AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene26877


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene26877.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 5.14e-31 115
MS.gene26877.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 1.16e-21 89.7
MS.gene26877.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 4.20e-18 80.1
MS.gene26877.t1 MTR_4g112730 57.971 69 28 1 143 211 2 69 7.91e-18 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 1.4:-80109125 MS.gene26877:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 1.4:-80109145 MS.gene26877:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 1.4:+80108829 None:intergenic
CAAAAGATCCCAAGATCTTA+TGG 0.237847 1.4:-80109203 MS.gene26877:CDS
GATTCTTGAGGGAGAAGATT+TGG 0.253340 1.4:-80109322 MS.gene26877:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 1.4:-80109180 MS.gene26877:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 1.4:+80109371 None:intergenic
CACGACCTCCACCACGAAAA+TGG 0.277262 1.4:+80108713 None:intergenic
GATCTTATGGGACAAAATTA+AGG 0.310971 1.4:-80109190 MS.gene26877:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 1.4:-80108935 MS.gene26877:CDS
ATTCTTGAGGGAGAAGATTT+GGG 0.333151 1.4:-80109321 MS.gene26877:CDS
AGACAGGTAGTGTCATTCTT+TGG 0.342502 1.4:+80108457 None:intergenic
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 1.4:-80109301 MS.gene26877:CDS
GAAGAGGTTATATGAATTAC+AGG 0.363099 1.4:-80108690 MS.gene26877:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 1.4:+80108614 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 1.4:+80108779 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 1.4:-80108769 MS.gene26877:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 1.4:-80109179 MS.gene26877:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 1.4:-80109022 MS.gene26877:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 1.4:-80109137 MS.gene26877:CDS
CGTGGTGGAGGTCGTGGAAG+AGG 0.449888 1.4:-80108706 MS.gene26877:CDS
TCCTGCATGCTTTAGCCCAA+TGG 0.457473 1.4:+80108557 None:intergenic
AAAAGATCCCAAGATCTTAT+GGG 0.458748 1.4:-80109202 MS.gene26877:CDS
AACCATCAGTTGCGTCCTAC+AGG 0.459311 1.4:-80108865 MS.gene26877:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 1.4:-80109031 MS.gene26877:CDS
ATCTGTGGATGGAAAGGAAA+GGG 0.491819 1.4:-80108503 MS.gene26877:CDS
ATCAAGCACCACATTGATGA+TGG 0.492315 1.4:-80109249 MS.gene26877:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.495634 1.4:-80108580 MS.gene26877:CDS
CTGGCGACAACTACATAACC+TGG 0.502097 1.4:-80109389 MS.gene26877:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 1.4:+80109134 None:intergenic
ATGCGGAAAGAAAGGCCATT+GGG 0.516896 1.4:-80108572 MS.gene26877:CDS
TTTGATTGGTCATATTTGAG+AGG 0.522357 1.4:+80108667 None:intergenic
CAAAGAATCTGTGGATGGAA+AGG 0.532926 1.4:-80108509 MS.gene26877:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 1.4:+80109135 None:intergenic
CGTGGACGAGGTAGAAATCA+TGG 0.535808 1.4:-80108742 MS.gene26877:CDS
GGACTCGATAAGATTCTTGA+GGG 0.539399 1.4:-80109333 MS.gene26877:CDS
GCCATTGGGCTAAAGCATGC+AGG 0.539769 1.4:-80108558 MS.gene26877:CDS
CCCTCTAGAAATCATGATGA+TGG 0.541875 1.4:-80108604 MS.gene26877:CDS
TTCCTGTAGGACGCAACTGA+TGG 0.562606 1.4:+80108863 None:intergenic
AAAATCAGCAGCCTCAAGAC+AGG 0.562896 1.4:+80108441 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 1.4:-80109355 MS.gene26877:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 1.4:-80109354 MS.gene26877:CDS
TTTGGTTGCAGCCCTTCTAG+TGG 0.582793 1.4:-80108917 MS.gene26877:CDS
GATGCGGAAAGAAAGGCCAT+TGG 0.583841 1.4:-80108573 MS.gene26877:CDS
TTGTGCAATAATTTGATGCA+TGG 0.588693 1.4:+80109065 None:intergenic
TAAAAGATACAAAGAATCTG+TGG 0.594054 1.4:-80108518 MS.gene26877:CDS
AGATACAAAGAATCTGTGGA+TGG 0.602731 1.4:-80108514 MS.gene26877:CDS
GGGACTCGATAAGATTCTTG+AGG 0.606176 1.4:-80109334 MS.gene26877:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 1.4:+80108816 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 1.4:+80108980 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 1.4:-80108787 MS.gene26877:CDS
ACCATCATCATGATTTCTAG+AGG 0.616492 1.4:+80108603 None:intergenic
GGATACGACATTGTTCCTGT+AGG 0.627452 1.4:+80108850 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 1.4:-80108793 MS.gene26877:CDS
CCATCATCATGATTTCTAGA+GGG 0.647682 1.4:+80108604 None:intergenic
GAATGACACTACCTGTCTTG+AGG 0.649563 1.4:-80108452 MS.gene26877:CDS
AATCTGTGGATGGAAAGGAA+AGG 0.653361 1.4:-80108504 MS.gene26877:CDS
GATGATGGTTGTTATAGATG+CGG 0.696569 1.4:-80108589 MS.gene26877:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 1.4:-80108784 MS.gene26877:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 1.4:+80109241 None:intergenic
AGATTTGGGAGATGTCCCAG+AGG 0.741186 1.4:-80109307 MS.gene26877:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCAAAATTTTAAGCATAAC+TGG - chr1.4:80108435-80108454 MS.gene26877:CDS 20.0%
! ACAAAATTAAGGCAAGATTT+GGG - chr1.4:80108664-80108683 MS.gene26877:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG - chr1.4:80108908-80108927 MS.gene26877:CDS 25.0%
! CAATCAAACAAAAATCATCA+GGG - chr1.4:80109191-80109210 MS.gene26877:CDS 25.0%
! TAAAAGATACAAAGAATCTG+TGG - chr1.4:80109325-80109344 MS.gene26877:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG - chr1.4:80108821-80108840 MS.gene26877:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG - chr1.4:80108792-80108811 MS.gene26877:CDS 25.0%
!! TATCTTTTACATAGATACTC+TGG + chr1.4:80109314-80109333 None:intergenic 25.0%
!!! CAACAACAGTTTTATAATCT+TGG + chr1.4:80108746-80108765 None:intergenic 25.0%
!!! TGTTGAAGGAGATTTTAATA+TGG - chr1.4:80109424-80109443 MS.gene26877:CDS 25.0%
AAAAGATCCCAAGATCTTAT+GGG - chr1.4:80108641-80108660 MS.gene26877:CDS 30.0%
AACAAAAATCATCAGGGTAA+AGG - chr1.4:80109197-80109216 MS.gene26877:CDS 30.0%
CCAATCAAACAAAAATCATC+AGG - chr1.4:80109190-80109209 MS.gene26877:CDS 30.0%
GAAGAGGTTATATGAATTAC+AGG - chr1.4:80109153-80109172 MS.gene26877:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG - chr1.4:80108663-80108682 MS.gene26877:CDS 30.0%
GATCTTATGGGACAAAATTA+AGG - chr1.4:80108653-80108672 MS.gene26877:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG - chr1.4:80108718-80108737 MS.gene26877:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG - chr1.4:80108812-80108831 MS.gene26877:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG + chr1.4:80108711-80108730 None:intergenic 30.0%
TTGTGCAATAATTTGATGCA+TGG + chr1.4:80108781-80108800 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG + chr1.4:80108605-80108624 None:intergenic 30.0%
! AATTTTGTCCCATAAGATCT+TGG + chr1.4:80108652-80108671 None:intergenic 30.0%
! ATTTTGTCCCATAAGATCTT+GGG + chr1.4:80108651-80108670 None:intergenic 30.0%
! TTTGATTGGTCATATTTGAG+AGG + chr1.4:80109179-80109198 None:intergenic 30.0%
!! CCTGATGATTTTTGTTTGAT+TGG + chr1.4:80109193-80109212 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG - chr1.4:80109215-80109234 MS.gene26877:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG + chr1.4:80109017-80109036 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG - chr1.4:80108488-80108507 MS.gene26877:CDS 35.0%
AGATACAAAGAATCTGTGGA+TGG - chr1.4:80109329-80109348 MS.gene26877:CDS 35.0%
ATTCTTGAGGGAGAAGATTT+GGG - chr1.4:80108522-80108541 MS.gene26877:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG - chr1.4:80108489-80108508 MS.gene26877:CDS 35.0%
CAAAAGATCCCAAGATCTTA+TGG - chr1.4:80108640-80108659 MS.gene26877:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG + chr1.4:80108712-80108731 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG - chr1.4:80109263-80109282 MS.gene26877:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG - chr1.4:80109023-80109042 MS.gene26877:CDS 35.0%
! ACCATCATCATGATTTCTAG+AGG + chr1.4:80109243-80109262 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG - chr1.4:80109024-80109043 MS.gene26877:CDS 35.0%
! ATTTTGTTCAGCCACTAGAA+GGG + chr1.4:80108940-80108959 None:intergenic 35.0%
! CCATCATCATGATTTCTAGA+GGG + chr1.4:80109242-80109261 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG + chr1.4:80108475-80108494 None:intergenic 35.0%
! GATGATGGTTGTTATAGATG+CGG - chr1.4:80109254-80109273 MS.gene26877:CDS 35.0%
! TATTTTGTTCAGCCACTAGA+AGG + chr1.4:80108941-80108960 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG + chr1.4:80108554-80108573 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG + chr1.4:80108555-80108574 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG - chr1.4:80108698-80108717 MS.gene26877:CDS 35.0%
AATCTGTGGATGGAAAGGAA+AGG - chr1.4:80109339-80109358 MS.gene26877:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG + chr1.4:80109030-80109049 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG - chr1.4:80108594-80108613 MS.gene26877:CDS 40.0%
ATCTGTGGATGGAAAGGAAA+GGG - chr1.4:80109340-80109359 MS.gene26877:CDS 40.0%
CAAAGAATCTGTGGATGGAA+AGG - chr1.4:80109334-80109353 MS.gene26877:CDS 40.0%
GATTCTTGAGGGAGAAGATT+TGG - chr1.4:80108521-80108540 MS.gene26877:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG + chr1.4:80108866-80108885 None:intergenic 40.0%
GGACTCGATAAGATTCTTGA+GGG - chr1.4:80108510-80108529 MS.gene26877:CDS 40.0%
GGGTAAAGGTAAAAACATCC+AGG - chr1.4:80109211-80109230 MS.gene26877:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG - chr1.4:80109029-80109048 MS.gene26877:CDS 40.0%
! AGACAGGTAGTGTCATTCTT+TGG + chr1.4:80109389-80109408 None:intergenic 40.0%
! CCCTCTAGAAATCATGATGA+TGG - chr1.4:80109239-80109258 MS.gene26877:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG - chr1.4:80108706-80108725 MS.gene26877:CDS 40.0%
AAAATCAGCAGCCTCAAGAC+AGG + chr1.4:80109405-80109424 None:intergenic 45.0%
ATGCGGAAAGAAAGGCCATT+GGG - chr1.4:80109271-80109290 MS.gene26877:CDS 45.0%
GAATGACACTACCTGTCTTG+AGG - chr1.4:80109391-80109410 MS.gene26877:CDS 45.0%
GGATACGACATTGTTCCTGT+AGG + chr1.4:80108996-80109015 None:intergenic 45.0%
GGGACTCGATAAGATTCTTG+AGG - chr1.4:80108509-80108528 MS.gene26877:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG - chr1.4:80109050-80109069 MS.gene26877:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG - chr1.4:80109056-80109075 MS.gene26877:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG - chr1.4:80109119-80109138 MS.gene26877:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG - chr1.4:80109032-80109051 MS.gene26877:CDS 45.0%
!!! GAGGCTGCTGATTTTGTTGA+AGG - chr1.4:80109410-80109429 MS.gene26877:CDS 45.0%
AACCATCAGTTGCGTCCTAC+AGG - chr1.4:80108978-80108997 MS.gene26877:CDS 50.0%
AGATTTGGGAGATGTCCCAG+AGG - chr1.4:80108536-80108555 MS.gene26877:CDS 50.0%
CGTGGACGAGGTAGAAATCA+TGG - chr1.4:80109101-80109120 MS.gene26877:CDS 50.0%
CTGGCGACAACTACATAACC+TGG - chr1.4:80108454-80108473 MS.gene26877:CDS 50.0%
GATGCGGAAAGAAAGGCCAT+TGG - chr1.4:80109270-80109289 MS.gene26877:CDS 50.0%
TCCTGCATGCTTTAGCCCAA+TGG + chr1.4:80109289-80109308 None:intergenic 50.0%
TTCCTGTAGGACGCAACTGA+TGG + chr1.4:80108983-80109002 None:intergenic 50.0%
TTTGGTTGCAGCCCTTCTAG+TGG - chr1.4:80108926-80108945 MS.gene26877:CDS 50.0%
! CGAAACCATTTTCGTGGTGG+AGG - chr1.4:80109125-80109144 MS.gene26877:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG + chr1.4:80109232-80109251 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG - chr1.4:80109122-80109141 MS.gene26877:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG - chr1.4:80109083-80109102 MS.gene26877:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG - chr1.4:80109059-80109078 MS.gene26877:CDS 55.0%
CACGACCTCCACCACGAAAA+TGG + chr1.4:80109133-80109152 None:intergenic 55.0%
CATAGCCACCACGTCCTCTT+TGG + chr1.4:80109067-80109086 None:intergenic 55.0%
GCCATTGGGCTAAAGCATGC+AGG - chr1.4:80109285-80109304 MS.gene26877:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG - chr1.4:80108542-80108561 MS.gene26877:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG - chr1.4:80109074-80109093 MS.gene26877:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG - chr1.4:80109077-80109096 MS.gene26877:CDS 55.0%
!! CATTTTCGTGGTGGAGGTCG+TGG - chr1.4:80109131-80109150 MS.gene26877:CDS 55.0%
!! CGTTTTGGTGGTCGTGGACG+AGG - chr1.4:80109089-80109108 MS.gene26877:CDS 60.0%
! CGTGGTGGAGGTCGTGGAAG+AGG - chr1.4:80109137-80109156 MS.gene26877:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 80108414 80109451 80108414 ID=MS.gene26877
chr1.4 mRNA 80108414 80109451 80108414 ID=MS.gene26877.t1;Parent=MS.gene26877
chr1.4 exon 80108414 80109451 80108414 ID=MS.gene26877.t1.exon1;Parent=MS.gene26877.t1
chr1.4 CDS 80108414 80109451 80108414 ID=cds.MS.gene26877.t1;Parent=MS.gene26877.t1
Gene Sequence

>MS.gene26877

ATGTCAAATGTTAAGCATCAATTCAAAATTTTAAGCATAACTGGCGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGATAAGATTCTTGAGGGAGAAGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCAAATGCAAAAGATCCCAAGATCTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCCATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGAGAATTTACTGAATACTCTGATTTGGTTGCAGCCCTTCTAGTGGCTGAACAAAATAACGAGCTGCTCATTAAAAACCATCAGTTGCGTCCTACAGGAACAATGTCGTATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGACGAGGTAGAAATCATGGTCGAAACCATTTTCGTGGTGGAGGTCGTGGAAGAGGTTATATGAATTACAGGCCTCTCAAATATGACCAATCAAACAAAAATCATCAGGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATGGTTGTTATAGATGCGGAAAGAAAGGCCATTGGGCTAAAGCATGCAGGACACCAGAGTATCTATGTAAAAGATACAAAGAATCTGTGGATGGAAAGGAAAGGGAAGTTAATTTTAATGAAATTGAACCAAAGAATGACACTACCTGTCTTGAGGCTGCTGATTTTGTTGAAGGAGATTTTAATATGGATTAA

Protein sequence

>MS.gene26877.t1

MSNVKHQFKILSITGDNYITWNNNLIEYLACEGLDKILEGEDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVAALLVAEQNNELLIKNHQLRPTGTMSYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRNHGRNHFRGGGRGRGYMNYRPLKYDQSNKNHQGKGKNIQEGPSRNHDDGCYRCGKKGHWAKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDTTCLEAADFVEGDFNMD