AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0744640


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0744640 MtrunA17_Chr5g0441261 94.231 104 6 0 1 104 1 104 4.26e-67 196
Msa0744640 MtrunA17_Chr3g0093771 62.000 100 35 1 1 100 25 121 1.61e-38 125
Msa0744640 MtrunA17_Chr8g0354141 50.476 105 50 2 1 104 38 141 1.70e-31 110
Msa0744640 MtrunA17_Chr3g0097041 46.000 100 51 1 4 103 62 158 2.65e-21 82.8
Msa0744640 MtrunA17_Chr4g0076001 37.647 85 52 1 5 89 29 112 1.18e-14 64.3
Msa0744640 MtrunA17_Chr7g0255521 50.980 51 25 0 11 61 39 89 5.93e-11 54.7
Msa0744640 MtrunA17_Chr3g0096881 45.902 61 33 0 20 80 78 138 8.66e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0744640 AT3G12490.1 54.808 104 44 1 1 104 1 101 2.40e-35 118
Msa0744640 AT3G12490.2 54.808 104 44 1 1 104 34 134 2.65e-34 118
Msa0744640 AT2G40880.1 51.163 86 42 0 4 89 35 120 2.06e-27 97.4
Msa0744640 AT5G05110.1 51.064 94 45 1 4 96 45 138 8.52e-27 99.0
Msa0744640 AT5G12140.1 47.126 87 46 0 4 90 10 96 3.26e-25 91.3
Msa0744640 AT4G16500.2 44.444 72 39 1 22 92 46 117 1.06e-13 62.4
Msa0744640 AT4G16500.1 44.444 72 39 1 22 92 46 117 1.06e-13 62.4

Find 23 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAAGGAGCATCGTAATTT+TGG 0.195527 5_1:-65478948 None:intergenic
AAAGATAGAAATTAAATTAA+TGG 0.234510 5_1:+65477549 Msa0744640:exon
GCAAAGAAGCAAGTGGTTTC+TGG 0.255766 5_1:+65478805 Msa0744640:CDS
CCATAGCTTCTCTAAAATCT+TGG 0.357443 5_1:-65478887 None:intergenic
GAAGCTATGGTTGAACTTCA+AGG 0.441137 5_1:+65478900 Msa0744640:CDS
TCAAGAACACAATATCAAAC+AGG 0.464934 5_1:+65477648 Msa0744640:CDS
CTCTAAAGTGATGTCGTACA+AGG 0.516796 5_1:-65478830 None:intergenic
GTTGAACTTCAAGGAGGTGC+AGG 0.521993 5_1:+65478909 Msa0744640:CDS
ATTAAATTAATGGCGACTCT+AGG 0.533183 5_1:+65477559 Msa0744640:exon
AATGGATGGTGGGAAGCAAA+AGG 0.558878 5_1:+65478855 Msa0744640:CDS
CTTTAGAGACAATGGATGGT+GGG 0.567845 5_1:+65478845 Msa0744640:CDS
CGACATCACTTTAGAGACAA+TGG 0.568752 5_1:+65478837 Msa0744640:CDS
CTTGAACAGCAAAGATAGCA+AGG 0.570675 5_1:-65477630 None:intergenic
ATGCAGTTCTAGAGTTTGTG+AGG 0.589311 5_1:+65478773 Msa0744640:CDS
TCTAGGTGGTAGCACTGAGG+TGG 0.608936 5_1:+65477576 Msa0744640:CDS
ACTTTAGAGACAATGGATGG+TGG 0.617779 5_1:+65478844 Msa0744640:CDS
GTTAAATGCAAAGAAGCAAG+TGG 0.625710 5_1:+65478798 Msa0744640:CDS
AACTAAGTGCTAGATACAGA+AGG 0.629142 5_1:-65478964 None:intergenic
TGCAGTTCTAGAGTTTGTGA+GGG 0.629223 5_1:+65478774 Msa0744640:CDS
AAATTAATGGCGACTCTAGG+TGG 0.639281 5_1:+65477562 Msa0744640:exon
ATCACTTTAGAGACAATGGA+TGG 0.646105 5_1:+65478841 Msa0744640:CDS
GACTCTAGGTGGTAGCACTG+AGG 0.714011 5_1:+65477573 Msa0744640:CDS
