AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0580024780.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024780.01.T01 MTR_5g016350 98.361 61 1 0 21 81 459 519 4.82e-38 132
MsG0580024780.01.T01 MTR_5g016350 98.361 61 1 0 21 81 523 583 8.88e-38 132
MsG0580024780.01.T01 MTR_5g016370 95.082 61 3 0 21 81 535 595 1.40e-34 123
MsG0580024780.01.T01 MTR_4g095058 83.607 61 10 0 21 81 516 576 4.65e-33 119
MsG0580024780.01.T01 MTR_4g095058 83.607 61 10 0 21 81 518 578 4.69e-33 119
MsG0580024780.01.T02 MTR_5g016350 98.361 61 1 0 21 81 459 519 4.82e-38 132
MsG0580024780.01.T02 MTR_5g016350 98.361 61 1 0 21 81 523 583 8.88e-38 132
MsG0580024780.01.T02 MTR_5g016370 95.082 61 3 0 21 81 535 595 1.40e-34 123
MsG0580024780.01.T02 MTR_4g095058 83.607 61 10 0 21 81 516 576 4.65e-33 119
MsG0580024780.01.T02 MTR_4g095058 83.607 61 10 0 21 81 518 578 4.69e-33 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0580024780.01.T01 AT5G67320 80.328 61 12 0 21 81 553 613 2.81e-32 117
MsG0580024780.01.T02 AT5G67320 80.328 61 12 0 21 81 553 613 2.81e-32 117

Find 42 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAACTCCGTTGTAAGTTTA+TGG 0.077339 5:-9612894 MsG0580024780.01.T01:three_prime_UTR
ATTCAAGGACCATATATTTA+TGG 0.160905 5:+9613187 None:intergenic
ATATTGACAGAACTGTATTT+TGG 0.226598 5:-9612973 MsG0580024780.01.T01:three_prime_UTR
AGTCTTTGTGAGAGCATTAC+TGG 0.233950 5:-9612715 MsG0580024780.01.T02:three_prime_UTR
CAAGAATGGTTAAAACTTAA+AGG 0.236174 5:+9612916 None:intergenic
GGCTAAATACTCACCACATT+GGG 0.262508 5:+9613229 None:intergenic
TAACAATACAGTTTGCGTTT+TGG 0.312131 5:-9613072 MsG0580024780.01.T01:CDS
CATAATCATTAGTAACTAGT+AGG 0.373232 5:-9612871 MsG0580024780.01.T01:three_prime_UTR
AATGATCTTGCCATCATTCA+AGG 0.388091 5:+9613172 None:intergenic
ATGACAAATCCATAAATATA+TGG 0.390659 5:-9613196 MsG0580024780.01.T01:CDS
TGTTCTCATTGGGTAACTAT+TGG 0.393629 5:-9612749 MsG0580024780.01.T02:three_prime_UTR
GAACATACCTTGGAGCTATC+TGG 0.400897 5:+9612767 None:intergenic
GCTCCAAGGTATGTTCTCAT+TGG 0.435463 5:-9612760 MsG0580024780.01.T02:three_prime_UTR
TGAGAAGAGCCACCTTACTT+TGG 0.449886 5:-9613030 MsG0580024780.01.T01:three_prime_UTR
AAAGTAAGGTGGCTCTTCTC+AGG 0.459176 5:+9613032 None:intergenic
CTCCAAGGTATGTTCTCATT+GGG 0.465225 5:-9612759 MsG0580024780.01.T02:three_prime_UTR
ATTAAAACATACAACGGTAA+TGG 0.483414 5:-9613152 MsG0580024780.01.T01:CDS
GGATTTGTCATGGGACCCAC+TGG 0.485949 5:+9613208 None:intergenic
ATACAGTTCTGTCAATATCA+TGG 0.492139 5:+9612978 None:intergenic
