AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47668

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47668.t1 MTR_5g089100 92.191 397 28 2 1 395 1 396 0.0 726
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 70 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAACAAAAGAGGTGGATTT+TGG 0.178214 5.2:+75696663 MS.gene47668:CDS
TTGACATACCAATCTCATTT+TGG 0.200804 5.2:-75696885 None:intergenic
CTTTCTGATTCTTCTTTCAT+TGG 0.206679 5.2:-75696506 None:intergenic
TGAGGATTCATTGCCTACTA+TGG 0.314743 5.2:+75696067 MS.gene47668:CDS
CCTTCTGGAAAAGACATTAA+AGG 0.322160 5.2:-75696455 None:intergenic
TCGGTTGTTACATGAGCTTC+TGG 0.322517 5.2:+75696478 MS.gene47668:CDS
TCTTGCAAACGCCAACCCTT+TGG 0.323714 5.2:-75696549 None:intergenic
TTTCGGTTTGTCTTAGTTCT+CGG 0.336891 5.2:-75696008 None:intergenic
CTTGCAAACGCCAACCCTTT+GGG 0.352903 5.2:-75696548 None:intergenic
TCATGTAACAACCGACCTTC+TGG 0.353465 5.2:-75696470 None:intergenic
CCTCCAAGACTAGTTCAAAA+TGG 0.363341 5.2:+75696152 MS.gene47668:CDS
AGAATTAGAGAGGCACTCTT+TGG 0.366394 5.2:+75696784 MS.gene47668:CDS
TCTTAGTTCTCGGTTCACTA+TGG 0.371720 5.2:-75695998 None:intergenic
AGTTTAAGAGGCGGCATCAT+TGG 0.387438 5.2:-75696128 None:intergenic
TATGATGATCTTGGTGTTGT+AGG 0.396948 5.2:-75695918 None:intergenic
AAATTCAAACCGATCTAGAT+TGG 0.397332 5.2:-75695955 None:intergenic
GCATCTTCATATGATGATCT+TGG 0.413582 5.2:-75695927 None:intergenic
GAATGCACAGATTTCATGTC+AGG 0.415124 5.2:-75696815 None:intergenic
AGGGTTGGCGTTTGCAAGAC+AGG 0.418597 5.2:+75696553 MS.gene47668:CDS
TTCTCAAAAGCCACCTTGAA+TGG 0.424398 5.2:-75696272 None:intergenic
AGGTAAGAGAAGAGAAGAAA+GGG 0.440659 5.2:+75696294 MS.gene47668:CDS
TGGAGTAAAGATGATATATC+AGG 0.442029 5.2:+75696854 MS.gene47668:CDS
TTCTTCCACAAGCGTGCAAA+AGG 0.442067 5.2:-75696236 None:intergenic
TGAGTTTACCAAAATGAGAT+TGG 0.445183 5.2:+75696877 MS.gene47668:CDS
GAACACAGTGGTTATCAAAC+AGG 0.451484 5.2:+75695894 MS.gene47668:CDS
TTTCTTTGCCTGGGTTATGA+GGG 0.465352 5.2:+75696926 MS.gene47668:CDS
GAGAAGAAAGGGAAATCAAA+GGG 0.466521 5.2:+75696305 MS.gene47668:CDS
TCATCAGCAAATGCCATAGT+AGG 0.468021 5.2:-75696080 None:intergenic
TTGAGTCTGCTAGGACTAGT+TGG 0.469582 5.2:-75695864 None:intergenic
AGTCTTGGAGGAAGTTTAAG+AGG 0.473364 5.2:-75696140 None:intergenic
TTTGGTTTCTAATGTTGCTA+AGG 0.475219 5.2:+75696625 MS.gene47668:CDS
