AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28987

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28987.t1 MTR_2g012700 84.426 122 19 0 1 122 1 122 1.21e-73 215
MS.gene28987.t1 MTR_2g062330 80.833 120 22 1 3 122 23 141 6.48e-67 199
MS.gene28987.t1 MTR_7g117590 35.385 130 65 4 7 119 44 171 3.99e-21 83.6
MS.gene28987.t1 MTR_7g117585 36.634 101 62 1 18 116 42 142 4.70e-18 75.1
MS.gene28987.t1 MTR_0010s0310 41.758 91 51 1 22 110 150 240 8.68e-18 76.3
MS.gene28987.t1 MTR_3g008190 29.897 97 68 0 24 120 6 102 1.52e-16 69.7
MS.gene28987.t1 MTR_5g071410 34.653 101 64 1 18 116 165 265 3.13e-15 69.7
MS.gene28987.t1 MTR_6g477950 37.037 81 51 0 39 119 64 144 6.59e-14 66.6
MS.gene28987.t1 MTR_0010s0320 37.363 91 53 2 24 110 192 282 5.60e-13 63.9
MS.gene28987.t1 MTR_6g087720 33.721 86 56 1 24 108 214 299 9.32e-13 63.5
MS.gene28987.t1 MTR_0010s0290 37.363 91 53 2 24 110 223 313 1.05e-12 63.2
MS.gene28987.t1 MTR_5g078270 34.066 91 58 1 22 110 208 298 1.86e-12 62.4
MS.gene28987.t1 MTR_8g069780 25.843 89 66 0 31 119 67 155 8.01e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGTTACTGCTTCTATTT+TGG 0.123735 4.2:-32681353 MS.gene28987:CDS
AAAATTCCGATGTTCATTAT+TGG 0.199581 4.2:-32681381 MS.gene28987:CDS
GAAGTCAATGGTGCTGAATT+AGG 0.200131 4.2:-32681412 MS.gene28987:CDS
TACCAGTTTCTTCATCAAAA+AGG 0.252196 4.2:+32681162 None:intergenic
CCTCGACGTGTTGCCGAGAA+TGG 0.307864 4.2:-32681212 MS.gene28987:CDS
CGGTCAATAATCCTCCTAAT+AGG 0.355854 4.2:-32681019 MS.gene28987:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 4.2:-32681335 MS.gene28987:intron
AAGTCAATGGTGCTGAATTA+GGG 0.416476 4.2:-32681411 MS.gene28987:CDS
ACGGTAGCATACATCCTATT+AGG 0.440754 4.2:+32681005 None:intergenic
ATTGGTATACAAACCATTCT+CGG 0.470714 4.2:+32681199 None:intergenic
GCATGGATCAGAAATACATA+GGG 0.559318 4.2:-32681103 MS.gene28987:CDS
AGCATGGATCAGAAATACAT+AGG 0.564126 4.2:-32681104 MS.gene28987:CDS
CTTGAAAAGTGCCTAAAAGT+TGG 0.570138 4.2:-32681059 MS.gene28987:CDS
AGAAATACATAGGGAGAGGA+TGG 0.573439 4.2:-32681094 MS.gene28987:CDS
GATCAGAAATACATAGGGAG+AGG 0.587262 4.2:-32681098 MS.gene28987:CDS
TCACACTGCGTCAAGAAGCA+TGG 0.587686 4.2:-32681120 MS.gene28987:CDS
CCATTCTCGGCAACACGTCG+AGG 0.599354 4.2:+32681212 None:intergenic
GAGATTGGAGTTGAAGTCAA+TGG 0.619642 4.2:-32681424 MS.gene28987:CDS
GTAGCATACATCCTATTAGG+AGG 0.633251 4.2:+32681008 None:intergenic
ATACTTCCAATAATGAACAT+CGG 0.646998 4.2:+32681375 None:intergenic
TAATCAGTCACAGTTAACGA+CGG 0.738430 4.2:+32680986 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATTCCGATGTTCATTAT+TGG - chr4.2:32681038-32681057 MS.gene28987:CDS 25.0%
! ATACTTCCAATAATGAACAT+CGG + chr4.2:32681047-32681066 None:intergenic 25.0%
!! AAGGAGAATTTTAGATTGAT+TGG + chr4.2:32681241-32681260 None:intergenic 25.0%
!! TAATGTTACTGCTTCTATTT+TGG - chr4.2:32681066-32681085 MS.gene28987:CDS 25.0%
ATTGGTATACAAACCATTCT+CGG + chr4.2:32681223-32681242 None:intergenic 30.0%
TACCAGTTTCTTCATCAAAA+AGG + chr4.2:32681260-32681279 None:intergenic 30.0%
! AAACAACATCACCAACTTTT+AGG + chr4.2:32681374-32681393 None:intergenic 30.0%
! TTTGGATGGAAACAATGTTT+TGG - chr4.2:32681084-32681103 MS.gene28987:CDS 30.0%
AGCATGGATCAGAAATACAT+AGG - chr4.2:32681315-32681334 MS.gene28987:intron 35.0%
GCATGGATCAGAAATACATA+GGG - chr4.2:32681316-32681335 MS.gene28987:intron 35.0%
! AAGTCAATGGTGCTGAATTA+GGG - chr4.2:32681008-32681027 MS.gene28987:CDS 35.0%
! CTCCTTTTTGATGAAGAAAC+TGG - chr4.2:32681255-32681274 MS.gene28987:intron 35.0%
!! CTTGAAAAGTGCCTAAAAGT+TGG - chr4.2:32681360-32681379 MS.gene28987:CDS 35.0%
!! GTTACTGCTTCTATTTTGGA+TGG - chr4.2:32681070-32681089 MS.gene28987:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG - chr4.2:32681091-32681110 MS.gene28987:CDS 35.0%
!!! TGGTGATGTTGTTTTGTTCA+CGG - chr4.2:32681380-32681399 MS.gene28987:CDS 35.0%
ACGGTAGCATACATCCTATT+AGG + chr4.2:32681417-32681436 None:intergenic 40.0%
AGAAATACATAGGGAGAGGA+TGG - chr4.2:32681325-32681344 MS.gene28987:intron 40.0%
CGGTCAATAATCCTCCTAAT+AGG - chr4.2:32681400-32681419 MS.gene28987:CDS 40.0%
GAGATTGGAGTTGAAGTCAA+TGG - chr4.2:32680995-32681014 MS.gene28987:CDS 40.0%
GATCAGAAATACATAGGGAG+AGG - chr4.2:32681321-32681340 MS.gene28987:intron 40.0%
GTAGCATACATCCTATTAGG+AGG + chr4.2:32681414-32681433 None:intergenic 40.0%
! GAAGTCAATGGTGCTGAATT+AGG - chr4.2:32681007-32681026 MS.gene28987:CDS 40.0%
TCACACTGCGTCAAGAAGCA+TGG - chr4.2:32681299-32681318 MS.gene28987:intron 50.0%
CCATTCTCGGCAACACGTCG+AGG + chr4.2:32681210-32681229 None:intergenic 60.0%
CCTCGACGTGTTGCCGAGAA+TGG - chr4.2:32681207-32681226 MS.gene28987:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 32680989 32681452 32680989 ID=MS.gene28987
chr4.2 mRNA 32680989 32681452 32680989 ID=MS.gene28987.t1;Parent=MS.gene28987
chr4.2 exon 32681336 32681452 32681336 ID=MS.gene28987.t1.exon1;Parent=MS.gene28987.t1
chr4.2 CDS 32681336 32681452 32681336 ID=cds.MS.gene28987.t1;Parent=MS.gene28987.t1
chr4.2 exon 32680989 32681240 32680989 ID=MS.gene28987.t1.exon2;Parent=MS.gene28987.t1
chr4.2 CDS 32680989 32681240 32680989 ID=cds.MS.gene28987.t1;Parent=MS.gene28987.t1
Gene Sequence

