AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1366620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1366620 MtrunA17_Chr7g0269361 94.972 179 9 0 17 195 17 195 4.09e-124 348
Msa1366620 MtrunA17_Chr1g0195561 67.526 194 61 1 5 198 6 197 1.94e-93 271
Msa1366620 MtrunA17_Chr5g0398871 34.043 188 114 3 8 190 28 210 9.79e-32 114
Msa1366620 MtrunA17_Chr4g0067891 32.338 201 123 4 5 192 6 206 3.34e-31 112
Msa1366620 MtrunA17_Chr4g0018281 31.282 195 124 3 3 190 4 195 6.11e-31 112
Msa1366620 MtrunA17_Chr3g0079401 33.333 168 108 3 26 189 18 185 5.57e-30 108
Msa1366620 MtrunA17_Chr8g0391341 33.140 172 103 3 34 193 45 216 9.52e-30 109
Msa1366620 MtrunA17_Chr4g0018251 30.729 192 129 2 3 190 4 195 2.02e-29 107
Msa1366620 MtrunA17_Chr4g0018241 29.688 192 131 2 3 190 4 195 8.82e-28 103
Msa1366620 MtrunA17_Chr3g0079381 29.762 168 114 3 26 189 17 184 2.29e-26 99.8
Msa1366620 MtrunA17_Chr2g0301381 32.768 177 107 4 19 190 20 189 1.76e-25 97.8
Msa1366620 MtrunA17_Chr4g0056601 30.890 191 124 3 7 189 10 200 9.55e-25 95.9
Msa1366620 MtrunA17_Chr4g0011681 29.858 211 124 6 1 196 5 206 4.47e-22 89.4
Msa1366620 MtrunA17_Chr4g0070161 30.928 194 120 6 3 187 8 196 1.54e-21 87.8
Msa1366620 MtrunA17_Chr4g0011701 29.756 205 118 6 1 189 5 199 3.79e-21 86.7
Msa1366620 MtrunA17_Chr4g0011711 29.858 211 126 7 3 196 1 206 3.20e-20 84.3
Msa1366620 MtrunA17_Chr4g0011721 29.412 204 122 7 3 189 1 199 3.96e-19 81.6
Msa1366620 MtrunA17_Chr7g0272141 29.487 156 107 3 34 187 40 194 4.84e-17 78.6
Msa1366620 MtrunA17_Chr7g0269541 30.366 191 120 3 7 188 15 201 1.10e-16 77.4
Msa1366620 MtrunA17_Chr7g0230391 29.697 165 100 6 34 183 44 207 3.62e-16 73.9
Msa1366620 MtrunA17_Chr8g0345281 32.903 155 99 4 34 183 68 222 1.74e-15 73.9
Msa1366620 MtrunA17_Chr1g0147051 28.804 184 106 5 17 183 67 242 6.41e-15 72.4
Msa1366620 MtrunA17_Chr4g0067611 33.333 159 98 5 33 189 58 210 7.81e-15 72.0
Msa1366620 MtrunA17_Chr3g0126771 27.273 165 106 2 29 183 73 233 1.59e-14 71.2
Msa1366620 MtrunA17_Chr3g0079371 26.582 158 109 4 34 185 67 223 5.40e-14 68.2
Msa1366620 MtrunA17_Chr8g0354901 29.487 156 102 3 34 184 76 228 7.40e-14 69.3
Msa1366620 MtrunA17_Chr2g0295531 30.380 158 102 5 33 187 42 194 1.69e-13 68.2
Msa1366620 MtrunA17_Chr3g0092681 28.729 181 117 5 7 184 50 221 4.26e-13 65.5
Msa1366620 MtrunA17_Chr4g0067601 29.487 156 106 1 34 189 59 210 7.62e-13 66.2
Msa1366620 MtrunA17_Chr2g0295551 28.125 160 105 3 29 185 51 203 8.62e-13 66.2
Msa1366620 MtrunA17_Chr3g0080391 28.205 156 107 3 32 184 69 222 1.65e-12 65.5
Msa1366620 MtrunA17_Chr7g0272151 26.506 166 117 4 34 198 59 220 2.65e-12 64.7
Msa1366620 MtrunA17_Chr1g0192321 27.329 161 113 3 34 193 56 213 4.73e-12 63.9
Msa1366620 MtrunA17_Chr2g0295541 27.673 159 107 3 29 185 51 203 1.25e-11 62.8
Msa1366620 MtrunA17_Chr1g0192311 26.994 163 107 3 34 190 58 214 2.11e-11 62.0
Msa1366620 MtrunA17_Chr1g0192281 26.994 163 107 3 34 190 58 214 2.11e-11 62.0
Msa1366620 MtrunA17_Chr4g0069891 31.325 166 102 6 34 195 81 238 3.78e-11 61.2
Msa1366620 MtrunA17_Chr8g0345211 27.500 160 107 4 33 187 76 231 4.09e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1366620 AT3G62820.1 44.560 193 101 3 3 192 5 194 5.57e-53 168
Msa1366620 AT2G47670.1 47.531 162 80 3 34 192 49 208 3.73e-39 133
Msa1366620 AT5G62360.1 34.177 158 101 3 34 189 44 200 4.14e-30 110
Msa1366620 AT5G20740.1 33.684 190 118 4 9 190 7 196 6.54e-30 109
Msa1366620 AT5G20740.2 33.684 190 118 4 9 190 41 230 1.41e-29 109
Msa1366620 AT4G12390.1 35.758 165 99 2 32 189 38 202 2.03e-28 105
Msa1366620 AT1G62770.1 32.632 190 119 5 8 188 7 196 1.75e-27 103
Msa1366620 AT5G62350.1 32.121 165 106 3 32 190 37 201 6.90e-27 102
Msa1366620 AT4G25260.1 31.795 195 117 5 7 189 9 199 3.20e-26 100
Msa1366620 AT2G01610.1 31.818 176 102 4 34 191 45 220 1.36e-24 96.7
Msa1366620 AT1G62760.1 31.953 169 112 1 25 190 139 307 1.56e-24 98.2
Msa1366620 AT1G14890.1 33.333 168 94 4 34 191 59 218 4.89e-24 95.1
Msa1366620 AT1G70720.1 32.990 194 114 5 11 192 9 198 1.71e-22 90.5
Msa1366620 AT1G70720.2 32.353 204 120 6 1 192 13 210 2.26e-22 90.5
Msa1366620 AT1G23205.1 31.053 190 119 4 9 186 9 198 3.34e-22 89.7
Msa1366620 AT3G47380.1 30.061 163 108 3 32 188 37 199 7.45e-22 89.0
Msa1366620 AT3G14310.1 35.542 166 97 6 34 192 59 221 4.04e-21 90.9
Msa1366620 AT4G25250.1 27.660 188 122 5 8 184 9 193 7.39e-17 75.5
Msa1366620 AT3G05620.1 28.079 203 128 5 1 187 1 201 7.48e-17 78.6
Msa1366620 AT5G51520.1 30.256 195 120 8 9 187 8 202 3.10e-16 73.9
Msa1366620 AT3G05610.1 29.487 156 106 3 34 188 58 210 9.63e-16 75.1
Msa1366620 AT1G53830.1 32.530 166 102 6 34 192 62 224 3.75e-15 73.6
Msa1366620 AT4G00080.1 28.221 163 105 5 34 185 36 197 5.62e-15 70.9
Msa1366620 AT3G49220.2 30.921 152 97 4 34 183 132 277 2.12e-14 71.2
Msa1366620 AT5G04960.1 30.065 153 95 3 33 184 67 208 3.58e-14 70.5
Msa1366620 AT3G14300.1 27.807 187 123 5 13 188 250 435 5.11e-14 70.5
Msa1366620 AT3G49220.3 30.921 152 97 4 34 183 132 277 5.49e-14 70.1
Msa1366620 AT3G49220.1 30.921 152 97 4 34 183 87 232 6.10e-14 70.1
Msa1366620 AT5G27870.1 25.806 155 113 2 34 188 57 209 2.27e-13 68.6
