AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0893950


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0893950 MtrunA17_Chr6g0477091 100.000 93 0 0 1 93 1 93 2.34e-64 192
Msa0893950 MtrunA17_Chr1g0157771 46.575 73 32 1 21 93 12 77 1.12e-13 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0893950 AT5G23550.1 68.817 93 26 2 1 93 1 90 8.98e-42 135
Msa0893950 AT5G24170.2 49.153 59 29 1 36 93 20 78 6.03e-12 57.8
Msa0893950 AT5G24170.1 49.153 59 29 1 36 93 20 78 9.41e-12 57.8

Find 27 sgRNAs with CRISPR-Local

Find 141 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAAAGCTCCTTTGCTTTCA+TGG 0.121644 6_1:+78923577 Msa0893950:CDS
TTCCTCAAACCAATCAAGTT+TGG 0.259395 6_1:+78925670 Msa0893950:CDS
ATTTGTAACCAGAGATTATA+TGG 0.289160 6_1:+78925390 Msa0893950:intron
ACTATGGATCTGTGATTTAT+AGG 0.307110 6_1:-78923415 None:intergenic
TCCTCAAACCAATCAAGTTT+GGG 0.333791 6_1:+78925671 Msa0893950:CDS
AAGAAAGAGAGAAGAAACTA+TGG 0.344571 6_1:-78923431 None:intergenic
AATGTTATCCCAAACTTGAT+TGG 0.371483 6_1:-78925679 None:intergenic
TTTGCCATTTGCTTTGCTGC+TGG 0.373336 6_1:+78925414 Msa0893950:CDS
TCTTGGAAATTTGCTTTCAC+TGG 0.383477 6_1:+78925705 Msa0893950:CDS
TTTGGGATAACATTCACTCT+TGG 0.432757 6_1:+78925688 Msa0893950:CDS
TCCCAAACTTGATTGGTTTG+AGG 0.451750 6_1:-78925672 None:intergenic
CTTCGAGAAAGTGAAAATAA+TGG 0.460885 6_1:+78923505 Msa0893950:CDS
CTTGGAAATTTGCTTTCACT+GGG 0.482081 6_1:+78925706 Msa0893950:CDS
AGAGGCACAAGCTGCTGCAT+TGG 0.489920 6_1:+78923550 Msa0893950:CDS
AGTGAAAATAATGGTGGGAA+TGG 0.497361 6_1:+78923514 Msa0893950:CDS
TACTCCAGCAGCAAAGCAAA+TGG 0.511667 6_1:-78925418 None:intergenic
AATAATGGTGGGAATGGAAG+TGG 0.528796 6_1:+78923520 Msa0893950:CDS
CAAACTTACCAACAGTGTAC+AGG 0.533605 6_1:-78925442 None:intergenic
GAAATTTGCTTTCACTGGGA+AGG 0.539615 6_1:+78925710 Msa0893950:CDS
CGAGAAAGTGAAAATAATGG+TGG 0.551729 6_1:+78923508 Msa0893950:CDS
GAAATCATCCATGAAAGCAA+AGG 0.578107 6_1:-78923585 None:intergenic
TGGTTTGAGGAAAACAAGCA+TGG 0.594589 6_1:-78925659 None:intergenic
GAGAAAGTGAAAATAATGGT+GGG 0.615024 6_1:+78923509 Msa0893950:CDS
CTGTACTTTATCTAGAACAC+AGG 0.629338 6_1:+78923616 Msa0893950:CDS
AATGGAAGTGGAAGACGAAG+AGG 0.638493 6_1:+78923532 Msa0893950:CDS
GAGAAAGTGAGGGAAAACGA+TGG 0.677040 6_1:+78923466 Msa0893950:exon
TGGAGTAACCTGTACACTGT+TGG 0.688579 6_1:+78925434 Msa0893950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATAATATATACATACA+AGG + chr6_1:78925120-78925139 Msa0893950:intron 10.0%
