AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1162900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1162900 MtrunA17_Chr7g0259091 95.876 194 8 0 1 194 1 194 2.55e-138 384
Msa1162900 MtrunA17_Chr7g0259101 94.845 194 10 0 1 194 1 194 6.49e-134 380
Msa1162900 MtrunA17_Chr7g0259101 93.299 194 12 1 1 194 201 393 7.51e-130 370
Msa1162900 MtrunA17_Chr7g0259071 77.157 197 36 2 1 194 1 191 1.18e-109 311
Msa1162900 MtrunA17_Chr7g0259121 59.091 176 65 4 24 194 20 193 1.07e-70 214
Msa1162900 MtrunA17_Chr1g0175911 51.309 191 87 4 5 194 7 192 2.32e-60 186
Msa1162900 MtrunA17_Chr4g0005081 50.000 166 81 2 30 194 33 197 1.19e-57 180
Msa1162900 MtrunA17_Chr4g0005071 47.541 183 94 2 13 194 15 196 1.11e-56 177
Msa1162900 MtrunA17_Chr4g0005031 51.316 152 73 1 43 194 71 221 2.88e-53 169
Msa1162900 MtrunA17_Chr4g0005041 48.214 168 81 4 30 194 34 198 3.16e-52 166
Msa1162900 MtrunA17_Chr4g0005011 48.795 166 81 3 30 194 35 197 2.45e-51 164
Msa1162900 MtrunA17_Chr4g0037481 52.941 153 70 2 43 194 41 192 2.76e-51 163
Msa1162900 MtrunA17_Chr3g0136641 48.315 178 88 4 19 194 13 188 7.42e-51 162
Msa1162900 MtrunA17_Chr3g0136631 45.810 179 92 4 19 194 13 189 2.13e-49 158
Msa1162900 MtrunA17_Chr7g0243501 46.907 194 91 5 11 194 1 192 5.70e-49 157
Msa1162900 MtrunA17_Chr4g0005111 42.857 175 97 3 20 194 19 190 5.55e-46 150
Msa1162900 MtrunA17_Chr5g0446751 45.989 187 89 7 15 194 8 189 2.37e-45 148
Msa1162900 MtrunA17_Chr1g0177051 43.316 187 94 5 11 193 7 185 8.23e-44 144
Msa1162900 MtrunA17_Chr4g0005131 39.205 176 104 3 20 194 18 191 1.98e-42 140
Msa1162900 MtrunA17_Chr3g0085291 42.632 190 100 4 7 193 3 186 4.06e-41 137
Msa1162900 MtrunA17_Chr3g0085311 48.322 149 74 2 45 193 43 188 6.35e-41 137
Msa1162900 MtrunA17_Chr3g0090231 42.021 188 99 6 8 194 7 185 3.13e-40 135
Msa1162900 MtrunA17_Chr4g0040551 42.051 195 102 7 1 194 1 185 3.60e-40 135
Msa1162900 MtrunA17_Chr3g0085301 40.659 182 101 4 15 193 16 193 4.44e-38 130
Msa1162900 MtrunA17_Chr3g0085321 43.709 151 82 2 43 193 41 188 7.08e-37 126
Msa1162900 MtrunA17_Chr4g0005091 37.791 172 88 3 26 194 20 175 1.06e-33 118
Msa1162900 MtrunA17_Chr4g0068381 40.397 151 89 1 44 194 31 180 8.09e-30 108
Msa1162900 MtrunA17_Chr4g0068391 40.397 151 89 1 44 194 31 180 1.54e-29 107
Msa1162900 MtrunA17_Chr4g0024961 32.215 149 100 1 41 189 26 173 7.97e-21 85.1
Msa1162900 MtrunA17_Chr4g0024951 29.630 189 117 4 1 189 1 173 3.20e-20 83.6
Msa1162900 MtrunA17_Chr1g0169511 40.000 95 55 2 78 172 133 225 1.37e-13 67.0
Msa1162900 MtrunA17_Chr1g0169281 38.947 95 56 2 78 172 139 231 1.66e-13 67.0
Msa1162900 MtrunA17_Chr1g0169291 40.000 95 55 2 78 172 133 225 2.22e-13 66.6
Msa1162900 MtrunA17_Chr1g0212861 36.154 130 75 5 71 193 225 353 8.76e-13 65.9
Msa1162900 MtrunA17_Chr4g0030731 37.383 107 66 1 71 177 177 282 1.72e-12 64.7
Msa1162900 MtrunA17_Chr4g0030681 37.383 107 66 1 71 177 178 283 1.99e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1162900 AT5G42500.1 51.190 168 78 3 26 193 22 185 2.69e-55 174
Msa1162900 AT5G42510.1 50.000 162 77 3 32 193 25 182 1.82e-51 164
Msa1162900 AT1G65870.1 53.548 155 67 3 41 193 38 189 2.18e-51 164
Msa1162900 AT1G22900.1 48.295 176 87 3 18 193 22 193 1.00e-50 162
Msa1162900 AT1G58170.1 43.716 183 97 2 12 194 9 185 3.86e-49 158
Msa1162900 AT1G55210.1 40.000 190 108 4 7 194 2 187 1.07e-48 157
Msa1162900 AT1G55210.2 40.000 190 108 4 7 194 2 187 1.07e-48 157
Msa1162900 AT5G49040.1 39.791 191 111 3 7 194 2 191 1.51e-48 157
Msa1162900 AT3G13650.1 39.785 186 108 2 9 194 5 186 3.36e-48 155
Msa1162900 AT2G21100.1 43.503 177 99 1 17 193 12 187 7.66e-44 144
Msa1162900 AT2G21100.2 43.503 177 99 1 17 193 12 187 7.66e-44 144
Msa1162900 AT4G38700.1 41.579 190 103 5 10 194 4 190 5.12e-43 142
Msa1162900 AT3G13662.1 47.651 149 70 3 33 181 32 172 5.35e-43 142
Msa1162900 AT2G21110.1 44.371 151 79 2 48 194 37 186 5.35e-42 140
Msa1162900 AT5G49030.3 40.237 169 97 3 7 172 2 169 3.78e-38 139
Msa1162900 AT3G58090.1 54.206 107 48 1 87 193 166 271 3.67e-34 122
Msa1162900 AT3G13660.1 44.538 119 65 1 76 194 8 125 5.39e-33 115
Msa1162900 AT4G23690.1 34.586 133 75 5 43 169 36 162 3.55e-13 65.5

Find 56 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCCATTGTTGGCGGGAC+TGG 0.222462 7_4:+53827567 Msa1162900:CDS
TGGCCATTGTTGGCGGGACT+GGG 0.273301 7_4:+53827568 Msa1162900:CDS
GGCAGTGACAAGGGATATTA+TGG 0.286127 7_4:-53827172 None:intergenic
TGGAAGTACACTTAGCATAT+TGG 0.334562 7_4:+53827509 Msa1162900:CDS
CTTGAAAACCCAGCATTGTT+GGG 0.345342 7_4:-53827218 None:intergenic
ACAATGGCCATTTCTCTAAC+AGG 0.358166 7_4:-53827555 None:intergenic
AAAAGAAATTAGAAGAGTTA+TGG 0.360744 7_4:-53827133 None:intergenic
ACAAATACCATGCTAGGTTT+TGG 0.370876 7_4:-53827291 None:intergenic
GTAATACACCTAGCTAATAA+TGG 0.373810 7_4:-53827686 None:intergenic
GGAAGTACACTTAGCATATT+GGG 0.380807 7_4:+53827510 Msa1162900:CDS
TCTTGAAAACCCAGCATTGT+TGG 0.400814 7_4:-53827219 None:intergenic
CGTTCAGGACCAGCCGTCAA+TGG 0.424944 7_4:-53827378 None:intergenic
TACTTTCACGACATTGTGTC+AGG 0.427188 7_4:+53827267 Msa1162900:CDS
AAGCCTATCCCCAACAATGC+TGG 0.431336 7_4:+53827209 Msa1162900:CDS
TATTCCGTTGATTACACTAA+AGG 0.444889 7_4:+53827630 Msa1162900:CDS
GAGTGAACCTGTTAGAGAAA+TGG 0.463422 7_4:+53827548 Msa1162900:CDS
TTCACTGATGGAGATTTCAA+TGG 0.465136 7_4:+53827489 Msa1162900:CDS
GTTAGAGAAATGGCCATTGT+TGG 0.468463 7_4:+53827558 Msa1162900:CDS
TTCTATATCACAAGAGGAGA+TGG 0.477985 7_4:+53827440 Msa1162900:CDS
ACAAGTTTCGAGTCACGTTC+AGG 0.491447 7_4:-53827393 None:intergenic
ATTCGGGACGGTTGTGGCGA+TGG 0.502476 7_4:+53827350 Msa1162900:CDS
GTTGCCATTCGGGACGGTTG+TGG 0.502902 7_4:+53827344 Msa1162900:CDS
AGAGAAATGGCCATTGTTGG+CGG 0.509028 7_4:+53827561 Msa1162900:CDS
AGAAATTAGAAGAGTTATGG+AGG 0.509697 7_4:-53827130 None:intergenic
AGCCTATCCCCAACAATGCT+GGG 0.510899 7_4:+53827210 Msa1162900:CDS
GGCCATTGTTGGCGGGACTG+GGG 0.511798 7_4:+53827569 Msa1162900:CDS
GAGAAATGGCCATTGTTGGC+GGG 0.513679 7_4:+53827562 Msa1162900:CDS
GTTCAGGACCAGCCGTCAAT+GGG 0.519940 7_4:-53827377 None:intergenic
GGCGATGGATGACCCATTGA+CGG 0.521036 7_4:+53827365 Msa1162900:CDS
GTATTTGTAGCTGAGCCTAA+TGG 0.523113 7_4:+53827306 Msa1162900:CDS
GAACGTGACTCGAAACTTGT+GGG 0.527774 7_4:+53827396 Msa1162900:CDS
AGAGGAGATGGGACTAATGA+TGG 0.528699 7_4:+53827452 Msa1162900:CDS
TGACTCGAAACTTGTGGGTA+AGG 0.534298 7_4:+53827401 Msa1162900:CDS
ATGGATGACCCATTGACGGC+TGG 0.541350 7_4:+53827369 Msa1162900:CDS
AAACTTGTGGGTAAGGCTCA+AGG 0.545821 7_4:+53827408 Msa1162900:CDS
TCAGCTACAAATACCATGCT+AGG 0.557255 7_4:-53827297 None:intergenic
TTACACTTCTATATCACAAG+AGG 0.558364 7_4:+53827434 Msa1162900:CDS
AAATGCGTTGCCATTCGGGA+CGG 0.561926 7_4:+53827338 Msa1162900:CDS
TTGAAAACCCAGCATTGTTG+GGG 0.562104 7_4:-53827217 None:intergenic
ATGACCATGGCATTCACTGA+TGG 0.562304 7_4:+53827477 Msa1162900:CDS
AGCCCCAGTCCCGCCAACAA+TGG 0.563286 7_4:-53827571 None:intergenic
GTAATTAGTGGCAGTGACAA+GGG 0.567205 7_4:-53827181 None:intergenic
AGTAATTAGTGGCAGTGACA+AGG 0.571016 7_4:-53827182 None:intergenic
TGAACGTGACTCGAAACTTG+TGG 0.588799 7_4:+53827395 Msa1162900:CDS
CACTAAAGGAGATGCCATTG+TGG 0.590470 7_4:+53827644 Msa1162900:CDS
ATCGCCACAACCGTCCCGAA+TGG 0.592145 7_4:-53827348 None:intergenic
TCTATATCACAAGAGGAGAT+GGG 0.592301 7_4:+53827441 Msa1162900:CDS
ATCTCCTTTAGTGTAATCAA+CGG 0.597699 7_4:-53827634 None:intergenic
AACCCAGCATTGTTGGGGAT+AGG 0.607331 7_4:-53827212 None:intergenic
GTCAGGACCAAAACCTAGCA+TGG 0.622028 7_4:+53827284 Msa1162900:CDS
TGTAGCTGAGCCTAATGGCA+AGG 0.630219 7_4:+53827311 Msa1162900:CDS
ATCTCCATCAGTGAATGCCA+TGG 0.633818 7_4:-53827481 None:intergenic
TGTCGTGAAAGTAAAAGTGA+AGG 0.637192 7_4:-53827257 None:intergenic
GAATATATCATATTCCACAA+TGG 0.663555 7_4:-53827658 None:intergenic
TGACAAGGGATATTATGGAG+AGG 0.687653 7_4:-53827167 None:intergenic
ACTAATGATGGTGATGACCA+TGG 0.702330 7_4:+53827464 Msa1162900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAATTAGAAGAGTTA+TGG - chr7_4:53827136-53827155 None:intergenic 20.0%
!! TAGGCTTTTATAGTAATTAG+TGG - chr7_4:53827196-53827215 None:intergenic 25.0%
! GAATATATCATATTCCACAA+TGG - chr7_4:53827661-53827680 None:intergenic 25.0%
AGAAATTAGAAGAGTTATGG+AGG - chr7_4:53827133-53827152 None:intergenic 30.0%
TTACACTTCTATATCACAAG+AGG + chr7_4:53827434-53827453 Msa1162900:CDS 30.0%
! TATTCCGTTGATTACACTAA+AGG + chr7_4:53827630-53827649 Msa1162900:CDS 30.0%
ATCTCCTTTAGTGTAATCAA+CGG - chr7_4:53827637-53827656 None:intergenic 30.0%
TGTCGTGAAAGTAAAAGTGA+AGG - chr7_4:53827260-53827279 None:intergenic 35.0%
! ACAAATACCATGCTAGGTTT+TGG - chr7_4:53827294-53827313 None:intergenic 35.0%
!!! GCATTTTTTACCTTGCCATT+AGG - chr7_4:53827324-53827343 None:intergenic 35.0%
GTAAAAAATGCGTTGCCATT+CGG + chr7_4:53827333-53827352 Msa1162900:CDS 35.0%
TAAAAAATGCGTTGCCATTC+GGG + chr7_4:53827334-53827353 Msa1162900:CDS 35.0%
TTCTATATCACAAGAGGAGA+TGG + chr7_4:53827440-53827459 Msa1162900:CDS 35.0%
TCTATATCACAAGAGGAGAT+GGG + chr7_4:53827441-53827460 Msa1162900:CDS 35.0%
TTCACTGATGGAGATTTCAA+TGG + chr7_4:53827489-53827508 Msa1162900:CDS 35.0%
! TGGAAGTACACTTAGCATAT+TGG + chr7_4:53827509-53827528 Msa1162900:CDS 35.0%
! GGAAGTACACTTAGCATATT+GGG + chr7_4:53827510-53827529 Msa1162900:CDS 35.0%
TGACAAGGGATATTATGGAG+AGG - chr7_4:53827170-53827189 None:intergenic 40.0%
GTAATTAGTGGCAGTGACAA+GGG - chr7_4:53827184-53827203 None:intergenic 40.0%
AGTAATTAGTGGCAGTGACA+AGG - chr7_4:53827185-53827204 None:intergenic 40.0%
TTGAAAACCCAGCATTGTTG+GGG - chr7_4:53827220-53827239 None:intergenic 40.0%
CTTGAAAACCCAGCATTGTT+GGG - chr7_4:53827221-53827240 None:intergenic 40.0%
TCTTGAAAACCCAGCATTGT+TGG - chr7_4:53827222-53827241 None:intergenic 40.0%
TACTTTCACGACATTGTGTC+AGG + chr7_4:53827267-53827286 Msa1162900:CDS 40.0%
TCAGCTACAAATACCATGCT+AGG - chr7_4:53827300-53827319 None:intergenic 40.0%
GTATTTGTAGCTGAGCCTAA+TGG + chr7_4:53827306-53827325 Msa1162900:CDS 40.0%
! ACTAATGATGGTGATGACCA+TGG + chr7_4:53827464-53827483 Msa1162900:CDS 40.0%
GAGTGAACCTGTTAGAGAAA+TGG + chr7_4:53827548-53827567 Msa1162900:CDS 40.0%
ACAATGGCCATTTCTCTAAC+AGG - chr7_4:53827558-53827577 None:intergenic 40.0%
GTTAGAGAAATGGCCATTGT+TGG + chr7_4:53827558-53827577 Msa1162900:CDS 40.0%
GGCAGTGACAAGGGATATTA+TGG - chr7_4:53827175-53827194 None:intergenic 45.0%
! ACAAGTTTCGAGTCACGTTC+AGG - chr7_4:53827396-53827415 None:intergenic 45.0%
TGAACGTGACTCGAAACTTG+TGG + chr7_4:53827395-53827414 Msa1162900:CDS 45.0%
GAACGTGACTCGAAACTTGT+GGG + chr7_4:53827396-53827415 Msa1162900:CDS 45.0%
TGACTCGAAACTTGTGGGTA+AGG + chr7_4:53827401-53827420 Msa1162900:CDS 45.0%
AAACTTGTGGGTAAGGCTCA+AGG + chr7_4:53827408-53827427 Msa1162900:CDS 45.0%
AGAGGAGATGGGACTAATGA+TGG + chr7_4:53827452-53827471 Msa1162900:CDS 45.0%
ATGACCATGGCATTCACTGA+TGG + chr7_4:53827477-53827496 Msa1162900:CDS 45.0%
ATCTCCATCAGTGAATGCCA+TGG - chr7_4:53827484-53827503 None:intergenic 45.0%
AGAGAAATGGCCATTGTTGG+CGG + chr7_4:53827561-53827580 Msa1162900:CDS 45.0%
! GGGCTTTTCGTTTTGTACGT+GGG + chr7_4:53827589-53827608 Msa1162900:CDS 45.0%
CACTAAAGGAGATGCCATTG+TGG + chr7_4:53827644-53827663 Msa1162900:CDS 45.0%
AAGCCTATCCCCAACAATGC+TGG + chr7_4:53827209-53827228 Msa1162900:CDS 50.0%
AGCCTATCCCCAACAATGCT+GGG + chr7_4:53827210-53827229 Msa1162900:CDS 50.0%
AACCCAGCATTGTTGGGGAT+AGG - chr7_4:53827215-53827234 None:intergenic 50.0%
GTCAGGACCAAAACCTAGCA+TGG + chr7_4:53827284-53827303 Msa1162900:CDS 50.0%
TGTAGCTGAGCCTAATGGCA+AGG + chr7_4:53827311-53827330 Msa1162900:CDS 50.0%
AAATGCGTTGCCATTCGGGA+CGG + chr7_4:53827338-53827357 Msa1162900:CDS 50.0%
GAGAAATGGCCATTGTTGGC+GGG + chr7_4:53827562-53827581 Msa1162900:CDS 50.0%
! GGGGCTTTTCGTTTTGTACG+TGG + chr7_4:53827588-53827607 Msa1162900:CDS 50.0%
GGCGATGGATGACCCATTGA+CGG + chr7_4:53827365-53827384 Msa1162900:CDS 55.0%
ATGGATGACCCATTGACGGC+TGG + chr7_4:53827369-53827388 Msa1162900:CDS 55.0%
GTTCAGGACCAGCCGTCAAT+GGG - chr7_4:53827380-53827399 None:intergenic 55.0%
GTTGCCATTCGGGACGGTTG+TGG + chr7_4:53827344-53827363 Msa1162900:CDS 60.0%
ATCGCCACAACCGTCCCGAA+TGG - chr7_4:53827351-53827370 None:intergenic 60.0%
ATTCGGGACGGTTGTGGCGA+TGG + chr7_4:53827350-53827369 Msa1162900:CDS 60.0%
CGTTCAGGACCAGCCGTCAA+TGG - chr7_4:53827381-53827400 None:intergenic 60.0%
ATGGCCATTGTTGGCGGGAC+TGG + chr7_4:53827567-53827586 Msa1162900:CDS 60.0%
TGGCCATTGTTGGCGGGACT+GGG + chr7_4:53827568-53827587 Msa1162900:CDS 60.0%
GGCCATTGTTGGCGGGACTG+GGG + chr7_4:53827569-53827588 Msa1162900:CDS 65.0%
AGCCCCAGTCCCGCCAACAA+TGG - chr7_4:53827574-53827593 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 53827111 53827695 53827111 ID=Msa1162900;Name=Msa1162900
chr7_4 mRNA 53827111 53827695 53827111 ID=Msa1162900-mRNA-1;Parent=Msa1162900;Name=Msa1162900-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|194
chr7_4 exon 53827111 53827695 53827111 ID=Msa1162900-mRNA-1:exon:15560;Parent=Msa1162900-mRNA-1
chr7_4 CDS 53827111 53827695 53827111 ID=Msa1162900-mRNA-1:cds;Parent=Msa1162900-mRNA-1
Gene Sequence

>Msa1162900

ATGGCAAAATCTTCACAATCCTCCATAACTCTTCTAATTTCTTTTAACGTTACATTCCTCTCCATAATATCCCTTGTCACTGCCACTAATTACTATAAAAGCCTATCCCCAACAATGCTGGGTTTTCAAGAAGAGAAATTCACTCACCTTCACTTTTACTTTCACGACATTGTGTCAGGACCAAAACCTAGCATGGTATTTGTAGCTGAGCCTAATGGCAAGGTAAAAAATGCGTTGCCATTCGGGACGGTTGTGGCGATGGATGACCCATTGACGGCTGGTCCTGAACGTGACTCGAAACTTGTGGGTAAGGCTCAAGGAATTTACACTTCTATATCACAAGAGGAGATGGGACTAATGATGGTGATGACCATGGCATTCACTGATGGAGATTTCAATGGAAGTACACTTAGCATATTGGGCAGAAACATGATCATGAGTGAACCTGTTAGAGAAATGGCCATTGTTGGCGGGACTGGGGCTTTTCGTTTTGTACGTGGGTATGCTCAAGCTAAATTTTATTCCGTTGATTACACTAAAGGAGATGCCATTGTGGAATATGATATATTCGTTTTCCATTATTAG
Protein sequence

>Msa1162900

MAKSSQSSITLLISFNVTFLSIISLVTATNYYKSLSPTMLGFQEEKFTHLHFYFHDIVSGPKPSMVFVAEPNGKVKNALPFGTVVAMDDPLTAGPERDSKLVGKAQGIYTSISQEEMGLMMVMTMAFTDGDFNGSTLSILGRNMIMSEPVREMAIVGGTGAFRFVRGYAQAKFYSVDYTKGDAIVEYDIFVFHY*