AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0789600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789600 MtrunA17_Chr1g0207551 36.364 165 81 2 78 218 33 197 4.35e-26 105
Msa0789600 MtrunA17_Chr2g0329031 33.523 176 86 4 67 218 2 170 7.23e-22 93.2
Msa0789600 MtrunA17_Chr5g0448761 30.233 172 89 4 78 218 59 230 3.39e-18 82.8
Msa0789600 MtrunA17_Chr3g0080351 28.333 180 67 4 78 218 75 231 3.61e-17 79.7
Msa0789600 MtrunA17_Chr6g0451441 28.500 200 121 5 40 218 49 247 3.58e-14 70.9
Msa0789600 MtrunA17_Chr2g0287651 24.468 188 112 4 58 215 53 240 1.04e-13 69.7
Msa0789600 MtrunA17_Chr7g0258861 26.220 164 94 3 78 214 9 172 1.98e-12 65.1
Msa0789600 MtrunA17_Chr5g0440451 28.571 133 76 3 39 154 1 131 7.19e-12 64.3
Msa0789600 MtrunA17_Chr7g0233911 33.793 145 62 6 49 162 2 143 1.97e-11 61.2
Msa0789600 MtrunA17_Chr2g0324011 26.627 169 94 5 78 218 9 175 2.43e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789600 AT4G15090.1 35.023 217 104 6 39 218 1 217 8.49e-29 114
Msa0789600 AT4G15090.5 35.023 217 104 6 39 218 1 217 8.49e-29 114
Msa0789600 AT4G15090.3 35.023 217 104 6 39 218 1 217 8.49e-29 114
Msa0789600 AT4G15090.2 35.023 217 104 6 39 218 1 217 8.49e-29 114
Msa0789600 AT4G15090.4 35.023 217 104 6 39 218 1 217 8.49e-29 114
Msa0789600 AT4G38180.1 31.148 183 94 4 66 218 62 242 2.16e-21 92.4
Msa0789600 AT3G22170.2 27.273 242 101 7 30 218 7 226 1.13e-19 87.4
Msa0789600 AT3G22170.1 27.273 242 101 7 30 218 7 226 1.13e-19 87.4
Msa0789600 AT1G76320.2 31.875 160 79 4 83 218 1 154 1.16e-16 78.6
Msa0789600 AT1G76320.1 31.875 160 79 4 83 218 1 154 1.21e-16 78.6
Msa0789600 AT1G76320.4 31.875 160 79 4 83 218 1 154 1.21e-16 78.6
Msa0789600 AT1G76320.3 31.875 160 79 4 83 218 1 154 1.70e-16 78.2
Msa0789600 AT2G32250.5 37.500 112 45 3 82 170 41 150 6.23e-14 70.5
Msa0789600 AT2G32250.2 37.500 112 45 3 82 170 41 150 6.61e-14 70.5
Msa0789600 AT2G32250.4 37.500 112 45 3 82 170 41 150 6.61e-14 70.5
Msa0789600 AT2G32250.6 37.500 112 45 3 82 170 41 150 6.80e-14 70.5
Msa0789600 AT2G32250.1 37.500 112 45 3 82 170 41 150 6.80e-14 70.5
Msa0789600 AT2G32250.3 37.500 112 45 3 82 170 41 150 6.80e-14 70.5
Msa0789600 AT2G32250.8 36.937 111 45 3 83 170 1 109 5.13e-13 67.8
Msa0789600 AT2G32250.7 36.937 111 45 3 83 170 1 109 5.23e-13 67.8

Find 38 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGAAATATAGGAATTAA+TGG 0.248279 5_2:-78915902 Msa0789600:intron
CACTCTGCTATCATTCTTAA+AGG 0.277937 5_2:-78916170 Msa0789600:CDS
TTCATATCCTCCATATTGTT+TGG 0.293868 5_2:+78915354 None:intergenic
AAATCTGCGTCGTTGTTTAA+AGG 0.297168 5_2:-78915584 Msa0789600:CDS
GCCACTCTGGCCAAACAATA+TGG 0.314518 5_2:-78915364 Msa0789600:CDS
TCAAATTTCATTCCAATGTA+TGG 0.346422 5_2:+78915772 None:intergenic
GAGTAAAGTGTAATGAAAAT+TGG 0.367197 5_2:-78916272 None:intergenic
ATCAGAAATCATTTAGATAT+AGG 0.417224 5_2:-78915307 Msa0789600:CDS
CATTATTTCCTTTGCCATAG+AGG 0.426978 5_2:-78915457 Msa0789600:CDS
GAATTAATGGAAGTTGTTGA+TGG 0.448629 5_2:-78915889 Msa0789600:CDS
AATGATGACAATGTTATTGA+TGG 0.455364 5_2:-78915865 Msa0789600:CDS
AGGAAATAATGTGCATATGC+TGG 0.467902 5_2:+78915469 None:intergenic
AGCGTGTGTTGAAGGGAGTT+TGG 0.475218 5_2:+78916232 None:intergenic
TGCTATCATTCTTAAAGGTA+TGG 0.477048 5_2:-78916165 Msa0789600:intron
TGTGTGTGAGCGTGTGTTGA+AGG 0.481794 5_2:+78916224 None:intergenic
ACTTATGCTCGCACAAGATA+CGG 0.484780 5_2:-78915631 Msa0789600:CDS
AGAATGATTCATGTACGGTT+GGG 0.505397 5_2:-78915810 Msa0789600:CDS
GTGTGTGAGCGTGTGTTGAA+GGG 0.519552 5_2:+78916225 None:intergenic
TATTGATTCCTCTATGGCAA+AGG 0.524300 5_2:+78915449 None:intergenic
ACTACTGTAACATAAATCTT+CGG 0.535461 5_2:+78916194 None:intergenic
CTTATGCTCGCACAAGATAC+GGG 0.542745 5_2:-78915630 Msa0789600:CDS
AATTAATGGAAGTTGTTGAT+GGG 0.547188 5_2:-78915888 Msa0789600:CDS
ATTGAAACTATGCAAGATGT+TGG 0.548761 5_2:-78915409 Msa0789600:CDS
TCCATATTGTTTGGCCAGAG+TGG 0.548986 5_2:+78915363 None:intergenic
GAGAATGATTCATGTACGGT+TGG 0.560679 5_2:-78915811 Msa0789600:CDS
CTAATGAAAGAGCCATACAT+TGG 0.562140 5_2:-78915784 Msa0789600:CDS
AAGCAAAATTTATGCCACTC+TGG 0.565072 5_2:-78915377 Msa0789600:CDS
TCTGCGTCGTTGTTTAAAGG+TGG 0.568390 5_2:-78915581 Msa0789600:CDS
TTGTTTAAAGGTGGAATGTG+AGG 0.581351 5_2:-78915572 Msa0789600:CDS
TATGGAGGATATGAAAACAT+TGG 0.602190 5_2:-78915346 Msa0789600:CDS
TGTTGAGAATGATTCATGTA+CGG 0.602674 5_2:-78915815 Msa0789600:CDS
ATGATTCATGTACGGTTGGG+AGG 0.609038 5_2:-78915807 Msa0789600:CDS
GAAATCATTTAGATATAGGT+CGG 0.612130 5_2:-78915303 Msa0789600:CDS
GCACAAGATACGGGAAGACG+CGG 0.628660 5_2:-78915621 Msa0789600:CDS
ATGATGACAATGTTATTGAT+GGG 0.630031 5_2:-78915864 Msa0789600:CDS
ACTGTAACATAAATCTTCGG+TGG 0.635445 5_2:+78916197 None:intergenic
CACAAGATACGGGAAGACGC+GGG 0.645645 5_2:-78915620 Msa0789600:CDS
ACTCTGGCCAAACAATATGG+AGG 0.695583 5_2:-78915361 Msa0789600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGGTAAATATTACTATAAAA+TGG - chr5_2:78915412-78915431 Msa0789600:CDS 15.0%
!!! CTTATTTTTTTAGAAAAAGT+TGG + chr5_2:78915556-78915575 None:intergenic 15.0%
!!! GTTTTAATCTTTATTTTACT+CGG - chr5_2:78915575-78915594 Msa0789600:CDS 15.0%
!!! ACAGTTATAATTTGAAATAT+AGG - chr5_2:78915646-78915665 Msa0789600:intron 15.0%
!!! ATTTGAAATATAGGAATTAA+TGG - chr5_2:78915655-78915674 Msa0789600:intron 15.0%
!! TGGTAAATATTACTATAAAA+TGG - chr5_2:78915412-78915431 Msa0789600:CDS 15.0%
!!! CTTATTTTTTTAGAAAAAGT+TGG + chr5_2:78915556-78915575 None:intergenic 15.0%
!!! GTTTTAATCTTTATTTTACT+CGG - chr5_2:78915575-78915594 Msa0789600:CDS 15.0%
!!! ACAGTTATAATTTGAAATAT+AGG - chr5_2:78915646-78915665 Msa0789600:intron 15.0%
!!! ATTTGAAATATAGGAATTAA+TGG - chr5_2:78915655-78915674 Msa0789600:intron 15.0%
!! TAAAATGGAATAGAATTTGA+TGG - chr5_2:78915427-78915446 Msa0789600:CDS 20.0%
!! TAATATAAGCACTATATATG+TGG - chr5_2:78915469-78915488 Msa0789600:CDS 20.0%
!! CGTATTAAAAAAAATTGTGA+TGG - chr5_2:78916016-78916035 Msa0789600:intron 20.0%
!!! AAAAAAATTGTGATGGAAAA+TGG - chr5_2:78916023-78916042 Msa0789600:intron 20.0%
!! ATCAGAAATCATTTAGATAT+AGG - chr5_2:78916250-78916269 Msa0789600:CDS 20.0%
!! TAAAATGGAATAGAATTTGA+TGG - chr5_2:78915427-78915446 Msa0789600:CDS 20.0%
!! TAATATAAGCACTATATATG+TGG - chr5_2:78915469-78915488 Msa0789600:CDS 20.0%
!! CGTATTAAAAAAAATTGTGA+TGG - chr5_2:78916016-78916035 Msa0789600:intron 20.0%
!!! AAAAAAATTGTGATGGAAAA+TGG - chr5_2:78916023-78916042 Msa0789600:intron 20.0%
!! ATCAGAAATCATTTAGATAT+AGG - chr5_2:78916250-78916269 Msa0789600:CDS 20.0%
! ACTACTGTAACATAAATCTT+CGG + chr5_2:78915366-78915385 None:intergenic 25.0%
! AATTAATGGAAGTTGTTGAT+GGG - chr5_2:78915669-78915688 Msa0789600:intron 25.0%
! AATGATGACAATGTTATTGA+TGG - chr5_2:78915692-78915711 Msa0789600:intron 25.0%
! ATGATGACAATGTTATTGAT+GGG - chr5_2:78915693-78915712 Msa0789600:intron 25.0%
! TCAAATTTCATTCCAATGTA+TGG + chr5_2:78915788-78915807 None:intergenic 25.0%
! GAAATCATTTAGATATAGGT+CGG - chr5_2:78916254-78916273 Msa0789600:CDS 25.0%
! ACTACTGTAACATAAATCTT+CGG + chr5_2:78915366-78915385 None:intergenic 25.0%
! AATTAATGGAAGTTGTTGAT+GGG - chr5_2:78915669-78915688 Msa0789600:intron 25.0%
! AATGATGACAATGTTATTGA+TGG - chr5_2:78915692-78915711 Msa0789600:intron 25.0%
! ATGATGACAATGTTATTGAT+GGG - chr5_2:78915693-78915712 Msa0789600:intron 25.0%
! TCAAATTTCATTCCAATGTA+TGG + chr5_2:78915788-78915807 None:intergenic 25.0%
! GAAATCATTTAGATATAGGT+CGG - chr5_2:78916254-78916273 Msa0789600:CDS 25.0%
TGCTATCATTCTTAAAGGTA+TGG - chr5_2:78915392-78915411 Msa0789600:CDS 30.0%
GAATTAATGGAAGTTGTTGA+TGG - chr5_2:78915668-78915687 Msa0789600:intron 30.0%
TGTTGAGAATGATTCATGTA+CGG - chr5_2:78915742-78915761 Msa0789600:CDS 30.0%
TAAAATTAGTCGTCGTTCAA+AGG - chr5_2:78915872-78915891 Msa0789600:CDS 30.0%
!!! GAGTTTTATTGATTCCTCTA+TGG + chr5_2:78916117-78916136 None:intergenic 30.0%
ATTGAAACTATGCAAGATGT+TGG - chr5_2:78916148-78916167 Msa0789600:intron 30.0%
TTCATATCCTCCATATTGTT+TGG + chr5_2:78916206-78916225 None:intergenic 30.0%
TATGGAGGATATGAAAACAT+TGG - chr5_2:78916211-78916230 Msa0789600:CDS 30.0%
TGCTATCATTCTTAAAGGTA+TGG - chr5_2:78915392-78915411 Msa0789600:CDS 30.0%
GAATTAATGGAAGTTGTTGA+TGG - chr5_2:78915668-78915687 Msa0789600:intron 30.0%
TGTTGAGAATGATTCATGTA+CGG - chr5_2:78915742-78915761 Msa0789600:CDS 30.0%
TAAAATTAGTCGTCGTTCAA+AGG - chr5_2:78915872-78915891 Msa0789600:CDS 30.0%
!!! GAGTTTTATTGATTCCTCTA+TGG + chr5_2:78916117-78916136 None:intergenic 30.0%
ATTGAAACTATGCAAGATGT+TGG - chr5_2:78916148-78916167 Msa0789600:intron 30.0%
TTCATATCCTCCATATTGTT+TGG + chr5_2:78916206-78916225 None:intergenic 30.0%
TATGGAGGATATGAAAACAT+TGG - chr5_2:78916211-78916230 Msa0789600:CDS 30.0%
ACTGTAACATAAATCTTCGG+TGG + chr5_2:78915363-78915382 None:intergenic 35.0%
CACTCTGCTATCATTCTTAA+AGG - chr5_2:78915387-78915406 Msa0789600:CDS 35.0%
AGAATGATTCATGTACGGTT+GGG - chr5_2:78915747-78915766 Msa0789600:CDS 35.0%
CTAATGAAAGAGCCATACAT+TGG - chr5_2:78915773-78915792 Msa0789600:CDS 35.0%
AAATCTGCGTCGTTGTTTAA+AGG - chr5_2:78915973-78915992 Msa0789600:intron 35.0%
TTGTTTAAAGGTGGAATGTG+AGG - chr5_2:78915985-78916004 Msa0789600:intron 35.0%
CTGGAAAAAGCTCATGATTA+TGG + chr5_2:78916072-78916091 None:intergenic 35.0%
AGGAAATAATGTGCATATGC+TGG + chr5_2:78916091-78916110 None:intergenic 35.0%
CATTATTTCCTTTGCCATAG+AGG - chr5_2:78916100-78916119 Msa0789600:intron 35.0%
!! TATTGATTCCTCTATGGCAA+AGG + chr5_2:78916111-78916130 None:intergenic 35.0%
AAGCAAAATTTATGCCACTC+TGG - chr5_2:78916180-78916199 Msa0789600:CDS 35.0%
ACTGTAACATAAATCTTCGG+TGG + chr5_2:78915363-78915382 None:intergenic 35.0%
CACTCTGCTATCATTCTTAA+AGG - chr5_2:78915387-78915406 Msa0789600:CDS 35.0%
AGAATGATTCATGTACGGTT+GGG - chr5_2:78915747-78915766 Msa0789600:CDS 35.0%
CTAATGAAAGAGCCATACAT+TGG - chr5_2:78915773-78915792 Msa0789600:CDS 35.0%
