AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380011641.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380011641.01.T01 MTR_3g007670 98.630 73 1 0 1 73 1 73 8.37e-48 145
MsG0380011641.01.T01 MTR_7g028755 76.562 64 12 1 1 61 103 166 3.67e-27 97.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380011641.01.T01 AT5G14105 66.667 75 19 2 1 70 1 74 2.09e-23 84.7

Find 21 sgRNAs with CRISPR-Local

Find 139 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCTTTGATTGTAATTCTTT+TGG 0.221706 3:-2928424 None:intergenic
TCCTCCTTAGGTATGTCTTT+TGG 0.234032 3:-2928454 None:intergenic
CAGAGCACAGTGTGAGAGTT+AGG 0.302460 3:+2926232 None:intergenic
AATTTCATTCTGACGGTTGC+CGG 0.320649 3:+2926279 MsG0380011641.01.T01:CDS
ATGCTGGTAATAGGATGTTT+AGG 0.407528 3:+2928492 MsG0380011641.01.T01:three_prime_UTR
CTAGTGTGTATGCTGGTAAT+AGG 0.434426 3:+2928483 MsG0380011641.01.T01:exon
ACGTTAAACACATTCGTCAC+TGG 0.475083 3:+2926367 MsG0380011641.01.T01:CDS
TCCAAAAGAATTACAATCAA+AGG 0.475520 3:+2928423 MsG0380011641.01.T01:CDS
TAGATAAGAATCCGAATACA+AGG 0.522911 3:-2928658 None:intergenic
CACTAGTGCTTATCCTCCTT+AGG 0.532294 3:-2928466 None:intergenic
AAGCACCACGGCGCTTACAC+CGG 0.551645 3:-2926298 None:intergenic
ATAAGCACTAGTGTGTATGC+TGG 0.570458 3:+2928476 MsG0380011641.01.T01:exon
AGTTAGGAATCAGACATCAA+TGG 0.593442 3:+2926248 MsG0380011641.01.T01:exon
TCCAAAAGACATACCTAAGG+AGG 0.600639 3:+2928453 MsG0380011641.01.T01:CDS
ATATGAACATAATACAGTGA+TGG 0.619101 3:-2928595 None:intergenic
TCCTCCAAAAGACATACCTA+AGG 0.623303 3:+2928450 MsG0380011641.01.T01:CDS
GATAACGAATTTCATTCTGA+CGG 0.642842 3:+2926272 MsG0380011641.01.T01:CDS
TCACTTGGAAGAAGAAGTAG+CGG 0.670878 3:-2926403 None:intergenic
AGATAAGAATCCGAATACAA+GGG 0.699506 3:-2928657 None:intergenic
GGTTGCCGGTGTAAGCGCCG+TGG 0.713581 3:+2926293 MsG0380011641.01.T01:CDS
ACTTCGTAGAAGAAGCACCA+CGG 0.754179 3:-2926310 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATTGTAAAAAAATCTT+TGG - Chr3:2927759-2927778 None:intergenic 10.0%
!!! ATATAAAGTAGTTTTTATTT+AGG + Chr3:2928614-2928633 MsG0380011641.01.T01:three_prime_UTR 10.0%
!! ATTGTATATAAATCATTCAT+TGG + Chr3:2926587-2926606 MsG0380011641.01.T01:intron 15.0%
!! TAAAAATTTATGATAGCATA+TGG + Chr3:2926938-2926957 MsG0380011641.01.T01:intron 15.0%
!! TACAAATTTCAAACAAAAAA+AGG - Chr3:2926527-2926546 None:intergenic 15.0%
!!! AAAGTTTCAATTTTTATTAC+TGG + Chr3:2926440-2926459 MsG0380011641.01.T01:intron 15.0%
