AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180000878.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000878.01.T01 MTR_1g026820 96.923 130 4 0 1 130 1 130 2.10e-87 250
MsG0180000878.01.T01 MTR_1g026820 98.980 98 1 0 33 130 1 98 4.47e-65 192
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180000878.01.T01 AT1G30380 81.679 131 22 2 1 130 1 130 6.17e-73 214

Find 67 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTTCTTAACTGTAATATT+TGG 0.204969 1:-12630435 MsG0180000878.01.T01:three_prime_UTR
ATTGGTGTTGGTGTTGTTCT+TGG 0.263431 1:-12630570 MsG0180000878.01.T01:CDS
ATCTTCCAGCAAACAACATT+AGG 0.298751 1:+12630730 None:intergenic
TTTCCCTTGCGCCTTGTCAT+AGG 0.324595 1:+12631505 None:intergenic
GCGCAAGGGAAAGGGTGCTT+TGG 0.345906 1:-12631494 MsG0180000878.01.T01:CDS
GTTCACCCTTGCTGATACTT+TGG 0.359682 1:-12630616 MsG0180000878.01.T01:CDS
TTGCAGACTGGTGACCCAGC+TGG 0.370604 1:-12630639 MsG0180000878.01.T01:CDS
CGCAAGGGAAAGGGTGCTTT+GGG 0.371284 1:-12631493 MsG0180000878.01.T01:CDS
TTTCATTTAGTTTGATCAAA+TGG 0.373909 1:-12631883 MsG0180000878.01.T01:exon
ACCTTCTCCTATCCAGGGTT+TGG 0.377236 1:-12631805 MsG0180000878.01.T01:intron
ATGTTGTTTGCTGGAAGATT+TGG 0.379579 1:-12630726 MsG0180000878.01.T01:CDS
ACAATGCACCAATGTTCTTA+AGG 0.380011 1:+12630547 None:intergenic
TTGAAATCATACCACATTAG+TGG 0.382365 1:+12631444 None:intergenic
ATGATTGAATCCCATTCAAT+TGG 0.383708 1:+12630351 None:intergenic
GGAGTTCGTTGTGACTTCAT+TGG 0.392047 1:-12631472 MsG0180000878.01.T01:CDS
TCTTCCAGCAAACAACATTA+GGG 0.393888 1:+12630731 None:intergenic
ACAACCCTAATGTTGTTTGC+TGG 0.398888 1:-12630735 MsG0180000878.01.T01:CDS
GTTGCTTTCCTGTTTGCTGA+TGG 0.410830 1:+12630696 None:intergenic
TTTAGAATGCTGATATTAGA+TGG 0.415451 1:+12632035 None:intergenic
CCTTGCGCCTTGTCATAGGT+TGG 0.425942 1:+12631509 None:intergenic
AATCGAGTCATCCAATTGAA+TGG 0.428090 1:-12630362 MsG0180000878.01.T01:three_prime_UTR
TGCAGACTGGTGACCCAGCT+GGG 0.430536 1:-12630638 MsG0180000878.01.T01:CDS
ACTCAAACCTTCTCCTATCC+AGG 0.437202 1:-12631811 MsG0180000878.01.T01:CDS
GATTGGCTCCATCAGCAAAC+AGG 0.437905 1:-12630704 MsG0180000878.01.T01:CDS
TCAGCAAGGGTGAACCCAGC+TGG 0.438597 1:+12630624 None:intergenic
CTTGCGCCTTGTCATAGGTT+GGG 0.439768 1:+12631510 None:intergenic
GGATGACTCGATTGTATCAC+TGG 0.446726 1:+12630372 None:intergenic
TCGAACTATTGAGTCACATA+TGG 0.457571 1:+12630322 None:intergenic
ACAACTTTGCCTCAATTCAC+TGG 0.462189 1:-12631846 MsG0180000878.01.T01:CDS
AGCAACAGCAGGACTAAAGC+TGG 0.487183 1:-12630679 MsG0180000878.01.T01:CDS
ATCGAGTCATCCAATTGAAT+GGG 0.490042 1:-12630361 MsG0180000878.01.T01:three_prime_UTR
GTTTGCTGGAAGATTTGGAT+TGG 0.494741 1:-12630721 MsG0180000878.01.T01:CDS
TATGACAAGGCGCAAGGGAA+AGG 0.505007 1:-12631503 MsG0180000878.01.T01:CDS
ACTTTGGCCTGTGGAACTGT+TGG 0.509321 1:-12630600 MsG0180000878.01.T01:CDS
ATGACAAGGCGCAAGGGAAA+GGG 0.519777 1:-12631502 MsG0180000878.01.T01:CDS
CTTGCTGATACTTTGGCCTG+TGG 0.531365 1:-12630609 MsG0180000878.01.T01:CDS
GGAACTGTTGGACACATCAT+TGG 0.534067 1:-12630588 MsG0180000878.01.T01:CDS
AGGGACTCAGGCTTGCAGAC+TGG 0.536809 1:-12630651 MsG0180000878.01.T01:CDS
CAGGACTAAAGCTGGAGACA+AGG 0.539368 1:-12630671 MsG0180000878.01.T01:CDS
GGTTTAAGACCAGTGAATTG+AGG 0.543474 1:+12631837 None:intergenic
ATAGGAGAAGGTTTGAGTTG+TGG 0.551141 1:+12631816 None:intergenic
AAGATGTAAGCAGAATCTAA+TGG 0.553360 1:+12631989 None:intergenic
ACCAAACCCTGGATAGGAGA+AGG 0.553964 1:+12631804 None:intergenic
AAGCTGGAGACAAGGGACTC+AGG 0.559360 1:-12630663 MsG0180000878.01.T01:CDS
TTACAGTTAAGAAATAGTAA+AGG 0.561952 1:+12630442 None:intergenic
CAGCAAGGGTGAACCCAGCT+GGG 0.567280 1:+12630625 None:intergenic
GTTCTTGGCCTTAAGAACAT+TGG 0.570766 1:-12630555 MsG0180000878.01.T01:CDS
GATGTGTCCAACAGTTCCAC+AGG 0.576438 1:+12630593 None:intergenic
ACGTTGGATTAACGTATCTA+CGG 0.581668 1:-12632058 MsG0180000878.01.T01:five_prime_UTR
AGGCAAAGTTGTCATCATAG+AGG 0.584160 1:+12631857 None:intergenic
TTAATTACCAAACCCTGGAT+AGG 0.584959 1:+12631798 None:intergenic
CATTGGTTCATCCACTAATG+TGG 0.586749 1:-12631455 MsG0180000878.01.T01:intron
GGTGGTTAATTACCAAACCC+TGG 0.592935 1:+12631793 None:intergenic
AGGACTAAAGCTGGAGACAA+GGG 0.595838 1:-12630670 MsG0180000878.01.T01:CDS
CTCAAACCTTCTCCTATCCA+GGG 0.595941 1:-12631810 MsG0180000878.01.T01:CDS
CCAACCTATGACAAGGCGCA+AGG 0.600144 1:-12631509 MsG0180000878.01.T01:CDS
CACAGGCCAAAGTATCAGCA+AGG 0.601389 1:+12630610 None:intergenic
GTTGGACACATCATTGGTGT+TGG 0.612231 1:-12630582 MsG0180000878.01.T01:CDS
GCAAACAGGAAAGCAACAGC+AGG 0.614247 1:-12630690 MsG0180000878.01.T01:CDS
CAAATCACATAATGCCACGT+TGG 0.617191 1:-12632074 MsG0180000878.01.T01:five_prime_UTR
CAACCTATGACAAGGCGCAA+GGG 0.619501 1:-12631508 MsG0180000878.01.T01:CDS
ACAGGCCAAAGTATCAGCAA+GGG 0.672894 1:+12630611 None:intergenic
TTGCTGCCCAACCTATGACA+AGG 0.674324 1:-12631516 MsG0180000878.01.T01:CDS
TACAACACAAGTTCACAACA+TGG 0.692925 1:+12630514 None:intergenic
GATGACTCGATTGTATCACT+GGG 0.704301 1:+12630373 None:intergenic
ACATGTTGGACAGATTATGG+TGG 0.710941 1:-12630763 MsG0180000878.01.T01:intron
GTAGATACGTTAATCCAACG+TGG 0.821236 1:+12632060 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAGTTTTATAATTCTTA+AGG + Chr1:12630820-12630839 None:intergenic 10.0%
!! TATTTCTTAACTGTAATATT+TGG - Chr1:12632016-12632035 MsG0180000878.01.T01:five_prime_UTR 15.0%
!!! TTGGAATTTTAATTCATTAA+AGG - Chr1:12631509-12631528 MsG0180000878.01.T01:CDS 15.0%
!! ACTATTACTTCCATAATAAT+TGG + Chr1:12631217-12631236 None:intergenic 20.0%
!! ATATGTCAATATGTGTTTAT+AGG - Chr1:12631395-12631414 MsG0180000878.01.T01:intron 20.0%
!! ATGAATAAAAACATTGGAAT+TGG + Chr1:12631042-12631061 None:intergenic 20.0%
!! TATGTCAATATGTGTTTATA+GGG - Chr1:12631396-12631415 MsG0180000878.01.T01:intron 20.0%
!! TATTCTATATACTTACTTCT+TGG - Chr1:12630762-12630781 MsG0180000878.01.T01:intron 20.0%
!! TTACAGTTAAGAAATAGTAA+AGG + Chr1:12632012-12632031 None:intergenic 20.0%
!!! TGTGTTTTTTTTTTATGTGA+AGG - Chr1:12630912-12630931 MsG0180000878.01.T01:intron 20.0%
!!! TTTCATTTAGTTTGATCAAA+TGG - Chr1:12630568-12630587 MsG0180000878.01.T01:CDS 20.0%
! AAAACTATACACATCATGTT+TGG + Chr1:12631184-12631203 None:intergenic 25.0%
! ACAAAATGATGACATGAAAA+AGG + Chr1:12630682-12630701 None:intergenic 25.0%
! CTTATCTAGTCCAATTATTA+TGG - Chr1:12631204-12631223 MsG0180000878.01.T01:intron 25.0%
! GTAACCATATAAAAAATCTG+TGG + Chr1:12630443-12630462 None:intergenic 25.0%
! TAACGAGTTTCACAAAATTA+CGG + Chr1:12631159-12631178 None:intergenic 25.0%
! TATTGACATATCAGTTCTTA+TGG + Chr1:12631386-12631405 None:intergenic 25.0%
! TTAACTTCAATTAGTGAGAA+TGG - Chr1:12631597-12631616 MsG0180000878.01.T01:intron 25.0%
!! TATGGAAGTAATAGTCATTT+TGG - Chr1:12631222-12631241 MsG0180000878.01.T01:intron 25.0%
!! TTTAGAATGCTGATATTAGA+TGG + Chr1:12630419-12630438 None:intergenic 25.0%
!!! AAAGCCACAGATTTTTTATA+TGG - Chr1:12630436-12630455 MsG0180000878.01.T01:three_prime_UTR 25.0%
!!! GTGATTTGATTTCATTTTGT+GGG + Chr1:12630365-12630384 None:intergenic 25.0%
!!! TGTGATTTGATTTCATTTTG+TGG + Chr1:12630366-12630385 None:intergenic 25.0%
AAATGATGACATGAAAAAGG+TGG + Chr1:12630679-12630698 None:intergenic 30.0%
AAGATGTAAGCAGAATCTAA+TGG + Chr1:12630465-12630484 None:intergenic 30.0%
ATAACGAGTAGACATAATAG+TGG - Chr1:12631256-12631275 MsG0180000878.01.T01:intron 30.0%
ATGATTGAATCCCATTCAAT+TGG + Chr1:12632103-12632122 None:intergenic 30.0%
CGCACTATGAATAAAAACAT+TGG + Chr1:12631048-12631067 None:intergenic 30.0%
TGTCTACTCGTTATACATTA+AGG + Chr1:12631250-12631269 None:intergenic 30.0%
TTGAAATCATACCACATTAG+TGG + Chr1:12631010-12631029 None:intergenic 30.0%
! ACAATCAATGACGACTATTT+TGG - Chr1:12631490-12631509 MsG0180000878.01.T01:CDS 30.0%
! TATGATTGACTTTGACATGT+TGG - Chr1:12631674-12631693 MsG0180000878.01.T01:intron 30.0%
! TTGATTTCATTTTGTGGGAA+TGG + Chr1:12630360-12630379 None:intergenic 30.0%
! TTTTATTCATAGTGCGTGTT+TGG - Chr1:12631052-12631071 MsG0180000878.01.T01:intron 30.0%
AATCGAGTCATCCAATTGAA+TGG - Chr1:12632089-12632108 MsG0180000878.01.T01:five_prime_UTR 35.0%
ACAATGCACCAATGTTCTTA+AGG + Chr1:12631907-12631926 None:intergenic 35.0%
ACGTTGGATTAACGTATCTA+CGG - Chr1:12630393-12630412 MsG0180000878.01.T01:three_prime_UTR 35.0%
ATCGAGTCATCCAATTGAAT+GGG - Chr1:12632090-12632109 MsG0180000878.01.T01:five_prime_UTR 35.0%
ATCTTCCAGCAAACAACATT+AGG + Chr1:12631724-12631743 None:intergenic 35.0%
CCATATGTGACTCAATAGTT+CGG - Chr1:12632129-12632148 MsG0180000878.01.T01:five_prime_UTR 35.0%
TACAACACAAGTTCACAACA+TGG + Chr1:12631940-12631959 None:intergenic 35.0%
TCTTCCAGCAAACAACATTA+GGG + Chr1:12631723-12631742 None:intergenic 35.0%
TTAATTACCAAACCCTGGAT+AGG + Chr1:12630656-12630675 None:intergenic 35.0%
TTGACATGTTGGACAGATTA+TGG - Chr1:12631685-12631704 MsG0180000878.01.T01:intron 35.0%
! ATGTTGTTTGCTGGAAGATT+TGG - Chr1:12631725-12631744 MsG0180000878.01.T01:intron 35.0%
ACAACTTTGCCTCAATTCAC+TGG - Chr1:12630605-12630624 MsG0180000878.01.T01:CDS 40.0%
ACATGTTGGACAGATTATGG+TGG - Chr1:12631688-12631707 MsG0180000878.01.T01:intron 40.0%
AGGCAAAGTTGTCATCATAG+AGG + Chr1:12630597-12630616 None:intergenic 40.0%
ATAGTGCGTGTTTGGATTGA+AGG - Chr1:12631060-12631079 MsG0180000878.01.T01:intron 40.0%
CAAATCACATAATGCCACGT+TGG - Chr1:12630377-12630396 MsG0180000878.01.T01:three_prime_UTR 40.0%
GATGACTCGATTGTATCACT+GGG + Chr1:12632081-12632100 None:intergenic 40.0%
GTAGATACGTTAATCCAACG+TGG + Chr1:12630394-12630413 None:intergenic 40.0%
! ACAACCCTAATGTTGTTTGC+TGG - Chr1:12631716-12631735 MsG0180000878.01.T01:intron 40.0%
! GGTTTAAGACCAGTGAATTG+AGG + Chr1:12630617-12630636 None:intergenic 40.0%
! GTCACACACACAGATTTTGA+AGG + Chr1:12630510-12630529 None:intergenic 40.0%
! GTTTGCTGGAAGATTTGGAT+TGG - Chr1:12631730-12631749 MsG0180000878.01.T01:intron 40.0%
!! ATAGGAGAAGGTTTGAGTTG+TGG + Chr1:12630638-12630657 None:intergenic 40.0%
!! ATTGGTGTTGGTGTTGTTCT+TGG - Chr1:12631881-12631900 MsG0180000878.01.T01:exon 40.0%
!! CATTGGTTCATCCACTAATG+TGG - Chr1:12630996-12631015 MsG0180000878.01.T01:intron 40.0%
!! GTTCTTGGCCTTAAGAACAT+TGG - Chr1:12631896-12631915 MsG0180000878.01.T01:five_prime_UTR 40.0%
ACTCAAACCTTCTCCTATCC+AGG - Chr1:12630640-12630659 MsG0180000878.01.T01:CDS 45.0%
AGGACTAAAGCTGGAGACAA+GGG - Chr1:12631781-12631800 MsG0180000878.01.T01:intron 45.0%
CTCAAACCTTCTCCTATCCA+GGG - Chr1:12630641-12630660 MsG0180000878.01.T01:CDS 45.0%
GGAACTGTTGGACACATCAT+TGG - Chr1:12631863-12631882 MsG0180000878.01.T01:CDS 45.0%
GGAGTTCGTTGTGACTTCAT+TGG - Chr1:12630979-12630998 MsG0180000878.01.T01:intron 45.0%
GGATGACTCGATTGTATCAC+TGG + Chr1:12632082-12632101 None:intergenic 45.0%
GGTGGTTAATTACCAAACCC+TGG + Chr1:12630661-12630680 None:intergenic 45.0%
GTTCACCCTTGCTGATACTT+TGG - Chr1:12631835-12631854 MsG0180000878.01.T01:CDS 45.0%
GTTGGACACATCATTGGTGT+TGG - Chr1:12631869-12631888 MsG0180000878.01.T01:exon 45.0%
! ACAGGCCAAAGTATCAGCAA+GGG + Chr1:12631843-12631862 None:intergenic 45.0%
! GTTGCTTTCCTGTTTGCTGA+TGG + Chr1:12631758-12631777 None:intergenic 45.0%
!! AATTTAAATATATATTATGA+AGG + Chr1:12630856-12630875 None:intergenic 5.0%
!!! CATAATATATATTTAAATTT+TGG - Chr1:12630857-12630876 MsG0180000878.01.T01:intron 5.0%
ACCAAACCCTGGATAGGAGA+AGG + Chr1:12630650-12630669 None:intergenic 50.0%
ACCTTCTCCTATCCAGGGTT+TGG - Chr1:12630646-12630665 MsG0180000878.01.T01:CDS 50.0%
ACTTTGGCCTGTGGAACTGT+TGG - Chr1:12631851-12631870 MsG0180000878.01.T01:CDS 50.0%
AGCAACAGCAGGACTAAAGC+TGG - Chr1:12631772-12631791 MsG0180000878.01.T01:intron 50.0%
ATGACAAGGCGCAAGGGAAA+GGG - Chr1:12630949-12630968 MsG0180000878.01.T01:intron 50.0%
CAACCTATGACAAGGCGCAA+GGG - Chr1:12630943-12630962 MsG0180000878.01.T01:intron 50.0%
CAGGACTAAAGCTGGAGACA+AGG - Chr1:12631780-12631799 MsG0180000878.01.T01:intron 50.0%
CTTGCGCCTTGTCATAGGTT+GGG + Chr1:12630944-12630963 None:intergenic 50.0%
CTTGCTGATACTTTGGCCTG+TGG - Chr1:12631842-12631861 MsG0180000878.01.T01:CDS 50.0%
GATGTGTCCAACAGTTCCAC+AGG + Chr1:12631861-12631880 None:intergenic 50.0%
GCAAACAGGAAAGCAACAGC+AGG - Chr1:12631761-12631780 MsG0180000878.01.T01:intron 50.0%
TATGACAAGGCGCAAGGGAA+AGG - Chr1:12630948-12630967 MsG0180000878.01.T01:intron 50.0%
TTGCTGCCCAACCTATGACA+AGG - Chr1:12630935-12630954 MsG0180000878.01.T01:intron 50.0%
TTTCCCTTGCGCCTTGTCAT+AGG + Chr1:12630949-12630968 None:intergenic 50.0%
! CACAGGCCAAAGTATCAGCA+AGG + Chr1:12631844-12631863 None:intergenic 50.0%
! GATTGGCTCCATCAGCAAAC+AGG - Chr1:12631747-12631766 MsG0180000878.01.T01:intron 50.0%
AAGCTGGAGACAAGGGACTC+AGG - Chr1:12631788-12631807 MsG0180000878.01.T01:intron 55.0%
CCAACCTATGACAAGGCGCA+AGG - Chr1:12630942-12630961 MsG0180000878.01.T01:intron 55.0%
CCTTGCGCCTTGTCATAGGT+TGG + Chr1:12630945-12630964 None:intergenic 55.0%
!! CGCAAGGGAAAGGGTGCTTT+GGG - Chr1:12630958-12630977 MsG0180000878.01.T01:intron 55.0%
AGGGACTCAGGCTTGCAGAC+TGG - Chr1:12631800-12631819 MsG0180000878.01.T01:intron 60.0%
CAGCAAGGGTGAACCCAGCT+GGG + Chr1:12631829-12631848 None:intergenic 60.0%
TCAGCAAGGGTGAACCCAGC+TGG + Chr1:12631830-12631849 None:intergenic 60.0%
TGCAGACTGGTGACCCAGCT+GGG - Chr1:12631813-12631832 MsG0180000878.01.T01:CDS 60.0%
TTGCAGACTGGTGACCCAGC+TGG - Chr1:12631812-12631831 MsG0180000878.01.T01:CDS 60.0%
!! GCGCAAGGGAAAGGGTGCTT+TGG - Chr1:12630957-12630976 MsG0180000878.01.T01:intron 60.0%
Chromosome Type Strat End Strand Name
Chr1 gene 12630323 12632150 12630323 ID=MsG0180000878.01;Name=MsG0180000878.01
Chr1 mRNA 12630323 12632150 12630323 ID=MsG0180000878.01.T01;Parent=MsG0180000878.01;Name=MsG0180000878.01.T01;_AED=0.33;_eAED=0.33;_QI=264|1|1|1|1|1|3|222|130
Chr1 exon 12631806 12632150 12631806 ID=MsG0180000878.01.T01:exon:136;Parent=MsG0180000878.01.T01
Chr1 exon 12631456 12631539 12631456 ID=MsG0180000878.01.T01:exon:137;Parent=MsG0180000878.01.T01
Chr1 exon 12630323 12630772 12630323 ID=MsG0180000878.01.T01:exon:138;Parent=MsG0180000878.01.T01
Chr1 five_prime_UTR 12631887 12632150 12631887 ID=MsG0180000878.01.T01:five_prime_utr;Parent=MsG0180000878.01.T01
Chr1 CDS 12631806 12631886 12631806 ID=MsG0180000878.01.T01:cds;Parent=MsG0180000878.01.T01
Chr1 CDS 12631456 12631539 12631456 ID=MsG0180000878.01.T01:cds;Parent=MsG0180000878.01.T01
Chr1 CDS 12630545 12630772 12630545 ID=MsG0180000878.01.T01:cds;Parent=MsG0180000878.01.T01
Chr1 three_prime_UTR 12630323 12630544 12630323 ID=MsG0180000878.01.T01:three_prime_utr;Parent=MsG0180000878.01.T01
Gene Sequence

>MsG0180000878.01.T01

ATGGCAACCTCTATGATGACAACTTTGCCTCAATTCACTGGTCTTAAACCACAACTCAAACCTTCTCCTATCCAGGGTTTGGTTGCTGCCCAACCTATGACAAGGCGCAAGGGAAAGGGTGCTTTGGGAGTTCGTTGTGACTTCATTGGTTCATCCACTAATGTGATTATGGTGGCATCTACAACCCTAATGTTGTTTGCTGGAAGATTTGGATTGGCTCCATCAGCAAACAGGAAAGCAACAGCAGGACTAAAGCTGGAGACAAGGGACTCAGGCTTGCAGACTGGTGACCCAGCTGGGTTCACCCTTGCTGATACTTTGGCCTGTGGAACTGTTGGACACATCATTGGTGTTGGTGTTGTTCTTGGCCTTAAGAACATTGGTGCATTGTAA

Protein sequence

>MsG0180000878.01.T01

MATSMMTTLPQFTGLKPQLKPSPIQGLVAAQPMTRRKGKGALGVRCDFIGSSTNVIMVASTTLMLFAGRFGLAPSANRKATAGLKLETRDSGLQTGDPAGFTLADTLACGTVGHIIGVGVVLGLKNIGAL*