AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene69873

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69873.t1 MTR_0097s0070 94.937 158 8 0 16 173 44 201 2.10e-107 305
MS.gene69873.t1 MTR_8g089300 72.848 151 41 0 16 166 43 193 1.02e-70 212
MS.gene69873.t1 MTR_4g118810 34.351 131 80 3 16 143 50 177 9.58e-18 77.0
MS.gene69873.t1 MTR_0004s0210 28.846 156 101 2 12 164 9 157 6.17e-17 73.9
MS.gene69873.t1 MTR_7g108130 29.167 144 95 2 24 161 43 185 1.08e-15 71.6
MS.gene69873.t1 MTR_2g020060 27.815 151 98 3 16 161 40 184 6.24e-13 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene69873.t1 AT5G44550 56.954 151 65 0 16 166 35 185 9.27e-58 179
MS.gene69873.t1 AT4G20390 53.378 148 69 0 15 162 34 181 4.91e-44 144
MS.gene69873.t1 AT1G03700 28.000 125 83 2 40 164 41 158 8.86e-14 65.9
MS.gene69873.t1 AT1G14160 29.915 117 82 0 41 157 86 202 1.56e-13 66.2
MS.gene69873.t1 AT4G15630 28.082 146 103 2 17 161 45 189 1.70e-12 63.2
MS.gene69873.t1 AT4G03540 28.244 131 78 3 16 146 26 140 2.30e-12 62.0
MS.gene69873.t1 AT4G15620 28.767 146 102 2 17 161 45 189 5.57e-12 61.6
MS.gene69873.t1 AT4G15610 28.244 131 87 3 16 144 46 171 7.08e-12 61.2
MS.gene69873.t1 AT5G15290 32.692 104 68 2 42 144 64 166 1.25e-11 60.5

Find 40 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTGGAGTTTGATTAAATT+TGG 0.215698 2.1:-42288612 None:intergenic
GCCCTTATTGCTTCTTTCAT+TGG 0.228754 2.1:+42289451 MS.gene69873:CDS
GCAGAAAGAGTAGCAGTTAT+TGG 0.256041 2.1:-42288590 None:intergenic
AAGTCCTTTGTAATCATATT+GGG 0.274380 2.1:-42289150 None:intergenic
CAGAAAGAGTAGCAGTTATT+GGG 0.306576 2.1:-42288589 None:intergenic
GAAGTCCTTTGTAATCATAT+TGG 0.328703 2.1:-42289151 None:intergenic
AGCCAATGAAAGAAGCAATA+AGG 0.340360 2.1:-42289453 None:intergenic
AATGCCAATAACAAAACTAT+TGG 0.406397 2.1:-42288555 None:intergenic
TTTGAAAGCTATTGCAATAG+AGG 0.418883 2.1:+42289421 MS.gene69873:CDS
ATGTCAGCATTGGGAAGAAA+TGG 0.423404 2.1:+42289361 MS.gene69873:CDS
GCCAATGAAAGAAGCAATAA+GGG 0.431019 2.1:-42289452 None:intergenic
TTGAAAACTTACACAAAAGC+TGG 0.437745 2.1:-42288629 None:intergenic
ATGATTGCATTGGATATGTT+AGG 0.445999 2.1:+42289125 MS.gene69873:CDS
ATGCAATCATCACCAAGTTA+TGG 0.467360 2.1:-42289112 None:intergenic
GGAGCATGGTTAATGCGATT+AGG 0.484616 2.1:-42289526 None:intergenic
AGCAACATTCATGTCAGCAT+TGG 0.488005 2.1:+42289351 MS.gene69873:CDS
