AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86856

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86856.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 5.31e-31 115
MS.gene86856.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 1.07e-21 90.1
MS.gene86856.t1 MTR_4g112730 57.746 71 29 1 143 213 2 71 3.02e-18 79.0
MS.gene86856.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 4.20e-18 80.1
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 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 6.2:-52831489 MS.gene86856:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 6.2:-52831509 MS.gene86856:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 6.2:+52831193 None:intergenic
CAAAAGATCCCAAGATCTTA+TGG 0.237847 6.2:-52831567 MS.gene86856:CDS
GATTCTTGAGGGAGAAGATT+TGG 0.253340 6.2:-52831686 MS.gene86856:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 6.2:-52831544 MS.gene86856:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 6.2:+52831735 None:intergenic
CACGACCTCCACCACGAAAA+TGG 0.277262 6.2:+52831077 None:intergenic
GATCTTATGGGACAAAATTA+AGG 0.310971 6.2:-52831554 MS.gene86856:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 6.2:-52831299 MS.gene86856:CDS
ATTCTTGAGGGAGAAGATTT+GGG 0.333151 6.2:-52831685 MS.gene86856:CDS
AGACAGGTAGTGTCATTCTT+TGG 0.342502 6.2:+52830821 None:intergenic
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 6.2:-52831665 MS.gene86856:CDS
GAAGAGGTTATATGAATTAC+AGG 0.363099 6.2:-52831054 MS.gene86856:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 6.2:+52830978 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 6.2:+52831143 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 6.2:-52831133 MS.gene86856:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 6.2:-52831543 MS.gene86856:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 6.2:-52831386 MS.gene86856:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 6.2:-52831501 MS.gene86856:CDS
CGTGGTGGAGGTCGTGGAAG+AGG 0.449888 6.2:-52831070 MS.gene86856:CDS
TCCTGCATGCTTTAGCCCAA+TGG 0.457473 6.2:+52830921 None:intergenic
AAAAGATCCCAAGATCTTAT+GGG 0.458748 6.2:-52831566 MS.gene86856:CDS
AACCATCAGTTGCGTCCTAC+AGG 0.459311 6.2:-52831229 MS.gene86856:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 6.2:-52831395 MS.gene86856:CDS
ATCTGTGGATGGAAAGGAAA+GGG 0.491819 6.2:-52830867 MS.gene86856:CDS
ATCAAGCACCACATTGATGA+TGG 0.492315 6.2:-52831613 MS.gene86856:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.495634 6.2:-52830944 MS.gene86856:CDS
CTGGCGACAACTACATAACC+TGG 0.502097 6.2:-52831753 MS.gene86856:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 6.2:+52831498 None:intergenic
ATGCGGAAAGAAAGGCCATT+GGG 0.516896 6.2:-52830936 MS.gene86856:CDS
TTTGATTGGTCATATTTGAG+AGG 0.522357 6.2:+52831031 None:intergenic
CAAAGAATCTGTGGATGGAA+AGG 0.532926 6.2:-52830873 MS.gene86856:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 6.2:+52831499 None:intergenic
CGTGGACGAGGTAGAAATCA+TGG 0.535808 6.2:-52831106 MS.gene86856:CDS
GGACTCGATAAGATTCTTGA+GGG 0.539399 6.2:-52831697 MS.gene86856:CDS
GCCATTGGGCTAAAGCATGC+AGG 0.539769 6.2:-52830922 MS.gene86856:CDS
CCCTCTAGAAATCATGATGA+TGG 0.541875 6.2:-52830968 MS.gene86856:CDS
TTCCTGTAGGACGCAACTGA+TGG 0.562606 6.2:+52831227 None:intergenic
AAAATCAGCAGCCTCAAGAC+AGG 0.562896 6.2:+52830805 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 6.2:-52831719 MS.gene86856:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 6.2:-52831718 MS.gene86856:CDS
