AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180003527.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180003527.01.T02 MTR_1g063360 94.872 78 4 0 1 78 1 78 4.98e-54 163
MsG0180003527.01.T01 MTR_1g063360 96.000 100 4 0 1 100 1 100 2.79e-71 207
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180003527.01.T02 AT3G09860 66.234 77 25 1 1 77 1 76 2.99e-32 108
MsG0180003527.01.T01 AT3G09860 64.646 99 33 2 1 99 1 97 2.93e-41 131

Find 26 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGCAATATCACTGGAAAA+AGG 0.290029 1:-63674978 MsG0180003527.01.T01:CDS
GAGACCTAAGTGAAGTAAAT+AGG 0.302445 1:+63674758 None:intergenic
CGTTACTTTGGTTACAAACT+TGG 0.308381 1:-63674700 MsG0180003527.01.T01:three_prime_UTR
TAATGCGCAGCTGGCATGAT+AGG 0.310695 1:-63675012 MsG0180003527.01.T01:intron
TACAACGAAGAAGGGGCGGG+GGG 0.405609 1:+63674663 None:intergenic
GTACAACGAAGAAGGGGCGG+GGG 0.419977 1:+63674662 None:intergenic
GAGATTCATACTACTTCAAC+TGG 0.442393 1:-63674781 MsG0180003527.01.T01:CDS
AGTACAACGAAGAAGGGGCG+GGG 0.444937 1:+63674661 None:intergenic
AACGATAATACAACCACAGC+AGG 0.460779 1:+63674719 None:intergenic
ACAACGAAGAAGGGGCGGGG+GGG 0.464062 1:+63674664 None:intergenic
GAGTACAACGAAGAAGGGGC+GGG 0.508989 1:+63674660 None:intergenic
TGGTTGTATTATCGTTACTT+TGG 0.512725 1:-63674712 MsG0180003527.01.T01:three_prime_UTR
ATTTGAGAGTACAACGAAGA+AGG 0.513420 1:+63674654 None:intergenic
CTGGCCTATTTACTTCACTT+AGG 0.516226 1:-63674762 MsG0180003527.01.T01:exon
TTTGAGAGTACAACGAAGAA+GGG 0.520550 1:+63674655 None:intergenic
TGTTGCAGTGGAACAAGACT+TGG 0.544049 1:-63674817 MsG0180003527.01.T01:intron
AGCGATACGAGTTCAATGTA+TGG 0.545276 1:-63674940 MsG0180003527.01.T01:intron
AATGCGCAGCTGGCATGATA+GGG 0.546604 1:-63675011 MsG0180003527.01.T01:intron
AGAGTACAACGAAGAAGGGG+CGG 0.596445 1:+63674659 None:intergenic
GAAGTAGTATGAATCTCGGT+GGG 0.609044 1:+63674787 None:intergenic
AGTTGAAGTAGTATGAATCT+CGG 0.616389 1:+63674783 None:intergenic
ACGATAATACAACCACAGCA+GGG 0.628027 1:+63674720 None:intergenic
CGATAATACAACCACAGCAG+GGG 0.641610 1:+63674721 None:intergenic
TTGAGAGTACAACGAAGAAG+GGG 0.654172 1:+63674656 None:intergenic
TGAAGTAGTATGAATCTCGG+TGG 0.662856 1:+63674786 None:intergenic
GTTGCAGTGGAACAAGACTT+GGG 0.683328 1:-63674816 MsG0180003527.01.T01:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAATTAATTAATGATTT+AGG - Chr1:63675219-63675238 MsG0180003527.01.T01:intron 10.0%
!! TTAAAAATATAAGTTATTCA+AGG - Chr1:63675460-63675479 MsG0180003527.01.T01:intron 10.0%
!! AGTTACAATTAAATAACTTA+AGG - Chr1:63675489-63675508 MsG0180003527.01.T01:intron 15.0%
!! GTTAGAATTAAATAACTTAT+AGG - Chr1:63675520-63675539 MsG0180003527.01.T01:intron 15.0%
!!! ACCTTCTTTTTTTTTTTTTA+GGG - Chr1:63675276-63675295 MsG0180003527.01.T01:intron 15.0%
!!! GTTATTTAATTGTAACTTTT+AGG + Chr1:63675486-63675505 None:intergenic 15.0%
!!! TTTGAAATTTTGTTAATTTC+AGG + Chr1:63674971-63674990 None:intergenic 15.0%
!!! TTTTCTTTTTCAAAGATATT+TGG - Chr1:63675062-63675081 MsG0180003527.01.T01:intron 15.0%
!! AAAATATGTCAATTTAGTCT+CGG + Chr1:63675020-63675039 None:intergenic 20.0%
!! ATTATGAGATGTAAATGATT+TGG + Chr1:63675822-63675841 None:intergenic 20.0%
!! ATTATTTAACTGCAACAAAT+TGG - Chr1:63675344-63675363 MsG0180003527.01.T01:intron 20.0%
!! GTGAATTAATTGTAATAAGT+TGG - Chr1:63675382-63675401 MsG0180003527.01.T01:intron 20.0%
!! GTTGAAAAATAATTAGAGAA+GGG + Chr1:63674812-63674831 None:intergenic 20.0%
!! TCCCTAAAAAAAAAAAAAGA+AGG + Chr1:63675280-63675299 None:intergenic 20.0%
!! TGTTGAAAAATAATTAGAGA+AGG + Chr1:63674813-63674832 None:intergenic 20.0%
!!! CACCTTCTTTTTTTTTTTTT+AGG - Chr1:63675275-63675294 MsG0180003527.01.T01:intron 20.0%
! AAACTCTTGGAATAAACAAT+AGG + Chr1:63675564-63675583 None:intergenic 25.0%
! ACACAAATTCTCCTTAATTA+TGG - Chr1:63675769-63675788 MsG0180003527.01.T01:intron 25.0%
! TAGGTCAACAGTAATAATTT+GGG - Chr1:63675425-63675444 MsG0180003527.01.T01:intron 25.0%
!! AAATAGTTTGGTTCATATTG+AGG - Chr1:63675585-63675604 MsG0180003527.01.T01:intron 25.0%
!! GGACACTTTTATTATTGTTT+AGG - Chr1:63675297-63675316 MsG0180003527.01.T01:intron 25.0%
!! TTTGGAGTTTCGTTAATTTA+AGG - Chr1:63675080-63675099 MsG0180003527.01.T01:intron 25.0%
!!! GAGTTTATCTATTGATTTGT+TGG - Chr1:63675134-63675153 MsG0180003527.01.T01:intron 25.0%
AAAAAAAAGAAGGTGATTGC+AGG + Chr1:63675270-63675289 None:intergenic 30.0%
AAAAAAAGAAGGTGATTGCA+GGG + Chr1:63675269-63675288 None:intergenic 30.0%
AAAACAAACCAAAACAAACC+AGG + Chr1:63675717-63675736 None:intergenic 30.0%
AAAAGAAGAGAAGAGAAGAA+TGG - Chr1:63674620-63674639 MsG0180003527.01.T01:three_prime_UTR 30.0%
AACAATAGGCTAAATTACAC+TGG + Chr1:63675550-63675569 None:intergenic 30.0%
ACCAAACTATTTCAAACTCT+TGG + Chr1:63675577-63675596 None:intergenic 30.0%
ACCAAGCAAAACCATAATTA+AGG + Chr1:63675783-63675802 None:intergenic 30.0%
AGTTGAAGTAGTATGAATCT+CGG + Chr1:63676085-63676104 None:intergenic 30.0%
ATTATTACTGTTGACCTAGT+TGG + Chr1:63675423-63675442 None:intergenic 30.0%
CACTCATAAATATTGGATTC+AGG + Chr1:63674901-63674920 None:intergenic 30.0%
CTAGGTCAACAGTAATAATT+TGG - Chr1:63675424-63675443 MsG0180003527.01.T01:intron 30.0%
GACGATTCACTCATAAATAT+TGG + Chr1:63674908-63674927 None:intergenic 30.0%
GTATGCACATTGAAATCATA+TGG + Chr1:63675247-63675266 None:intergenic 30.0%
TATAATTAAGCAAAGCACAG+AGG + Chr1:63676017-63676036 None:intergenic 30.0%
TGGTTGTATTATCGTTACTT+TGG - Chr1:63676153-63676172 MsG0180003527.01.T01:CDS 30.0%
TTCATTGACAAACATGATTG+AGG - Chr1:63675038-63675057 MsG0180003527.01.T01:intron 30.0%
! ATTTAGTTTACCAAGCTGTA+GGG - Chr1:63674929-63674948 MsG0180003527.01.T01:intron 30.0%
! TATTGGATTCAGGTTAATCA+AGG + Chr1:63674891-63674910 None:intergenic 30.0%
! TATTTAGTTTACCAAGCTGT+AGG - Chr1:63674928-63674947 MsG0180003527.01.T01:intron 30.0%
! TCCAAGAGTTTGAAATAGTT+TGG - Chr1:63675573-63675592 MsG0180003527.01.T01:intron 30.0%
!! AAAATTTTGTGTTGTTGCAG+TGG - Chr1:63676036-63676055 MsG0180003527.01.T01:intron 30.0%
!! ATTATGGTTTTGCTTGGTAA+AGG - Chr1:63675785-63675804 MsG0180003527.01.T01:intron 30.0%
!! TCCTTAATTATGGTTTTGCT+TGG - Chr1:63675779-63675798 MsG0180003527.01.T01:intron 30.0%
!!! AAGTTTTTTCTGTACCAACT+AGG - Chr1:63675406-63675425 MsG0180003527.01.T01:intron 30.0%
AATAGGCTAAATTACACTGG+AGG + Chr1:63675547-63675566 None:intergenic 35.0%
CATATTGAGGTCTAAGCTTA+AGG - Chr1:63675598-63675617 MsG0180003527.01.T01:intron 35.0%
GAGACCTAAGTGAAGTAAAT+AGG + Chr1:63676110-63676129 None:intergenic 35.0%
GAGATTCATACTACTTCAAC+TGG - Chr1:63676084-63676103 MsG0180003527.01.T01:intron 35.0%
GCTAAACTCTCAAAAAGATG+AGG + Chr1:63675971-63675990 None:intergenic 35.0%
TATAGTCTGCTTGTGAGATT+CGG - Chr1:63675739-63675758 MsG0180003527.01.T01:intron 35.0%
TATTTCAGTTCAGCATATCG+TGG - Chr1:63674648-63674667 MsG0180003527.01.T01:three_prime_UTR 35.0%
TGAGCAATATCACTGGAAAA+AGG - Chr1:63675887-63675906 MsG0180003527.01.T01:intron 35.0%
TGATGAGAAATACTTGAAGC+TGG + Chr1:63674787-63674806 None:intergenic 35.0%
! ATTTGAGAGTACAACGAAGA+AGG + Chr1:63676214-63676233 None:intergenic 35.0%
! CGTTACTTTGGTTACAAACT+TGG - Chr1:63676165-63676184 MsG0180003527.01.T01:CDS 35.0%
! TTTGAGAGTACAACGAAGAA+GGG + Chr1:63676213-63676232 None:intergenic 35.0%
!! GCAATGACTTGCTATGATTA+TGG - Chr1:63675643-63675662 MsG0180003527.01.T01:intron 35.0%
!! TGCTTTTTGAGCAATATCAC+TGG - Chr1:63675880-63675899 MsG0180003527.01.T01:intron 35.0%
!!! TCTTTCTTCCTGGTTTGTTT+TGG - Chr1:63675706-63675725 MsG0180003527.01.T01:intron 35.0%
AACATTCTTTAATGCGCAGC+TGG - Chr1:63675844-63675863 MsG0180003527.01.T01:intron 40.0%
AACGATAATACAACCACAGC+AGG + Chr1:63676149-63676168 None:intergenic 40.0%
ACGATAATACAACCACAGCA+GGG + Chr1:63676148-63676167 None:intergenic 40.0%
AGCGATACGAGTTCAATGTA+TGG - Chr1:63675925-63675944 MsG0180003527.01.T01:intron 40.0%
ATTGTCTAAACCCTACAGCT+TGG + Chr1:63674942-63674961 None:intergenic 40.0%
CAAAAAGATGAGGCAGTAGA+GGG + Chr1:63675961-63675980 None:intergenic 40.0%
CGAACCAAATGTTGACGAAA+CGG + Chr1:63674704-63674723 None:intergenic 40.0%
CGTTTCGTCAACATTTGGTT+CGG - Chr1:63674702-63674721 MsG0180003527.01.T01:three_prime_UTR 40.0%
CTGGCCTATTTACTTCACTT+AGG - Chr1:63676103-63676122 MsG0180003527.01.T01:CDS 40.0%
GAAGTAGTATGAATCTCGGT+GGG + Chr1:63676081-63676100 None:intergenic 40.0%
GAATCTCACAAGCAGACTAT+AGG + Chr1:63675740-63675759 None:intergenic 40.0%
GCTGTAGGGTTTAGACAATT+TGG - Chr1:63674943-63674962 MsG0180003527.01.T01:intron 40.0%
TCAAAAAGATGAGGCAGTAG+AGG + Chr1:63675962-63675981 None:intergenic 40.0%
TCTAAGCTTAAGGTTATCCG+TGG - Chr1:63675608-63675627 MsG0180003527.01.T01:intron 40.0%
TGAAGTAGTATGAATCTCGG+TGG + Chr1:63676082-63676101 None:intergenic 40.0%
TGAGAAATACTTGAAGCTGG+AGG + Chr1:63674784-63674803 None:intergenic 40.0%
TTGTGTCTTGTCTTTCTTCC+TGG - Chr1:63675696-63675715 MsG0180003527.01.T01:intron 40.0%
! AACTGCAACAAATTGGTCTC+AGG - Chr1:63675351-63675370 MsG0180003527.01.T01:intron 40.0%
! TTGAGAGTACAACGAAGAAG+GGG + Chr1:63676212-63676231 None:intergenic 40.0%
!! TTATTTTTCTTCCCCTGCTG+TGG - Chr1:63676133-63676152 MsG0180003527.01.T01:CDS 40.0%
AATCCCTACTTCTGGCACAT+CGG - Chr1:63674756-63674775 MsG0180003527.01.T01:exon 45.0%
ACTGTGTCAATCCCTACTTC+TGG - Chr1:63674748-63674767 MsG0180003527.01.T01:exon 45.0%
ATTGCTTAAGATCCGCACCA+CGG + Chr1:63675628-63675647 None:intergenic 45.0%
CAAATGTTGACGAAACGGTG+TGG + Chr1:63674699-63674718 None:intergenic 45.0%
CACACCGTTTCGTCAACATT+TGG - Chr1:63674697-63674716 MsG0180003527.01.T01:three_prime_UTR 45.0%
CGATAATACAACCACAGCAG+GGG + Chr1:63676147-63676166 None:intergenic 45.0%
GTTGCAGTGGAACAAGACTT+GGG - Chr1:63676049-63676068 MsG0180003527.01.T01:intron 45.0%
TGTTGCAGTGGAACAAGACT+TGG - Chr1:63676048-63676067 MsG0180003527.01.T01:intron 45.0%
AAACGGTGTGGATCAGCATG+GGG + Chr1:63674687-63674706 None:intergenic 50.0%
AATGCGCAGCTGGCATGATA+GGG - Chr1:63675854-63675873 MsG0180003527.01.T01:intron 50.0%
AGAGTACAACGAAGAAGGGG+CGG + Chr1:63676209-63676228 None:intergenic 50.0%
AGTTGCAAGCAGTGAAGGCA+AGG + Chr1:63674731-63674750 None:intergenic 50.0%
GAAACGGTGTGGATCAGCAT+GGG + Chr1:63674688-63674707 None:intergenic 50.0%
GAACCGATGTGCCAGAAGTA+GGG + Chr1:63674762-63674781 None:intergenic 50.0%
GACACAGTTGCAAGCAGTGA+AGG + Chr1:63674736-63674755 None:intergenic 50.0%
GCTTAAGGTTATCCGTGGTG+CGG - Chr1:63675613-63675632 MsG0180003527.01.T01:intron 50.0%
TAATGCGCAGCTGGCATGAT+AGG - Chr1:63675853-63675872 MsG0180003527.01.T01:intron 50.0%
AGTACAACGAAGAAGGGGCG+GGG + Chr1:63676207-63676226 None:intergenic 55.0%
CGAAACGGTGTGGATCAGCA+TGG + Chr1:63674689-63674708 None:intergenic 55.0%
GAGTACAACGAAGAAGGGGC+GGG + Chr1:63676208-63676227 None:intergenic 55.0%
GGAACCGATGTGCCAGAAGT+AGG + Chr1:63674763-63674782 None:intergenic 55.0%
TCAGCATATCGTGGTGACCC+AGG - Chr1:63674657-63674676 MsG0180003527.01.T01:three_prime_UTR 55.0%
GATCAGCATGGGGTACGCCT+GGG + Chr1:63674677-63674696 None:intergenic 60.0%
GTACAACGAAGAAGGGGCGG+GGG + Chr1:63676206-63676225 None:intergenic 60.0%
TACAACGAAGAAGGGGCGGG+GGG + Chr1:63676205-63676224 None:intergenic 60.0%
ACAACGAAGAAGGGGCGGGG+GGG + Chr1:63676204-63676223 None:intergenic 65.0%
GGATCAGCATGGGGTACGCC+TGG + Chr1:63674678-63674697 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
Chr1 gene 63674617 63676270 63674617 ID=MsG0180003527.01;Name=MsG0180003527.01
Chr1 mRNA 63674617 63676270 63674617 ID=MsG0180003527.01.T01;Parent=MsG0180003527.01;Name=MsG0180003527.01.T01;_AED=0.50;_eAED=0.50;_QI=22|1|1|1|0|0.33|3|146|100
Chr1 exon 63674617 63674831 63674617 ID=MsG0180003527.01.T01:exon:50199;Parent=MsG0180003527.01.T01
Chr1 exon 63674946 63675024 63674946 ID=MsG0180003527.01.T01:exon:50198;Parent=MsG0180003527.01.T01
Chr1 five_prime_UTR 63676249 63676270 63676249 ID=MsG0180003527.01.T01:five_prime_utr;Parent=MsG0180003527.01.T01
Chr1 CDS 63676094 63676248 63676094 ID=MsG0180003527.01.T01:cds;Parent=MsG0180003527.01.T01
Chr1 CDS 63674946 63675024 63674946 ID=MsG0180003527.01.T01:cds;Parent=MsG0180003527.01.T01
Chr1 CDS 63674763 63674831 63674763 ID=MsG0180003527.01.T01:cds;Parent=MsG0180003527.01.T01
Chr1 three_prime_UTR 63674617 63674762 63674617 ID=MsG0180003527.01.T01:three_prime_utr;Parent=MsG0180003527.01.T01
Chr1 mRNA 63674898 63676270 63674898 ID=MsG0180003527.01.T02;Parent=MsG0180003527.01;Name=MsG0180003527.01.T02;_AED=0.50;_eAED=0.58;_QI=22|1|0.5|1|0|0.5|2|0|93
Chr1 exon 63674898 63675024 63674898 ID=MsG0180003527.01.T02:exon:50200;Parent=MsG0180003527.01.T02
Chr1 five_prime_UTR 63676249 63676270 63676249 ID=MsG0180003527.01.T02:five_prime_utr;Parent=MsG0180003527.01.T02
Chr1 CDS 63676094 63676248 63676094 ID=MsG0180003527.01.T02:cds;Parent=MsG0180003527.01.T02
Chr1 CDS 63674898 63675024 63674898 ID=MsG0180003527.01.T02:cds;Parent=MsG0180003527.01.T02
Gene Sequence

>MsG0180003527.01.T02

ATGGACAAGTATTTCAGTTCAGCATATCGTGGTGACCCAGGCGTACCCCATGCTGATCCACACCGTTTCGTCAACATTTGGTTCGGTTGCCTTGCCTTCACTGCTTGCAACTGTGTCAATCCCTACTTCTGGCACATCGGTTCCTCCAGCTTCAACTGGCATGATAGGGTAATGCTTTTTGAGCAATATCACTGGAAAAAGGCAATGAAGAAGAATCAGCGATACGAGTTCAATGTATGGTATTTTACGTCCCTCTACTGCCTCATCTTTTTGAGAGTTTAG

>MsG0180003527.01.T01

ATGGACAAGTATTTCAGTTCAGCATATCGTGGTGACCCAGGCGTACCCCATGCTGATCCACACCGTTTCGTCAACATTTGGTTCGGTTGCCTTGCCTTCACTGCTTGCAACTGTGTCAATCCCTACTTCTGGCACATCGGTTCCTCCAGCTTCAACTGGCATGATAGGGTAATGCTTTTTGAGCAATATCACTGGAAAAAGGCAATGAAGAAGAATCAGCGATACGAGTTCAATTGGAACAAGACTTGGGACAGAGCCCACCGAGATTCATACTACTTCAACTGGCCTATTTACTTCACTTAG
Protein sequence

>MsG0180003527.01.T02

MDKYFSSAYRGDPGVPHADPHRFVNIWFGCLAFTACNCVNPYFWHIGSSSFNWHDRVMLFEQYHWKKAMKKNQRYEFNVWYFTSLYCLIFLRV*

>MsG0180003527.01.T01

MDKYFSSAYRGDPGVPHADPHRFVNIWFGCLAFTACNCVNPYFWHIGSSSFNWHDRVMLFEQYHWKKAMKKNQRYEFNWNKTWDRAHRDSYYFNWPIYFT*