AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63450.t1 MTR_6g085000 97.906 191 4 0 1 191 1 191 2.18e-137 381
MS.gene63450.t1 MTR_6g021670 97.382 191 5 0 1 191 1 191 4.81e-137 380
MS.gene63450.t1 MTR_8g087480 63.636 44 8 1 145 188 51 86 8.01e-12 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63450.t1 AT1G48830 79.058 191 40 0 1 191 1 191 1.48e-114 324
MS.gene63450.t1 AT1G48830 79.058 191 40 0 1 191 1 191 1.48e-114 324
MS.gene63450.t1 AT3G02560 79.581 191 39 0 1 191 1 191 5.50e-113 320
MS.gene63450.t1 AT3G02560 79.581 191 39 0 1 191 1 191 5.50e-113 320
MS.gene63450.t1 AT3G02560 79.581 191 39 0 1 191 1 191 5.50e-113 320
MS.gene63450.t1 AT5G16130 80.319 188 37 0 1 188 1 188 1.92e-112 318

Find 51 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAGCCAAGTTGATGTTTC+TGG 0.145762 6.3:+79177547 MS.gene63450:intron
TCCTCAATCTGTAGGGGATA+TGG 0.261869 6.3:-79177591 None:intergenic
AGAATCTACGCCTCAGTAAC+AGG 0.280462 6.3:-79178667 None:intergenic
TGAGCAGCGGAGCCTTTCTT+TGG 0.288203 6.3:-79178219 None:intergenic
ATAGTTTACCTTCATGATCT+TGG 0.292174 6.3:-79178349 None:intergenic
AAATTCACGTCAAGCTCGTT+AGG 0.363074 6.3:+79177626 MS.gene63450:CDS
CGTACTAGATACAGAATTGA+TGG 0.367485 6.3:+79178324 MS.gene63450:CDS
GTTGCAGGCTTTGTTTGATC+TGG 0.412438 6.3:+79177386 MS.gene63450:intron
CGCTGAGCCTACTGAATTTG+AGG 0.426295 6.3:+79177253 MS.gene63450:CDS
GCAGCGGAGCCTTTCTTTGG+TGG 0.435938 6.3:-79178216 None:intergenic
TTGTGAATATGTTTACTTCA+AGG 0.441187 6.3:+79177207 None:intergenic
GCAGTTTACAGGAAACTCTC+AGG 0.456482 6.3:+79178622 MS.gene63450:CDS
ATTTGAGGAGTCAGTTGGAC+AGG 0.472058 6.3:+79177268 MS.gene63450:CDS
TGTTACCTGCTGAGATTGTT+GGG 0.479284 6.3:+79178298 MS.gene63450:CDS
TGGTGGCCTGACGATTCTCC+TGG 0.483590 6.3:-79178199 None:intergenic
GTGTTACCTGCTGAGATTGT+TGG 0.484291 6.3:+79178297 MS.gene63450:CDS
TCCCCTACAGATTGAGGAAG+GGG 0.499187 6.3:+79177596 MS.gene63450:CDS
CGTGGACAGCAGTGAGTGTA+CGG 0.505350 6.3:-79178254 None:intergenic
ATCGTCAGGCCACCAAAGAA+AGG 0.508890 6.3:+79178207 MS.gene63450:CDS
TTCTGGAAACCGCAAGGCTG+TGG 0.509249 6.3:+79177564 MS.gene63450:CDS
TCCATATCCCCTACAGATTG+AGG 0.509912 6.3:+79177590 MS.gene63450:CDS
TTGCCACCAGGAGAATCGTC+AGG 0.510117 6.3:+79178193 MS.gene63450:CDS
