AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0030850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0030850 MtrunA17_Chr5g0420351 68.421 57 18 0 1 57 1 57 1.40e-21 81.3
Msa0030850 MtrunA17_Chr1g0197461 63.636 55 20 0 3 57 2 56 4.59e-19 74.7
Msa0030850 MtrunA17_Chr1g0197321 57.895 57 24 0 1 57 1 57 4.10e-17 69.7
Msa0030850 MtrunA17_Chr1g0188681 59.649 57 23 0 1 57 1 57 6.05e-17 69.3
Msa0030850 MtrunA17_Chr4g0012761 68.421 57 18 0 1 57 1 57 1.49e-16 68.6
Msa0030850 MtrunA17_Chr1g0188661 64.912 57 20 0 1 57 1 57 2.97e-16 67.8
Msa0030850 MtrunA17_Chr1g0197261 56.140 57 25 0 1 57 1 57 1.98e-15 65.5
Msa0030850 MtrunA17_Chr1g0188651 63.158 57 21 0 1 57 1 57 5.05e-15 64.3
Msa0030850 MtrunA17_Chr7g0218151 63.158 57 21 0 1 57 1 57 5.30e-15 64.3
Msa0030850 MtrunA17_Chr1g0193311 63.158 57 21 0 1 57 1 57 1.32e-14 63.2
Msa0030850 MtrunA17_Chr8g0351751 45.614 57 31 0 1 57 1 57 2.85e-12 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0030850 AT3G05860.2 47.368 57 30 0 1 57 1 57 2.62e-13 61.2
Msa0030850 AT3G05860.3 47.368 57 30 0 1 57 1 57 6.31e-13 60.8
Msa0030850 AT3G05860.1 47.368 57 30 0 1 57 1 57 6.66e-13 60.8

Find 13 sgRNAs with CRISPR-Local

Find 11 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGAACTCAATATTCTTTA+TGG 0.214259 1_1:+57340413 Msa0030850:CDS
AGCCTTCCTTGCTAAATAAT+TGG 0.275040 1_1:-57340351 None:intergenic
TGCTAAATAATTGGAGATAA+AGG 0.292175 1_1:-57340342 None:intergenic
CTCCAATTATTTAGCAAGGA+AGG 0.449283 1_1:+57340349 Msa0030850:CDS
GCAAGGCCATGGCTAGGAGT+AGG 0.521343 1_1:+57340309 None:intergenic
CAAGGCCATGGCTAGGAGTA+GGG 0.537523 1_1:+57340310 None:intergenic
TGCCTACATGCGGAGAAAGA+AGG 0.549399 1_1:+57340373 Msa0030850:CDS
TGCATTGCAAGGCCATGGCT+AGG 0.571000 1_1:+57340303 None:intergenic
TTATCTCCAATTATTTAGCA+AGG 0.573320 1_1:+57340345 Msa0030850:CDS
AAAGAAGGCTCTCTTTGAGA+AGG 0.588827 1_1:+57340388 Msa0030850:CDS
TTTCACCCTACTCCTAGCCA+TGG 0.617946 1_1:-57340315 None:intergenic
CAAGGAAGGCTGCCTACATG+CGG 0.644135 1_1:+57340363 Msa0030850:CDS
AGCCTTCTTTCTCCGCATGT+AGG 0.644142 1_1:-57340375 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTAAATAATTGGAGATAA+AGG - chr1_1:57340345-57340364 None:intergenic 25.0%
! TTATCTCCAATTATTTAGCA+AGG + chr1_1:57340345-57340364 Msa0030850:CDS 25.0%
! AGAGAACTCAATATTCTTTA+TGG + chr1_1:57340413-57340432 Msa0030850:CDS 25.0%
!!! TCCTTTTAATTCTAAAACAG+AGG + chr1_1:57340463-57340482 Msa0030850:CDS 25.0%
!!! ACCTCTGTTTTAGAATTAAA+AGG - chr1_1:57340467-57340486 None:intergenic 25.0%
CTCCAATTATTTAGCAAGGA+AGG + chr1_1:57340349-57340368 Msa0030850:CDS 35.0%
AGCCTTCCTTGCTAAATAAT+TGG - chr1_1:57340354-57340373 None:intergenic 35.0%
! AAAGAAGGCTCTCTTTGAGA+AGG + chr1_1:57340388-57340407 Msa0030850:CDS 40.0%
TGCCTACATGCGGAGAAAGA+AGG + chr1_1:57340373-57340392 Msa0030850:CDS 50.0%
AGCCTTCTTTCTCCGCATGT+AGG - chr1_1:57340378-57340397 None:intergenic 50.0%
CAAGGAAGGCTGCCTACATG+CGG + chr1_1:57340363-57340382 Msa0030850:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 57340317 57340490 57340317 ID=Msa0030850;Name=Msa0030850
chr1_1 mRNA 57340317 57340490 57340317 ID=Msa0030850-mRNA-1;Parent=Msa0030850;Name=Msa0030850-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|57
chr1_1 exon 57340317 57340490 57340317 ID=Msa0030850-mRNA-1:exon:17324;Parent=Msa0030850-mRNA-1
chr1_1 CDS 57340317 57340490 57340317 ID=Msa0030850-mRNA-1:cds;Parent=Msa0030850-mRNA-1
Gene Sequence

>Msa0030850

ATGGCTAGGAGTAGGGTGAAACTTGCCTTTATCTCCAATTATTTAGCAAGGAAGGCTGCCTACATGCGGAGAAAGAAGGCTCTCTTTGAGAAGGTGAGAGAACTCAATATTCTTTATGGTATTTCAGCATGTGTTCTAATTTCTAATCCTTTTAATTCTAAAACAGAGGTGTGA
Protein sequence

>Msa0030850

MARSRVKLAFISNYLARKAAYMRRKKALFEKVRELNILYGISACVLISNPFNSKTEV*