TATATTTATGGATTTGTCAT+GGG 0.493957 5:+9613199 None:intergenic
AATATATGGTCCTTGAATGA+TGG 0.499260 5:-9613182 MsG0580024780.01.T01:CDS
TTGAGCAACTAGCCAAAGTA+AGG 0.500908 5:+9613018 None:intergenic
ATATATTTATGGATTTGTCA+TGG 0.524784 5:+9613198 None:intergenic
GTCTTTGTGAGAGCATTACT+GGG 0.543975 5:-9612714 MsG0580024780.01.T02:three_prime_UTR
TGGCTAAATACTCACCACAT+TGG 0.566696 5:+9613228 None:intergenic
ATAATCATTAGTAACTAGTA+GGG 0.569724 5:-9612870 MsG0580024780.01.T01:three_prime_UTR
CTCATTGGGTAACTATTGGT+AGG 0.580005 5:-9612745 MsG0580024780.01.T02:three_prime_UTR
TTACAACGGAGTTACAAGAA+TGG 0.580824 5:+9612902 None:intergenic
GAGGTCTGTTGGAACAAGGA+GGG 0.582876 5:-9613119 MsG0580024780.01.T01:CDS
AATGCTAACAAGTGCACCTA+CGG 0.584601 5:+9612940 None:intergenic
TACCCAATGAGAACATACCT+TGG 0.597919 5:+9612757 None:intergenic
GCTAAATACTCACCACATTG+GGG 0.606470 5:+9613230 None:intergenic
AAAACATACAACGGTAATGG+AGG 0.632250 5:-9613149 MsG0580024780.01.T01:CDS
CATGATAACGATTATACAGA+CGG 0.632999 5:+9612809 None:intergenic
GTGGTGAGTATTTAGCCAGT+GGG 0.634149 5:-9613223 MsG0580024780.01.T01:CDS
TGTGGTGAGTATTTAGCCAG+TGG 0.634330 5:-9613224 MsG0580024780.01.T01:CDS
TGAGGTCTGTTGGAACAAGG+AGG 0.635956 5:-9613120 MsG0580024780.01.T01:CDS
AGCAACTAGCCAAAGTAAGG+TGG 0.639749 5:+9613021 None:intergenic
AAGATCATTAAAACATACAA+CGG 0.654641 5:-9613158 MsG0580024780.01.T01:CDS
ATTATGCCATAAACTTACAA+CGG 0.661222 5:+9612888 None:intergenic
TCTGCTGCCAGATAGCTCCA+AGG 0.682890 5:-9612774 MsG0580024780.01.T01:three_prime_UTR
TATTGCATTCAGCCCCAATG+TGG 0.700673 5:-9613242 MsG0580024780.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGAAATTTATGATAATT+AGG + Chr5:9613243-9613262 None:intergenic 10.0%
!!! AAAGTTGTTTAATTTGATTA+TGG - Chr5:9612818-9612837 MsG0580024780.01.T01:three_prime_UTR 15.0%
!! AACTTCTATTATAGTTTATC+TGG - Chr5:9613656-9613675 MsG0580024780.01.T01:intron 20.0%
!! AAGATCATTAAAACATACAA+CGG - Chr5:9613862-9613881 MsG0580024780.01.T01:intron 20.0%
!! ACTTTATATGAAAAACTACA+CGG + Chr5:9612803-9612822 None:intergenic 20.0%
!! ATAATCATTAGTAACTAGTA+GGG - Chr5:9614150-9614169 MsG0580024780.01.T01:intron 20.0%
!! ATATATTTATGGATTTGTCA+TGG + Chr5:9613825-9613844 None:intergenic 20.0%
!! ATGACAAATCCATAAATATA+TGG - Chr5:9613824-9613843 MsG0580024780.01.T01:intron 20.0%
!! TATATTTATGGATTTGTCAT+GGG + Chr5:9613824-9613843 None:intergenic 20.0%
!! TGATAAAAACTAATACTTTG+AGG - Chr5:9612967-9612986 MsG0580024780.01.T01:three_prime_UTR 20.0%
!! TTAAGTATGAAATGAATGTT+AGG + Chr5:9613629-9613648 None:intergenic 20.0%
!!! ATAAGAATTTGAAGAGTTTT+AGG - Chr5:9613271-9613290 MsG0580024780.01.T01:intron 20.0%
! AAACTAATTCATAGCTTGAA+TGG - Chr5:9613480-9613499 MsG0580024780.01.T01:intron 25.0%
! AACTGTATTGTTAGAAAAAC+AGG + Chr5:9613941-9613960 None:intergenic 25.0%
! AATGACTAAATAGTGTCAAA+AGG + Chr5:9613403-9613422 None:intergenic 25.0%
! ATTAAAACATACAACGGTAA+TGG - Chr5:9613868-9613887 MsG0580024780.01.T01:intron 25.0%
! ATTATGCCATAAACTTACAA+CGG + Chr5:9614135-9614154 None:intergenic 25.0%
! ATTCAAGGACCATATATTTA+TGG + Chr5:9613836-9613855 None:intergenic 25.0%
! CAAGAATGGTTAAAACTTAA+AGG + Chr5:9614107-9614126 None:intergenic 25.0%
! CATAATCATTAGTAACTAGT+AGG - Chr5:9614149-9614168 MsG0580024780.01.T01:intron 25.0%
!! AATTTTGTAGAATGTGATGA+GGG + Chr5:9613172-9613191 None:intergenic 25.0%
!! AGCTTTTTATGTTATATCAG+TGG - Chr5:9613521-9613540 MsG0580024780.01.T01:intron 25.0%
!! ATATTGACAGAACTGTATTT+TGG - Chr5:9614047-9614066 MsG0580024780.01.T01:intron 25.0%
!!! TGCTTGTTGTCTTTTAAATT+TGG - Chr5:9612873-9612892 MsG0580024780.01.T01:three_prime_UTR 25.0%
!!! TTTAATTTGATTATGGTGAC+CGG - Chr5:9612825-9612844 MsG0580024780.01.T01:three_prime_UTR 25.0%
AATATATGGTCCTTGAATGA+TGG - Chr5:9613838-9613857 MsG0580024780.01.T01:intron 30.0%
ATACAGTTCTGTCAATATCA+TGG + Chr5:9614045-9614064 None:intergenic 30.0%
ATATCAGTGGCAAGAATATA+TGG - Chr5:9613534-9613553 MsG0580024780.01.T01:intron 30.0%
ATTATAGTTTATCTGGTGTC+TGG - Chr5:9613663-9613682 MsG0580024780.01.T01:intron 30.0%
TACTAGCTAATGTGTGATAT+TGG - Chr5:9612918-9612937 MsG0580024780.01.T01:three_prime_UTR 30.0%
! ATTTTGTAGAATGTGATGAG+GGG + Chr5:9613171-9613190 None:intergenic 30.0%
! CAAGGTTTAAAACAATGTAG+TGG + Chr5:9613053-9613072 None:intergenic 30.0%
! CATGATAACGATTATACAGA+CGG + Chr5:9614214-9614233 None:intergenic 30.0%
! GAATTTTGTAGAATGTGATG+AGG + Chr5:9613173-9613192 None:intergenic 30.0%
! TAACAATACAGTTTGCGTTT+TGG - Chr5:9613948-9613967 MsG0580024780.01.T01:intron 30.0%
!! ATATTTTGAACAGTGAGTAG+TGG + Chr5:9613078-9613097 None:intergenic 30.0%
!!! TTGGTTTTGACTGGTTTATT+TGG - Chr5:9613732-9613751 MsG0580024780.01.T01:intron 30.0%
AATGATCTTGCCATCATTCA+AGG + Chr5:9613851-9613870 None:intergenic 35.0%
CCAGTCAAAACCAAAAGAAT+TGG + Chr5:9613726-9613745 None:intergenic 35.0%
GTAACTCCGTTGTAAGTTTA+TGG - Chr5:9614126-9614145 MsG0580024780.01.T01:intron 35.0%
TGTTCTCATTGGGTAACTAT+TGG - Chr5:9614271-9614290 MsG0580024780.01.T01:intron 35.0%
TTACAACGGAGTTACAAGAA+TGG + Chr5:9614121-9614140 None:intergenic 35.0%
