AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062078

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062078.t1 MTR_2g045020 85.561 187 26 1 16 201 1 187 5.23e-109 310
MS.gene062078.t1 MTR_3g437790 62.234 188 55 5 16 195 1 180 6.60e-65 198
MS.gene062078.t1 MTR_8g022970 45.789 190 83 6 23 201 3 183 1.23e-41 139
MS.gene062078.t1 MTR_3g109930 49.254 134 64 3 50 182 23 153 1.49e-35 123
MS.gene062078.t1 MTR_2g105290 38.889 162 80 6 35 182 5 161 1.15e-19 82.4
MS.gene062078.t1 MTR_7g028448 34.586 133 73 3 51 182 34 153 7.82e-17 74.7
MS.gene062078.t1 MTR_4g036915 34.586 133 73 3 51 182 34 153 7.82e-17 74.7
MS.gene062078.t1 MTR_8g086290 35.465 172 90 7 35 196 10 170 7.23e-15 69.7
MS.gene062078.t1 MTR_5g053390 32.051 156 91 6 36 179 7 159 1.35e-12 64.7
MS.gene062078.t1 MTR_8g043650 32.571 175 77 9 23 176 2 156 4.35e-12 63.2
MS.gene062078.t1 MTR_3g052920 31.677 161 85 5 36 179 7 159 5.45e-12 63.2
MS.gene062078.t1 MTR_3g080940 32.168 143 77 6 50 182 30 162 7.33e-12 62.4
MS.gene062078.t1 MTR_1g106070 30.864 162 85 7 36 179 7 159 2.31e-11 60.5
MS.gene062078.t1 MTR_1g105910 31.613 155 87 6 36 176 7 156 3.98e-11 60.5
MS.gene062078.t1 MTR_5g055100 30.061 163 79 7 36 176 7 156 4.96e-11 60.5
MS.gene062078.t1 MTR_2g030740 29.697 165 92 7 30 179 4 159 9.35e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062078.t1 AT5G60440 31.618 136 82 5 51 179 29 160 1.35e-12 65.5
MS.gene062078.t1 AT2G24840 25.806 186 116 6 37 201 65 249 7.32e-12 63.2

Find 27 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGTAGCAATGTTTATATT+TGG 0.182142 2.3:+45268319 None:intergenic
GTTTATATTTGGATGTAAAT+TGG 0.187712 2.3:+45268330 None:intergenic
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2.3:-45268398 MS.gene062078:CDS
GAATAATTCTATTGATGATA+TGG 0.255478 2.3:-45268434 MS.gene062078:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.3:+45268548 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2.3:+45268446 None:intergenic
TGAAGAAGAGCAGGATACTT+TGG 0.413235 2.3:-45268512 MS.gene062078:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.3:+45268549 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2.3:+45268673 None:intergenic
GAATTCTTTGGAGAGTTTCA+AGG 0.479356 2.3:-45268386 MS.gene062078:CDS
ACGTTGAATGACAGCATCAC+AGG 0.479438 2.3:+45268639 None:intergenic
AATTCTTTGGAGAGTTTCAA+GGG 0.490979 2.3:-45268385 MS.gene062078:CDS
GATGCATGAAATCAAGAAAG+AGG 0.498636 2.3:-45268782 MS.gene062078:CDS
ATCCTCGACCATCATATGTC+CGG 0.509285 2.3:+45268609 None:intergenic
ACATGAATAAGAAAATTGCT+AGG 0.527390 2.3:-45268858 MS.gene062078:CDS
ATGAAATTGCTGAAACCCTA+AGG 0.528268 2.3:-45268564 MS.gene062078:CDS
GGACATATGATGGTCGAGGA+TGG 0.543275 2.3:-45268607 MS.gene062078:CDS
TGCAATCATCGTCAAATCGC+CGG 0.556447 2.3:-45268692 MS.gene062078:CDS
GACATATGATGGTCGAGGAT+GGG 0.560153 2.3:-45268606 MS.gene062078:CDS
CATGAATAAGAAAATTGCTA+GGG 0.586387 2.3:-45268857 MS.gene062078:CDS
CGTTGAATGACAGCATCACA+GGG 0.594896 2.3:+45268640 None:intergenic
GACCGGACATATGATGGTCG+AGG 0.605126 2.3:-45268611 MS.gene062078:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2.3:-45268667 MS.gene062078:CDS
GAACAAAACTGAACAACACA+CGG 0.651271 2.3:-45268813 MS.gene062078:CDS
GCTAGTGAGAGAAAGAACCC+TGG 0.692523 2.3:-45268835 MS.gene062078:CDS
GGAAGCTGTCAAAGTCACTG+AGG 0.723299 2.3:-45268491 MS.gene062078:CDS
GTTGAATGACAGCATCACAG+GGG 0.800398 2.3:+45268641 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTTATATTTGGATGTAAAT+TGG + chr2.3:45268892-45268911 None:intergenic 20.0%
!! TAAGTAGCAATGTTTATATT+TGG + chr2.3:45268903-45268922 None:intergenic 20.0%
!!! GAATAATTCTATTGATGATA+TGG - chr2.3:45268785-45268804 MS.gene062078:CDS 20.0%
! ACATGAATAAGAAAATTGCT+AGG - chr2.3:45268361-45268380 MS.gene062078:CDS 25.0%
! CATGAATAAGAAAATTGCTA+GGG - chr2.3:45268362-45268381 MS.gene062078:CDS 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG - chr2.3:45268821-45268840 MS.gene062078:CDS 25.0%
!!! ATTTTAATTTCCATGATTGG+TGG - chr2.3:45268763-45268782 MS.gene062078:CDS 25.0%
!!! GTGATTTTAATTTCCATGAT+TGG - chr2.3:45268760-45268779 MS.gene062078:CDS 25.0%
TAGAATTATTCCACCAATCA+TGG + chr2.3:45268776-45268795 None:intergenic 30.0%
! AATTCTTTGGAGAGTTTCAA+GGG - chr2.3:45268834-45268853 MS.gene062078:CDS 30.0%
AAGAACAAGTTCTATGCATG+TGG - chr2.3:45268552-45268571 MS.gene062078:CDS 35.0%
AGAAAAACTTGAAGAAGAGC+AGG - chr2.3:45268698-45268717 MS.gene062078:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG - chr2.3:45268655-45268674 MS.gene062078:CDS 35.0%
GAACAAAACTGAACAACACA+CGG - chr2.3:45268406-45268425 MS.gene062078:CDS 35.0%
GATGCATGAAATCAAGAAAG+AGG - chr2.3:45268437-45268456 MS.gene062078:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.3:45268673-45268692 None:intergenic 35.0%
! CGATGATTGCAGTTTTTGAT+TGG + chr2.3:45268518-45268537 None:intergenic 35.0%
! GAATTCTTTGGAGAGTTTCA+AGG - chr2.3:45268833-45268852 MS.gene062078:CDS 35.0%
!!! TGTTGTTCAGTTTTGTTCCA+GGG + chr2.3:45268404-45268423 None:intergenic 35.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.3:45268674-45268693 None:intergenic 40.0%
TGAAGAAGAGCAGGATACTT+TGG - chr2.3:45268707-45268726 MS.gene062078:CDS 40.0%
! GCATAGAACTTGTTCTTGTC+CGG + chr2.3:45268549-45268568 None:intergenic 40.0%
! GTCATTCAACGTTTTCTGAC+CGG - chr2.3:45268591-45268610 MS.gene062078:CDS 40.0%
! TTTTCTGACCGGACATATGA+TGG - chr2.3:45268602-45268621 MS.gene062078:CDS 40.0%
!!! GTGTTGTTCAGTTTTGTTCC+AGG + chr2.3:45268405-45268424 None:intergenic 40.0%
ACGTTGAATGACAGCATCAC+AGG + chr2.3:45268583-45268602 None:intergenic 45.0%
ATCCTCGACCATCATATGTC+CGG + chr2.3:45268613-45268632 None:intergenic 45.0%
CGTTGAATGACAGCATCACA+GGG + chr2.3:45268582-45268601 None:intergenic 45.0%
GACATATGATGGTCGAGGAT+GGG - chr2.3:45268613-45268632 MS.gene062078:CDS 45.0%
GAGGAAAAAGAACGCAGACT+CGG - chr2.3:45268456-45268475 MS.gene062078:CDS 45.0%
GTTGAATGACAGCATCACAG+GGG + chr2.3:45268581-45268600 None:intergenic 45.0%
TGCAATCATCGTCAAATCGC+CGG - chr2.3:45268527-45268546 MS.gene062078:CDS 45.0%
GCTAGTGAGAGAAAGAACCC+TGG - chr2.3:45268384-45268403 MS.gene062078:CDS 50.0%
GGAAGCTGTCAAAGTCACTG+AGG - chr2.3:45268728-45268747 MS.gene062078:CDS 50.0%
GGACATATGATGGTCGAGGA+TGG - chr2.3:45268612-45268631 MS.gene062078:CDS 50.0%
GACCGGACATATGATGGTCG+AGG - chr2.3:45268608-45268627 MS.gene062078:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 45268318 45268923 45268318 ID=MS.gene062078
chr2.3 mRNA 45268318 45268923 45268318 ID=MS.gene062078.t1;Parent=MS.gene062078
chr2.3 exon 45268318 45268923 45268318 ID=MS.gene062078.t1.exon1;Parent=MS.gene062078.t1
chr2.3 CDS 45268318 45268923 45268318 ID=cds.MS.gene062078.t1;Parent=MS.gene062078.t1
Gene Sequence

>MS.gene062078

ATGTTATCAGATAATTCATCATCAGTGATGTTGTATGAAACAGACATGAATAAGAAAATTGCTAGGGCTAGTGAGAGAAAGAACCCTGGAACAAAACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAGGAAAAAGAACGCAGACTCGGAATTTTCAACAAAGCAATAGAGCTGTCTATTCTATGCCAATCAAAAACTGCAATCATCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCAACGTTTTCTGACCGGACATATGATGGTCGAGGATGGGAAAAAGAAGAAAGAAAACGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGCAGGATACTTTGGAAGCTGTCAAAGTCACTGAGGCACAAAAGAGTGATTTTAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGGATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTCAAGGGTAATTTACGTTCAGCAAGCGAAGCAGAGAAGTCCAATTTACATCCAAATATAAACATTGCTACTTAA
Protein sequence

>MS.gene062078.t1

MLSDNSSSVMLYETDMNKKIARASERKNPGTKLNNTRKRKMHEIKKEEKERRLGIFNKAIELSILCQSKTAIIVKSPDKNKFYACGYPCDAVIQRFLTGHMMVEDGKKKKENDEIAETLRLQYEALQEKLEEEQDTLEAVKVTEAQKSDFNFHDWWNNSIDDMDLASLEDFKNSLESFKGNLRSASEAEKSNLHPNINIAT