AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000163.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000163.01.T01 MTR_7g062720 40.541 148 80 3 1 146 1 142 1.49e-31 116
MsG0180000163.01.T01 MTR_5g061150 35.354 99 64 0 52 150 38 136 3.85e-18 80.1
MsG0180000163.01.T01 MTR_4g037355 40.800 125 58 3 155 272 1 116 9.59e-16 73.6
MsG0180000163.01.T01 MTR_4g112730 68.085 47 15 0 143 189 2 48 1.74e-14 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 58 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:-2240861 MsG0180000163.01.T01:CDS
AGTCTTATTGCCCTCATTAA+TGG 0.201947 1:-2240881 MsG0180000163.01.T01:CDS
GACAAAATTAAGGCAAGATT+TGG 0.257188 1:-2240916 MsG0180000163.01.T01:CDS
GATTCTTGAGGGAGACGATT+TGG 0.271296 1:-2241058 MsG0180000163.01.T01:CDS
CTCAATTAAGTTGTTGTTCC+AGG 0.274617 1:+2241107 None:intergenic
CACGGCCTCCACCACGAAAA+TGG 0.277262 1:+2240449 None:intergenic
CATAGGAGAAGATATTAATA+TGG 0.311554 1:-2240155 MsG0180000163.01.T01:CDS
ATTTACTGAATACTCTGATT+TGG 0.313227 1:-2240671 MsG0180000163.01.T01:CDS
GAAGAGGTTATATGAATTAT+AGG 0.339571 1:-2240426 MsG0180000163.01.T01:CDS
GGGAGATGTCCCAGAGGAAT+TGG 0.345733 1:-2241037 MsG0180000163.01.T01:CDS
ATTCTTGAGGGAGACGATTT+GGG 0.354692 1:-2241057 MsG0180000163.01.T01:CDS
AAGACAGGTAGTATCATTCT+TGG 0.359896 1:+2240192 None:intergenic
CTTGAGGCTGCTGATTTCAT+AGG 0.363536 1:-2240172 MsG0180000163.01.T01:CDS
GATTTCTAGAGGGACCTTCC+TGG 0.373636 1:+2240350 None:intergenic
CATAGCCACCACGTCCTCTT+TGG 0.374275 1:+2240515 None:intergenic
CGTGGTGGCTATGCTCGTTT+TGG 0.395091 1:-2240505 MsG0180000163.01.T01:CDS
ACAAAATTAAGGCAAGATTT+GGG 0.416566 1:-2240915 MsG0180000163.01.T01:CDS
TATAACTGAAAAGGAAAAGT+TGG 0.422757 1:-2240758 MsG0180000163.01.T01:CDS
CGTGGTGGAGGCCGTGGAAG+AGG 0.431707 1:-2240442 MsG0180000163.01.T01:CDS
TGCCCTCATTAATGGATCAA+TGG 0.432677 1:-2240873 MsG0180000163.01.T01:CDS
AGATACAAAGAATCTGTTGA+TGG 0.446469 1:-2240250 MsG0180000163.01.T01:CDS
TGGCAAAACTATAACTGAAA+AGG 0.467052 1:-2240767 MsG0180000163.01.T01:CDS
ATCTGTTGATGGAAAGGAAA+AGG 0.477668 1:-2240239 MsG0180000163.01.T01:CDS
AGACAGGTAGTATCATTCTT+GGG 0.483328 1:+2240193 None:intergenic
TTGTTCATGTAGGACGCAAC+TGG 0.484249 1:+2240596 None:intergenic
ATCAAGCACCACATTGATGA+TGG 0.492315 1:-2240985 MsG0180000163.01.T01:CDS
