AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64298

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64298.t1 MTR_1g046810 86.032 315 44 0 1 315 1 315 0.0 527
MS.gene64298.t1 MTR_1g052185 37.082 329 119 12 5 310 12 275 5.15e-39 139
MS.gene64298.t1 MTR_1g053530 37.168 226 95 7 63 281 39 224 4.00e-28 109
MS.gene64298.t1 MTR_1g085590 35.926 270 85 10 71 315 16 222 6.44e-27 107
MS.gene64298.t1 MTR_1g063150 35.945 217 57 7 94 310 36 170 2.24e-25 100
MS.gene64298.t1 MTR_1g063140 40.361 166 45 8 147 311 1 113 1.67e-17 79.3
MS.gene64298.t1 MTR_5g098470 30.144 209 84 9 14 210 46 204 7.55e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 58 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATTGTTATATATGTCTTA+TGG 0.192869 1.3:+28397294 MS.gene64298:CDS
AGCGAAGATGAAACTGAATT+AGG 0.276288 1.3:+28397540 MS.gene64298:CDS
CATTGTTATATATGTCTTAT+GGG 0.313934 1.3:+28397295 MS.gene64298:CDS
AGGTTGAAGAAGAGTGTTAG+AGG 0.343983 1.3:-28396875 None:intergenic
CTTTGAATGGACATATTAGA+TGG 0.355165 1.3:+28397070 MS.gene64298:CDS
ATTATCATCCACCGTATTGC+TGG 0.360275 1.3:-28397352 None:intergenic
ATCAGCAATACGCCTTCTCC+TGG 0.390025 1.3:-28397241 None:intergenic
GCGAAGATGAAACTGAATTA+GGG 0.399498 1.3:+28397541 MS.gene64298:CDS
TCAAAATTCCTGACAACTCT+TGG 0.403974 1.3:-28397564 None:intergenic
GTTATGAGGGATCAACTAAA+AGG 0.407447 1.3:+28397319 MS.gene64298:CDS
TATTAGATGGCATGCTCAAA+AGG 0.408209 1.3:+28397083 MS.gene64298:CDS
CATGATCATGCTGTGAATAA+TGG 0.410602 1.3:+28396916 MS.gene64298:CDS
GACTTTGTTCCAAGGAAGAT+GGG 0.419216 1.3:-28397143 None:intergenic
CACAAGCATAATCATGATGA+TGG 0.420773 1.3:+28396991 MS.gene64298:CDS
TCATCCAACAATGCTTTGAA+TGG 0.423695 1.3:+28397057 MS.gene64298:CDS
AACAGAAAAGAAACACTAAC+TGG 0.431171 1.3:-28397625 None:intergenic
TGACTTTGTTCCAAGGAAGA+TGG 0.439982 1.3:-28397144 None:intergenic
ACCGACTGCCCCATCTTCCT+TGG 0.446430 1.3:+28397134 MS.gene64298:CDS
TACTTTGACAAGTCAGTAGA+TGG 0.459060 1.3:-28397180 None:intergenic
AACTGTAGATTCTTGAACCT+GGG 0.459451 1.3:-28396786 None:intergenic
ATGTCCATTCAAAGCATTGT+TGG 0.483556 1.3:-28397061 None:intergenic
CAACTGTAGATTCTTGAACC+TGG 0.492609 1.3:-28396787 None:intergenic
TGCTCAAAAGGGTTCGAAGA+AGG 0.502364 1.3:+28397095 MS.gene64298:CDS
AATTAGGGCCAAGAGTTGTC+AGG 0.505315 1.3:+28397556 MS.gene64298:CDS
CATTATTCACAGCATGATCA+TGG 0.508716 1.3:-28396915 None:intergenic
TGTCACAAAACATTTACCTC+TGG 0.513939 1.3:+28396817 MS.gene64298:CDS
