AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00511

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00511.t1 MTR_1g017950 99.487 195 1 0 1 195 1 195 4.05e-146 404
MS.gene00511.t1 MTR_4g106800 66.857 175 57 1 2 176 3 176 1.70e-87 255
MS.gene00511.t1 MTR_3g070050 58.757 177 69 2 1 175 1 175 3.02e-70 212
MS.gene00511.t1 MTR_8g031490 50.820 183 83 3 1 182 1 177 2.64e-61 189
MS.gene00511.t1 MTR_8g097300 54.802 177 68 4 1 175 1 167 9.79e-61 188
MS.gene00511.t1 MTR_7g076720 50.857 175 82 2 1 175 1 171 3.28e-60 187
MS.gene00511.t1 MTR_3g070050 53.731 134 58 2 44 175 2 133 3.89e-45 146
MS.gene00511.t1 MTR_3g070050 47.826 69 36 0 3 71 61 129 1.42e-18 78.6
MS.gene00511.t1 MTR_1g106100 58.559 111 40 2 59 168 20 125 6.39e-38 128
MS.gene00511.t1 MTR_3g070033 66.038 53 18 0 123 175 6 58 3.58e-18 75.5
MS.gene00511.t1 MTR_3g070033 46.939 49 26 0 23 71 6 54 6.90e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00511.t1 AT1G10200 85.246 183 27 0 1 183 1 183 2.62e-116 328
MS.gene00511.t1 AT1G10200 82.014 139 25 0 45 183 3 141 2.77e-82 241
MS.gene00511.t1 AT1G10200 44.444 72 40 0 3 74 61 132 2.24e-16 72.8
MS.gene00511.t1 AT2G39900 58.192 177 69 2 1 175 1 174 2.13e-69 210
MS.gene00511.t1 AT3G55770 55.307 179 70 2 1 175 1 173 2.52e-67 205
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.85e-16 73.2
MS.gene00511.t1 AT3G55770 55.307 179 70 2 1 175 1 173 2.52e-67 205
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.85e-16 73.2
MS.gene00511.t1 AT3G55770 55.307 179 70 2 1 175 1 173 2.52e-67 205
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.85e-16 73.2
MS.gene00511.t1 AT3G55770 55.307 179 70 2 1 175 1 173 2.52e-67 205
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.85e-16 73.2
MS.gene00511.t1 AT2G45800 50.000 186 86 2 1 183 1 182 3.75e-61 190
MS.gene00511.t1 AT1G01780 48.649 185 87 3 1 183 1 179 2.17e-60 187
MS.gene00511.t1 AT3G61230 47.917 192 93 3 2 190 3 190 8.55e-60 186
MS.gene00511.t1 AT3G61230 36.792 106 67 0 3 108 100 205 3.58e-17 76.6
MS.gene00511.t1 AT3G55770 46.479 213 70 3 1 175 1 207 1.60e-59 186
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 1.44e-15 72.8
MS.gene00511.t1 AT3G55770 48.201 139 61 3 1 135 1 132 2.16e-40 134
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.56e-17 74.3
