AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066126


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066126.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 1.76e-31 116
MS.gene066126.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 1.50e-22 92.0
MS.gene066126.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 3.99e-18 80.1
MS.gene066126.t1 MTR_4g112730 57.971 69 28 1 143 211 2 69 1.20e-17 77.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 66 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 1.4:+47232656 MS.gene066126:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 1.4:+47232636 MS.gene066126:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 1.4:-47232952 None:intergenic
GATAAAATTAAGGCAAGATT+TGG 0.254283 1.4:+47232601 MS.gene066126:CDS
GATTCTTGAGGGAGACGATT+TGG 0.271296 1.4:+47232459 MS.gene066126:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 1.4:-47232410 None:intergenic
CACGGCCTCCACCACGAAAA+TGG 0.277262 1.4:-47233068 None:intergenic
CATAGGAGAAGAAATTAATA+TGG 0.282788 1.4:+47233362 MS.gene066126:CDS
AAGACAGGTAATATCATTCT+TGG 0.288759 1.4:-47233325 None:intergenic
ATTTACTGAATACTCTGATT+TGG 0.313227 1.4:+47232846 MS.gene066126:CDS
CTTGAGGTTGCTGATTTCAT+AGG 0.313595 1.4:+47233345 MS.gene066126:CDS
CTTGATGATTCTTGTTGGTT+TGG 0.339105 1.4:-47233128 None:intergenic
GAAGAGGTTATATGAATTAT+AGG 0.339571 1.4:+47233091 MS.gene066126:CDS
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 1.4:+47232480 MS.gene066126:CDS
ATTCTTGAGGGAGACGATTT+GGG 0.354692 1.4:+47232460 MS.gene066126:CDS
CGTGGTGGTTATGCTCGTTT+TGG 0.361113 1.4:+47233012 MS.gene066126:CDS
TTTACCTTGATGATTCTTGT+TGG 0.362649 1.4:-47233133 None:intergenic
GATTTCTAGAGGGACCTTCC+TGG 0.373636 1.4:-47233167 None:intergenic
CATAACCACCACGTCCTCTT+TGG 0.378867 1.4:-47233002 None:intergenic
TATAACTGAAAAGGAAAAGT+TGG 0.422757 1.4:+47232759 MS.gene066126:CDS
CGTGGTGGAGGCCGTGGAAG+AGG 0.431707 1.4:+47233075 MS.gene066126:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 1.4:+47232644 MS.gene066126:CDS
ATAAAATTAAGGCAAGATTT+GGG 0.433877 1.4:+47232602 MS.gene066126:CDS
AGATACAAAGAATCTGTTGA+TGG 0.446469 1.4:+47233267 MS.gene066126:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 1.4:+47232750 MS.gene066126:CDS
AACCACCAGTTGCGTCCTAC+AGG 0.478404 1.4:+47232916 MS.gene066126:CDS
TTGTTCCTGTAGGACGCAAC+TGG 0.480977 1.4:-47232921 None:intergenic
AGACAGGTAATATCATTCTT+GGG 0.483328 1.4:-47233324 None:intergenic
ATCAAGCACCACATTGATGA+TGG 0.492315 1.4:+47232532 MS.gene066126:CDS
TGCAACAACAATATAGAATG+AGG 0.496917 1.4:+47232821 MS.gene066126:CDS
CTGGAGACAACTACATAACC+TGG 0.502040 1.4:+47232392 MS.gene066126:CDS
AACAAGAATCATCAAGGTAA+AGG 0.504207 1.4:+47233135 MS.gene066126:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 1.4:-47232647 None:intergenic
CAAAGAATCTGTTGATGGAA+AGG 0.510693 1.4:+47233272 MS.gene066126:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.513070 1.4:+47233201 MS.gene066126:CDS
ATCTGTTGATGGAAAGGAAA+GGG 0.513746 1.4:+47233278 MS.gene066126:CDS
GAAATCAGCAACCTCAAGAC+AGG 0.522716 1.4:-47233340 None:intergenic
TTCCATTGATCCATTAATGA+GGG 0.533283 1.4:-47232646 None:intergenic
GATGCGGAAAGAAAGGTCAT+TGG 0.533423 1.4:+47233208 MS.gene066126:CDS
GGACTCGACAAGATTCTTGA+GGG 0.539594 1.4:+47232448 MS.gene066126:CDS
TTGGTTTGGTCATATTTGAG+AGG 0.544297 1.4:-47233114 None:intergenic
CGTGGTCGAGGCAGAAGTCA+TGG 0.554869 1.4:+47233039 MS.gene066126:CDS
AATTGAGTATCTTGCATGTG+AGG 0.565013 1.4:+47232426 MS.gene066126:CDS
