AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1169550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1169550 MtrunA17_Chr8g0392101 55.769 52 23 0 3 54 48 99 1.20e-15 66.2
Msa1169550 MtrunA17_Chr4g0075191 53.846 52 24 0 3 54 631 682 1.45e-14 67.0
Msa1169550 MtrunA17_Chr2g0327491 59.184 49 20 0 6 54 1 49 2.54e-14 61.2
Msa1169550 MtrunA17_Chr5g0411291 50.000 52 26 0 3 54 565 616 2.72e-14 66.2
Msa1169550 MtrunA17_Chr8g0354181 51.562 64 31 0 3 66 190 253 7.85e-14 64.7
Msa1169550 MtrunA17_Chr6g0479711 47.458 59 31 0 3 61 39 97 1.46e-13 60.5
Msa1169550 MtrunA17_Chr5g0447591 50.943 53 26 0 9 61 3 55 2.00e-13 58.9
Msa1169550 MtrunA17_Chr8g0336101 51.923 52 25 0 3 54 163 214 1.48e-12 60.5
Msa1169550 MtrunA17_Chr5g0423411 50.000 58 29 0 6 63 457 514 2.14e-12 60.8
Msa1169550 MtrunA17_Chr7g0243691 48.980 49 25 0 6 54 42 90 8.45e-12 56.2
Msa1169550 MtrunA17_Chr5g0397461 65.306 49 17 0 6 54 7 55 1.05e-11 54.7
Msa1169550 MtrunA17_Chr8g0383421 49.020 51 26 0 3 53 124 174 2.23e-11 56.6
Msa1169550 MtrunA17_Chr7g0267681 42.308 52 30 0 3 54 26 77 2.53e-11 54.7
Msa1169550 MtrunA17_Chr5g0423161 53.488 43 20 0 12 54 3 45 4.31e-11 53.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGACACATAACAATATT+TGG 0.095345 7_4:+62595188 None:intergenic
ATAACAATATTTGGGTTATT+TGG 0.130012 7_4:+62595197 Msa1169550:CDS
TTTAGTAGGTTCAGCAATTA+TGG 0.180567 7_4:+62595722 Msa1169550:intron
AGCAAAGCCGCACGCAAGCC+TGG 0.347113 7_4:-62595560 None:intergenic
TGTTCGGTGGGAGGCTCTCC+AGG 0.371380 7_4:+62595542 Msa1169550:CDS
AATGACACATAACAATATTT+GGG 0.382379 7_4:+62595189 None:intergenic
TTCAAACCCACTCGTAAAAC+AGG 0.411499 7_4:-62595336 None:intergenic
TGCGTGCGGCTTTGCTGTTT+AGG 0.415135 7_4:+62595567 Msa1169550:CDS
TTGACTTGGAGATGGTTGTC+AGG 0.424578 7_4:+62595292 Msa1169550:CDS
TTTGGGTTATTTGGAGAGCT+AGG 0.426784 7_4:+62595206 Msa1169550:CDS
TTAGTAGGTTCAGCAATTAT+GGG 0.431171 7_4:+62595723 Msa1169550:intron
GTGCTGCAGTATACTGCTGC+AGG 0.451649 7_4:+62595515 Msa1169550:intron
TCAATGCGGTTGTGAAAAGA+TGG 0.472987 7_4:+62595242 Msa1169550:CDS
TACTGCTGCAGGGTGCTGTT+CGG 0.473609 7_4:+62595526 Msa1169550:CDS
CAATTATGGGTGTTGACGTA+GGG 0.483160 7_4:+62595736 Msa1169550:CDS
TGCTGCAGGGTGCTGTTCGG+TGG 0.502269 7_4:+62595529 Msa1169550:CDS
GCTGCAGGGTGCTGTTCGGT+GGG 0.514881 7_4:+62595530 Msa1169550:CDS