MS.gene00511.t1 AT2G45800 45.455 154 76 3 34 184 4 152 4.96e-39 132
MS.gene00511.t1 AT2G45800 50.725 69 34 0 3 71 68 136 1.35e-16 74.7
MS.gene00511.t1 AT3G55770 48.462 130 57 2 1 126 1 124 1.92e-38 129
MS.gene00511.t1 AT3G55770 43.678 87 49 0 103 189 3 89 5.92e-17 73.9

Find 37 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATTATCTATATTTCTTTC+TGG 0.117591 1.2:-5152687 None:intergenic
TCCCTCATGTGCTATGTAAT+TGG 0.275186 1.2:-5153247 None:intergenic
AGCATTTGAAACAACTCTTA+TGG 0.319973 1.2:-5153197 None:intergenic
TTTATAAAGGTTACAGTGAA+TGG 0.352930 1.2:+5153165 MS.gene00511:intron
TTTGCTTGATCAGTTGAATA+TGG 0.353364 1.2:-5153290 None:intergenic
GATCAACTGTTCAAAAGAAC+TGG 0.398776 1.2:+5152523 MS.gene00511:CDS
AGGAAAAGAATGGCATTTGC+AGG 0.400538 1.2:+5151918 None:intergenic
CTTGAGGCTTTAGCTGCTGC+AGG 0.425078 1.2:-5152805 None:intergenic
TATTCAACTGATCAAGCAAA+AGG 0.432443 1.2:+5153293 MS.gene00511:CDS
GCTAAAGCCTCAAGTATGTT+TGG 0.441559 1.2:+5152814 MS.gene00511:CDS
ACACTAATTACCTTCTCTGT+TGG 0.465114 1.2:-5152880 None:intergenic
GGAAATTTGAGCCAGCTTGA+AGG 0.475377 1.2:+5153315 MS.gene00511:CDS
GGAACAAGGGACAAATGTTC+TGG 0.477611 1.2:+5152838 MS.gene00511:CDS
TCTCATGGTCACCTTCAAGC+TGG 0.480325 1.2:-5153326 None:intergenic
CAAGTATGTTTGGTGGAACA+AGG 0.495604 1.2:+5152824 MS.gene00511:CDS
TTGAAACAACTCTTATGGTA+AGG 0.498185 1.2:-5153192 None:intergenic
AGAAAGAAATATAGATAATG+AGG 0.518674 1.2:+5152689 MS.gene00511:CDS
CCTTGAGGGTTCCTTTGCAG+TGG 0.520760 1.2:-5152040 None:intergenic
GAGAGAGACATAGACCTTGA+GGG 0.525903 1.2:-5152054 None:intergenic
GACTAATAGTACACCCTCCA+TGG 0.536605 1.2:-5153221 None:intergenic
AGGAACAACTCAGAAGTGTA+TGG 0.560932 1.2:+5151938 MS.gene00511:CDS
ATTCAACTGATCAAGCAAAA+GGG 0.562604 1.2:+5153294 MS.gene00511:CDS
AGTTGTTTCAAATGCTGCCA+TGG 0.564010 1.2:+5153204 MS.gene00511:CDS
GACATCTGAAACAAGCTTTG+TGG 0.565667 1.2:-5152016 None:intergenic
TTCCAATTACATAGCACATG+AGG 0.574672 1.2:+5153245 MS.gene00511:CDS
TTCAGATGTCACCACTGCAA+AGG 0.582786 1.2:+5152029 MS.gene00511:CDS
GCTTGATCAGTTGAATATGG+TGG 0.582930 1.2:-5153287 None:intergenic
AAAGCCTCAAGTATGTTTGG+TGG 0.587944 1.2:+5152817 MS.gene00511:CDS
GTTTCAAATGCTGCCATGGA+GGG 0.597804 1.2:+5153208 MS.gene00511:CDS
TTGAACAGTTGATCAAAGTG+TGG 0.606620 1.2:-5152514 None:intergenic
TGTTCCACCAAACATACTTG+AGG 0.606764 1.2:-5152821 None:intergenic