GGATATGTCATTGTTCCTGT+AGG 0.570307 1.4:-47232931 None:intergenic
CAAACCAACAAGAATCATCA+AGG 0.574004 1.4:+47233129 MS.gene066126:CDS
AGGTAAAGGTAAAAGCATCC+AGG 0.575090 1.4:+47233149 MS.gene066126:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 1.4:+47232427 MS.gene066126:CDS
GCAACAACAATATAGAATGA+GGG 0.579939 1.4:+47232822 MS.gene066126:CDS
GAATGATATTACCTGTCTTG+AGG 0.586627 1.4:+47233329 MS.gene066126:CDS
TTCCTGTAGGACGCAACTGG+TGG 0.593030 1.4:-47232918 None:intergenic
AATTCATATAACCTCTTCCA+CGG 0.595635 1.4:-47233086 None:intergenic
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 1.4:-47232965 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 1.4:-47232801 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 1.4:+47232994 MS.gene066126:CDS
GGGACTCGACAAGATTCTTG+AGG 0.610766 1.4:+47232447 MS.gene066126:CDS
TGTTGATGGAAAGGAAAGGG+AGG 0.620365 1.4:+47233281 MS.gene066126:CDS
ACGATCATCATGATTTCTAG+AGG 0.627654 1.4:-47233178 None:intergenic
GTCATTGGTCTAAAGCATGT+AGG 0.629444 1.4:+47233223 MS.gene066126:CDS
GATGATCGTTGTTATAGATG+CGG 0.637106 1.4:+47233192 MS.gene066126:CDS
CGATCATCATGATTTCTAGA+GGG 0.638172 1.4:-47233177 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 1.4:+47232988 MS.gene066126:CDS
AATCTGTTGATGGAAAGGAA+AGG 0.653361 1.4:+47233277 MS.gene066126:CDS
AAAGGTAAAAGCATCCAGGA+AGG 0.661440 1.4:+47233153 MS.gene066126:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.703312 1.4:+47232997 MS.gene066126:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 1.4:-47232540 None:intergenic
CGATTTGGGAGATGTCCCAG+AGG 0.725435 1.4:+47232474 MS.gene066126:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATGTTTAAAATTTTGAAT+TGG - chr1.4:47232372-47232391 None:intergenic 10.0%
!!! TTCAAAATTTTAAACATAAC+TGG + chr1.4:47232373-47232392 MS.gene066126:CDS 15.0%
!! ATAAAATTAAGGCAAGATTT+GGG + chr1.4:47232602-47232621 MS.gene066126:CDS 20.0%
!!! AATTTTATCCCATAAAATCT+TGG - chr1.4:47232590-47232609 None:intergenic 20.0%
!!! ATTTTATCCCATAAAATCTT+GGG - chr1.4:47232589-47232608 None:intergenic 20.0%
!!! GATTTTATGGGATAAAATTA+AGG + chr1.4:47232591-47232610 MS.gene066126:CDS 20.0%
! ATTTACTGAATACTCTGATT+TGG + chr1.4:47232846-47232865 MS.gene066126:CDS 25.0%
! CATAGGAGAAGAAATTAATA+TGG + chr1.4:47233362-47233381 MS.gene066126:CDS 25.0%
! GAAGAGGTTATATGAATTAT+AGG + chr1.4:47233091-47233110 MS.gene066126:CDS 25.0%
! GATAAAATTAAGGCAAGATT+TGG + chr1.4:47232601-47232620 MS.gene066126:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG + chr1.4:47232759-47232778 MS.gene066126:CDS 25.0%
!! AAAAGATCCCAAGATTTTAT+GGG + chr1.4:47232579-47232598 MS.gene066126:CDS 25.0%
!! ATTGCACAATTAGAATTTTG+TGG + chr1.4:47232730-47232749 MS.gene066126:CDS 25.0%
!!! CAACAACAGTTTTATAATCT+TGG - chr1.4:47232684-47232703 None:intergenic 25.0%
AACAAGAATCATCAAGGTAA+AGG + chr1.4:47233135-47233154 MS.gene066126:CDS 30.0%
AAGACAGGTAATATCATTCT+TGG - chr1.4:47233328-47233347 None:intergenic 30.0%
AATTCATATAACCTCTTCCA+CGG - chr1.4:47233089-47233108 None:intergenic 30.0%
AGACAGGTAATATCATTCTT+GGG - chr1.4:47233327-47233346 None:intergenic 30.0%
AGATACAAAGAATCTGTTGA+TGG + chr1.4:47233267-47233286 MS.gene066126:CDS 30.0%
GCAACAACAATATAGAATGA+GGG + chr1.4:47232822-47232841 MS.gene066126:CDS 30.0%
TGCAACAACAATATAGAATG+AGG + chr1.4:47232821-47232840 MS.gene066126:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG + chr1.4:47232656-47232675 MS.gene066126:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG + chr1.4:47232750-47232769 MS.gene066126:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG - chr1.4:47232649-47232668 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG - chr1.4:47232543-47232562 None:intergenic 30.0%
