AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0232840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0232840 MtrunA17_Chr2g0280291 86.420 162 22 0 1 162 274 435 3.94e-105 307
Msa0232840 MtrunA17_Chr2g0280291 83.974 156 22 2 1 156 1 153 9.39e-91 270
Msa0232840 MtrunA17_Chr2g0281271 84.722 144 22 0 19 162 1 144 1.13e-93 268
Msa0232840 MtrunA17_Chr2g0280331 67.456 169 44 7 1 162 1 165 6.87e-77 226
Msa0232840 MtrunA17_Chr2g0280311 70.779 154 38 4 14 162 14 165 2.27e-76 224
Msa0232840 MtrunA17_Chr2g0280301 68.519 162 24 3 1 162 1 135 3.78e-70 208
Msa0232840 MtrunA17_Chr2g0280351 60.000 170 58 5 1 162 1 168 2.34e-68 204
Msa0232840 MtrunA17_Chr2g0295371 54.938 162 71 1 1 162 5 164 8.59e-67 201
Msa0232840 MtrunA17_Chr2g0280321 59.036 166 61 5 1 162 1 163 8.40e-65 195
Msa0232840 MtrunA17_Chr4g0049151 56.886 167 64 4 1 162 1 164 3.59e-60 184
Msa0232840 MtrunA17_Chr2g0280341 53.086 162 68 5 6 162 179 337 1.07e-51 167
Msa0232840 MtrunA17_Chr2g0280341 56.338 142 55 4 1 137 1 140 1.36e-44 149
Msa0232840 MtrunA17_Chr2g0280281 46.541 159 76 4 9 162 4 158 9.23e-51 159
Msa0232840 MtrunA17_Chr4g0049191 46.012 163 83 4 1 162 1 159 1.27e-48 154
Msa0232840 MtrunA17_Chr4g0072781 51.111 135 63 2 29 162 41 173 7.69e-45 145
Msa0232840 MtrunA17_Chr4g0072791 45.652 138 71 3 28 162 70 206 2.37e-41 137
Msa0232840 MtrunA17_Chr1g0181941 38.686 137 79 4 28 161 73 207 1.66e-32 115
Msa0232840 MtrunA17_Chr8g0373921 37.681 138 82 4 28 162 36 172 1.12e-26 99.0
Msa0232840 MtrunA17_Chr5g0403201 33.813 139 88 3 28 162 47 185 8.28e-25 94.4
Msa0232840 MtrunA17_Chr5g0403191 30.851 94 60 3 74 162 10 103 4.42e-13 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0232840 AT4G33720.1 59.627 161 62 2 2 162 6 163 3.36e-67 202
Msa0232840 AT2G14580.1 60.976 164 57 4 1 162 3 161 2.45e-65 197
Msa0232840 AT5G26130.1 57.962 157 65 1 6 162 11 166 8.57e-64 193
Msa0232840 AT2G14610.1 59.236 157 59 3 6 162 10 161 1.35e-61 187
Msa0232840 AT4G33710.1 61.702 141 53 1 22 162 27 166 1.94e-59 182
Msa0232840 AT3G19690.1 53.459 159 67 4 6 162 8 161 3.59e-57 176
Msa0232840 AT4G25790.1 53.676 136 60 2 28 162 77 210 1.69e-50 161
Msa0232840 AT1G50060.1 51.807 166 71 5 1 162 1 161 8.11e-49 155
Msa0232840 AT5G57625.1 52.593 135 61 2 29 162 75 207 1.01e-48 156
Msa0232840 AT2G19990.1 49.635 137 67 1 26 162 42 176 2.17e-48 154
Msa0232840 AT3G09590.1 48.905 137 66 2 28 162 52 186 3.75e-45 147
Msa0232840 AT4G25780.1 50.725 138 64 3 28 162 54 190 4.97e-45 146
Msa0232840 AT4G30320.1 45.695 151 78 3 13 162 14 161 1.35e-44 144
Msa0232840 AT1G50050.2 53.614 166 69 5 1 162 1 162 1.84e-44 144
Msa0232840 AT4G33730.1 52.174 138 61 4 26 162 39 172 2.49e-44 144
Msa0232840 AT5G02730.1 45.985 137 70 2 28 162 59 193 1.80e-40 135
Msa0232840 AT1G50050.1 52.564 156 69 4 6 160 9 160 2.53e-39 133
Msa0232840 AT1G01310.1 45.588 136 70 3 28 162 87 219 9.70e-39 132
Msa0232840 AT4G31470.1 46.324 136 69 3 28 162 53 185 2.44e-38 129
Msa0232840 AT5G66590.1 45.000 140 68 3 29 162 49 185 5.03e-37 126
Msa0232840 AT4G07820.1 43.662 142 75 4 21 162 24 160 5.71e-36 122
Msa0232840 AT2G19970.1 38.971 136 70 6 26 152 35 166 3.92e-24 92.8
Msa0232840 AT2G19980.1 34.706 170 90 8 3 162 7 165 4.82e-23 89.7

Find 41 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAGTCTGTTGGTGAGTTT+TGG 0.180317 2_2:-5103858 None:intergenic
CCGGTGGTGGTGGCCGTTAC+GGG 0.193193 2_2:+5104004 Msa0232840:CDS
TTAGGCTTATTTCTCATTAT+TGG 0.210544 2_2:+5103820 Msa0232840:CDS
TCCGGTGGTGGTGGCCGTTA+CGG 0.303334 2_2:+5104003 Msa0232840:CDS
TATTAATCATGCACTTAGTA+TGG 0.322170 2_2:-5104273 None:intergenic
TTGGTGTTGCAAATGTTGTT+TGG 0.348141 2_2:+5103911 Msa0232840:CDS
GCCATTATACTCAGGTGGTT+TGG 0.358578 2_2:+5104145 Msa0232840:CDS
GTTACTATTATAGTTATAAT+CGG 0.390895 2_2:-5104097 None:intergenic
TCCAAACCACCTGAGTATAA+TGG 0.398812 2_2:-5104146 None:intergenic
TGGTGTTGCAAATGTTGTTT+GGG 0.411343 2_2:+5103912 Msa0232840:CDS
CTGACGTCTTGCTTCGTTGT+GGG 0.413555 2_2:-5103887 None:intergenic
CCCGTAACGGCCACCACCAC+CGG 0.429882 2_2:-5104004 None:intergenic
TGGAGAAACACAAAGCGTAT+TGG 0.455942 2_2:+5104165 Msa0232840:CDS
GCACAGATGCAGTGAGGTTG+TGG 0.462999 2_2:+5104061 Msa0232840:CDS
ATTATTATCACATTTCACTT+TGG 0.463790 2_2:-5104193 None:intergenic
TTGATCCACTCCGGTGGTGG+TGG 0.492178 2_2:+5103994 Msa0232840:CDS
GTGAAATGTGATAATAATAG+AGG 0.492513 2_2:+5104198 Msa0232840:CDS
GAGAATCTAGCGTGGAGCTC+CGG 0.500119 2_2:+5104027 Msa0232840:CDS
ATCTGTGCCACTCATGTCGC+CGG 0.501762 2_2:-5104046 None:intergenic
CCTGACGTCTTGCTTCGTTG+TGG 0.534137 2_2:-5103888 None:intergenic
CGATTGATCCACTCCGGTGG+TGG 0.538844 2_2:+5103991 Msa0232840:CDS
CACAGATGCAGTGAGGTTGT+GGG 0.544377 2_2:+5104062 Msa0232840:CDS
CGGTGGTGGTGGCCGTTACG+GGG 0.566376 2_2:+5104005 Msa0232840:CDS
CCACAACGAAGCAAGACGTC+AGG 0.568340 2_2:+5103888 Msa0232840:CDS
TGGGCGTTCACATAGTCTGT+TGG 0.581596 2_2:-5103868 None:intergenic
TGGAGCTCCGGCGACATGAG+TGG 0.603470 2_2:+5104039 Msa0232840:CDS
AGACTATGCTAATCAACGCA+AGG 0.607234 2_2:+5103960 Msa0232840:CDS
GATCCACCAGGCAACTATGT+TGG 0.607501 2_2:+5104243 Msa0232840:CDS
AACGGCCACCACCACCGGAG+TGG 0.614459 2_2:-5103999 None:intergenic
TGACCAACATAGTTGCCTGG+TGG 0.614666 2_2:-5104246 None:intergenic
GACTATGCTAATCAACGCAA+GGG 0.626800 2_2:+5103961 Msa0232840:CDS
GTGTGGCCATTATACTCAGG+TGG 0.627875 2_2:+5104140 Msa0232840:CDS
GATTGTCGATTGATCCACTC+CGG 0.648727 2_2:+5103985 Msa0232840:CDS
AGTGTGTGGCCATTATACTC+AGG 0.651003 2_2:+5104137 Msa0232840:CDS
AACGAAGCAAGACGTCAGGT+TGG 0.655351 2_2:+5103892 Msa0232840:CDS
ACGCTAGATTCTCCCCGTAA+CGG 0.657514 2_2:-5104017 None:intergenic
ACTTGCAATTACGATCCACC+AGG 0.660677 2_2:+5104231 Msa0232840:CDS
GTTACGGGGAGAATCTAGCG+TGG 0.716019 2_2:+5104019 Msa0232840:CDS
TGTCGATTGATCCACTCCGG+TGG 0.719544 2_2:+5103988 Msa0232840:CDS
TGTGCTGCTAATAAAGTGTG+TGG 0.730769 2_2:+5104123 Msa0232840:CDS
TGAGTGGCACAGATGCAGTG+AGG 0.786885 2_2:+5104055 Msa0232840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTACTATTATAGTTATAAT+CGG - chr2_2:5104100-5104119 None:intergenic 15.0%
!! ATTATTATCACATTTCACTT+TGG - chr2_2:5104196-5104215 None:intergenic 20.0%
!! TTAGGCTTATTTCTCATTAT+TGG + chr2_2:5103820-5103839 Msa0232840:CDS 25.0%
! GTGAAATGTGATAATAATAG+AGG + chr2_2:5104198-5104217 Msa0232840:CDS 25.0%
! TTTTCTCTAATGTGTGTCTT+AGG + chr2_2:5103802-5103821 Msa0232840:CDS 30.0%
!! ATAGTCTGTTGGTGAGTTTT+GGG - chr2_2:5103860-5103879 None:intergenic 35.0%
!! TTGGTGTTGCAAATGTTGTT+TGG + chr2_2:5103911-5103930 Msa0232840:CDS 35.0%
!! TGGTGTTGCAAATGTTGTTT+GGG + chr2_2:5103912-5103931 Msa0232840:CDS 35.0%
!! CATAGTCTGTTGGTGAGTTT+TGG - chr2_2:5103861-5103880 None:intergenic 40.0%
AGACTATGCTAATCAACGCA+AGG + chr2_2:5103960-5103979 Msa0232840:CDS 40.0%
GACTATGCTAATCAACGCAA+GGG + chr2_2:5103961-5103980 Msa0232840:CDS 40.0%
! TGTGCTGCTAATAAAGTGTG+TGG + chr2_2:5104123-5104142 Msa0232840:CDS 40.0%
TCCAAACCACCTGAGTATAA+TGG - chr2_2:5104149-5104168 None:intergenic 40.0%
TGGAGAAACACAAAGCGTAT+TGG + chr2_2:5104165-5104184 Msa0232840:CDS 40.0%
! TTTTGACCAACATAGTTGCC+TGG - chr2_2:5104252-5104271 None:intergenic 40.0%
! GATTGTCGATTGATCCACTC+CGG + chr2_2:5103985-5104004 Msa0232840:CDS 45.0%
AGTGTGTGGCCATTATACTC+AGG + chr2_2:5104137-5104156 Msa0232840:CDS 45.0%
GCCATTATACTCAGGTGGTT+TGG + chr2_2:5104145-5104164 Msa0232840:CDS 45.0%
ACTTGCAATTACGATCCACC+AGG + chr2_2:5104231-5104250 Msa0232840:CDS 45.0%
TGGGCGTTCACATAGTCTGT+TGG - chr2_2:5103871-5103890 None:intergenic 50.0%
CTGACGTCTTGCTTCGTTGT+GGG - chr2_2:5103890-5103909 None:intergenic 50.0%
AACGAAGCAAGACGTCAGGT+TGG + chr2_2:5103892-5103911 Msa0232840:CDS 50.0%
ACGCTAGATTCTCCCCGTAA+CGG - chr2_2:5104020-5104039 None:intergenic 50.0%
CACAGATGCAGTGAGGTTGT+GGG + chr2_2:5104062-5104081 Msa0232840:CDS 50.0%
