AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0658050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0658050 MtrunA17_Chr8g0380791 97.351 151 4 0 6 156 617 767 2.41e-103 312
Msa0658050 MtrunA17_Chr1g0180261 54.015 137 56 3 18 153 686 816 6.99e-43 150
Msa0658050 MtrunA17_Chr3g0115111 45.918 98 43 2 66 154 634 730 5.28e-23 94.4
Msa0658050 MtrunA17_Chr1g0171491 45.192 104 54 2 49 149 685 788 3.69e-22 91.7
Msa0658050 MtrunA17_Chr3g0131001 45.361 97 44 3 66 154 608 703 5.92e-21 88.2
Msa0658050 MtrunA17_Chr5g0424301 45.161 93 42 2 66 149 635 727 1.32e-20 87.4
Msa0658050 MtrunA17_Chr7g0256301 48.315 89 43 2 68 154 703 790 1.44e-20 87.4
Msa0658050 MtrunA17_Chr8g0385201 43.956 91 48 2 66 154 576 665 5.29e-19 82.8
Msa0658050 MtrunA17_Chr3g0082501 38.732 142 71 5 16 154 631 759 1.00e-15 73.2
Msa0658050 MtrunA17_Chr8g0353121 42.308 104 56 3 53 154 648 749 9.91e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0658050 AT1G10900.2 72.535 142 38 1 13 154 612 752 9.50e-68 219
Msa0658050 AT1G10900.1 72.535 142 38 1 13 154 612 752 9.50e-68 219
Msa0658050 AT1G10900.3 72.535 142 38 1 13 154 612 752 9.50e-68 219
Msa0658050 AT1G60890.1 69.014 142 43 1 13 154 627 767 7.89e-64 208
Msa0658050 AT1G60890.2 69.014 142 43 1 13 154 639 779 9.05e-64 208
Msa0658050 AT3G09920.3 52.258 155 67 5 1 154 663 811 2.77e-42 149
Msa0658050 AT3G09920.4 52.258 155 67 5 1 154 663 811 2.77e-42 149
Msa0658050 AT3G09920.2 52.258 155 67 5 1 154 663 811 2.77e-42 149
Msa0658050 AT3G09920.1 52.258 155 67 5 1 154 663 811 2.77e-42 149
Msa0658050 AT3G07960.1 41.732 127 69 4 32 154 588 713 9.89e-23 94.0
Msa0658050 AT2G41210.1 44.860 107 50 3 49 149 663 766 1.65e-22 93.2
Msa0658050 AT1G77740.2 44.231 104 51 2 52 149 646 748 2.31e-22 92.8
Msa0658050 AT1G77740.1 44.231 104 51 2 52 149 646 748 2.31e-22 92.8
Msa0658050 AT1G21980.1 42.727 110 54 3 52 154 644 751 4.25e-22 92.0
Msa0658050 AT3G56960.2 44.643 112 58 3 46 154 667 777 1.30e-21 90.5
Msa0658050 AT3G56960.1 44.643 112 58 3 46 154 667 777 1.30e-21 90.5
Msa0658050 AT2G26420.1 40.157 127 62 5 36 149 574 699 3.01e-20 86.7
Msa0658050 AT2G26420.2 37.143 140 62 5 36 149 574 713 1.95e-19 84.3
Msa0658050 AT2G26420.3 37.143 140 62 5 36 149 574 713 1.95e-19 84.3
Msa0658050 AT4G01190.1 39.326 89 47 1 66 154 312 393 1.46e-17 78.6
Msa0658050 AT4G01190.3 39.326 89 47 1 66 154 322 403 1.48e-17 78.6
Msa0658050 AT4G01190.2 39.326 89 47 1 66 154 322 403 1.48e-17 78.6
Msa0658050 AT1G01460.1 40.404 99 49 3 56 154 334 422 4.02e-17 77.4

Find 39 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACATGACACTTAATTATT+TGG 0.050932 4_3:-68087512 Msa0658050:three_prime_UTR
CATCAATTTCATGGATAAAA+AGG 0.210898 4_3:-68087776 Msa0658050:CDS
TACAGACATCACGGTATTTC+CGG 0.243562 4_3:+68087748 None:intergenic
CAAATCAATCATATACTAAA+TGG 0.293412 4_3:+68087545 None:intergenic
AATTCAAACAGCTCAATAAA+AGG 0.308780 4_3:-68087576 Msa0658050:three_prime_UTR
CACATGACACTTAATTATTT+GGG 0.310401 4_3:-68087511 Msa0658050:three_prime_UTR
TGAACGTTTCATCAATTTCA+TGG 0.329150 4_3:-68087785 Msa0658050:CDS
CTCAGATTGCCGGTGCAATT+AGG 0.361997 4_3:-68088021 Msa0658050:intron
GTACACAATCATTCATCCTT+TGG 0.396078 4_3:+68087674 None:intergenic
ACAGACATCACGGTATTTCC+GGG 0.414756 4_3:+68087749 None:intergenic
GGGAATAATAGATATACTTC+AGG 0.414956 4_3:-68087899 Msa0658050:CDS
ACGCCTGGACCTCACATTAG+AGG 0.416249 4_3:-68088235 Msa0658050:CDS
AGCTTCGTCAACGCGACGCC+TGG 0.420191 4_3:-68088250 Msa0658050:CDS
ATGAATGTTCCTCAGATTGC+CGG 0.428484 4_3:-68088031 Msa0658050:intron
ATCAAACTGCAGTGATTTGT+AGG 0.464399 4_3:+68087846 None:intergenic
GCAACTAACAACAAGCCTTT+CGG 0.464606 4_3:+68088283 None:intergenic
AAATACTCACCTTGCAGTAC+CGG 0.481918 4_3:+68088159 None:intergenic
TTTGTAATTAATTGTTCCAA+AGG 0.483454 4_3:-68087690 Msa0658050:three_prime_UTR
TCTGTTACTGATATAGTCAT+AGG 0.486890 4_3:+68087823 None:intergenic
TTATGATGTGGTACTCTACA+TGG 0.514200 4_3:-68087920 Msa0658050:CDS
CACTAGATTTACTCAAACAA+GGG 0.520368 4_3:-68088321 Msa0658050:CDS
ATCAACTTCCTTGTTACCGA+TGG 0.520731 4_3:+68088192 None:intergenic
TTCCCTCTAATGTGAGGTCC+AGG 0.521447 4_3:+68088232 None:intergenic
GGCGTCGCGTTGACGAAGCT+CGG 0.526121 4_3:+68088253 None:intergenic
CGCCTGGACCTCACATTAGA+GGG 0.534333 4_3:-68088234 Msa0658050:CDS
ATGTTTACTCCTAATTGCAC+CGG 0.562596 4_3:+68088012 None:intergenic
AGCATACTCCATCGGTAACA+AGG 0.571690 4_3:-68088200 Msa0658050:CDS
GCACTAGATTTACTCAAACA+AGG 0.574901 4_3:-68088322 Msa0658050:CDS
AATACTCACCTTGCAGTACC+GGG 0.588020 4_3:+68088160 None:intergenic
AGCAAACTAGTAGCTTGAGC+CGG 0.603192 4_3:+68087988 None:intergenic
TAGTTTGCTTCAAGAAGACA+AGG 0.625211 4_3:-68087974 Msa0658050:CDS
AATGTATTCCCTCTAATGTG+AGG 0.644444 4_3:+68088226 None:intergenic
TAACAAATATACAGACATCA+CGG 0.648800 4_3:+68087739 None:intergenic
TATGATGTGGTACTCTACAT+GGG 0.652027 4_3:-68087919 Msa0658050:CDS
GCAATTAGGAGTAAACATGC+CGG 0.652141 4_3:-68088007 Msa0658050:CDS
ACTAGATTTACTCAAACAAG+GGG 0.654789 4_3:-68088320 Msa0658050:CDS
GAGCAGTTGATCATTCCGAA+AGG 0.659532 4_3:-68088298 Msa0658050:CDS
ACATTGAGAGCATACTCCAT+CGG 0.662326 4_3:-68088208 Msa0658050:CDS
TTTGCTTCAAGAAGACAAGG+TGG 0.679586 4_3:-68087971 Msa0658050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTGTTATCTTTTCATTT+TGG - chr4_3:68088097-68088116 Msa0658050:intron 15.0%
!!! TATTTGTTATCTTTTCATTT+TGG - chr4_3:68088097-68088116 Msa0658050:intron 15.0%
!! TTTGTAATTAATTGTTCCAA+AGG - chr4_3:68088132-68088151 Msa0658050:intron 20.0%
!! CAAATCAATCATATACTAAA+TGG + chr4_3:68088280-68088299 None:intergenic 20.0%
!! TTTGTAATTAATTGTTCCAA+AGG - chr4_3:68088132-68088151 Msa0658050:intron 20.0%
!! CAAATCAATCATATACTAAA+TGG + chr4_3:68088280-68088299 None:intergenic 20.0%
!! AAACGTTCAGCATAAATTTT+AGG + chr4_3:68088026-68088045 None:intergenic 25.0%
! CATCAATTTCATGGATAAAA+AGG - chr4_3:68088046-68088065 Msa0658050:intron 25.0%
! TAACAAATATACAGACATCA+CGG + chr4_3:68088086-68088105 None:intergenic 25.0%
! AATTCAAACAGCTCAATAAA+AGG - chr4_3:68088246-68088265 Msa0658050:CDS 25.0%
! TCACATGACACTTAATTATT+TGG - chr4_3:68088310-68088329 Msa0658050:CDS 25.0%
! CACATGACACTTAATTATTT+GGG - chr4_3:68088311-68088330 Msa0658050:CDS 25.0%
!! AAACGTTCAGCATAAATTTT+AGG + chr4_3:68088026-68088045 None:intergenic 25.0%
! CATCAATTTCATGGATAAAA+AGG - chr4_3:68088046-68088065 Msa0658050:intron 25.0%
! TAACAAATATACAGACATCA+CGG + chr4_3:68088086-68088105 None:intergenic 25.0%
! AATTCAAACAGCTCAATAAA+AGG - chr4_3:68088246-68088265 Msa0658050:CDS 25.0%
! TCACATGACACTTAATTATT+TGG - chr4_3:68088310-68088329 Msa0658050:CDS 25.0%
! CACATGACACTTAATTATTT+GGG - chr4_3:68088311-68088330 Msa0658050:CDS 25.0%
CACTAGATTTACTCAAACAA+GGG - chr4_3:68087501-68087520 Msa0658050:three_prime_UTR 30.0%
ACTAGATTTACTCAAACAAG+GGG - chr4_3:68087502-68087521 Msa0658050:three_prime_UTR 30.0%
GAACTTAAGATCACTAAACT+AGG - chr4_3:68087727-68087746 Msa0658050:three_prime_UTR 30.0%
GGGAATAATAGATATACTTC+AGG - chr4_3:68087923-68087942 Msa0658050:CDS 30.0%
TCTGTTACTGATATAGTCAT+AGG + chr4_3:68088002-68088021 None:intergenic 30.0%
TGAACGTTTCATCAATTTCA+TGG - chr4_3:68088037-68088056 Msa0658050:intron 30.0%
!! TGAGATTTGTTTTTCCTGTT+TGG - chr4_3:68088209-68088228 Msa0658050:CDS 30.0%
CACTAGATTTACTCAAACAA+GGG - chr4_3:68087501-68087520 Msa0658050:three_prime_UTR 30.0%
ACTAGATTTACTCAAACAAG+GGG - chr4_3:68087502-68087521 Msa0658050:three_prime_UTR 30.0%
GAACTTAAGATCACTAAACT+AGG - chr4_3:68087727-68087746 Msa0658050:three_prime_UTR 30.0%
GGGAATAATAGATATACTTC+AGG - chr4_3:68087923-68087942 Msa0658050:CDS 30.0%
TCTGTTACTGATATAGTCAT+AGG + chr4_3:68088002-68088021 None:intergenic 30.0%
TGAACGTTTCATCAATTTCA+TGG - chr4_3:68088037-68088056 Msa0658050:intron 30.0%
!! TGAGATTTGTTTTTCCTGTT+TGG - chr4_3:68088209-68088228 Msa0658050:CDS 30.0%
GCACTAGATTTACTCAAACA+AGG - chr4_3:68087500-68087519 Msa0658050:three_prime_UTR 35.0%
AATGTATTCCCTCTAATGTG+AGG + chr4_3:68087599-68087618 None:intergenic 35.0%
ATGTTTACTCCTAATTGCAC+CGG + chr4_3:68087813-68087832 None:intergenic 35.0%
!! TAGTTTGCTTCAAGAAGACA+AGG - chr4_3:68087848-68087867 Msa0658050:CDS 35.0%
TTATGATGTGGTACTCTACA+TGG - chr4_3:68087902-68087921 Msa0658050:CDS 35.0%
TATGATGTGGTACTCTACAT+GGG - chr4_3:68087903-68087922 Msa0658050:CDS 35.0%
! ATCAAACTGCAGTGATTTGT+AGG + chr4_3:68087979-68087998 None:intergenic 35.0%
!! CATGGATAAAAAGGTATTCC+CGG - chr4_3:68088055-68088074 Msa0658050:intron 35.0%
GTACACAATCATTCATCCTT+TGG + chr4_3:68088151-68088170 None:intergenic 35.0%
! TTTTTCCTGTTTGGCAAAAG+AGG - chr4_3:68088218-68088237 Msa0658050:CDS 35.0%
AATCTAGTGCAAGTAAGTCA+AGG + chr4_3:68087490-68087509 None:intergenic 35.0%
GCACTAGATTTACTCAAACA+AGG - chr4_3:68087500-68087519 Msa0658050:three_prime_UTR 35.0%
AATGTATTCCCTCTAATGTG+AGG + chr4_3:68087599-68087618 None:intergenic 35.0%
ATGTTTACTCCTAATTGCAC+CGG + chr4_3:68087813-68087832 None:intergenic 35.0%
!! TAGTTTGCTTCAAGAAGACA+AGG - chr4_3:68087848-68087867 Msa0658050:CDS 35.0%
TTATGATGTGGTACTCTACA+TGG - chr4_3:68087902-68087921 Msa0658050:CDS 35.0%
TATGATGTGGTACTCTACAT+GGG - chr4_3:68087903-68087922 Msa0658050:CDS 35.0%
! ATCAAACTGCAGTGATTTGT+AGG + chr4_3:68087979-68087998 None:intergenic 35.0%
!! CATGGATAAAAAGGTATTCC+CGG - chr4_3:68088055-68088074 Msa0658050:intron 35.0%
GTACACAATCATTCATCCTT+TGG + chr4_3:68088151-68088170 None:intergenic 35.0%
! TTTTTCCTGTTTGGCAAAAG+AGG - chr4_3:68088218-68088237 Msa0658050:CDS 35.0%
GCAACTAACAACAAGCCTTT+CGG + chr4_3:68087542-68087561 None:intergenic 40.0%
! ACATTGAGAGCATACTCCAT+CGG - chr4_3:68087614-68087633 Msa0658050:three_prime_UTR 40.0%
ATCAACTTCCTTGTTACCGA+TGG + chr4_3:68087633-68087652 None:intergenic 40.0%
!! GAAGTTGATCTTTTACTGCC+CGG - chr4_3:68087644-68087663 Msa0658050:three_prime_UTR 40.0%
AAATACTCACCTTGCAGTAC+CGG + chr4_3:68087666-68087685 None:intergenic 40.0%
GTTCCTAATGTAATAGCGAG+CGG + chr4_3:68087711-68087730 None:intergenic 40.0%
ATGAATGTTCCTCAGATTGC+CGG - chr4_3:68087791-68087810 Msa0658050:CDS 40.0%
GCAATTAGGAGTAAACATGC+CGG - chr4_3:68087815-68087834 Msa0658050:CDS 40.0%
TTTGCTTCAAGAAGACAAGG+TGG - chr4_3:68087851-68087870 Msa0658050:CDS 40.0%