ACGAGATCAAGGTGTTGACT+TGG 0.548103 7_4:+62595278 Msa1169550:CDS
GCAATTATGGGTGTTGACGT+AGG 0.551542 7_4:+62595735 Msa1169550:CDS
GCAGGGTGCTGTTCGGTGGG+AGG 0.552219 7_4:+62595533 Msa1169550:CDS
TGCGGCTTTGCTGTTTAGGA+AGG 0.553113 7_4:+62595571 Msa1169550:CDS
AGAGGTGGTAGACGAGATCA+AGG 0.580064 7_4:+62595267 Msa1169550:CDS
TGCTGCAGTATACTGCTGCA+GGG 0.582602 7_4:+62595516 Msa1169550:intron
CAATGCGGTTGTGAAAAGAT+GGG 0.615268 7_4:+62595243 Msa1169550:CDS
TCAAGGTGTTGACTTGGAGA+TGG 0.617912 7_4:+62595284 Msa1169550:CDS
TGTGAAAAGATGGGAAGAGG+TGG 0.635735 7_4:+62595252 Msa1169550:CDS
TGACTTGGAGATGGTTGTCA+GGG 0.640187 7_4:+62595293 Msa1169550:CDS
AATTATGGGTGTTGACGTAG+GGG 0.644593 7_4:+62595737 Msa1169550:CDS
GGTTGTGAAAAGATGGGAAG+AGG 0.645183 7_4:+62595249 Msa1169550:CDS
ACCCACTCGTAAAACAGGCA+CGG 0.645325 7_4:-62595331 None:intergenic
AGGCTCTCCAGGCTTGCGTG+CGG 0.652658 7_4:+62595553 Msa1169550:CDS
GAATGATAGCATCTTCAATG+CGG 0.737371 7_4:+62595228 Msa1169550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAACAATATTTGGGTTATT+TGG + chr7_4:62595197-62595216 Msa1169550:CDS 20.0%
! GACTGTATGATTAGATAATT+TGG + chr7_4:62595367-62595386 Msa1169550:intron 25.0%
! TGATTAGATAATTTGGTGAC+AGG + chr7_4:62595374-62595393 Msa1169550:intron 30.0%
TTTAGTAGGTTCAGCAATTA+TGG + chr7_4:62595722-62595741 Msa1169550:intron 30.0%
TTAGTAGGTTCAGCAATTAT+GGG + chr7_4:62595723-62595742 Msa1169550:intron 30.0%
GAATGATAGCATCTTCAATG+CGG + chr7_4:62595228-62595247 Msa1169550:CDS 35.0%
TATCTAATCATACAGTCACG+TGG - chr7_4:62595364-62595383 None:intergenic 35.0%
AAAAACCTGCTAAAAACCAC+AGG - chr7_4:62595691-62595710 None:intergenic 35.0%
!!! GTGGTTTTTAGCAGGTTTTT+TGG + chr7_4:62595691-62595710 Msa1169550:intron 35.0%
! TTTGGGTTATTTGGAGAGCT+AGG + chr7_4:62595206-62595225 Msa1169550:CDS 40.0%
TCAATGCGGTTGTGAAAAGA+TGG + chr7_4:62595242-62595261 Msa1169550:CDS 40.0%
CAATGCGGTTGTGAAAAGAT+GGG + chr7_4:62595243-62595262 Msa1169550:CDS 40.0%
TTCAAACCCACTCGTAAAAC+AGG - chr7_4:62595339-62595358 None:intergenic 40.0%
! GAAGGATGCTGCTGTATTTT+TGG + chr7_4:62595589-62595608 Msa1169550:intron 40.0%
!!! ATGCTGCTGTATTTTTGGTG+TGG + chr7_4:62595594-62595613 Msa1169550:intron 40.0%
!!! TTTAGCAGGTTTTTTGGCAC+TGG + chr7_4:62595697-62595716 Msa1169550:intron 40.0%
!!! TTTTGGCACTGGTCTTTAGT+AGG + chr7_4:62595708-62595727 Msa1169550:intron 40.0%
