AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1031930


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1031930 MtrunA17_Chr7g0253661 88.406 207 18 2 1 206 1 202 2.82e-114 324
Msa1031930 MtrunA17_Chr6g0481571 40.000 105 55 2 1 102 1 100 1.62e-19 81.6
Msa1031930 MtrunA17_Chr5g0440291 38.947 95 53 1 8 102 11 100 2.81e-17 77.4
Msa1031930 MtrunA17_Chr5g0440311 35.200 125 67 4 8 123 10 129 3.42e-16 74.7
Msa1031930 MtrunA17_Chr5g0440321 31.111 135 80 4 8 136 10 137 5.50e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1031930 AT1G54400.1 40.566 106 57 2 1 106 5 104 3.45e-20 84.3
Msa1031930 AT2G27140.1 33.945 109 66 2 5 112 7 110 5.02e-16 73.9
Msa1031930 AT5G20970.1 34.615 104 63 1 9 112 8 106 7.37e-15 71.2
Msa1031930 AT5G04890.1 32.692 104 60 3 11 109 16 114 1.07e-13 69.3

Find 29 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATCTTCATTGCAATATTT+TGG 0.150093 7_1:-66694631 Msa1031920:intron
TCTGGCATTTGTTCTTCTTC+TGG 0.224256 7_1:-66694730 Msa1031920:intron
ACATATCAGAGTTTGGAATT+TGG 0.240193 7_1:+66694787 Msa1031930:CDS
ACCGTTGAGCTTCATCTTCC+AGG 0.311460 7_1:+66694291 Msa1031930:CDS
TACACAACAGACAACAAGTT+TGG 0.336570 7_1:+66694856 Msa1031930:CDS
AGAGGTTGCTCTTAAATTCA+TGG 0.354880 7_1:+66694903 Msa1031930:CDS
GTCCATTTGATGGAACTAAA+TGG 0.359566 7_1:+66694581 Msa1031930:CDS
ATATCCTCATCTTCAAGTTC+TGG 0.365913 7_1:-66694748 Msa1031920:intron
CGAATTCAAATCAACCATCT+TGG 0.372715 7_1:+66694535 Msa1031930:CDS
TTCCATTTAGTTCCATCAAA+TGG 0.385038 7_1:-66694583 Msa1031920:intron
AGTGGAGAGCGTCCATTTGA+TGG 0.411520 7_1:+66694571 Msa1031930:CDS
GAATTCAAATCAACCATCTT+GGG 0.419246 7_1:+66694536 Msa1031930:CDS
GGTTGTGATAATTGTTGTAA+TGG 0.450646 7_1:+66694924 Msa1031930:CDS
AACACAAACATGCACATAAC+CGG 0.451506 7_1:+66694214 Msa1031930:CDS
TCTTCTTCTGGTTCCTCTTG+AGG 0.457813 7_1:-66694718 Msa1031920:intron
GGTTATTGTAAATTATCTTG+TGG 0.496692 7_1:+66694945 Msa1031930:CDS
TGCAATGAAGATGCCATTCG+TGG 0.501501 7_1:+66694640 Msa1031930:CDS
TATCAGAGTTTGGAATTTGG+AGG 0.521412 7_1:+66694790 Msa1031930:CDS
ATACATGAAATTGACATGCC+TGG 0.528684 7_1:-66694309 Msa1031920:intron
TTGCATGAAATTGCCACGAA+TGG 0.562966 7_1:-66694653 Msa1031920:intron
AGCAAAACCGTCATGGCTCA+AGG 0.573165 7_1:+66694973 Msa1031930:CDS
GATCAAAATCTTCATAAGAC+CGG 0.586407 7_1:-66694233 Msa1031920:intron
AATGCCAGAACTTGAAGATG+AGG 0.591611 7_1:+66694744 Msa1031930:CDS
AGTTGATCTGATACCTCAAG+AGG 0.599832 7_1:+66694705 Msa1031930:CDS
TGATTGACCTTGAGCCATGA+CGG 0.602155 7_1:-66694980 Msa1031920:intron
GATGAAGCTCAACGGTGTCA+CGG 0.610092 7_1:-66694284 Msa1031920:intron
GCCTGGAAGATGAAGCTCAA+CGG 0.610375 7_1:-66694292 Msa1031920:intron
GGATATGAGCAAAACCGTCA+TGG 0.621622 7_1:+66694966 Msa1031930:CDS
TGATGTAGAAACTACTAGAG+AGG 0.643103 7_1:+66694885 Msa1031930:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATGTATCTAAATTATATA+TGG + chr7_1:66694324-66694343 Msa1031930:intron 15.0%
!!! CATTGTTTTTGTTAAATTTA+CGG - chr7_1:66694427-66694446 Msa1031920:intron 15.0%
!! TCATGTATCTAAATTATATA+TGG + chr7_1:66694324-66694343 Msa1031930:intron 15.0%
!!! CATTGTTTTTGTTAAATTTA+CGG - chr7_1:66694427-66694446 Msa1031920:intron 15.0%
!! AAATGAAATTGAACTAAACA+AGG - chr7_1:66694351-66694370 Msa1031920:intron 20.0%
!! AAATGAAATTGAACTAAACA+AGG - chr7_1:66694351-66694370 Msa1031920:intron 20.0%
!!! ATTTTGATCCTGTTTTTAAG+TGG + chr7_1:66694247-66694266 Msa1031930:CDS 25.0%
! GAAAAATACATATCAGAGTT+TGG + chr7_1:66694780-66694799 Msa1031930:CDS 25.0%