! AAAACATACAACGGTAATGG+AGG - Chr5:9613871-9613890 MsG0580024780.01.T01:intron 35.0%
! AATTTTGTAGAAGCGATGAG+GGG + Chr5:9613129-9613148 None:intergenic 35.0%
! AGAATTTTGTAGAAGCGATG+AGG + Chr5:9613131-9613150 None:intergenic 35.0%
! GAATTTTGTAGAAGCGATGA+GGG + Chr5:9613130-9613149 None:intergenic 35.0%
! TGTTTTCTTGGCAACATTTC+AGG - Chr5:9613687-9613706 MsG0580024780.01.T01:intron 35.0%
! TTTTGTAGAATGTGATGAGG+GGG + Chr5:9613170-9613189 None:intergenic 35.0%
!! ACTGGTTTATTTGGTTCTAC+AGG - Chr5:9613741-9613760 MsG0580024780.01.T01:intron 35.0%
!! CTGGTTTATTTGGTTCTACA+GGG - Chr5:9613742-9613761 MsG0580024780.01.T01:intron 35.0%
!!! CCAATTCTTTTGGTTTTGAC+TGG - Chr5:9613723-9613742 MsG0580024780.01.T01:intron 35.0%
!!! GACAGAACTGTATTTTGGTT+CGG - Chr5:9614052-9614071 MsG0580024780.01.T01:intron 35.0%
AAGACAACAAGCATAGTTGC+AGG + Chr5:9612866-9612885 None:intergenic 40.0%
AATGCTAACAAGTGCACCTA+CGG + Chr5:9614083-9614102 None:intergenic 40.0%
ATGATTATCAACCCGGTTGT+AGG - Chr5:9612704-9612723 MsG0580024780.01.T02:three_prime_UTR 40.0%
CAGTGGCAAGAATATATGGA+TGG - Chr5:9613538-9613557 MsG0580024780.01.T01:intron 40.0%
CTCATTGGGTAACTATTGGT+AGG - Chr5:9614275-9614294 MsG0580024780.01.T01:intron 40.0%
CTCCAAGGTATGTTCTCATT+GGG - Chr5:9614261-9614280 MsG0580024780.01.T01:intron 40.0%
GCTAAATACTCACCACATTG+GGG + Chr5:9613793-9613812 None:intergenic 40.0%
GGCTAAATACTCACCACATT+GGG + Chr5:9613794-9613813 None:intergenic 40.0%
TACCCAATGAGAACATACCT+TGG + Chr5:9614266-9614285 None:intergenic 40.0%
TGACTCTACCGTAAAGCTAT+GGG - Chr5:9613443-9613462 MsG0580024780.01.T01:intron 40.0%
TGATTATCAACCCGGTTGTA+GGG - Chr5:9612705-9612724 MsG0580024780.01.T02:three_prime_UTR 40.0%
TGGCTAAATACTCACCACAT+TGG + Chr5:9613795-9613814 None:intergenic 40.0%
TTCATAGCTTGAATGGACAC+AGG - Chr5:9613487-9613506 MsG0580024780.01.T01:intron 40.0%
TTGAGCAACTAGCCAAAGTA+AGG + Chr5:9614005-9614024 None:intergenic 40.0%
!! AGTCTTTGTGAGAGCATTAC+TGG - Chr5:9614305-9614324 MsG0580024780.01.T01:intron 40.0%
!! GTCTTTGTGAGAGCATTACT+GGG - Chr5:9614306-9614325 MsG0580024780.01.T01:intron 40.0%
!!! CGGTAATGGAGGTATTTTTG+AGG - Chr5:9613882-9613901 MsG0580024780.01.T01:intron 40.0%
!!! GAGGTATTTTTGAGGTCTGT+TGG - Chr5:9613890-9613909 MsG0580024780.01.T01:intron 40.0%
!!! GTAGTTGGTGCCAATTCTTT+TGG - Chr5:9613713-9613732 MsG0580024780.01.T01:intron 40.0%
!!! TTTTGAGGTCTGTTGGAACA+AGG - Chr5:9613897-9613916 MsG0580024780.01.T01:intron 40.0%
AAAGTAAGGTGGCTCTTCTC+AGG + Chr5:9613991-9614010 None:intergenic 45.0%