TATCATCTTCAAGAGTCTGT+TGG 0.516591 1.3:-28396756 None:intergenic
AACAAGGTGTGCTGCTAACA+AGG 0.519240 1.3:+28397388 MS.gene64298:CDS
GGATCTAGCTGTGATATTGA+AGG 0.530396 1.3:+28397504 MS.gene64298:CDS
ACCTCTGGTAAATCACTTGG+TGG 0.531173 1.3:+28396832 MS.gene64298:CDS
TTGGTCTTATATGATATTGG+CGG 0.539661 1.3:-28397207 None:intergenic
CTCAAGTTGACTTTGTTCCA+AGG 0.540256 1.3:-28397151 None:intergenic
CACATGTGATGTTTGTAACA+AGG 0.542154 1.3:+28397029 MS.gene64298:CDS
ATTGTTATATATGTCTTATG+GGG 0.542437 1.3:+28397296 MS.gene64298:CDS
TCAAACATCGCAAGATTGCA+AGG 0.542865 1.3:+28397473 MS.gene64298:CDS
ATTAGATGGCATGCTCAAAA+GGG 0.543610 1.3:+28397084 MS.gene64298:CDS
GCAGAAGATTTCCAGCAATA+CGG 0.546299 1.3:+28397341 MS.gene64298:CDS
TCAAACGAATGGTGAGAAGA+AGG 0.549246 1.3:-28396703 None:intergenic
TTTACCTCTGGTAAATCACT+TGG 0.558168 1.3:+28396829 MS.gene64298:CDS
GAAGAAGAGTGTTAGAGGAG+CGG 0.560783 1.3:-28396870 None:intergenic
CAAGATTGCAAGGAACCTGC+AGG 0.562783 1.3:+28397483 MS.gene64298:CDS
GCTCAAAAGGGTTCGAAGAA+GGG 0.568620 1.3:+28397096 MS.gene64298:CDS
GGATGATAATGAGAAGATGA+AGG 0.579672 1.3:+28397365 MS.gene64298:CDS
ACAAGCATAATCATGATGAT+GGG 0.583581 1.3:+28396992 MS.gene64298:CDS
ATATCACAGCTAGATCCTGC+AGG 0.585006 1.3:-28397498 None:intergenic
AAGATGGGGCAGTCGGTGAG+TGG 0.586640 1.3:-28397128 None:intergenic
TCAGCAATACGCCTTCTCCT+GGG 0.592381 1.3:-28397240 None:intergenic
TTGTTATATATGTCTTATGG+GGG 0.593530 1.3:+28397297 MS.gene64298:CDS
TCATCTTCGAAATCATCACT+TGG 0.604104 1.3:-28397600 None:intergenic
AATGAGAAGATGAAGGAACA+AGG 0.607433 1.3:+28397372 MS.gene64298:CDS
TCCAAGGAAGATGGGGCAGT+CGG 0.610571 1.3:-28397135 None:intergenic
TCTGTTGGTGATAATGATCA+TGG 0.616583 1.3:-28396741 None:intergenic
ACTTTGTTCCAAGGAAGATG+GGG 0.644016 1.3:-28397142 None:intergenic
GCGTATTGCTGATAATGATG+AGG 0.644357 1.3:+28397251 MS.gene64298:CDS
GAAGATTTCCAGCAATACGG+TGG 0.664760 1.3:+28397344 MS.gene64298:CDS
TGTTACAAACATCACATGTG+CGG 0.682061 1.3:-28397026 None:intergenic
ACCACCAAGTGATTTACCAG+AGG 0.717389 1.3:-28396833 None:intergenic
GATCATGCTGTGAATAATGG+CGG 0.744855 1.3:+28396919 MS.gene64298:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATTGTTATATATGTCTTA+TGG + chr1.3:28397294-28397313 MS.gene64298:CDS 20.0%
!! ATTGTTATATATGTCTTATG+GGG + chr1.3:28397296-28397315 MS.gene64298:CDS 20.0%
!! CATTGTTATATATGTCTTAT+GGG + chr1.3:28397295-28397314 MS.gene64298:CDS 20.0%
!! TATCATATAAGACCAAAAAA+CGG + chr1.3:28397214-28397233 MS.gene64298:CDS 20.0%
!!! TTTTTGGTCTTATATGATAT+TGG - chr1.3:28397213-28397232 None:intergenic 20.0%
! AGAAGACTACAAAAATTACT+TGG + chr1.3:28396950-28396969 MS.gene64298:CDS 25.0%
! GAAGACTACAAAAATTACTT+GGG + chr1.3:28396951-28396970 MS.gene64298:CDS 25.0%
! GTTTGAAAAATCTTGTCTTT+AGG - chr1.3:28397459-28397478 None:intergenic 25.0%
! TTGTTATATATGTCTTATGG+GGG + chr1.3:28397297-28397316 MS.gene64298:CDS 25.0%
!! AATTTTTGTAGTCTTCTTCA+AGG - chr1.3:28396947-28396966 None:intergenic 25.0%
ACAAGCATAATCATGATGAT+GGG + chr1.3:28396992-28397011 MS.gene64298:CDS 30.0%
CTTTGAATGGACATATTAGA+TGG + chr1.3:28397070-28397089 MS.gene64298:CDS 30.0%
!! ATAATGATCATGGCTGTTTT+TGG - chr1.3:28396734-28396753 None:intergenic 30.0%
!! TGGATCTGTTTGTTTGTTTT+AGG - chr1.3:28396898-28396917 None:intergenic 30.0%
!! TTGGTCTTATATGATATTGG+CGG - chr1.3:28397210-28397229 None:intergenic 30.0%
!!! TAATGATCATGGCTGTTTTT+GGG - chr1.3:28396733-28396752 None:intergenic 30.0%
!!! TTTTGGGTTTATCAAACGAA+TGG - chr1.3:28396717-28396736 None:intergenic 30.0%
AACTGTAGATTCTTGAACCT+GGG - chr1.3:28396789-28396808 None:intergenic 35.0%
AATGAGAAGATGAAGGAACA+AGG + chr1.3:28397372-28397391 MS.gene64298:CDS 35.0%
AGCGAAGATGAAACTGAATT+AGG + chr1.3:28397540-28397559 MS.gene64298:CDS 35.0%
ATTAGATGGCATGCTCAAAA+GGG + chr1.3:28397084-28397103 MS.gene64298:CDS 35.0%
CACAAGCATAATCATGATGA+TGG + chr1.3:28396991-28397010 MS.gene64298:CDS 35.0%
CACATGTGATGTTTGTAACA+AGG + chr1.3:28397029-28397048 MS.gene64298:CDS 35.0%
CATGATCATGCTGTGAATAA+TGG + chr1.3:28396916-28396935 MS.gene64298:CDS 35.0%
CATTATTCACAGCATGATCA+TGG - chr1.3:28396918-28396937 None:intergenic 35.0%
GAAGATGATAAGAAAAACCC+AGG + chr1.3:28396769-28396788 MS.gene64298:CDS 35.0%
GCGAAGATGAAACTGAATTA+GGG + chr1.3:28397541-28397560 MS.gene64298:CDS 35.0%
GTTATGAGGGATCAACTAAA+AGG + chr1.3:28397319-28397338 MS.gene64298:CDS 35.0%
TACTTTGACAAGTCAGTAGA+TGG - chr1.3:28397183-28397202 None:intergenic 35.0%
TATCATCTTCAAGAGTCTGT+TGG - chr1.3:28396759-28396778 None:intergenic 35.0%
TATTAGATGGCATGCTCAAA+AGG + chr1.3:28397083-28397102 MS.gene64298:CDS 35.0%
TCAAAATTCCTGACAACTCT+TGG - chr1.3:28397567-28397586 None:intergenic 35.0%
TCATCTTCGAAATCATCACT+TGG - chr1.3:28397603-28397622 None:intergenic 35.0%
TGTCACAAAACATTTACCTC+TGG + chr1.3:28396817-28396836 MS.gene64298:CDS 35.0%
TGTTACAAACATCACATGTG+CGG - chr1.3:28397029-28397048 None:intergenic 35.0%
TTGCCACAACGAAAAAAACT+TGG + chr1.3:28397416-28397435 MS.gene64298:CDS 35.0%
TTTACCTCTGGTAAATCACT+TGG + chr1.3:28396829-28396848 MS.gene64298:CDS 35.0%
! GGATGATAATGAGAAGATGA+AGG + chr1.3:28397365-28397384 MS.gene64298:CDS 35.0%
! TCATCCAACAATGCTTTGAA+TGG + chr1.3:28397057-28397076 MS.gene64298:CDS 35.0%
!! ATGTCCATTCAAAGCATTGT+TGG - chr1.3:28397064-28397083 None:intergenic 35.0%
!! TCTGTTGGTGATAATGATCA+TGG - chr1.3:28396744-28396763 None:intergenic 35.0%
ACTTTGTTCCAAGGAAGATG+GGG - chr1.3:28397145-28397164 None:intergenic 40.0%
ATGTCTTATGGGGGTTATGA+GGG + chr1.3:28397306-28397325 MS.gene64298:CDS 40.0%
ATTATCATCCACCGTATTGC+TGG - chr1.3:28397355-28397374 None:intergenic 40.0%
CAACTGTAGATTCTTGAACC+TGG - chr1.3:28396790-28396809 None:intergenic 40.0%
GACTTTGTTCCAAGGAAGAT+GGG - chr1.3:28397146-28397165 None:intergenic 40.0%
GATCATGCTGTGAATAATGG+CGG + chr1.3:28396919-28396938 MS.gene64298:CDS 40.0%
GCAGAAGATTTCCAGCAATA+CGG + chr1.3:28397341-28397360 MS.gene64298:CDS 40.0%
GGATCTAGCTGTGATATTGA+AGG + chr1.3:28397504-28397523 MS.gene64298:CDS 40.0%
TATGTCTTATGGGGGTTATG+AGG + chr1.3:28397305-28397324 MS.gene64298:CDS 40.0%
TCAAACATCGCAAGATTGCA+AGG + chr1.3:28397473-28397492 MS.gene64298:CDS 40.0%
TCAAACGAATGGTGAGAAGA+AGG - chr1.3:28396706-28396725 None:intergenic 40.0%
TGACTTTGTTCCAAGGAAGA+TGG - chr1.3:28397147-28397166 None:intergenic 40.0%
! GCGTATTGCTGATAATGATG+AGG + chr1.3:28397251-28397270 MS.gene64298:CDS 40.0%
!! ACGAAAAAAACTTGGTGCTG+AGG + chr1.3:28397424-28397443 MS.gene64298:CDS 40.0%
!! AGGTTGAAGAAGAGTGTTAG+AGG - chr1.3:28396878-28396897 None:intergenic 40.0%
!! CTCAAGTTGACTTTGTTCCA+AGG - chr1.3:28397154-28397173 None:intergenic 40.0%
!!! GCACCAAGTTTTTTTCGTTG+TGG - chr1.3:28397422-28397441 None:intergenic 40.0%
AATTAGGGCCAAGAGTTGTC+AGG + chr1.3:28397556-28397575 MS.gene64298:CDS 45.0%
ACCACCAAGTGATTTACCAG+AGG - chr1.3:28396836-28396855 None:intergenic 45.0%
ACCTCTGGTAAATCACTTGG+TGG + chr1.3:28396832-28396851 MS.gene64298:CDS 45.0%
ATATCACAGCTAGATCCTGC+AGG - chr1.3:28397501-28397520 None:intergenic 45.0%
GAAGATTTCCAGCAATACGG+TGG + chr1.3:28397344-28397363 MS.gene64298:CDS 45.0%
GCTCAAAAGGGTTCGAAGAA+GGG + chr1.3:28397096-28397115 MS.gene64298:CDS 45.0%
TGCTCAAAAGGGTTCGAAGA+AGG + chr1.3:28397095-28397114 MS.gene64298:CDS 45.0%
! AACAAGGTGTGCTGCTAACA+AGG + chr1.3:28397388-28397407 MS.gene64298:CDS 45.0%
!! GAAGAAGAGTGTTAGAGGAG+CGG - chr1.3:28396873-28396892 None:intergenic 45.0%
AAAAACGGAGTCCCAGGAGA+AGG + chr1.3:28397229-28397248 MS.gene64298:CDS 50.0%
AGACCAAAAAACGGAGTCCC+AGG + chr1.3:28397223-28397242 MS.gene64298:CDS 50.0%
ATCAGCAATACGCCTTCTCC+TGG - chr1.3:28397244-28397263 None:intergenic 50.0%
CAAGATTGCAAGGAACCTGC+AGG + chr1.3:28397483-28397502 MS.gene64298:CDS 50.0%
TCAGCAATACGCCTTCTCCT+GGG - chr1.3:28397243-28397262 None:intergenic 50.0%
!!! TCTCCTGGGACTCCGTTTTT+TGG - chr1.3:28397229-28397248 None:intergenic 50.0%
TCCAAGGAAGATGGGGCAGT+CGG - chr1.3:28397138-28397157 None:intergenic 55.0%
AAGATGGGGCAGTCGGTGAG+TGG - chr1.3:28397131-28397150 None:intergenic 60.0%
ACCGACTGCCCCATCTTCCT+TGG + chr1.3:28397134-28397153 MS.gene64298:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 28396682 28397632 28396682 ID=MS.gene64298
chr1.3 mRNA 28396682 28397632 28396682 ID=MS.gene64298.t1;Parent=MS.gene64298
chr1.3 exon 28396682 28397632 28396682 ID=MS.gene64298.t1.exon1;Parent=MS.gene64298.t1
chr1.3 CDS 28396682 28397632 28396682 ID=cds.MS.gene64298.t1;Parent=MS.gene64298.t1
Gene Sequence

>MS.gene64298

ATGAACAAACACTATTCTTCACCTTCTTCTCACCATTCGTTTGATAAACCCAAAAACAGCCATGATCATTATCACCAACAGACTCTTGAAGATGATAAGAAAAACCCAGGTTCAAGAATCTACAGTTGTGAGTTCTGTCACAAAACATTTACCTCTGGTAAATCACTTGGTGGTCACAAAACTATTCACCGCTCCTCTAACACTCTTCTTCAACCTAAAACAAACAAACAGATCCATGATCATGCTGTGAATAATGGCGGCACCTTGAAGAAGACTACAAAAATTACTTGGGTTTTTTCTTCTTCTCTTCACAAGCATAATCATGATGATGGGAAACTGAAGAACCGCACATGTGATGTTTGTAACAAGGTTTTTTCATCCAACAATGCTTTGAATGGACATATTAGATGGCATGCTCAAAAGGGTTCGAAGAAGGGTGTTATTATCCACTCACCGACTGCCCCATCTTCCTTGGAACAAAGTCAACTTGAGTTTCTACCATCTACTGACTTGTCAAAGTACTTGCCGCCAATATCATATAAGACCAAAAAACGGAGTCCCAGGAGAAGGCGTATTGCTGATAATGATGAGGAAATTACTATTGCTGCAAAAACATTGTTATATATGTCTTATGGGGGTTATGAGGGATCAACTAAAAGGCAGAAGATTTCCAGCAATACGGTGGATGATAATGAGAAGATGAAGGAACAAGGTGTGCTGCTAACAAGGTGTGTTTGCCACAACGAAAAAAACTTGGTGCTGAGGTTGAAGATTCCTAAAGACAAGATTTTTCAAACATCGCAAGATTGCAAGGAACCTGCAGGATCTAGCTGTGATATTGAAGGCAAGAAGAATATTAGCGAAGATGAAACTGAATTAGGGCCAAGAGTTGTCAGGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTCGAAGATGAAACCAGTTAG
Protein sequence

>MS.gene64298.t1

MNKHYSSPSSHHSFDKPKNSHDHYHQQTLEDDKKNPGSRIYSCEFCHKTFTSGKSLGGHKTIHRSSNTLLQPKTNKQIHDHAVNNGGTLKKTTKITWVFSSSLHKHNHDDGKLKNRTCDVCNKVFSSNNALNGHIRWHAQKGSKKGVIIHSPTAPSSLEQSQLEFLPSTDLSKYLPPISYKTKKRSPRRRRIADNDEEITIAAKTLLYMSYGGYEGSTKRQKISSNTVDDNEKMKEQGVLLTRCVCHNEKNLVLRLKIPKDKIFQTSQDCKEPAGSSCDIEGKKNISEDETELGPRVVRNFDLNELPSDDFEDETS