AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96931

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96931.t1 MTR_1g046810 86.076 316 44 0 1 316 1 316 0.0 533
MS.gene96931.t1 MTR_1g052185 37.690 329 117 13 5 310 12 275 9.71e-41 143
MS.gene96931.t1 MTR_1g085590 37.037 270 82 9 71 315 16 222 1.05e-30 117
MS.gene96931.t1 MTR_1g053530 37.611 226 94 7 63 281 39 224 6.69e-30 114
MS.gene96931.t1 MTR_1g063150 38.249 217 52 7 94 310 36 170 4.21e-29 110
MS.gene96931.t1 MTR_4g073310 32.039 309 112 10 13 314 10 227 8.00e-21 89.4
MS.gene96931.t1 MTR_1g063140 41.212 165 43 8 147 310 1 112 5.77e-18 80.5
MS.gene96931.t1 MTR_5g098470 29.851 201 95 7 14 210 46 204 1.00e-11 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 57 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATTGTTATATATGTCTTA+TGG 0.192869 1.4:+31526446 MS.gene96931:CDS
AGCGAAGATGAAACTGAATT+AGG 0.276698 1.4:+31526692 MS.gene96931:CDS
CATTGTTATATATGTCTTAT+GGG 0.313934 1.4:+31526447 MS.gene96931:CDS
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.4:-31526027 None:intergenic
ATTATCATCCACCGTATTGC+TGG 0.360275 1.4:-31526504 None:intergenic
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.4:-31526393 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.4:+31526471 MS.gene96931:CDS
GCGAAGATGAAACTGAATTA+GGG 0.408376 1.4:+31526693 MS.gene96931:CDS
GACTTTGTTCCGAGGAAGAT+GGG 0.414040 1.4:-31526295 None:intergenic
CACAAGCATAATCATGATGA+TGG 0.420773 1.4:+31526143 MS.gene96931:CDS
AACAGAAAAGAAACACTAAC+TGG 0.431171 1.4:-31526777 None:intergenic
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.4:-31526332 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.4:-31525938 None:intergenic
TCATCCAACAGTGCTTTGAA+TGG 0.470969 1.4:+31526209 MS.gene96931:CDS
TGACTTTGTTCCGAGGAAGA+TGG 0.476518 1.4:-31526296 None:intergenic
TATGAGATGGCATACTCAAA+AGG 0.486406 1.4:+31526235 MS.gene96931:CDS
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.4:-31525939 None:intergenic
TGTTACAAACATCACATGTA+TGG 0.493822 1.4:-31526178 None:intergenic
TACTCAAAAGGGTTCGAAGA+AGG 0.504806 1.4:+31526247 MS.gene96931:CDS
AATTAGGGTCAAGAGTTGTC+AGG 0.507473 1.4:+31526708 MS.gene96931:CDS
CGTTATTCACAGCATGATCA+TGG 0.509884 1.4:-31526067 None:intergenic
TGTCACAAAACATTTACCTC+TGG 0.513939 1.4:+31525969 MS.gene96931:CDS
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.4:-31525908 None:intergenic
ACCGACTGCCCCATCTTCCT+CGG 0.517275 1.4:+31526286 MS.gene96931:CDS
CATGATCATGCTGTGAATAA+CGG 0.518528 1.4:+31526068 MS.gene96931:CDS
AACAAGGTGTGCTGCTAACA+AGG 0.519240 1.4:+31526540 MS.gene96931:CDS
ATGAGATGGCATACTCAAAA+GGG 0.526510 1.4:+31526236 MS.gene96931:CDS
GGATCTAGCTGTGATATTGA+AGG 0.530396 1.4:+31526656 MS.gene96931:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.531173 1.4:+31525984 MS.gene96931:CDS
ATTGTTATATATGTCTTATG+GGG 0.542437 1.4:+31526448 MS.gene96931:CDS
TCAAACATCGCAAGATTGCA+AGG 0.542865 1.4:+31526625 MS.gene96931:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.4:+31526493 MS.gene96931:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.4:-31525855 None:intergenic
TTGGTCTTATACGATATTGG+CGG 0.553676 1.4:-31526359 None:intergenic
ACTCAAAAGGGTTCGAAGAA+GGG 0.553906 1.4:+31526248 MS.gene96931:CDS
TTTACCTCTGGTAAATCACT+TGG 0.558168 1.4:+31525981 MS.gene96931:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.4:-31526022 None:intergenic
CAAGATTGCAAGGAACCTGC+AGG 0.562783 1.4:+31526635 MS.gene96931:CDS
CTCAATTTGACTTTGTTCCG+AGG 0.565511 1.4:-31526303 None:intergenic
ATGTCCATTCAAAGCACTGT+TGG 0.568123 1.4:-31526213 None:intergenic
GGATGATAATGAGAAGATGA+AGG 0.579672 1.4:+31526517 MS.gene96931:CDS
ACAAGCATAATCATGATGAT+GGG 0.583581 1.4:+31526144 MS.gene96931:CDS
ATATCACAGCTAGATCCTGC+AGG 0.585006 1.4:-31526650 None:intergenic
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.4:-31526280 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.4:-31526392 None:intergenic
TTGTTATATATGTCTTATGG+GGG 0.593530 1.4:+31526449 MS.gene96931:CDS
TCATCTTCGAAATCATCACT+TGG 0.604104 1.4:-31526752 None:intergenic
TACATGTGATGTTTGTAACA+AGG 0.605489 1.4:+31526181 MS.gene96931:CDS
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.4:+31526524 MS.gene96931:CDS
TCCGAGGAAGATGGGGCAGT+CGG 0.608551 1.4:-31526287 None:intergenic
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.4:-31525893 None:intergenic
GCGTATTGCTGATAATGATG+AGG 0.644357 1.4:+31526403 MS.gene96931:CDS
ACTTTGTTCCGAGGAAGATG+GGG 0.648774 1.4:-31526294 None:intergenic
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.4:+31526496 MS.gene96931:CDS
CTTTGAATGGACATATGAGA+TGG 0.684064 1.4:+31526222 MS.gene96931:CDS
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.4:-31525985 None:intergenic
GATCATGCTGTGAATAACGG+CGG 0.741138 1.4:+31526071 MS.gene96931:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+TGG + chr1.4:31526446-31526465 MS.gene96931:CDS 20.0%
!! ATTGTTATATATGTCTTATG+GGG + chr1.4:31526448-31526467 MS.gene96931:CDS 20.0%
!! CATTGTTATATATGTCTTAT+GGG + chr1.4:31526447-31526466 MS.gene96931:CDS 20.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.4:31526102-31526121 MS.gene96931:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.4:31526103-31526122 MS.gene96931:CDS 25.0%
! GTTTGAAAAATCTTGTCTTT+AGG - chr1.4:31526611-31526630 None:intergenic 25.0%
! TATCGTATAAGACCAAAAAA+CGG + chr1.4:31526366-31526385 MS.gene96931:CDS 25.0%
! TTGTTATATATGTCTTATGG+GGG + chr1.4:31526449-31526468 MS.gene96931:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.4:31526099-31526118 None:intergenic 25.0%
!!! TTTTTGGTCTTATACGATAT+TGG - chr1.4:31526365-31526384 None:intergenic 25.0%
ACAAGCATAATCATGATGAT+GGG + chr1.4:31526144-31526163 MS.gene96931:CDS 30.0%
TACATGTGATGTTTGTAACA+AGG + chr1.4:31526181-31526200 MS.gene96931:CDS 30.0%
TGTTACAAACATCACATGTA+TGG - chr1.4:31526181-31526200 None:intergenic 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.4:31525886-31525905 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.4:31526050-31526069 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.4:31525885-31525904 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.4:31525869-31525888 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.4:31525941-31525960 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.4:31526524-31526543 MS.gene96931:CDS 35.0%
AGCGAAGATGAAACTGAATT+AGG + chr1.4:31526692-31526711 MS.gene96931:CDS 35.0%
ATGAGATGGCATACTCAAAA+GGG + chr1.4:31526236-31526255 MS.gene96931:CDS 35.0%
CACAAGCATAATCATGATGA+TGG + chr1.4:31526143-31526162 MS.gene96931:CDS 35.0%
CATGATCATGCTGTGAATAA+CGG + chr1.4:31526068-31526087 MS.gene96931:CDS 35.0%
CTTTGAATGGACATATGAGA+TGG + chr1.4:31526222-31526241 MS.gene96931:CDS 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.4:31525921-31525940 MS.gene96931:CDS 35.0%
GCGAAGATGAAACTGAATTA+GGG + chr1.4:31526693-31526712 MS.gene96931:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.4:31526471-31526490 MS.gene96931:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.4:31526335-31526354 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.4:31525911-31525930 None:intergenic 35.0%
TATGAGATGGCATACTCAAA+AGG + chr1.4:31526235-31526254 MS.gene96931:CDS 35.0%
TCATCTTCGAAATCATCACT+TGG - chr1.4:31526755-31526774 None:intergenic 35.0%
TGTCACAAAACATTTACCTC+TGG + chr1.4:31525969-31525988 MS.gene96931:CDS 35.0%
TTGCCACAACGAAAAAAACT+TGG + chr1.4:31526568-31526587 MS.gene96931:CDS 35.0%
TTTACCTCTGGTAAATCACT+TGG + chr1.4:31525981-31526000 MS.gene96931:CDS 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.4:31526517-31526536 MS.gene96931:CDS 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.4:31525896-31525915 None:intergenic 35.0%
!! TTGGTCTTATACGATATTGG+CGG - chr1.4:31526362-31526381 None:intergenic 35.0%
AATTAGGGTCAAGAGTTGTC+AGG + chr1.4:31526708-31526727 MS.gene96931:CDS 40.0%
ACTCAAAAGGGTTCGAAGAA+GGG + chr1.4:31526248-31526267 MS.gene96931:CDS 40.0%
ATGTCTTATGGGGGTTATGA+GGG + chr1.4:31526458-31526477 MS.gene96931:CDS 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.4:31526507-31526526 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.4:31525942-31525961 None:intergenic 40.0%
CGTTATTCACAGCATGATCA+TGG - chr1.4:31526070-31526089 None:intergenic 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.4:31526493-31526512 MS.gene96931:CDS 40.0%
GGATCTAGCTGTGATATTGA+AGG + chr1.4:31526656-31526675 MS.gene96931:CDS 40.0%
TACTCAAAAGGGTTCGAAGA+AGG + chr1.4:31526247-31526266 MS.gene96931:CDS 40.0%
TATGTCTTATGGGGGTTATG+AGG + chr1.4:31526457-31526476 MS.gene96931:CDS 40.0%
TCAAACATCGCAAGATTGCA+AGG + chr1.4:31526625-31526644 MS.gene96931:CDS 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.4:31525858-31525877 None:intergenic 40.0%
! CTCAATTTGACTTTGTTCCG+AGG - chr1.4:31526306-31526325 None:intergenic 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.4:31526403-31526422 MS.gene96931:CDS 40.0%
! TCATCCAACAGTGCTTTGAA+TGG + chr1.4:31526209-31526228 MS.gene96931:CDS 40.0%
!! ACGAAAAAAACTTGGTGCTG+AGG + chr1.4:31526576-31526595 MS.gene96931:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.4:31526030-31526049 None:intergenic 40.0%
!! ATGTCCATTCAAAGCACTGT+TGG - chr1.4:31526216-31526235 None:intergenic 40.0%
!!! GCACCAAGTTTTTTTCGTTG+TGG - chr1.4:31526574-31526593 None:intergenic 40.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.4:31525988-31526007 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.4:31525984-31526003 MS.gene96931:CDS 45.0%
ACTTTGTTCCGAGGAAGATG+GGG - chr1.4:31526297-31526316 None:intergenic 45.0%
ATATCACAGCTAGATCCTGC+AGG - chr1.4:31526653-31526672 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.4:31526496-31526515 MS.gene96931:CDS 45.0%
GACTTTGTTCCGAGGAAGAT+GGG - chr1.4:31526298-31526317 None:intergenic 45.0%
GATCATGCTGTGAATAACGG+CGG + chr1.4:31526071-31526090 MS.gene96931:CDS 45.0%
TGACTTTGTTCCGAGGAAGA+TGG - chr1.4:31526299-31526318 None:intergenic 45.0%
! AACAAGGTGTGCTGCTAACA+AGG + chr1.4:31526540-31526559 MS.gene96931:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.4:31526025-31526044 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.4:31526381-31526400 MS.gene96931:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.4:31526375-31526394 MS.gene96931:CDS 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.4:31526396-31526415 None:intergenic 50.0%
CAAGATTGCAAGGAACCTGC+AGG + chr1.4:31526635-31526654 MS.gene96931:CDS 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.4:31526395-31526414 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.4:31526381-31526400 None:intergenic 50.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.4:31526283-31526302 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+CGG + chr1.4:31526286-31526305 MS.gene96931:CDS 60.0%
TCCGAGGAAGATGGGGCAGT+CGG - chr1.4:31526290-31526309 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 31525834 31526784 31525834 ID=MS.gene96931
chr1.4 mRNA 31525834 31526784 31525834 ID=MS.gene96931.t1;Parent=MS.gene96931
chr1.4 exon 31525834 31526784 31525834 ID=MS.gene96931.t1.exon1;Parent=MS.gene96931.t1
chr1.4 CDS 31525834 31526784 31525834 ID=cds.MS.gene96931.t1;Parent=MS.gene96931.t1
Gene Sequence

>MS.gene96931

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTCTGTCACAAAACATTTACCTCTGGTAAATCACTTGGTGGTCACAAAACTATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAACGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAGCATAATCATGATGATGGGAAACAGAAGAGCCATACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAGTGCTTTGAATGGACATATGAGATGGCATACTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTCGGAACAAAGTCAAATTGAGTTTCTACCATCTACTGACTTGTCAAAGTACTTGCCGCCAATATCGTATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATTGCTGCAAAAACATTGTTATATATGTCTTATGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGCTGCTAACAAGGTGTGTTTGCCACAACGAAAAAAACTTGGTGCTGAGGTTGAAGATTCCTAAAGACAAGATTTTTCAAACATCGCAAGATTGCAAGGAACCTGCAGGATCTAGCTGTGATATTGAAGGCAAGAAGAATATTAGCGAAGATGAAACTGAATTAGGGTCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTCGAAGATGAAACCAGTTAG
Protein sequence

>MS.gene96931.t1

MNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKQKSHTCDVCNKVFSSNSALNGHMRWHTQKGSKKGVIIHSPTAPSSSEQSQIEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVLLTRCVCHNEKNLVLRLKIPKDKIFQTSQDCKEPAGSSCDIEGKKNISEDETELGSRVVRNFDLNELPSDDFEDETS