AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0665000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0665000 MtrunA17_Chr4g0003091 90.625 192 4 3 1 190 1 180 2.25e-118 333
Msa0665000 MtrunA17_Chr2g0282361 35.450 189 81 10 16 184 83 250 7.78e-14 67.8
Msa0665000 MtrunA17_Chr2g0317321 36.598 194 92 8 16 190 65 246 2.79e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0665000 AT1G80450.1 41.206 199 56 7 11 189 10 167 2.85e-30 109
Msa0665000 AT1G28280.1 35.789 190 91 10 16 184 57 236 1.89e-14 69.7
Msa0665000 AT1G28280.2 35.789 190 91 10 16 184 57 236 1.89e-14 69.7
Msa0665000 AT5G08480.2 34.054 185 86 5 11 186 12 169 3.33e-13 65.1
Msa0665000 AT5G08480.3 34.054 185 86 5 11 186 12 169 3.33e-13 65.1
Msa0665000 AT3G15300.1 33.679 193 88 8 16 184 37 213 2.03e-12 63.9
Msa0665000 AT2G33780.1 32.065 184 98 8 16 189 36 202 7.38e-12 62.0
Msa0665000 AT5G53830.1 34.314 204 94 9 16 188 49 243 5.68e-11 60.1

Find 44 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGTGGAGGACGGTGGGCT+TGG 0.256659 4_4:-4293756 None:intergenic
GAGGACGGTGGGCTTGGGCT+TGG 0.257828 4_4:-4293750 None:intergenic
CAACATGCGAAGTGTTATTA+TGG 0.268568 4_4:+4293942 Msa0665000:CDS
TCATGTTATTGTTGTTGTTT+TGG 0.291134 4_4:-4293888 None:intergenic
AGGACGGTGGGCTTGGGCTT+GGG 0.306796 4_4:-4293749 None:intergenic
TAATATTCCAATGGTGAAAC+TGG 0.334222 4_4:-4293970 None:intergenic
TGGTGGAGGACGGTGGGCTT+GGG 0.338898 4_4:-4293755 None:intergenic
TTGTGTTTGGTTGTGTTGTT+AGG 0.343814 4_4:-4293612 None:intergenic
GGTTCCATGGTGGTTGTTGT+TGG 0.392587 4_4:-4293775 None:intergenic
TCCATGGTGGTTGTTGTTGG+TGG 0.405900 4_4:-4293772 None:intergenic
GCTTGTACAAAGGTTGTGTT+TGG 0.409951 4_4:-4293625 None:intergenic
ACAACTTGTCGGAAATTTGA+TGG 0.417823 4_4:-4293652 None:intergenic
GCGTTCGTGGAGTTTGAAGT+TGG 0.435488 4_4:-4293818 None:intergenic
TAAGAATGAGATTGAGAGGA+AGG 0.443832 4_4:-4294135 None:intergenic
CGTTCGTGGAGTTTGAAGTT+GGG 0.446220 4_4:-4293817 None:intergenic
TGGTTGTTGTTGGTGGAGGA+CGG 0.455302 4_4:-4293765 None:intergenic
TAAGCCCATTGGTGGTTCCA+TGG 0.464436 4_4:-4293788 None:intergenic
ACCATGCATTCACCAACATA+TGG 0.465787 4_4:+4293583 None:intergenic
GGCTTCACCAGTTTCACCAT+TGG 0.477870 4_4:+4293963 Msa0665000:CDS
TGTTGTTGGTGGAGGACGGT+GGG 0.481918 4_4:-4293761 None:intergenic
AAAACTCCAACTCAACGTTT+CGG 0.499017 4_4:+4293849 Msa0665000:CDS
AGACGAGAAGGGAGTGTGAG+TGG 0.503781 4_4:-4293721 None:intergenic