!!! AAGTTTCAATTTTTATTACT+GGG + Chr3:2926441-2926460 MsG0380011641.01.T01:intron 15.0%
!!! ATGCTATCATAAATTTTTAA+GGG - Chr3:2926937-2926956 None:intergenic 15.0%
!!! CATAACTTACATTTTTTATA+GGG - Chr3:2927809-2927828 None:intergenic 15.0%
!!! TATGCTATCATAAATTTTTA+AGG - Chr3:2926938-2926957 None:intergenic 15.0%
!!! TCATAACTTACATTTTTTAT+AGG - Chr3:2927810-2927829 None:intergenic 15.0%
!! AGAAATAAAACTATTGTAGT+TGG + Chr3:2927687-2927706 MsG0380011641.01.T01:intron 20.0%
!! ATTGTAAAAAAATCTTTGGA+TGG - Chr3:2927755-2927774 None:intergenic 20.0%
!! CGTAAATTATAATTAGGAAT+TGG + Chr3:2926710-2926729 MsG0380011641.01.T01:intron 20.0%
!! TGTGATCGTAAATTATAATT+AGG + Chr3:2926704-2926723 MsG0380011641.01.T01:intron 20.0%
!! TTAAATCAATTGTATACGTT+TGG - Chr3:2927176-2927195 None:intergenic 20.0%
!! TTTCACAATACTTCATAATT+TGG - Chr3:2927545-2927564 None:intergenic 20.0%
!!! ACAAGTTTTCATATACTTTA+GGG - Chr3:2928233-2928252 None:intergenic 20.0%
!!! ATGTAAGTTATGAATCTTTT+CGG + Chr3:2927817-2927836 MsG0380011641.01.T01:intron 20.0%
!!! TAATTTAGACTTGTTAACTA+TGG + Chr3:2927110-2927129 MsG0380011641.01.T01:intron 20.0%
!!! TACAAGATTTTTCTAAAAGA+CGG - Chr3:2927638-2927657 None:intergenic 20.0%
!!! TGATTCTATAAACTTGATTT+TGG - Chr3:2927377-2927396 None:intergenic 20.0%
!!! TTATTTCTTTTCAAACAAGA+GGG - Chr3:2927675-2927694 None:intergenic 20.0%
!!! TTTATTTCTTTTCAAACAAG+AGG - Chr3:2927676-2927695 None:intergenic 20.0%
! AAAGTATATGAAAACTTGTC+AGG + Chr3:2928234-2928253 MsG0380011641.01.T01:intron 25.0%
! AAATTAGATAGTGATGCTTT+AGG + Chr3:2928302-2928321 MsG0380011641.01.T01:intron 25.0%
! AACTTCTCTAAATATAAGGT+AGG - Chr3:2927929-2927948 None:intergenic 25.0%
! AATTAGATAGTGATGCTTTA+GGG + Chr3:2928303-2928322 MsG0380011641.01.T01:intron 25.0%
! ACCTTTCGTTTAAAAATAGT+TGG - Chr3:2927985-2928004 None:intergenic 25.0%
! ATAAAACTATTGTAGTTGGT+TGG + Chr3:2927691-2927710 MsG0380011641.01.T01:intron 25.0%
! ATATGAACATAATACAGTGA+TGG - Chr3:2928598-2928617 None:intergenic 25.0%
! CCCAAAATACATATAATAAG+CGG - Chr3:2928278-2928297 None:intergenic 25.0%
! GATAATGATTTGATGAGTTT+CGG + Chr3:2927839-2927858 MsG0380011641.01.T01:intron 25.0%
! GGTTATGTGATCATATATTA+CGG + Chr3:2926833-2926852 MsG0380011641.01.T01:intron 25.0%
! TATAAAGAATAAGACTCACT+TGG - Chr3:2926421-2926440 None:intergenic 25.0%
! TCCAAAAGAATTACAATCAA+AGG + Chr3:2928423-2928442 MsG0380011641.01.T01:CDS 25.0%
