AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49927


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49927.t1 MTR_6g085000 100.000 191 0 0 1 191 1 191 4.48e-139 385
MS.gene49927.t1 MTR_6g021670 99.476 191 1 0 1 191 1 191 7.51e-139 385
MS.gene49927.t1 MTR_8g087480 65.909 44 7 1 145 188 51 86 1.77e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49927.t1 AT1G48830 81.152 191 36 0 1 191 1 191 2.55e-116 328
MS.gene49927.t1 AT1G48830 81.152 191 36 0 1 191 1 191 2.55e-116 328
MS.gene49927.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene49927.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene49927.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene49927.t1 AT5G16130 81.383 188 35 0 1 188 1 188 2.24e-113 321

Find 51 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAGCCAAGTTGATGTTTC+TGG 0.170905 6.4:+59095731 MS.gene49927:intron
TCAGTATTGTTTCTCTCCTT+TGG 0.234939 6.4:-59096720 None:intergenic
CAGTATTGTTTCTCTCCTTT+GGG 0.277926 6.4:-59096719 None:intergenic
AGAATCTAGGCCTCAGTAAC+AGG 0.289126 6.4:-59096810 None:intergenic
ATAGTTTACCTTCATGATCT+TGG 0.292174 6.4:-59096501 None:intergenic
AAATTCACGTCAGGCTCGTT+AGG 0.322256 6.4:+59095810 MS.gene49927:CDS
GGATCCATCAATTCTGTATC+TGG 0.328918 6.4:-59096480 None:intergenic
TGAGCAGCAGAGCCTTTCTT+TGG 0.360132 6.4:-59096371 None:intergenic
CGTACCAGATACAGAATTGA+TGG 0.382090 6.4:+59096476 MS.gene49927:CDS
GTTGCAGGCTCTGTTTGATC+TGG 0.398358 6.4:+59095574 MS.gene49927:intron
TCGTGAAAATGTTTACTTCA+AGG 0.415835 6.4:+59095395 None:intergenic
CGCTGAGCCTACTGAATTTG+AGG 0.426295 6.4:+59095441 MS.gene49927:CDS
GCAGCAGAGCCTTTCTTTGG+TGG 0.437765 6.4:-59096368 None:intergenic
ATTTGAGGAGTCAGTTGGAC+AGG 0.472058 6.4:+59095456 MS.gene49927:CDS
TCCTCAATCTGTAGGGGACA+TGG 0.482798 6.4:-59095775 None:intergenic
TGGTGGCCTGACGATTCTCC+TGG 0.483590 6.4:-59096351 None:intergenic
GTTTCCGCAAAATTCACGTC+AGG 0.487674 6.4:+59095801 MS.gene49927:CDS
GTTTGAGTACCCTGTTACTG+AGG 0.503056 6.4:+59096800 MS.gene49927:CDS
CGTGGACAGCAGTGAGTGTA+CGG 0.505350 6.4:-59096406 None:intergenic
TTCTGGCAACCGCAAGGCTG+TGG 0.507229 6.4:+59095748 MS.gene49927:CDS
GTGTTGCCTGCTGAGATTGT+TGG 0.507352 6.4:+59096449 MS.gene49927:CDS
ATCGTCAGGCCACCAAAGAA+AGG 0.508890 6.4:+59096359 MS.gene49927:CDS
TTGCCACCAGGAGAATCGTC+AGG 0.510117 6.4:+59096345 MS.gene49927:CDS
GAAGAAAATCAGCAAGGACA+AGG 0.510615 6.4:+59095417 MS.gene49927:CDS
GAAACCCTTCCTCAATCTGT+AGG 0.511555 6.4:-59095783 None:intergenic
TCCATGTCCCCTACAGATTG+AGG 0.519730 6.4:+59095774 MS.gene49927:CDS
GCAGTTTACAGGAAACTCTC+AGG 0.525392 6.4:+59096765 MS.gene49927:CDS
AAACCCTTCCTCAATCTGTA+GGG 0.532886 6.4:-59095782 None:intergenic
AATTCACGTCAGGCTCGTTA+GGG 0.538364 6.4:+59095811 MS.gene49927:CDS
ACTGAATTTGAGGAGTCAGT+TGG 0.548538 6.4:+59095451 MS.gene49927:CDS
CGTTTGCCAACAATCTCAGC+AGG 0.559003 6.4:-59096455 None:intergenic
TGTCCCCTACAGATTGAGGA+AGG 0.573232 6.4:+59095778 MS.gene49927:CDS
ATGTAATCCTCATTGCCACC+AGG 0.584954 6.4:+59096333 MS.gene49927:CDS
CGATTCTCCTGGTGGCAATG+AGG 0.590532 6.4:-59096340 None:intergenic
AAGAAAATCAGCAAGGACAA+GGG 0.599976 6.4:+59095418 MS.gene49927:CDS
TGATGTTTCTGGCAACCGCA+AGG 0.602547 6.4:+59095742 MS.gene49927:CDS
GGTTGCCAGAAACATCAACT+TGG 0.607356 6.4:-59095736 None:intergenic
TGAGAAGAAATTCAGCGGAA+AGG 0.621961 6.4:+59095838 MS.gene49927:CDS
ACTGACTCCTCAAATTCAGT+AGG 0.622702 6.4:-59095448 None:intergenic
TGATGGATCCAAGATCATGA+AGG 0.639271 6.4:+59096493 MS.gene49927:CDS
GTCCCCTACAGATTGAGGAA+GGG 0.640329 6.4:+59095779 MS.gene49927:CDS
AACCCTTCCTCAATCTGTAG+GGG 0.640960 6.4:-59095781 None:intergenic
TGTCCACGAGGCAATGCTCG+AGG 0.642990 6.4:+59096421 MS.gene49927:CDS
TTCAAGGAAGAAAATCAGCA+AGG 0.648771 6.4:+59095411 MS.gene49927:CDS
GCAGTGAGTGTACGGCTGCG+TGG 0.657285 6.4:-59096398 None:intergenic
TACACTCACTGCTGTCCACG+AGG 0.659160 6.4:+59096409 MS.gene49927:CDS
TGGCCTGACGATTCTCCTGG+TGG 0.662830 6.4:-59096348 None:intergenic
GAATCTAGGCCTCAGTAACA+GGG 0.677360 6.4:-59096809 None:intergenic
CATCCTCGAGCATTGCCTCG+TGG 0.690997 6.4:-59096424 None:intergenic
CATGGATAACCACAGCCTTG+CGG 0.691240 6.4:-59095757 None:intergenic
GAGCTTGAGAAGAAATTCAG+CGG 0.694607 6.4:+59095833 MS.gene49927:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAATAAGAAATAATGTTAA+TGG + chr6.4:59096660-59096679 MS.gene49927:intron 15.0%
!! ATTAGTATACAATAAAGTTA+AGG - chr6.4:59096295-59096314 None:intergenic 15.0%
!! AAATTGGAACAAAAAATTGT+CGG - chr6.4:59095935-59095954 None:intergenic 20.0%
!! AGAATAAAGTTCTTGAAATA+AGG - chr6.4:59095984-59096003 None:intergenic 20.0%