GAAGAAAATCAGCAAGGACA+AGG 0.510615 6.3:+79177229 MS.gene63450:CDS
GAACCCCTTCCTCAATCTGT+AGG 0.515858 6.3:-79177599 None:intergenic
AACCCCTTCCTCAATCTGTA+GGG 0.520673 6.3:-79177598 None:intergenic
ACTGAATTTGAGGAGTCAGT+TGG 0.548538 6.3:+79177263 MS.gene63450:CDS
AATTCACGTCAAGCTCGTTA+GGG 0.550766 6.3:+79177627 MS.gene63450:CDS
GCTGCGTGGACGCTGAGCAG+CGG 0.558388 6.3:-79178232 None:intergenic
CGTTTCCCAACAATCTCAGC+AGG 0.558735 6.3:-79178303 None:intergenic
GTTTGAGTACCCTGTTACTG+AGG 0.572498 6.3:+79178657 MS.gene63450:CDS
TATCCCCTACAGATTGAGGA+AGG 0.573232 6.3:+79177594 MS.gene63450:CDS
GGTTTCCAGAAACATCAACT+TGG 0.575562 6.3:-79177552 None:intergenic
ATGTAATCCTCATTGCCACC+AGG 0.584954 6.3:+79178181 MS.gene63450:CDS
CGATTCTCCTGGTGGCAATG+AGG 0.590532 6.3:-79178188 None:intergenic
AAGAAAATCAGCAAGGACAA+GGG 0.599976 6.3:+79177230 MS.gene63450:CDS
CAGTTTACAGGAAACTCTCA+GGG 0.612531 6.3:+79178623 MS.gene63450:CDS
TGAGAAGAAATTCAGCGGAA+AGG 0.621961 6.3:+79177654 MS.gene63450:CDS
TGATGTTTCTGGAAACCGCA+AGG 0.622049 6.3:+79177558 MS.gene63450:CDS
ATCCCCTACAGATTGAGGAA+GGG 0.622569 6.3:+79177595 MS.gene63450:CDS
ACTGACTCCTCAAATTCAGT+AGG 0.622702 6.3:-79177260 None:intergenic
ACCCCTTCCTCAATCTGTAG+GGG 0.633929 6.3:-79177597 None:intergenic
TGATGGATCCAAGATCATGA+AGG 0.639271 6.3:+79178341 MS.gene63450:CDS
TGTCCACGAGGCAATGCTCG+AGG 0.642990 6.3:+79178269 MS.gene63450:CDS
TTCAAGGAAGAAAATCAGCA+AGG 0.648771 6.3:+79177223 MS.gene63450:CDS
GCAGTGAGTGTACGGCTGCG+TGG 0.657285 6.3:-79178246 None:intergenic
TACACTCACTGCTGTCCACG+AGG 0.659160 6.3:+79178257 MS.gene63450:CDS
TGGCCTGACGATTCTCCTGG+TGG 0.662830 6.3:-79178196 None:intergenic
TATGGATAACCACAGCCTTG+CGG 0.675676 6.3:-79177573 None:intergenic
GAATCTACGCCTCAGTAACA+GGG 0.678065 6.3:-79178666 None:intergenic
CATCCTCGAGCATTGCCTCG+TGG 0.690997 6.3:-79178272 None:intergenic
GAGCTTGAGAAGAAATTCAG+CGG 0.694607 6.3:+79177649 MS.gene63450:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTGGAACAAAAAATTGT+CGG - chr6.3:79177751-79177770 None:intergenic 20.0%
!! AGAATAAAGTTCTTGAAATA+AGG - chr6.3:79177800-79177819 None:intergenic 20.0%
!! CAAATTATTTAGTGTATGTT+TGG - chr6.3:79178065-79178084 None:intergenic 20.0%
!! TTAAAGCAATTTAAAAACCA+AGG - chr6.3:79177835-79177854 None:intergenic 20.0%
