AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene071842

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene071842.t1 MTR_2g035150 96.835 158 5 0 1 158 1 158 8.52e-108 304
MS.gene071842.t1 MTR_2g035130 89.172 157 17 0 1 157 1 157 1.96e-99 283
MS.gene071842.t1 MTR_2g035120 87.342 158 20 0 1 158 1 158 1.78e-97 278
MS.gene071842.t1 MTR_2g035100 85.350 157 23 0 1 157 1 157 2.43e-94 270
MS.gene071842.t1 MTR_2g035105 84.076 157 25 0 1 157 1 157 5.85e-93 266
MS.gene071842.t1 MTR_6g033450 74.684 158 40 0 1 158 1 158 1.19e-82 240
MS.gene071842.t1 MTR_4g120970 74.684 158 40 0 1 158 1 158 1.19e-82 240
MS.gene071842.t1 MTR_2g035320 66.242 157 53 0 1 157 1 157 1.25e-69 207
MS.gene071842.t1 MTR_2g035190 64.331 157 56 0 1 157 1 157 4.83e-67 201
MS.gene071842.t1 MTR_2g035210 63.057 157 58 0 1 157 1 157 1.35e-65 197
MS.gene071842.t1 MTR_2g035220 63.057 157 58 0 1 157 1 157 8.72e-64 192
MS.gene071842.t1 MTR_2g035170 58.599 157 65 0 1 157 1 157 1.31e-61 187
MS.gene071842.t1 MTR_2g035320 60.606 99 39 0 59 157 24 122 7.10e-37 123
MS.gene071842.t1 MTR_2g435310 39.103 156 94 1 1 155 1 156 9.16e-37 124
MS.gene071842.t1 MTR_4g120950 45.062 162 82 5 1 158 1 159 5.44e-36 122
MS.gene071842.t1 MTR_4g120760 39.744 156 93 1 1 155 1 156 1.22e-35 121
MS.gene071842.t1 MTR_4g120760 39.744 156 93 1 1 155 1 156 1.31e-35 121
MS.gene071842.t1 MTR_4g120940 64.045 89 29 1 70 158 35 120 3.34e-32 111
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATTTCAACACTCTTGA+TGG 0.245294 2.2:+53745593 None:intergenic
TGATGGCATCAATAACCTTT+GGG 0.301288 2.2:+53745610 None:intergenic
TTGATGGCATCAATAACCTT+TGG 0.345179 2.2:+53745609 None:intergenic
GGCTATAGAGGGTTACTGTT+TGG 0.394448 2.2:-53745085 MS.gene071842:CDS
CTTAGTAGATGATGCTAACT+TGG 0.397103 2.2:-53745304 MS.gene071842:CDS
GCTTACAACTACAGCATTGT+TGG 0.405129 2.2:-53745282 MS.gene071842:CDS
TTTGCAATGGATCCTCCATT+TGG 0.420662 2.2:+53745198 None:intergenic
TATATGCTTTAGTTGTAGTC+AGG 0.421813 2.2:+53745057 None:intergenic
TACAGCATTGTTGGAGGTGT+TGG 0.427537 2.2:-53745273 MS.gene071842:CDS
GAGATCTTCTCTATTGTGTC+TGG 0.431898 2.2:+53745246 None:intergenic
CATCAATAACCTTTGGGGTA+AGG 0.433870 2.2:+53745616 None:intergenic
AAGAGTGTTGAAATTGTTGA+AGG 0.434561 2.2:-53745588 MS.gene071842:CDS
CACTTTGTGCAACACATGCT+TGG 0.457459 2.2:+53745329 None:intergenic
AGAGCTTTGTAAAGTGTAGC+AGG 0.477836 2.2:+53745657 None:intergenic
AAATTGTCTGCAGGTCCAAA+TGG 0.485800 2.2:-53745213 MS.gene071842:CDS
ACTTTACAAAGCTCTAGTTA+AGG 0.493500 2.2:-53745649 MS.gene071842:CDS
AATAGAGAAGATCTCATTTG+AGG 0.494265 2.2:-53745238 MS.gene071842:CDS
CTCTTGAGTTCCTCTTCACT+AGG 0.501934 2.2:+53745138 None:intergenic
AATGTGAAATACTTCACAAA+AGG 0.503374 2.2:-53745171 MS.gene071842:CDS
TTTCACATTAAGCTTTGCAA+TGG 0.512266 2.2:+53745185 None:intergenic
GTTGAAGGAAACGGTGGTGC+CGG 0.528042 2.2:-53745573 MS.gene071842:CDS
ACTCAAGAGTGGCAAAGCTA+AGG 0.529920 2.2:-53745124 MS.gene071842:CDS
CTCAAGAGTGGCAAAGCTAA+GGG 0.532020 2.2:-53745123 MS.gene071842:CDS
TTTGAGGCTAAATTGTCTGC+AGG 0.535432 2.2:-53745222 MS.gene071842:CDS
GTTGAAATTGTTGAAGGAAA+CGG 0.548798 2.2:-53745582 MS.gene071842:CDS
AGCAGGAGCTACAGTGGAGG+TGG 0.552452 2.2:+53745674 None:intergenic
AAGTGTAGCAGGAGCTACAG+TGG 0.556963 2.2:+53745668 None:intergenic
TACAACTACAGCATTGTTGG+AGG 0.566488 2.2:-53745279 MS.gene071842:CDS
CAAGCATGTGTTGCACAAAG+TGG 0.568932 2.2:-53745328 MS.gene071842:CDS
GATGGCATCAATAACCTTTG+GGG 0.578696 2.2:+53745611 None:intergenic
AGTGGCAAAGCTAAGGGTGA+TGG 0.593000 2.2:-53745117 MS.gene071842:CDS
TTCTGACAACCTTACCCCAA+AGG 0.596498 2.2:-53745625 MS.gene071842:CDS
AGATGTTACTCCTAGTGAAG+AGG 0.628737 2.2:-53745148 MS.gene071842:CDS
TTGTCTGCAGGTCCAAATGG+AGG 0.646240 2.2:-53745210 MS.gene071842:CDS
TGTAGCAGGAGCTACAGTGG+AGG 0.673221 2.2:+53745671 None:intergenic
AGTGAAGAGGAACTCAAGAG+TGG 0.684104 2.2:-53745135 MS.gene071842:CDS
GAAATTGTTGAAGGAAACGG+TGG 0.749751 2.2:-53745579 MS.gene071842:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATGTGAAATACTTCACAAA+AGG - chr2.2:53745596-53745615 MS.gene071842:CDS 25.0%
AAAAAACTCACATTCGTTGA+AGG - chr2.2:53745224-53745243 MS.gene071842:CDS 30.0%
AACAATTTCAACACTCTTGA+TGG + chr2.2:53745177-53745196 None:intergenic 30.0%
AATAGAGAAGATCTCATTTG+AGG - chr2.2:53745529-53745548 MS.gene071842:intron 30.0%
CTTCAAATATGAAGAGATGT+AGG + chr2.2:53745365-53745384 None:intergenic 30.0%
GTTGAAATTGTTGAAGGAAA+CGG - chr2.2:53745185-53745204 MS.gene071842:CDS 30.0%
TGATGTTTGTGATTGTGAAA+CGG - chr2.2:53745394-53745413 MS.gene071842:intron 30.0%
TTTCACATTAAGCTTTGCAA+TGG + chr2.2:53745585-53745604 None:intergenic 30.0%
! ACTTTACAAAGCTCTAGTTA+AGG - chr2.2:53745118-53745137 MS.gene071842:CDS 30.0%
!! AAGAGTGTTGAAATTGTTGA+AGG - chr2.2:53745179-53745198 MS.gene071842:CDS 30.0%
!!! TGTGAGTTTTTTGATAGTTC+CGG + chr2.2:53745216-53745235 None:intergenic 30.0%
CTTAGTAGATGATGCTAACT+TGG - chr2.2:53745463-53745482 MS.gene071842:intron 35.0%
TGATGGCATCAATAACCTTT+GGG + chr2.2:53745160-53745179 None:intergenic 35.0%
! TTGATGGCATCAATAACCTT+TGG + chr2.2:53745161-53745180 None:intergenic 35.0%
AAATTGTCTGCAGGTCCAAA+TGG - chr2.2:53745554-53745573 MS.gene071842:CDS 40.0%
AACTCACATTCGTTGAAGGT+CGG - chr2.2:53745228-53745247 MS.gene071842:CDS 40.0%
AGATGTTACTCCTAGTGAAG+AGG - chr2.2:53745619-53745638 MS.gene071842:CDS 40.0%
GAAATTGTTGAAGGAAACGG+TGG - chr2.2:53745188-53745207 MS.gene071842:CDS 40.0%
GAGATCTTCTCTATTGTGTC+TGG + chr2.2:53745524-53745543 None:intergenic 40.0%
GATGGCATCAATAACCTTTG+GGG + chr2.2:53745159-53745178 None:intergenic 40.0%
GCTTACAACTACAGCATTGT+TGG - chr2.2:53745485-53745504 MS.gene071842:intron 40.0%
TACAACTACAGCATTGTTGG+AGG - chr2.2:53745488-53745507 MS.gene071842:intron 40.0%
TTTGCAATGGATCCTCCATT+TGG + chr2.2:53745572-53745591 None:intergenic 40.0%
! AGAGCTTTGTAAAGTGTAGC+AGG + chr2.2:53745113-53745132 None:intergenic 40.0%
! TTTGAGGCTAAATTGTCTGC+AGG - chr2.2:53745545-53745564 MS.gene071842:CDS 40.0%
!! CATCAATAACCTTTGGGGTA+AGG + chr2.2:53745154-53745173 None:intergenic 40.0%
!! GGTCTTTTCAAGGCTATAGA+GGG - chr2.2:53745671-53745690 MS.gene071842:CDS 40.0%
!! TAAGGGTGATGGTCTTTTCA+AGG - chr2.2:53745661-53745680 MS.gene071842:CDS 40.0%
!! TGGTCTTTTCAAGGCTATAG+AGG - chr2.2:53745670-53745689 MS.gene071842:CDS 40.0%
ACTCAAGAGTGGCAAAGCTA+AGG - chr2.2:53745643-53745662 MS.gene071842:CDS 45.0%
AGTGAAGAGGAACTCAAGAG+TGG - chr2.2:53745632-53745651 MS.gene071842:CDS 45.0%
CAAGCATGTGTTGCACAAAG+TGG - chr2.2:53745439-53745458 MS.gene071842:intron 45.0%
CACTTTGTGCAACACATGCT+TGG + chr2.2:53745441-53745460 None:intergenic 45.0%
CTCAAGAGTGGCAAAGCTAA+GGG - chr2.2:53745644-53745663 MS.gene071842:CDS 45.0%
CTCTTGAGTTCCTCTTCACT+AGG + chr2.2:53745632-53745651 None:intergenic 45.0%
GAAACGGATCAATGTGCAGA+TGG - chr2.2:53745410-53745429 MS.gene071842:intron 45.0%
GGCTATAGAGGGTTACTGTT+TGG - chr2.2:53745682-53745701 MS.gene071842:CDS 45.0%
TTCTGACAACCTTACCCCAA+AGG - chr2.2:53745142-53745161 MS.gene071842:CDS 45.0%
! TACAGCATTGTTGGAGGTGT+TGG - chr2.2:53745494-53745513 MS.gene071842:intron 45.0%
AAGTGTAGCAGGAGCTACAG+TGG + chr2.2:53745102-53745121 None:intergenic 50.0%
AGTGGCAAAGCTAAGGGTGA+TGG - chr2.2:53745650-53745669 MS.gene071842:CDS 50.0%
TTGTCTGCAGGTCCAAATGG+AGG - chr2.2:53745557-53745576 MS.gene071842:CDS 50.0%
GTTGAAGGAAACGGTGGTGC+CGG - chr2.2:53745194-53745213 MS.gene071842:CDS 55.0%
TGTAGCAGGAGCTACAGTGG+AGG + chr2.2:53745099-53745118 None:intergenic 55.0%
AGCAGGAGCTACAGTGGAGG+TGG + chr2.2:53745096-53745115 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 53745065 53745724 53745065 ID=MS.gene071842
chr2.2 mRNA 53745065 53745724 53745065 ID=MS.gene071842.t1;Parent=MS.gene071842
chr2.2 exon 53745544 53745724 53745544 ID=MS.gene071842.t1.exon1;Parent=MS.gene071842.t1
chr2.2 CDS 53745544 53745724 53745544 ID=cds.MS.gene071842.t1;Parent=MS.gene071842.t1
chr2.2 exon 53745065 53745360 53745065 ID=MS.gene071842.t1.exon2;Parent=MS.gene071842.t1
chr2.2 CDS 53745065 53745360 53745065 ID=cds.MS.gene071842.t1;Parent=MS.gene071842.t1
Gene Sequence

