AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048891

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048891.t1 MTR_8g099115 98.413 189 3 0 1 189 1 189 1.42e-139 387
MS.gene048891.t1 MTR_8g099135 63.830 188 62 2 2 189 4 185 1.19e-88 258
MS.gene048891.t1 MTR_4g073950 34.351 131 78 3 39 168 48 171 1.25e-17 77.0
MS.gene048891.t1 MTR_4g013335 33.835 133 77 3 41 172 57 179 3.06e-17 76.3
MS.gene048891.t1 MTR_4g122110 31.818 154 92 5 34 185 31 173 5.05e-17 75.1
MS.gene048891.t1 MTR_4g013320 33.835 133 79 3 41 172 58 182 6.74e-17 75.5
MS.gene048891.t1 MTR_4g013330 37.984 129 73 4 41 168 56 178 1.20e-16 74.7
MS.gene048891.t1 MTR_4g013310 32.353 136 81 4 41 174 58 184 4.29e-16 73.2
MS.gene048891.t1 MTR_3g034030 30.412 194 116 7 1 186 1 183 5.52e-16 72.8
MS.gene048891.t1 MTR_4g013325 33.835 133 79 3 41 172 58 182 1.11e-15 72.0
MS.gene048891.t1 MTR_1g054525 31.792 173 100 6 6 170 13 175 1.39e-15 71.6
MS.gene048891.t1 MTR_4g013350 33.333 129 77 3 41 168 56 176 3.73e-15 70.5
MS.gene048891.t1 MTR_4g122130 27.586 174 109 5 1 172 5 163 7.19e-15 69.7
MS.gene048891.t1 MTR_1g056370 30.994 171 99 6 8 168 4 165 1.51e-14 68.9
MS.gene048891.t1 MTR_4g013345 33.333 129 77 3 41 168 55 175 1.88e-14 68.6
MS.gene048891.t1 MTR_4g078885 29.897 194 117 7 1 186 1 183 2.05e-14 68.6
MS.gene048891.t1 MTR_4g049550 31.944 144 89 3 30 172 26 161 1.32e-13 66.2
MS.gene048891.t1 MTR_7g070390 29.932 147 73 4 39 174 50 177 3.43e-12 62.4
MS.gene048891.t1 MTR_7g093790 28.902 173 90 8 6 164 13 166 7.98e-12 61.6
MS.gene048891.t1 MTR_7g093870 32.540 126 75 5 41 162 47 166 1.07e-11 61.6
MS.gene048891.t1 MTR_4g013770 33.333 135 78 4 41 172 49 174 2.70e-11 60.1
MS.gene048891.t1 MTR_3g105640 30.178 169 108 5 7 172 10 171 3.82e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048891.t1 AT4G23690 54.878 164 66 2 27 189 31 187 3.90e-62 191
MS.gene048891.t1 AT1G64160 50.581 172 72 3 19 189 23 182 2.06e-61 189
MS.gene048891.t1 AT4G11210 45.652 184 91 3 8 189 7 183 4.41e-56 175
MS.gene048891.t1 AT4G11190 44.565 184 94 2 7 189 7 183 1.92e-54 171
MS.gene048891.t1 AT4G11180 42.391 184 97 3 8 189 9 185 1.70e-44 146
MS.gene048891.t1 AT1G22900 32.484 157 95 4 11 164 23 171 2.83e-18 79.0
MS.gene048891.t1 AT2G21100 31.214 173 107 5 4 172 7 171 7.89e-15 69.7
MS.gene048891.t1 AT2G21100 31.214 173 107 5 4 172 7 171 7.89e-15 69.7
MS.gene048891.t1 AT5G42500 33.544 158 92 6 14 168 20 167 8.62e-15 69.3
MS.gene048891.t1 AT2G21110 32.061 131 84 2 39 168 39 165 1.10e-14 69.3
MS.gene048891.t1 AT1G65870 32.394 142 85 4 33 171 39 172 4.04e-14 67.8
MS.gene048891.t1 AT5G42510 32.704 159 89 6 14 168 20 164 8.52e-14 66.6
MS.gene048891.t1 AT1G58170 30.526 190 112 7 3 189 9 181 1.14e-13 66.6
MS.gene048891.t1 AT5G49040 27.222 180 114 5 2 172 3 174 5.46e-13 64.7
MS.gene048891.t1 AT3G13662 28.571 126 82 2 48 172 50 168 6.58e-13 64.3
MS.gene048891.t1 AT4G38700 28.646 192 118 9 7 186 6 190 1.92e-12 63.2
MS.gene048891.t1 AT3G13650 28.788 132 82 3 42 172 49 169 3.20e-12 62.8
MS.gene048891.t1 AT1G55210 28.070 171 100 6 4 162 1 160 3.29e-12 62.8
MS.gene048891.t1 AT1G55210 28.070 171 100 6 4 162 1 160 3.29e-12 62.8
MS.gene048891.t1 AT5G49030 27.407 135 89 3 39 172 48 174 5.64e-12 63.9

Find 38 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAGGGACATTTCGGTAAT+TGG 0.217142 4.2:+5133372 MS.gene048891:CDS
TTAGCAAACCAAAACCATTT+TGG 0.234540 4.2:+5133153 MS.gene048891:CDS
CCAAATCACCAAAATGGTTT+TGG 0.244201 4.2:-5133161 None:intergenic
CTCCAACAAGATCAAGAAAA+AGG 0.244585 4.2:+5133004 MS.gene048891:CDS
AAACAACCAAATCACCAAAA+TGG 0.349103 4.2:-5133167 None:intergenic
CTCTCAACAGATTCATTTGA+AGG 0.380353 4.2:+5133435 MS.gene048891:CDS
GAATAAGACTAGGGACATTT+CGG 0.391298 4.2:+5133365 MS.gene048891:CDS
CTTCAACTCTACTCAACATA+AGG 0.398508 4.2:+5133308 MS.gene048891:CDS
CTGGTGATTTCTTCATGACT+AGG 0.418903 4.2:+5133400 MS.gene048891:CDS
AGGAATATGTCAATGAGATT+AGG 0.442216 4.2:-5132975 None:intergenic
AACTTACACTCACGACCAAT+TGG 0.452615 4.2:+5133216 MS.gene048891:CDS
TTTGGTTTGCTAATATGGTT+CGG 0.454869 4.2:-5133143 None:intergenic
AAGTTATTGTCCAAAGTGAT+TGG 0.456707 4.2:-5133198 None:intergenic
AATCCTTGAGCACGACCAAT+TGG 0.466958 4.2:-5133231 None:intergenic
AGATTAACTTGTACGAATGT+TGG 0.479766 4.2:+5133484 MS.gene048891:CDS
AATTGTAGGCACACCGGCAT+GGG 0.485148 4.2:+5133116 MS.gene048891:CDS
TGATCTTGTTGGAGTGGCAG+AGG 0.486276 4.2:-5132995 None:intergenic
CGACCAATTGGTCGTGCTCA+AGG 0.488935 4.2:+5133228 MS.gene048891:CDS
TGGTGATTTCTTCATGACTA+GGG 0.508367 4.2:+5133401 MS.gene048891:CDS
AATGCCACATCAGCAATTGT+AGG 0.509448 4.2:+5133102 MS.gene048891:CDS
CAATTGTAGGCACACCGGCA+TGG 0.515586 4.2:+5133115 MS.gene048891:CDS
ATTTCGGTAATTGGTGGGAC+TGG 0.519957 4.2:+5133381 MS.gene048891:CDS
AGATTAGGAGCAAGAAGAAG+AGG 0.538005 4.2:-5132960 None:intergenic
TAAAACACCAATGTCTTGCA+TGG 0.555621 4.2:-5133042 None:intergenic
TCCCTAGTCTTATTCATCAA+AGG 0.569008 4.2:-5133357 None:intergenic
TTCAACTCTACTCAACATAA+GGG 0.569068 4.2:+5133309 MS.gene048891:CDS
AAATGAATCTGTTGAGAGAG+TGG 0.569288 4.2:-5133430 None:intergenic
TCCTTTGATGAATAAGACTA+GGG 0.578401 4.2:+5133356 MS.gene048891:CDS
ATGGTTCGGTTACCCCATGC+CGG 0.588762 4.2:-5133129 None:intergenic
GGGACATTTCGGTAATTGGT+GGG 0.592368 4.2:+5133376 MS.gene048891:CDS
AGGGACATTTCGGTAATTGG+TGG 0.596783 4.2:+5133375 MS.gene048891:CDS
ATCCTTTGATGAATAAGACT+AGG 0.600343 4.2:+5133355 MS.gene048891:CDS
TGTGCCTACAATTGCTGATG+TGG 0.600935 4.2:-5133106 None:intergenic
TCATAAACCATGCAAGACAT+TGG 0.605259 4.2:+5133035 MS.gene048891:CDS
TTTCATGACATTATTTACAA+CGG 0.616702 4.2:+5133066 MS.gene048891:CDS
GGTGATTTCTTCATGACTAG+GGG 0.631660 4.2:+5133402 MS.gene048891:CDS
ATCAGCAATTGTAGGCACAC+CGG 0.631729 4.2:+5133110 MS.gene048891:CDS
ATTGTAGGCACACCGGCATG+GGG 0.649487 4.2:+5133117 MS.gene048891:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTCATGACATTATTTACAA+CGG + chr4.2:5133066-5133085 MS.gene048891:CDS 20.0%
!!! TTGAAGGTGAAGTTTATTTT+AGG + chr4.2:5133451-5133470 MS.gene048891:CDS 25.0%
AAACAACCAAATCACCAAAA+TGG - chr4.2:5133170-5133189 None:intergenic 30.0%
AAGTTATTGTCCAAAGTGAT+TGG - chr4.2:5133201-5133220 None:intergenic 30.0%
AGGAATATGTCAATGAGATT+AGG - chr4.2:5132978-5132997 None:intergenic 30.0%
ATCCTTTGATGAATAAGACT+AGG + chr4.2:5133355-5133374 MS.gene048891:CDS 30.0%
TCCAACAAGATCAAGAAAAA+GGG + chr4.2:5133005-5133024 MS.gene048891:CDS 30.0%
TCCTTTGATGAATAAGACTA+GGG + chr4.2:5133356-5133375 MS.gene048891:CDS 30.0%
TTCAACTCTACTCAACATAA+GGG + chr4.2:5133309-5133328 MS.gene048891:CDS 30.0%
! AGAAAGAAATTTTCACTGCT+TGG + chr4.2:5133268-5133287 MS.gene048891:CDS 30.0%
! TTAGCAAACCAAAACCATTT+TGG + chr4.2:5133153-5133172 MS.gene048891:CDS 30.0%
!! AGATTAACTTGTACGAATGT+TGG + chr4.2:5133484-5133503 MS.gene048891:CDS 30.0%
!! TTTGGTTTGCTAATATGGTT+CGG - chr4.2:5133146-5133165 None:intergenic 30.0%
!! TTTTGATGATCCAATCACTT+TGG + chr4.2:5133188-5133207 MS.gene048891:CDS 30.0%
!!! ATGGTTTTGGTTTGCTAATA+TGG - chr4.2:5133151-5133170 None:intergenic 30.0%
AAATGAATCTGTTGAGAGAG+TGG - chr4.2:5133433-5133452 None:intergenic 35.0%
CTCCAACAAGATCAAGAAAA+AGG + chr4.2:5133004-5133023 MS.gene048891:CDS 35.0%
CTCTCAACAGATTCATTTGA+AGG + chr4.2:5133435-5133454 MS.gene048891:CDS 35.0%
CTTCAACTCTACTCAACATA+AGG + chr4.2:5133308-5133327 MS.gene048891:CDS 35.0%
GAATAAGACTAGGGACATTT+CGG + chr4.2:5133365-5133384 MS.gene048891:CDS 35.0%
TAAAACACCAATGTCTTGCA+TGG - chr4.2:5133045-5133064 None:intergenic 35.0%
TCATAAACCATGCAAGACAT+TGG + chr4.2:5133035-5133054 MS.gene048891:CDS 35.0%
TGGTGATTTCTTCATGACTA+GGG + chr4.2:5133401-5133420 MS.gene048891:CDS 35.0%
! AAGGGTAGCATAAATTTTGC+TGG + chr4.2:5133327-5133346 MS.gene048891:CDS 35.0%
! AATTGCTGATGTGGCATTTT+TGG - chr4.2:5133100-5133119 None:intergenic 35.0%
! CCAAATCACCAAAATGGTTT+TGG - chr4.2:5133164-5133183 None:intergenic 35.0%
! TTTTCTTGATCTTGTTGGAG+TGG - chr4.2:5133004-5133023 None:intergenic 35.0%
!! CCAAAACCATTTTGGTGATT+TGG + chr4.2:5133161-5133180 MS.gene048891:CDS 35.0%
!! TCCCTAGTCTTATTCATCAA+AGG - chr4.2:5133360-5133379 None:intergenic 35.0%
!!! AGTTTATTTTAGGCTTCGTG+CGG + chr4.2:5133461-5133480 MS.gene048891:CDS 35.0%