AGAGAAGAAAGGGAAATCAA+AGG 0.475466 5.2:+75696304 MS.gene47668:CDS
GTTTGAGGCTAAGAAGACTT+TGG 0.477506 5.2:+75696607 MS.gene47668:CDS
TAGATCCCTTTCTCCATTGA+GGG 0.480062 5.2:+75696352 MS.gene47668:CDS
TCTATTAATTTGAGTCTGCT+AGG 0.481735 5.2:-75695873 None:intergenic
AAGGTAAGAGAAGAGAAGAA+AGG 0.483464 5.2:+75696293 MS.gene47668:CDS
AGCATTGATCCTGGAGACTT+AGG 0.489838 5.2:-75696206 None:intergenic
TTGTTGTTGAAGTCCCTCAA+TGG 0.492128 5.2:-75696365 None:intergenic
GGCTAATGATACAAAGTTTG+AGG 0.498660 5.2:+75696592 MS.gene47668:CDS
TTTGCCTGGGTTATGAGGGA+TGG 0.505640 5.2:+75696930 MS.gene47668:CDS
AGAATCAGAAAGAGAAAGTA+CGG 0.508154 5.2:+75696517 MS.gene47668:CDS
CTAGATCCCTTTCTCCATTG+AGG 0.518421 5.2:+75696351 MS.gene47668:CDS
GGAAGCCTAAGCATTGATCC+TGG 0.520514 5.2:-75696215 None:intergenic
GAAGTCCCTCAATGGAGAAA+GGG 0.528545 5.2:-75696357 None:intergenic
AGTCTCCAGGATCAATGCTT+AGG 0.529586 5.2:+75696210 MS.gene47668:CDS
TGAAGTCCCTCAATGGAGAA+AGG 0.529754 5.2:-75696358 None:intergenic
ACAGGTGAGACAAGTGGAAG+TGG 0.533037 5.2:+75696571 MS.gene47668:CDS
CCCAGGCAAAGAAAAGACTT+TGG 0.534703 5.2:-75696917 None:intergenic
TTTCTTTGGGAGTTCAAACA+AGG 0.537134 5.2:+75696721 MS.gene47668:CDS
GTAGAGAGCATAGTTTAAGA+AGG 0.548216 5.2:+75696327 MS.gene47668:CDS
ATGCATTTGAGCAGCATCAA+AGG 0.548678 5.2:+75696039 MS.gene47668:CDS
ACTCATATAGCATAACTCAT+TGG 0.552715 5.2:-75695796 None:intergenic
GCGACGTCTCCTAAGTCTCC+AGG 0.561265 5.2:+75696197 MS.gene47668:CDS
AAAGATGAGAACAAAAGAGG+TGG 0.561338 5.2:+75696656 MS.gene47668:CDS
AAGAAAGATGAGAACAAAAG+AGG 0.562093 5.2:+75696653 MS.gene47668:CDS
AAATGAGATTGGTATGTCAA+AGG 0.597742 5.2:+75696888 MS.gene47668:CDS
ATGCAAACACCAATCTAGAT+CGG 0.598062 5.2:+75695946 MS.gene47668:CDS
CAAAGAAAAGACTTTGGCAA+TGG 0.599126 5.2:-75696911 None:intergenic
GTACGGTATCTGAGCCCAAA+GGG 0.602552 5.2:+75696534 MS.gene47668:CDS
GCAGCATCAAAGGCTTTGTG+AGG 0.620784 5.2:+75696049 MS.gene47668:CDS
GGTATCTGAGCCCAAAGGGT+TGG 0.621729 5.2:+75696538 MS.gene47668:CDS
CTTTCCATCCCTCATAACCC+AGG 0.625041 5.2:-75696934 None:intergenic
AGTACGGTATCTGAGCCCAA+AGG 0.630219 5.2:+75696533 MS.gene47668:CDS
CAACAAGTGTGACAAACATG+AGG 0.637422 5.2:+75696382 MS.gene47668:CDS
TGCAAGACAGGTGAGACAAG+TGG 0.641832 5.2:+75696565 MS.gene47668:CDS