! TTGTATGAATTTGACCATTT+GGG + Chr3:2927519-2927538 MsG0380011641.01.T01:intron 25.0%
!! AATTGGTGGTTTATTCATAT+AGG + Chr3:2928330-2928349 MsG0380011641.01.T01:intron 25.0%
!! ACAATTGATTTAAACCTGTT+TGG + Chr3:2927183-2927202 MsG0380011641.01.T01:intron 25.0%
!! ACCGCTTATTATATGTATTT+TGG + Chr3:2928274-2928293 MsG0380011641.01.T01:intron 25.0%
!! ACCTTTGATTGTAATTCTTT+TGG - Chr3:2928427-2928446 None:intergenic 25.0%
!! ATGATTTTTGTCATCTTTTC+AGG + Chr3:2928398-2928417 MsG0380011641.01.T01:intron 25.0%
!! ATTAATTTTGCCTTCGAAAT+TGG + Chr3:2927221-2927240 MsG0380011641.01.T01:intron 25.0%
!! CCGCTTATTATATGTATTTT+GGG + Chr3:2928275-2928294 MsG0380011641.01.T01:intron 25.0%
!! CGCTTATTATATGTATTTTG+GGG + Chr3:2928276-2928295 MsG0380011641.01.T01:intron 25.0%
!! GACAAGTTTTCATATACTTT+AGG - Chr3:2928234-2928253 None:intergenic 25.0%
!! GATGGATTTCATATACTTAT+GGG - Chr3:2928202-2928221 None:intergenic 25.0%
!! TGATAAAAGTATAGAAGAGA+AGG + Chr3:2926642-2926661 MsG0380011641.01.T01:intron 25.0%
!! TGATTTTTGTCATCTTTTCA+GGG + Chr3:2928399-2928418 MsG0380011641.01.T01:intron 25.0%
!! TTTTTAAACGAAAGGTAGAA+TGG + Chr3:2927989-2928008 MsG0380011641.01.T01:intron 25.0%
!!! AAGTATTGTGAAAACTCTTT+TGG + Chr3:2927552-2927571 MsG0380011641.01.T01:intron 25.0%
!!! AATTTGAGAGGTTGATATTT+TGG - Chr3:2928148-2928167 None:intergenic 25.0%
!!! GTTTTTATTTAGGTTTCTCT+TGG + Chr3:2928624-2928643 MsG0380011641.01.T01:three_prime_UTR 25.0%
!!! TAAATTTTTAAGGGCATGTT+TGG - Chr3:2926928-2926947 None:intergenic 25.0%
!!! TGATGGATTTCATATACTTA+TGG - Chr3:2928203-2928222 None:intergenic 25.0%
AAACCATGATTTCAACAGAT+AGG - Chr3:2928058-2928077 None:intergenic 30.0%
ACTTGGAAAAAAAGAAGAGA+TGG - Chr3:2927725-2927744 None:intergenic 30.0%
AGATAAGAATCCGAATACAA+GGG - Chr3:2928660-2928679 None:intergenic 30.0%
ATTGATGAACTGTGATTGAA+TGG + Chr3:2926812-2926831 MsG0380011641.01.T01:intron 30.0%
ATTTAGGGACTAAATTTGAG+AGG - Chr3:2928160-2928179 None:intergenic 30.0%
CGAGAACTTCTCTAAATATA+AGG - Chr3:2927933-2927952 None:intergenic 30.0%
CTTGGAAAAAAAGAAGAGAT+GGG - Chr3:2927724-2927743 None:intergenic 30.0%
CTTGTATGAATTTGACCATT+TGG + Chr3:2927518-2927537 MsG0380011641.01.T01:intron 30.0%
GAAAGATTGATGAGAATATG+AGG + Chr3:2927070-2927089 MsG0380011641.01.T01:intron 30.0%
GATAACGAATTTCATTCTGA+CGG + Chr3:2926272-2926291 MsG0380011641.01.T01:CDS 30.0%