AACAGTGTATCCAACAGAGA+AGG 0.613878 1.2:+5152870 MS.gene00511:CDS
TCCAATTACATAGCACATGA+GGG 0.619052 1.2:+5153246 MS.gene00511:CDS
TCATGTGCTATGTAATTGGA+AGG 0.623562 1.2:-5153243 None:intergenic
AAGTATGTTTGGTGGAACAA+GGG 0.641097 1.2:+5152825 MS.gene00511:CDS
CCACTGCAAAGGAACCCTCA+AGG 0.664342 1.2:+5152040 MS.gene00511:CDS
TGTTTCAAATGCTGCCATGG+AGG 0.668776 1.2:+5153207 MS.gene00511:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACTCAAAAATAATTTTGTT+CGG - chr1.2:5153030-5153049 None:intergenic 15.0%
!!! TCAATAATTTGCATTTATAA+AGG + chr1.2:5153152-5153171 MS.gene00511:intron 15.0%
!! AGAAAGAAATATAGATAATG+AGG + chr1.2:5152689-5152708 MS.gene00511:CDS 20.0%
!! GTTCATTAACATGAAAATTA+CGG - chr1.2:5152356-5152375 None:intergenic 20.0%
!! TCATTATCTATATTTCTTTC+TGG - chr1.2:5152690-5152709 None:intergenic 20.0%
! AAACAGCTCAAAAAATCATA+TGG - chr1.2:5152775-5152794 None:intergenic 25.0%
! AATGAACTTCTTTCATCATT+TGG + chr1.2:5152369-5152388 MS.gene00511:intron 25.0%
! AGGTAATGAATTCTAAATCT+AGG + chr1.2:5152709-5152728 MS.gene00511:intron 25.0%
! AGGTAATTAGTGTATATGTT+TGG + chr1.2:5152890-5152909 MS.gene00511:intron 25.0%
! CATAGCTTAAGTAAAAACTA+TGG + chr1.2:5152242-5152261 MS.gene00511:intron 25.0%
! GAAAATTGTTACTGCATATT+TGG - chr1.2:5152295-5152314 None:intergenic 25.0%
! TTAGTACATGTTTCAATAGA+CGG + chr1.2:5152169-5152188 MS.gene00511:intron 25.0%
! TTTATAAAGGTTACAGTGAA+TGG + chr1.2:5153165-5153184 MS.gene00511:intron 25.0%
!! AAGCAATTACAATTCTTTTG+AGG + chr1.2:5152474-5152493 MS.gene00511:CDS 25.0%
!! AGCAATTACAATTCTTTTGA+GGG + chr1.2:5152475-5152494 MS.gene00511:CDS 25.0%
!! AGTGTATATGTTTGGAATTA+CGG + chr1.2:5152898-5152917 MS.gene00511:intron 25.0%
!!! AAGTTTTGTATTCAACATCA+GGG - chr1.2:5153114-5153133 None:intergenic 25.0%
!!! TAAGTTTTGTATTCAACATC+AGG - chr1.2:5153115-5153134 None:intergenic 25.0%
!!! TGTAGCTTTTTCTAAAATCA+TGG + chr1.2:5152971-5152990 MS.gene00511:intron 25.0%
!!! TTTTGAGTTTGTGATTAGTT+TGG + chr1.2:5153041-5153060 MS.gene00511:intron 25.0%
AAAAATGCTGGGAAAATCAA+TGG + chr1.2:5153348-5153367 MS.gene00511:CDS 30.0%
ACCAAAAAGAAATGTCTAAG+AGG - chr1.2:5152084-5152103 None:intergenic 30.0%
ATTCAACTGATCAAGCAAAA+GGG + chr1.2:5153294-5153313 MS.gene00511:CDS 30.0%
CATTAACATGAAAATTACGG+TGG - chr1.2:5152353-5152372 None:intergenic 30.0%
TATTCAACTGATCAAGCAAA+AGG + chr1.2:5153293-5153312 MS.gene00511:CDS 30.0%
TGAAAATGCTTATGAACAAC+TGG - chr1.2:5152323-5152342 None:intergenic 30.0%
TTACTGCATATTTGGATTCA+CGG - chr1.2:5152287-5152306 None:intergenic 30.0%
TTGAAACAACTCTTATGGTA+AGG - chr1.2:5153195-5153214 None:intergenic 30.0%
TTTGCTTGATCAGTTGAATA+TGG - chr1.2:5153293-5153312 None:intergenic 30.0%
! ACCTCTTAGACATTTCTTTT+TGG + chr1.2:5152080-5152099 MS.gene00511:intron 30.0%
! AGCATTTGAAACAACTCTTA+TGG - chr1.2:5153200-5153219 None:intergenic 30.0%
! TTCTTTCATCATTTGGCTTA+TGG + chr1.2:5152376-5152395 MS.gene00511:intron 30.0%
!! AAAGCTTTGAAGGTAAACAA+AGG + chr1.2:5152557-5152576 MS.gene00511:intron 30.0%
!!! ACTTTTGTTTTGCATACCTA+GGG + chr1.2:5152646-5152665 MS.gene00511:intron 30.0%
!!! AGCTTTTTCTAAAATCATGG+TGG + chr1.2:5152974-5152993 MS.gene00511:intron 30.0%
!!! CTTTCTGGTTTGACAATTTT+TGG - chr1.2:5152675-5152694 None:intergenic 30.0%
!!! TACCTTCAAAGCTTTTTTCA+AGG - chr1.2:5152552-5152571 None:intergenic 30.0%
!!! TACTTTTGTTTTGCATACCT+AGG + chr1.2:5152645-5152664 MS.gene00511:intron 30.0%
ACACTAATTACCTTCTCTGT+TGG - chr1.2:5152883-5152902 None:intergenic 35.0%
CTAACAGATCCAATACTAGA+AGG - chr1.2:5152132-5152151 None:intergenic 35.0%
GATCAACTGTTCAAAAGAAC+TGG + chr1.2:5152523-5152542 MS.gene00511:CDS 35.0%
TCATGTGCTATGTAATTGGA+AGG - chr1.2:5153246-5153265 None:intergenic 35.0%
TCCAATTACATAGCACATGA+GGG + chr1.2:5153246-5153265 MS.gene00511:CDS 35.0%
TTCCAATTACATAGCACATG+AGG + chr1.2:5153245-5153264 MS.gene00511:CDS 35.0%
TTGAACAGTTGATCAAAGTG+TGG - chr1.2:5152517-5152536 None:intergenic 35.0%
! AAGTATGTTTGGTGGAACAA+GGG + chr1.2:5152825-5152844 MS.gene00511:CDS 35.0%
! AGCCTTGAAAAAAGCTTTGA+AGG + chr1.2:5152547-5152566 MS.gene00511:CDS 35.0%
! CTAGTTTAGCCTTCTAGTAT+TGG + chr1.2:5152120-5152139 MS.gene00511:intron 35.0%
! TTTCATCATTTGGCTTATGG+AGG + chr1.2:5152379-5152398 MS.gene00511:intron 35.0%
! TTTTCCCAGCATTTTTCTCA+TGG - chr1.2:5153344-5153363 None:intergenic 35.0%
!! CGGCTAGTTTAACAATATCA+CGG + chr1.2:5152918-5152937 MS.gene00511:intron 35.0%
AAAGCCTCAAGTATGTTTGG+TGG + chr1.2:5152817-5152836 MS.gene00511:CDS 40.0%
AACAGTGTATCCAACAGAGA+AGG + chr1.2:5152870-5152889 MS.gene00511:CDS 40.0%
GCTAAAGCCTCAAGTATGTT+TGG + chr1.2:5152814-5152833 MS.gene00511:CDS 40.0%
GCTTGATCAGTTGAATATGG+TGG - chr1.2:5153290-5153309 None:intergenic 40.0%
GTGACCATGAGAAAAATGCT+GGG + chr1.2:5153337-5153356 MS.gene00511:CDS 40.0%
GTTCGGATTTGTGATGAGTT+TGG - chr1.2:5153013-5153032 None:intergenic 40.0%
TCCCTCATGTGCTATGTAAT+TGG - chr1.2:5153250-5153269 None:intergenic 40.0%
TGCAACTTTCGCCAAAATCA+CGG - chr1.2:5153085-5153104 None:intergenic 40.0%
TGTTCCACCAAACATACTTG+AGG - chr1.2:5152824-5152843 None:intergenic 40.0%
! AGGAACAACTCAGAAGTGTA+TGG + chr1.2:5151938-5151957 MS.gene00511:CDS 40.0%
! AGTTGTTTCAAATGCTGCCA+TGG + chr1.2:5153204-5153223 MS.gene00511:CDS 40.0%
! CAAGTATGTTTGGTGGAACA+AGG + chr1.2:5152824-5152843 MS.gene00511:CDS 40.0%
! GACATCTGAAACAAGCTTTG+TGG - chr1.2:5152019-5152038 None:intergenic 40.0%
!!! TGACAATTTTTGGTGTCCCT+AGG - chr1.2:5152665-5152684 None:intergenic 40.0%
GACTAATAGTACACCCTCCA+TGG - chr1.2:5153224-5153243 None:intergenic 45.0%
GAGAGAGACATAGACCTTGA+GGG - chr1.2:5152057-5152076 None:intergenic 45.0%
GATGAGTTTGGCAGAATCTG+TGG - chr1.2:5153001-5153020 None:intergenic 45.0%
GGAAATTTGAGCCAGCTTGA+AGG + chr1.2:5153315-5153334 MS.gene00511:CDS 45.0%
GGAACAAGGGACAAATGTTC+TGG + chr1.2:5152838-5152857 MS.gene00511:CDS 45.0%
GGTGACCATGAGAAAAATGC+TGG + chr1.2:5153336-5153355 MS.gene00511:CDS 45.0%
GTTTCAAATGCTGCCATGGA+GGG + chr1.2:5153208-5153227 MS.gene00511:CDS 45.0%
TGAGAGAGACATAGACCTTG+AGG - chr1.2:5152058-5152077 None:intergenic 45.0%
TGTTTCAAATGCTGCCATGG+AGG + chr1.2:5153207-5153226 MS.gene00511:CDS 45.0%
TTCAGATGTCACCACTGCAA+AGG + chr1.2:5152029-5152048 MS.gene00511:CDS 45.0%
! TCATTGTGCGACCGTGATTT+TGG + chr1.2:5153071-5153090 MS.gene00511:intron 45.0%
TCTCATGGTCACCTTCAAGC+TGG - chr1.2:5153329-5153348 None:intergenic 50.0%
CCACTGCAAAGGAACCCTCA+AGG + chr1.2:5152040-5152059 MS.gene00511:CDS 55.0%
CCTTGAGGGTTCCTTTGCAG+TGG - chr1.2:5152043-5152062 None:intergenic 55.0%
! CTTGAGGCTTTAGCTGCTGC+AGG - chr1.2:5152808-5152827 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 5151927 5153395 5151927 ID=MS.gene00511
chr1.2 mRNA 5151927 5153395 5151927 ID=MS.gene00511.t1;Parent=MS.gene00511
chr1.2 exon 5151927 5152061 5151927 ID=MS.gene00511.t1.exon1;Parent=MS.gene00511.t1
chr1.2 CDS 5151927 5152061 5151927 ID=cds.MS.gene00511.t1;Parent=MS.gene00511.t1
chr1.2 exon 5152472 5152568 5152472 ID=MS.gene00511.t1.exon2;Parent=MS.gene00511.t1
chr1.2 CDS 5152472 5152568 5152472 ID=cds.MS.gene00511.t1;Parent=MS.gene00511.t1
