AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0971100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0971100 MtrunA17_Chr6g0450121 97.790 181 4 0 1 181 1 181 2.75e-124 347
Msa0971100 MtrunA17_Chr8g0372561 34.815 135 70 2 64 180 60 194 2.33e-16 73.2
Msa0971100 MtrunA17_Chr7g0234831 34.351 131 76 2 60 180 86 216 6.19e-15 70.1
Msa0971100 MtrunA17_Chr2g0293431 33.333 141 84 3 48 178 12 152 3.71e-14 67.4
Msa0971100 MtrunA17_Chr2g0293341 49.254 67 34 0 110 176 119 185 1.91e-13 65.5
Msa0971100 MtrunA17_Chr2g0310131 33.333 132 76 2 60 180 85 215 3.56e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0971100 AT3G27850.1 61.170 188 58 5 7 181 2 187 4.90e-53 167
Msa0971100 AT3G27830.2 64.596 161 50 3 28 181 31 191 9.40e-52 164
Msa0971100 AT3G27830.1 64.596 161 50 3 28 181 31 191 9.40e-52 164
Msa0971100 AT3G27840.1 51.497 167 64 3 31 180 26 192 1.39e-44 146
Msa0971100 AT4G36420.1 36.301 146 79 3 49 180 33 178 5.56e-18 77.4
Msa0971100 AT3G06040.3 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0971100 AT3G06040.2 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0971100 AT3G06040.1 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0971100 AT1G70190.2 34.074 135 75 2 60 180 73 207 6.53e-13 64.7
Msa0971100 AT1G70190.1 34.074 135 75 2 60 180 73 207 6.53e-13 64.7
Msa0971100 AT4G37660.1 32.258 155 93 3 38 180 12 166 2.55e-12 62.4

Find 52 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGGGAGATGGAGAGGGGTT+TGG 0.285418 6_4:-2766759 None:intergenic
GAGGTAGTCGACGAGGTCTT+TGG 0.313141 6_4:-2766876 None:intergenic
TTCAATTACCACATCGAATT+CGG 0.338695 6_4:-2766993 None:intergenic
TTCTTCGACTACTGCGACTT+CGG 0.340678 6_4:-2766966 None:intergenic
GTTAGAGCTTTGACGAGTTT+AGG 0.347699 6_4:+2767055 Msa0971100:CDS
GCGGTGGTGGTGGTGGGAGA+TGG 0.358819 6_4:-2766771 None:intergenic
GGAGATGGAGAGGGGTTTGG+AGG 0.359975 6_4:-2766756 None:intergenic
GGTGGTGGTGGGAGATGGAG+AGG 0.376909 6_4:-2766766 None:intergenic
TGGTGGTGGGAGATGGAGAG+GGG 0.379049 6_4:-2766764 None:intergenic
GACGAGTGCGGTGGTGGTGG+TGG 0.381640 6_4:-2766778 None:intergenic
ACACCTTCTTTAAATTTCTT+CGG 0.390394 6_4:-2767112 None:intergenic
GGGAAATTGAGAGTGGAGAT+TGG 0.393088 6_4:-2766734 None:intergenic
GTGGTGGTGGGAGATGGAGA+GGG 0.406108 6_4:-2766765 None:intergenic
AGCGGCGACAGTGGCGGCGG+CGG 0.407686 6_4:-2766936 None:intergenic
GCCGCAATTCTCGCGTTACT+AGG 0.408930 6_4:-2767022 None:intergenic
GTCGACGAGGTCTTTGGCTT+GGG 0.415248 6_4:-2766870 None:intergenic
TTCAGTGGCCACGGCGGAGA+TGG 0.416551 6_4:-2766807 None:intergenic
AGATGGAGAGGGGTTTGGAG+GGG 0.419977 6_4:-2766754 None:intergenic
GCGGCGACAGTGGCGGCGGC+GGG 0.421106 6_4:-2766935 None:intergenic
GGCGGCGGGAGCGAAGGAAG+CGG 0.431011 6_4:-2766921 None:intergenic
GGAGACGAGTGCGGTGGTGG+TGG 0.449627 6_4:-2766781 None:intergenic
TGGAGCGGCGACAGTGGCGG+CGG 0.453386 6_4:-2766939 None:intergenic
AGTCGACGAGGTCTTTGGCT+TGG 0.457705 6_4:-2766871 None:intergenic
ACGAGTGCGGTGGTGGTGGT+GGG 0.464166 6_4:-2766777 None:intergenic
GAAGCGAAGGAATTGATTGA+AGG 0.470442 6_4:+2767085 Msa0971100:CDS
GGCTGGAGCGGCGACAGTGG+CGG 0.474590 6_4:-2766942 None:intergenic
ACTACTGCGACTTCGGCGGC+TGG 0.482100 6_4:-2766959 None:intergenic
GACGGAGACGAGTGCGGTGG+TGG 0.484373 6_4:-2766784 None:intergenic
TGCGACTTCGGCGGCTGGAG+CGG 0.489099 6_4:-2766954 None:intergenic
AGTGGCGGCGGCGGGAGCGA+AGG 0.497332 6_4:-2766927 None:intergenic
TTGCCGAAGAAATTTAAAGA+AGG 0.505106 6_4:+2767109 Msa0971100:CDS
GAGATGGAGAGGGGTTTGGA+GGG 0.520932 6_4:-2766755 None:intergenic
TCAGTGGCCACGGCGGAGAT+GGG 0.542642 6_4:-2766806 None:intergenic
TCCTAGTAACGCGAGAATTG+CGG 0.544335 6_4:+2767021 Msa0971100:CDS
GTGGTGAGAAAGTGTGAGGG+TGG 0.553869 6_4:-2766693 None:intergenic
GGCGGCTGGAGCGGCGACAG+TGG 0.556006 6_4:-2766945 None:intergenic
AAGAAACAACTTGAAGCTGC+AGG 0.564071 6_4:+2767160 Msa0971100:CDS
TGGCCACGGCGGAGATGGGA+CGG 0.564429 6_4:-2766802 None:intergenic
CTTTGGCTTGGGAGAGAGTG+AGG 0.565773 6_4:-2766859 None:intergenic
TTTAGGATTGAAAGAAGCGA+AGG 0.566913 6_4:+2767072 Msa0971100:CDS
TTTGGAGGGGAAATTGAGAG+TGG 0.570125 6_4:-2766741 None:intergenic
GGCGGGAGCGAAGGAAGCGG+CGG 0.574913 6_4:-2766918 None:intergenic
GGTGTGGTGAGAAAGTGTGA+GGG 0.597396 6_4:-2766696 None:intergenic
GGGTGTGGTGAGAAAGTGTG+AGG 0.603340 6_4:-2766697 None:intergenic
TTCGACTACTGCGACTTCGG+CGG 0.637460 6_4:-2766963 None:intergenic
GAGAATTGCGGCGATTAAAG+CGG 0.638455 6_4:+2767033 Msa0971100:CDS
TTCTATTTCAGTGGCCACGG+CGG 0.638885 6_4:-2766813 None:intergenic
GGTGGAGATAGTTGTGAAAG+CGG 0.640687 6_4:-2766675 None:intergenic
TCTCCGTCCCATCTCCGCCG+TGG 0.646628 6_4:+2766799 Msa0971100:CDS
AGATGGGACGGAGACGAGTG+CGG 0.648615 6_4:-2766790 None:intergenic
TTTCTTGGAGGTAGTCGACG+AGG 0.676894 6_4:-2766883 None:intergenic
TGGGACGGAGACGAGTGCGG+TGG 0.682439 6_4:-2766787 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACACCTTCTTTAAATTTCTT+CGG - chr6_4:2767115-2767134 None:intergenic 25.0%
TTCAATTACCACATCGAATT+CGG - chr6_4:2766996-2767015 None:intergenic 30.0%
TTGCCGAAGAAATTTAAAGA+AGG + chr6_4:2767109-2767128 Msa0971100:CDS 30.0%
!!! AGATTGGTTTTTTTGAGAGG+GGG - chr6_4:2766721-2766740 None:intergenic 35.0%
!!! GAGATTGGTTTTTTTGAGAG+GGG - chr6_4:2766722-2766741 None:intergenic 35.0%
!!! GGAGATTGGTTTTTTTGAGA+GGG - chr6_4:2766723-2766742 None:intergenic 35.0%
!!! TGGAGATTGGTTTTTTTGAG+AGG - chr6_4:2766724-2766743 None:intergenic 35.0%
! TTTTTCTATTTCAGTGGCCA+CGG - chr6_4:2766819-2766838 None:intergenic 35.0%
GCCACTGAAATAGAAAAACT+CGG + chr6_4:2766821-2766840 Msa0971100:CDS 35.0%
AGAAAAAACCGAATTCGATG+TGG + chr6_4:2766985-2767004 Msa0971100:CDS 35.0%
! TTTAGGATTGAAAGAAGCGA+AGG + chr6_4:2767072-2767091 Msa0971100:CDS 35.0%
!!! GATTGGTTTTTTTGAGAGGG+GGG - chr6_4:2766720-2766739 None:intergenic 40.0%
! GCCGAGTTTTTCTATTTCAG+TGG - chr6_4:2766825-2766844 None:intergenic 40.0%
GACTACCTCCAAGAAAAACT+CGG + chr6_4:2766890-2766909 Msa0971100:CDS 40.0%
! GTTAGAGCTTTGACGAGTTT+AGG + chr6_4:2767055-2767074 Msa0971100:CDS 40.0%
GAAGCGAAGGAATTGATTGA+AGG + chr6_4:2767085-2767104 Msa0971100:CDS 40.0%
AAGAAACAACTTGAAGCTGC+AGG + chr6_4:2767160-2767179 Msa0971100:CDS 40.0%
GGTGGAGATAGTTGTGAAAG+CGG - chr6_4:2766678-2766697 None:intergenic 45.0%
GGGAAATTGAGAGTGGAGAT+TGG - chr6_4:2766737-2766756 None:intergenic 45.0%
TTTGGAGGGGAAATTGAGAG+TGG - chr6_4:2766744-2766763 None:intergenic 45.0%
TTCTTCGACTACTGCGACTT+CGG - chr6_4:2766969-2766988 None:intergenic 45.0%
TCCTAGTAACGCGAGAATTG+CGG + chr6_4:2767021-2767040 Msa0971100:CDS 45.0%
GAGAATTGCGGCGATTAAAG+CGG + chr6_4:2767033-2767052 Msa0971100:CDS 45.0%
! GGTGTGGTGAGAAAGTGTGA+GGG - chr6_4:2766699-2766718 None:intergenic 50.0%
!!! GTTTTTTTGAGAGGGGGGTG+TGG - chr6_4:2766715-2766734 None:intergenic 50.0%
TTCTATTTCAGTGGCCACGG+CGG - chr6_4:2766816-2766835 None:intergenic 50.0%
TTTCTTGGAGGTAGTCGACG+AGG - chr6_4:2766886-2766905 None:intergenic 50.0%
! TGACGCCGAGTTTTTCTTGG+AGG - chr6_4:2766898-2766917 None:intergenic 50.0%
! GTGGTGAGAAAGTGTGAGGG+TGG - chr6_4:2766696-2766715 None:intergenic 55.0%
! GGGTGTGGTGAGAAAGTGTG+AGG - chr6_4:2766700-2766719 None:intergenic 55.0%
AGATGGAGAGGGGTTTGGAG+GGG - chr6_4:2766757-2766776 None:intergenic 55.0%
GAGATGGAGAGGGGTTTGGA+GGG - chr6_4:2766758-2766777 None:intergenic 55.0%
!! CTTTGGCTTGGGAGAGAGTG+AGG - chr6_4:2766862-2766881 None:intergenic 55.0%
! GTCGACGAGGTCTTTGGCTT+GGG - chr6_4:2766873-2766892 None:intergenic 55.0%
AGTCGACGAGGTCTTTGGCT+TGG - chr6_4:2766874-2766893 None:intergenic 55.0%
GAGGTAGTCGACGAGGTCTT+TGG - chr6_4:2766879-2766898 None:intergenic 55.0%
! CGGTGACGCCGAGTTTTTCT+TGG - chr6_4:2766901-2766920 None:intergenic 55.0%
TTCGACTACTGCGACTTCGG+CGG - chr6_4:2766966-2766985 None:intergenic 55.0%
GCCGCAATTCTCGCGTTACT+AGG - chr6_4:2767025-2767044 None:intergenic 55.0%
GGAGATGGAGAGGGGTTTGG+AGG - chr6_4:2766759-2766778 None:intergenic 60.0%
GTGGGAGATGGAGAGGGGTT+TGG - chr6_4:2766762-2766781 None:intergenic 60.0%
!! TGGTGGTGGGAGATGGAGAG+GGG - chr6_4:2766767-2766786 None:intergenic 60.0%
!! GTGGTGGTGGGAGATGGAGA+GGG - chr6_4:2766768-2766787 None:intergenic 60.0%
AGATGGGACGGAGACGAGTG+CGG - chr6_4:2766793-2766812 None:intergenic 60.0%
!! GGTGGTGGTGGGAGATGGAG+AGG - chr6_4:2766769-2766788 None:intergenic 65.0%
!! ACGAGTGCGGTGGTGGTGGT+GGG - chr6_4:2766780-2766799 None:intergenic 65.0%
TCAGTGGCCACGGCGGAGAT+GGG - chr6_4:2766809-2766828 None:intergenic 65.0%
TTCAGTGGCCACGGCGGAGA+TGG - chr6_4:2766810-2766829 None:intergenic 65.0%
ACTACTGCGACTTCGGCGGC+TGG - chr6_4:2766962-2766981 None:intergenic 65.0%
!! GCGGTGGTGGTGGTGGGAGA+TGG - chr6_4:2766774-2766793 None:intergenic 70.0%
!! GACGAGTGCGGTGGTGGTGG+TGG - chr6_4:2766781-2766800 None:intergenic 70.0%
! GGAGACGAGTGCGGTGGTGG+TGG - chr6_4:2766784-2766803 None:intergenic 70.0%
GACGGAGACGAGTGCGGTGG+TGG - chr6_4:2766787-2766806 None:intergenic 70.0%
TGGGACGGAGACGAGTGCGG+TGG - chr6_4:2766790-2766809 None:intergenic 70.0%
TCTCCGTCCCATCTCCGCCG+TGG + chr6_4:2766799-2766818 Msa0971100:CDS 70.0%
TGGCCACGGCGGAGATGGGA+CGG - chr6_4:2766805-2766824 None:intergenic 70.0%
TGCGACTTCGGCGGCTGGAG+CGG - chr6_4:2766957-2766976 None:intergenic 70.0%
GGCGGGAGCGAAGGAAGCGG+CGG - chr6_4:2766921-2766940 None:intergenic 75.0%
GGCGGCGGGAGCGAAGGAAG+CGG - chr6_4:2766924-2766943 None:intergenic 75.0%
TGGAGCGGCGACAGTGGCGG+CGG - chr6_4:2766942-2766961 None:intergenic 75.0%
GGCTGGAGCGGCGACAGTGG+CGG - chr6_4:2766945-2766964 None:intergenic 75.0%
! AGTGGCGGCGGCGGGAGCGA+AGG - chr6_4:2766930-2766949 None:intergenic 80.0%
! AGCGGCGACAGTGGCGGCGG+CGG - chr6_4:2766939-2766958 None:intergenic 80.0%
! GGCGGCTGGAGCGGCGACAG+TGG - chr6_4:2766948-2766967 None:intergenic 80.0%
! GCGGCGACAGTGGCGGCGGC+GGG - chr6_4:2766938-2766957 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 2766659 2767204 2766659 ID=Msa0971100;Name=Msa0971100
chr6_4 mRNA 2766659 2767204 2766659 ID=Msa0971100-mRNA-1;Parent=Msa0971100;Name=Msa0971100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|181
chr6_4 exon 2766659 2767204 2766659 ID=Msa0971100-mRNA-1:exon:1344;Parent=Msa0971100-mRNA-1
chr6_4 CDS 2766659 2767204 2766659 ID=Msa0971100-mRNA-1:cds;Parent=Msa0971100-mRNA-1
Gene Sequence

>Msa0971100

ATGGCATTATCAACAACCGCTTTCACAACTATCTCCACCCTCACACTTTCTCACCACACCCCCCTCTCAAAAAAACCAATCTCCACTCTCAATTTCCCCTCCAAACCCCTCTCCATCTCCCACCACCACCACCGCACTCGTCTCCGTCCCATCTCCGCCGTGGCCACTGAAATAGAAAAACTCGGCAACGACATCTCTGACCTCACTCTCTCCCAAGCCAAAGACCTCGTCGACTACCTCCAAGAAAAACTCGGCGTCACCGCCGCTTCCTTCGCTCCCGCCGCCGCCACTGTCGCCGCTCCAGCCGCCGAAGTCGCAGTAGTCGAAGAAAAAACCGAATTCGATGTGGTAATTGAAGATGTTCCTAGTAACGCGAGAATTGCGGCGATTAAAGCGGTTAGAGCTTTGACGAGTTTAGGATTGAAAGAAGCGAAGGAATTGATTGAAGGTTTGCCGAAGAAATTTAAAGAAGGTGTGAGTAAAGATGAAGCTGATGATGCTAAGAAACAACTTGAAGCTGCAGGTGCTAAAGTTACTATTGCTTAA

Protein sequence

>Msa0971100

MALSTTAFTTISTLTLSHHTPLSKKPISTLNFPSKPLSISHHHHRTRLRPISAVATEIEKLGNDISDLTLSQAKDLVDYLQEKLGVTAASFAPAAATVAAPAAEVAVVEEKTEFDVVIEDVPSNARIAAIKAVRALTSLGLKEAKELIEGLPKKFKEGVSKDEADDAKKQLEAAGAKVTIA*