AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068909

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068909.t1 MTR_2g045020 78.075 187 28 2 10 196 1 174 2.06e-94 273
MS.gene068909.t1 MTR_3g437790 65.455 165 53 4 35 197 12 174 8.55e-61 187
MS.gene068909.t1 MTR_8g022970 50.000 178 82 5 24 197 3 177 2.84e-46 150
MS.gene068909.t1 MTR_3g109930 52.448 143 64 3 56 197 21 160 2.42e-41 138
MS.gene068909.t1 MTR_2g105290 37.037 162 90 6 36 190 5 161 9.79e-18 77.4
MS.gene068909.t1 MTR_7g028448 34.559 136 75 3 56 190 31 153 1.07e-17 77.0
MS.gene068909.t1 MTR_4g036915 34.559 136 75 3 56 190 31 153 1.07e-17 77.0
MS.gene068909.t1 MTR_8g086290 35.443 158 93 6 36 190 10 161 7.26e-15 69.7
MS.gene068909.t1 MTR_1g012570 30.723 166 100 7 29 187 2 159 7.41e-13 65.5
MS.gene068909.t1 MTR_5g055100 30.909 165 95 6 29 184 2 156 8.19e-13 65.1
MS.gene068909.t1 MTR_2g085280 30.588 170 90 8 37 191 7 163 3.31e-12 63.5
MS.gene068909.t1 MTR_2g085250 30.588 170 90 8 37 191 7 163 4.01e-12 63.2
MS.gene068909.t1 MTR_1g108510 32.934 167 95 7 29 187 2 159 1.66e-11 61.6
MS.gene068909.t1 MTR_3g030770 33.533 167 94 8 29 187 2 159 2.51e-11 60.8
MS.gene068909.t1 MTR_3g080940 27.607 163 97 6 38 190 11 162 4.17e-11 60.1
MS.gene068909.t1 MTR_1g105920 31.361 169 95 7 29 187 2 159 9.57e-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.gene068909.t1 AT2G24840 28.289 152 105 4 38 187 65 214 2.33e-13 67.0