GTGTGGCCATTATACTCAGG+TGG + chr2_2:5104140-5104159 Msa0232840:CDS 50.0%
GATCCACCAGGCAACTATGT+TGG + chr2_2:5104243-5104262 Msa0232840:CDS 50.0%
TGACCAACATAGTTGCCTGG+TGG - chr2_2:5104249-5104268 None:intergenic 50.0%
CCTGACGTCTTGCTTCGTTG+TGG - chr2_2:5103891-5103910 None:intergenic 55.0%
CCACAACGAAGCAAGACGTC+AGG + chr2_2:5103888-5103907 Msa0232840:CDS 55.0%
! TGTCGATTGATCCACTCCGG+TGG + chr2_2:5103988-5104007 Msa0232840:CDS 55.0%
GTTACGGGGAGAATCTAGCG+TGG + chr2_2:5104019-5104038 Msa0232840:CDS 55.0%
GAGAATCTAGCGTGGAGCTC+CGG + chr2_2:5104027-5104046 Msa0232840:CDS 55.0%
! ATCTGTGCCACTCATGTCGC+CGG - chr2_2:5104049-5104068 None:intergenic 55.0%
TGAGTGGCACAGATGCAGTG+AGG + chr2_2:5104055-5104074 Msa0232840:CDS 55.0%
GCACAGATGCAGTGAGGTTG+TGG + chr2_2:5104061-5104080 Msa0232840:CDS 55.0%
CGATTGATCCACTCCGGTGG+TGG + chr2_2:5103991-5104010 Msa0232840:CDS 60.0%
! TTGATCCACTCCGGTGGTGG+TGG + chr2_2:5103994-5104013 Msa0232840:CDS 60.0%
!! TCCGGTGGTGGTGGCCGTTA+CGG + chr2_2:5104003-5104022 Msa0232840:CDS 65.0%
TGGAGCTCCGGCGACATGAG+TGG + chr2_2:5104039-5104058 Msa0232840:CDS 65.0%
AACGGCCACCACCACCGGAG+TGG - chr2_2:5104002-5104021 None:intergenic 70.0%
CCCGTAACGGCCACCACCAC+CGG - chr2_2:5104007-5104026 None:intergenic 70.0%
!! CCGGTGGTGGTGGCCGTTAC+GGG + chr2_2:5104004-5104023 Msa0232840:CDS 70.0%
!! CGGTGGTGGTGGCCGTTACG+GGG + chr2_2:5104005-5104024 Msa0232840:CDS 70.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 5103793 5104281 5103793 ID=Msa0232840;Name=Msa0232840
chr2_2 mRNA 5103793 5104281 5103793 ID=Msa0232840-mRNA-1;Parent=Msa0232840;Name=Msa0232840-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|162
chr2_2 exon 5103793 5104281 5103793 ID=Msa0232840-mRNA-1:exon:2251;Parent=Msa0232840-mRNA-1
chr2_2 CDS 5103793 5104281 5103793 ID=Msa0232840-mRNA-1:cds;Parent=Msa0232840-mRNA-1
Gene Sequence

>Msa0232840

ATGAGTTCATTTTCTCTAATGTGTGTCTTAGGCTTATTTCTCATTATTGGTCACGTTGCACATGCCCAAAACTCACCAACAGACTATGTGAACGCCCACAACGAAGCAAGACGTCAGGTTGGTGTTGCAAATGTTGTTTGGGACAATAACGTTGCTGCTTTTGCACAAGACTATGCTAATCAACGCAAGGGTGATTGTCGATTGATCCACTCCGGTGGTGGTGGCCGTTACGGGGAGAATCTAGCGTGGAGCTCCGGCGACATGAGTGGCACAGATGCAGTGAGGTTGTGGGTGAATGAGAGAGCCGATTATAACTATAATAGTAACACATGTGCTGCTAATAAAGTGTGTGGCCATTATACTCAGGTGGTTTGGAGAAACACAAAGCGTATTGGATGTGCCAAAGTGAAATGTGATAATAATAGAGGAACATTCATTACTTGCAATTACGATCCACCAGGCAACTATGTTGGTCAAAAGCCATACTAA
Protein sequence

>Msa0232840

MSSFSLMCVLGLFLIIGHVAHAQNSPTDYVNAHNEARRQVGVANVVWDNNVAAFAQDYANQRKGDCRLIHSGGGGRYGENLAWSSGDMSGTDAVRLWVNERADYNYNSNTCAANKVCGHYTQVVWRNTKRIGCAKVKCDNNRGTFITCNYDPPGNYVGQKPY*