AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0725030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0725030 MtrunA17_Chr5g0416431 98.925 93 1 0 1 93 1 93 7.68e-61 180
Msa0725030 MtrunA17_Chr8g0362131 79.762 84 16 1 10 93 10 92 1.71e-42 134
Msa0725030 MtrunA17_Chr7g0217141 72.826 92 24 1 1 92 1 91 8.00e-41 129
Msa0725030 MtrunA17_Chr6g0453041 69.737 76 23 0 17 92 15 90 3.68e-34 112
Msa0725030 MtrunA17_Chr3g0093001 74.026 77 18 1 17 93 17 91 3.81e-34 112
Msa0725030 MtrunA17_Chr7g0237771 45.946 74 40 0 8 81 3 76 9.86e-12 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0725030 AT1G26945.1 83.784 74 12 0 19 92 19 92 3.26e-39 125
Msa0725030 AT3G28857.1 64.894 94 30 2 1 93 1 92 3.87e-36 118
Msa0725030 AT3G47710.1 69.149 94 25 3 1 93 1 91 3.62e-35 115
Msa0725030 AT5G15160.1 73.333 75 19 1 19 92 18 92 3.39e-32 108
Msa0725030 AT1G74500.1 72.727 77 18 2 17 92 17 91 3.08e-31 105
Msa0725030 AT5G39860.1 65.385 78 26 1 17 93 15 92 1.80e-30 103

Find 47 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGATAATAAAATTAAATT+TGG 0.194346 5_1:+24364930 None:intergenic
GCTAGACATTGTTATAATTA+AGG 0.199410 5_1:+24364686 None:intergenic
TATCTGTGTAGGGTTTAATT+TGG 0.245749 5_1:-24363872 Msa0725030:three_prime_UTR
TGACCGATTGTCACAACTTT+TGG 0.275530 5_1:-24364047 Msa0725030:CDS
GAGCGGCTAGCGCGAAGTTC+GGG 0.276939 5_1:+24364573 None:intergenic
TTCTATAGCTATAAATAAAA+TGG 0.297131 5_1:-24363720 None:intergenic
GTGCTCAAGCAGCTATTATT+AGG 0.330670 5_1:-24364006 Msa0725030:CDS
GGAGCGGCTAGCGCGAAGTT+CGG 0.362273 5_1:+24364572 None:intergenic
GAAGTTATGTGAAATGAGTA+TGG 0.366690 5_1:+24364835 None:intergenic
GTTATTCTCTTATCTGTGTA+GGG 0.379197 5_1:-24363882 Msa0725030:three_prime_UTR
CTTATAGGTTTCAGCTACTA+AGG 0.382941 5_1:-24364128 Msa0725030:intron
TGTTATTCTCTTATCTGTGT+AGG 0.387894 5_1:-24363883 Msa0725030:three_prime_UTR
AGAGGAACCACCGGATTGTC+TGG 0.389390 5_1:+24364650 None:intergenic
GGGGATAAGTTGTTGTAACT+TGG 0.418381 5_1:+24364593 None:intergenic
GGAGGAGAGTGAAGAGGAGT+GGG 0.429020 5_1:+24364956 None:intergenic
GGTTTGTAGACCAAGGCAAA+AGG 0.461588 5_1:-24363851 Msa0725030:three_prime_UTR
AGAGAGGAAATGAGGTTGGT+TGG 0.463003 5_1:+24364783 None:intergenic
AAATAAACAAAGAGAAAGAG+AGG 0.468720 5_1:+24364767 None:intergenic
GATAATAAAATTAAATTTGG+AGG 0.476768 5_1:+24364933 None:intergenic
AGAAAGAGAGGAAATGAGGT+TGG 0.479603 5_1:+24364779 None:intergenic
GGTTGGTTGGTTGTCAGAGA+AGG 0.483101 5_1:+24364796 None:intergenic
ATAATAAAATTAAATTTGGA+GGG 0.484167 5_1:+24364934 None:intergenic
AAAGAGAAAGAGAGGAAATG+AGG 0.488212 5_1:+24364775 None:intergenic
AAGAGAGAAATAAATAAAAG+TGG 0.494133 5_1:+24364879 None:intergenic
AATAGCTGCTTGAGCACTGT+TGG 0.496664 5_1:+24364012 None:intergenic
TGTTATAATTAAGGAGGTAG+TGG 0.505098 5_1:+24364695 None:intergenic
TAAAATTAAATTTGGAGGGG+AGG 0.505190 5_1:+24364938 None:intergenic
TGTGAAATGAGTATGGAGTA+AGG 0.505231 5_1:+24364842 None:intergenic
AAGCCAAAAGTTGTGACAAT+CGG 0.524888 5_1:+24364044 None:intergenic
GTTTGTAGACCAAGGCAAAA+GGG 0.528021 5_1:-24363850 Msa0725030:three_prime_UTR
AAAATTAAACTAATTAATCA+AGG 0.530033 5_1:+24363802 None:intergenic
AGATCTCGTTCCAGACAATC+CGG 0.532260 5_1:-24364660 Msa0725030:CDS
GGGAGGAGAGTGAAGAGGAG+TGG 0.537209 5_1:+24364955 None:intergenic
TGGAGGGGAGGAGAGTGAAG+AGG 0.555226 5_1:+24364950 None:intergenic
GTGAAATGAGTATGGAGTAA+GGG 0.559416 5_1:+24364843 None:intergenic
GTTGAATTGTTGAATTGAAG+AGG 0.578890 5_1:+24364978 None:intergenic
TTAATTTGGTTTGTAGACCA+AGG 0.581266 5_1:-24363858 Msa0725030:three_prime_UTR
TAATAAAATTAAATTTGGAG+GGG 0.593264 5_1:+24364935 None:intergenic
AAATAAATACCTTGTTGGAG+CGG 0.605762 5_1:+24364556 None:intergenic
AGACATTGTTATAATTAAGG+AGG 0.612299 5_1:+24364689 None:intergenic
TCGCGCTAGCCGCTCCAACA+AGG 0.613710 5_1:-24364565 Msa0725030:intron
AGTGATCTCAGAGGAACCAC+CGG 0.628272 5_1:+24364641 None:intergenic
AGCGGCTAGCGCGAAGTTCG+GGG 0.650397 5_1:+24364574 None:intergenic
AATTAATCAAGGACTAACAA+AGG 0.658512 5_1:+24363813 None:intergenic
AATAACAATAAAGTGAGACA+AGG 0.708908 5_1:+24363899 None:intergenic
TCTCGTTCCAGACAATCCGG+TGG 0.728257 5_1:-24364657 Msa0725030:CDS
TTGAGCATCAGTGATCTCAG+AGG 0.728981 5_1:+24364632 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATAAAATTAAATTTGGA+GGG + chr5_1:24363775-24363794 None:intergenic 10.0%
!! AAAATTAAACTAATTAATCA+AGG + chr5_1:24364907-24364926 None:intergenic 10.0%
!! ATAATAAAATTAAATTTGGA+GGG + chr5_1:24363775-24363794 None:intergenic 10.0%
!! AAAATTAAACTAATTAATCA+AGG + chr5_1:24364907-24364926 None:intergenic 10.0%
!! TAATAAAATTAAATTTGGAG+GGG + chr5_1:24363774-24363793 None:intergenic 15.0%
!! GATAATAAAATTAAATTTGG+AGG + chr5_1:24363776-24363795 None:intergenic 15.0%
!!! ATTTTTTTTTATGGTCTTAT+AGG - chr5_1:24364563-24364582 Msa0725030:intron 15.0%
!! TAATAAAATTAAATTTGGAG+GGG + chr5_1:24363774-24363793 None:intergenic 15.0%
!! GATAATAAAATTAAATTTGG+AGG + chr5_1:24363776-24363795 None:intergenic 15.0%
!!! ATTTTTTTTTATGGTCTTAT+AGG - chr5_1:24364563-24364582 Msa0725030:intron 15.0%
!! AAGAGAGAAATAAATAAAAG+TGG + chr5_1:24363830-24363849 None:intergenic 20.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5_1:24364158-24364177 None:intergenic 20.0%
!! AAGAGAGAAATAAATAAAAG+TGG + chr5_1:24363830-24363849 None:intergenic 20.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5_1:24364158-24364177 None:intergenic 20.0%
!!! TGTTTTTTGTAATGTTGCTA+AGG + chr5_1:24363802-24363821 None:intergenic 25.0%
! AAATAAACAAAGAGAAAGAG+AGG + chr5_1:24363942-24363961 None:intergenic 25.0%
! AGACATTGTTATAATTAAGG+AGG + chr5_1:24364020-24364039 None:intergenic 25.0%
! GCTAGACATTGTTATAATTA+AGG + chr5_1:24364023-24364042 None:intergenic 25.0%
! AATAACAATAAAGTGAGACA+AGG + chr5_1:24364810-24364829 None:intergenic 25.0%
! AATTAATCAAGGACTAACAA+AGG + chr5_1:24364896-24364915 None:intergenic 25.0%
!!! TGTTTTTTGTAATGTTGCTA+AGG + chr5_1:24363802-24363821 None:intergenic 25.0%
! AAATAAACAAAGAGAAAGAG+AGG + chr5_1:24363942-24363961 None:intergenic 25.0%
! AGACATTGTTATAATTAAGG+AGG + chr5_1:24364020-24364039 None:intergenic 25.0%
! GCTAGACATTGTTATAATTA+AGG + chr5_1:24364023-24364042 None:intergenic 25.0%
! AATAACAATAAAGTGAGACA+AGG + chr5_1:24364810-24364829 None:intergenic 25.0%
! AATTAATCAAGGACTAACAA+AGG + chr5_1:24364896-24364915 None:intergenic 25.0%
GTTGAATTGTTGAATTGAAG+AGG + chr5_1:24363731-24363750 None:intergenic 30.0%
TAAAATTAAATTTGGAGGGG+AGG + chr5_1:24363771-24363790 None:intergenic 30.0%
GAAGTTATGTGAAATGAGTA+TGG + chr5_1:24363874-24363893 None:intergenic 30.0%
TGTTATAATTAAGGAGGTAG+TGG + chr5_1:24364014-24364033 None:intergenic 30.0%
AAATAAATACCTTGTTGGAG+CGG + chr5_1:24364153-24364172 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5_1:24364415-24364434 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5_1:24364623-24364642 Msa0725030:CDS 30.0%
TGTTATTCTCTTATCTGTGT+AGG - chr5_1:24364823-24364842 Msa0725030:five_prime_UTR 30.0%
GTTATTCTCTTATCTGTGTA+GGG - chr5_1:24364824-24364843 Msa0725030:five_prime_UTR 30.0%
TATCTGTGTAGGGTTTAATT+TGG - chr5_1:24364834-24364853 Msa0725030:five_prime_UTR 30.0%
!! TTAATTTGGTTTGTAGACCA+AGG - chr5_1:24364848-24364867 Msa0725030:five_prime_UTR 30.0%
GTTGAATTGTTGAATTGAAG+AGG + chr5_1:24363731-24363750 None:intergenic 30.0%
TAAAATTAAATTTGGAGGGG+AGG + chr5_1:24363771-24363790 None:intergenic 30.0%
GAAGTTATGTGAAATGAGTA+TGG + chr5_1:24363874-24363893 None:intergenic 30.0%
TGTTATAATTAAGGAGGTAG+TGG + chr5_1:24364014-24364033 None:intergenic 30.0%
AAATAAATACCTTGTTGGAG+CGG + chr5_1:24364153-24364172 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5_1:24364415-24364434 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5_1:24364623-24364642 Msa0725030:CDS 30.0%
TGTTATTCTCTTATCTGTGT+AGG - chr5_1:24364823-24364842 Msa0725030:five_prime_UTR 30.0%
GTTATTCTCTTATCTGTGTA+GGG - chr5_1:24364824-24364843 Msa0725030:five_prime_UTR 30.0%
TATCTGTGTAGGGTTTAATT+TGG - chr5_1:24364834-24364853 Msa0725030:five_prime_UTR 30.0%
!! TTAATTTGGTTTGTAGACCA+AGG - chr5_1:24364848-24364867 Msa0725030:five_prime_UTR 30.0%
GTGAAATGAGTATGGAGTAA+GGG + chr5_1:24363866-24363885 None:intergenic 35.0%
TGTGAAATGAGTATGGAGTA+AGG + chr5_1:24363867-24363886 None:intergenic 35.0%
AAAGAGAAAGAGAGGAAATG+AGG + chr5_1:24363934-24363953 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5_1:24364277-24364296 None:intergenic 35.0%
GATACAATGCACATATTGTG+TGG - chr5_1:24364332-24364351 Msa0725030:intron 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5_1:24364348-24364367 Msa0725030:intron 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5_1:24364578-24364597 Msa0725030:CDS 35.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5_1:24364665-24364684 None:intergenic 35.0%
GTGAAATGAGTATGGAGTAA+GGG + chr5_1:24363866-24363885 None:intergenic 35.0%
TGTGAAATGAGTATGGAGTA+AGG + chr5_1:24363867-24363886 None:intergenic 35.0%
AAAGAGAAAGAGAGGAAATG+AGG + chr5_1:24363934-24363953 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5_1:24364277-24364296 None:intergenic 35.0%
GATACAATGCACATATTGTG+TGG - chr5_1:24364332-24364351 Msa0725030:intron 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5_1:24364348-24364367 Msa0725030:intron 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5_1:24364578-24364597 Msa0725030:CDS 35.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5_1:24364665-24364684 None:intergenic 35.0%
AGAAAGAGAGGAAATGAGGT+TGG + chr5_1:24363930-24363949 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5_1:24364116-24364135 None:intergenic 40.0%
GTGCATGTGAATGATGACTT+GGG + chr5_1:24364301-24364320 None:intergenic 40.0%
TGTGCATGTGAATGATGACT+TGG + chr5_1:24364302-24364321 None:intergenic 40.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5_1:24364402-24364421 None:intergenic 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5_1:24364659-24364678 Msa0725030:CDS 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5_1:24364700-24364719 Msa0725030:five_prime_UTR 40.0%
GTTTGTAGACCAAGGCAAAA+GGG - chr5_1:24364856-24364875 Msa0725030:five_prime_UTR 40.0%
! TATAGTAAGCCCTTTTGCCT+TGG + chr5_1:24364868-24364887 None:intergenic 40.0%
AGAAAGAGAGGAAATGAGGT+TGG + chr5_1:24363930-24363949 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5_1:24364116-24364135 None:intergenic 40.0%
GTGCATGTGAATGATGACTT+GGG + chr5_1:24364301-24364320 None:intergenic 40.0%
TGTGCATGTGAATGATGACT+TGG + chr5_1:24364302-24364321 None:intergenic 40.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5_1:24364402-24364421 None:intergenic 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5_1:24364659-24364678 Msa0725030:CDS 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5_1:24364700-24364719 Msa0725030:five_prime_UTR 40.0%
GTTTGTAGACCAAGGCAAAA+GGG - chr5_1:24364856-24364875 Msa0725030:five_prime_UTR 40.0%
! TATAGTAAGCCCTTTTGCCT+TGG + chr5_1:24364868-24364887 None:intergenic 40.0%
! AGAGAGGAAATGAGGTTGGT+TGG + chr5_1:24363926-24363945 None:intergenic 45.0%
AGATCTCGTTCCAGACAATC+CGG - chr5_1:24364046-24364065 Msa0725030:CDS 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5_1:24364077-24364096 None:intergenic 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5_1:24364476-24364495 Msa0725030:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5_1:24364477-24364496 Msa0725030:intron 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5_1:24364697-24364716 None:intergenic 45.0%
GGTTTGTAGACCAAGGCAAA+AGG - chr5_1:24364855-24364874 Msa0725030:five_prime_UTR 45.0%
! AGAGAGGAAATGAGGTTGGT+TGG + chr5_1:24363926-24363945 None:intergenic 45.0%
AGATCTCGTTCCAGACAATC+CGG - chr5_1:24364046-24364065 Msa0725030:CDS 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5_1:24364077-24364096 None:intergenic 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5_1:24364476-24364495 Msa0725030:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5_1:24364477-24364496 Msa0725030:intron 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5_1:24364697-24364716 None:intergenic 45.0%
GGTTTGTAGACCAAGGCAAA+AGG - chr5_1:24364855-24364874 Msa0725030:five_prime_UTR 45.0%
!! TATGATAATAAAATTAAATT+TGG + chr5_1:24363779-24363798 None:intergenic 5.0%
!!! TTAATTTGTATTTTTTTTTA+TGG - chr5_1:24364554-24364573 Msa0725030:intron 5.0%
!! TATGATAATAAAATTAAATT+TGG + chr5_1:24363779-24363798 None:intergenic 5.0%
!!! TTAATTTGTATTTTTTTTTA+TGG - chr5_1:24364554-24364573 Msa0725030:intron 5.0%