!! TTGTTAAGTAAAATTTATAT+CGG + chr6_1:78925588-78925607 Msa0893950:intron 10.0%
!!! AAAAATATATATTTTGTGTC+TGG - chr6_1:78923798-78923817 None:intergenic 15.0%
!! TTTGTAAAAAGATGAAATTA+AGG + chr6_1:78924812-78924831 Msa0893950:intron 15.0%
!!! AAGAAATTGCTTAGATTTTA+AGG - chr6_1:78923364-78923383 None:intergenic 20.0%
!! AATTATTGTATTATGAAGCA+CGG + chr6_1:78923763-78923782 Msa0893950:intron 20.0%
!! AATAGGAAAAATGGATATTT+AGG + chr6_1:78923842-78923861 Msa0893950:intron 20.0%
!!! CAAGTAATTTGAAACTATTT+TGG - chr6_1:78924179-78924198 None:intergenic 20.0%
!! TTGTTTATCTGAAAATTATG+TGG + chr6_1:78924458-78924477 Msa0893950:intron 20.0%
!!! TACGAATTTTCATTAAGATA+TGG + chr6_1:78924607-78924626 Msa0893950:intron 20.0%
!! ATAGAGATTATCATTTATTG+TGG + chr6_1:78924688-78924707 Msa0893950:intron 20.0%
!!! TTTAGAGTTTTGTATATTGT+TGG + chr6_1:78924722-78924741 Msa0893950:intron 20.0%
!! GAAATTAAGGAAAAATTTGT+CGG + chr6_1:78924825-78924844 Msa0893950:intron 20.0%
!! GATGAATAATCACTAATTAA+TGG + chr6_1:78925615-78925634 Msa0893950:intron 20.0%
!!! TGCTTAGATTTTAAGGAATT+GGG - chr6_1:78923357-78923376 None:intergenic 25.0%
!!! TTGCTTAGATTTTAAGGAAT+TGG - chr6_1:78923358-78923377 None:intergenic 25.0%
!! TCTTCAAATTGAAGTTGTTT+TGG + chr6_1:78923728-78923747 Msa0893950:intron 25.0%
!!! TTTAGGTTTTGATTTGAGTA+TGG + chr6_1:78923859-78923878 Msa0893950:intron 25.0%
! TACCTCATAAATATAACATG+CGG - chr6_1:78924017-78924036 None:intergenic 25.0%
! TTCAAATTACTTGAGAATTG+AGG + chr6_1:78924186-78924205 Msa0893950:intron 25.0%
!!! AAAGTTTTGTCCTTTGTAAA+AGG - chr6_1:78924227-78924246 None:intergenic 25.0%
! TTACAAAGGACAAAACTTTA+AGG + chr6_1:78924228-78924247 Msa0893950:intron 25.0%
! TACAAAGGACAAAACTTTAA+GGG + chr6_1:78924229-78924248 Msa0893950:intron 25.0%
! TATTCGGATAGAAAATAACT+GGG + chr6_1:78924428-78924447 Msa0893950:intron 25.0%
!!! AATCTGATGTTTTTACAAAC+AGG - chr6_1:78924758-78924777 None:intergenic 25.0%
!!! AGATTGGTTTTATGAATTAC+AGG + chr6_1:78924985-78925004 Msa0893950:intron 25.0%
! CAAAGGAAACATAAGAATTT+AGG + chr6_1:78925014-78925033 Msa0893950:intron 25.0%
!!! AAGCATAATTTTTTTGTCAC+TGG + chr6_1:78925037-78925056 Msa0893950:intron 25.0%
! ATATTGAAATATGTAGCAAC+AGG - chr6_1:78925221-78925240 None:intergenic 25.0%
! ATTTGTAACCAGAGATTATA+TGG + chr6_1:78925390-78925409 Msa0893950:intron 25.0%
! CAAACTAATACACTATGTAA+AGG - chr6_1:78925571-78925590 None:intergenic 25.0%
!! GATTTTAAGGAATTGGGTTT+GGG - chr6_1:78923351-78923370 None:intergenic 30.0%
!! AGATTTTAAGGAATTGGGTT+TGG - chr6_1:78923352-78923371 None:intergenic 30.0%
ACTATGGATCTGTGATTTAT+AGG - chr6_1:78923418-78923437 None:intergenic 30.0%
AAGAAAGAGAGAAGAAACTA+TGG - chr6_1:78923434-78923453 None:intergenic 30.0%
! CATTATTTTCACTTTCTCGA+AGG - chr6_1:78923507-78923526 None:intergenic 30.0%
CTTCGAGAAAGTGAAAATAA+TGG + chr6_1:78923505-78923524 Msa0893950:CDS 30.0%
GAGAAAGTGAAAATAATGGT+GGG + chr6_1:78923509-78923528 Msa0893950:CDS 30.0%
CTAACTCAAATTATTCTCCT+CGG - chr6_1:78923980-78923999 None:intergenic 30.0%
! TTTTTCACAAAACCCTAAAG+CGG - chr6_1:78924044-78924063 None:intergenic 30.0%
TGTAAAGAACAAAACTGTGA+CGG - chr6_1:78924067-78924086 None:intergenic 30.0%
!!! ACAGTTTTGTTCTTTACACA+AGG + chr6_1:78924069-78924088 Msa0893950:intron 30.0%
CAAGAGATGTAAGTTGTATT+CGG + chr6_1:78924412-78924431 Msa0893950:intron 30.0%
GTATTCGGATAGAAAATAAC+TGG + chr6_1:78924427-78924446 Msa0893950:intron 30.0%
!! ACTATTTTTCCTCAACAACA+TGG - chr6_1:78924552-78924571 None:intergenic 30.0%
GACTACAAATCTTTATGAAC+TGG + chr6_1:78924887-78924906 Msa0893950:intron 30.0%
TGAATTACAGGATGAAACAA+AGG + chr6_1:78924997-78925016 Msa0893950:intron 30.0%
!!! CATAATTTTTTTGTCACTGG+AGG + chr6_1:78925040-78925059 Msa0893950:intron 30.0%
!! TTTCTAGTTTACGAGACTAA+GGG + chr6_1:78925485-78925504 Msa0893950:intron 30.0%
AATGTTATCCCAAACTTGAT+TGG - chr6_1:78925682-78925701 None:intergenic 30.0%
! TCATTTTCTCGAGAAAGTGA+GGG + chr6_1:78923456-78923475 Msa0893950:five_prime_UTR 35.0%
CGAGAAAGTGAAAATAATGG+TGG + chr6_1:78923508-78923527 Msa0893950:CDS 35.0%
! AGTGAAAATAATGGTGGGAA+TGG + chr6_1:78923514-78923533 Msa0893950:CDS 35.0%
GAAATCATCCATGAAAGCAA+AGG - chr6_1:78923588-78923607 None:intergenic 35.0%
! CTGTACTTTATCTAGAACAC+AGG + chr6_1:78923616-78923635 Msa0893950:CDS 35.0%
CGCACTCATAATAGGAAAAA+TGG + chr6_1:78923833-78923852 Msa0893950:intron 35.0%
GGATATTTGACACTGTGATA+CGG + chr6_1:78923880-78923899 Msa0893950:intron 35.0%
GACCGCATGTTATATTTATG+AGG + chr6_1:78924012-78924031 Msa0893950:intron 35.0%
TTGAGAATTGAGGCTACTTA+TGG + chr6_1:78924196-78924215 Msa0893950:intron 35.0%
!!! TATGGAGGTACCTTTTACAA+AGG + chr6_1:78924214-78924233 Msa0893950:intron 35.0%
ACATGGTATTGCAAATCTGA+AGG - chr6_1:78924535-78924554 None:intergenic 35.0%
TTTGCAATACCATGTTGTTG+AGG + chr6_1:78924540-78924559 Msa0893950:intron 35.0%
ATGGTAACATTTGTCTTCTC+AGG + chr6_1:78924626-78924645 Msa0893950:intron 35.0%
AACTGGATTAATCGAGAATG+TGG + chr6_1:78924904-78924923 Msa0893950:intron 35.0%
CAAAATACGATCCTCCAAAT+AGG - chr6_1:78924930-78924949 None:intergenic 35.0%
! ATTTGGAGGATCGTATTTTG+AGG + chr6_1:78924930-78924949 Msa0893950:intron 35.0%
TGGAGGTTCTTGTAATTGTT+AGG + chr6_1:78925057-78925076 Msa0893950:intron 35.0%
GTAAGGAATAAAACTTGAGG+AGG - chr6_1:78925273-78925292 None:intergenic 35.0%
TGGCAAAACCATATAATCTC+TGG - chr6_1:78925401-78925420 None:intergenic 35.0%
CTTAGTCTCGTAAACTAGAA+AGG - chr6_1:78925486-78925505 None:intergenic 35.0%
!! CTTTCTAGTTTACGAGACTA+AGG + chr6_1:78925484-78925503 Msa0893950:intron 35.0%
TTCCTCAAACCAATCAAGTT+TGG + chr6_1:78925670-78925689 Msa0893950:CDS 35.0%
TCCTCAAACCAATCAAGTTT+GGG + chr6_1:78925671-78925690 Msa0893950:CDS 35.0%
! TTTGGGATAACATTCACTCT+TGG + chr6_1:78925688-78925707 Msa0893950:CDS 35.0%
! TCTTGGAAATTTGCTTTCAC+TGG + chr6_1:78925705-78925724 Msa0893950:CDS 35.0%
! CTTGGAAATTTGCTTTCACT+GGG + chr6_1:78925706-78925725 Msa0893950:CDS 35.0%
! CTCATTTTCTCGAGAAAGTG+AGG + chr6_1:78923455-78923474 Msa0893950:five_prime_UTR 40.0%
! AATAATGGTGGGAATGGAAG+TGG + chr6_1:78923520-78923539 Msa0893950:CDS 40.0%
TATTTGACACTGTGATACGG+TGG + chr6_1:78923883-78923902 Msa0893950:intron 40.0%
!! TATGAGGTATTGTCCGCTTT+AGG + chr6_1:78924028-78924047 Msa0893950:intron 40.0%
!! ATGAGGTATTGTCCGCTTTA+GGG + chr6_1:78924029-78924048 Msa0893950:intron 40.0%
!! TTTACACAAGGCATCGTCTT+TGG + chr6_1:78924081-78924100 Msa0893950:intron 40.0%
AGAATTGAGGCTACTTATGG+AGG + chr6_1:78924199-78924218 Msa0893950:intron 40.0%
CTTTGCACAAAACCACAAAG+TGG + chr6_1:78924252-78924271 Msa0893950:intron 40.0%
TGGACACTATCTTGGAAATG+TGG + chr6_1:78924272-78924291 Msa0893950:intron 40.0%
TATCTTGGAAATGTGGCTAG+AGG + chr6_1:78924279-78924298 Msa0893950:intron 40.0%
TTCAGATTGACGATGTCTAC+GGG - chr6_1:78924360-78924379 None:intergenic 40.0%
CTTCAGATTGACGATGTCTA+CGG - chr6_1:78924361-78924380 None:intergenic 40.0%
! ACATCGTCAATCTGAAGTGT+CGG + chr6_1:78924364-78924383 Msa0893950:intron 40.0%
! GGAGTACTACTATACTTGAG+AGG + chr6_1:78924479-78924498 Msa0893950:intron 40.0%
TTAGAAAACCAGCACTCATG+AGG - chr6_1:78924586-78924605 None:intergenic 40.0%
TCTTCTCAGGTGATGTCATA+TGG + chr6_1:78924639-78924658 Msa0893950:intron 40.0%
CTTCTCAGGTGATGTCATAT+GGG + chr6_1:78924640-78924659 Msa0893950:intron 40.0%
TGTCGGAATACGAAATGAAC+TGG + chr6_1:78924842-78924861 Msa0893950:intron 40.0%
TACGAAATGAACTGGATGAG+TGG + chr6_1:78924850-78924869 Msa0893950:intron 40.0%