TTTGGTTGCAGCCCTTCTAG+TGG 0.582793 6.2:-52831281 MS.gene86856:CDS
GATGCGGAAAGAAAGGCCAT+TGG 0.583841 6.2:-52830937 MS.gene86856:CDS
TTGTGCAATAATTTGATGCA+TGG 0.588693 6.2:+52831429 None:intergenic
TAAAAGATACAAAGAATCTG+TGG 0.594054 6.2:-52830882 MS.gene86856:CDS
AGATACAAAGAATCTGTGGA+TGG 0.602731 6.2:-52830878 MS.gene86856:CDS
GGGACTCGATAAGATTCTTG+AGG 0.606176 6.2:-52831698 MS.gene86856:CDS
GCAATATCACTTGAGATGCA+TGG 0.608661 6.2:+52831344 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 6.2:-52831151 MS.gene86856:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.609769 6.2:+52831180 None:intergenic
ACCATCATCATGATTTCTAG+AGG 0.616492 6.2:+52830967 None:intergenic
GGATACGACATTGTTCCTGT+AGG 0.627452 6.2:+52831214 None:intergenic
AGTGGTTATAATCGCCAAAG+AGG 0.642086 6.2:-52831157 MS.gene86856:CDS
CCATCATCATGATTTCTAGA+GGG 0.647682 6.2:+52830968 None:intergenic
GAATGACACTACCTGTCTTG+AGG 0.649563 6.2:-52830816 MS.gene86856:CDS
AATCTGTGGATGGAAAGGAA+AGG 0.653361 6.2:-52830868 MS.gene86856:CDS
GATGATGGTTGTTATAGATG+CGG 0.696569 6.2:-52830953 MS.gene86856:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 6.2:-52831148 MS.gene86856:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 6.2:+52831605 None:intergenic
AGATTTGGGAGATGTCCCAG+AGG 0.741186 6.2:-52831671 MS.gene86856:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCAAAATTTTAAGCATAAC+TGG - chr6.2:52830799-52830818 MS.gene86856:CDS 20.0%
! ACAAAATTAAGGCAAGATTT+GGG - chr6.2:52831028-52831047 MS.gene86856:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG - chr6.2:52831272-52831291 MS.gene86856:CDS 25.0%
! CAATCAAACAAAAATCATCA+GGG - chr6.2:52831555-52831574 MS.gene86856:CDS 25.0%
! TAAAAGATACAAAGAATCTG+TGG - chr6.2:52831689-52831708 MS.gene86856:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG - chr6.2:52831185-52831204 MS.gene86856:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG - chr6.2:52831156-52831175 MS.gene86856:CDS 25.0%
!! TATCTTTTACATAGATACTC+TGG + chr6.2:52831678-52831697 None:intergenic 25.0%
!!! CAACAACAGTTTTATAATCT+TGG + chr6.2:52831110-52831129 None:intergenic 25.0%
!!! TGTTGAAGGAGATTTTAATA+TGG - chr6.2:52831788-52831807 MS.gene86856:CDS 25.0%
AAAAGATCCCAAGATCTTAT+GGG - chr6.2:52831005-52831024 MS.gene86856:CDS 30.0%
AACAAAAATCATCAGGGTAA+AGG - chr6.2:52831561-52831580 MS.gene86856:CDS 30.0%
CCAATCAAACAAAAATCATC+AGG - chr6.2:52831554-52831573 MS.gene86856:CDS 30.0%
GAAGAGGTTATATGAATTAC+AGG - chr6.2:52831517-52831536 MS.gene86856:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG - chr6.2:52831027-52831046 MS.gene86856:CDS 30.0%
GATCTTATGGGACAAAATTA+AGG - chr6.2:52831017-52831036 MS.gene86856:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG - chr6.2:52831082-52831101 MS.gene86856:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG - chr6.2:52831176-52831195 MS.gene86856:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG + chr6.2:52831075-52831094 None:intergenic 30.0%
TTGTGCAATAATTTGATGCA+TGG + chr6.2:52831145-52831164 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG + chr6.2:52830969-52830988 None:intergenic 30.0%
! AATTTTGTCCCATAAGATCT+TGG + chr6.2:52831016-52831035 None:intergenic 30.0%
! ATTTTGTCCCATAAGATCTT+GGG + chr6.2:52831015-52831034 None:intergenic 30.0%
! TTTGATTGGTCATATTTGAG+AGG + chr6.2:52831543-52831562 None:intergenic 30.0%
!! CCTGATGATTTTTGTTTGAT+TGG + chr6.2:52831557-52831576 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG - chr6.2:52831579-52831598 MS.gene86856:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG + chr6.2:52831381-52831400 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG - chr6.2:52830852-52830871 MS.gene86856:CDS 35.0%
AGATACAAAGAATCTGTGGA+TGG - chr6.2:52831693-52831712 MS.gene86856:CDS 35.0%
ATTCTTGAGGGAGAAGATTT+GGG - chr6.2:52830886-52830905 MS.gene86856:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG - chr6.2:52830853-52830872 MS.gene86856:CDS 35.0%
CAAAAGATCCCAAGATCTTA+TGG - chr6.2:52831004-52831023 MS.gene86856:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG + chr6.2:52831076-52831095 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG - chr6.2:52831627-52831646 MS.gene86856:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG - chr6.2:52831387-52831406 MS.gene86856:CDS 35.0%
! ACCATCATCATGATTTCTAG+AGG + chr6.2:52831607-52831626 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG - chr6.2:52831388-52831407 MS.gene86856:CDS 35.0%
! ATTTTGTTCAGCCACTAGAA+GGG + chr6.2:52831304-52831323 None:intergenic 35.0%
! CCATCATCATGATTTCTAGA+GGG + chr6.2:52831606-52831625 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG + chr6.2:52830839-52830858 None:intergenic 35.0%
! GATGATGGTTGTTATAGATG+CGG - chr6.2:52831618-52831637 MS.gene86856:CDS 35.0%
! TATTTTGTTCAGCCACTAGA+AGG + chr6.2:52831305-52831324 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG + chr6.2:52830918-52830937 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG + chr6.2:52830919-52830938 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG - chr6.2:52831062-52831081 MS.gene86856:CDS 35.0%
AATCTGTGGATGGAAAGGAA+AGG - chr6.2:52831703-52831722 MS.gene86856:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG + chr6.2:52831394-52831413 None:intergenic 40.0%
AGTGGTTATAATCGCCAAAG+AGG - chr6.2:52831414-52831433 MS.gene86856:CDS 40.0%
ATCAAGCACCACATTGATGA+TGG - chr6.2:52830958-52830977 MS.gene86856:CDS 40.0%
ATCTGTGGATGGAAAGGAAA+GGG - chr6.2:52831704-52831723 MS.gene86856:CDS 40.0%
CAAAGAATCTGTGGATGGAA+AGG - chr6.2:52831698-52831717 MS.gene86856:CDS 40.0%
GATTCTTGAGGGAGAAGATT+TGG - chr6.2:52830885-52830904 MS.gene86856:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG + chr6.2:52831230-52831249 None:intergenic 40.0%
GGACTCGATAAGATTCTTGA+GGG - chr6.2:52830874-52830893 MS.gene86856:CDS 40.0%
GGGTAAAGGTAAAAACATCC+AGG - chr6.2:52831575-52831594 MS.gene86856:CDS 40.0%
! AGACAGGTAGTGTCATTCTT+TGG + chr6.2:52831753-52831772 None:intergenic 40.0%
! CCCTCTAGAAATCATGATGA+TGG - chr6.2:52831603-52831622 MS.gene86856:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG - chr6.2:52831070-52831089 MS.gene86856:CDS 40.0%
!! ACTTTTAATCAAGGGCGTAG+TGG - chr6.2:52831396-52831415 MS.gene86856:CDS 40.0%
AAAATCAGCAGCCTCAAGAC+AGG + chr6.2:52831769-52831788 None:intergenic 45.0%
ATGCGGAAAGAAAGGCCATT+GGG - chr6.2:52831635-52831654 MS.gene86856:CDS 45.0%
GAATGACACTACCTGTCTTG+AGG - chr6.2:52831755-52831774 MS.gene86856:CDS 45.0%
GGATACGACATTGTTCCTGT+AGG + chr6.2:52831360-52831379 None:intergenic 45.0%
GGGACTCGATAAGATTCTTG+AGG - chr6.2:52830873-52830892 MS.gene86856:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG - chr6.2:52831420-52831439 MS.gene86856:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG - chr6.2:52831483-52831502 MS.gene86856:CDS 45.0%
!!! GAGGCTGCTGATTTTGTTGA+AGG - chr6.2:52831774-52831793 MS.gene86856:CDS 45.0%
AACCATCAGTTGCGTCCTAC+AGG - chr6.2:52831342-52831361 MS.gene86856:CDS 50.0%
AGATTTGGGAGATGTCCCAG+AGG - chr6.2:52830900-52830919 MS.gene86856:CDS 50.0%
CGTGGACGAGGTAGAAATCA+TGG - chr6.2:52831465-52831484 MS.gene86856:CDS 50.0%
CTGGCGACAACTACATAACC+TGG - chr6.2:52830818-52830837 MS.gene86856:CDS 50.0%
GATGCGGAAAGAAAGGCCAT+TGG - chr6.2:52831634-52831653 MS.gene86856:CDS 50.0%
TCCTGCATGCTTTAGCCCAA+TGG + chr6.2:52831653-52831672 None:intergenic 50.0%
TTCCTGTAGGACGCAACTGA+TGG + chr6.2:52831347-52831366 None:intergenic 50.0%
TTTGGTTGCAGCCCTTCTAG+TGG - chr6.2:52831290-52831309 MS.gene86856:CDS 50.0%
! CGAAACCATTTTCGTGGTGG+AGG - chr6.2:52831489-52831508 MS.gene86856:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG + chr6.2:52831596-52831615 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG - chr6.2:52831486-52831505 MS.gene86856:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG - chr6.2:52831447-52831466 MS.gene86856:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG - chr6.2:52831423-52831442 MS.gene86856:CDS 55.0%
CACGACCTCCACCACGAAAA+TGG + chr6.2:52831497-52831516 None:intergenic 55.0%
CATAGCCACCACGTCCTCTT+TGG + chr6.2:52831431-52831450 None:intergenic 55.0%
GCCATTGGGCTAAAGCATGC+AGG - chr6.2:52831649-52831668 MS.gene86856:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG - chr6.2:52830906-52830925 MS.gene86856:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG - chr6.2:52831438-52831457 MS.gene86856:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG - chr6.2:52831441-52831460 MS.gene86856:CDS 55.0%
!! CATTTTCGTGGTGGAGGTCG+TGG - chr6.2:52831495-52831514 MS.gene86856:CDS 55.0%
!! CGTTTTGGTGGTCGTGGACG+AGG - chr6.2:52831453-52831472 MS.gene86856:CDS 60.0%
! CGTGGTGGAGGTCGTGGAAG+AGG - chr6.2:52831501-52831520 MS.gene86856:CDS 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 52830778 52831815 52830778 ID=MS.gene86856
chr6.2 mRNA 52830778 52831815 52830778 ID=MS.gene86856.t1;Parent=MS.gene86856
chr6.2 exon 52830778 52831815 52830778 ID=MS.gene86856.t1.exon1;Parent=MS.gene86856.t1
chr6.2 CDS 52830778 52831815 52830778 ID=cds.MS.gene86856.t1;Parent=MS.gene86856.t1
Gene Sequence

>MS.gene86856

ATGTCAAATGTTAAGCATCAATTCAAAATTTTAAGCATAACTGGCGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGATAAGATTCTTGAGGGAGAAGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCAAATGCAAAAGATCCCAAGATCTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCCATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGAGAATTTACTGAATACTCTGATTTGGTTGCAGCCCTTCTAGTGGCTGAACAAAATAACGAGCTGCTCATTAAAAACCATCAGTTGCGTCCTACAGGAACAATGTCGTATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTAGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGACGAGGTAGAAATCATGGTCGAAACCATTTTCGTGGTGGAGGTCGTGGAAGAGGTTATATGAATTACAGGCCTCTCAAATATGACCAATCAAACAAAAATCATCAGGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATGGTTGTTATAGATGCGGAAAGAAAGGCCATTGGGCTAAAGCATGCAGGACACCAGAGTATCTATGTAAAAGATACAAAGAATCTGTGGATGGAAAGGAAAGGGAAGTTAATTTTAATGAAATTGAACCAAAGAATGACACTACCTGTCTTGAGGCTGCTGATTTTGTTGAAGGAGATTTTAATATGGATTAA
Protein sequence

>MS.gene86856.t1

MSNVKHQFKILSITGDNYITWNNNLIEYLACEGLDKILEGEDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVAALLVAEQNNELLIKNHQLRPTGTMSYPEINATTFNQGRSGYNRQRGRGGYARFGGRGRGRNHGRNHFRGGGRGRGYMNYRPLKYDQSNKNHQGKGKNIQEGPSRNHDDGCYRCGKKGHWAKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDTTCLEAADFVEGDFNMD