AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0878090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0878090 MtrunA17_Chr6g0460641 91.837 98 8 0 1 98 1 98 2.94e-63 186
Msa0878090 MtrunA17_Chr6g0460651 72.449 98 25 2 1 98 4 99 8.24e-44 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCACTGCCTCTTATTCTTTA+TGG 0.062997 6_1:+18502290 Msa0878090:CDS
CAATAATAGGAAAATGTTAT+TGG 0.164891 6_1:+18502681 Msa0878090:intron
ATGTTATTGGATTAAGTATT+GGG 0.250615 6_1:+18502694 Msa0878090:CDS
TTGATAAAGGAGAAGAATTC+AGG 0.251868 6_1:+18502727 Msa0878090:CDS
CAAACTCTTCCAGGTGGGTT+GGG 0.258199 6_1:-18502816 None:intergenic
GGTAAAGGAAAGGATGAATT+TGG 0.265021 6_1:+18502749 Msa0878090:CDS
TTCCAGGTGGGTTGGGGTCA+TGG 0.304052 6_1:-18502809 None:intergenic
GGGGAAGATTCATTTGATAA+AGG 0.323817 6_1:+18502714 Msa0878090:CDS
TTCATTGCTCAAACTCTTCC+AGG 0.325067 6_1:-18502825 None:intergenic
AATGCAAACTTCAATGGTTA+AGG 0.330001 6_1:+18502512 Msa0878090:CDS
AACAAATTTCATGTCTTATG+AGG 0.357442 6_1:+18502156 Msa0878090:five_prime_UTR
CACGTTAATGCAAACTTCAA+TGG 0.399282 6_1:+18502506 Msa0878090:CDS
AATGTTATTGGATTAAGTAT+TGG 0.412576 6_1:+18502693 Msa0878090:CDS
TCAAACTCTTCCAGGTGGGT+TGG 0.420140 6_1:-18502817 None:intergenic
AAACTCTTCCAGGTGGGTTG+GGG 0.423196 6_1:-18502815 None:intergenic
AGAAAACCATAAAGAATAAG+AGG 0.424821 6_1:-18502296 None:intergenic
TTGGAAATAGAAGACTATCC+AGG 0.442550 6_1:+18502768 Msa0878090:CDS
TAAAGAATAAGAGGCAGTGC+AGG 0.455063 6_1:-18502287 None:intergenic
TGGTTGTTTGCACCTGTCCC+TGG 0.458930 6_1:-18502786 None:intergenic
CACCATGACCCCAACCCACC+TGG 0.483419 6_1:+18502807 Msa0878090:CDS
TATCATCCATTAGAAAATAG+TGG 0.485206 6_1:-18502939 None:intergenic
AGGAGAAGAATTCAGGGTAA+AGG 0.485386 6_1:+18502734 Msa0878090:CDS
TGATAAAGGAGAAGAATTCA+GGG 0.515012 6_1:+18502728 Msa0878090:CDS
CATTGAAGTTTGCATTAACG+TGG 0.532124 6_1:-18502505 None:intergenic
TTGCTCAAACTCTTCCAGGT+GGG 0.533660 6_1:-18502821 None:intergenic
ATTATTACATACATGTCATG+TGG 0.555327 6_1:+18502876 Msa0878090:three_prime_UTR
ATAGAAGACTATCCAGGGAC+AGG 0.563265 6_1:+18502774 Msa0878090:CDS
TTATTACATACATGTCATGT+GGG 0.566063 6_1:+18502877 Msa0878090:three_prime_UTR
AAGAATTCAGGGTAAAGGAA+AGG 0.570547 6_1:+18502739 Msa0878090:CDS
TGGAAATAGAAGACTATCCA+GGG 0.571908 6_1:+18502769 Msa0878090:CDS
TGTTATTGGATTAAGTATTG+GGG 0.590218 6_1:+18502695 Msa0878090:CDS
CAGGTGGGTTGGGGTCATGG+TGG 0.598616 6_1:-18502806 None:intergenic
ATTGCTCAAACTCTTCCAGG+TGG 0.612682 6_1:-18502822 None:intergenic
AAAGAATAAGAGGCAGTGCA+GGG 0.628073 6_1:-18502286 None:intergenic
CGTGGATAAGATAAGAGCTG+AGG 0.644222 6_1:-18502229 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTAATAAAAAATAATA+AGG - chr6_1:18502415-18502434 None:intergenic 0.0%
!! TTAATTAATAAAAAATAATA+AGG - chr6_1:18502415-18502434 None:intergenic 0.0%
!! ATATATTTATAAGTTCATAT+GGG - chr6_1:18502550-18502569 None:intergenic 10.0%
!! AATATATTTATAAGTTCATA+TGG - chr6_1:18502551-18502570 None:intergenic 10.0%
!! ATATATTTATAAGTTCATAT+GGG - chr6_1:18502550-18502569 None:intergenic 10.0%
!! AATATATTTATAAGTTCATA+TGG - chr6_1:18502551-18502570 None:intergenic 10.0%
!! ATAAAAAATAATAAGGAGAT+GGG - chr6_1:18502408-18502427 None:intergenic 15.0%
!! AATAAAAAATAATAAGGAGA+TGG - chr6_1:18502409-18502428 None:intergenic 15.0%
!! ATAAAAAATAATAAGGAGAT+GGG - chr6_1:18502408-18502427 None:intergenic 15.0%
!! AATAAAAAATAATAAGGAGA+TGG - chr6_1:18502409-18502428 None:intergenic 15.0%
!!! TTTTCCATTTTATTTTTTGC+AGG + chr6_1:18502456-18502475 Msa0878090:intron 20.0%
!! TCTAACTATTAACCAAATTA+AGG + chr6_1:18502635-18502654 Msa0878090:intron 20.0%
!! CTAACTATTAACCAAATTAA+GGG + chr6_1:18502636-18502655 Msa0878090:intron 20.0%
!! CAATAATAGGAAAATGTTAT+TGG + chr6_1:18502681-18502700 Msa0878090:intron 20.0%
!! AATGTTATTGGATTAAGTAT+TGG + chr6_1:18502693-18502712 Msa0878090:CDS 20.0%
!! ATGTTATTGGATTAAGTATT+GGG + chr6_1:18502694-18502713 Msa0878090:CDS 20.0%
!!! TTTTCCATTTTATTTTTTGC+AGG + chr6_1:18502456-18502475 Msa0878090:intron 20.0%
!! TCTAACTATTAACCAAATTA+AGG + chr6_1:18502635-18502654 Msa0878090:intron 20.0%
!! CTAACTATTAACCAAATTAA+GGG + chr6_1:18502636-18502655 Msa0878090:intron 20.0%
!! CAATAATAGGAAAATGTTAT+TGG + chr6_1:18502681-18502700 Msa0878090:intron 20.0%
!! AATGTTATTGGATTAAGTAT+TGG + chr6_1:18502693-18502712 Msa0878090:CDS 20.0%
!! ATGTTATTGGATTAAGTATT+GGG + chr6_1:18502694-18502713 Msa0878090:CDS 20.0%
! AACAAATTTCATGTCTTATG+AGG + chr6_1:18502156-18502175 Msa0878090:five_prime_UTR 25.0%
! AGAAAACCATAAAGAATAAG+AGG - chr6_1:18502299-18502318 None:intergenic 25.0%
! TCTTCCTGCAAAAAATAAAA+TGG - chr6_1:18502463-18502482 None:intergenic 25.0%
! AATAAGTTAGACCCTTAATT+TGG - chr6_1:18502650-18502669 None:intergenic 25.0%
! TTAATGCCTTTCTCAATAAT+AGG + chr6_1:18502668-18502687 Msa0878090:intron 25.0%
!! CATTTTCCTATTATTGAGAA+AGG - chr6_1:18502677-18502696 None:intergenic 25.0%
!! TGTTATTGGATTAAGTATTG+GGG + chr6_1:18502695-18502714 Msa0878090:CDS 25.0%
! ATTATTACATACATGTCATG+TGG + chr6_1:18502876-18502895 Msa0878090:three_prime_UTR 25.0%
! TTATTACATACATGTCATGT+GGG + chr6_1:18502877-18502896 Msa0878090:three_prime_UTR 25.0%
!! GGGACATACTTATATATTTT+TGG + chr6_1:18502897-18502916 Msa0878090:three_prime_UTR 25.0%
! TATCATCCATTAGAAAATAG+TGG - chr6_1:18502942-18502961 None:intergenic 25.0%
! AACAAATTTCATGTCTTATG+AGG + chr6_1:18502156-18502175 Msa0878090:five_prime_UTR 25.0%
! AGAAAACCATAAAGAATAAG+AGG - chr6_1:18502299-18502318 None:intergenic 25.0%
! TCTTCCTGCAAAAAATAAAA+TGG - chr6_1:18502463-18502482 None:intergenic 25.0%
! AATAAGTTAGACCCTTAATT+TGG - chr6_1:18502650-18502669 None:intergenic 25.0%
! TTAATGCCTTTCTCAATAAT+AGG + chr6_1:18502668-18502687 Msa0878090:intron 25.0%
!! CATTTTCCTATTATTGAGAA+AGG - chr6_1:18502677-18502696 None:intergenic 25.0%
!! TGTTATTGGATTAAGTATTG+GGG + chr6_1:18502695-18502714 Msa0878090:CDS 25.0%
! ATTATTACATACATGTCATG+TGG + chr6_1:18502876-18502895 Msa0878090:three_prime_UTR 25.0%
! TTATTACATACATGTCATGT+GGG + chr6_1:18502877-18502896 Msa0878090:three_prime_UTR 25.0%
!! GGGACATACTTATATATTTT+TGG + chr6_1:18502897-18502916 Msa0878090:three_prime_UTR 25.0%
! TATCATCCATTAGAAAATAG+TGG - chr6_1:18502942-18502961 None:intergenic 25.0%
GTTGAACAAAAAAGAAAACG+TGG - chr6_1:18502250-18502269 None:intergenic 30.0%
AATGCAAACTTCAATGGTTA+AGG + chr6_1:18502512-18502531 Msa0878090:CDS 30.0%
TAGAAGCAAAATATAGAGCT+TGG - chr6_1:18502619-18502638 None:intergenic 30.0%
TTGATAAAGGAGAAGAATTC+AGG + chr6_1:18502727-18502746 Msa0878090:CDS 30.0%
TGATAAAGGAGAAGAATTCA+GGG + chr6_1:18502728-18502747 Msa0878090:CDS 30.0%
! TTTCAGCCACTATTTTCTAA+TGG + chr6_1:18502933-18502952 Msa0878090:three_prime_UTR 30.0%
GTTGAACAAAAAAGAAAACG+TGG - chr6_1:18502250-18502269 None:intergenic 30.0%
AATGCAAACTTCAATGGTTA+AGG + chr6_1:18502512-18502531 Msa0878090:CDS 30.0%
TAGAAGCAAAATATAGAGCT+TGG - chr6_1:18502619-18502638 None:intergenic 30.0%
TTGATAAAGGAGAAGAATTC+AGG + chr6_1:18502727-18502746 Msa0878090:CDS 30.0%
TGATAAAGGAGAAGAATTCA+GGG + chr6_1:18502728-18502747 Msa0878090:CDS 30.0%
! TTTCAGCCACTATTTTCTAA+TGG + chr6_1:18502933-18502952 Msa0878090:three_prime_UTR 30.0%
! TGCAGGAAGATTTTTGTCAA+AGG + chr6_1:18502473-18502492 Msa0878090:intron 35.0%
CATTGAAGTTTGCATTAACG+TGG - chr6_1:18502508-18502527 None:intergenic 35.0%
CACGTTAATGCAAACTTCAA+TGG + chr6_1:18502506-18502525 Msa0878090:CDS 35.0%
CAAAATATAGAGCTTGGTAG+AGG - chr6_1:18502613-18502632 None:intergenic 35.0%
GGGGAAGATTCATTTGATAA+AGG + chr6_1:18502714-18502733 Msa0878090:CDS 35.0%
AAGAATTCAGGGTAAAGGAA+AGG + chr6_1:18502739-18502758 Msa0878090:CDS 35.0%
GGTAAAGGAAAGGATGAATT+TGG + chr6_1:18502749-18502768 Msa0878090:CDS 35.0%
TTGGAAATAGAAGACTATCC+AGG + chr6_1:18502768-18502787 Msa0878090:CDS 35.0%
TGGAAATAGAAGACTATCCA+GGG + chr6_1:18502769-18502788 Msa0878090:CDS 35.0%
! TGCAGGAAGATTTTTGTCAA+AGG + chr6_1:18502473-18502492 Msa0878090:intron 35.0%
CATTGAAGTTTGCATTAACG+TGG - chr6_1:18502508-18502527 None:intergenic 35.0%
CACGTTAATGCAAACTTCAA+TGG + chr6_1:18502506-18502525 Msa0878090:CDS 35.0%
CAAAATATAGAGCTTGGTAG+AGG - chr6_1:18502613-18502632 None:intergenic 35.0%
GGGGAAGATTCATTTGATAA+AGG + chr6_1:18502714-18502733 Msa0878090:CDS 35.0%
AAGAATTCAGGGTAAAGGAA+AGG + chr6_1:18502739-18502758 Msa0878090:CDS 35.0%
GGTAAAGGAAAGGATGAATT+TGG + chr6_1:18502749-18502768 Msa0878090:CDS 35.0%
TTGGAAATAGAAGACTATCC+AGG + chr6_1:18502768-18502787 Msa0878090:CDS 35.0%
TGGAAATAGAAGACTATCCA+GGG + chr6_1:18502769-18502788 Msa0878090:CDS 35.0%
AAAGAATAAGAGGCAGTGCA+GGG - chr6_1:18502289-18502308 None:intergenic 40.0%
TAAAGAATAAGAGGCAGTGC+AGG - chr6_1:18502290-18502309 None:intergenic 40.0%
GCACTGCCTCTTATTCTTTA+TGG + chr6_1:18502290-18502309 Msa0878090:CDS 40.0%
AGGAGAAGAATTCAGGGTAA+AGG + chr6_1:18502734-18502753 Msa0878090:CDS 40.0%
TTCATTGCTCAAACTCTTCC+AGG - chr6_1:18502828-18502847 None:intergenic 40.0%
AAAGAATAAGAGGCAGTGCA+GGG - chr6_1:18502289-18502308 None:intergenic 40.0%
TAAAGAATAAGAGGCAGTGC+AGG - chr6_1:18502290-18502309 None:intergenic 40.0%
GCACTGCCTCTTATTCTTTA+TGG + chr6_1:18502290-18502309 Msa0878090:CDS 40.0%
AGGAGAAGAATTCAGGGTAA+AGG + chr6_1:18502734-18502753 Msa0878090:CDS 40.0%
TTCATTGCTCAAACTCTTCC+AGG - chr6_1:18502828-18502847 None:intergenic 40.0%
CGTGGATAAGATAAGAGCTG+AGG - chr6_1:18502232-18502251 None:intergenic 45.0%
ATAGAAGACTATCCAGGGAC+AGG + chr6_1:18502774-18502793 Msa0878090:CDS 45.0%
TTGCTCAAACTCTTCCAGGT+GGG - chr6_1:18502824-18502843 None:intergenic 45.0%
ATTGCTCAAACTCTTCCAGG+TGG - chr6_1:18502825-18502844 None:intergenic 45.0%
CGTGGATAAGATAAGAGCTG+AGG - chr6_1:18502232-18502251 None:intergenic 45.0%
ATAGAAGACTATCCAGGGAC+AGG + chr6_1:18502774-18502793 Msa0878090:CDS 45.0%
TTGCTCAAACTCTTCCAGGT+GGG - chr6_1:18502824-18502843 None:intergenic 45.0%
ATTGCTCAAACTCTTCCAGG+TGG - chr6_1:18502825-18502844 None:intergenic 45.0%
!! TTAAATTATTTATTTGTATA+TGG + chr6_1:18502376-18502395 Msa0878090:intron 5.0%
!! TTAAATTATTTATTTGTATA+TGG + chr6_1:18502376-18502395 Msa0878090:intron 5.0%
!! AAACTCTTCCAGGTGGGTTG+GGG - chr6_1:18502818-18502837 None:intergenic 50.0%