AATCGAGAATGTGGCCTATT+TGG + chr6_1:78924913-78924932 Msa0893950:intron 40.0%
GAAAACCAAAGCAAACATGC+TGG + chr6_1:78924958-78924977 Msa0893950:intron 40.0%
TAACACCAGCATGTTTGCTT+TGG - chr6_1:78924966-78924985 None:intergenic 40.0%
! CAAACATGCTGGTGTTAGAT+TGG + chr6_1:78924969-78924988 Msa0893950:intron 40.0%
TCCTGCTAAAGCAGTTGATT+AGG + chr6_1:78925170-78925189 Msa0893950:intron 40.0%
CCTGCTAAAGCAGTTGATTA+GGG + chr6_1:78925171-78925190 Msa0893950:intron 40.0%
CGCGTAAGGAATAAAACTTG+AGG - chr6_1:78925276-78925295 None:intergenic 40.0%
CAAACTTACCAACAGTGTAC+AGG - chr6_1:78925445-78925464 None:intergenic 40.0%
CTTTGTCATGTAGATGTGCT+AGG + chr6_1:78925532-78925551 Msa0893950:intron 40.0%
! AACAAGCATGGACTGTAAGA+TGG - chr6_1:78925650-78925669 None:intergenic 40.0%
TGGTTTGAGGAAAACAAGCA+TGG - chr6_1:78925662-78925681 None:intergenic 40.0%
!! TCCCAAACTTGATTGGTTTG+AGG - chr6_1:78925675-78925694 None:intergenic 40.0%
GAGAAAGTGAGGGAAAACGA+TGG + chr6_1:78923466-78923485 Msa0893950:exon 45.0%
AATGGAAGTGGAAGACGAAG+AGG + chr6_1:78923532-78923551 Msa0893950:CDS 45.0%
CGAAAGCTCCTTTGCTTTCA+TGG + chr6_1:78923577-78923596 Msa0893950:CDS 45.0%
GCAACAAGCGCACTCATAAT+AGG + chr6_1:78923825-78923844 Msa0893950:intron 45.0%
GGTATTATGCGTGTACGTGT+CGG - chr6_1:78923959-78923978 None:intergenic 45.0%
! AGGCATCGTCTTTGGAAATG+AGG + chr6_1:78924089-78924108 Msa0893950:intron 45.0%
! GGCATCGTCTTTGGAAATGA+GGG + chr6_1:78924090-78924109 Msa0893950:intron 45.0%
AAGCTACGCAATAGACCCTT+TGG + chr6_1:78924116-78924135 Msa0893950:intron 45.0%
CCAAGATAGTGTCCACTTTG+TGG - chr6_1:78924267-78924286 None:intergenic 45.0%
CCACAAAGTGGACACTATCT+TGG + chr6_1:78924264-78924283 Msa0893950:intron 45.0%
TTGGAAATGTGGCTAGAGGT+CGG + chr6_1:78924283-78924302 Msa0893950:intron 45.0%
CCCTAATCAACTGCTTTAGC+AGG - chr6_1:78925174-78925193 None:intergenic 45.0%
AGATGACTGAAGTTCGCGTA+AGG - chr6_1:78925290-78925309 None:intergenic 45.0%
! TTTGCCATTTGCTTTGCTGC+TGG + chr6_1:78925414-78925433 Msa0893950:CDS 45.0%
TACTCCAGCAGCAAAGCAAA+TGG - chr6_1:78925421-78925440 None:intergenic 45.0%
TGGAGTAACCTGTACACTGT+TGG + chr6_1:78925434-78925453 Msa0893950:CDS 45.0%
! AGCATGGACTGTAAGATGGT+AGG - chr6_1:78925646-78925665 None:intergenic 45.0%
CACGTACACGCATAATACCG+AGG + chr6_1:78923960-78923979 Msa0893950:intron 50.0%
TGGAAATGTGGCTAGAGGTC+GGG + chr6_1:78924284-78924303 Msa0893950:intron 50.0%
CGGCGCTACATAGTGATTGT+TGG + chr6_1:78924384-78924403 Msa0893950:intron 50.0%
