AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene02809

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02809.t1 MTR_2g014550 94.787 211 10 1 6 216 1 210 2.09e-148 411
MS.gene02809.t1 MTR_2g014520 84.541 207 32 0 10 216 1 207 2.83e-131 368
MS.gene02809.t1 MTR_4g088335 69.543 197 60 0 20 216 10 206 9.73e-106 303
MS.gene02809.t1 MTR_4g078870 52.356 191 89 2 25 214 14 203 2.64e-73 221
MS.gene02809.t1 MTR_5g044580 41.848 184 102 3 31 210 32 214 1.15e-46 154
MS.gene02809.t1 MTR_2g020850 41.420 169 96 1 47 215 23 188 1.72e-46 152
MS.gene02809.t1 MTR_7g010890 40.000 185 106 3 30 210 31 214 9.23e-44 146
MS.gene02809.t1 MTR_4g118470 40.314 191 100 3 29 215 18 198 4.54e-42 142
MS.gene02809.t1 MTR_4g118480 38.537 205 112 3 15 215 2 196 2.38e-40 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02809.t1 AT5G46090 60.748 214 77 3 6 214 1 212 1.18e-96 280
MS.gene02809.t1 AT4G18425 58.019 212 87 2 6 215 1 212 1.27e-90 265
MS.gene02809.t1 AT4G28485 48.731 197 99 2 20 214 2 198 2.04e-64 198
MS.gene02809.t1 AT3G02430 44.340 212 94 3 27 216 6 215 9.15e-63 194
MS.gene02809.t1 AT4G24310 48.438 192 92 3 28 214 18 207 1.95e-59 186
MS.gene02809.t1 AT3G21550 43.605 172 91 2 42 212 6 172 1.34e-43 144
MS.gene02809.t1 AT1G09157 36.957 184 104 1 39 210 56 239 2.99e-40 138
MS.gene02809.t1 AT5G39650 36.559 186 102 2 39 210 57 240 1.63e-39 136
MS.gene02809.t1 AT3G21520 40.000 160 89 2 54 211 33 187 1.94e-37 129
MS.gene02809.t1 AT4G28485 54.545 99 45 0 116 214 65 163 5.85e-32 114
MS.gene02809.t1 AT5G27370 36.932 176 96 4 50 210 11 186 1.31e-30 111

Find 47 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAGGCTCCTCTCAGCTTC+TGG 0.270180 2.3:+60758863 None:intergenic
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.3:-60758632 MS.gene02809:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.3:-60758631 MS.gene02809:CDS
AAGGGCATGTGGGTTATTGA+TGG 0.393194 2.3:-60758596 MS.gene02809:CDS
ATTTCAGAGCACCGGACATT+TGG 0.394083 2.3:-60758819 MS.gene02809:CDS
TTATGGGTTTGCCACCTTCA+AGG 0.406503 2.3:-60758615 MS.gene02809:CDS
TGCAACTTGAGGTGGAAGTT+TGG 0.409649 2.3:+60758568 None:intergenic
CAATTATTAACTTGTTGAAA+GGG 0.415154 2.3:+60758325 None:intergenic
ATGGCGATGCCTGTGGCAAT+TGG 0.419997 2.3:-60758407 MS.gene02809:CDS
TATGGGTTTGCCACCTTCAA+GGG 0.422703 2.3:-60758614 MS.gene02809:CDS
CCTACTGAGAGACATGGAAT+AGG 0.427667 2.3:-60758353 MS.gene02809:CDS
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.3:+60758846 None:intergenic
GCATGCGGTGATGTCAATTC+TGG 0.434994 2.3:-60758513 MS.gene02809:CDS
AGAACCATCAAAAGAGATAC+AGG 0.448641 2.3:-60758438 MS.gene02809:CDS
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.3:+60758792 None:intergenic
TCAATTATTAACTTGTTGAA+AGG 0.463534 2.3:+60758324 None:intergenic
TGCTATCAGTAAAGTTTAGC+AGG 0.467137 2.3:+60758663 None:intergenic
TTGCCACCTTCAAGGGCATG+TGG 0.474826 2.3:-60758607 MS.gene02809:CDS
TAAGAATAACGATGAACAAA+AGG 0.479910 2.3:-60758912 MS.gene02809:CDS
AATAACCCACATGCCCTTGA+AGG 0.501829 2.3:+60758601 None:intergenic
TAGAAGGTTTGCCAAATGTC+CGG 0.511649 2.3:+60758808 None:intergenic
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.3:-60758800 MS.gene02809:CDS
CTGGAACATCCGCATTCCGC+AGG 0.537897 2.3:+60758882 None:intergenic
TCTGTACTTGTGTCTCTATG+TGG 0.542497 2.3:-60758698 MS.gene02809:CDS
AATTATTAACTTGTTGAAAG+GGG 0.546060 2.3:+60758326 None:intergenic
AGACACAAGTACAGAAGTCA+TGG 0.561323 2.3:+60758706 None:intergenic
TCCAGAAGCTGAGAGGAGCC+TGG 0.563140 2.3:-60758864 MS.gene02809:CDS
CCTATTCCATGTCTCTCAGT+AGG 0.565915 2.3:+60758353 None:intergenic
TGCCACCTTCAAGGGCATGT+GGG 0.570413 2.3:-60758606 MS.gene02809:CDS
AGTTCGACATTTCAGAGCAC+CGG 0.577759 2.3:-60758827 MS.gene02809:CDS
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.3:-60758648 MS.gene02809:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.3:-60758528 MS.gene02809:CDS
AGAGATACAGGAAATTCTCA+TGG 0.587742 2.3:-60758426 MS.gene02809:CDS
ATTATTAACTTGTTGAAAGG+GGG 0.590301 2.3:+60758327 None:intergenic
AATTCTCATGGCGATGCCTG+TGG 0.604206 2.3:-60758414 MS.gene02809:CDS
AACCCACATGCCCTTGAAGG+TGG 0.607741 2.3:+60758604 None:intergenic
AACAAAAGGTTCCACTCCTG+CGG 0.611057 2.3:-60758898 MS.gene02809:CDS
ACATCCGCATTCCGCAGGAG+TGG 0.617607 2.3:+60758887 None:intergenic
GGTTCCACTCCTGCGGAATG+CGG 0.617826 2.3:-60758891 MS.gene02809:CDS
AAAGGAGGTTGTATACGCGA+TGG 0.625075 2.3:-60758963 None:intergenic
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.3:-60758477 MS.gene02809:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.3:-60758647 MS.gene02809:CDS
GCATTTCCTACTGAGAGACA+TGG 0.643869 2.3:-60758359 MS.gene02809:CDS
CGGATGTTCCAGAAGCTGAG+AGG 0.669051 2.3:-60758871 MS.gene02809:CDS
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.3:+60758785 None:intergenic
TATCAGTAAAGTTTAGCAGG+AGG 0.692885 2.3:+60758666 None:intergenic
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.3:-60758646 MS.gene02809:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAGAATAACGATGAACAAA+AGG - chr2.3:60758378-60758397 MS.gene02809:CDS 25.0%
! TTGCCAACATTTGTAAAAAT+CGG + chr2.3:60758544-60758563 None:intergenic 25.0%
GTTTATAGATTTCATGCATG+CGG - chr2.3:60758762-60758781 MS.gene02809:CDS 30.0%
TAAAAATCGGTGACAAAAGT+TGG + chr2.3:60758531-60758550 None:intergenic 30.0%
! ATTTCCTGTATCTCTTTTGA+TGG + chr2.3:60758859-60758878 None:intergenic 30.0%
!!! TCACCGATTTTTACAAATGT+TGG - chr2.3:60758538-60758557 MS.gene02809:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG + chr2.3:60758447-60758466 None:intergenic 35.0%
AGAACCATCAAAAGAGATAC+AGG - chr2.3:60758852-60758871 MS.gene02809:CDS 35.0%
AGAGATACAGGAAATTCTCA+TGG - chr2.3:60758864-60758883 MS.gene02809:CDS 35.0%
TATCAGTAAAGTTTAGCAGG+AGG + chr2.3:60758627-60758646 None:intergenic 35.0%
TGCATTGTTTGATCAGAATG+TGG - chr2.3:60758813-60758832 MS.gene02809:CDS 35.0%
TGCTATCAGTAAAGTTTAGC+AGG + chr2.3:60758630-60758649 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG - chr2.3:60758658-60758677 MS.gene02809:CDS 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG - chr2.3:60758659-60758678 MS.gene02809:CDS 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG + chr2.3:60758853-60758872 None:intergenic 35.0%
AGACACAAGTACAGAAGTCA+TGG + chr2.3:60758587-60758606 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG - chr2.3:60758644-60758663 MS.gene02809:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG - chr2.3:60758643-60758662 MS.gene02809:CDS 40.0%
TAGAAGGTTTGCCAAATGTC+CGG + chr2.3:60758485-60758504 None:intergenic 40.0%
TCTGTACTTGTGTCTCTATG+TGG - chr2.3:60758592-60758611 MS.gene02809:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG - chr2.3:60758642-60758661 MS.gene02809:CDS 40.0%
! CGATATTTTGCTGCAACTTG+AGG + chr2.3:60758736-60758755 None:intergenic 40.0%
! TATTTTGCTGCAACTTGAGG+TGG + chr2.3:60758733-60758752 None:intergenic 40.0%
AACAAAAGGTTCCACTCCTG+CGG - chr2.3:60758392-60758411 MS.gene02809:CDS 45.0%
AATAACCCACATGCCCTTGA+AGG + chr2.3:60758692-60758711 None:intergenic 45.0%
AATGCAAGAACAGTGCCTGT+AGG + chr2.3:60758508-60758527 None:intergenic 45.0%
AGTTCGACATTTCAGAGCAC+CGG - chr2.3:60758463-60758482 MS.gene02809:CDS 45.0%
CAAAAAACGCCAATTGCCAC+AGG + chr2.3:60758895-60758914 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+AGG - chr2.3:60758937-60758956 MS.gene02809:CDS 45.0%
CCTATTCCATGTCTCTCAGT+AGG + chr2.3:60758940-60758959 None:intergenic 45.0%
GCATTTCCTACTGAGAGACA+TGG - chr2.3:60758931-60758950 MS.gene02809:CDS 45.0%
TATGGGTTTGCCACCTTCAA+GGG - chr2.3:60758676-60758695 MS.gene02809:CDS 45.0%
TGCAACTTGAGGTGGAAGTT+TGG + chr2.3:60758725-60758744 None:intergenic 45.0%
TTATGGGTTTGCCACCTTCA+AGG - chr2.3:60758675-60758694 MS.gene02809:CDS 45.0%
TTGGCAAACCTTCTACCTAC+AGG - chr2.3:60758490-60758509 MS.gene02809:CDS 45.0%
! AAGGGCATGTGGGTTATTGA+TGG - chr2.3:60758694-60758713 MS.gene02809:CDS 45.0%
!! ATTTCAGAGCACCGGACATT+TGG - chr2.3:60758471-60758490 MS.gene02809:CDS 45.0%
AATTCTCATGGCGATGCCTG+TGG - chr2.3:60758876-60758895 MS.gene02809:CDS 50.0%
GAACAGTGCCTGTAGGTAGA+AGG + chr2.3:60758501-60758520 None:intergenic 50.0%
GCATGCGGTGATGTCAATTC+TGG - chr2.3:60758777-60758796 MS.gene02809:CDS 50.0%
AACCCACATGCCCTTGAAGG+TGG + chr2.3:60758689-60758708 None:intergenic 55.0%
ATGGCGATGCCTGTGGCAAT+TGG - chr2.3:60758883-60758902 MS.gene02809:CDS 55.0%
CGGATGTTCCAGAAGCTGAG+AGG - chr2.3:60758419-60758438 MS.gene02809:CDS 55.0%
! TGCCACCTTCAAGGGCATGT+GGG - chr2.3:60758684-60758703 MS.gene02809:CDS 55.0%
! TTGCCACCTTCAAGGGCATG+TGG - chr2.3:60758683-60758702 MS.gene02809:CDS 55.0%
ACATCCGCATTCCGCAGGAG+TGG + chr2.3:60758406-60758425 None:intergenic 60.0%
ACCAGGCTCCTCTCAGCTTC+TGG + chr2.3:60758430-60758449 None:intergenic 60.0%
CTGGAACATCCGCATTCCGC+AGG + chr2.3:60758411-60758430 None:intergenic 60.0%
GGTTCCACTCCTGCGGAATG+CGG - chr2.3:60758399-60758418 MS.gene02809:CDS 60.0%
TCCAGAAGCTGAGAGGAGCC+TGG - chr2.3:60758426-60758445 MS.gene02809:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 60758331 60758981 60758331 ID=MS.gene02809
chr2.3 mRNA 60758331 60758981 60758331 ID=MS.gene02809.t1;Parent=MS.gene02809
chr2.3 exon 60758331 60758981 60758331 ID=MS.gene02809.t1.exon1;Parent=MS.gene02809.t1
chr2.3 CDS 60758331 60758981 60758331 ID=cds.MS.gene02809.t1;Parent=MS.gene02809.t1
Gene Sequence

>MS.gene02809

GAGGTTGTATACGCGATGGACATCAATTTAGAAATCGACGATGACTCTAAGAATAACGATGAACAAAAGGTTCCACTCCTGCGGAATGCGGATGTTCCAGAAGCTGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGCACCGGACATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCGATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGTCTCTATGTGGTGCATCATGCCTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAGGGCATGTGGGTTATTGATGGATCAACCAAACTTCCACCTCAAGTTGCAGCAAAATATCGCATAAAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTGGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGTTTTTTTCCAGAACCATCAAAAGAGATACAGGAAATTCTCATGGCGATGCCTGTGGCAATTGGCGTTTTTTGCAGCATGATTTTCGTTGCATTTCCTACTGAGAGACATGGAATAGGCTTCCCCCTTTCAACAAGTTAA
Protein sequence

>MS.gene02809.t1

EVVYAMDINLEIDDDSKNNDEQKVPLLRNADVPEAERSLVQKAISSTFQSTGHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVSLCGASCLLLNFTDSIRDSKGNICYGFATFKGMWVIDGSTKLPPQVAAKYRIKFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILMAMPVAIGVFCSMIFVAFPTERHGIGFPLSTS