AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066839

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066839.t1 MTR_4g012060 96.727 275 7 2 1 274 1 274 0.0 533
MS.gene066839.t1 MTR_2g102140 48.344 302 121 9 1 274 1 295 5.46e-77 236
MS.gene066839.t1 MTR_1g072110 56.061 66 26 2 186 249 167 231 1.24e-15 74.7
MS.gene066839.t1 MTR_7g095150 47.826 69 34 1 183 249 129 197 3.41e-13 67.4
MS.gene066839.t1 MTR_1g103640 30.370 135 74 4 119 249 58 176 5.24e-12 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066839.t1 AT1G79960 37.333 300 134 11 1 268 1 278 1.00e-40 142
MS.gene066839.t1 AT4G14860 52.542 59 27 1 192 249 109 167 1.94e-13 67.4
MS.gene066839.t1 AT1G05420 34.343 99 63 1 153 249 117 215 5.00e-12 64.3
MS.gene066839.t1 AT1G05420 34.343 99 63 1 153 249 133 231 5.86e-12 64.3

Find 51 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGACCAATCCATTTCTTAG+AGG 0.317572 4.2:-88054276 None:intergenic
TTCGTTTATCCTCTAAGAAA+TGG 0.318720 4.2:+88054267 MS.gene066839:CDS
CGCTTCCACCGTTTCTTGCA+TGG 0.350979 4.2:-88054801 None:intergenic
AACACAACAACACAATTATC+AGG 0.354650 4.2:-88054740 None:intergenic
AAAGAGAAAGAAGGAGTTCT+AGG 0.365664 4.2:-88054314 None:intergenic
CGGGGAAGCCGCGGAGCGTT+CGG 0.387389 4.2:+88054975 MS.gene066839:CDS
ACAAACACATTTGAAGAAAC+AGG 0.393177 4.2:+88054644 MS.gene066839:CDS
TGAAAATGAGTTAACATTGA+AGG 0.394547 4.2:-88054696 None:intergenic
AAGTGTTGATTGGGATTTCA+TGG 0.402630 4.2:+88054841 MS.gene066839:CDS
GCGTTCGGACGGTTAGGATT+GGG 0.405374 4.2:+88054990 MS.gene066839:CDS
CGAACGCTCCGCGGCTTCCC+CGG 0.413484 4.2:-88054974 None:intergenic
TTTAGTGTTGTTGTTACAAT+CGG 0.422967 4.2:-88054447 None:intergenic
CGGTTTCTTTGTCATCTTCG+AGG 0.434566 4.2:-88054427 None:intergenic
GAAGAGTTCGGAGACTAAAC+CGG 0.441402 4.2:+88054955 MS.gene066839:CDS
GGAACAATGAAAGTGTTGAT+TGG 0.441448 4.2:+88054831 MS.gene066839:CDS
AGCGTTCGGACGGTTAGGAT+TGG 0.441450 4.2:+88054989 MS.gene066839:CDS
CGCGGAGCGTTCGGACGGTT+AGG 0.454970 4.2:+88054984 MS.gene066839:CDS
TGATAATTGTGTTGTTGTGT+TGG 0.457949 4.2:+88054742 MS.gene066839:CDS
AGGATAAACGAAGTTGTGTT+GGG 0.458162 4.2:-88054256 None:intergenic
ACGAAGTTGTGTTGGGCGAT+TGG 0.459516 4.2:-88054249 None:intergenic
CGAAAATCATCATAAGGACT+TGG 0.467264 4.2:-88054773 None:intergenic
GAGACACCATTGGATCTTTG+TGG 0.467751 4.2:+88054569 MS.gene066839:CDS
GAACAATGAAAGTGTTGATT+GGG 0.470006 4.2:+88054832 MS.gene066839:CDS