AGCAACTAGCCAAAGTAAGG+TGG + Chr5:9614002-9614021 None:intergenic 45.0%
AGCATCCTGCTTGTAATGTG+CGG - Chr5:9613586-9613605 MsG0580024780.01.T01:intron 45.0%
CAACATTTCAGGCTGGTAGT+TGG - Chr5:9613698-9613717 MsG0580024780.01.T01:intron 45.0%
CACATTACAAGCAGGATGCT+GGG + Chr5:9613586-9613605 None:intergenic 45.0%
GAACATACCTTGGAGCTATC+TGG + Chr5:9614256-9614275 None:intergenic 45.0%
GATTATCAACCCGGTTGTAG+GGG - Chr5:9612706-9612725 MsG0580024780.01.T02:three_prime_UTR 45.0%
GCTCCAAGGTATGTTCTCAT+TGG - Chr5:9614260-9614279 MsG0580024780.01.T01:intron 45.0%
GTGACTCTACCGTAAAGCTA+TGG - Chr5:9613442-9613461 MsG0580024780.01.T01:intron 45.0%
GTGGTGAGTATTTAGCCAGT+GGG - Chr5:9613797-9613816 MsG0580024780.01.T01:intron 45.0%
TACCGTAAAGCTATGGGATG+CGG - Chr5:9613449-9613468 MsG0580024780.01.T01:intron 45.0%
TATTGCATTCAGCCCCAATG+TGG - Chr5:9613778-9613797 MsG0580024780.01.T01:intron 45.0%
TCACTGATGCACTGTACAGA+AGG + Chr5:9613426-9613445 None:intergenic 45.0%
TGAGAAGAGCCACCTTACTT+TGG - Chr5:9613990-9614009 MsG0580024780.01.T01:intron 45.0%
TGTGGTGAGTATTTAGCCAG+TGG - Chr5:9613796-9613815 MsG0580024780.01.T01:intron 45.0%
TTCTTGGCAACATTTCAGGC+TGG - Chr5:9613691-9613710 MsG0580024780.01.T01:intron 45.0%
! GAACAGTGAGTAGTGGAACA+AGG + Chr5:9613071-9613090 None:intergenic 45.0%
! TTCCGCATCCCATAGCTTTA+CGG + Chr5:9613454-9613473 None:intergenic 45.0%
!! CTGGTGTCTGGTTGTTTTCT+TGG - Chr5:9613675-9613694 MsG0580024780.01.T01:intron 45.0%
AAGCTATGGGATGCGGAACT+CGG - Chr5:9613456-9613475 MsG0580024780.01.T01:intron 50.0%
ACAAGCATAGTTGCAGGTGC+AGG + Chr5:9612860-9612879 None:intergenic 50.0%
ATTACAAGCAGGATGCTGGG+AGG + Chr5:9613583-9613602 None:intergenic 50.0%
GAGGTCTGTTGGAACAAGGA+GGG - Chr5:9613901-9613920 MsG0580024780.01.T01:intron 50.0%
GCACATTACAAGCAGGATGC+TGG + Chr5:9613587-9613606 None:intergenic 50.0%
GTTGACCGCACATTACAAGC+AGG + Chr5:9613594-9613613 None:intergenic 50.0%
TGAGGTCTGTTGGAACAAGG+AGG - Chr5:9613900-9613919 MsG0580024780.01.T01:intron 50.0%
!!! TTTTGGTTCGGTAGTGCCGT+AGG - Chr5:9614064-9614083 MsG0580024780.01.T01:intron 50.0%
AGCTATGGGATGCGGAACTC+GGG - Chr5:9613457-9613476 MsG0580024780.01.T01:intron 55.0%
CAGGTGCAGGCACAGATATC+CGG + Chr5:9612847-9612866 None:intergenic 55.0%
GGATTTGTCATGGGACCCAC+TGG + Chr5:9613815-9613834 None:intergenic 55.0%
TCTGCTGCCAGATAGCTCCA+AGG - Chr5:9614246-9614265 MsG0580024780.01.T01:intron 55.0%
ACAAGCAGGATGCTGGGAGG+AGG + Chr5:9613580-9613599 None:intergenic 60.0%
TCCCAGCTGACCCCTACAAC+CGG + Chr5:9612719-9612738 None:intergenic 60.0%