chr1.2 exon 5152667 5152710 5152667 ID=MS.gene00511.t1.exon3;Parent=MS.gene00511.t1
chr1.2 CDS 5152667 5152710 5152667 ID=cds.MS.gene00511.t1;Parent=MS.gene00511.t1
chr1.2 exon 5152802 5152891 5152802 ID=MS.gene00511.t1.exon4;Parent=MS.gene00511.t1
chr1.2 CDS 5152802 5152891 5152802 ID=cds.MS.gene00511.t1;Parent=MS.gene00511.t1
chr1.2 exon 5153174 5153395 5153174 ID=MS.gene00511.t1.exon5;Parent=MS.gene00511.t1
chr1.2 CDS 5153174 5153395 5153174 ID=cds.MS.gene00511.t1;Parent=MS.gene00511.t1
Gene Sequence

>MS.gene00511

ATGGCATTTGCAGGAACAACTCAGAAGTGTATGGCTTGTAGCAAAACAGTTTATCTTGTTGATAAGTTAACTGCTGATAATAGAATTTTCCACAAAGCTTGTTTCAGATGTCACCACTGCAAAGGAACCCTCAAGGTCTATGTCTCTCTCATAACCTCTTAGACATTTCTTTTTGGTCTTATATATATAGTCTCTAGTTTAGCCTTCTAGTATTGGATCTGTTAGAATCATAATCATCAAATTTAGTACATGTTTCAATAGACGGTGAGTTTAGCGAAATGACAATAACACTGTAATTTTATTGAAGCTACAAAGCATAGCTTAAGTAAAAACTATGGTAGCACACAATGAAAATCGCCGTGAATCCAAATATGCAGTAACAATTTTCTTTAACCAGTTGTTCATAAGCATTTTCATCTCAGACCACCGTAATTTTCATGTTAATGAACTTCTTTCATCATTTGGCTTATGGAGGTATGTTGTTACTACATTGAAATAATTTTCATATACAAGTTTGCTGATAGATTAACGTATATACAATTCAGCTAAGCAATTACAATTCTTTTGAGGGAGTTCTTTACTGCAGACCACACTTTGATCAACTGTTCAAAAGAACTGGTAGCCTTGAAAAAAGCTTTGAAGGTAAACAAAGGATACATAATTGAATTTGTTAATTAAATGTCAACACAGTACTTTTTTCTTGTCAGTGTCTCAATTGTACTTTTGTTTTGCATACCTAGGGACACCAAAAATTGTCAAACCAGAAAGAAATATAGATAATGAGGTAATGAATTCTAAATCTAGGTGTTTACAATTCACAGTAGTAAATTCATGTTTTCAGCATTCCATATGATTTTTTGAGCTGTTTTAATCAGAAACCTGCAGCAGCTAAAGCCTCAAGTATGTTTGGTGGAACAAGGGACAAATGTTCTGGTTGTCAGAAAACAGTGTATCCAACAGAGAAGGTAATTAGTGTATATGTTTGGAATTACGGCTAGTTTAACAATATCACGGTGACACTGTAATTTTGTTGTAATTCTAAAGTGTAGCTTTTTCTAAAATCATGGTGGACCACAGATTCTGCCAAACTCATCACAAATCCGAACAAAATTATTTTTGAGTTTGTGATTAGTTTGGCAAAATCTCATTGTGCGACCGTGATTTTGGCGAAAGTTGCATCTAAACCCTGATGTTGAATACAAAACTTATTGTTCTACTAATGAAATCAATAATTTGCATTTATAAAGGTTACAGTGAATGGAACTCCTTACCATAAGAGTTGTTTCAAATGCTGCCATGGAGGGTGTACTATTAGTCCTTCCAATTACATAGCACATGAGGGAAAACTCTACTGCAAACACCACCATATTCAACTGATCAAGCAAAAGGGAAATTTGAGCCAGCTTGAAGGTGACCATGAGAAAAATGCTGGGAAAATCAATGGCGAAGAAGTTGCAGCTGAAACTTGA
Protein sequence

>MS.gene00511.t1

MAFAGTTQKCMACSKTVYLVDKLTADNRIFHKACFRCHHCKGTLKLSNYNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPERNIDNEKPAAAKASSMFGGTRDKCSGCQKTVYPTEKVTVNGTPYHKSCFKCCHGGCTISPSNYIAHEGKLYCKHHHIQLIKQKGNLSQLEGDHEKNAGKINGEEVAAET