TGATGGGTCTTGTGATGCTC+CGG 0.504118 4_4:-4293686 None:intergenic
ATGGTGGTTGTTGTTGGTGG+AGG 0.515633 4_4:-4293769 None:intergenic
AACCACCATGGAACCACCAA+TGG 0.516253 4_4:+4293783 Msa0665000:CDS
ACCACCATGGAACCACCAAT+GGG 0.535319 4_4:+4293784 Msa0665000:CDS
GTTTGGTTGTGTTGTTAGGT+CGG 0.535973 4_4:-4293608 None:intergenic
GCTTGGGCTGTTAGACGAGA+AGG 0.539771 4_4:-4293733 None:intergenic
TTGTTGTTGGTGGAGGACGG+TGG 0.540140 4_4:-4293762 None:intergenic
TAATTAAGAATGAGATTGAG+AGG 0.547532 4_4:-4294139 None:intergenic
TGATGGGTCTGCTTGTACAA+AGG 0.550070 4_4:-4293635 None:intergenic
GGACTATAGTAATATTCCAA+TGG 0.550459 4_4:-4293979 None:intergenic
CAACTTGTCGGAAATTTGAT+GGG 0.562610 4_4:-4293651 None:intergenic
TGTTGAGAAGCTCTAGGAGA+GGG 0.563092 4_4:-4294072 None:intergenic
TGAGAGGAAGGAGAATGCAA+AGG 0.574115 4_4:-4294123 None:intergenic
GGTTGTTGTTGAGAAGCTCT+AGG 0.576546 4_4:-4294078 None:intergenic
GTTAGGTCGGATCCATATGT+TGG 0.606638 4_4:-4293595 None:intergenic
AAAAGAGGTAAAAGTTCAGG+TGG 0.608567 4_4:-4294099 None:intergenic
TCCATATGTTGGTGAATGCA+TGG 0.614670 4_4:-4293584 None:intergenic
CTTGGGCTGTTAGACGAGAA+GGG 0.624849 4_4:-4293732 None:intergenic
TTGTTGAGAAGCTCTAGGAG+AGG 0.644100 4_4:-4294073 None:intergenic
TCCACCAACAACAACCACCA+TGG 0.648779 4_4:+4293771 Msa0665000:CDS
GCCCATTGGTGGTTCCATGG+TGG 0.657294 4_4:-4293785 None:intergenic
GTTGAGAAGCTCTAGGAGAG+GGG 0.657383 4_4:-4294071 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTTTCTTCATTTTCATT+TGG - chr4_4:4294012-4294031 None:intergenic 20.0%
!!! TCATGTTATTGTTGTTGTTT+TGG - chr4_4:4293891-4293910 None:intergenic 25.0%
!!! TCATTTTCATTTGGTGATTT+TGG - chr4_4:4294003-4294022 None:intergenic 25.0%
!! TTAGTTTTTGGACAACTTGT+CGG - chr4_4:4293666-4293685 None:intergenic 30.0%
!!! TTGTTGTTTTGGAACATCAT+GGG - chr4_4:4293880-4293899 None:intergenic 30.0%
TAATATTCCAATGGTGAAAC+TGG - chr4_4:4293973-4293992 None:intergenic 30.0%
GGACTATAGTAATATTCCAA+TGG - chr4_4:4293982-4294001 None:intergenic 30.0%
GAAAAAGTGATAGCTGAAAA+AGG + chr4_4:4294036-4294055 Msa0665000:CDS 30.0%
! TTGTGTTTGGTTGTGTTGTT+AGG - chr4_4:4293615-4293634 None:intergenic 35.0%
CAACTTGTCGGAAATTTGAT+GGG - chr4_4:4293654-4293673 None:intergenic 35.0%
ACAACTTGTCGGAAATTTGA+TGG - chr4_4:4293655-4293674 None:intergenic 35.0%
CAAGTTGTCCAAAAACTAAC+CGG + chr4_4:4293667-4293686 Msa0665000:CDS 35.0%
!!! TTGGGTTTTTTTAAGCCCAT+TGG - chr4_4:4293802-4293821 None:intergenic 35.0%
!!! TGAGTTGGAGTTTTTTAGAG+CGG - chr4_4:4293843-4293862 None:intergenic 35.0%
AAAACTCCAACTCAACGTTT+CGG + chr4_4:4293849-4293868 Msa0665000:CDS 35.0%
!!! GTTGTTGTTTTGGAACATCA+TGG - chr4_4:4293881-4293900 None:intergenic 35.0%
! CAACATGCGAAGTGTTATTA+TGG + chr4_4:4293942-4293961 Msa0665000:CDS 35.0%
AAAAGAGGTAAAAGTTCAGG+TGG - chr4_4:4294102-4294121 None:intergenic 35.0%
GGAAAAAGAGGTAAAAGTTC+AGG - chr4_4:4294105-4294124 None:intergenic 35.0%
TAAGAATGAGATTGAGAGGA+AGG - chr4_4:4294138-4294157 None:intergenic 35.0%
! GTTTGGTTGTGTTGTTAGGT+CGG - chr4_4:4293611-4293630 None:intergenic 40.0%
GCTTGTACAAAGGTTGTGTT+TGG - chr4_4:4293628-4293647 None:intergenic 40.0%
! GAGTGTGAGTGGAAGTTTTT+GGG - chr4_4:4293713-4293732 None:intergenic 40.0%
!!! GGTTTTTTTAAGCCCATTGG+TGG - chr4_4:4293799-4293818 None:intergenic 40.0%
! GATTTTCCGAAACGTTGAGT+TGG - chr4_4:4293858-4293877 None:intergenic 40.0%
GGAGAATGCAAAGGAAAAAG+AGG - chr4_4:4294117-4294136 None:intergenic 40.0%
GTTAGGTCGGATCCATATGT+TGG - chr4_4:4293598-4293617 None:intergenic 45.0%
! TGATGGGTCTGCTTGTACAA+AGG - chr4_4:4293638-4293657 None:intergenic 45.0%
!!! GTGATGCTCCGGTTAGTTTT+TGG - chr4_4:4293678-4293697 None:intergenic 45.0%
!! GTGGAAGTTTTTGGGCTGAT+GGG - chr4_4:4293705-4293724 None:intergenic 45.0%
!! AGTGGAAGTTTTTGGGCTGA+TGG - chr4_4:4293706-4293725 None:intergenic 45.0%
! GGAGTGTGAGTGGAAGTTTT+TGG - chr4_4:4293714-4293733 None:intergenic 45.0%
! CGTTCGTGGAGTTTGAAGTT+GGG - chr4_4:4293820-4293839 None:intergenic 45.0%
!! TGTTGAGAAGCTCTAGGAGA+GGG - chr4_4:4294075-4294094 None:intergenic 45.0%
!! TTGTTGAGAAGCTCTAGGAG+AGG - chr4_4:4294076-4294095 None:intergenic 45.0%
! GGTTGTTGTTGAGAAGCTCT+AGG - chr4_4:4294081-4294100 None:intergenic 45.0%
TGAGAGGAAGGAGAATGCAA+AGG - chr4_4:4294126-4294145 None:intergenic 45.0%
! TGATGGGTCTTGTGATGCTC+CGG - chr4_4:4293689-4293708 None:intergenic 50.0%
CTTGGGCTGTTAGACGAGAA+GGG - chr4_4:4293735-4293754 None:intergenic 50.0%
! TGGTTGTTGTTGGTGGAGGA+CGG - chr4_4:4293768-4293787 None:intergenic 50.0%
! ATGGTGGTTGTTGTTGGTGG+AGG - chr4_4:4293772-4293791 None:intergenic 50.0%
TCCACCAACAACAACCACCA+TGG + chr4_4:4293771-4293790 Msa0665000:CDS 50.0%
! TCCATGGTGGTTGTTGTTGG+TGG - chr4_4:4293775-4293794 None:intergenic 50.0%
GGTTCCATGGTGGTTGTTGT+TGG - chr4_4:4293778-4293797 None:intergenic 50.0%
AACCACCATGGAACCACCAA+TGG + chr4_4:4293783-4293802 Msa0665000:CDS 50.0%
