AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene018779

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018779.t1 MTR_1g053575 90.164 244 16 1 1 244 1 236 8.09e-160 446
MS.gene018779.t1 MTR_1g045470 62.451 253 69 8 1 243 1 237 3.05e-92 275
MS.gene018779.t1 MTR_7g116460 60.000 205 55 5 1 183 1 200 3.67e-77 232
MS.gene018779.t1 MTR_1g019820 41.216 148 63 4 102 240 5 137 7.08e-23 93.2
MS.gene018779.t1 MTR_7g005280 32.143 168 91 9 11 170 19 171 3.05e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAAGAATCCTTGGGATATT+TGG 0.040443 1.2:-39540392 MS.gene018779:CDS
CCACCATTTGATTCGTTTCT+TGG 0.076491 1.2:+39539735 None:intergenic
AAATATCCCAAGGATTCTTT+AGG 0.262491 1.2:+39540394 None:intergenic
CCAAGAGAGACAACCATTCT+TGG 0.271875 1.2:-39539639 MS.gene018779:CDS
TCAAAAGTAGTTCGTTCTAT+TGG 0.321604 1.2:-39540282 MS.gene018779:CDS
AAAGAATCCTTGGGATATTT+GGG 0.338135 1.2:-39540391 MS.gene018779:CDS
TGGGATATTTGGGAAGAGTT+TGG 0.341365 1.2:-39540381 MS.gene018779:CDS
AGTTGGGCAGAGATTTGTTA+TGG 0.350279 1.2:+39540451 None:intergenic
ATTCTTGAATACGATTTGTT+TGG 0.353129 1.2:-39540420 MS.gene018779:CDS
GTAGTTCGTTCTATTGGAAT+TGG 0.365191 1.2:-39540276 MS.gene018779:CDS
ATCTTTGATAAGAAATCCTT+TGG 0.365896 1.2:-39540106 MS.gene018779:intron
TCTCAATTCTTCTTCAAGTA+AGG 0.366602 1.2:-39540529 MS.gene018779:CDS
AATATCCCAAGGATTCTTTA+GGG 0.371252 1.2:+39540395 None:intergenic
TGGACACAATGGCACAAATA+TGG 0.371907 1.2:-39539715 MS.gene018779:CDS
TAGTGGTAGATTTCTTCTCT+AGG 0.391403 1.2:+39540307 None:intergenic
TGTAGGACTTACAAATTTGT+TGG 0.396611 1.2:+39539605 None:intergenic
TTAAGGTAGTGAAGAAGTAT+AGG 0.409073 1.2:+39540331 None:intergenic
CCAAGAATGGTTGTCTCTCT+TGG 0.410667 1.2:+39539639 None:intergenic
AGATTTCTTCTCTAGGGTTA+AGG 0.417289 1.2:+39540314 None:intergenic
GAAAGAAAGACCATTGTTCC+TGG 0.417462 1.2:-39539938 MS.gene018779:CDS
TTGGTACCCTAAAGAATCCT+TGG 0.424102 1.2:-39540401 MS.gene018779:CDS
TTCAAGAATGGTGATATAGT+TGG 0.425134 1.2:+39540434 None:intergenic
AATCAAGTAACTTACAGATA+TGG 0.426262 1.2:+39539901 None:intergenic
TCTGCATAGAACATAATTGT+TGG 0.465415 1.2:+39539991 None:intergenic
TCAAGAATGGTGATATAGTT+GGG 0.477899 1.2:+39540435 None:intergenic
TGGTACCCTAAAGAATCCTT+GGG 0.489046 1.2:-39540400 MS.gene018779:CDS
AGTGGTAGATTTCTTCTCTA+GGG 0.491270 1.2:+39540308 None:intergenic
GAACCAAGAAACGAATCAAA+TGG 0.503929 1.2:-39539738 MS.gene018779:CDS
GTTCTATTGGAATTGGTGCA+TGG 0.508402 1.2:-39540269 MS.gene018779:CDS
AAACAAATCGTATTCAAGAA+TGG 0.519788 1.2:+39540422 None:intergenic
GGCTGCTTCGAGTCCAAGAA+TGG 0.535306 1.2:+39539626 None:intergenic