! CAAACTCTTCCAGGTGGGTT+GGG - chr6_1:18502819-18502838 None:intergenic 50.0%
TCAAACTCTTCCAGGTGGGT+TGG - chr6_1:18502820-18502839 None:intergenic 50.0%
!! AAACTCTTCCAGGTGGGTTG+GGG - chr6_1:18502818-18502837 None:intergenic 50.0%
! CAAACTCTTCCAGGTGGGTT+GGG - chr6_1:18502819-18502838 None:intergenic 50.0%
TCAAACTCTTCCAGGTGGGT+TGG - chr6_1:18502820-18502839 None:intergenic 50.0%
TGGTTGTTTGCACCTGTCCC+TGG - chr6_1:18502789-18502808 None:intergenic 55.0%
TGGTTGTTTGCACCTGTCCC+TGG - chr6_1:18502789-18502808 None:intergenic 55.0%
!! TTCCAGGTGGGTTGGGGTCA+TGG - chr6_1:18502812-18502831 None:intergenic 60.0%
!! TTCCAGGTGGGTTGGGGTCA+TGG - chr6_1:18502812-18502831 None:intergenic 60.0%
!! CAGGTGGGTTGGGGTCATGG+TGG - chr6_1:18502809-18502828 None:intergenic 65.0%
CACCATGACCCCAACCCACC+TGG + chr6_1:18502807-18502826 Msa0878090:CDS 65.0%
!! CAGGTGGGTTGGGGTCATGG+TGG - chr6_1:18502809-18502828 None:intergenic 65.0%
CACCATGACCCCAACCCACC+TGG + chr6_1:18502807-18502826 Msa0878090:CDS 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 18502154 18503084 18502154 ID=Msa0878090;Name=Msa0878090
chr6_1 mRNA 18502154 18503084 18502154 ID=Msa0878090-mRNA-1;Parent=Msa0878090;Name=Msa0878090-mRNA-1;_AED=0.25;_eAED=0.25;_QI=116|0.5|0.66|1|1|1|3|245|98
chr6_1 exon 18502154 18502357 18502154 ID=Msa0878090-mRNA-1:exon:5046;Parent=Msa0878090-mRNA-1
chr6_1 exon 18502478 18502536 18502478 ID=Msa0878090-mRNA-1:exon:5047;Parent=Msa0878090-mRNA-1
chr6_1 exon 18502690 18503084 18502690 ID=Msa0878090-mRNA-1:exon:5048;Parent=Msa0878090-mRNA-1
chr6_1 five_prime_UTR 18502154 18502269 18502154 ID=Msa0878090-mRNA-1:five_prime_utr;Parent=Msa0878090-mRNA-1
chr6_1 CDS 18502270 18502357 18502270 ID=Msa0878090-mRNA-1:cds;Parent=Msa0878090-mRNA-1
chr6_1 CDS 18502478 18502536 18502478 ID=Msa0878090-mRNA-1:cds;Parent=Msa0878090-mRNA-1
chr6_1 CDS 18502690 18502839 18502690 ID=Msa0878090-mRNA-1:cds;Parent=Msa0878090-mRNA-1
chr6_1 three_prime_UTR 18502840 18503084 18502840 ID=Msa0878090-mRNA-1:three_prime_utr;Parent=Msa0878090-mRNA-1
Gene Sequence

>Msa0878090

ATGTTCAACAAATTTGCCCTGCACTGCCTCTTATTCTTTATGGTTTTCTCATGTCTTCTTCTTTCATCTTCTTCTCTACAAACAACAAGAAGATTTTTGTCAAAGGATGAAAAATCCACGTTAATGCAAACTTCAATGGTTAAGGTTGAAAATGTTATTGGATTAAGTATTGGGGAAGATTCATTTGATAAAGGAGAAGAATTCAGGGTAAAGGAAAGGATGAATTTGGAAATAGAAGACTATCCAGGGACAGGTGCAAACAACCACCATGACCCCAACCCACCTGGAAGAGTTTGA

Protein sequence

>Msa0878090

MFNKFALHCLLFFMVFSCLLLSSSSLQTTRRFLSKDEKSTLMQTSMVKVENVIGLSIGEDSFDKGEEFRVKERMNLEIEDYPGTGANNHHDPNPPGRV*