Find 27 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2.1:-45964391 MS.gene068909:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.1:+45964541 None:intergenic
TGATGTTGAATAAAACAAAC+TGG 0.355767 2.1:-45964920 MS.gene068909:CDS
TAGAATTATTCCACCAATCA+TGG 0.397833 2.1:+45964439 None:intergenic
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.1:+45964542 None:intergenic
GTGATGTCAATTTCCATGAT+TGG 0.461626 2.1:-45964452 MS.gene068909:CDS
GCATAGAGCTTGTTCTTGTC+CGG 0.461752 2.1:+45964666 None:intergenic
ACGATGAATGACAGCATCAC+AGG 0.499770 2.1:+45964632 None:intergenic
ATCCTCGGCCATCATATGTC+CGG 0.508496 2.1:+45964602 None:intergenic
GACATATGATGGCCGAGGAT+GGG 0.528388 2.1:-45964599 MS.gene068909:CDS
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2.1:-45964756 MS.gene068909:CDS
TGTCTGAAAAGAACACTGCT+AGG 0.558447 2.1:-45964872 MS.gene068909:CDS
TCTTGTCCGGCGATTTGACG+AGG 0.561634 2.1:+45964679 None:intergenic
TGCACTCCTCGTCAAATCGC+CGG 0.565424 2.1:-45964685 MS.gene068909:CDS
GGACATATGATGGCCGAGGA+TGG 0.572212 2.1:-45964600 MS.gene068909:CDS
ATGCAATTGCTGAAACCCTA+AGG 0.573132 2.1:-45964557 MS.gene068909:CDS
GCTTCTGAGAGAAAGAATGC+TGG 0.579951 2.1:-45964849 MS.gene068909:CDS
GACCGGACATATGATGGCCG+AGG 0.586444 2.1:-45964604 MS.gene068909:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2.1:-45964354 MS.gene068909:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2.1:+45964633 None:intergenic
GTCTGAAAAGAACACTGCTA+GGG 0.626438 2.1:-45964871 MS.gene068909:CDS
ATGTCAATTTCCATGATTGG+TGG 0.630551 2.1:-45964449 MS.gene068909:CDS
GAACAAAACTGAACAACACA+CGG 0.651271 2.1:-45964827 MS.gene068909:CDS
AAGAACAAGCTCTATGCATG+TGG 0.661717 2.1:-45964660 MS.gene068909:CDS
GATGTTGAATAAAACAAACT+GGG 0.674271 2.1:-45964919 MS.gene068909:CDS
GAAAGCTGTCAAAGTCACCG+AGG 0.773790 2.1:-45964484 MS.gene068909:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2.1:+45964634 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAGAAGAAAAACTGAA+CGG - chr2.1:45964482-45964501 MS.gene068909:CDS 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG - chr2.1:45964874-45964893 MS.gene068909:CDS 25.0%
!!! AATTCTTTGGAGAGTTTTAA+GGG - chr2.1:45964887-45964906 MS.gene068909:CDS 25.0%
AGAAAGAAGAAAAACTGAAC+GGG - chr2.1:45964483-45964502 MS.gene068909:CDS 30.0%
TAGAATTATTCCACCAATCA+TGG + chr2.1:45964829-45964848 None:intergenic 30.0%
TCAAGAAAAACTTGAAGAAG+AGG - chr2.1:45964748-45964767 MS.gene068909:CDS 30.0%
!! GAATTCTTTGGAGAGTTTTA+AGG - chr2.1:45964886-45964905 MS.gene068909:CDS 30.0%
ATGTCAATTTCCATGATTGG+TGG - chr2.1:45964816-45964835 MS.gene068909:CDS 35.0%
GAACAAAACTGAACAACACA+CGG - chr2.1:45964438-45964457 MS.gene068909:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG - chr2.1:45964813-45964832 MS.gene068909:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.1:45964726-45964745 None:intergenic 35.0%
! TTTCTTCTTTTTCCCATCCT+CGG + chr2.1:45964681-45964700 None:intergenic 35.0%
AAGAACAAGCTCTATGCATG+TGG - chr2.1:45964605-45964624 MS.gene068909:CDS 40.0%
ATGCAATTGCTGAAACCCTA+AGG - chr2.1:45964708-45964727 MS.gene068909:CDS 40.0%
GTCTGAAAAGAACACTGCTA+GGG - chr2.1:45964394-45964413 MS.gene068909:CDS 40.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.1:45964727-45964746 None:intergenic 40.0%
TGTCTGAAAAGAACACTGCT+AGG - chr2.1:45964393-45964412 MS.gene068909:CDS 40.0%
! GTCATTCATCGTTTTCTGAC+CGG - chr2.1:45964644-45964663 MS.gene068909:CDS 40.0%
! TTTTCTGACCGGACATATGA+TGG - chr2.1:45964655-45964674 MS.gene068909:CDS 40.0%
AATTTACGTGCAGCAAGCGA+AGG - chr2.1:45964911-45964930 MS.gene068909:CDS 45.0%
ACGATGAATGACAGCATCAC+AGG + chr2.1:45964636-45964655 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG + chr2.1:45964635-45964654 None:intergenic 45.0%
GAGTTCTCAAGACGCAAACT+CGG - chr2.1:45964509-45964528 MS.gene068909:CDS 45.0%
GATGAATGACAGCATCACAG+GGG + chr2.1:45964634-45964653 None:intergenic 45.0%
! GACATCACTCTTTTGTGCCT+CGG + chr2.1:45964801-45964820 None:intergenic 45.0%
! GCATAGAGCTTGTTCTTGTC+CGG + chr2.1:45964602-45964621 None:intergenic 45.0%
! GCTTCTGAGAGAAAGAATGC+TGG - chr2.1:45964416-45964435 MS.gene068909:CDS 45.0%
!! CGAGGAGTGCAGTTTTTGAT+TGG + chr2.1:45964571-45964590 None:intergenic 45.0%
ATCCTCGGCCATCATATGTC+CGG + chr2.1:45964666-45964685 None:intergenic 50.0%
GAAAGCTGTCAAAGTCACCG+AGG - chr2.1:45964781-45964800 MS.gene068909:CDS 50.0%
GACATATGATGGCCGAGGAT+GGG - chr2.1:45964666-45964685 MS.gene068909:CDS 50.0%
GGACATATGATGGCCGAGGA+TGG - chr2.1:45964665-45964684 MS.gene068909:CDS 55.0%
TCTTGTCCGGCGATTTGACG+AGG + chr2.1:45964589-45964608 None:intergenic 55.0%
TGCACTCCTCGTCAAATCGC+CGG - chr2.1:45964580-45964599 MS.gene068909:CDS 55.0%
GACCGGACATATGATGGCCG+AGG - chr2.1:45964661-45964680 MS.gene068909:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 45964347 45964940 45964347 ID=MS.gene068909
chr2.1 mRNA 45964347 45964940 45964347 ID=MS.gene068909.t1;Parent=MS.gene068909
chr2.1 exon 45964347 45964940 45964347 ID=MS.gene068909.t1.exon1;Parent=MS.gene068909.t1
chr2.1 CDS 45964347 45964940 45964347 ID=cds.MS.gene068909.t1;Parent=MS.gene068909.t1
Gene Sequence

>MS.gene068909

ATGTTGAATAAAACAAACTGGGACAACATGAATAAAAATTGTGAACTGTCTGAAAAGAACACTGCTAGGGCTTCTGAGAGAAAGAATGCTGGAACAAAACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGGTCTGAGTTCTCAAGACGCAAACTCGGAATTTTCAACAAAGCAATAGAGCTGTCTATTCTATGCCAATCAAAAACTGCACTCCTCGTCAAATCGCCGGACAAGAACAAGCTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTGACCGGACATATGATGGCCGAGGATGGGAAAAAGAAGAAACAAGATGATGCAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGATGATAATTTGAAAGCTGTCAAAGTCACCGAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTTAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>MS.gene068909.t1

MLNKTNWDNMNKNCELSEKNTARASERKNAGTKLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTALLVKSPDKNKLYACGYPCDAVIHRFLTGHMMAEDGKKKKQDDAIAETLRLQYEALQEKLEEEDDNLKAVKVTEAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK