AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048411

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048411.t1 MTR_8g067635 64.796 196 18 1 1 145 253 448 1.01e-77 240
MS.gene048411.t1 MTR_8g067650 64.467 197 18 2 1 145 243 439 8.72e-77 238
MS.gene048411.t1 MTR_8g069935 52.101 119 56 1 1 118 234 352 3.62e-31 117
MS.gene048411.t1 MTR_2g024380 33.333 213 61 4 1 162 184 366 7.76e-26 102
MS.gene048411.t1 MTR_6g053200 33.173 208 83 3 1 166 248 441 8.11e-22 91.3
MS.gene048411.t1 MTR_7g105000 41.525 118 63 3 1 116 226 339 5.58e-21 88.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048411.t1 AT4G01250 34.694 147 66 8 16 155 63 186 1.66e-12 64.3

Find 40 sgRNAs with CRISPR-Local

Find 93 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAATTTGATGACATATTC+TGG 0.180052 8.3:+35515904 None:intergenic
CGAAAACAGACACTCGATTT+TGG 0.221712 8.3:+35517469 None:intergenic
TGGGGTTCTTGTGGTTCTAA+TGG 0.273735 8.3:+35517390 None:intergenic
TGGATGTGGAGACCCTTTAA+TGG 0.287579 8.3:+35517049 None:intergenic
TAAAGTTGTAGAACTGGTTT+GGG 0.308186 8.3:+35517335 None:intergenic
CAGAATATGTCATCAAATTC+AGG 0.324509 8.3:-35515903 MS.gene048411:CDS
GTTGAGTTCAGGATGAAAAT+TGG 0.333089 8.3:+35517416 None:intergenic
TCATGGAGATGGAGAAAATA+TGG 0.338703 8.3:-35517080 MS.gene048411:CDS
ATAAGATTTCAGAAGATTCA+TGG 0.343013 8.3:-35517097 MS.gene048411:CDS
GTAAAGTTGTAGAACTGGTT+TGG 0.369929 8.3:+35517334 None:intergenic
GTAGTCGATTATGATTTCTC+TGG 0.378001 8.3:+35517370 None:intergenic
GGATGTGGAGACCCTTTAAT+GGG 0.385486 8.3:+35517050 None:intergenic
ATTCAGTAAAGTTGTAGAAC+TGG 0.405398 8.3:+35517329 None:intergenic
ACTCGAGCCTTGCTGCTCTC+TGG 0.411380 8.3:+35515795 None:intergenic
TTGAGCAACATCCAGCTTCT+CGG 0.416229 8.3:+35515868 None:intergenic
TCTAATGGATGGTTGAGTTC+AGG 0.423106 8.3:+35517405 None:intergenic
TTGCTCAAACGTTAGAAACT+TGG 0.430903 8.3:-35515853 MS.gene048411:CDS
TAGTCGATTATGATTTCTCT+GGG 0.436337 8.3:+35517371 None:intergenic
TGCTGCAACATTACCACATT+AGG 0.438405 8.3:+35515825 None:intergenic
GTTCTTGTGGTTCTAATGGA+TGG 0.440210 8.3:+35517394 None:intergenic
TCATCAAATTCAGGATTAGA+TGG 0.442631 8.3:-35515894 MS.gene048411:CDS
TGAATTTGATGACATATTCT+GGG 0.443651 8.3:+35515905 None:intergenic
TGTTGTTGTTCAACGAGCAT+TGG 0.450106 8.3:+35517504 None:intergenic
TTAGATGGTGTCCGAGAAGC+TGG 0.454965 8.3:-35515879 MS.gene048411:CDS
AATGCTCGTTGAACAACAAC+AGG 0.486815 8.3:-35517502 MS.gene048411:CDS
TGCTCAAACGTTAGAAACTT+GGG 0.493239 8.3:-35515852 MS.gene048411:CDS
CTGGTTTGGGGTAGTAGAAT+CGG 0.494141 8.3:+35517348 None:intergenic
TGATTTCTCTGGGGTTCTTG+TGG 0.495150 8.3:+35517381 None:intergenic
TTTCAGAAGATTCATGGAGA+TGG 0.509856 8.3:-35517091 MS.gene048411:CDS
