AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025390

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025390.t1 MTR_2g045020 86.631 187 24 1 16 201 1 187 2.38e-110 313
MS.gene025390.t1 MTR_3g437790 61.702 188 56 5 16 195 1 180 1.37e-64 197
MS.gene025390.t1 MTR_8g022970 45.789 190 83 6 23 201 3 183 5.62e-42 140
MS.gene025390.t1 MTR_3g109930 48.175 137 67 3 50 185 23 156 1.03e-35 124
MS.gene025390.t1 MTR_2g105290 37.288 177 90 7 35 195 5 176 2.39e-19 81.6
MS.gene025390.t1 MTR_7g028448 34.586 133 73 3 51 182 34 153 5.19e-17 75.1
MS.gene025390.t1 MTR_4g036915 34.586 133 73 3 51 182 34 153 5.19e-17 75.1
MS.gene025390.t1 MTR_8g086290 35.465 172 90 7 35 196 10 170 6.65e-15 69.7
MS.gene025390.t1 MTR_5g053390 32.051 156 91 6 36 179 7 159 9.18e-13 65.1
MS.gene025390.t1 MTR_8g043650 32.571 175 77 9 23 176 2 156 3.00e-12 63.9
MS.gene025390.t1 MTR_3g080940 32.867 143 76 6 50 182 30 162 3.04e-12 63.2
MS.gene025390.t1 MTR_1g106070 30.864 162 85 7 36 179 7 159 1.73e-11 60.8
MS.gene025390.t1 MTR_3g052920 31.056 161 86 5 36 179 7 159 1.98e-11 61.6
MS.gene025390.t1 MTR_1g105910 31.613 155 87 6 36 176 7 156 2.87e-11 60.8
MS.gene025390.t1 MTR_5g055100 30.061 163 79 7 36 176 7 156 3.26e-11 60.8
MS.gene025390.t1 MTR_2g030740 29.341 167 94 7 28 179 2 159 4.53e-11 60.5
MS.gene025390.t1 MTR_4g127140 36.364 143 75 6 51 182 34 171 7.92e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025390.t1 AT5G60440 32.353 136 81 5 51 179 29 160 6.48e-13 66.2
MS.gene025390.t1 AT2G24840 26.344 186 115 6 37 201 65 249 2.69e-12 64.3

