AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60629

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60629.t1 MTR_0856s0010 43.023 172 84 4 3 173 2 160 4.03e-37 127
MS.gene60629.t1 MTR_7g446060 50.667 75 37 0 130 204 7 81 2.48e-19 81.3
MS.gene60629.t1 MTR_1g019850 30.303 165 98 6 17 175 43 196 1.10e-15 73.9
MS.gene60629.t1 MTR_7g115320 58.333 60 21 2 132 190 3 59 2.91e-15 68.9
MS.gene60629.t1 MTR_0402s0040 23.958 192 132 4 48 225 26 217 1.29e-11 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGTTGACGTTTCGGATTC+CGG 0.204382 1.2:-69700221 MS.gene60629:CDS
GATTGCAAACCCTTGTTTCA+TGG 0.302647 1.2:+69700094 None:intergenic
GTGTTGACGTTTCGGATTCC+GGG 0.344560 1.2:-69700220 MS.gene60629:CDS
TTGCTTTAAAGAAGGGTCTA+TGG 0.361166 1.2:-69699923 MS.gene60629:CDS
TGCGGCTCGTGTTGACGTTT+CGG 0.362249 1.2:-69700228 MS.gene60629:CDS
ACTAAATCACGGTTGTTTGC+TGG 0.375082 1.2:-69699855 MS.gene60629:CDS
TTGTACAATTGTGGCAATCC+AGG 0.394673 1.2:+69699653 None:intergenic
AAAGGATGATCGATCAATAT+AGG 0.415391 1.2:+69700281 None:intergenic
TTGGTGGTATGTTTGATTCA+TGG 0.433399 1.2:+69699997 None:intergenic
GCAAACAACCGTGATTTAGT+TGG 0.439208 1.2:+69699858 None:intergenic
TGTGGCAATCCAGGGAATCT+TGG 0.442923 1.2:+69699662 None:intergenic
CCATCAGCTAGCTCTCCGTC+AGG 0.451558 1.2:+69700251 None:intergenic
AAAACTAGAAACTCTAAGAA+AGG 0.460138 1.2:-69700071 MS.gene60629:CDS
AAACTAGAAACTCTAAGAAA+GGG 0.460938 1.2:-69700070 MS.gene60629:CDS
GATAACGGTTGCTTTAAAGA+AGG 0.473052 1.2:-69699931 MS.gene60629:CDS
GAGCAATCAAGTTTCTTCGT+TGG 0.480101 1.2:+69699960 None:intergenic
CACTTATGCTCGATGGCTGA+TGG 0.482201 1.2:-69700308 None:intergenic
ATTTGTTGTTTCAAAGGTCC+CGG 0.485747 1.2:+69700202 None:intergenic
GACAGCATTTGTTGTTTCAA+AGG 0.491833 1.2:+69700196 None:intergenic
CTTGTTTCATGGCATATTCA+CGG 0.492232 1.2:+69700105 None:intergenic
CGTGAATATGCCATGAAACA+AGG 0.498225 1.2:-69700104 MS.gene60629:CDS
TAGCATCTACCAAGATTCCC+TGG 0.498228 1.2:-69699671 MS.gene60629:CDS
TTAAAAGACATACCGATAGT+AGG 0.501742 1.2:+69700155 None:intergenic
GTTGGATTCGTCTTCAAAGT+TGG 0.502236 1.2:+69699978 None:intergenic
TTACGAAAATCTAACATTTG+TGG 0.512305 1.2:-69699727 MS.gene60629:CDS
AAACGATCAGGCAGGTGTAC+GGG 0.512319 1.2:-69699790 MS.gene60629:CDS
CGTTCCATGGTATGTGATGC+CGG 0.512631 1.2:-69699753 MS.gene60629:CDS
ATAACGGTTGCTTTAAAGAA+GGG 0.522275 1.2:-69699930 MS.gene60629:CDS
GAACAAAAGTTTCCGTTCCA+TGG 0.529264 1.2:-69699766 MS.gene60629:CDS
GGATTCGTCTTCAAAGTTGG+TGG 0.530111 1.2:+69699981 None:intergenic
TAAACGATCAGGCAGGTGTA+CGG 0.533293 1.2:-69699791 MS.gene60629:CDS
CATCAGCTAGCTCTCCGTCA+GGG 0.541329 1.2:+69700252 None:intergenic
TGTACAATTGTGGCAATCCA+GGG 0.548653 1.2:+69699654 None:intergenic
TGATTGCTCAGCTAAGATAA+CGG 0.550952 1.2:-69699946 MS.gene60629:CDS
GATAAATTCACGCCTACTAT+CGG 0.551302 1.2:-69700167 MS.gene60629:CDS
ATTCTAACTTGTGCAAGAGA+AGG 0.552020 1.2:-69700023 MS.gene60629:CDS
GATGTACAAGACTACACAGC+TGG 0.552704 1.2:-69699699 MS.gene60629:CDS
AACTCTAAGAAAGGGGCCGA+TGG 0.560180 1.2:-69700062 MS.gene60629:CDS
CTGTGCAATTTGTACAATTG+TGG 0.565025 1.2:+69699644 None:intergenic
ATCAGCTAGCTCTCCGTCAG+GGG 0.582853 1.2:+69700253 None:intergenic
GTGAATATGCCATGAAACAA+GGG 0.602322 1.2:-69700103 MS.gene60629:CDS
ACCACCGGCATCACATACCA+TGG 0.613048 1.2:+69699749 None:intergenic
CCTGACGGAGAGCTAGCTGA+TGG 0.623440 1.2:-69700251 MS.gene60629:CDS
CGGCATCACATACCATGGAA+CGG 0.625469 1.2:+69699754 None:intergenic
AACTAGAAACTCTAAGAAAG+GGG 0.633083 1.2:-69700069 MS.gene60629:CDS
GGATGATCGATCAATATAGG+AGG 0.639611 1.2:+69700284 None:intergenic
AGATAAGTCCAACTAAATCA+CGG 0.645312 1.2:-69699866 MS.gene60629:CDS
TCAGCTAGCTCTCCGTCAGG+GGG 0.662037 1.2:+69700254 None:intergenic
CGGAGAGCTAGCTGATGGTG+CGG 0.662675 1.2:-69700246 MS.gene60629:CDS
TCCATGGTATGTGATGCCGG+TGG 0.764195 1.2:-69699750 MS.gene60629:CDS
AGATTGATATGCATGCACAG+CGG 0.798983 1.2:-69699824 MS.gene60629:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTACGAAAATCTAACATTTG+TGG - chr1.2:69700198-69700217 MS.gene60629:CDS 25.0%
!! AAAACTAGAAACTCTAAGAA+AGG - chr1.2:69699854-69699873 MS.gene60629:CDS 25.0%
!! AAACTAGAAACTCTAAGAAA+GGG - chr1.2:69699855-69699874 MS.gene60629:CDS 25.0%
!! TATCGGTATGTCTTTTAAAT+CGG - chr1.2:69699775-69699794 MS.gene60629:CDS 25.0%
!!! GAAATATTTTAACATGCCAT+CGG + chr1.2:69699882-69699901 None:intergenic 25.0%
AAAGGATGATCGATCAATAT+AGG + chr1.2:69699647-69699666 None:intergenic 30.0%
AGATAAGTCCAACTAAATCA+CGG - chr1.2:69700059-69700078 MS.gene60629:CDS 30.0%
TTAAAAGACATACCGATAGT+AGG + chr1.2:69699773-69699792 None:intergenic 30.0%
! AACTAGAAACTCTAAGAAAG+GGG - chr1.2:69699856-69699875 MS.gene60629:CDS 30.0%
!! ATAACGGTTGCTTTAAAGAA+GGG - chr1.2:69699995-69700014 MS.gene60629:CDS 30.0%
!! GACAATTTTGATAAACGATC+AGG - chr1.2:69700123-69700142 MS.gene60629:CDS 30.0%
CTGTGCAATTTGTACAATTG+TGG + chr1.2:69700284-69700303 None:intergenic 35.0%