! GGTTATTGTAAATTATCTTG+TGG + chr7_1:66694945-66694964 Msa1031930:CDS 25.0%
!!! ATTTTGATCCTGTTTTTAAG+TGG + chr7_1:66694247-66694266 Msa1031930:CDS 25.0%
! GAAAAATACATATCAGAGTT+TGG + chr7_1:66694780-66694799 Msa1031930:CDS 25.0%
! GGTTATTGTAAATTATCTTG+TGG + chr7_1:66694945-66694964 Msa1031930:CDS 25.0%
GATCAAAATCTTCATAAGAC+CGG - chr7_1:66694236-66694255 Msa1031920:intron 30.0%
!!! TTAGACTTTTTTCACAGACT+AGG + chr7_1:66694450-66694469 Msa1031930:intron 30.0%
!!! TAGACTTTTTTCACAGACTA+GGG + chr7_1:66694451-66694470 Msa1031930:intron 30.0%
!! GCTTTATTTGAGAGTTATGA+GGG + chr7_1:66694473-66694492 Msa1031930:intron 30.0%
! CTTTATTTGAGAGTTATGAG+GGG + chr7_1:66694474-66694493 Msa1031930:intron 30.0%
!!! GGGGTTATTAATTTGTTTTC+AGG + chr7_1:66694493-66694512 Msa1031930:intron 30.0%
GAATTCAAATCAACCATCTT+GGG + chr7_1:66694536-66694555 Msa1031930:CDS 30.0%
! TTCCATTTAGTTCCATCAAA+TGG - chr7_1:66694586-66694605 Msa1031920:intron 30.0%
! GCATCTTCATTGCAATATTT+TGG - chr7_1:66694634-66694653 Msa1031920:intron 30.0%
!!! GGTATCAGATCAACTTTTTT+TGG - chr7_1:66694700-66694719 Msa1031920:intron 30.0%
! ACATATCAGAGTTTGGAATT+TGG + chr7_1:66694787-66694806 Msa1031930:CDS 30.0%
GGTTGTGATAATTGTTGTAA+TGG + chr7_1:66694924-66694943 Msa1031930:CDS 30.0%
GATCAAAATCTTCATAAGAC+CGG - chr7_1:66694236-66694255 Msa1031920:intron 30.0%
!!! TTAGACTTTTTTCACAGACT+AGG + chr7_1:66694450-66694469 Msa1031930:intron 30.0%
!!! TAGACTTTTTTCACAGACTA+GGG + chr7_1:66694451-66694470 Msa1031930:intron 30.0%
!! GCTTTATTTGAGAGTTATGA+GGG + chr7_1:66694473-66694492 Msa1031930:intron 30.0%
! CTTTATTTGAGAGTTATGAG+GGG + chr7_1:66694474-66694493 Msa1031930:intron 30.0%
!!! GGGGTTATTAATTTGTTTTC+AGG + chr7_1:66694493-66694512 Msa1031930:intron 30.0%
GAATTCAAATCAACCATCTT+GGG + chr7_1:66694536-66694555 Msa1031930:CDS 30.0%
! TTCCATTTAGTTCCATCAAA+TGG - chr7_1:66694586-66694605 Msa1031920:intron 30.0%
! GCATCTTCATTGCAATATTT+TGG - chr7_1:66694634-66694653 Msa1031920:intron 30.0%
!!! GGTATCAGATCAACTTTTTT+TGG - chr7_1:66694700-66694719 Msa1031920:intron 30.0%
! ACATATCAGAGTTTGGAATT+TGG + chr7_1:66694787-66694806 Msa1031930:CDS 30.0%
GGTTGTGATAATTGTTGTAA+TGG + chr7_1:66694924-66694943 Msa1031930:CDS 30.0%
AACACAAACATGCACATAAC+CGG + chr7_1:66694214-66694233 Msa1031930:CDS 35.0%
ATACATGAAATTGACATGCC+TGG - chr7_1:66694312-66694331 Msa1031920:intron 35.0%
!! GGCTTTATTTGAGAGTTATG+AGG + chr7_1:66694472-66694491 Msa1031930:intron 35.0%
CGAATTCAAATCAACCATCT+TGG + chr7_1:66694535-66694554 Msa1031930:CDS 35.0%
! AATCAACCATCTTGGGTTTT+TGG + chr7_1:66694543-66694562 Msa1031930:CDS 35.0%
TTATCACCAAAAACCCAAGA+TGG - chr7_1:66694552-66694571 Msa1031920:intron 35.0%
GTCCATTTGATGGAACTAAA+TGG + chr7_1:66694581-66694600 Msa1031930:CDS 35.0%
! ATATCCTCATCTTCAAGTTC+TGG - chr7_1:66694751-66694770 Msa1031920:intron 35.0%
! TATCAGAGTTTGGAATTTGG+AGG + chr7_1:66694790-66694809 Msa1031930:CDS 35.0%
TACACAACAGACAACAAGTT+TGG + chr7_1:66694856-66694875 Msa1031930:CDS 35.0%
TGATGTAGAAACTACTAGAG+AGG + chr7_1:66694885-66694904 Msa1031930:CDS 35.0%
AGAGGTTGCTCTTAAATTCA+TGG + chr7_1:66694903-66694922 Msa1031930:CDS 35.0%
AACACAAACATGCACATAAC+CGG + chr7_1:66694214-66694233 Msa1031930:CDS 35.0%
ATACATGAAATTGACATGCC+TGG - chr7_1:66694312-66694331 Msa1031920:intron 35.0%
!! GGCTTTATTTGAGAGTTATG+AGG + chr7_1:66694472-66694491 Msa1031930:intron 35.0%
CGAATTCAAATCAACCATCT+TGG + chr7_1:66694535-66694554 Msa1031930:CDS 35.0%
! AATCAACCATCTTGGGTTTT+TGG + chr7_1:66694543-66694562 Msa1031930:CDS 35.0%
TTATCACCAAAAACCCAAGA+TGG - chr7_1:66694552-66694571 Msa1031920:intron 35.0%
GTCCATTTGATGGAACTAAA+TGG + chr7_1:66694581-66694600 Msa1031930:CDS 35.0%
! ATATCCTCATCTTCAAGTTC+TGG - chr7_1:66694751-66694770 Msa1031920:intron 35.0%
! TATCAGAGTTTGGAATTTGG+AGG + chr7_1:66694790-66694809 Msa1031930:CDS 35.0%
TACACAACAGACAACAAGTT+TGG + chr7_1:66694856-66694875 Msa1031930:CDS 35.0%
TGATGTAGAAACTACTAGAG+AGG + chr7_1:66694885-66694904 Msa1031930:CDS 35.0%
AGAGGTTGCTCTTAAATTCA+TGG + chr7_1:66694903-66694922 Msa1031930:CDS 35.0%
TCTCTACGCCACTTAAAAAC+AGG - chr7_1:66694258-66694277 Msa1031920:intron 40.0%
!!! CTTGGGTTTTTGGTGATAAG+TGG + chr7_1:66694553-66694572 Msa1031930:CDS 40.0%
TTGCATGAAATTGCCACGAA+TGG - chr7_1:66694656-66694675 Msa1031920:intron 40.0%
AGTTGATCTGATACCTCAAG+AGG + chr7_1:66694705-66694724 Msa1031930:CDS 40.0%
TCTGGCATTTGTTCTTCTTC+TGG - chr7_1:66694733-66694752 Msa1031920:intron 40.0%
AATGCCAGAACTTGAAGATG+AGG + chr7_1:66694744-66694763 Msa1031930:CDS 40.0%
TCTCTACGCCACTTAAAAAC+AGG - chr7_1:66694258-66694277 Msa1031920:intron 40.0%
!!! CTTGGGTTTTTGGTGATAAG+TGG + chr7_1:66694553-66694572 Msa1031930:CDS 40.0%
TTGCATGAAATTGCCACGAA+TGG - chr7_1:66694656-66694675 Msa1031920:intron 40.0%
AGTTGATCTGATACCTCAAG+AGG + chr7_1:66694705-66694724 Msa1031930:CDS 40.0%
TCTGGCATTTGTTCTTCTTC+TGG - chr7_1:66694733-66694752 Msa1031920:intron 40.0%
AATGCCAGAACTTGAAGATG+AGG + chr7_1:66694744-66694763 Msa1031930:CDS 40.0%
TGCAATGAAGATGCCATTCG+TGG + chr7_1:66694640-66694659 Msa1031930:CDS 45.0%
!! TCTTCTTCTGGTTCCTCTTG+AGG - chr7_1:66694721-66694740 Msa1031920:intron 45.0%
GGATATGAGCAAAACCGTCA+TGG + chr7_1:66694966-66694985 Msa1031930:CDS 45.0%
TGATTGACCTTGAGCCATGA+CGG - chr7_1:66694983-66695002 Msa1031920:intron 45.0%
TGCAATGAAGATGCCATTCG+TGG + chr7_1:66694640-66694659 Msa1031930:CDS 45.0%
!! TCTTCTTCTGGTTCCTCTTG+AGG - chr7_1:66694721-66694740 Msa1031920:intron 45.0%
GGATATGAGCAAAACCGTCA+TGG + chr7_1:66694966-66694985 Msa1031930:CDS 45.0%
TGATTGACCTTGAGCCATGA+CGG - chr7_1:66694983-66695002 Msa1031920:intron 45.0%
! GATGAAGCTCAACGGTGTCA+CGG - chr7_1:66694287-66694306 Msa1031920:intron 50.0%
ACCGTTGAGCTTCATCTTCC+AGG + chr7_1:66694291-66694310 Msa1031930:CDS 50.0%
GCCTGGAAGATGAAGCTCAA+CGG - chr7_1:66694295-66694314 Msa1031920:intron 50.0%
!! AGTGGAGAGCGTCCATTTGA+TGG + chr7_1:66694571-66694590 Msa1031930:CDS 50.0%
AGCAAAACCGTCATGGCTCA+AGG + chr7_1:66694973-66694992 Msa1031930:CDS 50.0%
! GATGAAGCTCAACGGTGTCA+CGG - chr7_1:66694287-66694306 Msa1031920:intron 50.0%
ACCGTTGAGCTTCATCTTCC+AGG + chr7_1:66694291-66694310 Msa1031930:CDS 50.0%
GCCTGGAAGATGAAGCTCAA+CGG - chr7_1:66694295-66694314 Msa1031920:intron 50.0%
!! AGTGGAGAGCGTCCATTTGA+TGG + chr7_1:66694571-66694590 Msa1031930:CDS 50.0%
AGCAAAACCGTCATGGCTCA+AGG + chr7_1:66694973-66694992 Msa1031930:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 66694210 66695017 66694210 ID=Msa1031930;Name=Msa1031930
chr7_1 mRNA 66694210 66695017 66694210 ID=Msa1031930-mRNA-1;Parent=Msa1031930;Name=Msa1031930-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|206
chr7_1 exon 66694210 66694327 66694210 ID=Msa1031930-mRNA-1:exon:15084;Parent=Msa1031930-mRNA-1
chr7_1 exon 66694515 66695017 66694515 ID=Msa1031930-mRNA-1:exon:15085;Parent=Msa1031930-mRNA-1
chr7_1 CDS 66694210 66694327 66694210 ID=Msa1031930-mRNA-1:cds;Parent=Msa1031930-mRNA-1
chr7_1 CDS 66694515 66695017 66694515 ID=Msa1031930-mRNA-1:cds;Parent=Msa1031930-mRNA-1
Gene Sequence

>Msa1031930

ATGGAACACAAACATGCACATAACCGGTCTTATGAAGATTTTGATCCTGTTTTTAAGTGGCGTAGAGAACAAGACCGTGACACCGTTGAGCTTCATCTTCCAGGCATGTCAATTTCATGTTTTAAGAGAGAGCAAATACGAATTCAAATCAACCATCTTGGGTTTTTGGTGATAAGTGGAGAGCGTCCATTTGATGGAACTAAATGGAAACGTTTCAAGAAAGAATTTGAACTTCCAAAATATTGCAATGAAGATGCCATTCGTGGCAATTTCATGCAAAACATTCTTTCAGTAGTATTGCCAAAAAAAGTTGATCTGATACCTCAAGAGGAACCAGAAGAAGAACAAATGCCAGAACTTGAAGATGAGGATATATATCAAGAGAAAAATACATATCAGAGTTTGGAATTTGGAGGAAGAAATAGAGAAGCAGAGATTGAAAAACTATCAGAATATAATTACACAACAGACAACAAGTTTGGAGAAAATGATGTAGAAACTACTAGAGAGGTTGCTCTTAAATTCATGGTTGTGATAATTGTTGTAATGGTTATTGTAAATTATCTTGTGGATATGAGCAAAACCGTCATGGCTCAAGGTCAATCATATTTTCAAAATTAG

Protein sequence

>Msa1031930

MEHKHAHNRSYEDFDPVFKWRREQDRDTVELHLPGMSISCFKREQIRIQINHLGFLVISGERPFDGTKWKRFKKEFELPKYCNEDAIRGNFMQNILSVVLPKKVDLIPQEEPEEEQMPELEDEDIYQEKNTYQSLEFGGRNREAEIEKLSEYNYTTDNKFGENDVETTREVALKFMVVIIVVMVIVNYLVDMSKTVMAQGQSYFQN*