CTCTATCATGAGGAAGAGTT+CGG 0.473366 4.2:+88054943 MS.gene066839:CDS
GATCTTCGAAAATCATCATA+AGG 0.481189 4.2:-88054779 None:intergenic
AAATGTGTTTGTTGTTGTTG+TGG 0.483665 4.2:-88054633 None:intergenic
TGAAATTCTCAAAGAGAAAA+CGG 0.493044 4.2:-88054394 None:intergenic
GAGGATAAACGAAGTTGTGT+TGG 0.494329 4.2:-88054257 None:intergenic
AGAAGATGATGATGAAGAAG+AGG 0.508127 4.2:+88054490 MS.gene066839:CDS
TTATCCTCTAAGAAATGGAT+TGG 0.514704 4.2:+88054272 MS.gene066839:CDS
TCGAAGATCCATGCAAGAAA+CGG 0.523834 4.2:+88054793 MS.gene066839:CDS
AAACGGTGGAAGCGAGGTTG+AGG 0.524180 4.2:+88054810 MS.gene066839:CDS
TGTGTTTGTTGTTGTTGTGG+TGG 0.541664 4.2:-88054630 None:intergenic
AAGAGTTCGGAGACTAAACC+GGG 0.547011 4.2:+88054956 MS.gene066839:CDS
TTCATCCAACGAGACACCAT+TGG 0.547786 4.2:+88054559 MS.gene066839:CDS
TTGTTGTCAAAAGAGAAAGA+AGG 0.565659 4.2:-88054323 None:intergenic
GACGGTTAGGATTGGGACTG+AGG 0.576913 4.2:+88054997 MS.gene066839:CDS
AGACTAAACCGGGGAAGCCG+CGG 0.578732 4.2:+88054966 MS.gene066839:CDS
AAGATCCAATGGTGTCTCGT+TGG 0.579089 4.2:-88054564 None:intergenic
AAGAAATGGATTGGTCTCAA+AGG 0.580257 4.2:+88054281 MS.gene066839:CDS
GAAGCCGCGGAGCGTTCGGA+CGG 0.591522 4.2:+88054979 MS.gene066839:CDS
CTCGTTGGATGAATCAAACA+AGG 0.592816 4.2:-88054549 None:intergenic
TGCAAGAAACGGTGGAAGCG+AGG 0.598163 4.2:+88054804 MS.gene066839:CDS
GTGACTTGATCTCTATCATG+AGG 0.602549 4.2:+88054933 MS.gene066839:CDS
TTAGATCCACAAAGATCCAA+TGG 0.615900 4.2:-88054575 None:intergenic
ACGGTCAACATCTTCGAGTG+TGG 0.632740 4.2:-88054375 None:intergenic
TTGGATGAATCAAACAAGGT+GGG 0.642701 4.2:-88054545 None:intergenic
AAGATCCATGCAAGAAACGG+TGG 0.645271 4.2:+88054796 MS.gene066839:CDS
GTTGGATGAATCAAACAAGG+TGG 0.690695 4.2:-88054546 None:intergenic
CTAACCGTCCGAACGCTCCG+CGG 0.714481 4.2:-88054983 None:intergenic
AGAGTTCGGAGACTAAACCG+GGG 0.806429 4.2:+88054957 MS.gene066839:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCATAGTAAAAAAAAAATAT+TGG + chr4.2:88055325-88055344 MS.gene066839:intron 10.0%
!! GAAGAAAAATATTCAAAACA+AGG + chr4.2:88054521-88054540 MS.gene066839:CDS 20.0%
!!! ACTAAATTCTATTTTTGTTG+TGG - chr4.2:88055644-88055663 None:intergenic 20.0%
!!! CTAAATTCTATTTTTGTTGT+GGG - chr4.2:88055643-88055662 None:intergenic 20.0%
!!! CTTGGTCTAAATTAATATTT+TGG - chr4.2:88055505-88055524 None:intergenic 20.0%
!!! GAATTTAGTTATGAGTTTTA+AGG + chr4.2:88055655-88055674 MS.gene066839:intron 20.0%
!!! GTATGATTTATTTTCAATGT+TGG + chr4.2:88055198-88055217 MS.gene066839:intron 20.0%
!!! TTTATCTTTTGTATGTCTTT+TGG + chr4.2:88055102-88055121 MS.gene066839:intron 20.0%
! ATAAGAATCTCACTTCAAAT+AGG + chr4.2:88055284-88055303 MS.gene066839:intron 25.0%
! ATCGATGAAAATTCGTAATT+AGG + chr4.2:88055562-88055581 MS.gene066839:intron 25.0%
! ATTAATTTAGACCAAGTTTG+AGG + chr4.2:88055509-88055528 MS.gene066839:intron 25.0%
! TGAAAATGAGTTAACATTGA+AGG - chr4.2:88054699-88054718 None:intergenic 25.0%
! TGAAATTCTCAAAGAGAAAA+CGG - chr4.2:88054397-88054416 None:intergenic 25.0%
!! ACCTAAATTTCTTTTATCCA+AGG + chr4.2:88055717-88055736 MS.gene066839:intron 25.0%
!! CAATGTTAACTCATTTTCAA+AGG + chr4.2:88054700-88054719 MS.gene066839:CDS 25.0%
!! CCTAAATTTCTTTTATCCAA+GGG + chr4.2:88055718-88055737 MS.gene066839:intron 25.0%
!! TTTAGTGTTGTTGTTACAAT+CGG - chr4.2:88054450-88054469 None:intergenic 25.0%
!!! GAATTAACTTTAGAGTTTGA+AGG + chr4.2:88055040-88055059 MS.gene066839:intron 25.0%
AACACAACAACACAATTATC+AGG - chr4.2:88054743-88054762 None:intergenic 30.0%
ACAAACACATTTGAAGAAAC+AGG + chr4.2:88054644-88054663 MS.gene066839:CDS 30.0%
CCCTTGGATAAAAGAAATTT+AGG - chr4.2:88055721-88055740 None:intergenic 30.0%
GAAAATTCGTAATTAGGCTT+TGG + chr4.2:88055568-88055587 MS.gene066839:intron 30.0%
GATCTTCGAAAATCATCATA+AGG - chr4.2:88054782-88054801 None:intergenic 30.0%
TAAATGTCAACGAATTTCAG+TGG + chr4.2:88055231-88055250 MS.gene066839:intron 30.0%
TTGTTGTCAAAAGAGAAAGA+AGG - chr4.2:88054326-88054345 None:intergenic 30.0%
! AATAGATTCTTTTTGACACG+TGG + chr4.2:88054596-88054615 MS.gene066839:CDS 30.0%
! GAGTTAACATTGAAGGTTTT+TGG - chr4.2:88054692-88054711 None:intergenic 30.0%
! TGATAATTGTGTTGTTGTGT+TGG + chr4.2:88054742-88054761 MS.gene066839:CDS 30.0%
! TGTTAACTCATTTTCAAAGG+AGG + chr4.2:88054703-88054722 MS.gene066839:CDS 30.0%
! TTATCCTCTAAGAAATGGAT+TGG + chr4.2:88054272-88054291 MS.gene066839:CDS 30.0%
! TTCGTTTATCCTCTAAGAAA+TGG + chr4.2:88054267-88054286 MS.gene066839:CDS 30.0%
! TTTGGAGAGGTAATTTTGAA+GGG - chr4.2:88054222-88054241 None:intergenic 30.0%
!! AAATATTGGTGTTAACCATC+CGG + chr4.2:88055339-88055358 MS.gene066839:intron 30.0%
!! AAATGTGTTTGTTGTTGTTG+TGG - chr4.2:88054636-88054655 None:intergenic 30.0%
!! AGGGATTTTTGAAAGTTCTT+TGG - chr4.2:88054203-88054222 None:intergenic 30.0%
!! GAACAATGAAAGTGTTGATT+GGG + chr4.2:88054832-88054851 MS.gene066839:CDS 30.0%
!! TTTTGGAGAGGTAATTTTGA+AGG - chr4.2:88054223-88054242 None:intergenic 30.0%
AAAGAGAAAGAAGGAGTTCT+AGG - chr4.2:88054317-88054336 None:intergenic 35.0%
AGGATAAACGAAGTTGTGTT+GGG - chr4.2:88054259-88054278 None:intergenic 35.0%
CAAGAAAAACAACGACAACA+AGG + chr4.2:88054343-88054362 MS.gene066839:CDS 35.0%
CGAAAATCATCATAAGGACT+TGG - chr4.2:88054776-88054795 None:intergenic 35.0%
TTAGATCCACAAAGATCCAA+TGG - chr4.2:88054578-88054597 None:intergenic 35.0%
TTGGATGAATCAAACAAGGT+GGG - chr4.2:88054548-88054567 None:intergenic 35.0%
! AGAAGATGATGATGAAGAAG+AGG + chr4.2:88054490-88054509 MS.gene066839:CDS 35.0%
!! AAGAAATGGATTGGTCTCAA+AGG + chr4.2:88054281-88054300 MS.gene066839:CDS 35.0%
!! AAGTGTTGATTGGGATTTCA+TGG + chr4.2:88054841-88054860 MS.gene066839:CDS 35.0%
!! GGAACAATGAAAGTGTTGAT+TGG + chr4.2:88054831-88054850 MS.gene066839:CDS 35.0%
!!! ATAGGTTTGTCGACTTTTCT+CGG + chr4.2:88055302-88055321 MS.gene066839:intron 35.0%
!!! GATTGGTTTTGATTTTGGAG+AGG - chr4.2:88054235-88054254 None:intergenic 35.0%
!!! TTTTTTTCACCCTAGTCTTG+TGG + chr4.2:88055129-88055148 MS.gene066839:intron 35.0%
ATTAGCAAGCCACAAGACTA+GGG - chr4.2:88055141-88055160 None:intergenic 40.0%
CTCGTTGGATGAATCAAACA+AGG - chr4.2:88054552-88054571 None:intergenic 40.0%
CTCTATCATGAGGAAGAGTT+CGG + chr4.2:88054943-88054962 MS.gene066839:CDS 40.0%
GAGACCAATCCATTTCTTAG+AGG - chr4.2:88054279-88054298 None:intergenic 40.0%
GAGGATAAACGAAGTTGTGT+TGG - chr4.2:88054260-88054279 None:intergenic 40.0%
GTCTCAAAGTCTCACTATGA+CGG - chr4.2:88055377-88055396 None:intergenic 40.0%
GTGACTTGATCTCTATCATG+AGG + chr4.2:88054933-88054952 MS.gene066839:CDS 40.0%
GTTGGATGAATCAAACAAGG+TGG - chr4.2:88054549-88054568 None:intergenic 40.0%
TATTAGCAAGCCACAAGACT+AGG - chr4.2:88055142-88055161 None:intergenic 40.0%
TCGAAGATCCATGCAAGAAA+CGG + chr4.2:88054793-88054812 MS.gene066839:CDS 40.0%
TCTCAAAGTCTCACTATGAC+GGG - chr4.2:88055376-88055395 None:intergenic 40.0%
TTCAGTGGTCGTTAATAGAC+AGG + chr4.2:88055246-88055265 MS.gene066839:intron 40.0%
!! TGTGTTTGTTGTTGTTGTGG+TGG - chr4.2:88054633-88054652 None:intergenic 40.0%
!!! GACTCGAGTTAGTTTTGAAG+TGG + chr4.2:88055604-88055623 MS.gene066839:intron 40.0%
!!! TGGGCGATTGGTTTTGATTT+TGG - chr4.2:88054240-88054259 None:intergenic 40.0%
AAGAGTTCGGAGACTAAACC+GGG + chr4.2:88054956-88054975 MS.gene066839:CDS 45.0%
AAGATCCAATGGTGTCTCGT+TGG - chr4.2:88054567-88054586 None:intergenic 45.0%
AAGATCCATGCAAGAAACGG+TGG + chr4.2:88054796-88054815 MS.gene066839:CDS 45.0%
ATCCCAGAACTCACATGAGT+CGG - chr4.2:88055686-88055705 None:intergenic 45.0%
CGCAACACATACCTCAAACT+TGG - chr4.2:88055523-88055542 None:intergenic 45.0%
CGGTTTCTTTGTCATCTTCG+AGG - chr4.2:88054430-88054449 None:intergenic 45.0%
GAAGAGTTCGGAGACTAAAC+CGG + chr4.2:88054955-88054974 MS.gene066839:CDS 45.0%
GAGACACCATTGGATCTTTG+TGG + chr4.2:88054569-88054588 MS.gene066839:CDS 45.0%
TTAGGATTGGGACTGAGGTA+AGG + chr4.2:88055002-88055021 MS.gene066839:intron 45.0%
TTCATCCAACGAGACACCAT+TGG + chr4.2:88054559-88054578 MS.gene066839:CDS 45.0%
! CTTTTTGACACGTGGCTTCT+CGG + chr4.2:88054604-88054623 MS.gene066839:CDS 45.0%
! TTTTTGACACGTGGCTTCTC+GGG + chr4.2:88054605-88054624 MS.gene066839:CDS 45.0%
ACGAAGTTGTGTTGGGCGAT+TGG - chr4.2:88054252-88054271 None:intergenic 50.0%
ACGGTCAACATCTTCGAGTG+TGG - chr4.2:88054378-88054397 None:intergenic 50.0%
AGAGTTCGGAGACTAAACCG+GGG + chr4.2:88054957-88054976 MS.gene066839:CDS 50.0%
TCCCAGAACTCACATGAGTC+GGG - chr4.2:88055685-88055704 None:intergenic 50.0%
! ATGACGGGAGAATGCGATAC+CGG - chr4.2:88055361-88055380 None:intergenic 50.0%
AAACGGTGGAAGCGAGGTTG+AGG + chr4.2:88054810-88054829 MS.gene066839:CDS 55.0%
AGCGTTCGGACGGTTAGGAT+TGG + chr4.2:88054989-88055008 MS.gene066839:CDS 55.0%
CCCAGAACTCACATGAGTCG+GGG - chr4.2:88055684-88055703 None:intergenic 55.0%
CCCCGACTCATGTGAGTTCT+GGG + chr4.2:88055681-88055700 MS.gene066839:intron 55.0%
CGCTTCCACCGTTTCTTGCA+TGG - chr4.2:88054804-88054823 None:intergenic 55.0%
GACGGTTAGGATTGGGACTG+AGG + chr4.2:88054997-88055016 MS.gene066839:CDS 55.0%
GCGTTCGGACGGTTAGGATT+GGG + chr4.2:88054990-88055009 MS.gene066839:CDS 55.0%
GGATTGGGACTGAGGTAAGG+CGG + chr4.2:88055005-88055024 MS.gene066839:intron 55.0%
TGCAAGAAACGGTGGAAGCG+AGG + chr4.2:88054804-88054823 MS.gene066839:CDS 55.0%
AGACTAAACCGGGGAAGCCG+CGG + chr4.2:88054966-88054985 MS.gene066839:CDS 60.0%
CGGGAGAATGCGATACCGGA+TGG - chr4.2:88055357-88055376 None:intergenic 60.0%
GCCCCGACTCATGTGAGTTC+TGG + chr4.2:88055680-88055699 MS.gene066839:intron 60.0%
CTAACCGTCCGAACGCTCCG+CGG - chr4.2:88054986-88055005 None:intergenic 65.0%
! CGCGGAGCGTTCGGACGGTT+AGG + chr4.2:88054984-88055003 MS.gene066839:CDS 70.0%
! GAAGCCGCGGAGCGTTCGGA+CGG + chr4.2:88054979-88054998 MS.gene066839:CDS 70.0%
CGAACGCTCCGCGGCTTCCC+CGG - chr4.2:88054977-88054996 None:intergenic 75.0%
! CGGGGAAGCCGCGGAGCGTT+CGG + chr4.2:88054975-88054994 MS.gene066839:CDS 75.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 88054197 88055747 88054197 ID=MS.gene066839
chr4.2 mRNA 88054197 88055747 88054197 ID=MS.gene066839.t1;Parent=MS.gene066839
chr4.2 exon 88054197 88055018 88054197 ID=MS.gene066839.t1.exon1;Parent=MS.gene066839.t1
chr4.2 CDS 88054197 88055018 88054197 ID=cds.MS.gene066839.t1;Parent=MS.gene066839.t1
chr4.2 exon 88055739 88055747 88055739 ID=MS.gene066839.t1.exon2;Parent=MS.gene066839.t1
chr4.2 CDS 88055739 88055747 88055739 ID=cds.MS.gene066839.t1;Parent=MS.gene066839.t1
Gene Sequence

>MS.gene066839

ATGCCAAAGAACTTTCAAAAATCCCTTCAAAATTACCTCTCCAAAATCAAAACCAATCGCCCAACACAACTTCGTTTATCCTCTAAGAAATGGATTGGTCTCAAAGGTTGCAAACATCCTAGAACTCCTTCTTTCTCTTTTGACAACAAGAAAAACAACGACAACAAGGACGATGAAGCCACACTCGAAGATGTTGACCGTTTTCTCTTTGAGAATTTCAAGTCTTTATACCTCGAAGATGACAAAGAAACCGATTGTAACAACAACACTAAAAGTGTTGTCTCATCAGACGAAGAAGATGATGATGAAGAAGAGGAAACTCGTGAAGAAAAATATTCAAAACAAGGTCCCACCTTGTTTGATTCATCCAACGAGACACCATTGGATCTTTGTGGATCTAATAGATTCTTTTTGACACGTGGCTTCTCGGGCTCCACCACAACAACAACAAACACATTTGAAGAAACAGGATCATGCTCAAACTCGTCAACACCAAAAACCTTCAATGTTAACTCATTTTCAAAGGAGGATCAAATGAATATTCCTGATAATTGTGTTGTTGTGTTGGCAAGTTCGCCAAGTCCTTATGATGATTTTCGAAGATCCATGCAAGAAACGGTGGAAGCGAGGTTGAGGAACAATGAAAGTGTTGATTGGGATTTCATGGAAGAGCTTTTGTTTTGTTATATGAACTTAAATGAGAAGAAATCTTATAAGTTTATACTAAGTGCTTTTTGTGACTTGATCTCTATCATGAGGAAGAGTTCGGAGACTAAACCGGGGAAGCCGCGGAGCGTTCGGACGGTTAGGATTGGGACTGAGGTAAGGCGGAAGAAGATTAAAGAATTAACTTTAGAGTTTGAAGGTTCAAGATAATGAATAAAATTTGACAGATTTTCGAGTTATTTATCTTTTGTATGTCTTTTGGATTTTTTTTTTCACCCTAGTCTTGTGGCTTGCTAATAACATGTACTATGATTATGATTTTTTTTTTTTATGATGTATGATTTATTTTCAATGTTGGAGAAAATAAATAAATGTCAACGAATTTCAGTGGTCGTTAATAGACAGGTCATATATATGTTTCATAAGAATCTCACTTCAAATAGGTTTGTCGACTTTTCTCGGTCATAGTAAAAAAAAAATATTGGTGTTAACCATCCGGTATCGCATTCTCCCGTCATAGTGAGACTTTGAGACATAACTTATTTAAATTTTCACTTAAAAAGTAAATAAATAAACAAATTAAATAAAATGATAAAGTAAATAAATAAACAAATTAAATAAAATGATCATAGTTTAAGTCCAAAATATTAATTTAGACCAAGTTTGAGGTATGTGTTGCGTTGATATTATAAGATATACATCGATGAAAATTCGTAATTAGGCTTTGGTAGTGAGAAACGTGACTCGAGTTAGTTTTGAAGTGGAGTACAATCTTTTCCCACAACAAAAATAGAATTTAGTTATGAGTTTTAAGGTTGCCCCGACTCATGTGAGTTCTGGGATTTCAACTAATCACCTAAATTTCTTTTATCCAAGGGTCCATGA
Protein sequence

>MS.gene066839.t1

MPKNFQKSLQNYLSKIKTNRPTQLRLSSKKWIGLKGCKHPRTPSFSFDNKKNNDNKDDEATLEDVDRFLFENFKSLYLEDDKETDCNNNTKSVVSSDEEDDDEEEETREEKYSKQGPTLFDSSNETPLDLCGSNRFFLTRGFSGSTTTTTNTFEETGSCSNSSTPKTFNVNSFSKEDQMNIPDNCVVVLASSPSPYDDFRRSMQETVEARLRNNESVDWDFMEELLFCYMNLNEKKSYKFILSAFCDLISIMRKSSETKPGKPRSVRTVRIGTEGP