AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063009

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene063009.t1 MTR_4g073310 69.149 282 29 3 1 279 1 227 7.75e-114 327
MS.gene063009.t1 MTR_1g052185 45.791 297 117 10 1 275 1 275 1.28e-54 178
MS.gene063009.t1 MTR_1g046810 34.091 308 134 11 20 279 28 314 1.16e-31 119
MS.gene063009.t1 MTR_1g053530 34.884 215 112 6 23 236 25 212 9.08e-23 94.4
MS.gene063009.t1 MTR_6g011180 77.778 36 8 0 167 202 200 235 6.80e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGATCATGAACATCTTAA+TGG 0.235891 4.2:+35172508 MS.gene063009:CDS
TTTCTCATCATCGTCCTTAA+TGG 0.261776 4.2:-35172254 None:intergenic
AGAAGAACATGGATTATAAA+AGG 0.308077 4.2:-35172104 None:intergenic
AAATTCATAACAACTCCTTT+TGG 0.331715 4.2:-35172850 None:intergenic
ATGTCTTGCGCTGCGGCTGC+TGG 0.338853 4.2:+35172550 MS.gene063009:CDS
CCGCCGCTCTCATACCATTA+AGG 0.353355 4.2:+35172240 MS.gene063009:CDS
CCTCCTGATAGAACGTTTGT+TGG 0.361348 4.2:-35172476 None:intergenic
TGCGCTGCGGCTGCTGGTGG+TGG 0.361962 4.2:+35172556 MS.gene063009:CDS
AAATACTTGGTTAAGTCAAT+TGG 0.389715 4.2:-35172433 None:intergenic
AAACCAACAAACGTTCTATC+AGG 0.407703 4.2:+35172473 MS.gene063009:CDS
GGACTTTGGTGGCAAATACT+TGG 0.426874 4.2:-35172446 None:intergenic
ATGTCCGCGAAAAGCCTTGT+TGG 0.435044 4.2:-35172317 None:intergenic
GCTGCTGGTGGTGGTGATCA+TGG 0.448558 4.2:+35172565 MS.gene063009:CDS
GAAACAGAAACATAGTTGTC+TGG 0.459864 4.2:+35172273 MS.gene063009:CDS
AAATCACACTCATACATTCT+CGG 0.462757 4.2:-35172163 None:intergenic
TATGATATTGCACCATGAAA+AGG 0.464373 4.2:+35172339 MS.gene063009:CDS
GGTTGACGATTGAATACTCT+TGG 0.485743 4.2:-35172365 None:intergenic
TCTAATGAATTGAAGCCAAA+AGG 0.489056 4.2:+35172835 MS.gene063009:CDS
TCATGTGCAACATCTTCTGT+TGG 0.490922 4.2:-35172889 None:intergenic
TTGAAATTGTTCCAAGGATG+TGG 0.492696 4.2:-35172386 None:intergenic
TCAATCGTCAACCACATCCT+TGG 0.496081 4.2:+35172375 MS.gene063009:CDS
GAACAATTTCAATTTCAAGT+TGG 0.498276 4.2:+35172397 MS.gene063009:CDS
TTCAGCTCTGGCAACGCACT+CGG 0.503636 4.2:+35172199 MS.gene063009:CDS
TTGAAATTGAAATTGTTCCA+AGG 0.519609 4.2:-35172392 None:intergenic
ATTATTATTGTCCTTCACCT+TGG 0.520250 4.2:-35172677 None:intergenic
ATGATATTGCACCATGAAAA+GGG 0.521004 4.2:+35172340 MS.gene063009:CDS
TCTTGCGCTGCGGCTGCTGG+TGG 0.523708 4.2:+35172553 MS.gene063009:CDS
CTTGCACTCATGAGGAAGAA+AGG 0.532255 4.2:+35172067 None:intergenic
TACTTGGTTAAGTCAATTGG+TGG 0.543017 4.2:-35172430 None:intergenic
TAGTTGTCTGGTTTGCAACA+AGG 0.558698 4.2:+35172285 MS.gene063009:CDS
GACAAGATCGAGAAACAAGT+TGG 0.568686 4.2:+35172631 MS.gene063009:CDS
TCTTTAATCTTGAATATCAG+CGG 0.572245 4.2:-35172733 None:intergenic
TGGTGACATTGATGAAACTT+CGG 0.577161 4.2:+35172651 MS.gene063009:CDS
AAGGTCTCGCAATGCAGCCA+AGG 0.578454 4.2:+35172760 MS.gene063009:CDS
TGATGAAACTTCGGCGACCA+AGG 0.579505 4.2:+35172660 MS.gene063009:CDS
GATGATAATGAGAAATCTCA+AGG 0.595352 4.2:+35172139 MS.gene063009:CDS
TTGGTTAAGTCAATTGGTGG+TGG 0.603616 4.2:-35172427 None:intergenic
TGAAGGTGGTGAAACTGCAA+TGG 0.611497 4.2:+35172804 MS.gene063009:CDS
AGCTCTGGCAACGCACTCGG+TGG 0.612484 4.2:+35172202 MS.gene063009:CDS
CTTCAATATGTCTTGCGCTG+CGG 0.618324 4.2:+35172543 MS.gene063009:CDS
AACTTCGGCGACCAAGGTGA+AGG 0.625913 4.2:+35172666 MS.gene063009:CDS
GGATTATAAAAGGAACAAGA+AGG 0.636811 4.2:-35172094 None:intergenic
AATGAATGAAAAGAAGAACA+TGG 0.641497 4.2:-35172115 None:intergenic
CCAACAAACGTTCTATCAGG+AGG 0.665230 4.2:+35172476 MS.gene063009:CDS
GCTCAAAGTTTCAAGCAATG+TGG 0.669423 4.2:+35172603 MS.gene063009:CDS
ATTCAAGATTAAAGACAACA+AGG 0.676790 4.2:+35172741 MS.gene063009:CDS
CCTTAATGGTATGAGAGCGG+CGG 0.689827 4.2:-35172240 None:intergenic
CGTCCTTAATGGTATGAGAG+CGG 0.691522 4.2:-35172243 None:intergenic
ATGTATGAGTGTGATTTGTG+CGG 0.720837 4.2:+35172169 MS.gene063009:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAAGAAGAAAAATAATGA+AGG + chr4.2:35172787-35172806 MS.gene063009:CDS 20.0%
! AAATACTTGGTTAAGTCAAT+TGG - chr4.2:35172436-35172455 None:intergenic 25.0%
! AAGAAGAAAAATAATGAAGG+TGG + chr4.2:35172790-35172809 MS.gene063009:CDS 25.0%
! AATGAATGAAAAGAAGAACA+TGG - chr4.2:35172118-35172137 None:intergenic 25.0%
! ATTCAAGATTAAAGACAACA+AGG + chr4.2:35172741-35172760 MS.gene063009:CDS 25.0%
! ATTGATCATGAACATCTTAA+TGG + chr4.2:35172508-35172527 MS.gene063009:CDS 25.0%
! TCTTTAATCTTGAATATCAG+CGG - chr4.2:35172736-35172755 None:intergenic 25.0%
! TTGAAATTGAAATTGTTCCA+AGG - chr4.2:35172395-35172414 None:intergenic 25.0%
!! AAATTCATAACAACTCCTTT+TGG - chr4.2:35172853-35172872 None:intergenic 25.0%
!! AGAAGAACATGGATTATAAA+AGG - chr4.2:35172107-35172126 None:intergenic 25.0%
!! GAACAATTTCAATTTCAAGT+TGG + chr4.2:35172397-35172416 MS.gene063009:CDS 25.0%
AAATCACACTCATACATTCT+CGG - chr4.2:35172166-35172185 None:intergenic 30.0%
ATGATATTGCACCATGAAAA+GGG + chr4.2:35172340-35172359 MS.gene063009:CDS 30.0%
ATTATTATTGTCCTTCACCT+TGG - chr4.2:35172680-35172699 None:intergenic 30.0%
GGATTATAAAAGGAACAAGA+AGG - chr4.2:35172097-35172116 None:intergenic 30.0%