GCTATGGTTGAACTTCAAGG+AGG 0.769675 5_1:+65478903 Msa0744640:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATATAT+AGG + chr5_1:65478220-65478239 Msa0744640:intron 0.0%
!! ATATATATATATATATATAT+AGG + chr5_1:65478220-65478239 Msa0744640:intron 0.0%
!! AAAGATAGAAATTAAATTAA+TGG + chr5_1:65477549-65477568 Msa0744640:exon 10.0%
!! ATAAATGAACATTAAATAAA+TGG + chr5_1:65477982-65478001 Msa0744640:intron 10.0%
!! AACTTATTCATAATTTATTA+GGG - chr5_1:65478186-65478205 None:intergenic 10.0%
!! TAACTTATTCATAATTTATT+AGG - chr5_1:65478187-65478206 None:intergenic 10.0%
!! TTAATCTAACTAAAATTAAT+TGG + chr5_1:65478693-65478712 Msa0744640:intron 10.0%
!! AAAGATAGAAATTAAATTAA+TGG + chr5_1:65477549-65477568 Msa0744640:exon 10.0%
!! ATAAATGAACATTAAATAAA+TGG + chr5_1:65477982-65478001 Msa0744640:intron 10.0%
!! AACTTATTCATAATTTATTA+GGG - chr5_1:65478186-65478205 None:intergenic 10.0%
!! TAACTTATTCATAATTTATT+AGG - chr5_1:65478187-65478206 None:intergenic 10.0%
!! TTAATCTAACTAAAATTAAT+TGG + chr5_1:65478693-65478712 Msa0744640:intron 10.0%
!!! TTCTATACTATATTTTACAA+AGG - chr5_1:65477747-65477766 None:intergenic 15.0%
!! ACTTATTCATAATTTATTAG+GGG - chr5_1:65478185-65478204 None:intergenic 15.0%
!! ATGAATAAGTTATTAACATT+TGG + chr5_1:65478195-65478214 Msa0744640:intron 15.0%
!! TAATCATTAATATAACGATT+TGG - chr5_1:65478344-65478363 None:intergenic 15.0%
!!! TTCTATACTATATTTTACAA+AGG - chr5_1:65477747-65477766 None:intergenic 15.0%
!! ACTTATTCATAATTTATTAG+GGG - chr5_1:65478185-65478204 None:intergenic 15.0%
!! ATGAATAAGTTATTAACATT+TGG + chr5_1:65478195-65478214 Msa0744640:intron 15.0%
!! TAATCATTAATATAACGATT+TGG - chr5_1:65478344-65478363 None:intergenic 15.0%
!! TTAATGTTTATCTCTTTACA+CGG - chr5_1:65477896-65477915 None:intergenic 20.0%
!! TGAGATTCACTTATTAAAAA+GGG + chr5_1:65477926-65477945 Msa0744640:intron 20.0%
!! ATATATATAGGCAAATTCTA+TGG + chr5_1:65478288-65478307 Msa0744640:intron 20.0%
!! ACTCAAATGCATATATATTA+TGG + chr5_1:65478547-65478566 Msa0744640:intron 20.0%
!! TTAATGTTTATCTCTTTACA+CGG - chr5_1:65477896-65477915 None:intergenic 20.0%
!! TGAGATTCACTTATTAAAAA+GGG + chr5_1:65477926-65477945 Msa0744640:intron 20.0%
!! ATATATATAGGCAAATTCTA+TGG + chr5_1:65478288-65478307 Msa0744640:intron 20.0%
!! ACTCAAATGCATATATATTA+TGG + chr5_1:65478547-65478566 Msa0744640:intron 20.0%
!! CTATATTTTACAAAGGAAAC+TGG - chr5_1:65477740-65477759 None:intergenic 25.0%
!!! TTCAAAAGTACTAAGAGTTT+CGG - chr5_1:65477820-65477839 None:intergenic 25.0%
! GTGAGATTCACTTATTAAAA+AGG + chr5_1:65477925-65477944 Msa0744640:intron 25.0%
!! TATCATTGTATTAGTCTAGA+AGG + chr5_1:65478077-65478096 Msa0744640:intron 25.0%
!! CTATATTTTACAAAGGAAAC+TGG - chr5_1:65477740-65477759 None:intergenic 25.0%
!!! TTCAAAAGTACTAAGAGTTT+CGG - chr5_1:65477820-65477839 None:intergenic 25.0%
! GTGAGATTCACTTATTAAAA+AGG + chr5_1:65477925-65477944 Msa0744640:intron 25.0%
!! TATCATTGTATTAGTCTAGA+AGG + chr5_1:65478077-65478096 Msa0744640:intron 25.0%
ATTAAATTAATGGCGACTCT+AGG + chr5_1:65477559-65477578 Msa0744640:exon 30.0%
TCAAGAACACAATATCAAAC+AGG + chr5_1:65477648-65477667 Msa0744640:CDS 30.0%
AGGACAGAACAAAATTGAAA+TGG - chr5_1:65477683-65477702 None:intergenic 30.0%
TTATCAAGCAAACAAAACAC+AGG - chr5_1:65477703-65477722 None:intergenic 30.0%
GAATAAAAGTTCCTTTGTAC+CGG + chr5_1:65477764-65477783 Msa0744640:intron 30.0%
AATAAAAGTTCCTTTGTACC+GGG + chr5_1:65477765-65477784 Msa0744640:intron 30.0%
!! AATATAACGATTTGGTGTAC+CGG - chr5_1:65478336-65478355 None:intergenic 30.0%
!! TTTTATTTCGTCGAAGCTTT+TGG - chr5_1:65478435-65478454 None:intergenic 30.0%
ATTAAATTAATGGCGACTCT+AGG + chr5_1:65477559-65477578 Msa0744640:exon 30.0%
TCAAGAACACAATATCAAAC+AGG + chr5_1:65477648-65477667 Msa0744640:CDS 30.0%
AGGACAGAACAAAATTGAAA+TGG - chr5_1:65477683-65477702 None:intergenic 30.0%
TTATCAAGCAAACAAAACAC+AGG - chr5_1:65477703-65477722 None:intergenic 30.0%
GAATAAAAGTTCCTTTGTAC+CGG + chr5_1:65477764-65477783 Msa0744640:intron 30.0%
AATAAAAGTTCCTTTGTACC+GGG + chr5_1:65477765-65477784 Msa0744640:intron 30.0%
!! AATATAACGATTTGGTGTAC+CGG - chr5_1:65478336-65478355 None:intergenic 30.0%
!! TTTTATTTCGTCGAAGCTTT+TGG - chr5_1:65478435-65478454 None:intergenic 30.0%
AAATCGATCATGAAATGACC+CGG - chr5_1:65477786-65477805 None:intergenic 35.0%
ACCCAAAAATTTGAGTGTAC+CGG + chr5_1:65478314-65478333 Msa0744640:intron 35.0%
! ACCGGTACACTCAAATTTTT+GGG - chr5_1:65478318-65478337 None:intergenic 35.0%
! TACCGGTACACTCAAATTTT+TGG - chr5_1:65478319-65478338 None:intergenic 35.0%
GTTAAATGCAAAGAAGCAAG+TGG + chr5_1:65478798-65478817 Msa0744640:CDS 35.0%
! ATCACTTTAGAGACAATGGA+TGG + chr5_1:65478841-65478860 Msa0744640:CDS 35.0%
!! CCATAGCTTCTCTAAAATCT+TGG - chr5_1:65478890-65478909 None:intergenic 35.0%
!! CCAAGATTTTAGAGAAGCTA+TGG + chr5_1:65478887-65478906 Msa0744640:CDS 35.0%
AAATCGATCATGAAATGACC+CGG - chr5_1:65477786-65477805 None:intergenic 35.0%
ACCCAAAAATTTGAGTGTAC+CGG + chr5_1:65478314-65478333 Msa0744640:intron 35.0%
! ACCGGTACACTCAAATTTTT+GGG - chr5_1:65478318-65478337 None:intergenic 35.0%
! TACCGGTACACTCAAATTTT+TGG - chr5_1:65478319-65478338 None:intergenic 35.0%
GTTAAATGCAAAGAAGCAAG+TGG + chr5_1:65478798-65478817 Msa0744640:CDS 35.0%
! ATCACTTTAGAGACAATGGA+TGG + chr5_1:65478841-65478860 Msa0744640:CDS 35.0%
!! CCATAGCTTCTCTAAAATCT+TGG - chr5_1:65478890-65478909 None:intergenic 35.0%
!! CCAAGATTTTAGAGAAGCTA+TGG + chr5_1:65478887-65478906 Msa0744640:CDS 35.0%
AAATTAATGGCGACTCTAGG+TGG + chr5_1:65477562-65477581 Msa0744640:exon 40.0%
CTTGAACAGCAAAGATAGCA+AGG - chr5_1:65477633-65477652 None:intergenic 40.0%
!! AAGGAGTATCCAACTGGTTT+GGG + chr5_1:65478096-65478115 Msa0744640:intron 40.0%
GTGAAGGAGTTATATGCAGT+AGG + chr5_1:65478128-65478147 Msa0744640:intron 40.0%
CGTGACATAATAATGAGACG+TGG + chr5_1:65478634-65478653 Msa0744640:intron 40.0%
TTCTGCGCATTTAAGCATCA+AGG - chr5_1:65478754-65478773 None:intergenic 40.0%
!! ATGCAGTTCTAGAGTTTGTG+AGG + chr5_1:65478773-65478792 Msa0744640:CDS 40.0%
!! TGCAGTTCTAGAGTTTGTGA+GGG + chr5_1:65478774-65478793 Msa0744640:CDS 40.0%
!! CTCTAAAGTGATGTCGTACA+AGG - chr5_1:65478833-65478852 None:intergenic 40.0%
! CGACATCACTTTAGAGACAA+TGG + chr5_1:65478837-65478856 Msa0744640:CDS 40.0%
! ACTTTAGAGACAATGGATGG+TGG + chr5_1:65478844-65478863 Msa0744640:CDS 40.0%
! CTTTAGAGACAATGGATGGT+GGG + chr5_1:65478845-65478864 Msa0744640:CDS 40.0%
GAAGCTATGGTTGAACTTCA+AGG + chr5_1:65478900-65478919 Msa0744640:CDS 40.0%
!!! CAGAAGGAGCATCGTAATTT+TGG - chr5_1:65478951-65478970 None:intergenic 40.0%
AAATTAATGGCGACTCTAGG+TGG + chr5_1:65477562-65477581 Msa0744640:exon 40.0%
CTTGAACAGCAAAGATAGCA+AGG - chr5_1:65477633-65477652 None:intergenic 40.0%
!! AAGGAGTATCCAACTGGTTT+GGG + chr5_1:65478096-65478115 Msa0744640:intron 40.0%
GTGAAGGAGTTATATGCAGT+AGG + chr5_1:65478128-65478147 Msa0744640:intron 40.0%
CGTGACATAATAATGAGACG+TGG + chr5_1:65478634-65478653 Msa0744640:intron 40.0%
TTCTGCGCATTTAAGCATCA+AGG - chr5_1:65478754-65478773 None:intergenic 40.0%
!! ATGCAGTTCTAGAGTTTGTG+AGG + chr5_1:65478773-65478792 Msa0744640:CDS 40.0%
!! TGCAGTTCTAGAGTTTGTGA+GGG + chr5_1:65478774-65478793 Msa0744640:CDS 40.0%
!! CTCTAAAGTGATGTCGTACA+AGG - chr5_1:65478833-65478852 None:intergenic 40.0%
! CGACATCACTTTAGAGACAA+TGG + chr5_1:65478837-65478856 Msa0744640:CDS 40.0%
! ACTTTAGAGACAATGGATGG+TGG + chr5_1:65478844-65478863 Msa0744640:CDS 40.0%
! CTTTAGAGACAATGGATGGT+GGG + chr5_1:65478845-65478864 Msa0744640:CDS 40.0%
GAAGCTATGGTTGAACTTCA+AGG + chr5_1:65478900-65478919 Msa0744640:CDS 40.0%
!!! CAGAAGGAGCATCGTAATTT+TGG - chr5_1:65478951-65478970 None:intergenic 40.0%
CATGAAATGACCCGGTACAA+AGG - chr5_1:65477778-65477797 None:intergenic 45.0%
!! GTCTAGAAGGAGTATCCAAC+TGG + chr5_1:65478090-65478109 Msa0744640:intron 45.0%
!! GAAGGAGTATCCAACTGGTT+TGG + chr5_1:65478095-65478114 Msa0744640:intron 45.0%
GCAAAGAAGCAAGTGGTTTC+TGG + chr5_1:65478805-65478824 Msa0744640:CDS 45.0%