AACTTACACTCACGACCAAT+TGG + chr4.2:5133216-5133235 MS.gene048891:CDS 40.0%
AATGCCACATCAGCAATTGT+AGG + chr4.2:5133102-5133121 MS.gene048891:CDS 40.0%
ACTAGGGACATTTCGGTAAT+TGG + chr4.2:5133372-5133391 MS.gene048891:CDS 40.0%
AGATTAGGAGCAAGAAGAAG+AGG - chr4.2:5132963-5132982 None:intergenic 40.0%
CTGGTGATTTCTTCATGACT+AGG + chr4.2:5133400-5133419 MS.gene048891:CDS 40.0%
GGTGATTTCTTCATGACTAG+GGG + chr4.2:5133402-5133421 MS.gene048891:CDS 40.0%
! GAAATTTTCACTGCTTGGCT+TGG + chr4.2:5133273-5133292 MS.gene048891:CDS 40.0%
! GCCCTTTTTCTTGATCTTGT+TGG - chr4.2:5133009-5133028 None:intergenic 40.0%
AATCCTTGAGCACGACCAAT+TGG - chr4.2:5133234-5133253 None:intergenic 45.0%
AGGGACATTTCGGTAATTGG+TGG + chr4.2:5133375-5133394 MS.gene048891:CDS 45.0%
ATCAGCAATTGTAGGCACAC+CGG + chr4.2:5133110-5133129 MS.gene048891:CDS 45.0%
ATTTCGGTAATTGGTGGGAC+TGG + chr4.2:5133381-5133400 MS.gene048891:CDS 45.0%
GGGACATTTCGGTAATTGGT+GGG + chr4.2:5133376-5133395 MS.gene048891:CDS 45.0%
TGTGCCTACAATTGCTGATG+TGG - chr4.2:5133109-5133128 None:intergenic 45.0%
AATTGTAGGCACACCGGCAT+GGG + chr4.2:5133116-5133135 MS.gene048891:CDS 50.0%
TGATCTTGTTGGAGTGGCAG+AGG - chr4.2:5132998-5133017 None:intergenic 50.0%
ATTGTAGGCACACCGGCATG+GGG + chr4.2:5133117-5133136 MS.gene048891:CDS 55.0%
CAATTGTAGGCACACCGGCA+TGG + chr4.2:5133115-5133134 MS.gene048891:CDS 55.0%
CGACCAATTGGTCGTGCTCA+AGG + chr4.2:5133228-5133247 MS.gene048891:CDS 55.0%
!! ATGGTTCGGTTACCCCATGC+CGG - chr4.2:5133132-5133151 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 5132940 5133509 5132940 ID=MS.gene048891
chr4.2 mRNA 5132940 5133509 5132940 ID=MS.gene048891.t1;Parent=MS.gene048891
chr4.2 exon 5132940 5133509 5132940 ID=MS.gene048891.t1.exon1;Parent=MS.gene048891.t1
chr4.2 CDS 5132940 5133509 5132940 ID=cds.MS.gene048891.t1;Parent=MS.gene048891.t1
Gene Sequence

>MS.gene048891

ATGAAGCTCATTTCAACTCTCCTCTTCTTCTTGCTCCTAATCTCATTGACATATTCCTCTGCCACTCCAACAAGATCAAGAAAAAGGGCTCGTGTTCATAAACCATGCAAGACATTGGTGTTTTATTTTCATGACATTATTTACAACGGTCACAACTCCAAAAATGCCACATCAGCAATTGTAGGCACACCGGCATGGGGTAACCGAACCATATTAGCAAACCAAAACCATTTTGGTGATTTGGTTGTTTTTGATGATCCAATCACTTTGGACAATAACTTACACTCACGACCAATTGGTCGTGCTCAAGGATTTTACATTTATGATAAGAAAGAAATTTTCACTGCTTGGCTTGGTTTCTCATTTGTCTTCAACTCTACTCAACATAAGGGTAGCATAAATTTTGCTGGTGCTGATCCTTTGATGAATAAGACTAGGGACATTTCGGTAATTGGTGGGACTGGTGATTTCTTCATGACTAGGGGAGTAGCCACTCTCTCAACAGATTCATTTGAAGGTGAAGTTTATTTTAGGCTTCGTGCGGAGATTAACTTGTACGAATGTTGGTAA
Protein sequence

>MS.gene048891.t1

MKLISTLLFFLLLISLTYSSATPTRSRKRARVHKPCKTLVFYFHDIIYNGHNSKNATSAIVGTPAWGNRTILANQNHFGDLVVFDDPITLDNNLHSRPIGRAQGFYIYDKKEIFTAWLGFSFVFNSTQHKGSINFAGADPLMNKTRDISVIGGTGDFFMTRGVATLSTDSFEGEVYFRLRAEINLYECW