ACTATGGCTCTGGCATCAGC+TGG 0.494373 2.1:+42289319 MS.gene69873:CDS
GCGATTAGGCTTGAGAAGCT+TGG 0.494528 2.1:-42289512 None:intergenic
GCAACATTCATGTCAGCATT+GGG 0.495269 2.1:+42289352 MS.gene69873:CDS
AAATGCTAGTCTCCATAACT+TGG 0.496794 2.1:+42289100 MS.gene69873:CDS
GGTGAAGTTAACTATGGCTC+TGG 0.500555 2.1:+42289309 MS.gene69873:intron
ATGGAGACTAGCATTTCCAT+TGG 0.506652 2.1:-42289093 None:intergenic
ATGTTAATCATATCAAGGAC+TGG 0.510976 2.1:-42289548 None:intergenic
TGGAGACTAGCATTTCCATT+GGG 0.512268 2.1:-42289092 None:intergenic
TGGTAATTCACATGCAAGAT+GGG 0.512674 2.1:+42289381 MS.gene69873:CDS
ATGGTAATTCACATGCAAGA+TGG 0.522902 2.1:+42289380 MS.gene69873:CDS
GCTCTGGCATCAGCTGGAGA+TGG 0.540036 2.1:+42289325 MS.gene69873:CDS
TAACTTGGTGATGATTGCAT+TGG 0.550469 2.1:+42289115 MS.gene69873:CDS
CATATCAAGGACTGGGAGCA+TGG 0.559515 2.1:-42289540 None:intergenic
TGTTAATCATATCAAGGACT+GGG 0.560345 2.1:-42289547 None:intergenic
AGGCTTGAGAAGCTTGGCAA+TGG 0.561801 2.1:-42289506 None:intergenic
AGGTTCTTTGTGATACCCAA+TGG 0.564051 2.1:+42289077 MS.gene69873:intron
CTAAAATTGCAATAAATGCA+AGG 0.578209 2.1:-42289175 None:intergenic
AGCTATTGCAATAGAGGTGG+TGG 0.598102 2.1:+42289427 MS.gene69873:CDS
GAAAGCTATTGCAATAGAGG+TGG 0.619990 2.1:+42289424 MS.gene69873:CDS
TCACAGTGATAATCAAGAGA+AGG 0.626568 2.1:-42289480 None:intergenic
AGTCCTTTGTAATCATATTG+GGG 0.628572 2.1:-42289149 None:intergenic
AGAAAGAGTAGCAGTTATTG+GGG 0.633112 2.1:-42288588 None:intergenic
TTGTTGAGTGCCATCACAAG+TGG 0.646450 2.1:-42288527 None:intergenic
GGACCCCAATATGATTACAA+AGG 0.686673 2.1:+42289146 MS.gene69873:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTAATTTTTTTTCTT+AGG + chr2.1:42289240-42289259 MS.gene69873:intron 10.0%
!!! TTTTTATAGGTAAATATTAG+TGG - chr2.1:42288884-42288903 None:intergenic 15.0%
!! TTACCTATAAAAAATGTAAG+AGG + chr2.1:42288891-42288910 MS.gene69873:intron 20.0%
!!! AATATTAGTGGTTAATTTGT+CGG - chr2.1:42288872-42288891 None:intergenic 20.0%
!!! ACACAAAAAAAGTTTTATGT+AGG + chr2.1:42288804-42288823 MS.gene69873:intron 20.0%
!!! ATTTATTGCAATTTTAGACA+TGG + chr2.1:42289181-42289200 MS.gene69873:CDS 20.0%
!!! TTTCCTCTTACATTTTTTAT+AGG - chr2.1:42288897-42288916 None:intergenic 20.0%
! AACGAACATAAATAGAAAAG+AGG - chr2.1:42288691-42288710 None:intergenic 25.0%
! AAGTCCTTTGTAATCATATT+GGG - chr2.1:42289153-42289172 None:intergenic 25.0%
! AATGCCAATAACAAAACTAT+TGG - chr2.1:42288558-42288577 None:intergenic 25.0%
! AATTTCATCGCTTAATTCAA+AGG + chr2.1:42288949-42288968 MS.gene69873:intron 25.0%
! CTAAAATTGCAATAAATGCA+AGG - chr2.1:42289178-42289197 None:intergenic 25.0%
! TTACATTAACACATCATTGT+GGG + chr2.1:42289047-42289066 MS.gene69873:intron 25.0%
! TTTACATTAACACATCATTG+TGG + chr2.1:42289046-42289065 MS.gene69873:intron 25.0%
!! ATTGGATTCTTTTATCTCTT+AGG + chr2.1:42288488-42288507 MS.gene69873:CDS 25.0%
!! TTGGATTCTTTTATCTCTTA+GGG + chr2.1:42288489-42288508 MS.gene69873:CDS 25.0%
!!! ATATTAGTGGTTAATTTGTC+GGG - chr2.1:42288871-42288890 None:intergenic 25.0%
!!! CAAAAAAAGTTTTATGTAGG+AGG + chr2.1:42288807-42288826 MS.gene69873:intron 25.0%
AGCTGGAGTTTGATTAAATT+TGG - chr2.1:42288615-42288634 None:intergenic 30.0%
AGTCCTTTGTAATCATATTG+GGG - chr2.1:42289152-42289171 None:intergenic 30.0%
ATGATTGCATTGGATATGTT+AGG + chr2.1:42289125-42289144 MS.gene69873:CDS 30.0%
GAAGTCCTTTGTAATCATAT+TGG - chr2.1:42289154-42289173 None:intergenic 30.0%
TACATTAACACATCATTGTG+GGG + chr2.1:42289048-42289067 MS.gene69873:intron 30.0%
TGTAAGAGGAAAATAGAGAA+AGG + chr2.1:42288905-42288924 MS.gene69873:intron 30.0%
TTGAAAACTTACACAAAAGC+TGG - chr2.1:42288632-42288651 None:intergenic 30.0%
TTTGAAAGCTATTGCAATAG+AGG + chr2.1:42289421-42289440 MS.gene69873:CDS 30.0%
!! TATTAGTGGTTAATTTGTCG+GGG - chr2.1:42288870-42288889 None:intergenic 30.0%
!!! CAGACCAATAGTTTTGTTAT+TGG + chr2.1:42288551-42288570 MS.gene69873:CDS 30.0%
!!! TTTTTGGGTGAAGTTAACTA+TGG + chr2.1:42289303-42289322 MS.gene69873:intron 30.0%
AGAAAGAGTAGCAGTTATTG+GGG - chr2.1:42288591-42288610 None:intergenic 35.0%
AGCCAATGAAAGAAGCAATA+AGG - chr2.1:42289456-42289475 None:intergenic 35.0%
ATGCAATCATCACCAAGTTA+TGG - chr2.1:42289115-42289134 None:intergenic 35.0%
ATGGTAATTCACATGCAAGA+TGG + chr2.1:42289380-42289399 MS.gene69873:CDS 35.0%
CAGAAAGAGTAGCAGTTATT+GGG - chr2.1:42288592-42288611 None:intergenic 35.0%
GCCAATGAAAGAAGCAATAA+GGG - chr2.1:42289455-42289474 None:intergenic 35.0%
TAGTAGAAGAGGTCGAATTT+CGG - chr2.1:42288834-42288853 None:intergenic 35.0%
TCACAGTGATAATCAAGAGA+AGG - chr2.1:42289483-42289502 None:intergenic 35.0%
TGGTAATTCACATGCAAGAT+GGG + chr2.1:42289381-42289400 MS.gene69873:CDS 35.0%
! AAATGCTAGTCTCCATAACT+TGG + chr2.1:42289100-42289119 MS.gene69873:CDS 35.0%
