AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene058515


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene058515.t1 MTR_7g062720 40.541 148 80 3 1 146 1 142 1.71e-30 114
MS.gene058515.t1 MTR_4g037355 40.441 136 61 4 155 290 1 116 2.05e-22 91.7
MS.gene058515.t1 MTR_5g061150 35.354 99 64 0 52 150 38 136 1.32e-18 81.6
MS.gene058515.t1 MTR_4g112730 57.971 69 28 1 143 211 2 69 7.68e-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 66 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGATCAATGGAACAAATTA+AGG 0.196151 7.4:-27300805 MS.gene058515:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 7.4:-27300825 MS.gene058515:CDS
AAAGTTGTGGCGTTTATTTC+AGG 0.203868 7.4:+27300509 None:intergenic
GACAAAATTAAGGCAAGATT+TGG 0.257188 7.4:-27300860 MS.gene058515:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 7.4:+27301051 None:intergenic
CACGGCCTCCACCACGAAAA+TGG 0.277262 7.4:+27300393 None:intergenic
GATTCTTGAGGGAGGCGATT+TGG 0.283776 7.4:-27301002 MS.gene058515:CDS
ATTCTTGAGGGAGGCGATTT+GGG 0.289346 7.4:-27301001 MS.gene058515:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 7.4:-27300615 MS.gene058515:CDS
CTTGATGATTCTTGTTGGTT+TGG 0.339105 7.4:+27300333 None:intergenic
GAAGAGGTTATATGAATTAT+AGG 0.339571 7.4:-27300370 MS.gene058515:CDS
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 7.4:-27300981 MS.gene058515:CDS
AAGACAGGTAGTATCATTCT+TGG 0.359896 7.4:+27300136 None:intergenic
TTTACCTTGATGATTCTTGT+TGG 0.362649 7.4:+27300328 None:intergenic
CTTGAGACTGCTGATTTCAT+AGG 0.373343 7.4:-27300116 MS.gene058515:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 7.4:+27300294 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 7.4:+27300459 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 7.4:-27300449 MS.gene058515:CDS
CAAAGAATCTGTTGATGAAA+AGG 0.401541 7.4:-27300189 MS.gene058515:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 7.4:-27300859 MS.gene058515:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 7.4:-27300702 MS.gene058515:CDS
CGTGGTGGAGGCCGTGGAAG+AGG 0.431707 7.4:-27300386 MS.gene058515:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 7.4:-27300817 MS.gene058515:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 7.4:-27300711 MS.gene058515:CDS
TGATTTCATAGGAGAAGAAA+TGG 0.469590 7.4:-27300105 MS.gene058515:CDS
AACCACCAGTTGCGTCCTAC+AGG 0.478404 7.4:-27300545 MS.gene058515:CDS
TTGTTCCTGTAGGACGCAAC+TGG 0.480977 7.4:+27300540 None:intergenic
AGACAGGTAGTATCATTCTT+GGG 0.483328 7.4:+27300137 None:intergenic
ATCAAGCACCACATTGATGA+TGG 0.492315 7.4:-27300929 MS.gene058515:CDS
CTGGAGACAACTACATAACC+TGG 0.502040 7.4:-27301069 MS.gene058515:CDS
AACAAGAATCATCAAGGTAA+AGG 0.504207 7.4:-27300326 MS.gene058515:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 7.4:+27300814 None:intergenic
ATCTGTTGATGAAAAGGAAA+GGG 0.514509 7.4:-27300183 MS.gene058515:CDS
ATGATCGTTGTTATAGATGC+GGG 0.530476 7.4:-27300268 MS.gene058515:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 7.4:+27300815 None:intergenic
GATGCGGGAAGAAATGTCAT+TGG 0.541206 7.4:-27300253 MS.gene058515:CDS
TTGGTTTGGTCATATTTGAG+AGG 0.544297 7.4:+27300347 None:intergenic
TGCAACAACAATATAGAATG+AGG 0.547994 7.4:-27300640 MS.gene058515:CDS
GGACTCGACAAGATTCTTGA+GGG 0.549561 7.4:-27301013 MS.gene058515:CDS
AATCTGTTGATGAAAAGGAA+AGG 0.552428 7.4:-27300184 MS.gene058515:CDS
CGTGGTCGAGGCAGAAGTCA+TGG 0.554869 7.4:-27300422 MS.gene058515:CDS
GAAATCAGCAGTCTCAAGAC+AGG 0.562148 7.4:+27300121 None:intergenic
CTTAATTGAGTATCTTGCAT+GGG 0.562250 7.4:-27301038 MS.gene058515:CDS
AATTGAGTATCTTGCATGGG+AGG 0.573842 7.4:-27301035 MS.gene058515:CDS
CAAACCAACAAGAATCATCA+AGG 0.574004 7.4:-27300332 MS.gene058515:CDS
TTTGGTTACAGCTCTTCTAG+TGG 0.574259 7.4:-27300597 MS.gene058515:CDS
ATTGAGTATCTTGCATGGGA+GGG 0.578262 7.4:-27301034 MS.gene058515:CDS
GGATATGCCATTGTTCCTGT+AGG 0.578642 7.4:+27300530 None:intergenic
TTCCTGTAGGACGCAACTGG+TGG 0.593030 7.4:+27300543 None:intergenic
GGGACTCGACAAGATTCTTG+AGG 0.594343 7.4:-27301014 MS.gene058515:CDS
AATTCATATAACCTCTTCCA+CGG 0.595635 7.4:+27300375 None:intergenic
TGTTGATGAAAAGGAAAGGG+AGG 0.595996 7.4:-27300180 MS.gene058515:CDS
ACGCCCTTGATTAAAAGTTG+TGG 0.608515 7.4:+27300496 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 7.4:+27300660 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 7.4:-27300467 MS.gene058515:CDS
GATGATCGTTGTTATAGATG+CGG 0.611305 7.4:-27300269 MS.gene058515:CDS
ACTTAATTGAGTATCTTGCA+TGG 0.611509 7.4:-27301039 MS.gene058515:CDS
GTCATTGGTCTAAAGCATGT+AGG 0.614634 7.4:-27300238 MS.gene058515:CDS
ACGATCATCATGATTTCTAG+AGG 0.627654 7.4:+27300283 None:intergenic
CGATCATCATGATTTCTAGA+GGG 0.638172 7.4:+27300284 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.642086 7.4:-27300473 MS.gene058515:CDS
CTCGACAAGATTCTTGAGGG+AGG 0.648718 7.4:-27301010 MS.gene058515:CDS
GTTGCGTCCTACAGGAACAA+TGG 0.661047 7.4:-27300537 MS.gene058515:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 7.4:-27300464 MS.gene058515:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 7.4:+27300921 None:intergenic
CGATTTGGGAGATGTCCCAG+AGG 0.724045 7.4:-27300987 MS.gene058515:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATGTTTAAAATTTTGAAT+TGG + chr7.4:27300120-27300139 None:intergenic 10.0%
!!! TTCAAAATTTTAAACATAAC+TGG - chr7.4:27300121-27300140 MS.gene058515:CDS 15.0%
! ACAAAATTAAGGCAAGATTT+GGG - chr7.4:27300350-27300369 MS.gene058515:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG - chr7.4:27300594-27300613 MS.gene058515:CDS 25.0%
! GAAGAGGTTATATGAATTAT+AGG - chr7.4:27300839-27300858 MS.gene058515:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG - chr7.4:27300507-27300526 MS.gene058515:CDS 25.0%
!! AAAAGATCCCAAGATTTTAT+GGG - chr7.4:27300327-27300346 MS.gene058515:CDS 25.0%
!! AATTTTGTCCCATAAAATCT+TGG + chr7.4:27300338-27300357 None:intergenic 25.0%
!! ATTGCACAATTAGAATTTTG+TGG - chr7.4:27300478-27300497 MS.gene058515:CDS 25.0%
!! ATTTTGTCCCATAAAATCTT+GGG + chr7.4:27300337-27300356 None:intergenic 25.0%
!! GATTTTATGGGACAAAATTA+AGG - chr7.4:27300339-27300358 MS.gene058515:CDS 25.0%
!!! CAACAACAGTTTTATAATCT+TGG + chr7.4:27300432-27300451 None:intergenic 25.0%
AACAAGAATCATCAAGGTAA+AGG - chr7.4:27300883-27300902 MS.gene058515:CDS 30.0%
AATTCATATAACCTCTTCCA+CGG + chr7.4:27300837-27300856 None:intergenic 30.0%
ACTTAATTGAGTATCTTGCA+TGG - chr7.4:27300170-27300189 MS.gene058515:CDS 30.0%
CTTAATTGAGTATCTTGCAT+GGG - chr7.4:27300171-27300190 MS.gene058515:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG - chr7.4:27300349-27300368 MS.gene058515:CDS 30.0%
TGATTTCATAGGAGAAGAAA+TGG - chr7.4:27301104-27301123 MS.gene058515:CDS 30.0%
TGCAACAACAATATAGAATG+AGG - chr7.4:27300569-27300588 MS.gene058515:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG - chr7.4:27300404-27300423 MS.gene058515:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG - chr7.4:27300498-27300517 MS.gene058515:CDS 30.0%
TTCCATTGATCCATTAATGA+GGG + chr7.4:27300397-27300416 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG + chr7.4:27300291-27300310 None:intergenic 30.0%
! AATCTGTTGATGAAAAGGAA+AGG - chr7.4:27301025-27301044 MS.gene058515:CDS 30.0%
! ATCTGTTGATGAAAAGGAAA+GGG - chr7.4:27301026-27301045 MS.gene058515:CDS 30.0%
! CAAAAGATCCCAAGATTTTA+TGG - chr7.4:27300326-27300345 MS.gene058515:CDS 30.0%
! CAAAGAATCTGTTGATGAAA+AGG - chr7.4:27301020-27301039 MS.gene058515:CDS 30.0%
! TATCTTTTACACAGATACTC+TGG + chr7.4:27301000-27301019 None:intergenic 30.0%
! TTTACCTTGATGATTCTTGT+TGG + chr7.4:27300884-27300903 None:intergenic 30.0%
AAAGGTAAAAACATCCAGGA+AGG - chr7.4:27300901-27300920 MS.gene058515:CDS 35.0%
AAAGTTGTGGCGTTTATTTC+AGG + chr7.4:27300703-27300722 None:intergenic 35.0%
AAGACAGGTAGTATCATTCT+TGG + chr7.4:27301076-27301095 None:intergenic 35.0%
AGACAGGTAGTATCATTCTT+GGG + chr7.4:27301075-27301094 None:intergenic 35.0%
AGGTAAAGGTAAAAACATCC+AGG - chr7.4:27300897-27300916 MS.gene058515:CDS 35.0%
ATGATCGTTGTTATAGATGC+GGG - chr7.4:27300941-27300960 MS.gene058515:CDS 35.0%
CAAACCAACAAGAATCATCA+AGG - chr7.4:27300877-27300896 MS.gene058515:CDS 35.0%
GATGATCGTTGTTATAGATG+CGG - chr7.4:27300940-27300959 MS.gene058515:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG + chr7.4:27300398-27300417 None:intergenic 35.0%
! AACGCCACAACTTTTAATCA+AGG - chr7.4:27300709-27300728 MS.gene058515:CDS 35.0%
! ACGATCATCATGATTTCTAG+AGG + chr7.4:27300929-27300948 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG - chr7.4:27300710-27300729 MS.gene058515:CDS 35.0%
! CGATCATCATGATTTCTAGA+GGG + chr7.4:27300928-27300947 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG + chr7.4:27300161-27300180 None:intergenic 35.0%
! CTTGATGATTCTTGTTGGTT+TGG + chr7.4:27300879-27300898 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG + chr7.4:27300240-27300259 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG + chr7.4:27300241-27300260 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG - chr7.4:27300384-27300403 MS.gene058515:CDS 35.0%
!! TTGGTTTGGTCATATTTGAG+AGG + chr7.4:27300865-27300884 None:intergenic 35.0%
AATTGAGTATCTTGCATGGG+AGG - chr7.4:27300174-27300193 MS.gene058515:CDS 40.0%
ACGCCCTTGATTAAAAGTTG+TGG + chr7.4:27300716-27300735 None:intergenic 40.0%
ATCAAGCACCACATTGATGA+TGG - chr7.4:27300280-27300299 MS.gene058515:CDS 40.0%
ATTGAGTATCTTGCATGGGA+GGG - chr7.4:27300175-27300194 MS.gene058515:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG + chr7.4:27300552-27300571 None:intergenic 40.0%
TTTGGTTACAGCTCTTCTAG+TGG - chr7.4:27300612-27300631 MS.gene058515:CDS 40.0%
! ACAACTTTTAATCAAGGGCG+TGG - chr7.4:27300715-27300734 MS.gene058515:CDS 40.0%
! GTCATTGGTCTAAAGCATGT+AGG - chr7.4:27300971-27300990 MS.gene058515:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG - chr7.4:27300392-27300411 MS.gene058515:CDS 40.0%
! TGTTGATGAAAAGGAAAGGG+AGG - chr7.4:27301029-27301048 MS.gene058515:CDS 40.0%
!! CTTGAGACTGCTGATTTCAT+AGG - chr7.4:27301093-27301112 MS.gene058515:CDS 40.0%
ATTCTTGAGGGAGGCGATTT+GGG - chr7.4:27300208-27300227 MS.gene058515:CDS 45.0%
CTGGAGACAACTACATAACC+TGG - chr7.4:27300140-27300159 MS.gene058515:CDS 45.0%
GAAATCAGCAGTCTCAAGAC+AGG + chr7.4:27301091-27301110 None:intergenic 45.0%
GATGCGGGAAGAAATGTCAT+TGG - chr7.4:27300956-27300975 MS.gene058515:CDS 45.0%
GGACTCGACAAGATTCTTGA+GGG - chr7.4:27300196-27300215 MS.gene058515:CDS 45.0%
GGATATGCCATTGTTCCTGT+AGG + chr7.4:27300682-27300701 None:intergenic 45.0%
GGTGGTTATAATCGCCAAAG+AGG - chr7.4:27300736-27300755 MS.gene058515:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG - chr7.4:27300742-27300761 MS.gene058515:CDS 45.0%
! CATGGTCGAAACCATTTTCG+TGG - chr7.4:27300805-27300824 MS.gene058515:CDS 45.0%
!! ACTTTTAATCAAGGGCGTGG+TGG - chr7.4:27300718-27300737 MS.gene058515:CDS 45.0%
CTCGACAAGATTCTTGAGGG+AGG - chr7.4:27300199-27300218 MS.gene058515:CDS 50.0%
GATTCTTGAGGGAGGCGATT+TGG - chr7.4:27300207-27300226 MS.gene058515:CDS 50.0%
GGGACTCGACAAGATTCTTG+AGG - chr7.4:27300195-27300214 MS.gene058515:CDS 50.0%
GTTGCGTCCTACAGGAACAA+TGG - chr7.4:27300672-27300691 MS.gene058515:CDS 50.0%
TTGTTCCTGTAGGACGCAAC+TGG + chr7.4:27300672-27300691 None:intergenic 50.0%
! CGAAACCATTTTCGTGGTGG+AGG - chr7.4:27300811-27300830 MS.gene058515:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG + chr7.4:27300918-27300937 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG - chr7.4:27300808-27300827 MS.gene058515:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG - chr7.4:27300769-27300788 MS.gene058515:CDS 50.0%
AACCACCAGTTGCGTCCTAC+AGG - chr7.4:27300664-27300683 MS.gene058515:CDS 55.0%
AATCGCCAAAGAGGACGTGG+TGG - chr7.4:27300745-27300764 MS.gene058515:CDS 55.0%
CATAGCCACCACGTCCTCTT+TGG + chr7.4:27300753-27300772 None:intergenic 55.0%
GGGAGATGTCCCAGAGGAAT+TGG - chr7.4:27300228-27300247 MS.gene058515:CDS 55.0%
TTCCTGTAGGACGCAACTGG+TGG + chr7.4:27300669-27300688 None:intergenic 55.0%
! CGATTTGGGAGATGTCCCAG+AGG - chr7.4:27300222-27300241 MS.gene058515:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG - chr7.4:27300760-27300779 MS.gene058515:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG - chr7.4:27300763-27300782 MS.gene058515:CDS 55.0%
CACGGCCTCCACCACGAAAA+TGG + chr7.4:27300819-27300838 None:intergenic 60.0%
CGTGGTCGAGGCAGAAGTCA+TGG - chr7.4:27300787-27300806 MS.gene058515:CDS 60.0%
!! CATTTTCGTGGTGGAGGCCG+TGG - chr7.4:27300817-27300836 MS.gene058515:CDS 60.0%
!! CGTTTTGGTGGTCGTGGTCG+AGG - chr7.4:27300775-27300794 MS.gene058515:CDS 60.0%
! CGTGGTGGAGGCCGTGGAAG+AGG - chr7.4:27300823-27300842 MS.gene058515:CDS 70.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 27300100 27301131 27300100 ID=MS.gene058515
chr7.4 mRNA 27300100 27301131 27300100 ID=MS.gene058515.t1;Parent=MS.gene058515
chr7.4 exon 27300100 27301131 27300100 ID=MS.gene058515.t1.exon1;Parent=MS.gene058515.t1
chr7.4 CDS 27300100 27301131 27300100 ID=cds.MS.gene058515.t1;Parent=MS.gene058515.t1
Gene Sequence

>MS.gene058515

ATGTCAAATGTTAAGCACCAATTCAAAATTTTAAACATAACTGGAGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGGGAGGGACTCGACAAGATTCTTGAGGGAGGCGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCGAATGCAAAAGATCCCAAGATTTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGTTATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGGAAATTTACTGAATACTCTGATTTGGTTACAGCTCTTCTAGTGGCTGAACAAAATAATGAGTTGCTCATTAAAAACCACCAGTTGCGTCCTACAGGAACAATGGCATATCCTGAAATAAACGCCACAACTTTTAATCAAGGGCGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGTCGAGGCAGAAGTCATGGTCGAAACCATTTTCGTGGTGGAGGCCGTGGAAGAGGTTATATGAATTATAGGCCTCTCAAATATGACCAAACCAACAAGAATCATCAAGGTAAAGGTAAAAACATCCAGGAAGGTCCCTCTAGAAATCATGATGATCGTTGTTATAGATGCGGGAAGAAATGTCATTGGTCTAAAGCATGTAGGACACCAGAGTATCTGTGTAAAAGATACAAAGAATCTGTTGATGAAAAGGAAAGGGAGGTTAATTTTAATGAAATTGAACCCAAGAATGATACTACCTGTCTTGAGACTGCTGATTTCATAGGAGAAGAAATGGATTAA

Protein sequence

>MS.gene058515.t1

MSNVKHQFKILNITGDNYITWNNNLIEYLAWEGLDKILEGGDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSVMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMRKFTEYSDLVTALLVAEQNNELLIKNHQLRPTGTMAYPEINATTFNQGRGGYNRQRGRGGYARFGGRGRGRSHGRNHFRGGGRGRGYMNYRPLKYDQTNKNHQGKGKNIQEGPSRNHDDRCYRCGKKCHWSKACRTPEYLCKRYKESVDEKEREVNFNEIEPKNDTTCLETADFIGEEMD