ACCCGGTTGTAGGGGTCAGC+TGG - Chr5:9612714-9612733 MsG0580024780.01.T02:three_prime_UTR 65.0%
CCCAGCTGACCCCTACAACC+GGG + Chr5:9612718-9612737 None:intergenic 65.0%
CCCGGTTGTAGGGGTCAGCT+GGG - Chr5:9612715-9612734 MsG0580024780.01.T02:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
Chr5 gene 9612704 9614338 9612704 ID=MsG0580024780.01;Name=MsG0580024780.01
Chr5 mRNA 9612771 9614338 9612771 ID=MsG0580024780.01.T01;Parent=MsG0580024780.01;Name=MsG0580024780.01.T01;_AED=0.49;_eAED=0.51;_QI=0|0.5|0.66|1|0|0|3|267|81
Chr5 exon 9612771 9612940 9612771 ID=MsG0580024780.01.T01:exon:26525;Parent=MsG0580024780.01.T01
Chr5 exon 9612961 9613279 9612961 ID=MsG0580024780.01.T01:exon:26524;Parent=MsG0580024780.01.T01
Chr5 CDS 9614315 9614338 9614315 ID=MsG0580024780.01.T01:cds;Parent=MsG0580024780.01.T01
Chr5 CDS 9613058 9613279 9613058 ID=MsG0580024780.01.T01:cds;Parent=MsG0580024780.01.T01
Chr5 three_prime_UTR 9612961 9613057 9612961 ID=MsG0580024780.01.T01:three_prime_utr;Parent=MsG0580024780.01.T01
Chr5 three_prime_UTR 9612771 9612940 9612771 ID=MsG0580024780.01.T01:three_prime_utr;Parent=MsG0580024780.01.T01
Chr5 mRNA 9612704 9614338 9612704 ID=MsG0580024780.01.T02;Parent=MsG0580024780.01;Name=MsG0580024780.01.T02;_AED=0.49;_eAED=0.51;_QI=0|0|0.5|1|0|0|2|354|81
Chr5 exon 9612704 9613279 9612704 ID=MsG0580024780.01.T02:exon:26526;Parent=MsG0580024780.01.T02
Chr5 CDS 9614315 9614338 9614315 ID=MsG0580024780.01.T02:cds;Parent=MsG0580024780.01.T02
Chr5 CDS 9613058 9613279 9613058 ID=MsG0580024780.01.T02:cds;Parent=MsG0580024780.01.T02
Chr5 three_prime_UTR 9612704 9613057 9612704 ID=MsG0580024780.01.T02:three_prime_utr;Parent=MsG0580024780.01.T02
Gene Sequence

>MsG0580024780.01.T01

ATGATTATCAACCCGGTTGTAGGGGGATCGTGTATATACTATTGCATTCAGCCCCAATGTGGTGAGTATTTAGCCAGTGGGTCCCATGACAAATCCATAAATATATGGTCCTTGAATGATGGCAAGATCATTAAAACATACAACGGTAATGGAGGTATTTTTGAGGTCTGTTGGAACAAGGAGGGTGACAAGATCGCTGCCTGTTTTTCTAACAATACAGTTTGCGTTTTGGATTTCAGAATGTAA

>MsG0580024780.01.T02

ATGATTATCAACCCGGTTGTAGGGGGATCGTGTATATACTATTGCATTCAGCCCCAATGTGGTGAGTATTTAGCCAGTGGGTCCCATGACAAATCCATAAATATATGGTCCTTGAATGATGGCAAGATCATTAAAACATACAACGGTAATGGAGGTATTTTTGAGGTCTGTTGGAACAAGGAGGGTGACAAGATCGCTGCCTGTTTTTCTAACAATACAGTTTGCGTTTTGGATTTCAGAATGTAA
Protein sequence

>MsG0580024780.01.T01

MIINPVVGGSCIYYCIQPQCGEYLASGSHDKSINIWSLNDGKIIKTYNGNGGIFEVCWNKEGDKIAACFSNNTVCVLDFRM*

>MsG0580024780.01.T02

MIINPVVGGSCIYYCIQPQCGEYLASGSHDKSINIWSLNDGKIIKTYNGNGGIFEVCWNKEGDKIAACFSNNTVCVLDFRM*