_1:33513331-33513350 None:intergenic 70.0%
!! GGAAGTGGTGGTGGCGGTGG+TGG + chr7_1:33513334-33513353 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 33513309 33513719 33513309 ID=Msa1016570;Name=Msa1016570
chr7_1 mRNA 33513309 33513719 33513309 ID=Msa1016570-mRNA-1;Parent=Msa1016570;Name=Msa1016570-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|136
chr7_1 exon 33513309 33513719 33513309 ID=Msa1016570-mRNA-1:exon:6517;Parent=Msa1016570-mRNA-1
chr7_1 CDS 33513309 33513719 33513309 ID=Msa1016570-mRNA-1:cds;Parent=Msa1016570-mRNA-1
Gene Sequence

>Msa1016570

ATGAAACTCAACTCAATCACCACCACCACCGCCACCACCACTTCCTTTTTCTTCCCCAACCCATTCACCTCTCAAACCACCAACAAAAGACTAACCGCCAAAAAGAACCTCCTCACCCTCATCTCTGACCAAGACCGTGGCCTCAAGACCCAAAACAACCCCACCAAGCTAGTGTCGATCGTTACCGTGATCGATTCAATGGTCAAGCTTGGCATCGGTACAGTAACCACTGGTGATTCCCTATCGACAACTTGGCGATTGCTCTGGACTACTGAGAAGGAGCAGTTGTTCATCATTGAGAAGGCTGGATTGTTTGGAACTAAAGCTGGAGATGTTTTACAGGTTATTGATGTGAAGAATTTGAGTCTTAACAATGTTATTACTTTTCCTCCTGATGGTTTTTTTTTTTGA
Protein sequence

>Msa1016570

MKLNSITTTTATTTSFFFPNPFTSQTTNKRLTAKKNLLTLISDQDRGLKTQNNPTKLVSIVTVIDSMVKLGIGTVTTGDSLSTTWRLLWTTEKEQLFIIEKAGLFGTKAGDVLQVIDVKNLSLNNVITFPPDGFFF*