>MS.gene071842

ATGGGTGTGTTCAATTTTGAGGATGAAACCACCTCCACTGTAGCTCCTGCTACACTTTACAAAGCTCTAGTTAAGGATTCTGACAACCTTACCCCAAAGGTTATTGATGCCATCAAGAGTGTTGAAATTGTTGAAGGAAACGGTGGTGCCGGAACTATCAAAAAACTCACATTCGTTGAAGGTCGGTATAAATATATTTATGTTATTTTTATAGTCAAATATTAATAATTAATTGTTACGTTAGTGTTTAAAAAAATTATGTTTTCTACATCGAGTCTAAGTTCATCGTCTGAACTACCTACATCTCTTCATATTTGAAGTAATGCTGATGATGTTTGTGATTGTGAAACGGATCAATGTGCAGATGGTGAGACCAAGCATGTGTTGCACAAAGTGGACTTAGTAGATGATGCTAACTTGGCTTACAACTACAGCATTGTTGGAGGTGTTGGTCTTCCAGACACAATAGAGAAGATCTCATTTGAGGCTAAATTGTCTGCAGGTCCAAATGGAGGATCCATTGCAAAGCTTAATGTGAAATACTTCACAAAAGGAGATGTTACTCCTAGTGAAGAGGAACTCAAGAGTGGCAAAGCTAAGGGTGATGGTCTTTTCAAGGCTATAGAGGGTTACTGTTTGGCTAATCCTGACTACAACTAA
Protein sequence

>MS.gene071842.t1

MGVFNFEDETTSTVAPATLYKALVKDSDNLTPKVIDAIKSVEIVEGNGGAGTIKKLTFVEDGETKHVLHKVDLVDDANLAYNYSIVGGVGLPDTIEKISFEAKLSAGPNGGSIAKLNVKYFTKGDVTPSEEELKSGKAKGDGLFKAIEGYCLANPDYN