AAATCTGCGTCGTTGTTTAA+AGG - chr5_2:78915973-78915992 Msa0789600:intron 35.0%
TTGTTTAAAGGTGGAATGTG+AGG - chr5_2:78915985-78916004 Msa0789600:intron 35.0%
CTGGAAAAAGCTCATGATTA+TGG + chr5_2:78916072-78916091 None:intergenic 35.0%
AGGAAATAATGTGCATATGC+TGG + chr5_2:78916091-78916110 None:intergenic 35.0%
CATTATTTCCTTTGCCATAG+AGG - chr5_2:78916100-78916119 Msa0789600:intron 35.0%
!! TATTGATTCCTCTATGGCAA+AGG + chr5_2:78916111-78916130 None:intergenic 35.0%
AAGCAAAATTTATGCCACTC+TGG - chr5_2:78916180-78916199 Msa0789600:CDS 35.0%
GAGAATGATTCATGTACGGT+TGG - chr5_2:78915746-78915765 Msa0789600:CDS 40.0%
ATTACGCTGTCTGTTGGATT+TGG - chr5_2:78915840-78915859 Msa0789600:CDS 40.0%
TTACGCTGTCTGTTGGATTT+GGG - chr5_2:78915841-78915860 Msa0789600:CDS 40.0%
ACTTATGCTCGCACAAGATA+CGG - chr5_2:78915926-78915945 Msa0789600:intron 40.0%
GAGAATGATTCATGTACGGT+TGG - chr5_2:78915746-78915765 Msa0789600:CDS 40.0%
ATTACGCTGTCTGTTGGATT+TGG - chr5_2:78915840-78915859 Msa0789600:CDS 40.0%
TTACGCTGTCTGTTGGATTT+GGG - chr5_2:78915841-78915860 Msa0789600:CDS 40.0%
ACTTATGCTCGCACAAGATA+CGG - chr5_2:78915926-78915945 Msa0789600:intron 40.0%
ATGATTCATGTACGGTTGGG+AGG - chr5_2:78915750-78915769 Msa0789600:CDS 45.0%
ACACTCATTACGCTGTCTGT+TGG - chr5_2:78915834-78915853 Msa0789600:CDS 45.0%
CTTATGCTCGCACAAGATAC+GGG - chr5_2:78915927-78915946 Msa0789600:intron 45.0%
TCTGCGTCGTTGTTTAAAGG+TGG - chr5_2:78915976-78915995 Msa0789600:intron 45.0%
TCCATATTGTTTGGCCAGAG+TGG + chr5_2:78916197-78916216 None:intergenic 45.0%
ACTCTGGCCAAACAATATGG+AGG - chr5_2:78916196-78916215 Msa0789600:CDS 45.0%
ATGATTCATGTACGGTTGGG+AGG - chr5_2:78915750-78915769 Msa0789600:CDS 45.0%
ACACTCATTACGCTGTCTGT+TGG - chr5_2:78915834-78915853 Msa0789600:CDS 45.0%
CTTATGCTCGCACAAGATAC+GGG - chr5_2:78915927-78915946 Msa0789600:intron 45.0%
TCTGCGTCGTTGTTTAAAGG+TGG - chr5_2:78915976-78915995 Msa0789600:intron 45.0%
TCCATATTGTTTGGCCAGAG+TGG + chr5_2:78916197-78916216 None:intergenic 45.0%
ACTCTGGCCAAACAATATGG+AGG - chr5_2:78916196-78916215 Msa0789600:CDS 45.0%
AGCGTGTGTTGAAGGGAGTT+TGG + chr5_2:78915328-78915347 None:intergenic 50.0%
GTGTGTGAGCGTGTGTTGAA+GGG + chr5_2:78915335-78915354 None:intergenic 50.0%
TGTGTGTGAGCGTGTGTTGA+AGG + chr5_2:78915336-78915355 None:intergenic 50.0%
! ACGACGCAGATTTTGTGCAG+TGG + chr5_2:78915966-78915985 None:intergenic 50.0%
GCCACTCTGGCCAAACAATA+TGG - chr5_2:78916193-78916212 Msa0789600:CDS 50.0%
AGCGTGTGTTGAAGGGAGTT+TGG + chr5_2:78915328-78915347 None:intergenic 50.0%
GTGTGTGAGCGTGTGTTGAA+GGG + chr5_2:78915335-78915354 None:intergenic 50.0%
TGTGTGTGAGCGTGTGTTGA+AGG + chr5_2:78915336-78915355 None:intergenic 50.0%
! ACGACGCAGATTTTGTGCAG+TGG + chr5_2:78915966-78915985 None:intergenic 50.0%
GCCACTCTGGCCAAACAATA+TGG - chr5_2:78916193-78916212 Msa0789600:CDS 50.0%
GCACAAGATACGGGAAGACG+CGG - chr5_2:78915936-78915955 Msa0789600:intron 55.0%
CACAAGATACGGGAAGACGC+GGG - chr5_2:78915937-78915956 Msa0789600:intron 55.0%
GCACAAGATACGGGAAGACG+CGG - chr5_2:78915936-78915955 Msa0789600:intron 55.0%
CACAAGATACGGGAAGACGC+GGG - chr5_2:78915937-78915956 Msa0789600:intron 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 78915297 78916282 78915297 ID=Msa0789600;Name=Msa0789600
chr5_2 mRNA 78915297 78916282 78915297 ID=Msa0789600-mRNA-1;Parent=Msa0789600;Name=Msa0789600-mRNA-1;_AED=0.31;_eAED=0.32;_QI=0|0|0|0.66|0.5|0.66|3|0|219
chr5_2 exon 78916166 78916282 78916166 ID=Msa0789600-mRNA-1:exon:23647;Parent=Msa0789600-mRNA-1
chr5_2 exon 78915732 78915911 78915732 ID=Msa0789600-mRNA-1:exon:23646;Parent=Msa0789600-mRNA-1
chr5_2 exon 78915297 78915659 78915297 ID=Msa0789600-mRNA-1:exon:23645;Parent=Msa0789600-mRNA-1
chr5_2 CDS 78916166 78916282 78916166 ID=Msa0789600-mRNA-1:cds;Parent=Msa0789600-mRNA-1
chr5_2 CDS 78915732 78915911 78915732 ID=Msa0789600-mRNA-1:cds;Parent=Msa0789600-mRNA-1
chr5_2 CDS 78915297 78915659 78915297 ID=Msa0789600-mRNA-1:cds;Parent=Msa0789600-mRNA-1
Gene Sequence

>Msa0789600

ATGAAAATTGGTATTGTCAAATTCTGTGCCAAACTCCCTTCAACACACGCTCACACACAAAAGCCACCGAAGATTTATGTTACAGTAGTGCACTCTGCTATCATTCTTAAAGGTATGGAATTAATGGAAGTTGTTGATGGGAATGATGACAATGTTATTGATGGGAATGAAGAGCAATCTTTCACTGAGATTGTTGAGAATGATTCATGTACGGTTGGGAGGCTAATGAAAGAGCCATACATTGGAATGAAATTTGATTCACAAGAAAATGCTTATTCATTCTACACTCATTACGCTTTATGCACTTATGCTCGCACAAGATACGGGAAGACGCGGGAATCCACTGCACAAAATCTGCGTCGTTGTTTAAAGGTGGAATGTGAGGCTAGCTTGCGTATTAAAAAAAATTGTGATGGAAAATGGATTGTTTACAACTTCATTAAAGACCATAATCATGAGCTTTTTCCAGCATATGCACATTATTTCCTTTGCCATAGAGGAATCAATAAAACTCAAAAGCATTGTATTGAAACTATGCAAGATGTTGGAGTGAGAACAAGCAAAATTTATGCCACTCTGGCCAAACAATATGGAGGATATGAAAACATTGGTTGTTTGCAGAAAGATATCAGAAATCATTTAGATATAGGTCGGTGTTGA

Protein sequence

>Msa0789600

MKIGIVKFCAKLPSTHAHTQKPPKIYVTVVHSAIILKGMELMEVVDGNDDNVIDGNEEQSFTEIVENDSCTVGRLMKEPYIGMKFDSQENAYSFYTHYALCTYARTRYGKTRESTAQNLRRCLKVECEASLRIKKNCDGKWIVYNFIKDHNHELFPAYAHYFLCHRGINKTQKHCIETMQDVGVRTSKIYATLAKQYGGYENIGCLQKDIRNHLDIGRC*