!!! AGGTTATATATTGATTACTA+CGG + chr6.3:79177288-79177307 MS.gene63450:intron 20.0%
! TATTTAGTGTATGTTTGGTT+TGG - chr6.3:79178060-79178079 None:intergenic 25.0%
!! TGTGAGAAAACAATTTTTCA+AGG - chr6.3:79178106-79178125 None:intergenic 25.0%
!!! AGTAACTTTTGGAAATTGTT+TGG - chr6.3:79178383-79178402 None:intergenic 25.0%
!!! TGCTTATTTTCACATTAGTT+TGG - chr6.3:79178439-79178458 None:intergenic 25.0%
AACAAAAACTCACGATTACA+TGG + chr6.3:79177958-79177977 MS.gene63450:intron 30.0%
ATAGTTTACCTTCATGATCT+TGG - chr6.3:79178352-79178371 None:intergenic 30.0%
CTAATGAACCTTAAACTTGT+AGG + chr6.3:79178158-79178177 MS.gene63450:intron 30.0%
CTGTAAAACTGAAGTTAATC+AGG + chr6.3:79177886-79177905 MS.gene63450:intron 30.0%
GACAGAATCGTAATAAAAGA+TGG - chr6.3:79177726-79177745 None:intergenic 30.0%
GATTACATCCTACAAGTTTA+AGG - chr6.3:79178169-79178188 None:intergenic 30.0%
TTAGAAAGAATAACTGGCAA+AGG - chr6.3:79177698-79177717 None:intergenic 30.0%
! TCTGTGTATATAGGTGTTTT+TGG + chr6.3:79178552-79178571 MS.gene63450:intron 30.0%
! TCTTGTGTTTCTGTGTATAT+AGG + chr6.3:79178543-79178562 MS.gene63450:intron 30.0%
!! CAGTATTGTTTTTCTCCTTT+GGG - chr6.3:79178579-79178598 None:intergenic 30.0%
!! TCAGTATTGTTTTTCTCCTT+TGG - chr6.3:79178580-79178599 None:intergenic 30.0%
!!! TGTTTTCAATTTGTTGTTGC+AGG + chr6.3:79177371-79177390 MS.gene63450:intron 30.0%
!!! TTCAAGCTTTGAGTAACTTT+TGG - chr6.3:79178394-79178413 None:intergenic 30.0%
AAGAAAATCAGCAAGGACAA+GGG + chr6.3:79177230-79177249 MS.gene63450:CDS 35.0%
CGAGTAGAAGACAAAGAAAT+TGG - chr6.3:79177767-79177786 None:intergenic 35.0%
CGTACTAGATACAGAATTGA+TGG + chr6.3:79178324-79178343 MS.gene63450:CDS 35.0%
GATAAAGAGAAGCTACAAAG+TGG - chr6.3:79177989-79178008 None:intergenic 35.0%
GTCTAAGCATGTGTTTGATT+TGG + chr6.3:79177914-79177933 MS.gene63450:intron 35.0%
GTGCAGTTAGAAAGAATAAC+TGG - chr6.3:79177704-79177723 None:intergenic 35.0%
GTGTAAGGATGTGTTCTTTA+TGG + chr6.3:79177465-79177484 MS.gene63450:intron 35.0%
TACATCAATTCTGCAGTGTA+AGG + chr6.3:79177450-79177469 MS.gene63450:intron 35.0%
TGGCTGTAGATAACAGAAAA+CGG - chr6.3:79177535-79177554 None:intergenic 35.0%
TTCAAGGAAGAAAATCAGCA+AGG + chr6.3:79177223-79177242 MS.gene63450:CDS 35.0%
! AAACGTTTTCTGCAGTTTAC+AGG + chr6.3:79178611-79178630 MS.gene63450:CDS 35.0%
! ACTATTGTTGTTGCTGTGAT+TGG + chr6.3:79177311-79177330 MS.gene63450:intron 35.0%
! ATTCTGTTTTGCAATCTCCT+TGG + chr6.3:79177815-79177834 MS.gene63450:intron 35.0%
AAATTCACGTCAAGCTCGTT+AGG + chr6.3:79177626-79177645 MS.gene63450:CDS 40.0%
AACTGAAGTTAATCAGGCTG+CGG + chr6.3:79177892-79177911 MS.gene63450:intron 40.0%
AATTCACGTCAAGCTCGTTA+GGG + chr6.3:79177627-79177646 MS.gene63450:CDS 40.0%
ACTGAATTTGAGGAGTCAGT+TGG + chr6.3:79177263-79177282 MS.gene63450:CDS 40.0%
CAGTTTACAGGAAACTCTCA+GGG + chr6.3:79178623-79178642 MS.gene63450:CDS 40.0%
GAAGAAAATCAGCAAGGACA+AGG + chr6.3:79177229-79177248 MS.gene63450:CDS 40.0%
GAGCTTGAGAAGAAATTCAG+CGG + chr6.3:79177649-79177668 MS.gene63450:CDS 40.0%
GGTTTCCAGAAACATCAACT+TGG - chr6.3:79177555-79177574 None:intergenic 40.0%
TGAGAAGAAATTCAGCGGAA+AGG + chr6.3:79177654-79177673 MS.gene63450:CDS 40.0%
TGTTACCTGCTGAGATTGTT+GGG + chr6.3:79178298-79178317 MS.gene63450:CDS 40.0%
! ACTGACTCCTCAAATTCAGT+AGG - chr6.3:79177263-79177282 None:intergenic 40.0%
! TGATGGATCCAAGATCATGA+AGG + chr6.3:79178341-79178360 MS.gene63450:CDS 40.0%
!! TACAGCCAAGTTGATGTTTC+TGG + chr6.3:79177547-79177566 MS.gene63450:intron 40.0%
!! TCAGATCACTTTTGAGCTCA+TGG - chr6.3:79177422-79177441 None:intergenic 40.0%
!!! ATAGGTGTTTTTGGACCCAA+AGG + chr6.3:79178561-79178580 MS.gene63450:intron 40.0%
AACCCCTTCCTCAATCTGTA+GGG - chr6.3:79177601-79177620 None:intergenic 45.0%
ATCCCCTACAGATTGAGGAA+GGG + chr6.3:79177595-79177614 MS.gene63450:CDS 45.0%
ATGCCTTGTAATCATGCGAG+TGG + chr6.3:79178021-79178040 MS.gene63450:intron 45.0%
ATGTAATCCTCATTGCCACC+AGG + chr6.3:79178181-79178200 MS.gene63450:CDS 45.0%
ATTTGAGGAGTCAGTTGGAC+AGG + chr6.3:79177268-79177287 MS.gene63450:CDS 45.0%
GCAGTTTACAGGAAACTCTC+AGG + chr6.3:79178622-79178641 MS.gene63450:CDS 45.0%
GTGTTACCTGCTGAGATTGT+TGG + chr6.3:79178297-79178316 MS.gene63450:CDS 45.0%
GTTTGAGTACCCTGTTACTG+AGG + chr6.3:79178657-79178676 MS.gene63450:CDS 45.0%
TATCCCCTACAGATTGAGGA+AGG + chr6.3:79177594-79177613 MS.gene63450:CDS 45.0%
TATGGATAACCACAGCCTTG+CGG - chr6.3:79177576-79177595 None:intergenic 45.0%
TCCATATCCCCTACAGATTG+AGG + chr6.3:79177590-79177609 MS.gene63450:CDS 45.0%
TCCTCAATCTGTAGGGGATA+TGG - chr6.3:79177594-79177613 None:intergenic 45.0%