TTTGTGCTCCTCATGAGTGC+TGG + chr6_1:78924575-78924594 Msa0893950:intron 50.0%
CGAGAATGTGGCCTATTTGG+AGG + chr6_1:78924916-78924935 Msa0893950:intron 50.0%
! AGAGGCACAAGCTGCTGCAT+TGG + chr6_1:78923550-78923569 Msa0893950:CDS 55.0%
GTTGAGGCTAAGCGGCCAAA+GGG - chr6_1:78924134-78924153 None:intergenic 55.0%
AGTTGAGGCTAAGCGGCCAA+AGG - chr6_1:78924135-78924154 None:intergenic 55.0%
TTTGGCCGCTTAGCCTCAAC+TGG + chr6_1:78924134-78924153 Msa0893950:intron 55.0%
TTGGCCGCTTAGCCTCAACT+GGG + chr6_1:78924135-78924154 Msa0893950:intron 55.0%
AAATGTGGCTAGAGGTCGGG+AGG + chr6_1:78924287-78924306 Msa0893950:intron 55.0%
AATGTGGCTAGAGGTCGGGA+GGG + chr6_1:78924288-78924307 Msa0893950:intron 55.0%
TGGCCGCTTAGCCTCAACTG+GGG + chr6_1:78924136-78924155 Msa0893950:intron 60.0%
GAACACTAGCCCCCCAGTTG+AGG - chr6_1:78924150-78924169 None:intergenic 60.0%
GGCCGCTTAGCCTCAACTGG+GGG + chr6_1:78924137-78924156 Msa0893950:intron 65.0%
GCCGCTTAGCCTCAACTGGG+GGG + chr6_1:78924138-78924157 Msa0893950:intron 65.0%
GCCCCCCAGTTGAGGCTAAG+CGG - chr6_1:78924142-78924161 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 78923270 78925729 78923270 ID=Msa0893950;Name=Msa0893950
chr6_1 mRNA 78923270 78925729 78923270 ID=Msa0893950-mRNA-1;Parent=Msa0893950;Name=Msa0893950-mRNA-1;_AED=0.00;_eAED=0.00;_QI=215|1|0.66|1|1|0.66|3|0|93
chr6_1 exon 78923270 78923637 78923270 ID=Msa0893950-mRNA-1:exon:13196;Parent=Msa0893950-mRNA-1
chr6_1 exon 78925402 78925455 78925402 ID=Msa0893950-mRNA-1:exon:13197;Parent=Msa0893950-mRNA-1
chr6_1 exon 78925658 78925729 78925658 ID=Msa0893950-mRNA-1:exon:13198;Parent=Msa0893950-mRNA-1
chr6_1 five_prime_UTR 78923270 78923484 78923270 ID=Msa0893950-mRNA-1:five_prime_utr;Parent=Msa0893950-mRNA-1
chr6_1 CDS 78923485 78923637 78923485 ID=Msa0893950-mRNA-1:cds;Parent=Msa0893950-mRNA-1
chr6_1 CDS 78925402 78925455 78925402 ID=Msa0893950-mRNA-1:cds;Parent=Msa0893950-mRNA-1
chr6_1 CDS 78925658 78925729 78925658 ID=Msa0893950-mRNA-1:cds;Parent=Msa0893950-mRNA-1
Gene Sequence

>Msa0893950

ATGGAAAAAATGAACAAAGCCTTCGAGAAAGTGAAAATAATGGTGGGAATGGAAGTGGAAGACGAAGAGGCACAAGCTGCTGCATTGGAAAACGAAAGCTCCTTTGCTTTCATGGATGATTTCAATCGCAACTGTACTTTATCTAGAACACAGAGATTATATGGTTTTGCCATTTGCTTTGCTGCTGGAGTAACCTGTACACTGTTGTCCATGCTTGTTTTCCTCAAACCAATCAAGTTTGGGATAACATTCACTCTTGGAAATTTGCTTTCACTGGGA

Protein sequence

>Msa0893950

MEKMNKAFEKVKIMVGMEVEDEEAQAAALENESSFAFMDDFNRNCTLSRTQRLYGFAICFAAGVTCTLLSMLVFLKPIKFGITFTLGNLLSLG