TATGATATTGCACCATGAAA+AGG + chr4.2:35172339-35172358 MS.gene063009:CDS 30.0%
TCTAATGAATTGAAGCCAAA+AGG + chr4.2:35172835-35172854 MS.gene063009:CDS 30.0%
! GATGATAATGAGAAATCTCA+AGG + chr4.2:35172139-35172158 MS.gene063009:CDS 30.0%
! TTTTCTTCTTTTCTTCACCT+TGG - chr4.2:35172780-35172799 None:intergenic 30.0%
!!! AGAACGTTTGTTGGTTTTAT+GGG - chr4.2:35172470-35172489 None:intergenic 30.0%
!!! TAGAACGTTTGTTGGTTTTA+TGG - chr4.2:35172471-35172490 None:intergenic 30.0%
AAACCAACAAACGTTCTATC+AGG + chr4.2:35172473-35172492 MS.gene063009:CDS 35.0%
GAAACAGAAACATAGTTGTC+TGG + chr4.2:35172273-35172292 MS.gene063009:CDS 35.0%
TACTTGGTTAAGTCAATTGG+TGG - chr4.2:35172433-35172452 None:intergenic 35.0%
TGGTGACATTGATGAAACTT+CGG + chr4.2:35172651-35172670 MS.gene063009:CDS 35.0%
TTGAAATTGTTCCAAGGATG+TGG - chr4.2:35172389-35172408 None:intergenic 35.0%
TTTCTCATCATCGTCCTTAA+TGG - chr4.2:35172257-35172276 None:intergenic 35.0%
! ATGTATGAGTGTGATTTGTG+CGG + chr4.2:35172169-35172188 MS.gene063009:CDS 35.0%
!!! CAAGGTTTTTTCATCCAACA+AGG + chr4.2:35172303-35172322 MS.gene063009:CDS 35.0%
!!! TTGTTGGTTTTATGGGACTT+TGG - chr4.2:35172463-35172482 None:intergenic 35.0%
GACAAGATCGAGAAACAAGT+TGG + chr4.2:35172631-35172650 MS.gene063009:CDS 40.0%
GCTCAAAGTTTCAAGCAATG+TGG + chr4.2:35172603-35172622 MS.gene063009:CDS 40.0%
GGTTGACGATTGAATACTCT+TGG - chr4.2:35172368-35172387 None:intergenic 40.0%
TCATGTGCAACATCTTCTGT+TGG - chr4.2:35172892-35172911 None:intergenic 40.0%
TTGGTTAAGTCAATTGGTGG+TGG - chr4.2:35172430-35172449 None:intergenic 40.0%
! TACTCTTGGAACCCTTTTCA+TGG - chr4.2:35172354-35172373 None:intergenic 40.0%
! TAGTTGTCTGGTTTGCAACA+AGG + chr4.2:35172285-35172304 MS.gene063009:CDS 40.0%
!!! TTGGTTTTATGGGACTTTGG+TGG - chr4.2:35172460-35172479 None:intergenic 40.0%
CCAACAAACGTTCTATCAGG+AGG + chr4.2:35172476-35172495 MS.gene063009:CDS 45.0%
CCTCCTGATAGAACGTTTGT+TGG - chr4.2:35172479-35172498 None:intergenic 45.0%
CGTCCTTAATGGTATGAGAG+CGG - chr4.2:35172246-35172265 None:intergenic 45.0%
CTTCAATATGTCTTGCGCTG+CGG + chr4.2:35172543-35172562 MS.gene063009:CDS 45.0%
TCAATCGTCAACCACATCCT+TGG + chr4.2:35172375-35172394 MS.gene063009:CDS 45.0%
TGAAGGTGGTGAAACTGCAA+TGG + chr4.2:35172804-35172823 MS.gene063009:CDS 45.0%
! GGACTTTGGTGGCAAATACT+TGG - chr4.2:35172449-35172468 None:intergenic 45.0%
! TCATCCAACAAGGCTTTTCG+CGG + chr4.2:35172313-35172332 MS.gene063009:CDS 45.0%
CCTTAATGGTATGAGAGCGG+CGG - chr4.2:35172243-35172262 None:intergenic 50.0%
TGATGAAACTTCGGCGACCA+AGG + chr4.2:35172660-35172679 MS.gene063009:CDS 50.0%
TGCGGCAAAAAGTTCAGCTC+TGG + chr4.2:35172187-35172206 MS.gene063009:CDS 50.0%
! ATGTCCGCGAAAAGCCTTGT+TGG - chr4.2:35172320-35172339 None:intergenic 50.0%
AACTTCGGCGACCAAGGTGA+AGG + chr4.2:35172666-35172685 MS.gene063009:CDS 55.0%
AAGGTCTCGCAATGCAGCCA+AGG + chr4.2:35172760-35172779 MS.gene063009:CDS 55.0%
CCGCCGCTCTCATACCATTA+AGG + chr4.2:35172240-35172259 MS.gene063009:CDS 55.0%
! AGCGGCGGTGAGATGTTTTG+TGG - chr4.2:35172228-35172247 None:intergenic 55.0%
! TTCAGCTCTGGCAACGCACT+CGG + chr4.2:35172199-35172218 MS.gene063009:CDS 55.0%
!! GCTGCTGGTGGTGGTGATCA+TGG + chr4.2:35172565-35172584 MS.gene063009:CDS 60.0%
ATGTCTTGCGCTGCGGCTGC+TGG + chr4.2:35172550-35172569 MS.gene063009:CDS 65.0%
! AGCTCTGGCAACGCACTCGG+TGG + chr4.2:35172202-35172221 MS.gene063009:CDS 65.0%
TCTTGCGCTGCGGCTGCTGG+TGG + chr4.2:35172553-35172572 MS.gene063009:CDS 70.0%
TGCGCTGCGGCTGCTGGTGG+TGG + chr4.2:35172556-35172575 MS.gene063009:CDS 75.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 35172076 35172915 35172076 ID=MS.gene063009
chr4.2 mRNA 35172076 35172915 35172076 ID=MS.gene063009.t1;Parent=MS.gene063009
chr4.2 exon 35172076 35172915 35172076 ID=MS.gene063009.t1.exon1;Parent=MS.gene063009.t1
chr4.2 CDS 35172076 35172915 35172076 ID=cds.MS.gene063009.t1;Parent=MS.gene063009.t1
Gene Sequence

>MS.gene063009

ATGAGGAAGAAAGGTACTCCTTCTTGTTCCTTTTATAATCCATGTTCTTCTTTTCATTCATTCGATGATAATGAGAAATCTCAAGGTCCGAGAATGTATGAGTGTGATTTGTGCGGCAAAAAGTTCAGCTCTGGCAACGCACTCGGTGGCCACAAAACATCTCACCGCCGCTCTCATACCATTAAGGACGATGATGAGAAACAGAAACATAGTTGTCTGGTTTGCAACAAGGTTTTTTCATCCAACAAGGCTTTTCGCGGACATATGATATTGCACCATGAAAAGGGTTCCAAGAGTATTCAATCGTCAACCACATCCTTGGAACAATTTCAATTTCAAGTTGGTATTGCACCACCACCAATTGACTTAACCAAGTATTTGCCACCAAAGTCCCATAAAACCAACAAACGTTCTATCAGGAGGAGAAATATCATTGATCATGAACATCTTAATGGAGCACAAACACTCTTCAATATGTCTTGCGCTGCGGCTGCTGGTGGTGGTGATCATGGTCACATACATAAAAAGCTCAAAGTTTCAAGCAATGTGGACGATGACAAGATCGAGAAACAAGTTGGTGACATTGATGAAACTTCGGCGACCAAGGTGAAGGACAATAATAATAATAATAATAATAATAACAGTAAAAAGAGTTTGCCGCTGATATTCAAGATTAAAGACAACAAGGTCTCGCAATGCAGCCAAGGTGAAGAAAAGAAGAAAAATAATGAAGGTGGTGAAACTGCAATGGAAGAGAGTTCTAATGAATTGAAGCCAAAAGGAGTTGTTATGAATTTTGATTTGAATGAGCTTCCAACAGAAGATGTTGCACATGAATGA
Protein sequence

>MS.gene063009.t1

MRKKGTPSCSFYNPCSSFHSFDDNEKSQGPRMYECDLCGKKFSSGNALGGHKTSHRRSHTIKDDDEKQKHSCLVCNKVFSSNKAFRGHMILHHEKGSKSIQSSTTSLEQFQFQVGIAPPPIDLTKYLPPKSHKTNKRSIRRRNIIDHEHLNGAQTLFNMSCAAAAGGGDHGHIHKKLKVSSNVDDDKIEKQVGDIDETSATKVKDNNNNNNNNNSKKSLPLIFKIKDNKVSQCSQGEEKKKNNEGGETAMEESSNELKPKGVVMNFDLNELPTEDVAHE