TTGCCACTCGCATGATTACA+AGG - chr6.3:79178027-79178046 None:intergenic 45.0%
! CGAGCTTGACGTGAATTTTG+CGG - chr6.3:79177624-79177643 None:intergenic 45.0%
!! GTTGCAGGCTTTGTTTGATC+TGG + chr6.3:79177386-79177405 MS.gene63450:intron 45.0%
!! TGATGTTTCTGGAAACCGCA+AGG + chr6.3:79177558-79177577 MS.gene63450:CDS 45.0%
ACCCCTTCCTCAATCTGTAG+GGG - chr6.3:79177600-79177619 None:intergenic 50.0%
ATCGTCAGGCCACCAAAGAA+AGG + chr6.3:79178207-79178226 MS.gene63450:CDS 50.0%
CGCTGAGCCTACTGAATTTG+AGG + chr6.3:79177253-79177272 MS.gene63450:CDS 50.0%
CGTTTCCCAACAATCTCAGC+AGG - chr6.3:79178306-79178325 None:intergenic 50.0%
GAACCCCTTCCTCAATCTGT+AGG - chr6.3:79177602-79177621 None:intergenic 50.0%
TCCCCTACAGATTGAGGAAG+GGG + chr6.3:79177596-79177615 MS.gene63450:CDS 50.0%
CGATTCTCCTGGTGGCAATG+AGG - chr6.3:79178191-79178210 None:intergenic 55.0%
CGTGGACAGCAGTGAGTGTA+CGG - chr6.3:79178257-79178276 None:intergenic 55.0%
TACACTCACTGCTGTCCACG+AGG + chr6.3:79178257-79178276 MS.gene63450:CDS 55.0%
TGAGCAGCGGAGCCTTTCTT+TGG - chr6.3:79178222-79178241 None:intergenic 55.0%
TTGCCACCAGGAGAATCGTC+AGG + chr6.3:79178193-79178212 MS.gene63450:CDS 55.0%
! TTCTGGAAACCGCAAGGCTG+TGG + chr6.3:79177564-79177583 MS.gene63450:CDS 55.0%
GCAGCGGAGCCTTTCTTTGG+TGG - chr6.3:79178219-79178238 None:intergenic 60.0%
TGGCCTGACGATTCTCCTGG+TGG - chr6.3:79178199-79178218 None:intergenic 60.0%
TGGTGGCCTGACGATTCTCC+TGG - chr6.3:79178202-79178221 None:intergenic 60.0%
TGTCCACGAGGCAATGCTCG+AGG + chr6.3:79178269-79178288 MS.gene63450:CDS 60.0%
! CATCCTCGAGCATTGCCTCG+TGG - chr6.3:79178275-79178294 None:intergenic 60.0%
GCAGTGAGTGTACGGCTGCG+TGG - chr6.3:79178249-79178268 None:intergenic 65.0%
GCTGCGTGGACGCTGAGCAG+CGG - chr6.3:79178235-79178254 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 79177215 79178684 79177215 ID=MS.gene63450
chr6.3 mRNA 79177215 79178684 79177215 ID=MS.gene63450.t1;Parent=MS.gene63450
chr6.3 exon 79177215 79177289 79177215 ID=MS.gene63450.t1.exon1;Parent=MS.gene63450.t1
chr6.3 CDS 79177215 79177289 79177215 ID=cds.MS.gene63450.t1;Parent=MS.gene63450.t1
chr6.3 exon 79177393 79177466 79177393 ID=MS.gene63450.t1.exon2;Parent=MS.gene63450.t1
chr6.3 CDS 79177393 79177466 79177393 ID=cds.MS.gene63450.t1;Parent=MS.gene63450.t1
chr6.3 exon 79177552 79177675 79177552 ID=MS.gene63450.t1.exon3;Parent=MS.gene63450.t1
chr6.3 CDS 79177552 79177675 79177552 ID=cds.MS.gene63450.t1;Parent=MS.gene63450.t1
chr6.3 exon 79178180 79178362 79178180 ID=MS.gene63450.t1.exon4;Parent=MS.gene63450.t1
chr6.3 CDS 79178180 79178362 79178180 ID=cds.MS.gene63450.t1;Parent=MS.gene63450.t1
chr6.3 exon 79178565 79178684 79178565 ID=MS.gene63450.t1.exon5;Parent=MS.gene63450.t1
chr6.3 CDS 79178565 79178684 79178565 ID=cds.MS.gene63450.t1;Parent=MS.gene63450.t1
Gene Sequence

>MS.gene63450

ATGTTTACTTCAAGGAAGAAAATCAGCAAGGACAAGGGCGCTGAGCCTACTGAATTTGAGGAGTCAGTTGGACAGGTTATATATTGATTACTACGGACTATTGTTGTTGCTGTGATTGGTGATTAGTCTCAATAATTACAAAATCTAAATCATTATTGTTTTCAATTTGTTGTTGCAGGCTTTGTTTGATCTGGAAAACACTAACCATGAGCTCAAAAGTGATCTGAAAGATTTATACATCAATTCTGCAGTGTAAGGATGTGTTCTTTATGGTTTGTTCGAAAATACATCTGTTTTTTTTTTGTGTCTCATGTCTACCGTTTTCTGTTATCTACAGCCAAGTTGATGTTTCTGGAAACCGCAAGGCTGTGGTTATCCATATCCCCTACAGATTGAGGAAGGGGTTCCGCAAAATTCACGTCAAGCTCGTTAGGGAGCTTGAGAAGAAATTCAGCGGAAAGGTAATCAAAGTCTTTTATACCTTTGCCAGTTATTCTTTCTAACTGCACCATCTTTTATTACGATTCTGTCTACCGACAATTTTTTGTTCCAATTTCTTTGTCTTCTACTCGTTATTTTTATCCTTATTTCAAGAACTTTATTCTGTTTTGCAATCTCCTTGGTTTTTAAATTGCTTTAATTTATATTTACTTGAGAGTAGTTCTATTCAGCTGTAAAACTGAAGTTAATCAGGCTGCGGTCTAAGCATGTGTTTGATTTGGCTTCATAGTTTTCATAATTACAACAAAAACTCACGATTACATGGAAGCTCCACTTTGTAGCTTCTCTTTATCACGACAGAATGCATGCCTTGTAATCATGCGAGTGGCAATGTAAAGAAGCCAAACCAAACATACACTAAATAATTTGATGATAGCATAACAATAGCCTTGAAAAATTGTTTTCTCACAGATTTATATTTGATGTTTCACTTTATTGTGTACTAATGAACCTTAAACTTGTAGGATGTAATCCTCATTGCCACCAGGAGAATCGTCAGGCCACCAAAGAAAGGCTCCGCTGCTCAGCGTCCACGCAGCCGTACACTCACTGCTGTCCACGAGGCAATGCTCGAGGATGTCGTGTTACCTGCTGAGATTGTTGGGAAACGTACTAGATACAGAATTGATGGATCCAAGATCATGAAGGTAAACTATACTAACAGCCAAACAATTTCCAAAAGTTACTCAAAGCTTGAATGAAAAATACATTTCGATTAAGCCAAACTAATGTGAAAATAAGCATACATGCTTTTATTATATACTACAATATTAAAATCATTAAGAAATGATGTTAATTCATTTCAAAAGAAATGATGTTAATTGAATTCTTGTGTTTCTGTGTATATAGGTGTTTTTGGACCCAAAGGAGAAAAACAATACTGAATACAAGCTCGAAACGTTTTCTGCAGTTTACAGGAAACTCTCAGGGAAAGATGTTGTGTTTGAGTACCCTGTTACTGAGGCGTAG

Protein sequence

>MS.gene63450.t1

MFTSRKKISKDKGAEPTEFEESVGQALFDLENTNHELKSDLKDLYINSAVQVDVSGNRKAVVIHIPYRLRKGFRKIHVKLVRELEKKFSGKDVILIATRRIVRPPKKGSAAQRPRSRTLTAVHEAMLEDVVLPAEIVGKRTRYRIDGSKIMKVFLDPKEKNNTEYKLETFSAVYRKLSGKDVVFEYPVTEA