!! TTAAAGCAATTTAAAAACCA+AGG - chr6.4:59096019-59096038 None:intergenic 20.0%
!!! AGGTTATATATTGATTACTA+CGG + chr6.4:59095476-59095495 MS.gene49927:intron 20.0%
!!! ATTTTTTAAGGCTAATGTTA+TGG - chr6.4:59096246-59096265 None:intergenic 20.0%
!!! GATGTATTTGTTTTAAGTTT+TGG - chr6.4:59096566-59096585 None:intergenic 20.0%
!!! TGTGAGAAAACAATTTTTTA+AGG - chr6.4:59096258-59096277 None:intergenic 20.0%
! CTGTAAAACTGAAATTAATC+AGG + chr6.4:59096070-59096089 MS.gene49927:intron 25.0%
! TAATGTTAATGGAATTCTTG+TGG + chr6.4:59096671-59096690 MS.gene49927:intron 25.0%
!!! TTGTTTTAAGTTTTGGTTGA+TGG - chr6.4:59096559-59096578 None:intergenic 25.0%
ACACAAAACAGGAAGTTATT+TGG - chr6.4:59096535-59096554 None:intergenic 30.0%
ATAGTTTACCTTCATGATCT+TGG - chr6.4:59096504-59096523 None:intergenic 30.0%
CAAATTCTTTAGTGTACGTT+TGG - chr6.4:59096217-59096236 None:intergenic 30.0%
GACAGAATCGTAATAAAAGA+TGG - chr6.4:59095910-59095929 None:intergenic 30.0%
GATTACATCCTACAAGTTAA+AGG - chr6.4:59096321-59096340 None:intergenic 30.0%
TTAGAAAGAATAACTGGCAA+AGG - chr6.4:59095882-59095901 None:intergenic 30.0%
! AAACATTTTCTGCAGTTTAC+AGG + chr6.4:59096754-59096773 MS.gene49927:CDS 30.0%
! TCTGTGTATATAGGTGTTTT+TGG + chr6.4:59096695-59096714 MS.gene49927:intron 30.0%
!! CTAATGAACCTTTAACTTGT+AGG + chr6.4:59096310-59096329 MS.gene49927:intron 30.0%
!! GTTATTTTGCAAAATCACTC+TGG + chr6.4:59096588-59096607 MS.gene49927:intron 30.0%
!!! TGTTTTGAATTTGTTGTTGC+AGG + chr6.4:59095559-59095578 MS.gene49927:intron 30.0%
AACTGAAATTAATCAGGCTG+CGG + chr6.4:59096076-59096095 MS.gene49927:intron 35.0%
AAGAAAATCAGCAAGGACAA+GGG + chr6.4:59095418-59095437 MS.gene49927:CDS 35.0%
CGAGTAGAAGACAAAGAAAT+TGG - chr6.4:59095951-59095970 None:intergenic 35.0%
GTCTAAGCATGTGTTTGATT+TGG + chr6.4:59096098-59096117 MS.gene49927:intron 35.0%
GTGCAGTTAGAAAGAATAAC+TGG - chr6.4:59095888-59095907 None:intergenic 35.0%
GTGTAAGGATGTGTTCTTTA+TGG + chr6.4:59095653-59095672 MS.gene49927:intron 35.0%
TACATCAATTCTGCAGTGTA+AGG + chr6.4:59095638-59095657 MS.gene49927:intron 35.0%
TCTTTAGTGTACGTTTGGTT+TGG - chr6.4:59096212-59096231 None:intergenic 35.0%
TTCAAGGAAGAAAATCAGCA+AGG + chr6.4:59095411-59095430 MS.gene49927:CDS 35.0%
! ATTCTGTTTTGCATTCTCCT+TGG + chr6.4:59095999-59096018 MS.gene49927:intron 35.0%
! CAGTATTGTTTCTCTCCTTT+GGG - chr6.4:59096722-59096741 None:intergenic 35.0%
! TCAGTATTGTTTCTCTCCTT+TGG - chr6.4:59096723-59096742 None:intergenic 35.0%
! TCTTGTGGTTCTGTGTATAT+AGG + chr6.4:59096686-59096705 MS.gene49927:intron 35.0%
AAACCCTTCCTCAATCTGTA+GGG - chr6.4:59095785-59095804 None:intergenic 40.0%
ACTGAATTTGAGGAGTCAGT+TGG + chr6.4:59095451-59095470 MS.gene49927:CDS 40.0%
CGTACCAGATACAGAATTGA+TGG + chr6.4:59096476-59096495 MS.gene49927:CDS 40.0%
GAAGAAAATCAGCAAGGACA+AGG + chr6.4:59095417-59095436 MS.gene49927:CDS 40.0%
GAGCTTGAGAAGAAATTCAG+CGG + chr6.4:59095833-59095852 MS.gene49927:CDS 40.0%
GGATCCATCAATTCTGTATC+TGG - chr6.4:59096483-59096502 None:intergenic 40.0%
TGAGAAGAAATTCAGCGGAA+AGG + chr6.4:59095838-59095857 MS.gene49927:CDS 40.0%
! ACTGACTCCTCAAATTCAGT+AGG - chr6.4:59095451-59095470 None:intergenic 40.0%
! TGATGGATCCAAGATCATGA+AGG + chr6.4:59096493-59096512 MS.gene49927:CDS 40.0%
!! TACAGCCAAGTTGATGTTTC+TGG + chr6.4:59095731-59095750 MS.gene49927:intron 40.0%
!! TGGTTGATGGAACACAAAAC+AGG - chr6.4:59096546-59096565 None:intergenic 40.0%
!!! ATAGGTGTTTTTGGACCCAA+AGG + chr6.4:59096704-59096723 MS.gene49927:intron 40.0%
AAATTCACGTCAGGCTCGTT+AGG + chr6.4:59095810-59095829 MS.gene49927:CDS 45.0%
AACCCTTCCTCAATCTGTAG+GGG - chr6.4:59095784-59095803 None:intergenic 45.0%
AATTCACGTCAGGCTCGTTA+GGG + chr6.4:59095811-59095830 MS.gene49927:CDS 45.0%
ATGCATGCCTTGTAATCGTG+TGG + chr6.4:59096169-59096188 MS.gene49927:intron 45.0%
ATGTAATCCTCATTGCCACC+AGG + chr6.4:59096333-59096352 MS.gene49927:CDS 45.0%
ATTTGAGGAGTCAGTTGGAC+AGG + chr6.4:59095456-59095475 MS.gene49927:CDS 45.0%
GAAACCCTTCCTCAATCTGT+AGG - chr6.4:59095786-59095805 None:intergenic 45.0%
GCAGTTTACAGGAAACTCTC+AGG + chr6.4:59096765-59096784 MS.gene49927:CDS 45.0%
GGTTGCCAGAAACATCAACT+TGG - chr6.4:59095739-59095758 None:intergenic 45.0%
GTTTCCGCAAAATTCACGTC+AGG + chr6.4:59095801-59095820 MS.gene49927:CDS 45.0%
GTTTGAGTACCCTGTTACTG+AGG + chr6.4:59096800-59096819 MS.gene49927:CDS 45.0%
TGCATGCCTTGTAATCGTGT+GGG + chr6.4:59096170-59096189 MS.gene49927:intron 45.0%
! ACGGACTATTGTTGTTGCTG+TGG + chr6.4:59095495-59095514 MS.gene49927:intron 45.0%
!! TCAGCTCACTTTTGAGCTCA+TGG - chr6.4:59095610-59095629 None:intergenic 45.0%
ATCGTCAGGCCACCAAAGAA+AGG + chr6.4:59096359-59096378 MS.gene49927:CDS 50.0%
CATGGATAACCACAGCCTTG+CGG - chr6.4:59095760-59095779 None:intergenic 50.0%
CGCTGAGCCTACTGAATTTG+AGG + chr6.4:59095441-59095460 MS.gene49927:CDS 50.0%
CGTTTGCCAACAATCTCAGC+AGG - chr6.4:59096458-59096477 None:intergenic 50.0%
CTGCAACCCACACGATTACA+AGG - chr6.4:59096179-59096198 None:intergenic 50.0%
GTCCCCTACAGATTGAGGAA+GGG + chr6.4:59095779-59095798 MS.gene49927:CDS 50.0%
GTGTTGCCTGCTGAGATTGT+TGG + chr6.4:59096449-59096468 MS.gene49927:CDS 50.0%
GTTGCAGGCTCTGTTTGATC+TGG + chr6.4:59095574-59095593 MS.gene49927:intron 50.0%
TCCATGTCCCCTACAGATTG+AGG + chr6.4:59095774-59095793 MS.gene49927:CDS 50.0%
TCCTCAATCTGTAGGGGACA+TGG - chr6.4:59095778-59095797 None:intergenic 50.0%
TGAGCAGCAGAGCCTTTCTT+TGG - chr6.4:59096374-59096393 None:intergenic 50.0%
TGTCCCCTACAGATTGAGGA+AGG + chr6.4:59095778-59095797 MS.gene49927:CDS 50.0%
! CGAGCCTGACGTGAATTTTG+CGG - chr6.4:59095808-59095827 None:intergenic 50.0%
!! TGATGTTTCTGGCAACCGCA+AGG + chr6.4:59095742-59095761 MS.gene49927:CDS 50.0%
CGATTCTCCTGGTGGCAATG+AGG - chr6.4:59096343-59096362 None:intergenic 55.0%
CGTGGACAGCAGTGAGTGTA+CGG - chr6.4:59096409-59096428 None:intergenic 55.0%
GCAGCAGAGCCTTTCTTTGG+TGG - chr6.4:59096371-59096390 None:intergenic 55.0%
TACACTCACTGCTGTCCACG+AGG + chr6.4:59096409-59096428 MS.gene49927:CDS 55.0%
TTGCCACCAGGAGAATCGTC+AGG + chr6.4:59096345-59096364 MS.gene49927:CDS 55.0%
TGGCCTGACGATTCTCCTGG+TGG - chr6.4:59096351-59096370 None:intergenic 60.0%
TGGTGGCCTGACGATTCTCC+TGG - chr6.4:59096354-59096373 None:intergenic 60.0%
TGTCCACGAGGCAATGCTCG+AGG + chr6.4:59096421-59096440 MS.gene49927:CDS 60.0%
TTCTGGCAACCGCAAGGCTG+TGG + chr6.4:59095748-59095767 MS.gene49927:CDS 60.0%
! CATCCTCGAGCATTGCCTCG+TGG - chr6.4:59096427-59096446 None:intergenic 60.0%
GCAGTGAGTGTACGGCTGCG+TGG - chr6.4:59096401-59096420 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.4 gene 59095403 59096827 59095403 ID=MS.gene49927
chr6.4 mRNA 59095403 59096827 59095403 ID=MS.gene49927.t1;Parent=MS.gene49927
chr6.4 exon 59095403 59095477 59095403 ID=MS.gene49927.t1.exon1;Parent=MS.gene49927.t1
chr6.4 CDS 59095403 59095477 59095403 ID=cds.MS.gene49927.t1;Parent=MS.gene49927.t1
chr6.4 exon 59095581 59095654 59095581 ID=MS.gene49927.t1.exon2;Parent=MS.gene49927.t1
chr6.4 CDS 59095581 59095654 59095581 ID=cds.MS.gene49927.t1;Parent=MS.gene49927.t1
chr6.4 exon 59095736 59095859 59095736 ID=MS.gene49927.t1.exon3;Parent=MS.gene49927.t1
chr6.4 CDS 59095736 59095859 59095736 ID=cds.MS.gene49927.t1;Parent=MS.gene49927.t1
chr6.4 exon 59096332 59096514 59096332 ID=MS.gene49927.t1.exon4;Parent=MS.gene49927.t1
chr6.4 CDS 59096332 59096514 59096332 ID=cds.MS.gene49927.t1;Parent=MS.gene49927.t1
chr6.4 exon 59096708 59096827 59096708 ID=MS.gene49927.t1.exon5;Parent=MS.gene49927.t1
chr6.4 CDS 59096708 59096827 59096708 ID=cds.MS.gene49927.t1;Parent=MS.gene49927.t1
Gene Sequence

>MS.gene49927

ATGTTTACTTCAAGGAAGAAAATCAGCAAGGACAAGGGCGCTGAGCCTACTGAATTTGAGGAGTCAGTTGGACAGGTTATATATTGATTACTACGGACTATTGTTGTTGCTGTGGTTGCTGATTAGTCTCTATAATTGCAAAATCTAAATCATTATTGTTTTGAATTTGTTGTTGCAGGCTCTGTTTGATCTGGAAAACACTAACCATGAGCTCAAAAGTGAGCTGAAAGATTTATACATCAATTCTGCAGTGTAAGGATGTGTTCTTTATGGTTTGTTTGAAAATACATCTGTTTTCTTCGTCTCATGTCTACTGTTTTCTGTTATCTACAGCCAAGTTGATGTTTCTGGCAACCGCAAGGCTGTGGTTATCCATGTCCCCTACAGATTGAGGAAGGGTTTCCGCAAAATTCACGTCAGGCTCGTTAGGGAGCTTGAGAAGAAATTCAGCGGAAAGGTAATCAAAGTCTTTTATACCTTTGCCAGTTATTCTTTCTAACTGCACCATCTTTTATTACGATTCTGTCTACCGACAATTTTTTGTTCCAATTTCTTTGTCTTCTACTCGTTATTTTTATCCTTATTTCAAGAACTTTATTCTGTTTTGCATTCTCCTTGGTTTTTAAATTGCTTTAATTTATATTTACTTGAGAGTAGTTCTATTCAGCTGTAAAACTGAAATTAATCAGGCTGCGGTCTAAGCATGTGTTTGATTTGGCTTCATAGTTTTCATAATCACTTTGTAGCTTCTCTTTATCACGACAGAATGCATGCCTTGTAATCGTGTGGGTTGCAGTGAAAAGAAGCCAAACCAAACGTACACTAAAGAATTTGATGATACCATAACATTAGCCTTAAAAAATTGTTTTCTCACAGATTTATATGTGATCCTTAACTTTATTGTATACTAATGAACCTTTAACTTGTAGGATGTAATCCTCATTGCCACCAGGAGAATCGTCAGGCCACCAAAGAAAGGCTCTGCTGCTCAGCGTCCACGCAGCCGTACACTCACTGCTGTCCACGAGGCAATGCTCGAGGATGTCGTGTTGCCTGCTGAGATTGTTGGCAAACGTACCAGATACAGAATTGATGGATCCAAGATCATGAAGGTAAACTATTCTAACAGCCAAATAACTTCCTGTTTTGTGTTCCATCAACCAAAACTTAAAACAAATACATCTCGTTATTTTGCAAAATCACTCTGGTGAAATTTATTTACATGATAGTCGTTTTTATTATGCTATAATATTAAAAAGAATAAGAAATAATGTTAATGGAATTCTTGTGGTTCTGTGTATATAGGTGTTTTTGGACCCAAAGGAGAGAAACAATACTGAATACAAGCTCGAAACATTTTCTGCAGTTTACAGGAAACTCTCAGGCAAAGATGTTGTGTTTGAGTACCCTGTTACTGAGGCCTAG

Protein sequence

>MS.gene49927.t1

MFTSRKKISKDKGAEPTEFEESVGQALFDLENTNHELKSELKDLYINSAVQVDVSGNRKAVVIHVPYRLRKGFRKIHVRLVRELEKKFSGKDVILIATRRIVRPPKKGSAAQRPRSRTLTAVHEAMLEDVVLPAEIVGKRTRYRIDGSKIMKVFLDPKERNNTEYKLETFSAVYRKLSGKDVVFEYPVTEA