ATGGTGGTTTCTGCACGTCC+AGG 0.545124 1.2:+39539920 None:intergenic
TTCTATTGGAATTGGTGCAT+GGG 0.546914 1.2:-39540268 MS.gene018779:CDS
GCAAGATCCATGCACCATCA+TGG 0.566204 1.2:+39540148 None:intergenic
TTCTTATCAAAGATTTGTCG+AGG 0.569506 1.2:+39540115 None:intergenic
AACTCTTCCCAAATATCCCA+AGG 0.585203 1.2:+39540384 None:intergenic
CAAGTAACTTACAGATATGG+TGG 0.592493 1.2:+39539904 None:intergenic
TTCTGCACGTCCAGGAACAA+TGG 0.595867 1.2:+39539928 None:intergenic
GAATCAAATGGTGGACACAA+TGG 0.599759 1.2:-39539726 MS.gene018779:CDS
AGAAAGAATATTCATGCACA+AGG 0.627598 1.2:-39539965 MS.gene018779:CDS
ATTGGAATTGGTGCATGGGA+AGG 0.630255 1.2:-39540264 MS.gene018779:CDS
GCACTTACCATGATGGTGCA+TGG 0.633065 1.2:-39540155 MS.gene018779:CDS
AATAGTGGCACTTACCATGA+TGG 0.645072 1.2:-39540162 MS.gene018779:CDS
TGGGAAGGTGAAGAAGACAC+TGG 0.669846 1.2:-39540249 MS.gene018779:CDS
CCAAGAAACGAATCAAATGG+TGG 0.672770 1.2:-39539735 MS.gene018779:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAGATGTTAGAAATATT+TGG - chr1.2:39540441-39540460 MS.gene018779:CDS 15.0%
!!! TGTATCTTTTTTTTTTTTGT+AGG - chr1.2:39540089-39540108 MS.gene018779:intron 15.0%
!! AGAAAAACAACAATAAATGT+AGG + chr1.2:39540518-39540537 None:intergenic 20.0%
!! CTTGATTCAAGATTTAATAA+TGG - chr1.2:39540235-39540254 MS.gene018779:CDS 20.0%
! AAACAAATCGTATTCAAGAA+TGG + chr1.2:39539684-39539703 None:intergenic 25.0%
! AATCAAGTAACTTACAGATA+TGG + chr1.2:39540205-39540224 None:intergenic 25.0%
! ATCTTTGATAAGAAATCCTT+TGG - chr1.2:39539997-39540016 MS.gene018779:intron 25.0%
! ATGTTAAGTAGAAAAACAAC+CGG + chr1.2:39540275-39540294 None:intergenic 25.0%
!! ATTCTTGAATACGATTTGTT+TGG - chr1.2:39539683-39539702 MS.gene018779:CDS 25.0%
!! CATTCTTGATTTGATATGTA+GGG - chr1.2:39540305-39540324 MS.gene018779:CDS 25.0%
AAAGAATCCTTGGGATATTT+GGG - chr1.2:39539712-39539731 MS.gene018779:CDS 30.0%
AAATATCCCAAGGATTCTTT+AGG + chr1.2:39539712-39539731 None:intergenic 30.0%
AATATCCCAAGGATTCTTTA+GGG + chr1.2:39539711-39539730 None:intergenic 30.0%
AATGGATACATTTCAAGATC+CGG - chr1.2:39540253-39540272 MS.gene018779:CDS 30.0%
AGAAAGAATATTCATGCACA+AGG - chr1.2:39540138-39540157 MS.gene018779:CDS 30.0%
TAAAGAATCCTTGGGATATT+TGG - chr1.2:39539711-39539730 MS.gene018779:CDS 30.0%
TCAAAAGTAGTTCGTTCTAT+TGG - chr1.2:39539821-39539840 MS.gene018779:intron 30.0%
TCAAGAATGGTGATATAGTT+GGG + chr1.2:39539671-39539690 None:intergenic 30.0%
TCTCAATTCTTCTTCAAGTA+AGG - chr1.2:39539574-39539593 MS.gene018779:intron 30.0%
TCTGCATAGAACATAATTGT+TGG + chr1.2:39540115-39540134 None:intergenic 30.0%
TGTAGGACTTACAAATTTGT+TGG + chr1.2:39540501-39540520 None:intergenic 30.0%