!! AATGGATGGTGGGAAGCAAA+AGG + chr5_1:65478855-65478874 Msa0744640:CDS 45.0%
GCTATGGTTGAACTTCAAGG+AGG + chr5_1:65478903-65478922 Msa0744640:CDS 45.0%
CATGAAATGACCCGGTACAA+AGG - chr5_1:65477778-65477797 None:intergenic 45.0%
!! GTCTAGAAGGAGTATCCAAC+TGG + chr5_1:65478090-65478109 Msa0744640:intron 45.0%
!! GAAGGAGTATCCAACTGGTT+TGG + chr5_1:65478095-65478114 Msa0744640:intron 45.0%
GCAAAGAAGCAAGTGGTTTC+TGG + chr5_1:65478805-65478824 Msa0744640:CDS 45.0%
!! AATGGATGGTGGGAAGCAAA+AGG + chr5_1:65478855-65478874 Msa0744640:CDS 45.0%
GCTATGGTTGAACTTCAAGG+AGG + chr5_1:65478903-65478922 Msa0744640:CDS 45.0%
GTGTTACAGCCCAAACCAGT+TGG - chr5_1:65478108-65478127 None:intergenic 50.0%
GTTTGGGCTGTAACACGTGA+AGG + chr5_1:65478112-65478131 Msa0744640:intron 50.0%
! GTTGAACTTCAAGGAGGTGC+AGG + chr5_1:65478909-65478928 Msa0744640:CDS 50.0%
GTGTTACAGCCCAAACCAGT+TGG - chr5_1:65478108-65478127 None:intergenic 50.0%
GTTTGGGCTGTAACACGTGA+AGG + chr5_1:65478112-65478131 Msa0744640:intron 50.0%
! GTTGAACTTCAAGGAGGTGC+AGG + chr5_1:65478909-65478928 Msa0744640:CDS 50.0%
GACTCTAGGTGGTAGCACTG+AGG + chr5_1:65477573-65477592 Msa0744640:CDS 55.0%
! TCTAGGTGGTAGCACTGAGG+TGG + chr5_1:65477576-65477595 Msa0744640:CDS 55.0%
GACTCTAGGTGGTAGCACTG+AGG + chr5_1:65477573-65477592 Msa0744640:CDS 55.0%
! TCTAGGTGGTAGCACTGAGG+TGG + chr5_1:65477576-65477595 Msa0744640:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 65477548 65478984 65477548 ID=Msa0744640;Name=Msa0744640
chr5_1 mRNA 65477548 65478984 65477548 ID=Msa0744640-mRNA-1;Parent=Msa0744640;Name=Msa0744640-mRNA-1;_AED=0.07;_eAED=0.07;_QI=20|1|0.5|1|1|1|2|0|104
chr5_1 exon 65477548 65477669 65477548 ID=Msa0744640-mRNA-1:exon:19432;Parent=Msa0744640-mRNA-1
chr5_1 exon 65478772 65478984 65478772 ID=Msa0744640-mRNA-1:exon:19433;Parent=Msa0744640-mRNA-1
chr5_1 five_prime_UTR 65477548 65477567 65477548 ID=Msa0744640-mRNA-1:five_prime_utr;Parent=Msa0744640-mRNA-1
chr5_1 CDS 65477568 65477669 65477568 ID=Msa0744640-mRNA-1:cds;Parent=Msa0744640-mRNA-1
chr5_1 CDS 65478772 65478984 65478772 ID=Msa0744640-mRNA-1:cds;Parent=Msa0744640-mRNA-1
Gene Sequence

>Msa0744640

ATGGCGACTCTAGGTGGTAGCACTGAGGTGGAATATACACAAAACAGTGTTGAGATAGATAACCTTGCTATCTTTGCTGTTCAAGAACACAATATCAAACAGAATGCAGTTCTAGAGTTTGTGAGGGTGTTAAATGCAAAGAAGCAAGTGGTTTCTGGCACCTTGTACGACATCACTTTAGAGACAATGGATGGTGGGAAGCAAAAGGTGTATGAAGCCAAGATTTTAGAGAAGCTATGGTTGAACTTCAAGGAGGTGCAGGAATTCAATCTCATTAGCCAAAATTACGATGCTCCTTCTGTATCTAGCACTTAG

Protein sequence

>Msa0744640

MATLGGSTEVEYTQNSVEIDNLAIFAVQEHNIKQNAVLEFVRVLNAKKQVVSGTLYDITLETMDGGKQKVYEAKILEKLWLNFKEVQEFNLISQNYDAPSVSST*