! ATCAGAAGTAGAGCTTTTCG+AGG - chr4_3:68087878-68087897 Msa0658050:CDS 40.0%
!! GCTTTTCGAGGTTTATGATG+TGG - chr4_3:68087890-68087909 Msa0658050:CDS 40.0%
TACAGACATCACGGTATTTC+CGG + chr4_3:68088077-68088096 None:intergenic 40.0%
GCAACTAACAACAAGCCTTT+CGG + chr4_3:68087542-68087561 None:intergenic 40.0%
! ACATTGAGAGCATACTCCAT+CGG - chr4_3:68087614-68087633 Msa0658050:three_prime_UTR 40.0%
ATCAACTTCCTTGTTACCGA+TGG + chr4_3:68087633-68087652 None:intergenic 40.0%
!! GAAGTTGATCTTTTACTGCC+CGG - chr4_3:68087644-68087663 Msa0658050:three_prime_UTR 40.0%
AAATACTCACCTTGCAGTAC+CGG + chr4_3:68087666-68087685 None:intergenic 40.0%
GTTCCTAATGTAATAGCGAG+CGG + chr4_3:68087711-68087730 None:intergenic 40.0%
ATGAATGTTCCTCAGATTGC+CGG - chr4_3:68087791-68087810 Msa0658050:CDS 40.0%
GCAATTAGGAGTAAACATGC+CGG - chr4_3:68087815-68087834 Msa0658050:CDS 40.0%
TTTGCTTCAAGAAGACAAGG+TGG - chr4_3:68087851-68087870 Msa0658050:CDS 40.0%
! ATCAGAAGTAGAGCTTTTCG+AGG - chr4_3:68087878-68087897 Msa0658050:CDS 40.0%
!! GCTTTTCGAGGTTTATGATG+TGG - chr4_3:68087890-68087909 Msa0658050:CDS 40.0%
TACAGACATCACGGTATTTC+CGG + chr4_3:68088077-68088096 None:intergenic 40.0%
GAGCAGTTGATCATTCCGAA+AGG - chr4_3:68087524-68087543 Msa0658050:three_prime_UTR 45.0%
AGCATACTCCATCGGTAACA+AGG - chr4_3:68087622-68087641 Msa0658050:three_prime_UTR 45.0%
AATACTCACCTTGCAGTACC+GGG + chr4_3:68087665-68087684 None:intergenic 45.0%
TTGCCGCTCGCTATTACATT+AGG - chr4_3:68087705-68087724 Msa0658050:three_prime_UTR 45.0%
AGCAAACTAGTAGCTTGAGC+CGG + chr4_3:68087837-68087856 None:intergenic 45.0%
ACAGACATCACGGTATTTCC+GGG + chr4_3:68088076-68088095 None:intergenic 45.0%
GAGCAGTTGATCATTCCGAA+AGG - chr4_3:68087524-68087543 Msa0658050:three_prime_UTR 45.0%
AGCATACTCCATCGGTAACA+AGG - chr4_3:68087622-68087641 Msa0658050:three_prime_UTR 45.0%
AATACTCACCTTGCAGTACC+GGG + chr4_3:68087665-68087684 None:intergenic 45.0%
TTGCCGCTCGCTATTACATT+AGG - chr4_3:68087705-68087724 Msa0658050:three_prime_UTR 45.0%
AGCAAACTAGTAGCTTGAGC+CGG + chr4_3:68087837-68087856 None:intergenic 45.0%
ACAGACATCACGGTATTTCC+GGG + chr4_3:68088076-68088095 None:intergenic 45.0%
TTCCCTCTAATGTGAGGTCC+AGG + chr4_3:68087593-68087612 None:intergenic 50.0%
! TTTTACTGCCCGGTACTGCA+AGG - chr4_3:68087654-68087673 Msa0658050:three_prime_UTR 50.0%
! CTAATTGCACCGGCAATCTG+AGG + chr4_3:68087803-68087822 None:intergenic 50.0%
CTCAGATTGCCGGTGCAATT+AGG - chr4_3:68087801-68087820 Msa0658050:CDS 50.0%
! GCAAGCCTCTTTTGCCAAAC+AGG + chr4_3:68088226-68088245 None:intergenic 50.0%
TTCCCTCTAATGTGAGGTCC+AGG + chr4_3:68087593-68087612 None:intergenic 50.0%
! TTTTACTGCCCGGTACTGCA+AGG - chr4_3:68087654-68087673 Msa0658050:three_prime_UTR 50.0%
! CTAATTGCACCGGCAATCTG+AGG + chr4_3:68087803-68087822 None:intergenic 50.0%
CTCAGATTGCCGGTGCAATT+AGG - chr4_3:68087801-68087820 Msa0658050:CDS 50.0%
! GCAAGCCTCTTTTGCCAAAC+AGG + chr4_3:68088226-68088245 None:intergenic 50.0%
ACGCCTGGACCTCACATTAG+AGG - chr4_3:68087587-68087606 Msa0658050:three_prime_UTR 55.0%
CGCCTGGACCTCACATTAGA+GGG - chr4_3:68087588-68087607 Msa0658050:three_prime_UTR 55.0%
ACGCCTGGACCTCACATTAG+AGG - chr4_3:68087587-68087606 Msa0658050:three_prime_UTR 55.0%
CGCCTGGACCTCACATTAGA+GGG - chr4_3:68087588-68087607 Msa0658050:three_prime_UTR 55.0%
! GGCGTCGCGTTGACGAAGCT+CGG + chr4_3:68087572-68087591 None:intergenic 65.0%
AGCTTCGTCAACGCGACGCC+TGG - chr4_3:68087572-68087591 Msa0658050:three_prime_UTR 65.0%
! GGCGTCGCGTTGACGAAGCT+CGG + chr4_3:68087572-68087591 None:intergenic 65.0%
AGCTTCGTCAACGCGACGCC+TGG - chr4_3:68087572-68087591 Msa0658050:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 68087488 68088356 68087488 ID=Msa0658050;Name=Msa0658050
chr4_3 mRNA 68087488 68088356 68087488 ID=Msa0658050-mRNA-1;Parent=Msa0658050;Name=Msa0658050-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|1|2|268|156
chr4_3 exon 68087488 68088038 68087488 ID=Msa0658050-mRNA-1:exon:19651;Parent=Msa0658050-mRNA-1
chr4_3 exon 68088169 68088356 68088169 ID=Msa0658050-mRNA-1:exon:19650;Parent=Msa0658050-mRNA-1
chr4_3 CDS 68088169 68088356 68088169 ID=Msa0658050-mRNA-1:cds;Parent=Msa0658050-mRNA-1
chr4_3 CDS 68087756 68088038 68087756 ID=Msa0658050-mRNA-1:cds;Parent=Msa0658050-mRNA-1
chr4_3 three_prime_UTR 68087488 68087755 68087488 ID=Msa0658050-mRNA-1:three_prime_utr;Parent=Msa0658050-mRNA-1
Gene Sequence

>Msa0658050

CTTGACTTACTTGCACTAGATTTACTCAAACAAGGGGAGCAGTTGATCATTCCGAAAGGCTTGTTGTTAGTTGCACATGAACCGAGCTTCGTCAACGCGACGCCTGGACCTCACATTAGAGGGAATACATTGAGAGCATACTCCATCGGTAACAAGGAAGTTGATCTTTTACTGCCCGGTACTGCAAGATTGCCGGTGCAATTAGGAGTAAACATGCCGGCTCAAGCTACTAGTTTGCTTCAAGAAGACAAGGTGGAAGAATCAGAAGTAGAGCTTTTCGAGGTTTATGATGTGGTACTCTACATGGGAATAATAGATATACTTCAGGAATACACTGTCAAAAAGAAACTTGAGCATGCCTACAAATCACTGCAGTTTGATCCTATGACTATATCAGTAACAGAACCTAAAATTTATGCTGAACGTTTCATCAATTTCATGGATAAAAAGGTATTCCCGGAAATACCGTGA
Protein sequence

>Msa0658050

LDLLALDLLKQGEQLIIPKGLLLVAHEPSFVNATPGPHIRGNTLRAYSIGNKEVDLLLPGTARLPVQLGVNMPAQATSLLQEDKVEESEVELFEVYDVVLYMGIIDILQEYTVKKKLEHAYKSLQFDPMTISVTEPKIYAERFINFMDKKVFPEIP*