! GATTCTTTTATCTCTTAGGG+TGG + chr2.1:42288492-42288511 MS.gene69873:CDS 35.0%
!! ATTAGTGGTTAATTTGTCGG+GGG - chr2.1:42288869-42288888 None:intergenic 35.0%
!! TAACTTGGTGATGATTGCAT+TGG + chr2.1:42289115-42289134 MS.gene69873:CDS 35.0%
!!! AGTTTTGTTATTGGCATTGC+TGG + chr2.1:42288560-42288579 MS.gene69873:CDS 35.0%
AGCAACATTCATGTCAGCAT+TGG + chr2.1:42289351-42289370 MS.gene69873:CDS 40.0%
AGGTTCTTTGTGATACCCAA+TGG + chr2.1:42289077-42289096 MS.gene69873:intron 40.0%
ATACGATTGGACTACTCGTT+CGG - chr2.1:42288751-42288770 None:intergenic 40.0%
ATGGAGACTAGCATTTCCAT+TGG - chr2.1:42289096-42289115 None:intergenic 40.0%
CCATCACAAGTGGCAAAAAA+TGG - chr2.1:42288520-42288539 None:intergenic 40.0%
GAAAGCTATTGCAATAGAGG+TGG + chr2.1:42289424-42289443 MS.gene69873:CDS 40.0%
GAGAGAGTTGTTAGTAGAAG+AGG - chr2.1:42288845-42288864 None:intergenic 40.0%
GCAACATTCATGTCAGCATT+GGG + chr2.1:42289352-42289371 MS.gene69873:CDS 40.0%
GCAGAAAGAGTAGCAGTTAT+TGG - chr2.1:42288593-42288612 None:intergenic 40.0%
GCCCTTATTGCTTCTTTCAT+TGG + chr2.1:42289451-42289470 MS.gene69873:CDS 40.0%
GGACCCCAATATGATTACAA+AGG + chr2.1:42289146-42289165 MS.gene69873:CDS 40.0%
TGGAGACTAGCATTTCCATT+GGG - chr2.1:42289095-42289114 None:intergenic 40.0%
TGTGTCTGAATCGATACGAT+TGG - chr2.1:42288789-42288808 None:intergenic 40.0%
! ATGTCAGCATTGGGAAGAAA+TGG + chr2.1:42289361-42289380 MS.gene69873:CDS 40.0%
!!! CCATTTTTTGCCACTTGTGA+TGG + chr2.1:42288517-42288536 MS.gene69873:CDS 40.0%
ACATCATTGTGGGGTGAAAC+AGG + chr2.1:42289057-42289076 MS.gene69873:intron 45.0%
AGCTATTGCAATAGAGGTGG+TGG + chr2.1:42289427-42289446 MS.gene69873:CDS 45.0%
GGAGCATGGTTAATGCGATT+AGG - chr2.1:42289529-42289548 None:intergenic 45.0%
GGTGAAGTTAACTATGGCTC+TGG + chr2.1:42289309-42289328 MS.gene69873:intron 45.0%
TACGATTGGACTACTCGTTC+GGG - chr2.1:42288750-42288769 None:intergenic 45.0%
TTGTTGAGTGCCATCACAAG+TGG - chr2.1:42288530-42288549 None:intergenic 45.0%
!!! TTGATAAATAATATTTTTTT+GGG + chr2.1:42289288-42289307 MS.gene69873:intron 5.0%
!!! TTTGATAAATAATATTTTTT+TGG + chr2.1:42289287-42289306 MS.gene69873:intron 5.0%
ACGATTGGACTACTCGTTCG+GGG - chr2.1:42288749-42288768 None:intergenic 50.0%
AGGCTTGAGAAGCTTGGCAA+TGG - chr2.1:42289509-42289528 None:intergenic 50.0%
GCGATTAGGCTTGAGAAGCT+TGG - chr2.1:42289515-42289534 None:intergenic 50.0%