ACCACCATGGAACCACCAAT+GGG + chr4_4:4293784-4293803 Msa0665000:CDS 50.0%
! TAAGCCCATTGGTGGTTCCA+TGG - chr4_4:4293791-4293810 None:intergenic 50.0%
! GCGTTCGTGGAGTTTGAAGT+TGG - chr4_4:4293821-4293840 None:intergenic 50.0%
!!! GTTTTTTAGAGCGGCGTTCG+TGG - chr4_4:4293834-4293853 None:intergenic 50.0%
GGCTTCACCAGTTTCACCAT+TGG + chr4_4:4293963-4293982 Msa0665000:CDS 50.0%
!! GTTGAGAAGCTCTAGGAGAG+GGG - chr4_4:4294074-4294093 None:intergenic 50.0%
! AGACGAGAAGGGAGTGTGAG+TGG - chr4_4:4293724-4293743 None:intergenic 55.0%
GCTTGGGCTGTTAGACGAGA+AGG - chr4_4:4293736-4293755 None:intergenic 55.0%
! TGTTGTTGGTGGAGGACGGT+GGG - chr4_4:4293764-4293783 None:intergenic 55.0%
! TTGTTGTTGGTGGAGGACGG+TGG - chr4_4:4293765-4293784 None:intergenic 55.0%
! GCCCATTGGTGGTTCCATGG+TGG - chr4_4:4293788-4293807 None:intergenic 60.0%
! AGGACGGTGGGCTTGGGCTT+GGG - chr4_4:4293752-4293771 None:intergenic 65.0%
! TGGTGGAGGACGGTGGGCTT+GGG - chr4_4:4293758-4293777 None:intergenic 65.0%
! TTGGTGGAGGACGGTGGGCT+TGG - chr4_4:4293759-4293778 None:intergenic 65.0%
! GAGGACGGTGGGCTTGGGCT+TGG - chr4_4:4293753-4293772 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 4293586 4294158 4293586 ID=Msa0665000;Name=Msa0665000
chr4_4 mRNA 4293586 4294158 4293586 ID=Msa0665000-mRNA-1;Parent=Msa0665000;Name=Msa0665000-mRNA-1;_AED=0.00;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|190
chr4_4 exon 4293586 4294158 4293586 ID=Msa0665000-mRNA-1:exon:1436;Parent=Msa0665000-mRNA-1
chr4_4 CDS 4293586 4294158 4293586 ID=Msa0665000-mRNA-1:cds;Parent=Msa0665000-mRNA-1
Gene Sequence

>Msa0665000

ATGCATTCACCAACATATGGATCCGACCTAACAACACAACCAAACACAACCTTTGTACAAGCAGACCCATCAAATTTCCGACAAGTTGTCCAAAAACTAACCGGAGCATCACAAGACCCATCAGCCCAAAAACTTCCACTCACACTCCCTTCTCGTCTAACAGCCCAAGCCCAAGCCCACCGTCCTCCACCAACAACAACCACCATGGAACCACCAATGGGCTTAAAAAAACCCAACTTCAAACTCCACGAACGCCGCTCTAAAAAACTCCAACTCAACGTTTCGGAAAATCCCATGATGTTCCAAAACAACAACAATAACATGATGATGATGTTAATGAATAGTAACAACAACAACAACATGCGAAGTGTTATTATGGCTTCACCAGTTTCACCATTGGAATATTACTATAGTCCAAAATCACCAAATGAAAATGAAGAAAAAGAAGAAGAAAAAGTGATAGCTGAAAAAGGTTTCTATTTGCACCCCTCTCCTAGAGCTTCTCAACAACAACCACCTGAACTTTTACCTCTTTTTCCTTTGCATTCTCCTTCCTCTCAATCTCATTCTTAA
Protein sequence

>Msa0665000

MHSPTYGSDLTTQPNTTFVQADPSNFRQVVQKLTGASQDPSAQKLPLTLPSRLTAQAQAHRPPPTTTTMEPPMGLKKPNFKLHERRSKKLQLNVSENPMMFQNNNNNMMMMLMNSNNNNNMRSVIMASPVSPLEYYYSPKSPNENEEKEEEKVIAEKGFYLHPSPRASQQQPPELLPLFPLHSPSSQSHS*