CTTGGAGGAAGTTTAAGAGG+CGG 0.649976 5.2:-75696137 None:intergenic
TTCTTTGGGAGTTCAAACAA+GGG 0.664937 5.2:+75696722 MS.gene47668:CDS
AACAAGTGTGACAAACATGA+GGG 0.675618 5.2:+75696383 MS.gene47668:CDS
ATTCAACAGAATCAACGACA+TGG 0.718349 5.2:+75696834 MS.gene47668:CDS
CTCAAATTAATAGAACACAG+TGG 0.795850 5.2:+75695882 MS.gene47668:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAAAACAGAATTAGAG+AGG + chr5.2:75696774-75696793 MS.gene47668:CDS 20.0%
!!! AGTATAAAGAAGTTTTTCTT+TGG + chr5.2:75696707-75696726 MS.gene47668:CDS 20.0%
!!! GTATAAAGAAGTTTTTCTTT+GGG + chr5.2:75696708-75696727 MS.gene47668:CDS 20.0%
AAATGAGATTGGTATGTCAA+AGG + chr5.2:75696888-75696907 MS.gene47668:CDS 30.0%
AAATTCAAACCGATCTAGAT+TGG - chr5.2:75695958-75695977 None:intergenic 30.0%
AAGAAAGATGAGAACAAAAG+AGG + chr5.2:75696653-75696672 MS.gene47668:CDS 30.0%
ACTCATATAGCATAACTCAT+TGG - chr5.2:75695799-75695818 None:intergenic 30.0%
AGAATCAGAAAGAGAAAGTA+CGG + chr5.2:75696517-75696536 MS.gene47668:CDS 30.0%
CTCAAATTAATAGAACACAG+TGG + chr5.2:75695882-75695901 MS.gene47668:CDS 30.0%
CTTTCTGATTCTTCTTTCAT+TGG - chr5.2:75696509-75696528 None:intergenic 30.0%
TGAGTTTACCAAAATGAGAT+TGG + chr5.2:75696877-75696896 MS.gene47668:CDS 30.0%
TGGAGTAAAGATGATATATC+AGG + chr5.2:75696854-75696873 MS.gene47668:CDS 30.0%
! CAAATGCATTCACATCTTTT+CGG - chr5.2:75696028-75696047 None:intergenic 30.0%
! TCTATTAATTTGAGTCTGCT+AGG - chr5.2:75695876-75695895 None:intergenic 30.0%
! TTGACATACCAATCTCATTT+TGG - chr5.2:75696888-75696907 None:intergenic 30.0%
! TTTGGTTTCTAATGTTGCTA+AGG + chr5.2:75696625-75696644 MS.gene47668:CDS 30.0%
!! TGATGATTTTGATCCATTCA+AGG + chr5.2:75696259-75696278 MS.gene47668:CDS 30.0%
AAAGATGAGAACAAAAGAGG+TGG + chr5.2:75696656-75696675 MS.gene47668:CDS 35.0%
AACAAGTGTGACAAACATGA+GGG + chr5.2:75696383-75696402 MS.gene47668:CDS 35.0%
AAGGTAAGAGAAGAGAAGAA+AGG + chr5.2:75696293-75696312 MS.gene47668:CDS 35.0%
AGAGAAGAAAGGGAAATCAA+AGG + chr5.2:75696304-75696323 MS.gene47668:CDS 35.0%
AGGTAAGAGAAGAGAAGAAA+GGG + chr5.2:75696294-75696313 MS.gene47668:CDS 35.0%
ATGCAAACACCAATCTAGAT+CGG + chr5.2:75695946-75695965 MS.gene47668:CDS 35.0%
ATTCAACAGAATCAACGACA+TGG + chr5.2:75696834-75696853 MS.gene47668:CDS 35.0%
CAAAGAAAAGACTTTGGCAA+TGG - chr5.2:75696914-75696933 None:intergenic 35.0%
GAGAAGAAAGGGAAATCAAA+GGG + chr5.2:75696305-75696324 MS.gene47668:CDS 35.0%
GCATCTTCATATGATGATCT+TGG - chr5.2:75695930-75695949 None:intergenic 35.0%
GGCTAATGATACAAAGTTTG+AGG + chr5.2:75696592-75696611 MS.gene47668:CDS 35.0%
! CCTTCTGGAAAAGACATTAA+AGG - chr5.2:75696458-75696477 None:intergenic 35.0%
! CCTTTAATGTCTTTTCCAGA+AGG + chr5.2:75696455-75696474 MS.gene47668:CDS 35.0%
! GTAGAGAGCATAGTTTAAGA+AGG + chr5.2:75696327-75696346 MS.gene47668:CDS 35.0%
! TAATGTCTTTTCCAGAAGGT+CGG + chr5.2:75696459-75696478 MS.gene47668:CDS 35.0%
! TTCTTTGGGAGTTCAAACAA+GGG + chr5.2:75696722-75696741 MS.gene47668:CDS 35.0%
! TTTCGGTTTGTCTTAGTTCT+CGG - chr5.2:75696011-75696030 None:intergenic 35.0%
! TTTCTTTGGGAGTTCAAACA+AGG + chr5.2:75696721-75696740 MS.gene47668:CDS 35.0%
!! AAAGAGGTGGATTTTGGAAA+AGG + chr5.2:75696669-75696688 MS.gene47668:CDS 35.0%
!! AGAACAAAAGAGGTGGATTT+TGG + chr5.2:75696663-75696682 MS.gene47668:CDS 35.0%
!! TATGATGATCTTGGTGTTGT+AGG - chr5.2:75695921-75695940 None:intergenic 35.0%
!! TCTCCATTTTGAACTAGTCT+TGG - chr5.2:75696158-75696177 None:intergenic 35.0%
!! TGATTTTGATCCATTCAAGG+TGG + chr5.2:75696262-75696281 MS.gene47668:CDS 35.0%
AGTCTTGGAGGAAGTTTAAG+AGG - chr5.2:75696143-75696162 None:intergenic 40.0%
ATGCATTTGAGCAGCATCAA+AGG + chr5.2:75696039-75696058 MS.gene47668:CDS 40.0%
CAACAAGTGTGACAAACATG+AGG + chr5.2:75696382-75696401 MS.gene47668:CDS 40.0%
GAACACAGTGGTTATCAAAC+AGG + chr5.2:75695894-75695913 MS.gene47668:CDS 40.0%
GAATGCACAGATTTCATGTC+AGG - chr5.2:75696818-75696837 None:intergenic 40.0%
TAGATCCCTTTCTCCATTGA+GGG + chr5.2:75696352-75696371 MS.gene47668:CDS 40.0%
TCATCAGCAAATGCCATAGT+AGG - chr5.2:75696083-75696102 None:intergenic 40.0%
TGAGGATTCATTGCCTACTA+TGG + chr5.2:75696067-75696086 MS.gene47668:CDS 40.0%
TTCTCAAAAGCCACCTTGAA+TGG - chr5.2:75696275-75696294 None:intergenic 40.0%
TTTCTTTGCCTGGGTTATGA+GGG + chr5.2:75696926-75696945 MS.gene47668:CDS 40.0%
! CCAAAGTCTTTTCTTTGCCT+GGG + chr5.2:75696917-75696936 MS.gene47668:CDS 40.0%
! CCTCCAAGACTAGTTCAAAA+TGG + chr5.2:75696152-75696171 MS.gene47668:CDS 40.0%
! GTTTGAGGCTAAGAAGACTT+TGG + chr5.2:75696607-75696626 MS.gene47668:CDS 40.0%
! TCTTAGTTCTCGGTTCACTA+TGG - chr5.2:75696001-75696020 None:intergenic 40.0%
! TTCTGACTTTTGTTGAGCAC+TGG - chr5.2:75696753-75696772 None:intergenic 40.0%
! TTGTTGTTGAAGTCCCTCAA+TGG - chr5.2:75696368-75696387 None:intergenic 40.0%
! TTTTCTTTGCCTGGGTTATG+AGG + chr5.2:75696925-75696944 MS.gene47668:CDS 40.0%
!! AGAATTAGAGAGGCACTCTT+TGG + chr5.2:75696784-75696803 MS.gene47668:CDS 40.0%
!! ATTCAAGGTGGCTTTTGAGA+AGG + chr5.2:75696274-75696293 MS.gene47668:CDS 40.0%
!! GCTGATGAGCTATTTTGTGA+TGG + chr5.2:75696095-75696114 MS.gene47668:CDS 40.0%
!!! CCATTTTGAACTAGTCTTGG+AGG - chr5.2:75696155-75696174 None:intergenic 40.0%
AGTCTCCAGGATCAATGCTT+AGG + chr5.2:75696210-75696229 MS.gene47668:CDS 45.0%
AGTTTAAGAGGCGGCATCAT+TGG - chr5.2:75696131-75696150 None:intergenic 45.0%
CCCAGGCAAAGAAAAGACTT+TGG - chr5.2:75696920-75696939 None:intergenic 45.0%
CTAGATCCCTTTCTCCATTG+AGG + chr5.2:75696351-75696370 MS.gene47668:CDS 45.0%
CTTGGAGGAAGTTTAAGAGG+CGG - chr5.2:75696140-75696159 None:intergenic 45.0%
GAAGTCCCTCAATGGAGAAA+GGG - chr5.2:75696360-75696379 None:intergenic 45.0%
TCATGTAACAACCGACCTTC+TGG - chr5.2:75696473-75696492 None:intergenic 45.0%
TCGGTTGTTACATGAGCTTC+TGG + chr5.2:75696478-75696497 MS.gene47668:CDS 45.0%
TGAAGTCCCTCAATGGAGAA+AGG - chr5.2:75696361-75696380 None:intergenic 45.0%
TTCTTCCACAAGCGTGCAAA+AGG - chr5.2:75696239-75696258 None:intergenic 45.0%
! GCCAAAGTCTTTTCTTTGCC+TGG + chr5.2:75696916-75696935 MS.gene47668:CDS 45.0%
! TTGAGTCTGCTAGGACTAGT+TGG - chr5.2:75695867-75695886 None:intergenic 45.0%
!! AGCATTGATCCTGGAGACTT+AGG - chr5.2:75696209-75696228 None:intergenic 45.0%
ACAGGTGAGACAAGTGGAAG+TGG + chr5.2:75696571-75696590 MS.gene47668:CDS 50.0%
AGTACGGTATCTGAGCCCAA+AGG + chr5.2:75696533-75696552 MS.gene47668:CDS 50.0%
CTTGCAAACGCCAACCCTTT+GGG - chr5.2:75696551-75696570 None:intergenic 50.0%
CTTTCCATCCCTCATAACCC+AGG - chr5.2:75696937-75696956 None:intergenic 50.0%
GTACGGTATCTGAGCCCAAA+GGG + chr5.2:75696534-75696553 MS.gene47668:CDS 50.0%
TCTTGCAAACGCCAACCCTT+TGG - chr5.2:75696552-75696571 None:intergenic 50.0%
TGCAAGACAGGTGAGACAAG+TGG + chr5.2:75696565-75696584 MS.gene47668:CDS 50.0%
TTTGCCTGGGTTATGAGGGA+TGG + chr5.2:75696930-75696949 MS.gene47668:CDS 50.0%
! GCAGCATCAAAGGCTTTGTG+AGG + chr5.2:75696049-75696068 MS.gene47668:CDS 50.0%
!! GGAAGCCTAAGCATTGATCC+TGG - chr5.2:75696218-75696237 None:intergenic 50.0%
GGTATCTGAGCCCAAAGGGT+TGG + chr5.2:75696538-75696557 MS.gene47668:CDS 55.0%
