AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006234

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006234.t1 MTR_1g105960 53.571 56 26 0 6 61 13 68 9.05e-14 60.8
MS.gene006234.t1 MTR_5g036670 50.000 60 30 0 6 65 55 114 7.21e-13 61.6
MS.gene006234.t1 MTR_6g008970 49.153 59 30 0 6 64 75 133 1.67e-12 60.5
MS.gene006234.t1 MTR_1g105955 57.447 47 20 0 15 61 116 162 1.80e-12 58.9
MS.gene006234.t1 MTR_1g105955 46.429 56 30 0 2 57 24 79 1.59e-11 56.6
MS.gene006234.t1 MTR_8g062700 46.875 64 34 0 2 65 50 113 3.58e-12 59.7
MS.gene006234.t1 MTR_8g062700 46.875 64 34 0 2 65 50 113 3.72e-12 59.7
MS.gene006234.t1 MTR_3g006185 60.417 48 19 0 14 61 119 166 1.00e-11 57.0
MS.gene006234.t1 MTR_3g006065 60.000 45 18 0 15 59 112 156 2.33e-11 56.2
MS.gene006234.t1 MTR_7g083950 53.061 49 23 0 7 55 27 75 4.49e-11 56.6
MS.gene006234.t1 MTR_7g013410 45.161 62 34 0 2 63 6 67 4.88e-11 54.3
MS.gene006234.t1 MTR_3g006010 55.319 47 21 0 17 63 32 78 5.93e-11 56.2
MS.gene006234.t1 MTR_3g006150 60.000 45 18 0 15 59 112 156 7.15e-11 54.3
MS.gene006234.t1 MTR_4g133470 50.000 58 29 0 6 63 184 241 8.17e-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
MS.gene006234.t1 AT1G24190 46.032 63 34 0 2 64 22 84 2.56e-12 60.1
MS.gene006234.t1 AT1G24190 46.032 63 34 0 2 64 22 84 2.71e-12 60.1
MS.gene006234.t1 AT1G24190 46.032 63 34 0 2 64 22 84 2.88e-12 60.1
MS.gene006234.t1 AT3G01320 46.774 62 33 0 2 63 65 126 8.86e-12 58.5
MS.gene006234.t1 AT3G01320 46.774 62 33 0 2 63 65 126 8.86e-12 58.5
MS.gene006234.t1 AT5G15025 45.763 59 32 0 6 64 59 117 2.26e-11 55.1
MS.gene006234.t1 AT1G70060 46.774 62 33 0 2 63 22 83 3.01e-11 57.0
MS.gene006234.t1 AT1G70060 46.774 62 33 0 2 63 22 83 3.01e-11 57.0
MS.gene006234.t1 AT5G15020 42.857 63 36 0 2 64 60 122 7.92e-11 55.8
MS.gene006234.t1 AT5G15020 42.857 63 36 0 2 64 60 122 8.08e-11 55.8