GGTTGTGAAAAGATGGGAAG+AGG + chr7_4:62595249-62595268 Msa1169550:CDS 45.0%
TGTGAAAAGATGGGAAGAGG+TGG + chr7_4:62595252-62595271 Msa1169550:CDS 45.0%
!! ACGAGATCAAGGTGTTGACT+TGG + chr7_4:62595278-62595297 Msa1169550:CDS 45.0%
!! TCAAGGTGTTGACTTGGAGA+TGG + chr7_4:62595284-62595303 Msa1169550:CDS 45.0%
!! TTGACTTGGAGATGGTTGTC+AGG + chr7_4:62595292-62595311 Msa1169550:CDS 45.0%
! TGACTTGGAGATGGTTGTCA+GGG + chr7_4:62595293-62595312 Msa1169550:CDS 45.0%
GCATACCAGTACACAGCAAA+GGG - chr7_4:62595466-62595485 None:intergenic 45.0%
AGCATACCAGTACACAGCAA+AGG - chr7_4:62595467-62595486 None:intergenic 45.0%
! TGTGTACTGGTATGCTGTGT+TGG + chr7_4:62595471-62595490 Msa1169550:intron 45.0%
! GTGTACTGGTATGCTGTGTT+GGG + chr7_4:62595472-62595491 Msa1169550:intron 45.0%
! TGTACTGGTATGCTGTGTTG+GGG + chr7_4:62595473-62595492 Msa1169550:intron 45.0%
!!! TATTTTTGGTGTGGTGCTGC+AGG + chr7_4:62595603-62595622 Msa1169550:intron 45.0%
!!! AGGTTCCTGTGGTTTTTAGC+AGG + chr7_4:62595683-62595702 Msa1169550:intron 45.0%
AGAGGTGGTAGACGAGATCA+AGG + chr7_4:62595267-62595286 Msa1169550:CDS 50.0%
ACCCACTCGTAAAACAGGCA+CGG - chr7_4:62595334-62595353 None:intergenic 50.0%
! TTGGTGACAGGTTGTGTAGC+AGG + chr7_4:62595386-62595405 Msa1169550:intron 50.0%
TGGTGACAGGTTGTGTAGCA+GGG + chr7_4:62595387-62595406 Msa1169550:intron 50.0%
! TTGCCTTCTGCTTGCGGTTT+TGG + chr7_4:62595427-62595446 Msa1169550:intron 50.0%
! TTCCTCCCTTTGCTGTGTAC+TGG + chr7_4:62595458-62595477 Msa1169550:intron 50.0%
TACCAGTACACAGCAAAGGG+AGG - chr7_4:62595463-62595482 None:intergenic 50.0%
TGCTGCAGTATACTGCTGCA+GGG + chr7_4:62595516-62595535 Msa1169550:intron 50.0%
!! TGCGGCTTTGCTGTTTAGGA+AGG + chr7_4:62595571-62595590 Msa1169550:CDS 50.0%
TCACAGACAGCAGCACTCAA+AGG - chr7_4:62595655-62595674 None:intergenic 50.0%
TGCTGCTGTCTGTGATTGCT+GGG + chr7_4:62595660-62595679 Msa1169550:intron 50.0%
! GCCGTGCCTGTTTTACGAGT+GGG + chr7_4:62595330-62595349 Msa1169550:CDS 55.0%
AGGTTGTGTAGCAGGGCTGT+TGG + chr7_4:62595394-62595413 Msa1169550:intron 55.0%
! TGTAGCAGGGCTGTTGGTCT+CGG + chr7_4:62595400-62595419 Msa1169550:intron 55.0%
GGCAGTTTGCCTTCTGCTTG+CGG + chr7_4:62595421-62595440 Msa1169550:intron 55.0%
CTGCCAAAACCGCAAGCAGA+AGG - chr7_4:62595433-62595452 None:intergenic 55.0%
ACACAGCAAAGGGAGGAAGC+AGG - chr7_4:62595456-62595475 None:intergenic 55.0%
! CTGTGTTGGGGTGTCTCTAC+TGG + chr7_4:62595485-62595504 Msa1169550:intron 55.0%
GTGCTGCAGTATACTGCTGC+AGG + chr7_4:62595515-62595534 Msa1169550:intron 55.0%
!! TACTGCTGCAGGGTGCTGTT+CGG + chr7_4:62595526-62595545 Msa1169550:CDS 55.0%
!! TGCGTGCGGCTTTGCTGTTT+AGG + chr7_4:62595567-62595586 Msa1169550:CDS 55.0%
! GTGCTGCTGTCTGTGATTGC+TGG + chr7_4:62595659-62595678 Msa1169550:intron 55.0%
TGCTGTCTGTGATTGCTGGG+AGG + chr7_4:62595663-62595682 Msa1169550:intron 55.0%
TGATTGCTGGGAGGTTCCTG+TGG + chr7_4:62595672-62595691 Msa1169550:intron 55.0%
! CGCCGTGCCTGTTTTACGAG+TGG + chr7_4:62595329-62595348 Msa1169550:CDS 60.0%
!! TGCTGCAGGGTGCTGTTCGG+TGG + chr7_4:62595529-62595548 Msa1169550:CDS 65.0%
!! GCTGCAGGGTGCTGTTCGGT+GGG + chr7_4:62595530-62595549 Msa1169550:CDS 65.0%
! TGTTCGGTGGGAGGCTCTCC+AGG + chr7_4:62595542-62595561 Msa1169550:CDS 65.0%
AGGCTCTCCAGGCTTGCGTG+CGG + chr7_4:62595553-62595572 Msa1169550:CDS 65.0%
AGCAAAGCCGCACGCAAGCC+TGG - chr7_4:62595563-62595582 None:intergenic 65.0%
!! GCAGGGTGCTGTTCGGTGGG+AGG + chr7_4:62595533-62595552 Msa1169550:CDS 70.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 62595190 62595756 62595190 ID=Msa1169550;Name=Msa1169550
chr7_4 mRNA 62595190 62595756 62595190 ID=Msa1169550-mRNA-1;Parent=Msa1169550;Name=Msa1169550-mRNA-1;_AED=0.65;_eAED=0.65;_QI=0|0|0|0.33|0|0.33|3|0|88
chr7_4 exon 62595190 62595351 62595190 ID=Msa1169550-mRNA-1:exon:19885;Parent=Msa1169550-mRNA-1
chr7_4 exon 62595524 62595601 62595524 ID=Msa1169550-mRNA-1:exon:19886;Parent=Msa1169550-mRNA-1
chr7_4 exon 62595730 62595756 62595730 ID=Msa1169550-mRNA-1:exon:19887;Parent=Msa1169550-mRNA-1
chr7_4 CDS 62595190 62595351 62595190 ID=Msa1169550-mRNA-1:cds;Parent=Msa1169550-mRNA-1
chr7_4 CDS 62595524 62595601 62595524 ID=Msa1169550-mRNA-1:cds;Parent=Msa1169550-mRNA-1
chr7_4 CDS 62595730 62595756 62595730 ID=Msa1169550-mRNA-1:cds;Parent=Msa1169550-mRNA-1
Gene Sequence

>Msa1169550

ATGACACATAACAATATTTGGGTTATTTGGAGAGCTAGGAATGATAGCATCTTCAATGCGGTTGTGAAAAGATGGGAAGAGGTGGTAGACGAGATCAAGGTGTTGACTTGGAGATGGTTGTCAGGGAGAAGCAAAGTGTCGCCGTGCCTGTTTTACGAGTGGTATACTGCTGCAGGGTGCTGTTCGGTGGGAGGCTCTCCAGGCTTGCGTGCGGCTTTGCTGTTTAGGAAGGATGCTGCTGTTCAGCAATTATGGGTGTTGACGTAG

Protein sequence

>Msa1169550

MTHNNIWVIWRARNDSIFNAVVKRWEEVVDEIKVLTWRWLSGRSKVSPCLFYEWYTAAGCCSVGGSPGLRAALLFRKDAAVQQLWVLT*