TTCAAGAATGGTGATATAGT+TGG + chr1.2:39539672-39539691 None:intergenic 30.0%
TTCTTATCAAAGATTTGTCG+AGG + chr1.2:39539991-39540010 None:intergenic 30.0%
! GCATTCTTGATTTGATATGT+AGG - chr1.2:39540304-39540323 MS.gene018779:CDS 30.0%
! TTAAGGTAGTGAAGAAGTAT+AGG + chr1.2:39539775-39539794 None:intergenic 30.0%
!! TGTTATGGATTTTGTTGTAG+AGG + chr1.2:39539640-39539659 None:intergenic 30.0%
!! TGTTTTCGATTTGAGAATAG+TGG - chr1.2:39539926-39539945 MS.gene018779:CDS 30.0%
!!! GAAAACATTTTTTCACACCA+AGG + chr1.2:39539913-39539932 None:intergenic 30.0%
AAAAACAAGAACCAACTCCT+TGG - chr1.2:39539893-39539912 MS.gene018779:intron 35.0%
AGTGGTAGATTTCTTCTCTA+GGG + chr1.2:39539798-39539817 None:intergenic 35.0%
CAAGTAACTTACAGATATGG+TGG + chr1.2:39540202-39540221 None:intergenic 35.0%
GAACCAAGAAACGAATCAAA+TGG - chr1.2:39540365-39540384 MS.gene018779:CDS 35.0%
GTAGTTCGTTCTATTGGAAT+TGG - chr1.2:39539827-39539846 MS.gene018779:intron 35.0%
TAGTGGTAGATTTCTTCTCT+AGG + chr1.2:39539799-39539818 None:intergenic 35.0%
TGTATCACATTGCTTACCAA+AGG + chr1.2:39540016-39540035 None:intergenic 35.0%
TTCTATTGGAATTGGTGCAT+GGG - chr1.2:39539835-39539854 MS.gene018779:intron 35.0%
!! AGATTTCTTCTCTAGGGTTA+AGG + chr1.2:39539792-39539811 None:intergenic 35.0%
!!! ATTTTTTCACACCAAGGAGT+TGG + chr1.2:39539907-39539926 None:intergenic 35.0%
AACTCTTCCCAAATATCCCA+AGG + chr1.2:39539722-39539741 None:intergenic 40.0%
AATAGTGGCACTTACCATGA+TGG - chr1.2:39539941-39539960 MS.gene018779:CDS 40.0%
CCAAGAAACGAATCAAATGG+TGG - chr1.2:39540368-39540387 MS.gene018779:CDS 40.0%
GAAAGAAAGACCATTGTTCC+TGG - chr1.2:39540165-39540184 MS.gene018779:CDS 40.0%
GTTCTATTGGAATTGGTGCA+TGG - chr1.2:39539834-39539853 MS.gene018779:intron 40.0%
TGGACACAATGGCACAAATA+TGG - chr1.2:39540388-39540407 MS.gene018779:CDS 40.0%
TGGGATATTTGGGAAGAGTT+TGG - chr1.2:39539722-39539741 MS.gene018779:CDS 40.0%
TGGTACCCTAAAGAATCCTT+GGG - chr1.2:39539703-39539722 MS.gene018779:CDS 40.0%
TTGGTACCCTAAAGAATCCT+TGG - chr1.2:39539702-39539721 MS.gene018779:CDS 40.0%
! CCACCATTTGATTCGTTTCT+TGG + chr1.2:39540371-39540390 None:intergenic 40.0%
!! ACGAACTACTTTTGAGCTAG+TGG + chr1.2:39539816-39539835 None:intergenic 40.0%
!! AGTTGGGCAGAGATTTGTTA+TGG + chr1.2:39539655-39539674 None:intergenic 40.0%
!! GAATCAAATGGTGGACACAA+TGG - chr1.2:39540377-39540396 MS.gene018779:CDS 40.0%
ATTGGAATTGGTGCATGGGA+AGG - chr1.2:39539839-39539858 MS.gene018779:intron 45.0%
CCAAGAATGGTTGTCTCTCT+TGG + chr1.2:39540467-39540486 None:intergenic 45.0%
CCAAGAGAGACAACCATTCT+TGG - chr1.2:39540464-39540483 MS.gene018779:CDS 45.0%
GCAAGATCCATGCACCATCA+TGG + chr1.2:39539958-39539977 None:intergenic 50.0%
