AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065955

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065955.t1 MTR_4g039380 78.632 117 17 2 1 109 1 117 4.32e-54 164
MS.gene065955.t1 MTR_4g039340 70.229 131 17 2 1 109 1 131 6.00e-52 160
MS.gene065955.t1 MTR_4g039640 78.632 117 17 2 1 109 1 117 2.97e-48 150
MS.gene065955.t1 MTR_4g039400 41.818 110 35 2 1 109 1 82 2.20e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4.3:+61313642 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.3:+61313462 None:intergenic
CTAGATTCTAATATATAATC+TGG 0.344499 4.3:+61313681 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.3:+61313463 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4.3:+61313648 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 4.3:+61313489 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.3:+61313510 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4.3:+61313645 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 4.3:+61313496 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.3:+61313522 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.3:+61313528 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.3:+61313726 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.3:+61313472 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 4.3:+61313492 None:intergenic
ATATTAGAATCTAGTAAACA+AGG 0.648272 4.3:-61313672 MS.gene065955:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.3:+61313525 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAGAATCTAGTAAACA+AGG - chr4.3:61313563-61313582 MS.gene065955:CDS 20.0%
!! CTAGATTCTAATATATAATC+TGG + chr4.3:61313557-61313576 None:intergenic 20.0%
! TGATGTTCAACATTTTGTGG+TGG + chr4.3:61313632-61313651 None:intergenic 35.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.3:61313629-61313648 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.3:61313635-61313654 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.3:61313716-61313735 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG + chr4.3:61313512-61313531 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.3:61313766-61313785 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.3:61313713-61313732 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG + chr4.3:61313749-61313768 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr4.3:61313596-61313615 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG + chr4.3:61313668-61313687 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.3:61313710-61313729 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG + chr4.3:61313746-61313765 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr4.3:61313728-61313747 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.3:61313593-61313612 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr4.3:61313614-61313633 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.3:61313590-61313609 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.3:61313698-61313717 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr4.3:61313604-61313623 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG + chr4.3:61313608-61313627 None:intergenic 50.0%
CGAAAGCTTGAACAGGAGGC+TGG + chr4.3:61313742-61313761 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.3:61313656-61313675 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 61313464 61313793 61313464 ID=MS.gene065955
chr4.3 mRNA 61313464 61313793 61313464 ID=MS.gene065955.t1;Parent=MS.gene065955
chr4.3 exon 61313464 61313793 61313464 ID=MS.gene065955.t1.exon1;Parent=MS.gene065955.t1
chr4.3 CDS 61313464 61313793 61313464 ID=cds.MS.gene065955.t1;Parent=MS.gene065955.t1
Gene Sequence

>MS.gene065955

ATGTCAAAGCAAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCTAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene065955.t1

MSKQEFLCSECDTMFPSREALAVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEHQPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE