AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0933320


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0933320 MtrunA17_Chr6g0450121 97.790 181 4 0 1 181 1 181 2.75e-124 347
Msa0933320 MtrunA17_Chr8g0372561 34.815 135 70 2 64 180 60 194 2.33e-16 73.2
Msa0933320 MtrunA17_Chr7g0234831 34.351 131 76 2 60 180 86 216 6.19e-15 70.1
Msa0933320 MtrunA17_Chr2g0293431 33.333 141 84 3 48 178 12 152 3.71e-14 67.4
Msa0933320 MtrunA17_Chr2g0293341 49.254 67 34 0 110 176 119 185 1.91e-13 65.5
Msa0933320 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
Msa0933320 AT3G27850.1 61.170 188 58 5 7 181 2 187 4.90e-53 167
Msa0933320 AT3G27830.2 64.596 161 50 3 28 181 31 191 9.40e-52 164
Msa0933320 AT3G27830.1 64.596 161 50 3 28 181 31 191 9.40e-52 164
Msa0933320 AT3G27840.1 51.497 167 64 3 31 180 26 192 1.39e-44 146
Msa0933320 AT4G36420.1 36.301 146 79 3 49 180 33 178 5.56e-18 77.4
Msa0933320 AT3G06040.3 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0933320 AT3G06040.2 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0933320 AT3G06040.1 46.667 75 40 0 102 176 107 181 5.29e-13 64.7
Msa0933320 AT1G70190.2 34.074 135 75 2 60 180 73 207 6.53e-13 64.7
Msa0933320 AT1G70190.1 34.074 135 75 2 60 180 73 207 6.53e-13 64.7
Msa0933320 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_3:-1817851 None:intergenic
GAGGTAGTCGACGAGGTCTT+TGG 0.313141 6_3:-1817968 None:intergenic
TTCAATTACCACATCGAATT+CGG 0.338695 6_3:-1818085 None:intergenic
TTCTTCGACTACTGCGACTT+CGG 0.340678 6_3:-1818058 None:intergenic
GTTAGAGCTTTGACGAGTTT+AGG 0.347699 6_3:+1818147 Msa0933320:CDS
GCGGTGGTGGTGGTGGGAGA+TGG 0.358819 6_3:-1817863 None:intergenic
GGAGATGGAGAGGGGTTTGG+AGG 0.359975 6_3:-1817848 None:intergenic
GGTGGTGGTGGGAGATGGAG+AGG 0.376909 6_3:-1817858 None:intergenic
TGGTGGTGGGAGATGGAGAG+GGG 0.379049 6_3:-1817856 None:intergenic
GACGAGTGCGGTGGTGGTGG+TGG 0.381640 6_3:-1817870 None:intergenic
ACACCTTCTTTAAATTTCTT+CGG 0.390394 6_3:-1818204 None:intergenic
GGGAAATTGAGAGTGGAGAT+TGG 0.393088 6_3:-1817826 None:intergenic
GTGGTGGTGGGAGATGGAGA+GGG 0.406108 6_3:-1817857 None:intergenic
AGCGGCGACAGTGGCGGCGG+CGG 0.407686 6_3:-1818028 None:intergenic
GCCGCAATTCTCGCGTTACT+AGG 0.408930 6_3:-1818114 None:intergenic
GTCGACGAGGTCTTTGGCTT+GGG 0.415248 6_3:-1817962 None:intergenic
TTCAGTGGCCACGGCGGAGA+TGG 0.416551 6_3:-1817899 None:intergenic
AGATGGAGAGGGGTTTGGAG+GGG 0.419977 6_3:-1817846 None:intergenic
GCGGCGACAGTGGCGGCGGC+GGG 0.421106 6_3:-1818027 None:intergenic
GGCGGCGGGAGCGAAGGAAG+CGG 0.431011 6_3:-1818013 None:intergenic
GGAGACGAGTGCGGTGGTGG+TGG 0.449627 6_3:-1817873 None:intergenic
TGGAGCGGCGACAGTGGCGG+CGG 0.453386 6_3:-1818031 None:intergenic