CTTGTTTCATGGCATATTCA+CGG + chr1.2:69699823-69699842 None:intergenic 35.0%
GATAAATTCACGCCTACTAT+CGG - chr1.2:69699758-69699777 MS.gene60629:CDS 35.0%
GTGAATATGCCATGAAACAA+GGG - chr1.2:69699822-69699841 MS.gene60629:CDS 35.0%
TGATTGCTCAGCTAAGATAA+CGG - chr1.2:69699979-69699998 MS.gene60629:CDS 35.0%
! ATTCTAACTTGTGCAAGAGA+AGG - chr1.2:69699902-69699921 MS.gene60629:CDS 35.0%
! TGTTAGATTTTCGTAACCAC+CGG + chr1.2:69700194-69700213 None:intergenic 35.0%
! TTGGTGGTATGTTTGATTCA+TGG + chr1.2:69699931-69699950 None:intergenic 35.0%
!! ATTTGTTGTTTCAAAGGTCC+CGG + chr1.2:69699726-69699745 None:intergenic 35.0%
!! ATTTTGATAAACGATCAGGC+AGG - chr1.2:69700127-69700146 MS.gene60629:CDS 35.0%
!! GACAGCATTTGTTGTTTCAA+AGG + chr1.2:69699732-69699751 None:intergenic 35.0%
!! GATAACGGTTGCTTTAAAGA+AGG - chr1.2:69699994-69700013 MS.gene60629:CDS 35.0%
!! TTGCTTTAAAGAAGGGTCTA+TGG - chr1.2:69700002-69700021 MS.gene60629:CDS 35.0%
ACTAAATCACGGTTGTTTGC+TGG - chr1.2:69700070-69700089 MS.gene60629:CDS 40.0%
AGATTGATATGCATGCACAG+CGG - chr1.2:69700101-69700120 MS.gene60629:CDS 40.0%
CGTGAATATGCCATGAAACA+AGG - chr1.2:69699821-69699840 MS.gene60629:CDS 40.0%
GAACAAAAGTTTCCGTTCCA+TGG - chr1.2:69700159-69700178 MS.gene60629:CDS 40.0%
GAGCAATCAAGTTTCTTCGT+TGG + chr1.2:69699968-69699987 None:intergenic 40.0%
GCAAACAACCGTGATTTAGT+TGG + chr1.2:69700070-69700089 None:intergenic 40.0%
GGATGATCGATCAATATAGG+AGG + chr1.2:69699644-69699663 None:intergenic 40.0%
GTTGGATTCGTCTTCAAAGT+TGG + chr1.2:69699950-69699969 None:intergenic 40.0%
TGTACAATTGTGGCAATCCA+GGG + chr1.2:69700274-69700293 None:intergenic 40.0%
TTGTACAATTGTGGCAATCC+AGG + chr1.2:69700275-69700294 None:intergenic 40.0%
! GATTGCAAACCCTTGTTTCA+TGG + chr1.2:69699834-69699853 None:intergenic 40.0%
CATCCTTTATTACCCCCTGA+CGG - chr1.2:69699659-69699678 MS.gene60629:CDS 45.0%
GATGTACAAGACTACACAGC+TGG - chr1.2:69700226-69700245 MS.gene60629:CDS 45.0%
GGATTCGTCTTCAAAGTTGG+TGG + chr1.2:69699947-69699966 None:intergenic 45.0%
TAAACGATCAGGCAGGTGTA+CGG - chr1.2:69700134-69700153 MS.gene60629:CDS 45.0%
TAGCATCTACCAAGATTCCC+TGG - chr1.2:69700254-69700273 MS.gene60629:CDS 45.0%
AAACGATCAGGCAGGTGTAC+GGG - chr1.2:69700135-69700154 MS.gene60629:CDS 50.0%
CGGCATCACATACCATGGAA+CGG + chr1.2:69700174-69700193 None:intergenic 50.0%
CGTTCCATGGTATGTGATGC+CGG - chr1.2:69700172-69700191 MS.gene60629:CDS 50.0%
TCTCCGTCAGGGGGTAATAA+AGG + chr1.2:69699665-69699684 None:intergenic 50.0%
TGTGGCAATCCAGGGAATCT+TGG + chr1.2:69700266-69700285 None:intergenic 50.0%
! AACTCTAAGAAAGGGGCCGA+TGG - chr1.2:69699863-69699882 MS.gene60629:CDS 50.0%
! CGTGTTGACGTTTCGGATTC+CGG - chr1.2:69699704-69699723 MS.gene60629:CDS 50.0%
! GTGTTGACGTTTCGGATTCC+GGG - chr1.2:69699705-69699724 MS.gene60629:CDS 50.0%
ACCACCGGCATCACATACCA+TGG + chr1.2:69700179-69700198 None:intergenic 55.0%
TCCATGGTATGTGATGCCGG+TGG - chr1.2:69700175-69700194 MS.gene60629:CDS 55.0%
! ATCAGCTAGCTCTCCGTCAG+GGG + chr1.2:69699675-69699694 None:intergenic 55.0%
! CATCAGCTAGCTCTCCGTCA+GGG + chr1.2:69699676-69699695 None:intergenic 55.0%
! TGCGGCTCGTGTTGACGTTT+CGG - chr1.2:69699697-69699716 MS.gene60629:CDS 55.0%
CCTGACGGAGAGCTAGCTGA+TGG - chr1.2:69699674-69699693 MS.gene60629:CDS 60.0%
! CCATCAGCTAGCTCTCCGTC+AGG + chr1.2:69699677-69699696 None:intergenic 60.0%
! CGGAGAGCTAGCTGATGGTG+CGG - chr1.2:69699679-69699698 MS.gene60629:CDS 60.0%
! TCAGCTAGCTCTCCGTCAGG+GGG + chr1.2:69699674-69699693 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 69699629 69700318 69699629 ID=MS.gene60629
chr1.2 mRNA 69699629 69700318 69699629 ID=MS.gene60629.t1;Parent=MS.gene60629
chr1.2 exon 69699629 69700318 69699629 ID=MS.gene60629.t1.exon1;Parent=MS.gene60629.t1
chr1.2 CDS 69699629 69700318 69699629 ID=cds.MS.gene60629.t1;Parent=MS.gene60629.t1
Gene Sequence

>MS.gene60629

ATGGCTGATGGTCCTCCTATATTGATCGATCATCCTTTATTACCCCCTGACGGAGAGCTAGCTGATGGTGCGGCTCGTGTTGACGTTTCGGATTCCGGGACCTTTGAAACAACAAATGCTGTCGCAACAGATAAATTCACGCCTACTATCGGTATGTCTTTTAAATCGGTTGCAGATTGTAAGTCTTTTTACCGTGAATATGCCATGAAACAAGGGTTTGCAATCAAAACTAGAAACTCTAAGAAAGGGGCCGATGGCATGTTAAAATATTTCATTCTAACTTGTGCAAGAGAAGGTCACCATGAATCAAACATACCACCAACTTTGAAGACGAATCCAACGAAGAAACTTGATTGCTCAGCTAAGATAACGGTTGCTTTAAAGAAGGGTCTATGGACTATTTTGTCTTTTAATTCATGTCATAATCATGAGATAAGTCCAACTAAATCACGGTTGTTTGCTGGCAATAAGAAGATTGATATGCATGCACAGCGGACAATTTTGATAAACGATCAGGCAGGTGTACGGGTGAACAAAAGTTTCCGTTCCATGGTATGTGATGCCGGTGGTTACGAAAATCTAACATTTGTGGAGAGAGATGTACAAGACTACACAGCTGGACTCTTAGCATCTACCAAGATTCCCTGGATTGCCACAATTGTACAAATTGCACAGATAGCATGTGAATAA
Protein sequence

>MS.gene60629.t1

MADGPPILIDHPLLPPDGELADGAARVDVSDSGTFETTNAVATDKFTPTIGMSFKSVADCKSFYREYAMKQGFAIKTRNSKKGADGMLKYFILTCAREGHHESNIPPTLKTNPTKKLDCSAKITVALKKGLWTILSFNSCHNHEISPTKSRLFAGNKKIDMHAQRTILINDQAGVRVNKSFRSMVCDAGGYENLTFVERDVQDYTAGLLASTKIPWIATIVQIAQIACE