TGGGAAGGTGAAGAAGACAC+TGG - chr1.2:39539854-39539873 MS.gene018779:intron 50.0%
TTCTGCACGTCCAGGAACAA+TGG + chr1.2:39540178-39540197 None:intergenic 50.0%
! GCACTTACCATGATGGTGCA+TGG - chr1.2:39539948-39539967 MS.gene018779:CDS 50.0%
ATGGTGGTTTCTGCACGTCC+AGG + chr1.2:39540186-39540205 None:intergenic 55.0%
GGCTGCTTCGAGTCCAAGAA+TGG + chr1.2:39540480-39540499 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 39539569 39540556 39539569 ID=MS.gene018779
chr1.2 mRNA 39539569 39540556 39539569 ID=MS.gene018779.t1;Parent=MS.gene018779
chr1.2 exon 39540107 39540556 39540107 ID=MS.gene018779.t1.exon1;Parent=MS.gene018779.t1
chr1.2 CDS 39540107 39540556 39540107 ID=cds.MS.gene018779.t1;Parent=MS.gene018779.t1
chr1.2 exon 39539916 39540014 39539916 ID=MS.gene018779.t1.exon2;Parent=MS.gene018779.t1
chr1.2 CDS 39539916 39540014 39539916 ID=cds.MS.gene018779.t1;Parent=MS.gene018779.t1
chr1.2 exon 39539617 39539799 39539617 ID=MS.gene018779.t1.exon3;Parent=MS.gene018779.t1
chr1.2 CDS 39539617 39539799 39539617 ID=cds.MS.gene018779.t1;Parent=MS.gene018779.t1
chr1.2 exon 39539569 39539577 39539569 ID=MS.gene018779.t1.exon4;Parent=MS.gene018779.t1
chr1.2 CDS 39539569 39539577 39539569 ID=cds.MS.gene018779.t1;Parent=MS.gene018779.t1
Gene Sequence

>MS.gene018779

ATGGCTCTCAATTCTTCTTCAAGTAAGGATTTCAAATTCACACTCAGAGATGATGAACTTCTACGTTTCCTCTACAACAAAATCCATAACAAATCTCTGCCCAACTATATCACCATTCTTGAATACGATTTGTTTGGTACCCTAAAGAATCCTTGGGATATTTGGGAAGAGTTTGGAGCTTCTCGCTCATATTGTGAAAAAGACCTATACTTCTTCACTACCTTAACCCTAGAGAAGAAATCTACCACTAGCTCAAAAGTAGTTCGTTCTATTGGAATTGGTGCATGGGAAGGTGAAGAAGACACTGGAAAAATTATAGTTGCAAAAAACAAGAACCAACTCCTTGGTGTGAAAAAATGTTTTCGATTTGAGAATAGTGGCACTTACCATGATGGTGCATGGATCTTGCATGAATATAGCCTCGACAAATCTTTGATAAGAAATCCTTTGGTAAGCAATGTGATACATTTACATTATTAATTTTTCTTGTTTTTTGAAGCATATTTATATAATTTGATTTTGTATCTTTTTTTTTTTTGTAGGCCAACAATTATGTTCTATGCAGATTTAGAAAGAATATTCATGCACAAGGTAAAGAAAGAAAGACCATTGTTCCTGGACGTGCAGAAACCACCATATCTGTAAGTTACTTGATTAATTATGTTGCTTGATTCAAGATTTAATAATGGATACATTTCAAGATCCGGTTGTTTTTCTACTTAACATTGTTCTTTTGCATTCTTGATTTGATATGTAGGGAAATAAAGATTCGTTGACAAAATATATAATTTATAAAGAACCAAGAAACGAATCAAATGGTGGACACAATGGCACAAATATGGTTAATACAGAGTCTCATTATAAGAAAGAAGAAAAAGATGTTAGAAATATTTGGCCAAGAGAGACAACCATTCTTGGACTCGAAGCAGCCAACAAATTTGTAAGTCCTACATTTATTGTTGTTTTTCTTATTTTTTAGAGTTTCTAG
Protein sequence

>MS.gene018779.t1

MALNSSSSKDFKFTLRDDELLRFLYNKIHNKSLPNYITILEYDLFGTLKNPWDIWEEFGASRSYCEKDLYFFTTLTLEKKSTTSSKVVRSIGIGAWEGEEDTGKIIVAKNKNQLLGVKKCFRFENSGTYHDGAWILHEYSLDKSLIRNPLANNYVLCRFRKNIHAQGKERKTIVPGRAETTISGNKDSLTKYIIYKEPRNESNGGHNGTNMVNTESHYKKEEKDVRNIWPRETTILGLEAANKFSF