TGCAACAACAATATAGAATG+AGG 0.496917 1:-2240696 MsG0180000163.01.T01:CDS
CTGGAGACAACTACATAACC+TGG 0.502040 1:-2241125 MsG0180000163.01.T01:CDS
GTTCCATTGATCCATTAATG+AGG 0.509644 1:+2240870 None:intergenic
CAAAGAATCTGTTGATGGAA+AGG 0.510693 1:-2240245 MsG0180000163.01.T01:CDS
TGTTATAGATGCGGAAAGAA+AGG 0.513070 1:-2240316 MsG0180000163.01.T01:CDS
TTCCATTGATCCATTAATGA+GGG 0.533283 1:+2240871 None:intergenic
GATGCGGAAAGAAAGGTCAT+TGG 0.533423 1:-2240309 MsG0180000163.01.T01:CDS
GGACTCGACAAGATTCTTGA+GGG 0.539594 1:-2241069 MsG0180000163.01.T01:CDS
TTGGTTTGGTCATATTTGAG+AGG 0.543043 1:+2240403 None:intergenic
CGTGGTCGAGGCAGAAGTCA+TGG 0.554869 1:-2240478 MsG0180000163.01.T01:CDS
GAAATCAGCAGCCTCAAGAC+AGG 0.558951 1:+2240177 None:intergenic
AATTGAGTATCTTGCATGTG+AGG 0.565013 1:-2241091 MsG0180000163.01.T01:CDS
TTTGGTTACAGCTCTTCTAG+TGG 0.574259 1:-2240653 MsG0180000163.01.T01:CDS
AGGTAAAGGTAAAAGCATCC+AGG 0.575090 1:-2240368 MsG0180000163.01.T01:CDS
ATTGAGTATCTTGCATGTGA+GGG 0.575966 1:-2241090 MsG0180000163.01.T01:CDS
GCAACAACAATATAGAATGA+GGG 0.579939 1:-2240695 MsG0180000163.01.T01:CDS
AATTCATATAACCTCTTCCA+CGG 0.595635 1:+2240431 None:intergenic
GCAATATCACTTGAGATGCA+TGG 0.608661 1:+2240716 None:intergenic
TATAATCGCCAAAGAGGACG+TGG 0.608957 1:-2240523 MsG0180000163.01.T01:CDS
GGGACTCGACAAGATTCTTG+AGG 0.610766 1:-2241070 MsG0180000163.01.T01:CDS
TGTTGATGGAAAGGAAAAGG+AGG 0.612844 1:-2240236 MsG0180000163.01.T01:CDS
TTCATGTAGGACGCAACTGG+TGG 0.624154 1:+2240599 None:intergenic
ACGATCATCATGATTTCTAG+AGG 0.627654 1:+2240339 None:intergenic
GTCATTGGTCTAAAGCATGT+AGG 0.629444 1:-2240294 MsG0180000163.01.T01:CDS
GATGATCGTTGTTATAGATG+CGG 0.637106 1:-2240325 MsG0180000163.01.T01:CDS
GAATGATACTACCTGTCTTG+AGG 0.637144 1:-2240188 MsG0180000163.01.T01:CDS
CGATCATCATGATTTCTAGA+GGG 0.638172 1:+2240340 None:intergenic
GGTGGTTATAATCGCCAAAG+AGG 0.652314 1:-2240529 MsG0180000163.01.T01:CDS
AAAGGTAAAAGCATCCAGGA+AGG 0.661440 1:-2240364 MsG0180000163.01.T01:CDS
AATCGCCAAAGAGGACGTGG+TGG 0.698905 1:-2240520 MsG0180000163.01.T01:CDS
TTTGTAATCCATCATCAATG+TGG 0.715751 1:+2240977 None:intergenic
CGATTTGGGAGATGTCCCAG+AGG 0.725435 1:-2241043 MsG0180000163.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATGTTTAAAATTTTGAAT+TGG + Chr1:2240170-2240189 None:intergenic 10.0%