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCCTCGTCATGGTAGTTC+TGG 0.199501 1.1:+71814786 None:intergenic
TGCCTCGTCATGGTAGTTCT+GGG 0.393485 1.1:+71814787 None:intergenic
AGTTTGATTTGATGTTCCTT+TGG 0.399942 1.1:+71814629 None:intergenic
TGATTTGATGTTCCTTTGGC+AGG 0.443659 1.1:+71814633 None:intergenic
AGAGTCAAGGAGCTGCTTGA+AGG 0.509677 1.1:-71814689 MS.gene006234:CDS
AGGTGCTGCGGCAAGAGTCA+AGG 0.534822 1.1:-71814702 MS.gene006234:CDS
TTGATGTTCCTTTGGCAGGA+AGG 0.538933 1.1:+71814637 None:intergenic
GAGTCAAGGAGCTGCTTGAA+GGG 0.541631 1.1:-71814688 MS.gene006234:CDS
AAAAGTCCTAAAAGATGTGA+AGG 0.543573 1.1:-71814744 MS.gene006234:CDS
CGAGGCAGTACAAGCTAATG+AGG 0.552124 1.1:-71814771 MS.gene006234:CDS
GCCTCGTCATGGTAGTTCTG+GGG 0.562928 1.1:+71814788 None:intergenic
CAAATCAAACTTGAGACCAC+TGG 0.570634 1.1:-71814617 MS.gene006234:CDS
CCTCGTCATGGTAGTTCTGG+GGG 0.607116 1.1:+71814789 None:intergenic
ATTCAATACCTTCCTGCCAA+AGG 0.612236 1.1:-71814645 MS.gene006234:CDS
GATCAAAGAATTTATACAAG+AGG 0.613874 1.1:-71814722 MS.gene006234:CDS
TAGCTTGTACTGCCTCGTCA+TGG 0.617598 1.1:+71814777 None:intergenic
AATTTATACAAGAGGTGCTG+CGG 0.636068 1.1:-71814714 MS.gene006234:CDS
AATGATAAATTACTAACCAG+TGG 0.644366 1.1:+71814601 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTATTATTCTGAATTAT+TGG - chr1.1:71814662-71814681 MS.gene006234:CDS 15.0%
!!! AAAAATCAATTATTCGAGTT+AGG + chr1.1:71814632-71814651 None:intergenic 20.0%
! GATCAAAGAATTTATACAAG+AGG - chr1.1:71814797-71814816 MS.gene006234:intron 25.0%
AAAAGTCCTAAAAGATGTGA+AGG - chr1.1:71814775-71814794 MS.gene006234:CDS 30.0%
! TTTGATCCTTCACATCTTTT+AGG + chr1.1:71814784-71814803 None:intergenic 30.0%
!! AGTTTGATTTGATGTTCCTT+TGG + chr1.1:71814893-71814912 None:intergenic 30.0%
!! AATTTATACAAGAGGTGCTG+CGG - chr1.1:71814805-71814824 MS.gene006234:intron 35.0%
ATTCAATACCTTCCTGCCAA+AGG - chr1.1:71814874-71814893 MS.gene006234:intron 40.0%
CAAATCAAACTTGAGACCAC+TGG - chr1.1:71814902-71814921 MS.gene006234:intron 40.0%
TGATTTGATGTTCCTTTGGC+AGG + chr1.1:71814889-71814908 None:intergenic 40.0%
! CAATTATTCGAGTTAGGACG+AGG + chr1.1:71814626-71814645 None:intergenic 40.0%
TTGATGTTCCTTTGGCAGGA+AGG + chr1.1:71814885-71814904 None:intergenic 45.0%
AGAGTCAAGGAGCTGCTTGA+AGG - chr1.1:71814830-71814849 MS.gene006234:intron 50.0%
CGAGGCAGTACAAGCTAATG+AGG - chr1.1:71814748-71814767 MS.gene006234:CDS 50.0%
GAGTCAAGGAGCTGCTTGAA+GGG - chr1.1:71814831-71814850 MS.gene006234:intron 50.0%
TGCCTCGTCATGGTAGTTCT+GGG + chr1.1:71814735-71814754 None:intergenic 50.0%
! TAGCTTGTACTGCCTCGTCA+TGG + chr1.1:71814745-71814764 None:intergenic 50.0%
CTGCCTCGTCATGGTAGTTC+TGG + chr1.1:71814736-71814755 None:intergenic 55.0%
! GCCTCGTCATGGTAGTTCTG+GGG + chr1.1:71814734-71814753 None:intergenic 55.0%
!! CCTCGTCATGGTAGTTCTGG+GGG + chr1.1:71814733-71814752 None:intergenic 55.0%
CCCCCAGAACTACCATGACG+AGG - chr1.1:71814730-71814749 MS.gene006234:CDS 60.0%
! AGGTGCTGCGGCAAGAGTCA+AGG - chr1.1:71814817-71814836 MS.gene006234:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 71814613 71814928 71814613 ID=MS.gene006234
chr1.1 mRNA 71814613 71814928 71814613 ID=MS.gene006234.t1;Parent=MS.gene006234
chr1.1 exon 71814926 71814928 71814926 ID=MS.gene006234.t1.exon1;Parent=MS.gene006234.t1
chr1.1 CDS 71814926 71814928 71814926 ID=cds.MS.gene006234.t1;Parent=MS.gene006234.t1
chr1.1 exon 71814613 71814813 71814613 ID=MS.gene006234.t1.exon2;Parent=MS.gene006234.t1
chr1.1 CDS 71814613 71814813 71814613 ID=cds.MS.gene006234.t1;Parent=MS.gene006234.t1
Gene Sequence

>MS.gene006234

ATGGTATGCTCCTCGTCCTAACTCGAATAATTGATTTTTGTTTTGTTTTGTTTTATTATTCTGAATTATTGGAATTAGTTATATTGAATCTTTACTTTTCTTAATAATGATGAAGATCCCCCAGAACTACCATGACGAGGCAGTACAAGCTAATGAGGTTTTAAAAGTCCTAAAAGATGTGAAGGATCAAAGAATTTATACAAGAGGTGCTGCGGCAAGAGTCAAGGAGCTGCTTGAAGGGCATACTCATTTAATTTTGAGATTCAATACCTTCCTGCCAAAGGAACATCAAATCAAACTTGAGACCACTGGTTAG
Protein sequence

>MS.gene006234.t1

MIPQNYHDEAVQANEVLKVLKDVKDQRIYTRGAAARVKELLEGHTHLILRFNTFLPKEHQIKLETTG