TACTCGTTCGGCGATACGAT+TGG - chr2.1:42288764-42288783 None:intergenic 50.0%
CGATTGGACTACTCGTTCGG+GGG - chr2.1:42288748-42288767 None:intergenic 55.0%
!! ACTATGGCTCTGGCATCAGC+TGG + chr2.1:42289319-42289338 MS.gene69873:CDS 55.0%
GCTCTGGCATCAGCTGGAGA+TGG + chr2.1:42289325-42289344 MS.gene69873:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 42288485 42289558 42288485 ID=MS.gene69873
chr2.1 mRNA 42288485 42289558 42288485 ID=MS.gene69873.t1;Parent=MS.gene69873
chr2.1 exon 42288485 42288639 42288485 ID=MS.gene69873.t1.exon1;Parent=MS.gene69873.t1
chr2.1 CDS 42288485 42288639 42288485 ID=cds.MS.gene69873.t1;Parent=MS.gene69873.t1
chr2.1 exon 42289079 42289202 42289079 ID=MS.gene69873.t1.exon2;Parent=MS.gene69873.t1
chr2.1 CDS 42289079 42289202 42289079 ID=cds.MS.gene69873.t1;Parent=MS.gene69873.t1
chr2.1 exon 42289316 42289558 42289316 ID=MS.gene69873.t1.exon3;Parent=MS.gene69873.t1
chr2.1 CDS 42289316 42289558 42289316 ID=cds.MS.gene69873.t1;Parent=MS.gene69873.t1
Gene Sequence

>MS.gene69873

ATGATTGGATTCTTTTATCTCTTAGGGTGGCTCCATTTTTTGCCACTTGTGATGGCACTCAACAAACAGACCAATAGTTTTGTTATTGGCATTGCTGGTAACACCCCAATAACTGCTACTCTTTCTGCCAAATTTAATCAAACTCCAGCTTTTGTGTAAGTTTTCAATAATTATATATATACAAATATTTATGATTCTACTTTCCTCTTTTCTATTTATGTTCGTTTGCAAGAAAACATATAAGTAGTAATAAATAGAGTCCCCCGAACGAGTAGTCCAATCGTATCGCCGAACGAGTAGTCCAATCGTATCGATTCAGACACAAAAAAAGTTTTATGTAGGAGGTCCGAAATTCGACCTCTTCTACTAACAACTCTCTCTCCCCCGACAAATTAACCACTAATATTTACCTATAAAAAATGTAAGAGGAAAATAGAGAAAGGAAATTGTTATGATCTGTCTCTAATTTCATCGCTTAATTCAAAGGCGATGAATTTAGAGATATGTTTAATTTTTTTGTGATGATATAGCTATTTTTATTTTATTATAGATTTTTATACATTTACATTAACACATCATTGTGGGGTGAAACAGGTTCTTTGTGATACCCAATGGAAATGCTAGTCTCCATAACTTGGTGATGATTGCATTGGATATGTTAGGACCCCAATATGATTACAAAGGACTTCGCCTTGCATTTATTGCAATTTTAGACATGGTAATTTTTGTTAATTAATTTTACATCAATTCTACAAGTTTTTTAATTTTTTTTCTTAGGATATCATTTATGTAAGAAAAAATGTTTGATAAATAATATTTTTTTGGGTGAAGTTAACTATGGCTCTGGCATCAGCTGGAGATGGTGCAGCAACATTCATGTCAGCATTGGGAAGAAATGGTAATTCACATGCAAGATGGGATAAGATTTGTGACAAATTTGAAAGCTATTGCAATAGAGGTGGTGGTGCCCTTATTGCTTCTTTCATTGGCTTCATCCTTCTCTTGATTATCACTGTGATGTCCATTGCCAAGCTTCTCAAGCCTAATCGCATTAACCATGCTCCCAGTCCTTGA
Protein sequence

>MS.gene69873.t1

MIGFFYLLGWLHFLPLVMALNKQTNSFVIGIAGNTPITATLSAKFNQTPAFVFFVIPNGNASLHNLVMIALDMLGPQYDYKGLRLAFIAILDMLTMALASAGDGAATFMSALGRNGNSHARWDKICDKFESYCNRGGGALIASFIGFILLLIITVMSIAKLLKPNRINHAPSP