!!! TTCAAAATTTTAAACATAAC+TGG - Chr1:2240171-2240190 MsG0180000163.01.T01:CDS 15.0%
! AACAAAAATCATCAAGGTAA+AGG - Chr1:2240933-2240952 MsG0180000163.01.T01:CDS 25.0%
! ACAAAATTAAGGCAAGATTT+GGG - Chr1:2240400-2240419 MsG0180000163.01.T01:CDS 25.0%
! ATTTACTGAATACTCTGATT+TGG - Chr1:2240644-2240663 MsG0180000163.01.T01:CDS 25.0%
! CATAGGAGAAGATATTAATA+TGG - Chr1:2241160-2241179 MsG0180000163.01.T01:CDS 25.0%
! GAAGAGGTTATATGAATTAT+AGG - Chr1:2240889-2240908 MsG0180000163.01.T01:CDS 25.0%
! TATAACTGAAAAGGAAAAGT+TGG - Chr1:2240557-2240576 MsG0180000163.01.T01:intron 25.0%
!! AAAAGATCCCAAGATTTTAT+GGG - Chr1:2240377-2240396 MsG0180000163.01.T01:CDS 25.0%
!! AATTTTGTCCCATAAAATCT+TGG + Chr1:2240388-2240407 None:intergenic 25.0%
!! ATTGCACAATTAGAATTTTG+TGG - Chr1:2240528-2240547 MsG0180000163.01.T01:CDS 25.0%
!! ATTTTGTCCCATAAAATCTT+GGG + Chr1:2240387-2240406 None:intergenic 25.0%
!! GATTTTATGGGACAAAATTA+AGG - Chr1:2240389-2240408 MsG0180000163.01.T01:CDS 25.0%
!!! CAACAACAGTTTTATAATCT+TGG + Chr1:2240482-2240501 None:intergenic 25.0%
!!! TTTACCTTGATGATTTTTGT+TGG + Chr1:2240934-2240953 None:intergenic 25.0%
AATTCATATAACCTCTTCCA+CGG + Chr1:2240887-2240906 None:intergenic 30.0%
AGATACAAAGAATCTGTTGA+TGG - Chr1:2241065-2241084 MsG0180000163.01.T01:CDS 30.0%
CAAACCAACAAAAATCATCA+AGG - Chr1:2240927-2240946 MsG0180000163.01.T01:CDS 30.0%
GACAAAATTAAGGCAAGATT+TGG - Chr1:2240399-2240418 MsG0180000163.01.T01:CDS 30.0%
GCAACAACAATATAGAATGA+GGG - Chr1:2240620-2240639 MsG0180000163.01.T01:CDS 30.0%
TGCAACAACAATATAGAATG+AGG - Chr1:2240619-2240638 MsG0180000163.01.T01:CDS 30.0%
TGGATCAATGGAACAAATTA+AGG - Chr1:2240454-2240473 MsG0180000163.01.T01:CDS 30.0%
TGGCAAAACTATAACTGAAA+AGG - Chr1:2240548-2240567 MsG0180000163.01.T01:intron 30.0%
TTCCATTGATCCATTAATGA+GGG + Chr1:2240447-2240466 None:intergenic 30.0%
TTTGTAATCCATCATCAATG+TGG + Chr1:2240341-2240360 None:intergenic 30.0%
! CAAAAGATCCCAAGATTTTA+TGG - Chr1:2240376-2240395 MsG0180000163.01.T01:CDS 30.0%
! TATCTTTTACACAGATACTC+TGG + Chr1:2241050-2241069 None:intergenic 30.0%
!! CTTGATGATTTTTGTTGGTT+TGG + Chr1:2240929-2240948 None:intergenic 30.0%
AAAGTTGTGGCGTTTATTTC+AGG + Chr1:2240753-2240772 None:intergenic 35.0%
AAGACAGGTAGTATCATTCT+TGG + Chr1:2241126-2241145 None:intergenic 35.0%
AATTGAGTATCTTGCATGTG+AGG - Chr1:2240224-2240243 MsG0180000163.01.T01:CDS 35.0%
ACACCCTTGATTAAAAGTTG+TGG + Chr1:2240766-2240785 None:intergenic 35.0%
AGACAGGTAGTATCATTCTT+GGG + Chr1:2241125-2241144 None:intergenic 35.0%
ATTGAGTATCTTGCATGTGA+GGG - Chr1:2240225-2240244 MsG0180000163.01.T01:CDS 35.0%
GATGATCGTTGTTATAGATG+CGG - Chr1:2240990-2241009 MsG0180000163.01.T01:CDS 35.0%
GTTCCATTGATCCATTAATG+AGG + Chr1:2240448-2240467 None:intergenic 35.0%
TGTTATAGATGCGGAAAGAA+AGG - Chr1:2240999-2241018 MsG0180000163.01.T01:CDS 35.0%
! AACGCCACAACTTTTAATCA+AGG - Chr1:2240759-2240778 MsG0180000163.01.T01:CDS 35.0%
! ACAACTTTTAATCAAGGGTG+TGG - Chr1:2240765-2240784 MsG0180000163.01.T01:CDS 35.0%
! ACGATCATCATGATTTCTAG+AGG + Chr1:2240979-2240998 None:intergenic 35.0%
! ACGCCACAACTTTTAATCAA+GGG - Chr1:2240760-2240779 MsG0180000163.01.T01:CDS 35.0%
! ATCTGTTGATGGAAAGGAAA+AGG - Chr1:2241076-2241095 MsG0180000163.01.T01:CDS 35.0%
! CAAAGAATCTGTTGATGGAA+AGG - Chr1:2241070-2241089 MsG0180000163.01.T01:CDS 35.0%
! CGATCATCATGATTTCTAGA+GGG + Chr1:2240978-2240997 None:intergenic 35.0%
! CTCAATTAAGTTGTTGTTCC+AGG + Chr1:2240211-2240230 None:intergenic 35.0%
! TTTTCTTTGCCAATTCCTCT+GGG + Chr1:2240290-2240309 None:intergenic 35.0%
! TTTTTCTTTGCCAATTCCTC+TGG + Chr1:2240291-2240310 None:intergenic 35.0%
!! AGTCTTATTGCCCTCATTAA+TGG - Chr1:2240434-2240453 MsG0180000163.01.T01:CDS 35.0%
!! TTGGTTTGGTCATATTTGAG+AGG + Chr1:2240915-2240934 None:intergenic 35.0%
ATCAAGCACCACATTGATGA+TGG - Chr1:2240330-2240349 MsG0180000163.01.T01:CDS 40.0%
ATTCTTGAGGGAGACGATTT+GGG - Chr1:2240258-2240277 MsG0180000163.01.T01:CDS 40.0%
GAATGATACTACCTGTCTTG+AGG - Chr1:2241127-2241146 MsG0180000163.01.T01:CDS 40.0%
GCAATATCACTTGAGATGCA+TGG + Chr1:2240602-2240621 None:intergenic 40.0%
GGATATGCCATTGTTCATGT+AGG + Chr1:2240732-2240751 None:intergenic 40.0%
TTTGGTTACAGCTCTTCTAG+TGG - Chr1:2240662-2240681 MsG0180000163.01.T01:CDS 40.0%
! GTCATTGGTCTAAAGCATGT+AGG - Chr1:2241021-2241040 MsG0180000163.01.T01:CDS 40.0%
! TGCCCTCATTAATGGATCAA+TGG - Chr1:2240442-2240461 MsG0180000163.01.T01:CDS 40.0%
! TGTTGATGGAAAGGAAAAGG+AGG - Chr1:2241079-2241098 MsG0180000163.01.T01:CDS 40.0%
!! AAAGGTAAAAGCATCCAGGA+AGG - Chr1:2240951-2240970 MsG0180000163.01.T01:CDS 40.0%
!! ACTTTTAATCAAGGGTGTGG+TGG - Chr1:2240768-2240787 MsG0180000163.01.T01:CDS 40.0%
!! AGGTAAAGGTAAAAGCATCC+AGG - Chr1:2240947-2240966 MsG0180000163.01.T01:CDS 40.0%
CTGGAGACAACTACATAACC+TGG - Chr1:2240190-2240209 MsG0180000163.01.T01:CDS 45.0%
GATGCGGAAAGAAAGGTCAT+TGG - Chr1:2241006-2241025 MsG0180000163.01.T01:CDS 45.0%
GATTCTTGAGGGAGACGATT+TGG - Chr1:2240257-2240276 MsG0180000163.01.T01:CDS 45.0%
GGACTCGACAAGATTCTTGA+GGG - Chr1:2240246-2240265 MsG0180000163.01.T01:CDS 45.0%
GGTGGTTATAATCGCCAAAG+AGG - Chr1:2240786-2240805 MsG0180000163.01.T01:CDS 45.0%
GTTGCGTCCTACATGAACAA+TGG - Chr1:2240722-2240741 MsG0180000163.01.T01:CDS 45.0%
TATAATCGCCAAAGAGGACG+TGG - Chr1:2240792-2240811 MsG0180000163.01.T01:CDS 45.0%
TTGTTCATGTAGGACGCAAC+TGG + Chr1:2240722-2240741 None:intergenic 45.0%
! CATGGTCGAAACCATTTTCG+TGG - Chr1:2240855-2240874 MsG0180000163.01.T01:CDS 45.0%
!! CTTGAGGCTGCTGATTTCAT+AGG - Chr1:2241143-2241162 MsG0180000163.01.T01:CDS 45.0%
GAAATCAGCAGCCTCAAGAC+AGG + Chr1:2241141-2241160 None:intergenic 50.0%
GGGACTCGACAAGATTCTTG+AGG - Chr1:2240245-2240264 MsG0180000163.01.T01:CDS 50.0%
TTCATGTAGGACGCAACTGG+TGG + Chr1:2240719-2240738 None:intergenic 50.0%
! CGAAACCATTTTCGTGGTGG+AGG - Chr1:2240861-2240880 MsG0180000163.01.T01:CDS 50.0%
! GATTTCTAGAGGGACCTTCC+TGG + Chr1:2240968-2240987 None:intergenic 50.0%
! GGTCGAAACCATTTTCGTGG+TGG - Chr1:2240858-2240877 MsG0180000163.01.T01:CDS 50.0%
!! TATGCTCGTTTTGGTGGTCG+TGG - Chr1:2240819-2240838 MsG0180000163.01.T01:CDS 50.0%
AATCGCCAAAGAGGACGTGG+TGG - Chr1:2240795-2240814 MsG0180000163.01.T01:CDS 55.0%
CATAGCCACCACGTCCTCTT+TGG + Chr1:2240803-2240822 None:intergenic 55.0%
GGGAGATGTCCCAGAGGAAT+TGG - Chr1:2240278-2240297 MsG0180000163.01.T01:CDS 55.0%
! CGATTTGGGAGATGTCCCAG+AGG - Chr1:2240272-2240291 MsG0180000163.01.T01:CDS 55.0%
! CGTGGTGGCTATGCTCGTTT+TGG - Chr1:2240810-2240829 MsG0180000163.01.T01:CDS 55.0%
! GGTGGCTATGCTCGTTTTGG+TGG - Chr1:2240813-2240832 MsG0180000163.01.T01:CDS 55.0%
CACGGCCTCCACCACGAAAA+TGG + Chr1:2240869-2240888 None:intergenic 60.0%
CGTGGTCGAGGCAGAAGTCA+TGG - Chr1:2240837-2240856 MsG0180000163.01.T01:CDS 60.0%
!! CATTTTCGTGGTGGAGGCCG+TGG - Chr1:2240867-2240886 MsG0180000163.01.T01:CDS 60.0%
!! CGTTTTGGTGGTCGTGGTCG+AGG - Chr1:2240825-2240844 MsG0180000163.01.T01:CDS 60.0%
! CGTGGTGGAGGCCGTGGAAG+AGG - Chr1:2240873-2240892 MsG0180000163.01.T01:CDS 70.0%
Chromosome Type Strat End Strand Name
Chr1 gene 2240150 2241187 2240150 ID=MsG0180000163.01;Name=MsG0180000163.01
Chr1 mRNA 2240150 2241187 2240150 ID=MsG0180000163.01.T01;Parent=MsG0180000163.01;Name=MsG0180000163.01.T01;_AED=0.49;_eAED=0.49;_QI=0|0|0|1|1|1|2|0|327
Chr1 exon 2240611 2241187 2240611 ID=MsG0180000163.01.T01:exon:6720;Parent=MsG0180000163.01.T01
Chr1 exon 2240150 2240556 2240150 ID=MsG0180000163.01.T01:exon:6721;Parent=MsG0180000163.01.T01
Chr1 CDS 2240611 2241187 2240611 ID=MsG0180000163.01.T01:cds;Parent=MsG0180000163.01.T01
Chr1 CDS 2240150 2240556 2240150 ID=MsG0180000163.01.T01:cds;Parent=MsG0180000163.01.T01
Gene Sequence

>MsG0180000163.01.T01

ATGTCAAATGTTAAGCACCAATTCAAAATTTTAAACATAACTGGAGACAACTACATAACCTGGAACAACAACTTAATTGAGTATCTTGCATGTGAGGGACTCGACAAGATTCTTGAGGGAGACGATTTGGGAGATGTCCCAGAGGAATTGGCAAAGAAAAAATCAAAAGTAAATCGTATAATCAAGCACCACATTGATGATGGATTACAAACAGAGTATTCGAATGCAAAAGATCCCAAGATTTTATGGGACAAAATTAAGGCAAGATTTGGGCATCAGAAGAAAGTCTTATTGCCCTCATTAATGGATCAATGGAACAAATTAAGGTTCCAAGATTATAAAACTGTTGTTGCATATAACTCTGCTATGCATCAAATTATTGCACAATTAGAATTTTGTGGCAAAACTATAACTGAAAAGGAAAAGTTGGAGAAAACATTCTCAACTTTCCATGCATCTCAAGTGATATTGCAACAACAATATAGAATGAGGGAATTTACTGAATACTCTGATTTGGTTACAGCTCTTCTAGTGGCTGAACAAAATAATGAGCTGCTCATTAAAAACCACCAGTTGCGGTGTGGTGGTTATAATCGCCAAAGAGGACGTGGTGGCTATGCTCGTTTTGGTGGTCGTGGTCGAGGCAGAAGTCATGGTCGAAACCATTTTCGTGGTGGAGGCCGTGGAAGAGGTTATATGAATTATAGGCCTCTCAAATATGACCAAACCAACAAAAATCATCAAGGTAAAGGTAAAAGCATCCAGGAAGGTCCCTCTAGAAATCATGATGATCGTTGTTATAGATGCGGAAAGAAAGGTCATTGGTCTAAAGCATGTAGGACACCAGAGTATCTGTGTAAAAGATACAAAGAATCTGTTGATGGAAAGGAAAAGGAGGTTAATTTTAATGAAATTGAACCCAAGAATGATACTACCTGTCTTGAGGCTGCTGATTTCATAGGAGAAGATATTAATATGGATTAA

Protein sequence

>MsG0180000163.01.T01

MSNVKHQFKILNITGDNYITWNNNLIEYLACEGLDKILEGDDLGDVPEELAKKKSKVNRIIKHHIDDGLQTEYSNAKDPKILWDKIKARFGHQKKVLLPSLMDQWNKLRFQDYKTVVAYNSAMHQIIAQLEFCGKTITEKEKLEKTFSTFHASQVILQQQYRMREFTEYSDLVTALLVAEQNNELLIKNHQLRCGGYNRQRGRGGYARFGGRGRGRSHGRNHFRGGGRGRGYMNYRPLKYDQTNKNHQGKGKSIQEGPSRNHDDRCYRCGKKGHWSKACRTPEYLCKRYKESVDGKEKEVNFNEIEPKNDTTCLEAADFIGEDINMD*