! AGGGTTGGCGTTTGCAAGAC+AGG + chr5.2:75696553-75696572 MS.gene47668:CDS 55.0%
! GGCTTCCTTTTGCACGCTTG+TGG + chr5.2:75696231-75696250 MS.gene47668:CDS 55.0%
GCGACGTCTCCTAAGTCTCC+AGG + chr5.2:75696197-75696216 MS.gene47668:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 75695777 75696964 75695777 ID=MS.gene47668
chr5.2 mRNA 75695777 75696964 75695777 ID=MS.gene47668.t1;Parent=MS.gene47668
chr5.2 exon 75695777 75696964 75695777 ID=MS.gene47668.t1.exon1;Parent=MS.gene47668.t1
chr5.2 CDS 75695777 75696964 75695777 ID=cds.MS.gene47668.t1;Parent=MS.gene47668.t1
Gene Sequence

>MS.gene47668

ATGATGGATATCTCATTTTCCAATGAGTTATGCTATATGAGTGCAAGTAGCTGCAATCAAGATAAAGATTTGTTCTTCTATAGTGCACCAACTAGTCCTAGCAGACTCAAATTAATAGAACACAGTGGTTATCAAACAGGTCCTACAACACCAAGATCATCATATGAAGATGCAAACACCAATCTAGATCGGTTTGAATTTGAAACAAGTCGTCGTTTCAACCATAGTGAACCGAGAACTAAGACAAACCGAAAAGATGTGAATGCATTTGAGCAGCATCAAAGGCTTTGTGAGGATTCATTGCCTACTATGGCATTTGCTGATGAGCTATTTTGTGATGGAAAAGTAATTCCAATGATGCCGCCTCTTAAACTTCCTCCAAGACTAGTTCAAAATGGAGATAGTACTCAAAGCTCAAGAGCGACGTCTCCTAAGTCTCCAGGATCAATGCTTAGGCTTCCTTTTGCACGCTTGTGGAAGAATGATGATTTTGATCCATTCAAGGTGGCTTTTGAGAAGGTAAGAGAAGAGAAGAAAGGGAAATCAAAGGGTAGAGAGCATAGTTTAAGAAGGACTAGATCCCTTTCTCCATTGAGGGACTTCAACAACAAGTGTGACAAACATGAGGGACTTTCAGAGTCACATAAACATGATCAATCGCATTGTTGTGAAAAACTTCCTTTAATGTCTTTTCCAGAAGGTCGGTTGTTACATGAGCTTCTGGAAGAGCCAATGAAAGAAGAATCAGAAAGAGAAAGTACGGTATCTGAGCCCAAAGGGTTGGCGTTTGCAAGACAGGTGAGACAAGTGGAAGTGGCTAATGATACAAAGTTTGAGGCTAAGAAGACTTTGGTTTCTAATGTTGCTAAGGAGACAAAGAAAGATGAGAACAAAAGAGGTGGATTTTGGAAAAGGAATAAAAAGTTAGAAAGTATAAAGAAGTTTTTCTTTGGGAGTTCAAACAAGGGTAAAGCCAGTGCTCAACAAAAGTCAGAAGATAAAAAAACAGAATTAGAGAGGCACTCTTTGGTGAAGAAACCTGACATGAAATCTGTGCATTCAACAGAATCAACGACATGGAGTAAAGATGATATATCAGGTGAGTTTACCAAAATGAGATTGGTATGTCAAAGGCCATTGCCAAAGTCTTTTCTTTGCCTGGGTTATGAGGGATGGAAAGTGAAGTGA
Protein sequence

>MS.gene47668.t1

MMDISFSNELCYMSASSCNQDKDLFFYSAPTSPSRLKLIEHSGYQTGPTTPRSSYEDANTNLDRFEFETSRRFNHSEPRTKTNRKDVNAFEQHQRLCEDSLPTMAFADELFCDGKVIPMMPPLKLPPRLVQNGDSTQSSRATSPKSPGSMLRLPFARLWKNDDFDPFKVAFEKVREEKKGKSKGREHSLRRTRSLSPLRDFNNKCDKHEGLSESHKHDQSHCCEKLPLMSFPEGRLLHELLEEPMKEESERESTVSEPKGLAFARQVRQVEVANDTKFEAKKTLVSNVAKETKKDENKRGGFWKRNKKLESIKKFFFGSSNKGKASAQQKSEDKKTELERHSLVKKPDMKSVHSTESTTWSKDDISGEFTKMRLVCQRPLPKSFLCLGYEGWKVK