AGTCGACGAGGTCTTTGGCT+TGG 0.457705 6_3:-1817963 None:intergenic
ACGAGTGCGGTGGTGGTGGT+GGG 0.464166 6_3:-1817869 None:intergenic
GAAGCGAAGGAATTGATTGA+AGG 0.470442 6_3:+1818177 Msa0933320:CDS
GGCTGGAGCGGCGACAGTGG+CGG 0.474590 6_3:-1818034 None:intergenic
ACTACTGCGACTTCGGCGGC+TGG 0.482100 6_3:-1818051 None:intergenic
GACGGAGACGAGTGCGGTGG+TGG 0.484373 6_3:-1817876 None:intergenic
TGCGACTTCGGCGGCTGGAG+CGG 0.489099 6_3:-1818046 None:intergenic
AGTGGCGGCGGCGGGAGCGA+AGG 0.497332 6_3:-1818019 None:intergenic
TTGCCGAAGAAATTTAAAGA+AGG 0.505106 6_3:+1818201 Msa0933320:CDS
GAGATGGAGAGGGGTTTGGA+GGG 0.520932 6_3:-1817847 None:intergenic
TCAGTGGCCACGGCGGAGAT+GGG 0.542642 6_3:-1817898 None:intergenic
TCCTAGTAACGCGAGAATTG+CGG 0.544335 6_3:+1818113 Msa0933320:CDS
GTGGTGAGAAAGTGTGAGGG+TGG 0.553869 6_3:-1817785 None:intergenic
GGCGGCTGGAGCGGCGACAG+TGG 0.556006 6_3:-1818037 None:intergenic
AAGAAACAACTTGAAGCTGC+AGG 0.564071 6_3:+1818252 Msa0933320:CDS
TGGCCACGGCGGAGATGGGA+CGG 0.564429 6_3:-1817894 None:intergenic
CTTTGGCTTGGGAGAGAGTG+AGG 0.565773 6_3:-1817951 None:intergenic
TTTAGGATTGAAAGAAGCGA+AGG 0.566913 6_3:+1818164 Msa0933320:CDS
TTTGGAGGGGAAATTGAGAG+TGG 0.570125 6_3:-1817833 None:intergenic
GGCGGGAGCGAAGGAAGCGG+CGG 0.574913 6_3:-1818010 None:intergenic
GGTGTGGTGAGAAAGTGTGA+GGG 0.597396 6_3:-1817788 None:intergenic
GGGTGTGGTGAGAAAGTGTG+AGG 0.603340 6_3:-1817789 None:intergenic
TTCGACTACTGCGACTTCGG+CGG 0.637460 6_3:-1818055 None:intergenic
GAGAATTGCGGCGATTAAAG+CGG 0.638455 6_3:+1818125 Msa0933320:CDS
TTCTATTTCAGTGGCCACGG+CGG 0.638885 6_3:-1817905 None:intergenic
GGTGGAGATAGTTGTGAAAG+CGG 0.640687 6_3:-1817767 None:intergenic
TCTCCGTCCCATCTCCGCCG+TGG 0.646628 6_3:+1817891 Msa0933320:CDS
AGATGGGACGGAGACGAGTG+CGG 0.648615 6_3:-1817882 None:intergenic
TTTCTTGGAGGTAGTCGACG+AGG 0.676894 6_3:-1817975 None:intergenic
TGGGACGGAGACGAGTGCGG+TGG 0.682439 6_3:-1817879 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACACCTTCTTTAAATTTCTT+CGG - chr6_3:1818207-1818226 None:intergenic 25.0%
TTCAATTACCACATCGAATT+CGG - chr6_3:1818088-1818107 None:intergenic 30.0%
TTGCCGAAGAAATTTAAAGA+AGG + chr6_3:1818201-1818220 Msa0933320:CDS 30.0%
!!! AGATTGGTTTTTTTGAGAGG+GGG - chr6_3:1817813-1817832 None:intergenic 35.0%
!!! GAGATTGGTTTTTTTGAGAG+GGG - chr6_3:1817814-1817833 None:intergenic 35.0%
!!! GGAGATTGGTTTTTTTGAGA+GGG - chr6_3:1817815-1817834 None:intergenic 35.0%
!!! TGGAGATTGGTTTTTTTGAG+AGG - chr6_3:1817816-1817835 None:intergenic 35.0%
! TTTTTCTATTTCAGTGGCCA+CGG - chr6_3:1817911-1817930 None:intergenic 35.0%
GCCACTGAAATAGAAAAACT+CGG + chr6_3:1817913-1817932 Msa0933320:CDS 35.0%
AGAAAAAACCGAATTCGATG+TGG + chr6_3:1818077-1818096 Msa0933320:CDS 35.0%
! TTTAGGATTGAAAGAAGCGA+AGG + chr6_3:1818164-1818183 Msa0933320:CDS 35.0%
!!! GATTGGTTTTTTTGAGAGGG+GGG - chr6_3:1817812-1817831 None:intergenic 40.0%
! GCCGAGTTTTTCTATTTCAG+TGG - chr6_3:1817917-1817936 None:intergenic 40.0%
GACTACCTCCAAGAAAAACT+CGG + chr6_3:1817982-1818001 Msa0933320:CDS 40.0%
! GTTAGAGCTTTGACGAGTTT+AGG + chr6_3:1818147-1818166 Msa0933320:CDS 40.0%
GAAGCGAAGGAATTGATTGA+AGG + chr6_3:1818177-1818196 Msa0933320:CDS 40.0%
AAGAAACAACTTGAAGCTGC+AGG + chr6_3:1818252-1818271 Msa0933320:CDS 40.0%
GGTGGAGATAGTTGTGAAAG+CGG - chr6_3:1817770-1817789 None:intergenic 45.0%
GGGAAATTGAGAGTGGAGAT+TGG - chr6_3:1817829-1817848 None:intergenic 45.0%
TTTGGAGGGGAAATTGAGAG+TGG - chr6_3:1817836-1817855 None:intergenic 45.0%
TTCTTCGACTACTGCGACTT+CGG - chr6_3:1818061-1818080 None:intergenic 45.0%
TCCTAGTAACGCGAGAATTG+CGG + chr6_3:1818113-1818132 Msa0933320:CDS 45.0%
GAGAATTGCGGCGATTAAAG+CGG + chr6_3:1818125-1818144 Msa0933320:CDS 45.0%
! GGTGTGGTGAGAAAGTGTGA+GGG - chr6_3:1817791-1817810 None:intergenic 50.0%
!!! GTTTTTTTGAGAGGGGGGTG+TGG - chr6_3:1817807-1817826 None:intergenic 50.0%
TTCTATTTCAGTGGCCACGG+CGG - chr6_3:1817908-1817927 None:intergenic 50.0%
TTTCTTGGAGGTAGTCGACG+AGG - chr6_3:1817978-1817997 None:intergenic 50.0%
! TGACGCCGAGTTTTTCTTGG+AGG - chr6_3:1817990-1818009 None:intergenic 50.0%
! GTGGTGAGAAAGTGTGAGGG+TGG - chr6_3:1817788-1817807 None:intergenic 55.0%
! GGGTGTGGTGAGAAAGTGTG+AGG - chr6_3:1817792-1817811 None:intergenic 55.0%
AGATGGAGAGGGGTTTGGAG+GGG - chr6_3:1817849-1817868 None:intergenic 55.0%
GAGATGGAGAGGGGTTTGGA+GGG - chr6_3:1817850-1817869 None:intergenic 55.0%
!! CTTTGGCTTGGGAGAGAGTG+AGG - chr6_3:1817954-1817973 None:intergenic 55.0%
! GTCGACGAGGTCTTTGGCTT+GGG - chr6_3:1817965-1817984 None:intergenic 55.0%
AGTCGACGAGGTCTTTGGCT+TGG - chr6_3:1817966-1817985 None:intergenic 55.0%
GAGGTAGTCGACGAGGTCTT+TGG - chr6_3:1817971-1817990 None:intergenic 55.0%
! CGGTGACGCCGAGTTTTTCT+TGG - chr6_3:1817993-1818012 None:intergenic 55.0%
TTCGACTACTGCGACTTCGG+CGG - chr6_3:1818058-1818077 None:intergenic 55.0%
GCCGCAATTCTCGCGTTACT+AGG - chr6_3:1818117-1818136 None:intergenic 55.0%
GGAGATGGAGAGGGGTTTGG+AGG - chr6_3:1817851-1817870 None:intergenic 60.0%
GTGGGAGATGGAGAGGGGTT+TGG - chr6_3:1817854-1817873 None:intergenic 60.0%
!! TGGTGGTGGGAGATGGAGAG+GGG - chr6_3:1817859-1817878 None:intergenic 60.0%
!! GTGGTGGTGGGAGATGGAGA+GGG - chr6_3:1817860-1817879 None:intergenic 60.0%
AGATGGGACGGAGACGAGTG+CGG - chr6_3:1817885-1817904 None:intergenic 60.0%
!! GGTGGTGGTGGGAGATGGAG+AGG - chr6_3:1817861-1817880 None:intergenic 65.0%
