AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene94537

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94537.t1 MTR_3g025510 52.564 156 66 4 1 151 1 153 3.56e-41 135
MS.gene94537.t1 MTR_3g025620 87.719 57 4 1 99 152 1 57 3.10e-28 99.8
MS.gene94537.t1 MTR_3g025380 45.455 154 67 5 1 150 1 141 6.06e-27 99.0
MS.gene94537.t1 MTR_3g025550 54.688 64 26 1 90 150 1 64 2.44e-18 74.7
MS.gene94537.t1 MTR_2g058360 53.623 69 29 2 83 148 73 141 1.85e-16 72.0
MS.gene94537.t1 MTR_5g041310 33.766 77 50 1 69 144 80 156 2.56e-11 60.1
MS.gene94537.t1 MTR_5g041330 40.000 55 33 0 90 144 92 146 2.60e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94537.t1 AT3G10815 41.667 60 32 1 89 145 104 163 7.41e-11 58.5
MS.gene94537.t1 AT1G60360 46.667 45 24 0 101 145 222 266 7.45e-11 59.7

Find 22 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTGCATGAACGAGATTT+TGG 0.201759 3.2:+15673242 MS.gene94537:CDS
ATGAAGAGTGTATTGTAAAA+TGG 0.302625 3.2:+15673421 MS.gene94537:CDS
GATTGTGACCAAGATGTCTT+TGG 0.344275 3.2:-15673290 None:intergenic
ATAAGCACGTAAGACATTAT+AGG 0.361737 3.2:-15673208 None:intergenic
GTCCGAAGCTTCTATATGTT+TGG 0.391153 3.2:+15673344 MS.gene94537:CDS
TCGGTTGCAACACTTCTTGT+AGG 0.395824 3.2:-15673063 None:intergenic
CATAATTGAATTGTTGTCTT+CGG 0.406577 3.2:-15673082 None:intergenic
TTCTGAACCTTCTTGATGAC+GGG 0.406773 3.2:-15673158 None:intergenic
CGCCAAACATATAGAAGCTT+CGG 0.444454 3.2:-15673346 None:intergenic
TGTTTGGCGGATCTCTCGGT+TGG 0.458821 3.2:+15673360 MS.gene94537:CDS
TATATGTTTGGCGGATCTCT+CGG 0.463458 3.2:+15673356 MS.gene94537:CDS
CTTCTGAACCTTCTTGATGA+CGG 0.466963 3.2:-15673159 None:intergenic
GAAACAAACCAAAGACATCT+TGG 0.470596 3.2:+15673282 MS.gene94537:CDS
CTTCTACAAATAATGCGATA+GGG 0.511833 3.2:-15673129 None:intergenic
TCTTCTACAAATAATGCGAT+AGG 0.512827 3.2:-15673130 None:intergenic
GTTTGGCGGATCTCTCGGTT+GGG 0.520272 3.2:+15673361 MS.gene94537:CDS
CGAAGCTTCTATATGTTTGG+CGG 0.523704 3.2:+15673347 MS.gene94537:CDS
TTCTACAAATAATGCGATAG+GGG 0.558963 3.2:-15673128 None:intergenic
TGAACCTTCTTGATGACGGG+TGG 0.560392 3.2:-15673155 None:intergenic
AAACAATACGACGACACAAA+GGG 0.563961 3.2:-15673464 None:intergenic
GATTCCACCCGTCATCAAGA+AGG 0.580470 3.2:+15673151 MS.gene94537:CDS
GAAACAATACGACGACACAA+AGG 0.619273 3.2:-15673465 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAAAATCAAAATTGATGA+AGG + chr3.2:15673315-15673334 MS.gene94537:CDS 20.0%
!!! ATTGTTTCTGATTTTTCTTT+GGG + chr3.2:15673480-15673499 MS.gene94537:CDS 20.0%
!!! TATTGTTTCTGATTTTTCTT+TGG + chr3.2:15673479-15673498 MS.gene94537:CDS 20.0%
! CATAATTGAATTGTTGTCTT+CGG - chr3.2:15673085-15673104 None:intergenic 25.0%
!! ATGAAGAGTGTATTGTAAAA+TGG + chr3.2:15673421-15673440 MS.gene94537:CDS 25.0%
!! ATTTTACAATACACTCTTCA+TGG - chr3.2:15673422-15673441 None:intergenic 25.0%
ATAAGCACGTAAGACATTAT+AGG - chr3.2:15673211-15673230 None:intergenic 30.0%
CTTCTACAAATAATGCGATA+GGG - chr3.2:15673132-15673151 None:intergenic 30.0%
TCTTCTACAAATAATGCGAT+AGG - chr3.2:15673133-15673152 None:intergenic 30.0%
TTCTACAAATAATGCGATAG+GGG - chr3.2:15673131-15673150 None:intergenic 30.0%
AAACAATACGACGACACAAA+GGG - chr3.2:15673467-15673486 None:intergenic 35.0%
GAAACAAACCAAAGACATCT+TGG + chr3.2:15673282-15673301 MS.gene94537:CDS 35.0%
CGAAGCTTCTATATGTTTGG+CGG + chr3.2:15673347-15673366 MS.gene94537:CDS 40.0%
CGCCAAACATATAGAAGCTT+CGG - chr3.2:15673349-15673368 None:intergenic 40.0%
CTTCTGAACCTTCTTGATGA+CGG - chr3.2:15673162-15673181 None:intergenic 40.0%
GAAACAATACGACGACACAA+AGG - chr3.2:15673468-15673487 None:intergenic 40.0%
GATTGTGACCAAGATGTCTT+TGG - chr3.2:15673293-15673312 None:intergenic 40.0%
GTCCGAAGCTTCTATATGTT+TGG + chr3.2:15673344-15673363 MS.gene94537:CDS 40.0%
! CAACTGCATGAACGAGATTT+TGG + chr3.2:15673242-15673261 MS.gene94537:CDS 40.0%
! TATATGTTTGGCGGATCTCT+CGG + chr3.2:15673356-15673375 MS.gene94537:CDS 40.0%
! TTCTGAACCTTCTTGATGAC+GGG - chr3.2:15673161-15673180 None:intergenic 40.0%
TCGGTTGCAACACTTCTTGT+AGG - chr3.2:15673066-15673085 None:intergenic 45.0%
GATTCCACCCGTCATCAAGA+AGG + chr3.2:15673151-15673170 MS.gene94537:CDS 50.0%
!! TGAACCTTCTTGATGACGGG+TGG - chr3.2:15673158-15673177 None:intergenic 50.0%
! GTTTGGCGGATCTCTCGGTT+GGG + chr3.2:15673361-15673380 MS.gene94537:CDS 55.0%
! TGTTTGGCGGATCTCTCGGT+TGG + chr3.2:15673360-15673379 MS.gene94537:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 15673045 15673533 15673045 ID=MS.gene94537
chr3.2 mRNA 15673045 15673533 15673045 ID=MS.gene94537.t1;Parent=MS.gene94537
chr3.2 exon 15673045 15673533 15673045 ID=MS.gene94537.t1.exon1;Parent=MS.gene94537.t1
chr3.2 CDS 15673045 15673533 15673045 ID=cds.MS.gene94537.t1;Parent=MS.gene94537.t1
Gene Sequence

>MS.gene94537

ATGGAGCAACAACAACTTCCTACAAGAAGTGTTGCAACCGAAGACAACAATTCAATTATGAGTCTTGATGATATTGATCTAAACCCCTATCGCATTATTTGTAGAAGATTCCACCCGTCATCAAGAAGGTTCAGAAGAAATCACATTCAAACAAGAATTGCTACCTATAATGTCTTACGTGCTTATGTAAACAACATCAACTGCATGAACGAGATTTTGGCGAGTACAAGAAATGTTGAAACAAACCAAAGACATCTTGGTCACAATCTTTCAAAAATCAAAATTGATGAAGGAATGAAGTCCGAAGCTTCTATATGTTTGGCGGATCTCTCGGTTGGGTCGATAGCAATTCAGTTGTCATGTTCGCATTTGTACCATGAAGAGTGTATTGTAAAATGGCTCGATAGATCAAACACTTGCCCTTTGTGTCGTCGTATTGTTTCTGATTTTTCTTTGGGACATGATTCATTCGACATTTATTTTTGTTAA
Protein sequence

>MS.gene94537.t1

MEQQQLPTRSVATEDNNSIMSLDDIDLNPYRIICRRFHPSSRRFRRNHIQTRIATYNVLRAYVNNINCMNEILASTRNVETNQRHLGHNLSKIKIDEGMKSEASICLADLSVGSIAIQLSCSHLYHEECIVKWLDRSNTCPLCRRIVSDFSLGHDSFDIYFC