GTCAAATTCATACAAGCAAA+AGG - Chr3:2927514-2927533 None:intergenic 30.0%
TAGATAAGAATCCGAATACA+AGG - Chr3:2928661-2928680 None:intergenic 30.0%
TCAATTGTATACGTTTGGAA+TGG - Chr3:2927171-2927190 None:intergenic 30.0%
TGTTAACTATGGTGTATGTT+TGG + Chr3:2927121-2927140 MsG0380011641.01.T01:intron 30.0%
TTCTAATCCCTACAATCTAA+TGG - Chr3:2926995-2927014 None:intergenic 30.0%
! AGGGATTAGAAATTTTGTAC+TGG + Chr3:2927004-2927023 MsG0380011641.01.T01:intron 30.0%
! CATCAATCTTTCAAGTCAAA+GGG - Chr3:2927062-2927081 None:intergenic 30.0%
! GATTAGAAATTTTGTACTGG+TGG + Chr3:2927007-2927026 MsG0380011641.01.T01:intron 30.0%
! TACTTTAGGGACTAAAATGA+TGG - Chr3:2928220-2928239 None:intergenic 30.0%
! TCATCAATCTTTCAAGTCAA+AGG - Chr3:2927063-2927082 None:intergenic 30.0%
!! ATAGTCTGCTTAAGTTGTTT+TGG + Chr3:2927450-2927469 MsG0380011641.01.T01:intron 30.0%
!! TAGTCTGCTTAAGTTGTTTT+GGG + Chr3:2927451-2927470 MsG0380011641.01.T01:intron 30.0%
!!! AAAGGTAGAATGGTTTTGTT+GGG + Chr3:2927999-2928018 MsG0380011641.01.T01:intron 30.0%
!!! GCCAACTATTTTTAAACGAA+AGG + Chr3:2927981-2928000 MsG0380011641.01.T01:intron 30.0%
ACTTCATAATTTGGCCCAAA+TGG - Chr3:2927536-2927555 None:intergenic 35.0%
AGTTAGGAATCAGACATCAA+TGG + Chr3:2926248-2926267 MsG0380011641.01.T01:exon 35.0%
ATGATTTGATGAGTTTCGGT+TGG + Chr3:2927843-2927862 MsG0380011641.01.T01:intron 35.0%
ATGCCTATCTGTTGAAATCA+TGG + Chr3:2928052-2928071 MsG0380011641.01.T01:intron 35.0%
ATGCTGGTAATAGGATGTTT+AGG + Chr3:2928492-2928511 MsG0380011641.01.T01:three_prime_UTR 35.0%
CAAGTAAGAACCAATTTCGA+AGG - Chr3:2927234-2927253 None:intergenic 35.0%
GATGAGACCATTAGATTGTA+GGG + Chr3:2926985-2927004 MsG0380011641.01.T01:intron 35.0%
GCAAATCTAGGTTTGAATTC+TGG + Chr3:2926960-2926979 MsG0380011641.01.T01:intron 35.0%
GTCAGGATTTCACATACTTT+AGG + Chr3:2928251-2928270 MsG0380011641.01.T01:intron 35.0%
TGATAGCATATGGCAAATCT+AGG + Chr3:2926948-2926967 MsG0380011641.01.T01:intron 35.0%
TGATGAGACCATTAGATTGT+AGG + Chr3:2926984-2927003 MsG0380011641.01.T01:intron 35.0%
TTCTTATTGTTTCCGCAACT+GGG + Chr3:2926483-2926502 MsG0380011641.01.T01:intron 35.0%
! CTTTGGATGGACATTTTACT+TGG - Chr3:2927742-2927761 None:intergenic 35.0%
! TTAGGAATTGGCACAAGTTT+TGG + Chr3:2926722-2926741 MsG0380011641.01.T01:intron 35.0%
! TTTTCGAAGACCCTTGTATT+CGG + Chr3:2928647-2928666 MsG0380011641.01.T01:three_prime_UTR 35.0%
!! GAAATTTTGTACTGGTGGAA+AGG + Chr3:2927012-2927031 MsG0380011641.01.T01:intron 35.0%
