AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062080.t1 MTR_2g045020 77.654 179 34 1 9 187 2 174 1.08e-91 266
MS.gene062080.t1 MTR_3g437790 64.242 165 55 4 26 188 12 174 5.33e-60 185
MS.gene062080.t1 MTR_8g022970 50.000 178 82 5 15 188 3 177 3.78e-46 150
MS.gene062080.t1 MTR_3g109930 50.000 158 74 4 32 188 7 160 1.39e-41 138
MS.gene062080.t1 MTR_7g028448 33.088 136 77 3 47 181 31 153 6.69e-17 74.7
MS.gene062080.t1 MTR_4g036915 33.088 136 77 3 47 181 31 153 6.69e-17 74.7
MS.gene062080.t1 MTR_2g105290 35.802 162 92 6 27 181 5 161 9.36e-17 74.3
MS.gene062080.t1 MTR_8g086290 35.443 158 93 6 27 181 10 161 5.91e-15 69.7
MS.gene062080.t1 MTR_8g043650 34.503 171 86 8 15 175 2 156 1.97e-14 69.3
MS.gene062080.t1 MTR_2g030740 34.483 174 88 8 15 178 2 159 2.12e-13 66.6
MS.gene062080.t1 MTR_5g053390 33.121 157 95 7 28 178 7 159 3.86e-13 65.9
MS.gene062080.t1 MTR_3g052920 35.366 164 82 8 28 178 7 159 4.65e-13 65.5
MS.gene062080.t1 MTR_1g106070 34.568 162 86 8 28 178 7 159 5.78e-13 64.3
MS.gene062080.t1 MTR_1g105910 34.783 161 81 8 28 175 7 156 2.13e-12 63.9
MS.gene062080.t1 MTR_1g012570 31.677 161 92 8 28 178 7 159 5.76e-12 62.8
MS.gene062080.t1 MTR_3g080940 27.607 163 97 6 29 181 11 162 2.79e-11 60.5
MS.gene062080.t1 MTR_3g030770 32.278 158 90 6 29 178 11 159 3.74e-11 60.5
MS.gene062080.t1 MTR_1g105920 33.537 164 85 8 28 178 7 159 7.69e-11 59.7
MS.gene062080.t1 MTR_1g108510 32.278 158 90 6 29 178 11 159 7.92e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062080.t1 AT5G60440 32.075 159 92 7 29 178 9 160 2.79e-13 67.0
MS.gene062080.t1 AT2G24840 28.289 152 105 4 29 178 65 214 3.48e-13 66.2

Find 26 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2.3:-45283156 MS.gene062080:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.3:+45283306 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2.3:+45283204 None:intergenic
TGATGTTGAATGAAACAAAC+TGG 0.408161 2.3:-45283658 MS.gene062080:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.3:+45283307 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2.3:+45283431 None:intergenic
GTGATGTCAATTTCCATGAT+TGG 0.461626 2.3:-45283217 MS.gene062080:CDS
ACGATGAATGACAGCATCAC+AGG 0.499770 2.3:+45283397 None:intergenic
GACATATGATGGTCGACGAT+GGG 0.514442 2.3:-45283364 MS.gene062080:CDS
ATGAAATTGCTGAAACCCTA+AGG 0.533334 2.3:-45283322 MS.gene062080:CDS
ATCGTCGACCATCATATGTC+CGG 0.542227 2.3:+45283367 None:intergenic
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2.3:-45283521 MS.gene062080:CDS
GGACAACATGAATGCTGCTA+GGG 0.558097 2.3:-45283636 MS.gene062080:CDS
TCTTGTCCGGCGATTTGACG+AGG 0.561634 2.3:+45283444 None:intergenic
GGACATATGATGGTCGACGA+TGG 0.562958 2.3:-45283365 MS.gene062080:CDS
GGGACAACATGAATGCTGCT+AGG 0.564881 2.3:-45283637 MS.gene062080:CDS
TGCACTCCTCGTCAAATCGC+CGG 0.565424 2.3:-45283450 MS.gene062080:CDS
GCTTCTGAGAGAAAGAATGC+TGG 0.579951 2.3:-45283614 MS.gene062080:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2.3:-45283119 MS.gene062080:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2.3:+45283398 None:intergenic
ATGTCAATTTCCATGATTGG+TGG 0.630551 2.3:-45283214 MS.gene062080:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2.3:-45283425 MS.gene062080:CDS
GAACAACACTGAACAACACA+CGG 0.651271 2.3:-45283592 MS.gene062080:CDS
GATGTTGAATGAAACAAACT+GGG 0.726719 2.3:-45283657 MS.gene062080:CDS
GAAAGCTGTCAAAGTCACCG+AGG 0.773790 2.3:-45283249 MS.gene062080:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2.3:+45283399 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAGAAGAAAAACTGAA+CGG - chr2.3:45283220-45283239 MS.gene062080:CDS 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG - chr2.3:45283612-45283631 MS.gene062080:CDS 25.0%
!!! AATTCTTTGGAGAGTTTTAA+GGG - chr2.3:45283625-45283644 MS.gene062080:CDS 25.0%
TAGAATTATTCCACCAATCA+TGG + chr2.3:45283567-45283586 None:intergenic 30.0%
TCAAGAAAAACTTGAAGAAG+AGG - chr2.3:45283486-45283505 MS.gene062080:CDS 30.0%
!! GAATTCTTTGGAGAGTTTTA+AGG - chr2.3:45283624-45283643 MS.gene062080:CDS 30.0%
AAGAACAAGTTCTATGCATG+TGG - chr2.3:45283343-45283362 MS.gene062080:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG - chr2.3:45283446-45283465 MS.gene062080:CDS 35.0%
ATGTCAATTTCCATGATTGG+TGG - chr2.3:45283554-45283573 MS.gene062080:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG - chr2.3:45283551-45283570 MS.gene062080:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.3:45283464-45283483 None:intergenic 35.0%
GAACAACACTGAACAACACA+CGG - chr2.3:45283176-45283195 MS.gene062080:CDS 40.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.3:45283465-45283484 None:intergenic 40.0%
! GCATAGAACTTGTTCTTGTC+CGG + chr2.3:45283340-45283359 None:intergenic 40.0%
! GTCATTCATCGTTTTCTGAC+CGG - chr2.3:45283382-45283401 MS.gene062080:CDS 40.0%
! TTTTCTGACCGGACATATGA+TGG - chr2.3:45283393-45283412 MS.gene062080:CDS 40.0%
AATTTACGTGCAGCAAGCGA+AGG - chr2.3:45283649-45283668 MS.gene062080:CDS 45.0%
ACGATGAATGACAGCATCAC+AGG + chr2.3:45283374-45283393 None:intergenic 45.0%
ATCGTCGACCATCATATGTC+CGG + chr2.3:45283404-45283423 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG + chr2.3:45283373-45283392 None:intergenic 45.0%
GACATATGATGGTCGACGAT+GGG - chr2.3:45283404-45283423 MS.gene062080:CDS 45.0%
GAGTTCTCAAGACGCAAACT+CGG - chr2.3:45283247-45283266 MS.gene062080:CDS 45.0%
GATGAATGACAGCATCACAG+GGG + chr2.3:45283372-45283391 None:intergenic 45.0%
GGACAACATGAATGCTGCTA+GGG - chr2.3:45283132-45283151 MS.gene062080:CDS 45.0%
! GACATCACTCTTTTGTGCCT+CGG + chr2.3:45283539-45283558 None:intergenic 45.0%
! GCTTCTGAGAGAAAGAATGC+TGG - chr2.3:45283154-45283173 MS.gene062080:CDS 45.0%
!! CGAGGAGTGCAGTTTTTGAT+TGG + chr2.3:45283309-45283328 None:intergenic 45.0%
GAAAGCTGTCAAAGTCACCG+AGG - chr2.3:45283519-45283538 MS.gene062080:CDS 50.0%
GGACATATGATGGTCGACGA+TGG - chr2.3:45283403-45283422 MS.gene062080:CDS 50.0%
GGGACAACATGAATGCTGCT+AGG - chr2.3:45283131-45283150 MS.gene062080:CDS 50.0%
TCTTGTCCGGCGATTTGACG+AGG + chr2.3:45283327-45283346 None:intergenic 55.0%
TGCACTCCTCGTCAAATCGC+CGG - chr2.3:45283318-45283337 MS.gene062080:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 45283112 45283678 45283112 ID=MS.gene062080
chr2.3 mRNA 45283112 45283678 45283112 ID=MS.gene062080.t1;Parent=MS.gene062080
chr2.3 exon 45283112 45283678 45283112 ID=MS.gene062080.t1.exon1;Parent=MS.gene062080.t1
chr2.3 CDS 45283112 45283678 45283112 ID=cds.MS.gene062080.t1;Parent=MS.gene062080.t1
Gene Sequence

>MS.gene062080

ATGTTGAATGAAACAAACTGGGACAACATGAATGCTGCTAGGGCTTCTGAGAGAAAGAATGCTGGAACAACACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGTTCTGAGTTCTCAAGACGCAAACTCGGAATATTCAACAAAGCAATAGAACTGTCTATTCTATGCCAATCAAAAACTGCACTCCTCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTGACCGGACATATGATGGTCGACGATGGGAAAAAGAAGAAACAAGATGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGATGATAATTTGAAAGCTGTCAAAGTCACCGAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTTAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>MS.gene062080.t1

MLNETNWDNMNAARASERKNAGTTLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTALLVKSPDKNKFYACGYPCDAVIHRFLTGHMMVDDGKKKKQDDEIAETLRLQYEALQEKLEEEDDNLKAVKVTEAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK