AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052448

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052448.t1 MTR_6g086760 80.723 83 12 1 10 88 8 90 5.40e-39 125
MS.gene052448.t1 MTR_6g086765 87.273 55 7 0 18 72 37 91 1.73e-23 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCATTCTCCTGCTGGTT+TGG 0.290743 6.1:+75373622 None:intergenic
TTAGATGTACCTTCTTCATT+TGG 0.332645 6.1:+75373658 None:intergenic
CTTAAGCTTCATTCTCCTGC+TGG 0.359038 6.1:+75373617 None:intergenic
AAATGAAGAAGGTACATCTA+AGG 0.414920 6.1:-75373656 MS.gene052448:CDS
AAGTGGAAGTGGAGGAAGCC+GGG 0.449093 6.1:+75374180 None:intergenic
TCGTCAATCACACTGCAAAC+AGG 0.488932 6.1:+75374153 None:intergenic
GTATGCAGCGCGGACTGCCC+TGG 0.503284 6.1:-75373800 MS.gene052448:CDS
GAAGTGGAAGTGGAGGAAGC+CGG 0.515793 6.1:+75374179 None:intergenic
AAACAGGAGGGAAGTGGAAG+TGG 0.519609 6.1:+75374169 None:intergenic
CACTGCAAACAGGAGGGAAG+TGG 0.520900 6.1:+75374163 None:intergenic
AGCTGAAGTTCCAAACCAGC+AGG 0.526615 6.1:-75373632 MS.gene052448:CDS
CAGGAGGGAAGTGGAAGTGG+AGG 0.585934 6.1:+75374172 None:intergenic
GCTGAAGTTCCAAATGAAGA+AGG 0.589203 6.1:-75373667 MS.gene052448:CDS
TCAATCACACTGCAAACAGG+AGG 0.629072 6.1:+75374156 None:intergenic
AAACCGCAAATGGCTCCACC+CGG 0.634759 6.1:-75374198 None:intergenic
CAATCACACTGCAAACAGGA+GGG 0.665161 6.1:+75374157 None:intergenic
TGGAAGTGGAGGAAGCCGGG+TGG 0.674546 6.1:+75374183 None:intergenic
TGGAGTTGTTGTATGCAGCG+CGG 0.721128 6.1:-75373810 MS.gene052448:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTAAAGAACTCAAAATA+TGG + chr6.1:75373783-75373802 None:intergenic 15.0%
!! AAATGTTAACTAAGTTTATG+GGG - chr6.1:75373711-75373730 MS.gene052448:CDS 20.0%
!! GAAATGTTAACTAAGTTTAT+GGG - chr6.1:75373710-75373729 MS.gene052448:CDS 20.0%
!! TGAAATGTTAACTAAGTTTA+TGG - chr6.1:75373709-75373728 MS.gene052448:CDS 20.0%
!!! ATATGAGCAATAGTAATTTT+AGG + chr6.1:75373839-75373858 None:intergenic 20.0%
!!! AGAAAGAAGCTGATTTTAAA+AGG - chr6.1:75374045-75374064 MS.gene052448:intron 25.0%
!!! GAAAGAAGCTGATTTTAAAA+GGG - chr6.1:75374046-75374065 MS.gene052448:intron 25.0%
TAAATTTAAAGAACTTGCCG+CGG + chr6.1:75373906-75373925 None:intergenic 30.0%
TTAGATGTACCTTCTTCATT+TGG + chr6.1:75374152-75374171 None:intergenic 30.0%
TTCATGAAAAAACTTGCCTT+GGG + chr6.1:75373693-75373712 None:intergenic 30.0%
TTTCATGAAAAAACTTGCCT+TGG + chr6.1:75373694-75373713 None:intergenic 30.0%
! AAATGAAGAAGGTACATCTA+AGG - chr6.1:75374151-75374170 MS.gene052448:intron 30.0%
AAATTTAAAGAACTTGCCGC+GGG + chr6.1:75373905-75373924 None:intergenic 35.0%
AGATGAAAAAGCTGCATCTA+AGG - chr6.1:75374115-75374134 MS.gene052448:intron 35.0%
! TTTTAGGCTTCAATTTCTGC+TGG + chr6.1:75373823-75373842 None:intergenic 35.0%
!! CTGCTTTTCAATTTCATCCA+GGG + chr6.1:75374027-75374046 None:intergenic 35.0%
!! TCTGCTTTTCAATTTCATCC+AGG + chr6.1:75374028-75374047 None:intergenic 35.0%
GCTGAAGTTCCAAATGAAGA+AGG - chr6.1:75374140-75374159 MS.gene052448:intron 40.0%
TTAACCTCTAAACCAGCAGT+TGG - chr6.1:75373977-75373996 MS.gene052448:intron 40.0%
CAATCACACTGCAAACAGGA+GGG + chr6.1:75373653-75373672 None:intergenic 45.0%
CATACAACAACTCCAACTGC+TGG + chr6.1:75373992-75374011 None:intergenic 45.0%
TCAATCACACTGCAAACAGG+AGG + chr6.1:75373654-75373673 None:intergenic 45.0%
TCGTCAATCACACTGCAAAC+AGG + chr6.1:75373657-75373676 None:intergenic 45.0%
TGTGTCTGATTTACAACCCG+CGG - chr6.1:75373886-75373905 MS.gene052448:intron 45.0%
!! AACTCCAACTGCTGGTTTAG+AGG + chr6.1:75373984-75374003 None:intergenic 45.0%
!! GCTGATTTTAAAAGGGCTGC+AGG - chr6.1:75374053-75374072 MS.gene052448:intron 45.0%
AAACAGGAGGGAAGTGGAAG+TGG + chr6.1:75373641-75373660 None:intergenic 50.0%
AGCTGAAGTTCCAAACCAGC+AGG - chr6.1:75374175-75374194 MS.gene052448:CDS 50.0%
CGAACTTTCTGCAGAACCCA+AGG - chr6.1:75373674-75373693 MS.gene052448:CDS 50.0%
TGGAGTTGTTGTATGCAGCG+CGG - chr6.1:75373997-75374016 MS.gene052448:intron 50.0%
! GCTTCATTCTCCTGCTGGTT+TGG + chr6.1:75374188-75374207 None:intergenic 50.0%
AAGTGGAAGTGGAGGAAGCC+GGG + chr6.1:75373630-75373649 None:intergenic 55.0%
CACTGCAAACAGGAGGGAAG+TGG + chr6.1:75373647-75373666 None:intergenic 55.0%
GAAGTGGAAGTGGAGGAAGC+CGG + chr6.1:75373631-75373650 None:intergenic 55.0%
CAGGAGGGAAGTGGAAGTGG+AGG + chr6.1:75373638-75373657 None:intergenic 60.0%
TGGAAGTGGAGGAAGCCGGG+TGG + chr6.1:75373627-75373646 None:intergenic 65.0%
! GTATGCAGCGCGGACTGCCC+TGG - chr6.1:75374007-75374026 MS.gene052448:intron 70.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 75373618 75374211 75373618 ID=MS.gene052448
chr6.1 mRNA 75373618 75374211 75373618 ID=MS.gene052448.t1;Parent=MS.gene052448
chr6.1 exon 75374164 75374211 75374164 ID=MS.gene052448.t1.exon1;Parent=MS.gene052448.t1
chr6.1 CDS 75374164 75374211 75374164 ID=cds.MS.gene052448.t1;Parent=MS.gene052448.t1
chr6.1 exon 75373618 75373836 75373618 ID=MS.gene052448.t1.exon2;Parent=MS.gene052448.t1
chr6.1 CDS 75373618 75373836 75373618 ID=cds.MS.gene052448.t1;Parent=MS.gene052448.t1
Gene Sequence

>MS.gene052448

ATGGCTCCACCCGGCTTCCTCCACTTCCACTTCCCTCCTGTTTGCAGTGTGATTGACGAACTTTCTGCAGAACCCAAGGCAAGTTTTTTCATGAAATGTTAACTAAGTTTATGGGGCTGAAGCAATACTTACTTCTTATAAAAACAATCTTATTTTCTTTGTCCATATTTTGAGTTCTTTAATAATATTTATCTCTATATCACCAGCAGAAATTGAAGCCTAAAATTACTATTGCTCATATTGAAAAGCTCGTGAGAACTGCGAAGACTGTGTCTGATTTACAACCCGCGGCAAGTTCTTTAAATTTAAGTTTCATACTTTTAGTTTCTTTGTTTATATTTTGAGTTCTTTAATATTAATTAACCTCTAAACCAGCAGTTGGAGTTGTTGTATGCAGCGCGGACTGCCCTGGATGAAATTGAAAAGCAGAAAGAAGCTGATTTTAAAAGGGCTGCAGGTGAAATTAAGAAACTGAGAGTTCAAATTCAAAAGAAGATAGATGAAAAAGCTGCATCTAAGGCAGCTGAAGTTCCAAATGAAGAAGGTACATCTAAGGCAGCTGAAGTTCCAAACCAGCAGGAGAATGAAGCTTAA
Protein sequence

>MS.gene052448.t1

MAPPGFLHFHFPPVCSQLELLYAARTALDEIEKQKEADFKRAAGEIKKLRVQIQKKIDEKAASKAAEVPNEEGTSKAAEVPNQQENEA