!! TGATGCTTTAGGGACTAAAT+TGG + Chr3:2928313-2928332 MsG0380011641.01.T01:intron 35.0%
!! TTTTAAGGGCATGTTTGGAT+GGG - Chr3:2926923-2926942 None:intergenic 35.0%
!! TTTTTAAGGGCATGTTTGGA+TGG - Chr3:2926924-2926943 None:intergenic 35.0%
!!! GAAAGGTAGAATGGTTTTGT+TGG + Chr3:2927998-2928017 MsG0380011641.01.T01:intron 35.0%
AATTTCATTCTGACGGTTGC+CGG + Chr3:2926279-2926298 MsG0380011641.01.T01:CDS 40.0%
ACGTTAAACACATTCGTCAC+TGG + Chr3:2926367-2926386 MsG0380011641.01.T01:CDS 40.0%
ATAAGCACTAGTGTGTATGC+TGG + Chr3:2928476-2928495 MsG0380011641.01.T01:exon 40.0%
CTAGTGTGTATGCTGGTAAT+AGG + Chr3:2928483-2928502 MsG0380011641.01.T01:exon 40.0%
CTATTGTAGTTGGTTGGACT+TGG + Chr3:2927697-2927716 MsG0380011641.01.T01:intron 40.0%
CTGCTAGAAAACATCCAAAC+AGG - Chr3:2927200-2927219 None:intergenic 40.0%
GTTCTTATTGTTTCCGCAAC+TGG + Chr3:2926482-2926501 MsG0380011641.01.T01:intron 40.0%
TCACTTGGAAGAAGAAGTAG+CGG - Chr3:2926406-2926425 None:intergenic 40.0%
TCATGGTTTATCTCGAGAGT+TGG + Chr3:2928069-2928088 MsG0380011641.01.T01:intron 40.0%
TCCAAAAGACATACCTAAGG+AGG + Chr3:2928453-2928472 MsG0380011641.01.T01:CDS 40.0%
TCCTCCAAAAGACATACCTA+AGG + Chr3:2928450-2928469 MsG0380011641.01.T01:CDS 40.0%
TGGGTGATATACATAAGCCA+TGG + Chr3:2927470-2927489 MsG0380011641.01.T01:intron 40.0%
! TCCTCCTTAGGTATGTCTTT+TGG - Chr3:2928457-2928476 None:intergenic 40.0%
! TCCTTAGGTATGTCTTTTGG+AGG - Chr3:2928454-2928473 None:intergenic 40.0%
! TGTATGTTTGGTTTCGCTCT+TGG + Chr3:2927133-2927152 MsG0380011641.01.T01:intron 40.0%
! TTTAAGGGCATGTTTGGATG+GGG - Chr3:2926922-2926941 None:intergenic 40.0%
!! GAATTGGCACAAGTTTTGGT+GGG + Chr3:2926726-2926745 MsG0380011641.01.T01:intron 40.0%
!! TGCTTTAGGGACTAAATTGG+TGG + Chr3:2928316-2928335 MsG0380011641.01.T01:intron 40.0%
!! TTAGGTATGTCTTTTGGAGG+AGG - Chr3:2928451-2928470 None:intergenic 40.0%
!!! AGAATGGTTTTGTTGGGAGT+AGG + Chr3:2928005-2928024 MsG0380011641.01.T01:intron 40.0%
CAACAACAAAGACCCAGTTG+CGG - Chr3:2926498-2926517 None:intergenic 45.0%
CAAGACGAACTTCAACACCA+TGG - Chr3:2927490-2927509 None:intergenic 45.0%
CACTAGTGCTTATCCTCCTT+AGG - Chr3:2928469-2928488 None:intergenic 45.0%
! TTAAGGGCATGTTTGGATGG+GGG - Chr3:2926921-2926940 None:intergenic 45.0%
!! AAGTTTTGGTGGGAAAGGGA+GGG + Chr3:2926736-2926755 MsG0380011641.01.T01:intron 45.0%
!! ACTTCGTAGAAGAAGCACCA+CGG - Chr3:2926313-2926332 None:intergenic 45.0%