GGTGGTTGTAGTCTTAATGC+AGG 0.525304 8.3:+35517437 None:intergenic
AAATAATAACCAAGTGACAT+TGG 0.536349 8.3:-35517138 MS.gene048411:CDS
CATAGCTCACCAATGTCACT+TGG 0.536490 8.3:+35517129 None:intergenic
AAACTTGGGTTCTCCTAATG+TGG 0.561663 8.3:-35515838 MS.gene048411:CDS
TTAAAGGGTCTCCACATCCA+AGG 0.584498 8.3:-35517046 MS.gene048411:intron
GAGTTCAGGATGAAAATTGG+TGG 0.596987 8.3:+35517419 None:intergenic
AGCAAGGCTCGAGTTCATGA+TGG 0.606224 8.3:-35515786 MS.gene048411:CDS
TGATCATCCAGAGAGCAGCA+AGG 0.696293 8.3:-35515802 MS.gene048411:CDS
GACATTGGTGAGCTATGTGA+AGG 0.706817 8.3:-35517123 MS.gene048411:CDS
AGTCGATTATGATTTCTCTG+GGG 0.721816 8.3:+35517372 None:intergenic
AAAGTTGTAGAACTGGTTTG+GGG 0.727319 8.3:+35517336 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAAAATTATATATTTTTA+GGG - chr8.3:35516906-35516925 MS.gene048411:intron 0.0%
!!! TTAAAAAATTATATATTTTT+AGG - chr8.3:35516905-35516924 MS.gene048411:intron 0.0%
!! AAAAAATGATGTAAATGTAA+GGG + chr8.3:35517048-35517067 None:intergenic 15.0%
!! AGGGTTAAAATTAATATTAA+AGG + chr8.3:35516757-35516776 None:intergenic 15.0%
!! TAAAAAATGATGTAAATGTA+AGG + chr8.3:35517049-35517068 None:intergenic 15.0%
!!! CAATATGAATAAATTTTGTA+GGG - chr8.3:35516805-35516824 MS.gene048411:intron 15.0%
!!! TATATGTATCATTTTTTGTT+TGG - chr8.3:35516602-35516621 MS.gene048411:intron 15.0%
!! AAAAATGATGTAAATGTAAG+GGG + chr8.3:35517047-35517066 None:intergenic 20.0%
!! AAAAATTTAAACCAGGAAAA+AGG - chr8.3:35515990-35516009 MS.gene048411:intron 20.0%
!! AAACAACAAAAATTTAAACC+AGG - chr8.3:35515983-35516002 MS.gene048411:intron 20.0%
!! AATATTTGTTCTTTAATGCT+TGG - chr8.3:35516686-35516705 MS.gene048411:intron 20.0%
!! CAAAAAATGATACATATACA+AGG + chr8.3:35516600-35516619 None:intergenic 20.0%
!! CCTACAAAATTTATTCATAT+TGG + chr8.3:35516807-35516826 None:intergenic 20.0%
!! TCATATAGACACATATAAAT+AGG + chr8.3:35517135-35517154 None:intergenic 20.0%
!! TTTGAATGAATAAAAAACCT+TGG + chr8.3:35516254-35516273 None:intergenic 20.0%
!!! AATTTTAACCCTTATATTGA+TGG - chr8.3:35516765-35516784 MS.gene048411:intron 20.0%
!!! ATTTTAACCCATCAATATAA+GGG + chr8.3:35516776-35516795 None:intergenic 20.0%
!!! ATTTTAACCCTTATATTGAT+GGG - chr8.3:35516766-35516785 MS.gene048411:intron 20.0%
!!! ATTTTTTCTACAAGAAAAGA+AGG + chr8.3:35516126-35516145 None:intergenic 20.0%
!!! CCAATATGAATAAATTTTGT+AGG - chr8.3:35516804-35516823 MS.gene048411:intron 20.0%
!!! GGTTTAAATTTTTGTTGTTT+CGG + chr8.3:35515983-35516002 None:intergenic 20.0%
!!! TTTTTTCTACAAGAAAAGAA+GGG + chr8.3:35516125-35516144 None:intergenic 20.0%
! AAATAATAACCAAGTGACAT+TGG - chr8.3:35516142-35516161 MS.gene048411:intron 25.0%
! ACTTATGAAGTGACATATAT+AGG - chr8.3:35517299-35517318 MS.gene048411:CDS 25.0%
! ATAAGATTTCAGAAGATTCA+TGG - chr8.3:35516183-35516202 MS.gene048411:intron 25.0%
! CAAACACTGAAATAAAAATG+TGG - chr8.3:35516842-35516861 MS.gene048411:intron 25.0%
! TCAAAAACAAAAGATCAAAG+AGG + chr8.3:35516658-35516677 None:intergenic 25.0%
! TTGTTTAGCAAAAAAACTAG+TGG - chr8.3:35517253-35517272 MS.gene048411:intron 25.0%
!! AAGAAGGGTAAGATAATTTT+CGG + chr8.3:35516110-35516129 None:intergenic 25.0%
!! ACTAATTAAAACCATTGGTT+TGG + chr8.3:35516353-35516372 None:intergenic 25.0%
!! TGAATTTGATGACATATTCT+GGG + chr8.3:35517378-35517397 None:intergenic 25.0%
!!! CTAATTAAAACCATTGGTTT+GGG + chr8.3:35516352-35516371 None:intergenic 25.0%
!!! GATTTTAACCCATCAATATA+AGG + chr8.3:35516777-35516796 None:intergenic 25.0%
AAGAATGATCAAAATGCATG+TGG + chr8.3:35516378-35516397 None:intergenic 30.0%
AATAATTGGAATTCCGTTGT+TGG - chr8.3:35517347-35517366 MS.gene048411:CDS 30.0%
ACAGAAAACCAGCAAATAAT+TGG - chr8.3:35517333-35517352 MS.gene048411:CDS 30.0%
ATGGACAAAAACCCATTAAA+GGG - chr8.3:35516219-35516238 MS.gene048411:intron 30.0%
ATGTATTATTTCACGTATCG+TGG - chr8.3:35517071-35517090 MS.gene048411:CDS 30.0%
ATTCAGTAAAGTTGTAGAAC+TGG + chr8.3:35515954-35515973 None:intergenic 30.0%
CAGAATATGTCATCAAATTC+AGG - chr8.3:35517377-35517396 MS.gene048411:CDS 30.0%
CTAGTGGAGAAAATAAAAAC+TGG - chr8.3:35517269-35517288 MS.gene048411:intron 30.0%
GACAAATATGATCTTGATAG+TGG - chr8.3:35516423-35516442 MS.gene048411:intron 30.0%
TAGTCGATTATGATTTCTCT+GGG + chr8.3:35515912-35515931 None:intergenic 30.0%
TATGGACAAAAACCCATTAA+AGG - chr8.3:35516218-35516237 MS.gene048411:intron 30.0%
TCATCAAATTCAGGATTAGA+TGG - chr8.3:35517386-35517405 MS.gene048411:CDS 30.0%
TGAATAAAAAACCTTGGATG+TGG + chr8.3:35516248-35516267 None:intergenic 30.0%
TGGTCACTAATTAAAACCAT+TGG + chr8.3:35516358-35516377 None:intergenic 30.0%
TGTAAATGTAAGGGGAAAAT+AGG + chr8.3:35517039-35517058 None:intergenic 30.0%
TGTATTATTTCACGTATCGT+GGG - chr8.3:35517072-35517091 MS.gene048411:CDS 30.0%
! CTGAATTTGATGACATATTC+TGG + chr8.3:35517379-35517398 None:intergenic 30.0%
! TAAAGTTGTAGAACTGGTTT+GGG + chr8.3:35515948-35515967 None:intergenic 30.0%
! TCAATTCTTTACCTTTTTCC+TGG + chr8.3:35516004-35516023 None:intergenic 30.0%
ACGGAATTCCAATTATTTGC+TGG + chr8.3:35517344-35517363 None:intergenic 35.0%
AGTCGATTATGATTTCTCTG+GGG + chr8.3:35515911-35515930 None:intergenic 35.0%
CAATCAATGAATGACTTTGC+AGG - chr8.3:35517201-35517220 MS.gene048411:intron 35.0%
GGAGAAAATAAAAACTGGAG+AGG - chr8.3:35517274-35517293 MS.gene048411:intron 35.0%
GTAAAGTTGTAGAACTGGTT+TGG + chr8.3:35515949-35515968 None:intergenic 35.0%
GTAGTCGATTATGATTTCTC+TGG + chr8.3:35515913-35515932 None:intergenic 35.0%
GTTGAGTTCAGGATGAAAAT+TGG + chr8.3:35515867-35515886 None:intergenic 35.0%
TCATGGAGATGGAGAAAATA+TGG - chr8.3:35516200-35516219 MS.gene048411:intron 35.0%
TGCTCAAACGTTAGAAACTT+GGG - chr8.3:35517428-35517447 MS.gene048411:CDS 35.0%
TTGCTCAAACGTTAGAAACT+TGG - chr8.3:35517427-35517446 MS.gene048411:CDS 35.0%
TTTCAGAAGATTCATGGAGA+TGG - chr8.3:35516189-35516208 MS.gene048411:intron 35.0%
!! AAAGTTGTAGAACTGGTTTG+GGG + chr8.3:35515947-35515966 None:intergenic 35.0%
AAACTTGGGTTCTCCTAATG+TGG - chr8.3:35517442-35517461 MS.gene048411:CDS 40.0%
GAGTTCAGGATGAAAATTGG+TGG + chr8.3:35515864-35515883 None:intergenic 40.0%
TGCTGCAACATTACCACATT+AGG + chr8.3:35517458-35517477 None:intergenic 40.0%
TTATTTCACGTATCGTGGGA+CGG - chr8.3:35517076-35517095 MS.gene048411:CDS 40.0%
! CGAAAACAGACACTCGATTT+TGG + chr8.3:35515814-35515833 None:intergenic 40.0%
! TCTAATGGATGGTTGAGTTC+AGG + chr8.3:35515878-35515897 None:intergenic 40.0%
!! AAAACCATTGGTTTGGGTGT+GGG + chr8.3:35516346-35516365 None:intergenic 40.0%
!! GTTCTTGTGGTTCTAATGGA+TGG + chr8.3:35515889-35515908 None:intergenic 40.0%
!! TAAAACCATTGGTTTGGGTG+TGG + chr8.3:35516347-35516366 None:intergenic 40.0%
CATAGCTCACCAATGTCACT+TGG + chr8.3:35516154-35516173 None:intergenic 45.0%
GACATTGGTGAGCTATGTGA+AGG - chr8.3:35516157-35516176 MS.gene048411:intron 45.0%
GGATGTGGAGACCCTTTAAT+GGG + chr8.3:35516233-35516252 None:intergenic 45.0%
TGGATGTGGAGACCCTTTAA+TGG + chr8.3:35516234-35516253 None:intergenic 45.0%
TTAAAGGGTCTCCACATCCA+AGG - chr8.3:35516234-35516253 MS.gene048411:intron 45.0%
TTGAGCAACATCCAGCTTCT+CGG + chr8.3:35517415-35517434 None:intergenic 45.0%
! ATTCTGGGAGCTACCAACAA+CGG + chr8.3:35517363-35517382 None:intergenic 45.0%
! GGTGGTTGTAGTCTTAATGC+AGG + chr8.3:35515846-35515865 None:intergenic 45.0%
!! CTGGTTTGGGGTAGTAGAAT+CGG + chr8.3:35515935-35515954 None:intergenic 45.0%
!! TGATTTCTCTGGGGTTCTTG+TGG + chr8.3:35515902-35515921 None:intergenic 45.0%
!! TGGGGTTCTTGTGGTTCTAA+TGG + chr8.3:35515893-35515912 None:intergenic 45.0%
!! TATAAAATATATTAAATAGT+AGG + chr8.3:35516029-35516048 None:intergenic 5.0%
!!! ATTTTGTTTTATATTAAAAT+TGG - chr8.3:35516729-35516748 MS.gene048411:intron 5.0%
AGCAAGGCTCGAGTTCATGA+TGG - chr8.3:35517494-35517513 MS.gene048411:CDS 50.0%
TGATCATCCAGAGAGCAGCA+AGG - chr8.3:35517478-35517497 MS.gene048411:CDS 50.0%
TGGGTGTGGGTGTGTGTATT+AGG + chr8.3:35516333-35516352 None:intergenic 50.0%
TTAGATGGTGTCCGAGAAGC+TGG - chr8.3:35517401-35517420 MS.gene048411:CDS 50.0%
CACACCCACACCCAAACCAA+TGG - chr8.3:35516339-35516358 MS.gene048411:intron 55.0%
ACTCGAGCCTTGCTGCTCTC+TGG + chr8.3:35517488-35517507 None:intergenic 60.0%
CACGTATCGTGGGACGGAGT+CGG - chr8.3:35517082-35517101 MS.gene048411:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 35515779 35517523 35515779 ID=MS.gene048411
chr8.3 mRNA 35515779 35517523 35515779 ID=MS.gene048411.t1;Parent=MS.gene048411
chr8.3 exon 35517291 35517523 35517291 ID=MS.gene048411.t1.exon1;Parent=MS.gene048411.t1
chr8.3 CDS 35517291 35517523 35517291 ID=cds.MS.gene048411.t1;Parent=MS.gene048411.t1
chr8.3 exon 35517047 35517163 35517047 ID=MS.gene048411.t1.exon2;Parent=MS.gene048411.t1
chr8.3 CDS 35517047 35517163 35517047 ID=cds.MS.gene048411.t1;Parent=MS.gene048411.t1
chr8.3 exon 35515779 35515929 35515779 ID=MS.gene048411.t1.exon3;Parent=MS.gene048411.t1
chr8.3 CDS 35515779 35515929 35515779 ID=cds.MS.gene048411.t1;Parent=MS.gene048411.t1
Gene Sequence

>MS.gene048411

ATGCTCGTTGAACAACAACAGGTTCAAGCAAACCAAAATCGAGTGTCTGTTTTCGACTCTATTTCCTGCATTAAGACTACAACCACCAATTTTCATCCTGAACTCAACCATCCATTAGAACCACAAGAACCCCAGAGAAATCATAATCGACTACCGATTCTACTACCCCAAACCAGTTCTACAACTTTACTGAATACAAAACCGAAACAACAAAAATTTAAACCAGGAAAAAGGTAAAGAATTGATTCCTACTATTTAATATATTTTATATGTAAATATATTTCATTTTATTGAAATTATTAAAATACTTTTACATAACTCATTTTTACCGAAAATTATCTTACCCTTCTTTTCTTGTAGAAAAAATAATAACCAAGTGACATTGGTGAGCTATGTGAAGGCAGATAAGATTTCAGAAGATTCATGGAGATGGAGAAAATATGGACAAAAACCCATTAAAGGGTCTCCACATCCAAGGTTTTTTATTCATTCAAAACTCTAACATTATCATAATTTTCTTTTTTTCTAATATTAACACAATATTTTTGTTACCTAATACACACACCCACACCCAAACCAATGGTTTTAATTAGTGACCACATGCATTTTGATCATTCTTATTGAAAAGAGTTTTAGTTAAATGTGACAAATATGATCTTGATAGTGGTTGCGTTTTCTTTTCAATTTCGATAAAAAATTGTTACTCTCATCTTTTCAATGAGAGTCATGTTTGCAAATTTTTTTTTTTTACAAAGTAAATGTCACTTTTAATTTTCTATGTAATGAGATTAGTTTTTACTTTAATATATGTTTTAAGACCTTGTATATGTATCATTTTTTGTTTGGTAAAAAAAATTATCATTTTTTTGCTTTTAACCTCTTTGATCTTTTGTTTTTGACTATCATAAATATTTGTTCTTTAATGCTTGGTATTTGTTTTAGTTCATGTAATTTTGTTTTATATTAAAATTGGTTCCTTTAATATTAATTTTAACCCTTATATTGATGGGTTAAAATCAAATATTCCAATATGAATAAATTTTGTAGGGACTAAACAAAACAACAAACACTGAAATAAAAATGTGGTATATTTGAAAAAGCTAAACAAATTAGAAAGACTAAATTTTTAAAAAATTATATATTTTTAGGGAACAAAAACATATTTAAATCTCACTTATTTTTCACAACTGTAAAATTTAATGAATATTAAGTGCATCACTCACATGTCTATATCTTTCACTTTAGAATTGTAAAACTCCTATTTTCCCCTTACATTTACATCATTTTTTAATATGTATTATTTCACGTATCGTGGGACGGAGTCGGATTTTAAATATATTTTTGAAAGCATCGCCTATTTATATGTGTCTATATGATATTAGATATTAAAATGTTACGATTTAGTGATGTTTGATATAAAAACAATCAATGAATGACTTTGCAGGAGCTACTTCAAATGTAGCAGTTTCAACGATTGTTTAGCAAAAAAACTAGTGGAGAAAATAAAAACTGGAGAGGACACTTATGAAGTGACATATATAGGAGAGCACAATCACAGAAAACCAGCAAATAATTGGAATTCCGTTGTTGGTAGCTCCCAGAATATGTCATCAAATTCAGGATTAGATGGTGTCCGAGAAGCTGGATGTTGCTCAAACGTTAGAAACTTGGGTTCTCCTAATGTGGTAATGTTGCAGCATGATCATCCAGAGAGCAGCAAGGCTCGAGTTCATGATGGTGAATAA
Protein sequence

>MS.gene048411.t1

MLVEQQQVQANQNRVSVFDSISCIKTTTTNFHPELNHPLEPQEPQRNHNRLPILLPQTSSTTLLNTKPKQQKFKPGKRKNNNQVTLVSYVKADKISEDSWRWRKYGQKPIKGSPHPSSQNMSSNSGLDGVREAGCCSNVRNLGSPNVVMLQHDHPESSKARVHDGE