AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84831

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 64 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGATTATATTCCACTTA+TGG 0.180908 4.1:-72683561 MS.gene84831:CDS
TTCATAGAGACTCTAAAATT+TGG 0.181573 4.1:-72682840 MS.gene84831:CDS
AGAAAGTACAAGAAGAAATT+AGG 0.193409 4.1:-72683059 MS.gene84831:CDS
GCAATAAACTGAATCTAAAT+AGG 0.205054 4.1:+72682544 None:intergenic
CTCTCAGGATAAAACTCTTC+TGG 0.230573 4.1:+72682811 None:intergenic
ATGATTTGTAGGATTGCTTT+TGG 0.269710 4.1:-72683671 None:intergenic
TGTACTTTCTTCATTACTCT+TGG 0.272705 4.1:+72683072 None:intergenic
TCTGATTATATTCCACTTAT+GGG 0.275846 4.1:-72683560 MS.gene84831:CDS
GAAAGTACAAGAAGAAATTA+GGG 0.290467 4.1:-72683058 MS.gene84831:CDS
ATCTTCTCTATTCATTTGAT+TGG 0.299448 4.1:-72682666 MS.gene84831:CDS
CCACGTCTGCCACAATAGTT+TGG 0.318253 4.1:-72683119 MS.gene84831:CDS
ACAAACGTTGTTTCTTCAAT+TGG 0.326370 4.1:+72683393 None:intergenic
TCATCTGTATGTTGTCTGTT+TGG 0.333689 4.1:+72683440 None:intergenic
GTACTTTCTTCATTACTCTT+GGG 0.359870 4.1:+72683073 None:intergenic
AGGGGTTATTGATGAACATT+TGG 0.362806 4.1:-72683465 MS.gene84831:CDS
GGTTGGATTGATAAACTATC+TGG 0.378220 4.1:-72683539 MS.gene84831:CDS
ACAAAATTTCGTCTATTTGA+AGG 0.395788 4.1:-72682995 MS.gene84831:CDS
TCTTCTCTATTCATTTGATT+GGG 0.409540 4.1:-72682665 MS.gene84831:CDS
TCTCAGGATAAAACTCTTCT+GGG 0.417358 4.1:+72682812 None:intergenic
ATTATATTCCACTTATGGGT+TGG 0.420893 4.1:-72683556 MS.gene84831:CDS
TAGGGGATCAAGAGTTAAGA+AGG 0.429807 4.1:-72683040 MS.gene84831:CDS
CAATAAACTGAATCTAAATA+GGG 0.430060 4.1:+72682545 None:intergenic
TTCTATCGCAGTTGCATCGT+TGG 0.438240 4.1:-72682704 MS.gene84831:CDS
CTGAATCTAAATAGGGACTT+TGG 0.439575 4.1:+72682552 None:intergenic
CAATAGTATATGTGAATGCT+TGG 0.454351 4.1:-72682867 MS.gene84831:CDS
GCGTCTTGAACGAAATTTCA+AGG 0.463177 4.1:-72683507 MS.gene84831:CDS
CGAACTCATGCAACATTCCA+TGG 0.464765 4.1:+72683609 None:intergenic
GAACTAATTCCGTTTGGAGC+AGG 0.467327 4.1:-72682748 MS.gene84831:CDS
ATTGATACAGAAATGTTGCC+AGG 0.469404 4.1:-72682613 MS.gene84831:CDS
CACGTCTGCCACAATAGTTT+GGG 0.484094 4.1:-72683118 MS.gene84831:CDS
GTTTCTCTTGGCAAAAGCAA+TGG 0.491693 4.1:+72682934 None:intergenic
TGAACGAAATTTCAAGGCGA+TGG 0.497520 4.1:-72683501 MS.gene84831:CDS
GAACTCTCTAAGAATCTCTC+AGG 0.498130 4.1:+72682796 None:intergenic
TTATCAATCCAACCCATAAG+TGG 0.515860 4.1:+72683548 None:intergenic
ATTCTACGGCCTGCTCCAAA+CGG 0.522210 4.1:+72682739 None:intergenic
AAATAGGGACTTTGGCTACA+AGG 0.522430 4.1:+72682560 None:intergenic
TGGAATGTTGCATGAGTTCG+AGG 0.522929 4.1:-72683606 MS.gene84831:CDS
TTGGGAATTACCACATGGGT+TGG 0.525961 4.1:-72682647 MS.gene84831:CDS
ATTACCACATGGGTTGGTAA+AGG 0.528712 4.1:-72682641 MS.gene84831:CDS
AAATACCTGGGCAAATTCTA+CGG 0.529429 4.1:+72682725 None:intergenic
AACAAAGAAAGCAGTCATCA+AGG 0.546880 4.1:+72683583 None:intergenic
GGGAAGAGGTACGAGAAACA+AGG 0.565351 4.1:-72683650 MS.gene84831:CDS
AATGTTCATCAATAACCCCT+TGG 0.567178 4.1:+72683468 None:intergenic
GCAACTGCGATAGAAATACC+TGG 0.569172 4.1:+72682712 None:intergenic
ACAAGAGAAAAGTGTATCGT+AGG 0.569253 4.1:-72682913 MS.gene84831:CDS
CTTGGCAAAAGCAATGGAGC+TGG 0.577987 4.1:+72682940 None:intergenic
ACGAGAAACAAGGGATTGAG+AGG 0.587447 4.1:-72683640 MS.gene84831:CDS
AGTCATAGCCCAAACTATTG+TGG 0.591714 4.1:+72683110 None:intergenic
ATGAATAGAGAAGATTAGCA+AGG 0.593996 4.1:+72682674 None:intergenic
CCAAACTATTGTGGCAGACG+TGG 0.594757 4.1:+72683119 None:intergenic
TCATATCAAAGGAGTCCTCA+TGG 0.609600 4.1:-72683348 MS.gene84831:intron
ATTGAGAGGAGTAAATTCCA+TGG 0.609832 4.1:-72683626 MS.gene84831:CDS
GCAAAAGCAATGGAGCTGGT+AGG 0.616646 4.1:+72682944 None:intergenic
TGAATAGAGAAGATTAGCAA+GGG 0.618501 4.1:+72682675 None:intergenic
AGAGAAAAGTGTATCGTAGG+TGG 0.618520 4.1:-72682910 MS.gene84831:CDS
TTGATACAGAAATGTTGCCA+GGG 0.619652 4.1:-72682612 MS.gene84831:CDS
GCAGGCCGTAGAATTTGCCC+AGG 0.626471 4.1:-72682730 MS.gene84831:CDS
TTTGATTGGGAATTACCACA+TGG 0.636196 4.1:-72682652 MS.gene84831:CDS
AAATTTCGTCTATTTGAAGG+CGG 0.648837 4.1:-72682992 MS.gene84831:CDS
GGAAGAGGTACGAGAAACAA+GGG 0.654353 4.1:-72683649 MS.gene84831:CDS
CAACTGCGATAGAAATACCT+GGG 0.659782 4.1:+72682713 None:intergenic
TTGATTGGGAATTACCACAT+GGG 0.665400 4.1:-72682651 MS.gene84831:CDS
AAAGTACAAGAAGAAATTAG+GGG 0.686279 4.1:-72683057 MS.gene84831:CDS
TCTTCCTTTACCAACCCATG+TGG 0.699620 4.1:+72682637 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAAGTATCAAATTCGAAA+AGG + chr4.1:72682910-72682929 None:intergenic 20.0%
! AAAGTACAAGAAGAAATTAG+GGG - chr4.1:72683161-72683180 MS.gene84831:intron 25.0%
! AATATTCTCTTGTAAAATGG+CGG - chr4.1:72682957-72682976 MS.gene84831:CDS 25.0%
! ACAAAATTTCGTCTATTTGA+AGG - chr4.1:72683223-72683242 MS.gene84831:intron 25.0%
! ATAAAAGTTAGCAACATAAC+TGG + chr4.1:72682985-72683004 None:intergenic 25.0%
! ATCTTCTCTATTCATTTGAT+TGG - chr4.1:72683552-72683571 MS.gene84831:CDS 25.0%
! GAGAATATTCTCTTGTAAAA+TGG - chr4.1:72682954-72682973 MS.gene84831:CDS 25.0%
! TCAATTTAAATCCACGATAT+CGG - chr4.1:72682932-72682951 MS.gene84831:CDS 25.0%
! TCTGATTATATTCCACTTAT+GGG - chr4.1:72682658-72682677 MS.gene84831:CDS 25.0%
! TCTTCTCTATTCATTTGATT+GGG - chr4.1:72683553-72683572 MS.gene84831:CDS 25.0%
! TTCTGATTATATTCCACTTA+TGG - chr4.1:72682657-72682676 MS.gene84831:CDS 25.0%
!! AGAAAGTACAAGAAGAAATT+AGG - chr4.1:72683159-72683178 MS.gene84831:intron 25.0%
!! GAAAGTACAAGAAGAAATTA+GGG - chr4.1:72683160-72683179 MS.gene84831:intron 25.0%
!! GAGAGTTCTATAAATTTTCT+TGG - chr4.1:72683437-72683456 MS.gene84831:CDS 25.0%
!!! ACATATACTATTGTTTTTGC+AGG + chr4.1:72683344-72683363 None:intergenic 25.0%
!!! GTTAAGAAGGATTTTTTAGA+TGG - chr4.1:72683191-72683210 MS.gene84831:intron 25.0%
!!! TACTCTTGGGTTTTTTATTA+GGG + chr4.1:72683135-72683154 None:intergenic 25.0%
!!! TTACTCTTGGGTTTTTTATT+AGG + chr4.1:72683136-72683155 None:intergenic 25.0%
!!! TTCATAGAGACTCTAAAATT+TGG - chr4.1:72683378-72683397 MS.gene84831:CDS 25.0%
AAATTTCGTCTATTTGAAGG+CGG - chr4.1:72683226-72683245 MS.gene84831:intron 30.0%
ATGAATAGAGAAGATTAGCA+AGG + chr4.1:72683547-72683566 None:intergenic 30.0%
ATTATATTCCACTTATGGGT+TGG - chr4.1:72682662-72682681 MS.gene84831:CDS 30.0%
CAATAGTATATGTGAATGCT+TGG - chr4.1:72683351-72683370 MS.gene84831:CDS 30.0%
GAATAAAACATCATACCATG+AGG + chr4.1:72682888-72682907 None:intergenic 30.0%
GTACTTTCTTCATTACTCTT+GGG + chr4.1:72683148-72683167 None:intergenic 30.0%
TGAATAGAGAAGATTAGCAA+GGG + chr4.1:72683546-72683565 None:intergenic 30.0%
TGTACTTTCTTCATTACTCT+TGG + chr4.1:72683149-72683168 None:intergenic 30.0%
! AGAGATGATTCTTTTTGTGT+TGG + chr4.1:72683637-72683656 None:intergenic 30.0%
! CGTAGTTAAGTACTTGTTAA+GGG + chr4.1:72683036-72683055 None:intergenic 30.0%
! GAGATGATTCTTTTTGTGTT+GGG + chr4.1:72683636-72683655 None:intergenic 30.0%
! GATTTTGAACTAATTCCGTT+TGG - chr4.1:72683464-72683483 MS.gene84831:CDS 30.0%
! TCGTAGTTAAGTACTTGTTA+AGG + chr4.1:72683037-72683056 None:intergenic 30.0%
!! ACAAACGTTGTTTCTTCAAT+TGG + chr4.1:72682828-72682847 None:intergenic 30.0%
!! CTCACTTTTGATCATATCAA+AGG - chr4.1:72682859-72682878 MS.gene84831:CDS 30.0%
!!! CTATTGTTTTTGCAGGAATA+TGG + chr4.1:72683337-72683356 None:intergenic 30.0%
AAATACCTGGGCAAATTCTA+CGG + chr4.1:72683496-72683515 None:intergenic 35.0%
AACAAAGAAAGCAGTCATCA+AGG + chr4.1:72682638-72682657 None:intergenic 35.0%
AATGTTCATCAATAACCCCT+TGG + chr4.1:72682753-72682772 None:intergenic 35.0%
AGGGGTTATTGATGAACATT+TGG - chr4.1:72682753-72682772 MS.gene84831:CDS 35.0%
ATTGAGAGGAGTAAATTCCA+TGG - chr4.1:72682592-72682611 MS.gene84831:CDS 35.0%
ATTGATACAGAAATGTTGCC+AGG - chr4.1:72683605-72683624 MS.gene84831:CDS 35.0%
GGTTGGATTGATAAACTATC+TGG - chr4.1:72682679-72682698 MS.gene84831:CDS 35.0%
TCATCTGTATGTTGTCTGTT+TGG + chr4.1:72682781-72682800 None:intergenic 35.0%
TCTCAGGATAAAACTCTTCT+GGG + chr4.1:72683409-72683428 None:intergenic 35.0%
TTATCAATCCAACCCATAAG+TGG + chr4.1:72682673-72682692 None:intergenic 35.0%
TTGATACAGAAATGTTGCCA+GGG - chr4.1:72683606-72683625 MS.gene84831:CDS 35.0%
TTGATTGGGAATTACCACAT+GGG - chr4.1:72683567-72683586 MS.gene84831:CDS 35.0%
TTTGATTGGGAATTACCACA+TGG - chr4.1:72683566-72683585 MS.gene84831:CDS 35.0%
! ACAAGAGAAAAGTGTATCGT+AGG - chr4.1:72683305-72683324 MS.gene84831:intron 35.0%
!! CACTTTTCTCTTGTTTCTCT+TGG + chr4.1:72683299-72683318 None:intergenic 35.0%
AAATAGGGACTTTGGCTACA+AGG + chr4.1:72683661-72683680 None:intergenic 40.0%
AGTCATAGCCCAAACTATTG+TGG + chr4.1:72683111-72683130 None:intergenic 40.0%
CAACTGCGATAGAAATACCT+GGG + chr4.1:72683508-72683527 None:intergenic 40.0%
CTCTCAGGATAAAACTCTTC+TGG + chr4.1:72683410-72683429 None:intergenic 40.0%
GAGAATATTCTCCGATATCG+TGG + chr4.1:72682946-72682965 None:intergenic 40.0%
GCGTCTTGAACGAAATTTCA+AGG - chr4.1:72682711-72682730 MS.gene84831:CDS 40.0%
GTTTCTCTTGGCAAAAGCAA+TGG + chr4.1:72683287-72683306 None:intergenic 40.0%
TACGAGTATTCTTCATGTGC+AGG - chr4.1:72683052-72683071 MS.gene84831:CDS 40.0%
TAGGGGATCAAGAGTTAAGA+AGG - chr4.1:72683178-72683197 MS.gene84831:intron 40.0%
TCATATCAAAGGAGTCCTCA+TGG - chr4.1:72682870-72682889 MS.gene84831:CDS 40.0%
TGAACGAAATTTCAAGGCGA+TGG - chr4.1:72682717-72682736 MS.gene84831:CDS 40.0%
TGTAGCCAAAGTCCCTATTT+AGG - chr4.1:72683661-72683680 MS.gene84831:CDS 40.0%
! AGAGAAAAGTGTATCGTAGG+TGG - chr4.1:72683308-72683327 MS.gene84831:intron 40.0%
! GAACTCTCTAAGAATCTCTC+AGG + chr4.1:72683425-72683444 None:intergenic 40.0%
! TTTTTGTGTTGGGTTATCCC+TGG + chr4.1:72683626-72683645 None:intergenic 40.0%
!! ATTACCACATGGGTTGGTAA+AGG - chr4.1:72683577-72683596 MS.gene84831:CDS 40.0%
ACGAGAAACAAGGGATTGAG+AGG - chr4.1:72682578-72682597 MS.gene84831:CDS 45.0%
CACGTCTGCCACAATAGTTT+GGG - chr4.1:72683100-72683119 MS.gene84831:CDS 45.0%
CGAACTCATGCAACATTCCA+TGG + chr4.1:72682612-72682631 None:intergenic 45.0%
GCAACTGCGATAGAAATACC+TGG + chr4.1:72683509-72683528 None:intergenic 45.0%
TCTTCCTTTACCAACCCATG+TGG + chr4.1:72683584-72683603 None:intergenic 45.0%
TGGAATGTTGCATGAGTTCG+AGG - chr4.1:72682612-72682631 MS.gene84831:CDS 45.0%
TTCTATCGCAGTTGCATCGT+TGG - chr4.1:72683514-72683533 MS.gene84831:CDS 45.0%
TTGGGAATTACCACATGGGT+TGG - chr4.1:72683571-72683590 MS.gene84831:CDS 45.0%
! CGATGGACGAGTTTTACCAA+GGG - chr4.1:72682734-72682753 MS.gene84831:CDS 45.0%
! GAACTAATTCCGTTTGGAGC+AGG - chr4.1:72683470-72683489 MS.gene84831:CDS 45.0%
! GATGGACGAGTTTTACCAAG+GGG - chr4.1:72682735-72682754 MS.gene84831:CDS 45.0%
! GGAAGAGGTACGAGAAACAA+GGG - chr4.1:72682569-72682588 MS.gene84831:CDS 45.0%
ATTCTACGGCCTGCTCCAAA+CGG + chr4.1:72683482-72683501 None:intergenic 50.0%
CCAAACTATTGTGGCAGACG+TGG + chr4.1:72683102-72683121 None:intergenic 50.0%
CCACGTCTGCCACAATAGTT+TGG - chr4.1:72683099-72683118 MS.gene84831:CDS 50.0%
CTTGGCAAAAGCAATGGAGC+TGG + chr4.1:72683281-72683300 None:intergenic 50.0%
GCAAAAGCAATGGAGCTGGT+AGG + chr4.1:72683277-72683296 None:intergenic 50.0%
! GCGATGGACGAGTTTTACCA+AGG - chr4.1:72682733-72682752 MS.gene84831:CDS 50.0%
! GGGAAGAGGTACGAGAAACA+AGG - chr4.1:72682568-72682587 MS.gene84831:CDS 50.0%
GCAGGCCGTAGAATTTGCCC+AGG - chr4.1:72683488-72683507 MS.gene84831:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 72682558 72683682 72682558 ID=MS.gene84831
chr4.1 mRNA 72682558 72683682 72682558 ID=MS.gene84831.t1;Parent=MS.gene84831
chr4.1 exon 72683349 72683682 72683349 ID=MS.gene84831.t1.exon1;Parent=MS.gene84831.t1
chr4.1 CDS 72683349 72683682 72683349 ID=cds.MS.gene84831.t1;Parent=MS.gene84831.t1
chr4.1 exon 72682558 72683166 72682558 ID=MS.gene84831.t1.exon2;Parent=MS.gene84831.t1
chr4.1 CDS 72682558 72683166 72682558 ID=cds.MS.gene84831.t1;Parent=MS.gene84831.t1
Gene Sequence

>MS.gene84831

GATTGCTTTTGGGAAGAGGTACGAGAAACAAGGGATTGAGAGGAGTAAATTCCATGGAATGTTGCATGAGTTCGAGGCCTTGATGACTGCTTTCTTTGTTTCTGATTATATTCCACTTATGGGTTGGATTGATAAACTATCTGGACTTCGTACGCGTCTTGAACGAAATTTCAAGGCGATGGACGAGTTTTACCAAGGGGTTATTGATGAACATTTGGATCCAAACAGACAACATACAGATGAAGAGTTTATTGTTGATGTCTTACTCCAATTGAAGAAACAACGTTTGTTTTCGATTGATCTCACTTTTGATCATATCAAAGGAGTCCTCATGGTATGATGTTTTATTCCTTTTCGAATTTGATACTTTTTACTCAATTTAAATCCACGATATCGGAGAATATTCTCTTGTAAAATGGCGGTTCCAGTTATGTTGCTAACTTTTATCTTGTCAATAGTAAGTATTTTACAAAATCCCTTAACAAGTACTTAACTACGAGTATTCTTCATGTGCAGGACATGCTTGTAGCTGCAACAGATACCACGTCTGCCACAATAGTTTGGGCTATGACTGCCCTAATAAAAAACCCAAGAGTAATGAAGAAAGTACAAGAAGAAATTAGGGGATCAAGAGTTAAGAAGGATTTTTTAGATGGAAATGATATACAAAATTTCGTCTATTTGAAGGCGGTGATAAAAGAGACATTGAGATTGTACCTACCAGCTCCATTGCTTTTGCCAAGAGAAACAAGAGAAAAGTGTATCGTAGGTGGCTACCATATTCCTGCAAAAACAATAGTATATGTGAATGCTTGGTCTATTCATAGAGACTCTAAAATTTGGAAAGACCCAGAAGAGTTTTATCCTGAGAGATTCTTAGAGAGTTCTATAAATTTTCTTGGACATGATTTTGAACTAATTCCGTTTGGAGCAGGCCGTAGAATTTGCCCAGGTATTTCTATCGCAGTTGCATCGTTGGAACTTACCCTTGCTAATCTTCTCTATTCATTTGATTGGGAATTACCACATGGGTTGGTAAAGGAAGATATTGATACAGAAATGTTGCCAGGGATAACCCAACACAAAAAGAATCATCTCTGCCTTGTAGCCAAAGTCCCTATTTAG
Protein sequence

>MS.gene84831.t1

DCFWEEVRETRDUEEUIPWNVAUVRGLDDCFLCFULYSTYGLDUUTIWTSYASUTKFQGDGRVLPRGYUUTFGSKQTTYRURVYCUCLTPIEETTFVFDUSHFUSYQRSPHGHACSCNRYHVCHNSLGYDCPNKKPKSNEESTRRNUGIKSUEGFFRWKUYTKFRLFEGGDKRDIEIVPTSSIAFAKRNKRKVYRRWLPYSCKNNSICECLVYSURLUNLERPRRVLSUEILREFYKFSWTUFUTNSVWSRPUNLPRYFYRSCIVGTYPCUSSLFIULGITTWVGKGRYUYRNVARDNPTQKESSLPCSQSPYL