Find 27 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGTAGCAATGTTTATATT+TGG 0.182142 2.2:+42142798 None:intergenic
GTTTATATTTGGATGTAAAT+TGG 0.187712 2.2:+42142809 None:intergenic
TGAGGACTTTAAGAATTCTT+TGG 0.239126 2.2:-42142877 MS.gene025390:CDS
GAATAATTCTATTGATGATA+TGG 0.255478 2.2:-42142913 MS.gene025390:CDS
ACATGAATAAGAAAATTTCT+AGG 0.307560 2.2:-42143337 MS.gene025390:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.2:+42143027 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2.2:+42142925 None:intergenic
TGAAGAAGAGCAGGATACTT+TGG 0.413235 2.2:-42142991 MS.gene025390:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.2:+42143028 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2.2:+42143152 None:intergenic
GAATTCTTTGGAGAGTTTCA+AGG 0.479356 2.2:-42142865 MS.gene025390:CDS
CATGAATAAGAAAATTTCTA+GGG 0.489642 2.2:-42143336 MS.gene025390:CDS
AATTCTTTGGAGAGTTTCAA+GGG 0.490979 2.2:-42142864 MS.gene025390:CDS
GATGCATGAAATCAAGAAAG+AGG 0.498636 2.2:-42143261 MS.gene025390:CDS
ATCCTCGACCATCATATGTC+CGG 0.509285 2.2:+42143088 None:intergenic
ATGAAATTGCTGAAACCCTA+AGG 0.528268 2.2:-42143043 MS.gene025390:CDS
GGACATATGATGGTCGAGGA+TGG 0.552906 2.2:-42143086 MS.gene025390:CDS
TGCAATCATCGTCAAATCGC+CGG 0.556447 2.2:-42143171 MS.gene025390:CDS
GACATATGATGGTCGAGGAT+GGG 0.560153 2.2:-42143085 MS.gene025390:CDS
GCTTCTGAGAGAAAGAATGC+TGG 0.579951 2.2:-42143314 MS.gene025390:CDS
CACCGGACATATGATGGTCG+AGG 0.592373 2.2:-42143090 MS.gene025390:CDS
CGTTGAATGACAGAGTCACA+AGG 0.630158 2.2:+42143119 None:intergenic
AAGAACAAGTTCTATGCATG+TGG 0.639320 2.2:-42143146 MS.gene025390:CDS
TATGGATTTAGCATCTCTTG+AGG 0.650206 2.2:-42142895 MS.gene025390:CDS
GAACAAAACTCAACAACACA+CGG 0.651271 2.2:-42143292 MS.gene025390:CDS
GGAAGCTGTCAAAGTCACTG+AGG 0.723299 2.2:-42142970 MS.gene025390:CDS
GTTGAATGACAGAGTCACAA+GGG 0.725206 2.2:+42143120 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATGAATAAGAAAATTTCT+AGG - chr2.2:42142840-42142859 MS.gene025390:CDS 20.0%
!! CATGAATAAGAAAATTTCTA+GGG - chr2.2:42142841-42142860 MS.gene025390:CDS 20.0%
!! GTTTATATTTGGATGTAAAT+TGG + chr2.2:42143371-42143390 None:intergenic 20.0%
!! TAAGTAGCAATGTTTATATT+TGG + chr2.2:42143382-42143401 None:intergenic 20.0%
!!! GAATAATTCTATTGATGATA+TGG - chr2.2:42143264-42143283 MS.gene025390:CDS 20.0%
!!! ATTTTAATTTCCATGATTGG+TGG - chr2.2:42143242-42143261 MS.gene025390:CDS 25.0%
!!! GTGATTTTAATTTCCATGAT+TGG - chr2.2:42143239-42143258 MS.gene025390:CDS 25.0%
TAGAATTATTCCACCAATCA+TGG + chr2.2:42143255-42143274 None:intergenic 30.0%
! AATTCTTTGGAGAGTTTCAA+GGG - chr2.2:42143313-42143332 MS.gene025390:CDS 30.0%
! TGAGGACTTTAAGAATTCTT+TGG - chr2.2:42143300-42143319 MS.gene025390:CDS 30.0%
AAGAACAAGTTCTATGCATG+TGG - chr2.2:42143031-42143050 MS.gene025390:CDS 35.0%
AGAAAAACTTGAAGAAGAGC+AGG - chr2.2:42143177-42143196 MS.gene025390:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG - chr2.2:42143134-42143153 MS.gene025390:CDS 35.0%
GAACAAAACTCAACAACACA+CGG - chr2.2:42142885-42142904 MS.gene025390:CDS 35.0%
GATGCATGAAATCAAGAAAG+AGG - chr2.2:42142916-42142935 MS.gene025390:CDS 35.0%
TATGGATTTAGCATCTCTTG+AGG - chr2.2:42143282-42143301 MS.gene025390:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.2:42143152-42143171 None:intergenic 35.0%
! CGATGATTGCAGTTTTTGAT+TGG + chr2.2:42142997-42143016 None:intergenic 35.0%
! GAATTCTTTGGAGAGTTTCA+AGG - chr2.2:42143312-42143331 MS.gene025390:CDS 35.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.2:42143153-42143172 None:intergenic 40.0%
GTTGAATGACAGAGTCACAA+GGG + chr2.2:42143060-42143079 None:intergenic 40.0%
TGAAGAAGAGCAGGATACTT+TGG - chr2.2:42143186-42143205 MS.gene025390:CDS 40.0%
! GCATAGAACTTGTTCTTGTC+CGG + chr2.2:42143028-42143047 None:intergenic 40.0%
! GTCATTCAACGTTTTCTCAC+CGG - chr2.2:42143070-42143089 MS.gene025390:CDS 40.0%
! TTTTCTCACCGGACATATGA+TGG - chr2.2:42143081-42143100 MS.gene025390:CDS 40.0%
ATCCTCGACCATCATATGTC+CGG + chr2.2:42143092-42143111 None:intergenic 45.0%
CGTTGAATGACAGAGTCACA+AGG + chr2.2:42143061-42143080 None:intergenic 45.0%
GACATATGATGGTCGAGGAT+GGG - chr2.2:42143092-42143111 MS.gene025390:CDS 45.0%
GAGGAAAAAGAACGCAGACT+CGG - chr2.2:42142935-42142954 MS.gene025390:CDS 45.0%
TGCAATCATCGTCAAATCGC+CGG - chr2.2:42143006-42143025 MS.gene025390:CDS 45.0%
! GCTTCTGAGAGAAAGAATGC+TGG - chr2.2:42142863-42142882 MS.gene025390:CDS 45.0%
GGAAGCTGTCAAAGTCACTG+AGG - chr2.2:42143207-42143226 MS.gene025390:CDS 50.0%
GGACATATGATGGTCGAGGA+TGG - chr2.2:42143091-42143110 MS.gene025390:CDS 50.0%
CACCGGACATATGATGGTCG+AGG - chr2.2:42143087-42143106 MS.gene025390:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 42142797 42143402 42142797 ID=MS.gene025390
chr2.2 mRNA 42142797 42143402 42142797 ID=MS.gene025390.t1;Parent=MS.gene025390
chr2.2 exon 42142797 42143402 42142797 ID=MS.gene025390.t1.exon1;Parent=MS.gene025390.t1
chr2.2 CDS 42142797 42143402 42142797 ID=cds.MS.gene025390.t1;Parent=MS.gene025390.t1
Gene Sequence

>MS.gene025390

ATGTTATCAGATAATTCATCATCAGTGATTTTGAATGAAACAAACATGAATAAGAAAATTTCTAGGGCTTCTGAGAGAAAGAATGCTGGAACAAAACTCAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAGGAAAAAGAACGCAGACTCGGAATTTTCAACAAAGCAATAGAGCTGTCTATTCTATGCCAATCAAAAACTGCAATCATCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCTTGTGACTCTGTCATTCAACGTTTTCTCACCGGACATATGATGGTCGAGGATGGGAAAAAGAAGAAAGAAAACGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGCAGGATACTTTGGAAGCTGTCAAAGTCACTGAGGCACAAAAGAGTGATTTTAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGGATTTAGCATCTCTTGAGGACTTTAAGAATTCTTTGGAGAGTTTCAAGGGTAATTTACGTTCAGCAAGCGAAGCAGAGAAGTCCAATTTACATCCAAATATAAACATTGCTACTTAA
Protein sequence

>MS.gene025390.t1

MLSDNSSSVILNETNMNKKISRASERKNAGTKLNNTRKRKMHEIKKEEKERRLGIFNKAIELSILCQSKTAIIVKSPDKNKFYACGYPCDSVIQRFLTGHMMVEDGKKKKENDEIAETLRLQYEALQEKLEEEQDTLEAVKVTEAQKSDFNFHDWWNNSIDDMDLASLEDFKNSLESFKGNLRSASEAEKSNLHPNINIAT