AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0746850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0746850 MtrunA17_Chr5g0394901 98.936 94 1 0 1 94 1 94 1.46e-59 191
Msa0746850 MtrunA17_Chr1g0205121 73.404 94 23 1 1 94 1 92 2.28e-39 137
Msa0746850 MtrunA17_Chr1g0185281 44.211 95 49 2 1 94 1 92 3.24e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0746850 AT1G05470.2 56.842 95 37 3 1 94 1 92 7.96e-24 94.0
Msa0746850 AT1G05470.1 56.842 95 37 3 1 94 1 92 7.96e-24 94.0
Msa0746850 AT2G32010.2 61.053 95 32 3 1 94 1 91 2.42e-17 75.5
Msa0746850 AT2G32010.1 61.053 95 32 3 1 94 1 91 2.42e-17 75.5
Msa0746850 AT2G32010.4 61.053 95 32 3 1 94 1 91 2.42e-17 75.5
Msa0746850 AT2G32010.3 61.053 95 32 3 1 94 1 91 2.42e-17 75.5
Msa0746850 AT3G63240.2 43.678 87 45 3 1 86 1 84 1.42e-12 62.0
Msa0746850 AT3G63240.1 43.678 87 45 3 1 86 1 84 1.42e-12 62.0

Find 37 sgRNAs with CRISPR-Local

Find 121 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTAAATTCAACACTTTAA+AGG 0.140919 5_1:-70491234 Msa0746850:five_prime_UTR
ATTAAATTCAACACTTTAAA+GGG 0.302092 5_1:-70491233 Msa0746850:five_prime_UTR
TAAAGTGTTGAATTTAATAA+TGG 0.302706 5_1:+70491238 None:intergenic
GTGTTTCAGTTTCTCTCTCT+TGG 0.329050 5_1:+70491331 None:intergenic
GCTCTCATGGTCAAAGAAAA+TGG 0.337468 5_1:-70490868 Msa0746850:CDS
TTATGGACATCTATAATTCT+AGG 0.373586 5_1:+70490383 None:intergenic
CAGGGCAAGGAAAGAAATAA+AGG 0.409618 5_1:+70491292 None:intergenic
AAGTAGCATACCTGTAGTTA+TGG 0.444576 5_1:+70490366 None:intergenic
CCTTCATTATTTCCTTACTT+AGG 0.451421 5_1:-70491183 Msa0746850:five_prime_UTR
ATTTAGCAGGAACTCGAGTC+AGG 0.458225 5_1:-70490435 Msa0746850:CDS
TTTCTCTCTCTTGGAAACAT+AGG 0.462677 5_1:+70491340 None:intergenic
GGTTTCTTCAATTACCAAGT+TGG 0.482493 5_1:-70491072 Msa0746850:five_prime_UTR
TAAAGACAAAGTCCTAAGTA+AGG 0.483982 5_1:+70491171 None:intergenic
GAAGGAAGTAAAAGAAAGTG+AGG 0.500585 5_1:+70491201 None:intergenic
CAAGACATTGTGACAGGGCA+AGG 0.524347 5_1:+70491279 None:intergenic
GCAGGAACTCGAGTCAGGTT+AGG 0.539731 5_1:-70490430 Msa0746850:CDS
GTAGAACAAGACATTGTGAC+AGG 0.541939 5_1:+70491273 None:intergenic
CCTAAGTAAGGAAATAATGA+AGG 0.542678 5_1:+70491183 None:intergenic
TTATAGATGTCCATAACTAC+AGG 0.550251 5_1:-70490376 None:intergenic
AATGTACAGAGAAATTTAGC+AGG 0.552127 5_1:-70490448 Msa0746850:intron
TGTACTTAATGAAGCTCTCA+TGG 0.553658 5_1:-70490881 Msa0746850:intron
AGGGCAAGGAAAGAAATAAA+GGG 0.557287 5_1:+70491293 None:intergenic
TGAGGACGCTACTCAACAAA+GGG 0.557372 5_1:-70490814 Msa0746850:CDS
GTGGCTTGGAATACAGAAGC+AGG 0.576308 5_1:-70490609 Msa0746850:CDS
TGCTGTTGTAGCAGAGAACA+AGG 0.578610 5_1:-70491364 Msa0746850:five_prime_UTR
CTGAGGACGCTACTCAACAA+AGG 0.588845 5_1:-70490815 Msa0746850:CDS
TTTCCTCAGAGTTACCAACT+TGG 0.605370 5_1:+70491058 None:intergenic
GGACATCTATAATTCTAGGA+TGG 0.608490 5_1:+70490387 None:intergenic
CGAGTCAGGTTAGGCGAGCG+AGG 0.613788 5_1:-70490421 Msa0746850:CDS
CTATAATTCTAGGATGGTCA+AGG 0.617072 5_1:+70490393 None:intergenic
AAGGAAGTAAAAGAAAGTGA+GGG 0.623001 5_1:+70491202 None:intergenic
GACGCTACTCAACAAAGGGA+TGG 0.637949 5_1:-70490810 Msa0746850:CDS
TGAGAATACCAAGAAAAGCA+AGG 0.646032 5_1:-70490984 Msa0746850:intron
TTACCAAGTTGGTAACTCTG+AGG 0.681107 5_1:-70491061 Msa0746850:five_prime_UTR
CAACATCAAATGCAAAACTG+AGG 0.684800 5_1:-70490832 Msa0746850:CDS
GCAAGGAAAGAAATAAAGGG+AGG 0.723683 5_1:+70491296 None:intergenic
TAGAACAAGACATTGTGACA+GGG 0.733705 5_1:+70491274 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAGTGTTGAATTTAATAA+TGG + chr5_1:70490516-70490535 None:intergenic 15.0%
!! TATTAAATTCAACACTTTAA+AGG - chr5_1:70490517-70490536 Msa0746850:intron 15.0%
!! ATTAAATTCAACACTTTAAA+GGG - chr5_1:70490518-70490537 Msa0746850:intron 15.0%
!!! TTTTTTATGAACAAAATCAA+AGG - chr5_1:70491016-70491035 Msa0746850:five_prime_UTR 15.0%
!!! ATCATTTTCAAATGAAAATA+AGG + chr5_1:70491245-70491264 None:intergenic 15.0%
!!! TAAAGTGTTGAATTTAATAA+TGG + chr5_1:70490516-70490535 None:intergenic 15.0%
!! TATTAAATTCAACACTTTAA+AGG - chr5_1:70490517-70490536 Msa0746850:intron 15.0%
!! ATTAAATTCAACACTTTAAA+GGG - chr5_1:70490518-70490537 Msa0746850:intron 15.0%
!!! TTTTTTATGAACAAAATCAA+AGG - chr5_1:70491016-70491035 Msa0746850:five_prime_UTR 15.0%
!!! ATCATTTTCAAATGAAAATA+AGG + chr5_1:70491245-70491264 None:intergenic 15.0%
!!! TTTGACTGTTTTTATGTGTT+TGG - chr5_1:70490847-70490866 Msa0746850:CDS 25.0%
!! TGAAAATAAGGCATTTCAAT+TGG + chr5_1:70491233-70491252 None:intergenic 25.0%
! TTATGGACATCTATAATTCT+AGG + chr5_1:70491371-70491390 None:intergenic 25.0%
!!! TTTGACTGTTTTTATGTGTT+TGG - chr5_1:70490847-70490866 Msa0746850:CDS 25.0%
!! TGAAAATAAGGCATTTCAAT+TGG + chr5_1:70491233-70491252 None:intergenic 25.0%
! TTATGGACATCTATAATTCT+AGG + chr5_1:70491371-70491390 None:intergenic 25.0%
AAGGAAGTAAAAGAAAGTGA+GGG + chr5_1:70490552-70490571 None:intergenic 30.0%
CCTAAGTAAGGAAATAATGA+AGG + chr5_1:70490571-70490590 None:intergenic 30.0%
CCTTCATTATTTCCTTACTT+AGG - chr5_1:70490568-70490587 Msa0746850:CDS 30.0%
TAAAGACAAAGTCCTAAGTA+AGG + chr5_1:70490583-70490602 None:intergenic 30.0%
AGAAGAGAAAAACAAGAAGA+AGG + chr5_1:70490630-70490649 None:intergenic 30.0%
!! AAAGCAAAAAGTGTTGAGTT+TGG - chr5_1:70490658-70490677 Msa0746850:intron 30.0%
!! GTAAAAAACCTTGCTTTTCT+TGG + chr5_1:70490778-70490797 None:intergenic 30.0%
! TGAAACATGTTTCCTTTTTC+AGG - chr5_1:70491117-70491136 Msa0746850:five_prime_UTR 30.0%
ACAATCAAAAAGAGCAAAAC+AGG - chr5_1:70491192-70491211 Msa0746850:five_prime_UTR 30.0%
TCTCTGTACATTACAATTGA+GGG + chr5_1:70491295-70491314 None:intergenic 30.0%
TTCTCTGTACATTACAATTG+AGG + chr5_1:70491296-70491315 None:intergenic 30.0%
AATGTACAGAGAAATTTAGC+AGG - chr5_1:70491303-70491322 Msa0746850:five_prime_UTR 30.0%
AAGGAAGTAAAAGAAAGTGA+GGG + chr5_1:70490552-70490571 None:intergenic 30.0%
CCTAAGTAAGGAAATAATGA+AGG + chr5_1:70490571-70490590 None:intergenic 30.0%
CCTTCATTATTTCCTTACTT+AGG - chr5_1:70490568-70490587 Msa0746850:CDS 30.0%
TAAAGACAAAGTCCTAAGTA+AGG + chr5_1:70490583-70490602 None:intergenic 30.0%
AGAAGAGAAAAACAAGAAGA+AGG + chr5_1:70490630-70490649 None:intergenic 30.0%
!! AAAGCAAAAAGTGTTGAGTT+TGG - chr5_1:70490658-70490677 Msa0746850:intron 30.0%
!! GTAAAAAACCTTGCTTTTCT+TGG + chr5_1:70490778-70490797 None:intergenic 30.0%
! TGAAACATGTTTCCTTTTTC+AGG - chr5_1:70491117-70491136 Msa0746850:five_prime_UTR 30.0%
ACAATCAAAAAGAGCAAAAC+AGG - chr5_1:70491192-70491211 Msa0746850:five_prime_UTR 30.0%
TCTCTGTACATTACAATTGA+GGG + chr5_1:70491295-70491314 None:intergenic 30.0%
TTCTCTGTACATTACAATTG+AGG + chr5_1:70491296-70491315 None:intergenic 30.0%
AATGTACAGAGAAATTTAGC+AGG - chr5_1:70491303-70491322 Msa0746850:five_prime_UTR 30.0%
TTTCTCTCTCTTGGAAACAT+AGG + chr5_1:70490414-70490433 None:intergenic 35.0%
AGGGCAAGGAAAGAAATAAA+GGG + chr5_1:70490461-70490480 None:intergenic 35.0%
TAGAACAAGACATTGTGACA+GGG + chr5_1:70490480-70490499 None:intergenic 35.0%
GAAGGAAGTAAAAGAAAGTG+AGG + chr5_1:70490553-70490572 None:intergenic 35.0%
AGAGAAAAACAAGAAGAAGG+TGG + chr5_1:70490627-70490646 None:intergenic 35.0%
GGTTTCTTCAATTACCAAGT+TGG - chr5_1:70490679-70490698 Msa0746850:intron 35.0%
!! GAGGAAAAAAAGCATTCTTG+AGG - chr5_1:70490709-70490728 Msa0746850:intron 35.0%
!! GAAAAAAAGCATTCTTGAGG+AGG - chr5_1:70490712-70490731 Msa0746850:intron 35.0%
TGAGAATACCAAGAAAAGCA+AGG - chr5_1:70490767-70490786 Msa0746850:intron 35.0%
TGTACTTAATGAAGCTCTCA+TGG - chr5_1:70490870-70490889 Msa0746850:CDS 35.0%
CAACATCAAATGCAAAACTG+AGG - chr5_1:70490919-70490938 Msa0746850:intron 35.0%
ACCAAGATGCAAATGCAAAA+GGG - chr5_1:70491040-70491059 Msa0746850:five_prime_UTR 35.0%
!!! AACATGTTTCCTTTTTCAGG+AGG - chr5_1:70491120-70491139 Msa0746850:five_prime_UTR 35.0%
!! TTGCTCTTTTTGATTGTGCT+TGG + chr5_1:70491189-70491208 None:intergenic 35.0%
!! CTATAATTCTAGGATGGTCA+AGG + chr5_1:70491361-70491380 None:intergenic 35.0%
! GGACATCTATAATTCTAGGA+TGG + chr5_1:70491367-70491386 None:intergenic 35.0%
TTTCTCTCTCTTGGAAACAT+AGG + chr5_1:70490414-70490433 None:intergenic 35.0%
AGGGCAAGGAAAGAAATAAA+GGG + chr5_1:70490461-70490480 None:intergenic 35.0%
TAGAACAAGACATTGTGACA+GGG + chr5_1:70490480-70490499 None:intergenic 35.0%
GAAGGAAGTAAAAGAAAGTG+AGG + chr5_1:70490553-70490572 None:intergenic 35.0%
AGAGAAAAACAAGAAGAAGG+TGG + chr5_1:70490627-70490646 None:intergenic 35.0%
GGTTTCTTCAATTACCAAGT+TGG - chr5_1:70490679-70490698 Msa0746850:intron 35.0%
!! GAGGAAAAAAAGCATTCTTG+AGG - chr5_1:70490709-70490728 Msa0746850:intron 35.0%
!! GAAAAAAAGCATTCTTGAGG+AGG - chr5_1:70490712-70490731 Msa0746850:intron 35.0%
TGAGAATACCAAGAAAAGCA+AGG - chr5_1:70490767-70490786 Msa0746850:intron 35.0%
TGTACTTAATGAAGCTCTCA+TGG - chr5_1:70490870-70490889 Msa0746850:CDS 35.0%
CAACATCAAATGCAAAACTG+AGG - chr5_1:70490919-70490938 Msa0746850:intron 35.0%
ACCAAGATGCAAATGCAAAA+GGG - chr5_1:70491040-70491059 Msa0746850:five_prime_UTR 35.0%
!!! AACATGTTTCCTTTTTCAGG+AGG - chr5_1:70491120-70491139 Msa0746850:five_prime_UTR 35.0%
!! TTGCTCTTTTTGATTGTGCT+TGG + chr5_1:70491189-70491208 None:intergenic 35.0%
!! CTATAATTCTAGGATGGTCA+AGG + chr5_1:70491361-70491380 None:intergenic 35.0%
! GGACATCTATAATTCTAGGA+TGG + chr5_1:70491367-70491386 None:intergenic 35.0%
GTGTTTCAGTTTCTCTCTCT+TGG + chr5_1:70490423-70490442 None:intergenic 40.0%
GCAAGGAAAGAAATAAAGGG+AGG + chr5_1:70490458-70490477 None:intergenic 40.0%
CAGGGCAAGGAAAGAAATAA+AGG + chr5_1:70490462-70490481 None:intergenic 40.0%
GTAGAACAAGACATTGTGAC+AGG + chr5_1:70490481-70490500 None:intergenic 40.0%
!! TTACCAAGTTGGTAACTCTG+AGG - chr5_1:70490690-70490709 Msa0746850:intron 40.0%
TTTCCTCAGAGTTACCAACT+TGG + chr5_1:70490696-70490715 None:intergenic 40.0%
GCTCTCATGGTCAAAGAAAA+TGG - chr5_1:70490883-70490902 Msa0746850:intron 40.0%
CACCAAGATGCAAATGCAAA+AGG - chr5_1:70491039-70491058 Msa0746850:five_prime_UTR 40.0%
! ACCCTTTTGCATTTGCATCT+TGG + chr5_1:70491044-70491063 None:intergenic 40.0%
!!! ATGTTTCCTTTTTCAGGAGG+TGG - chr5_1:70491123-70491142 Msa0746850:five_prime_UTR 40.0%
CTGCTACAACAGCAAAGTAT+CGG + chr5_1:70490381-70490400 None:intergenic 40.0%
GTGTTTCAGTTTCTCTCTCT+TGG + chr5_1:70490423-70490442 None:intergenic 40.0%
GCAAGGAAAGAAATAAAGGG+AGG + chr5_1:70490458-70490477 None:intergenic 40.0%
CAGGGCAAGGAAAGAAATAA+AGG + chr5_1:70490462-70490481 None:intergenic 40.0%
GTAGAACAAGACATTGTGAC+AGG + chr5_1:70490481-70490500 None:intergenic 40.0%
!! TTACCAAGTTGGTAACTCTG+AGG - chr5_1:70490690-70490709 Msa0746850:intron 40.0%
TTTCCTCAGAGTTACCAACT+TGG + chr5_1:70490696-70490715 None:intergenic 40.0%
GCTCTCATGGTCAAAGAAAA+TGG - chr5_1:70490883-70490902 Msa0746850:intron 40.0%
CACCAAGATGCAAATGCAAA+AGG - chr5_1:70491039-70491058 Msa0746850:five_prime_UTR 40.0%
! ACCCTTTTGCATTTGCATCT+TGG + chr5_1:70491044-70491063 None:intergenic 40.0%
!!! ATGTTTCCTTTTTCAGGAGG+TGG - chr5_1:70491123-70491142 Msa0746850:five_prime_UTR 40.0%
TGCTGTTGTAGCAGAGAACA+AGG - chr5_1:70490387-70490406 Msa0746850:CDS 45.0%
TGAGGACGCTACTCAACAAA+GGG - chr5_1:70490937-70490956 Msa0746850:intron 45.0%
!! CAAAGGGATGGTTTTGCTTC+TGG - chr5_1:70490953-70490972 Msa0746850:intron 45.0%
ATTTAGCAGGAACTCGAGTC+AGG - chr5_1:70491316-70491335 Msa0746850:five_prime_UTR 45.0%
TGCTGTTGTAGCAGAGAACA+AGG - chr5_1:70490387-70490406 Msa0746850:CDS 45.0%
TGAGGACGCTACTCAACAAA+GGG - chr5_1:70490937-70490956 Msa0746850:intron 45.0%
!! CAAAGGGATGGTTTTGCTTC+TGG - chr5_1:70490953-70490972 Msa0746850:intron 45.0%
ATTTAGCAGGAACTCGAGTC+AGG - chr5_1:70491316-70491335 Msa0746850:five_prime_UTR 45.0%
!!! AAAATGAATTTTTAATTTAA+AGG + chr5_1:70491000-70491019 None:intergenic 5.0%
!!! AAAATGAATTTTTAATTTAA+AGG + chr5_1:70491000-70491019 None:intergenic 5.0%
CAAGACATTGTGACAGGGCA+AGG + chr5_1:70490475-70490494 None:intergenic 50.0%
CTGAGGACGCTACTCAACAA+AGG - chr5_1:70490936-70490955 Msa0746850:intron 50.0%
GACGCTACTCAACAAAGGGA+TGG - chr5_1:70490941-70490960 Msa0746850:intron 50.0%
!! AGGGATGGTTTTGCTTCTGG+AGG - chr5_1:70490956-70490975 Msa0746850:intron 50.0%
!!! TCCTTTTTCAGGAGGTGGCT+TGG - chr5_1:70491128-70491147 Msa0746850:five_prime_UTR 50.0%
TCCAAGCCACCTCCTGAAAA+AGG + chr5_1:70491132-70491151 None:intergenic 50.0%
! GTGGCTTGGAATACAGAAGC+AGG - chr5_1:70491142-70491161 Msa0746850:five_prime_UTR 50.0%