!! GCACAAGTTTTGGTGGGAAA+GGG + Chr3:2926732-2926751 MsG0380011641.01.T01:intron 45.0%
!! GGAATTGGCACAAGTTTTGG+TGG + Chr3:2926725-2926744 MsG0380011641.01.T01:intron 45.0%
!! TAAATTATAAAAATAATAAG+TGG + Chr3:2928175-2928194 MsG0380011641.01.T01:intron 5.0%
!!! ACTTATTATTTTTATAATTT+AGG - Chr3:2928176-2928195 None:intergenic 5.0%
!!! CTTATTATTTTTATAATTTA+GGG - Chr3:2928175-2928194 None:intergenic 5.0%
CATGTTTGGATGGGGGAGTT+TGG - Chr3:2926914-2926933 None:intergenic 50.0%
!! AGTTTTGGTGGGAAAGGGAG+GGG + Chr3:2926737-2926756 MsG0380011641.01.T01:intron 50.0%
!! CAAGTTTTGGTGGGAAAGGG+AGG + Chr3:2926735-2926754 MsG0380011641.01.T01:intron 50.0%
!! GGCACAAGTTTTGGTGGGAA+AGG + Chr3:2926731-2926750 MsG0380011641.01.T01:intron 50.0%
GTTTGGATGGGGGAGTTTGG+AGG - Chr3:2926911-2926930 None:intergenic 55.0%
!! GTTTTGGTGGGAAAGGGAGG+GGG + Chr3:2926738-2926757 MsG0380011641.01.T01:intron 55.0%
AAGCACCACGGCGCTTACAC+CGG - Chr3:2926301-2926320 None:intergenic 60.0%
TGGTGGGAAAGGGAGGGGGA+AGG + Chr3:2926742-2926761 MsG0380011641.01.T01:intron 65.0%
! GGTTGCCGGTGTAAGCGCCG+TGG + Chr3:2926293-2926312 MsG0380011641.01.T01:CDS 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 2926238 2928707 2926238 ID=MsG0380011641.01;Name=MsG0380011641.01
Chr3 mRNA 2926238 2928707 2926238 ID=MsG0380011641.01.T01;Parent=MsG0380011641.01;Name=MsG0380011641.01.T01;_AED=0.49;_eAED=0.49;_QI=29|1|1|1|0|0|2|221|73
Chr3 exon 2926238 2926421 2926238 ID=MsG0380011641.01.T01:exon:1584;Parent=MsG0380011641.01.T01
Chr3 exon 2928420 2928707 2928420 ID=MsG0380011641.01.T01:exon:1585;Parent=MsG0380011641.01.T01
Chr3 five_prime_UTR 2926238 2926266 2926238 ID=MsG0380011641.01.T01:five_prime_utr;Parent=MsG0380011641.01.T01
Chr3 CDS 2926267 2926421 2926267 ID=MsG0380011641.01.T01:cds;Parent=MsG0380011641.01.T01
Chr3 CDS 2928420 2928486 2928420 ID=MsG0380011641.01.T01:cds;Parent=MsG0380011641.01.T01
Chr3 three_prime_UTR 2928487 2928707 2928487 ID=MsG0380011641.01.T01:three_prime_utr;Parent=MsG0380011641.01.T01
Gene Sequence

>MsG0380011641.01.T01

ATGGCGATAACGAATTTCATTCTGACGGTTGCCGGTGTAAGCGCCGTGGTGCTTCTTCTACGAAGTGATGTGAAGAAATCAGCTTCAATATTCAGACAAAACGTTAAACACATTCGTCACTGGCTTGAAGAAGAAACCGCTACTTCTTCTTCCAAGGTTCCAAAAGAATTACAATCAAAGGTTCCTCCTCCAAAAGACATACCTAAGGAGGATAAGCACTAG
Protein sequence

>MsG0380011641.01.T01

MAITNFILTVAGVSAVVLLLRSDVKKSASIFRQNVKHIRHWLEEETATSSSKVPKELQSKVPPPKDIPKEDKH*