>MS.gene28987

ATGAATGAGATTGGAGTTGAAGTCAATGGTGCTGAATTAGGGAATCTTCAAAATTCCGATGTTCATTATTGGAAGTATAATGTTACTGCTTCTATTTTGGATGGAAACAATGTTTTGGTTAGTGGCATTTACGAAGCATTTTTTGTTGTTTTCATGTTAAGTTGTTGTTGATTAATTATAGATTGTATGATTTCTTGACAAATCTATTGTAGAATTTTCCTCGACGTGTTGCCGAGAATGGTTTGTATACCAATCAATCTAAAATTCTCCTTTTTGATGAAGAAACTGGTAAATCTTATGACTGTGATGTTCACACTGCGTCAAGAAGCATGGATCAGAAATACATAGGGAGAGGATGGTACGACTTTGTTCTTGAAAAGTGCCTAAAAGTTGGTGATGTTGTTTTGTTCACGGTCAATAATCCTCCTAATAGGATGTATGCTACCGTCGTTAACTGTGACTGA
Protein sequence

>MS.gene28987.t1

MNEIGVEVNGAELGNLQNSDVHYWKYNVTASILDGNNVLNFPRRVAENGLYTNQSKILLFDEETGKSYDCDVHTASRSMDQKYIGRGWYDFVLEKCLKVGDVVLFTVNNPPNRMYATVVNCD