CAAGACATTGTGACAGGGCA+AGG + chr5_1:70490475-70490494 None:intergenic 50.0%
CTGAGGACGCTACTCAACAA+AGG - chr5_1:70490936-70490955 Msa0746850:intron 50.0%
GACGCTACTCAACAAAGGGA+TGG - chr5_1:70490941-70490960 Msa0746850:intron 50.0%
!! AGGGATGGTTTTGCTTCTGG+AGG - chr5_1:70490956-70490975 Msa0746850:intron 50.0%
!!! TCCTTTTTCAGGAGGTGGCT+TGG - chr5_1:70491128-70491147 Msa0746850:five_prime_UTR 50.0%
TCCAAGCCACCTCCTGAAAA+AGG + chr5_1:70491132-70491151 None:intergenic 50.0%
! GTGGCTTGGAATACAGAAGC+AGG - chr5_1:70491142-70491161 Msa0746850:five_prime_UTR 50.0%
GCAGGAACTCGAGTCAGGTT+AGG - chr5_1:70491321-70491340 Msa0746850:five_prime_UTR 55.0%
GCAGGAACTCGAGTCAGGTT+AGG - chr5_1:70491321-70491340 Msa0746850:five_prime_UTR 55.0%
CGAGTCAGGTTAGGCGAGCG+AGG - chr5_1:70491330-70491349 Msa0746850:five_prime_UTR 65.0%
CGAGTCAGGTTAGGCGAGCG+AGG - chr5_1:70491330-70491349 Msa0746850:five_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 70490379 70491394 70490379 ID=Msa0746850;Name=Msa0746850
chr5_1 mRNA 70490379 70491394 70490379 ID=Msa0746850-mRNA-1;Parent=Msa0746850;Name=Msa0746850-mRNA-1;_AED=0.00;_eAED=0.00;_QI=380|1|1|1|1|0.75|4|0|94
chr5_1 exon 70490379 70490461 70490379 ID=Msa0746850-mRNA-1:exon:20725;Parent=Msa0746850-mRNA-1
chr5_1 exon 70490560 70490634 70490560 ID=Msa0746850-mRNA-1:exon:20724;Parent=Msa0746850-mRNA-1
chr5_1 exon 70490796 70490889 70490796 ID=Msa0746850-mRNA-1:exon:20723;Parent=Msa0746850-mRNA-1
chr5_1 exon 70490985 70491394 70490985 ID=Msa0746850-mRNA-1:exon:20722;Parent=Msa0746850-mRNA-1
chr5_1 five_prime_UTR 70491015 70491394 70491015 ID=Msa0746850-mRNA-1:five_prime_utr;Parent=Msa0746850-mRNA-1
chr5_1 CDS 70490985 70491014 70490985 ID=Msa0746850-mRNA-1:cds;Parent=Msa0746850-mRNA-1
chr5_1 CDS 70490796 70490889 70490796 ID=Msa0746850-mRNA-1:cds;Parent=Msa0746850-mRNA-1
chr5_1 CDS 70490560 70490634 70490560 ID=Msa0746850-mRNA-1:cds;Parent=Msa0746850-mRNA-1
chr5_1 CDS 70490379 70490461 70490379 ID=Msa0746850-mRNA-1:cds;Parent=Msa0746850-mRNA-1
Gene Sequence

>Msa0746850

ATGAGAGATGAGAATACCAAGAAAAGCAAGCTCTCATGGTCAAAGAAAATGGTCAGAAAATTCTTCAACATCAAATGCAAAACTGAGGACGCTACTCAACAAAGGGATGGTTTTGCTTCTGGAGGAGGTGGCTTGGAATACAGAAGCAGGAGTAGCTTGTCTGAGAGAGAGCCAAGCACAATCAAAAAGAGCAAAACAGAGAAATTTAGCAGGAACTCGAGTCAGGTTAGGCGAGCGAGGATGAACCTTGACCATCCTAGAATTATAGATGTCCATAACTAC
Protein sequence

>Msa0746850

MRDENTKKSKLSWSKKMVRKFFNIKCKTEDATQQRDGFASGGGGLEYRSRSSLSEREPSTIKKSKTEKFSRNSSQVRRARMNLDHPRIIDVHNY