!! ACGAGTGCGGTGGTGGTGGT+GGG - chr6_3:1817872-1817891 None:intergenic 65.0%
TCAGTGGCCACGGCGGAGAT+GGG - chr6_3:1817901-1817920 None:intergenic 65.0%
TTCAGTGGCCACGGCGGAGA+TGG - chr6_3:1817902-1817921 None:intergenic 65.0%
ACTACTGCGACTTCGGCGGC+TGG - chr6_3:1818054-1818073 None:intergenic 65.0%
!! GCGGTGGTGGTGGTGGGAGA+TGG - chr6_3:1817866-1817885 None:intergenic 70.0%
!! GACGAGTGCGGTGGTGGTGG+TGG - chr6_3:1817873-1817892 None:intergenic 70.0%
! GGAGACGAGTGCGGTGGTGG+TGG - chr6_3:1817876-1817895 None:intergenic 70.0%
GACGGAGACGAGTGCGGTGG+TGG - chr6_3:1817879-1817898 None:intergenic 70.0%
TGGGACGGAGACGAGTGCGG+TGG - chr6_3:1817882-1817901 None:intergenic 70.0%
TCTCCGTCCCATCTCCGCCG+TGG + chr6_3:1817891-1817910 Msa0933320:CDS 70.0%
TGGCCACGGCGGAGATGGGA+CGG - chr6_3:1817897-1817916 None:intergenic 70.0%
TGCGACTTCGGCGGCTGGAG+CGG - chr6_3:1818049-1818068 None:intergenic 70.0%
GGCGGGAGCGAAGGAAGCGG+CGG - chr6_3:1818013-1818032 None:intergenic 75.0%
GGCGGCGGGAGCGAAGGAAG+CGG - chr6_3:1818016-1818035 None:intergenic 75.0%
TGGAGCGGCGACAGTGGCGG+CGG - chr6_3:1818034-1818053 None:intergenic 75.0%
GGCTGGAGCGGCGACAGTGG+CGG - chr6_3:1818037-1818056 None:intergenic 75.0%
! AGTGGCGGCGGCGGGAGCGA+AGG - chr6_3:1818022-1818041 None:intergenic 80.0%
! AGCGGCGACAGTGGCGGCGG+CGG - chr6_3:1818031-1818050 None:intergenic 80.0%
! GGCGGCTGGAGCGGCGACAG+TGG - chr6_3:1818040-1818059 None:intergenic 80.0%
! GCGGCGACAGTGGCGGCGGC+GGG - chr6_3:1818030-1818049 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 1817751 1818296 1817751 ID=Msa0933320;Name=Msa0933320
chr6_3 mRNA 1817751 1818296 1817751 ID=Msa0933320-mRNA-1;Parent=Msa0933320;Name=Msa0933320-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|181
chr6_3 exon 1817751 1818296 1817751 ID=Msa0933320-mRNA-1:exon:692;Parent=Msa0933320-mRNA-1
chr6_3 CDS 1817751 1818296 1817751 ID=Msa0933320-mRNA-1:cds;Parent=Msa0933320-mRNA-1
Gene Sequence

>Msa0933320

ATGGCATTATCAACAACCGCTTTCACAACTATCTCCACCCTCACACTTTCTCACCACACCCCCCTCTCAAAAAAACCAATCTCCACTCTCAATTTCCCCTCCAAACCCCTCTCCATCTCCCACCACCACCACCGCACTCGTCTCCGTCCCATCTCCGCCGTGGCCACTGAAATAGAAAAACTCGGCAACGACATCTCTGACCTCACTCTCTCCCAAGCCAAAGACCTCGTCGACTACCTCCAAGAAAAACTCGGCGTCACCGCCGCTTCCTTCGCTCCCGCCGCCGCCACTGTCGCCGCTCCAGCCGCCGAAGTCGCAGTAGTCGAAGAAAAAACCGAATTCGATGTGGTAATTGAAGATGTTCCTAGTAACGCGAGAATTGCGGCGATTAAAGCGGTTAGAGCTTTGACGAGTTTAGGATTGAAAGAAGCGAAGGAATTGATTGAAGGTTTGCCGAAGAAATTTAAAGAAGGTGTGAGTAAAGATGAAGCTGATGATGCTAAGAAACAACTTGAAGCTGCAGGTGCTAAAGTTACTATTGCTTAA

Protein sequence

>Msa0933320

MALSTTAFTTISTLTLSHHTPLSKKPISTLNFPSKPLSISHHHHRTRLRPISAVATEIEKLGNDISDLTLSQAKDLVDYLQEKLGVTAASFAPAAATVAAPAAEVAVVEEKTEFDVVIEDVPSNARIAAIKAVRALTSLGLKEAKELIEGLPKKFKEGVSKDEADDAKKQLEAAGAKVTIA*