! GGTTGGTTGGTTGTCAGAGA+AGG + chr5_1:24363913-24363932 None:intergenic 50.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5_1:24364068-24364087 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5_1:24364480-24364499 Msa0725030:intron 50.0%
! GGTTGGTTGGTTGTCAGAGA+AGG + chr5_1:24363913-24363932 None:intergenic 50.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5_1:24364068-24364087 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5_1:24364480-24364499 Msa0725030:intron 50.0%
GGAGGAGAGTGAAGAGGAGT+GGG + chr5_1:24363753-24363772 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5_1:24364049-24364068 Msa0725030:CDS 55.0%
AGAGGAACCACCGGATTGTC+TGG + chr5_1:24364059-24364078 None:intergenic 55.0%
GGAGGAGAGTGAAGAGGAGT+GGG + chr5_1:24363753-24363772 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5_1:24364049-24364068 Msa0725030:CDS 55.0%
AGAGGAACCACCGGATTGTC+TGG + chr5_1:24364059-24364078 None:intergenic 55.0%
GGGAGGAGAGTGAAGAGGAG+TGG + chr5_1:24363754-24363773 None:intergenic 60.0%
TGGAGGGGAGGAGAGTGAAG+AGG + chr5_1:24363759-24363778 None:intergenic 60.0%
GGGAGGAGAGTGAAGAGGAG+TGG + chr5_1:24363754-24363773 None:intergenic 60.0%
TGGAGGGGAGGAGAGTGAAG+AGG + chr5_1:24363759-24363778 None:intergenic 60.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5_1:24364135-24364154 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5_1:24364136-24364155 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5_1:24364137-24364156 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5_1:24364141-24364160 Msa0725030:intron 65.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5_1:24364135-24364154 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5_1:24364136-24364155 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5_1:24364137-24364156 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5_1:24364141-24364160 Msa0725030:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 24363723 24365005 24363723 ID=Msa0725030;Name=Msa0725030
chr5_1 mRNA 24363723 24365005 24363723 ID=Msa0725030-mRNA-1;Parent=Msa0725030;Name=Msa0725030-mRNA-1;_AED=0.03;_eAED=0.03;_QI=311|1|1|1|1|1|2|268|93
chr5_1 exon 24363723 24364143 24363723 ID=Msa0725030-mRNA-1:exon:8911;Parent=Msa0725030-mRNA-1
chr5_1 exon 24364566 24365005 24364566 ID=Msa0725030-mRNA-1:exon:8910;Parent=Msa0725030-mRNA-1
chr5_1 five_prime_UTR 24364695 24365005 24364695 ID=Msa0725030-mRNA-1:five_prime_utr;Parent=Msa0725030-mRNA-1
chr5_1 CDS 24364566 24364694 24364566 ID=Msa0725030-mRNA-1:cds;Parent=Msa0725030-mRNA-1
chr5_1 CDS 24363991 24364143 24363991 ID=Msa0725030-mRNA-1:cds;Parent=Msa0725030-mRNA-1
chr5_1 three_prime_UTR 24363723 24363990 24363723 ID=Msa0725030-mRNA-1:three_prime_utr;Parent=Msa0725030-mRNA-1
Gene Sequence

>Msa0725030

ATGTCTAGCAGAAGATCTCGTTCCAGACAATCCGGTGGTTCCTCTGAGATCACTGATGCTCAAATCACTGATCTCATTTCCAAGTTACAACAACTTATCCCCGAACTTCGCGCTAGCCGCTCCAACAAGGTTTCAGCTACTAAGGTATTGCAAGAGACTTGCAACTACATAAAAAACTTGCATAGAGAGGTTGATGATTTAAGTGACCGATTGTCACAACTTTTGGCTTCTACAGATTCCAACAGTGCTCAAGCAGCTATTATTAGGAGCTTACTTATGTAA
Protein sequence

>Msa0725030

MSSRRSRSRQSGGSSEITDAQITDLISKLQQLIPELRASRSNKVSATKVLQETCNYIKNLHREVDDLSDRLSQLLASTDSNSAQAAIIRSLLM*