! CAAAAGATCCCAAGATTTTA+TGG + chr1.4:47232578-47232597 MS.gene066126:CDS 30.0%
! TATCTTTTACACAGATACTC+TGG - chr1.4:47233252-47233271 None:intergenic 30.0%
! TTTACCTTGATGATTCTTGT+TGG - chr1.4:47233136-47233155 None:intergenic 30.0%
AAAGTTGTGGCGTTTATTTC+AGG - chr1.4:47232955-47232974 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG + chr1.4:47232426-47232445 MS.gene066126:CDS 35.0%
ATTGAGTATCTTGCATGTGA+GGG + chr1.4:47232427-47232446 MS.gene066126:CDS 35.0%
CAAACCAACAAGAATCATCA+AGG + chr1.4:47233129-47233148 MS.gene066126:CDS 35.0%
GAATGATATTACCTGTCTTG+AGG + chr1.4:47233329-47233348 MS.gene066126:CDS 35.0%
GATGATCGTTGTTATAGATG+CGG + chr1.4:47233192-47233211 MS.gene066126:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG - chr1.4:47232650-47232669 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG + chr1.4:47233201-47233220 MS.gene066126:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG + chr1.4:47232961-47232980 MS.gene066126:CDS 35.0%
! AATCTGTTGATGGAAAGGAA+AGG + chr1.4:47233277-47233296 MS.gene066126:CDS 35.0%
! ACGATCATCATGATTTCTAG+AGG - chr1.4:47233181-47233200 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG + chr1.4:47232962-47232981 MS.gene066126:CDS 35.0%
! ATCTGTTGATGGAAAGGAAA+GGG + chr1.4:47233278-47233297 MS.gene066126:CDS 35.0%
! CAAAGAATCTGTTGATGGAA+AGG + chr1.4:47233272-47233291 MS.gene066126:CDS 35.0%
! CGATCATCATGATTTCTAGA+GGG - chr1.4:47233180-47233199 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG - chr1.4:47232413-47232432 None:intergenic 35.0%
! CTTGATGATTCTTGTTGGTT+TGG - chr1.4:47233131-47233150 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG - chr1.4:47232492-47232511 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG - chr1.4:47232493-47232512 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG + chr1.4:47232636-47232655 MS.gene066126:CDS 35.0%
!! TTGGTTTGGTCATATTTGAG+AGG - chr1.4:47233117-47233136 None:intergenic 35.0%
ACGCCCTTGATTAAAAGTTG+TGG - chr1.4:47232968-47232987 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG + chr1.4:47232532-47232551 MS.gene066126:CDS 40.0%
ATTCTTGAGGGAGACGATTT+GGG + chr1.4:47232460-47232479 MS.gene066126:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG - chr1.4:47232804-47232823 None:intergenic 40.0%
GGATATGTCATTGTTCCTGT+AGG - chr1.4:47232934-47232953 None:intergenic 40.0%
! ACAACTTTTAATCAAGGGCG+TGG + chr1.4:47232967-47232986 MS.gene066126:CDS 40.0%
! GTCATTGGTCTAAAGCATGT+AGG + chr1.4:47233223-47233242 MS.gene066126:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG + chr1.4:47232644-47232663 MS.gene066126:CDS 40.0%
!! AAAGGTAAAAGCATCCAGGA+AGG + chr1.4:47233153-47233172 MS.gene066126:CDS 40.0%
!! AGGTAAAGGTAAAAGCATCC+AGG + chr1.4:47233149-47233168 MS.gene066126:CDS 40.0%
!! CTTGAGGTTGCTGATTTCAT+AGG + chr1.4:47233345-47233364 MS.gene066126:CDS 40.0%
CTGGAGACAACTACATAACC+TGG + chr1.4:47232392-47232411 MS.gene066126:CDS 45.0%
GAAATCAGCAACCTCAAGAC+AGG - chr1.4:47233343-47233362 None:intergenic 45.0%
GATGCGGAAAGAAAGGTCAT+TGG + chr1.4:47233208-47233227 MS.gene066126:CDS 45.0%
GATTCTTGAGGGAGACGATT+TGG + chr1.4:47232459-47232478 MS.gene066126:CDS 45.0%
GGACTCGACAAGATTCTTGA+GGG + chr1.4:47232448-47232467 MS.gene066126:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG + chr1.4:47232988-47233007 MS.gene066126:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG + chr1.4:47232994-47233013 MS.gene066126:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG + chr1.4:47233057-47233076 MS.gene066126:CDS 45.0%
! TGTTGATGGAAAGGAAAGGG+AGG + chr1.4:47233281-47233300 MS.gene066126:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG + chr1.4:47232970-47232989 MS.gene066126:CDS 45.0%
CATAACCACCACGTCCTCTT+TGG - chr1.4:47233005-47233024 None:intergenic 50.0%
GGGACTCGACAAGATTCTTG+AGG + chr1.4:47232447-47232466 MS.gene066126:CDS 50.0%
TTGTTCCTGTAGGACGCAAC+TGG - chr1.4:47232924-47232943 None:intergenic 50.0%
! CGAAACCATTTTCGTGGTGG+AGG + chr1.4:47233063-47233082 MS.gene066126:CDS 50.0%
! CGTGGTGGTTATGCTCGTTT+TGG + chr1.4:47233012-47233031 MS.gene066126:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG - chr1.4:47233170-47233189 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG + chr1.4:47233060-47233079 MS.gene066126:CDS 50.0%
! GGTGGTTATGCTCGTTTTGG+TGG + chr1.4:47233015-47233034 MS.gene066126:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG + chr1.4:47233021-47233040 MS.gene066126:CDS 50.0%
AACCACCAGTTGCGTCCTAC+AGG + chr1.4:47232916-47232935 MS.gene066126:CDS 55.0%
AATCGCCAAAGAGGACGTGG+TGG + chr1.4:47232997-47233016 MS.gene066126:CDS 55.0%
GGGAGATGTCCCAGAGGAAT+TGG + chr1.4:47232480-47232499 MS.gene066126:CDS 55.0%
TTCCTGTAGGACGCAACTGG+TGG - chr1.4:47232921-47232940 None:intergenic 55.0%
! CGATTTGGGAGATGTCCCAG+AGG + chr1.4:47232474-47232493 MS.gene066126:CDS 55.0%
CACGGCCTCCACCACGAAAA+TGG - chr1.4:47233071-47233090 None:intergenic 60.0%
CGTGGTCGAGGCAGAAGTCA+TGG + chr1.4:47233039-47233058 MS.gene066126:CDS 60.0%
!! CATTTTCGTGGTGGAGGCCG+TGG + chr1.4:47233069-47233088 MS.gene066126:CDS 60.0%
!! CGTTTTGGTGGTCGTGGTCG+AGG + chr1.4:47233027-47233046 MS.gene066126:CDS 60.0%
! CGTGGTGGAGGCCGTGGAAG+AGG + chr1.4:47233075-47233094 MS.gene066126:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 47232352 47233389 47232352 ID=MS.gene066126
chr1.4 mRNA 47232352 47233389 47232352 ID=MS.gene066126.t1;Parent=MS.gene066126
chr1.4 exon 47232352 47233389 47232352 ID=MS.gene066126.t1.exon1;Parent=MS.gene066126.t1
chr1.4 CDS 47232352 47233389 47232352 ID=cds.MS.gene066126.t1;Parent=MS.gene066126.t1
Gene Sequence

>MS.gene066126

ATGTCAAATGTTAAGCACCAATTCAAAATTTTAAACATAACTGGAGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGACAAGATTCTTGAGGGAGACGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCGAATGCAAAAGATCCCAAGATTTTATGGGATAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCTATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGGGAATTTACTGAATACTCTGATTTGGTTACAACTCTTCTAGTAGCTGAACAAAATAATGAGCTGCTCATTAAAAACCACCAGTTGCGTCCTACAGGAACAATGACATATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGTTATGCTCGTTTTGGTGGTCGTGGTCGAGGCAGAAGTCATGGTCGAAACCATTTTCGTGGTGGAGGCCGTGGAAGAGGTTATATGAATTATAGGCCTCTCAAATATGACCAAACCAACAAGAATCATCAAGGTAAAGGTAAAAGCATCCAGGAAGGTCCCTCTAGAAATCATGATGATCGTTGTTATAGATGCGGAAAGAAAGGTCATTGGTCTAAAGCATGTAGGACACCAGAGTATCTGTGTAAAAGATACAAAGAATCTGTTGATGGAAAGGAAAGGGAGGTTAATTTTAATGAAATTGAACCCAAGAATGATATTACCTGTCTTGAGGTTGCTGATTTCATAGGAGAAGAAATTAATATGGATTAA

Protein sequence

>MS.gene066126.t1

MSNVKHQFKILNITGDNYITWNNNLIEYLACEGLDKILEGDDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVTTLLVAEQNNELLIKNHQLRPTGTMTYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRSHGRNHFRGGGRGRGYMNYRPLKYDQTNKNHQGKGKSIQEGPSRNHDDRCYRCGKKGHWSKACRTPEYLCKRYKESVDGKEREVNFNEIEPKNDITCLEVADFIGEEINMD