Msa1366620 AT5G53370.2 29.412 153 101 3 34 183 111 259 3.38e-12 65.1
Msa1366620 AT5G53370.1 29.412 153 101 3 34 183 75 223 4.77e-12 64.3
Msa1366620 AT4G15980.1 27.273 154 105 3 38 187 52 202 7.92e-12 63.9
Msa1366620 AT4G15980.2 27.273 154 105 3 38 187 62 212 9.16e-12 63.5
Msa1366620 AT1G53840.1 28.144 167 109 4 33 189 72 237 5.60e-11 61.2
Msa1366620 AT3G10710.1 27.551 196 122 7 1 188 33 216 8.48e-11 60.8
Msa1366620 AT5G49180.1 28.497 193 124 6 2 184 17 205 9.19e-11 60.8

Find 34 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTAAATTGCTGCAAAATA+AGG 0.253916 tig0018459:-170191 Msa1366620:CDS
CGGCACGTGCCCATTTGCTT+GGG 0.271742 tig0018459:+170494 None:intergenic
TAAACTTGCTTCTACGGGTT+TGG 0.307810 tig0018459:-170122 Msa1366620:CDS
CCGGCACGTGCCCATTTGCT+TGG 0.317654 tig0018459:+170493 None:intergenic
TCAGATTGCATAGAAACTTT+TGG 0.319992 tig0018459:-170373 Msa1366620:CDS
GAAATACTAATAGTAAAATA+AGG 0.351810 tig0018459:+170659 None:intergenic
AATGAAGACACTTGCCTTGA+TGG 0.365286 tig0018459:-170238 Msa1366620:CDS
CAAGCAAATGGGCACGTGCC+GGG 0.387799 tig0018459:-170492 Msa1366620:CDS
CAGGAAGAACCCCAAGCAAA+TGG 0.388875 tig0018459:-170504 Msa1366620:CDS
AAACACATTTAGTACACAAA+TGG 0.389035 tig0018459:-170296 Msa1366620:CDS
GTGTGTGGATGCAAAGGTTT+TGG 0.415849 tig0018459:+170548 None:intergenic
CGTCGATAAACTTGCTTCTA+CGG 0.416581 tig0018459:-170128 Msa1366620:CDS
TGGGGTTCTTCCTGCTGTGT+TGG 0.420102 tig0018459:+170513 None:intergenic
ATGCACTTGATGATCTTCAT+AGG 0.431401 tig0018459:-170348 Msa1366620:CDS
ACTTGCCTTGATGGGTTTGA+AGG 0.437348 tig0018459:-170229 Msa1366620:CDS
AAACAAGAACAACAATGTTA+AGG 0.453205 tig0018459:-170593 Msa1366620:CDS
GTCGATAAACTTGCTTCTAC+GGG 0.464387 tig0018459:-170127 Msa1366620:CDS
AGCCAAATTGTATATGCAAA+AGG 0.474317 tig0018459:-170616 Msa1366620:CDS
ATAGGTCACTTGGTGTGCTT+AGG 0.475642 tig0018459:-170330 Msa1366620:CDS
AACACATTTAGTACACAAAT+GGG 0.486915 tig0018459:-170295 Msa1366620:CDS
CCAAGCAAATGGGCACGTGC+CGG 0.491123 tig0018459:-170493 Msa1366620:CDS
AGGAAGAACCCCAAGCAAAT+GGG 0.506154 tig0018459:-170503 Msa1366620:CDS
AAGCAAATGGGCACGTGCCG+GGG 0.507156 tig0018459:-170491 Msa1366620:CDS
ATGAAGACACTTGCCTTGAT+GGG 0.520738 tig0018459:-170237 Msa1366620:CDS
ATGGGCACGTGCCGGGGTGT+CGG 0.523182 tig0018459:-170485 Msa1366620:CDS
AAGATGAACGAGAAGATGAA+AGG 0.537634 tig0018459:-170415 Msa1366620:CDS
GGCACGTGCCCATTTGCTTG+GGG 0.543135 tig0018459:+170495 None:intergenic
GCACAATTCTCCAACACAGC+AGG 0.560783 tig0018459:-170523 Msa1366620:CDS
GATGATCTTCATAGGTCACT+TGG 0.570132 tig0018459:-170340 Msa1366620:CDS
TGGAGAATTGTGCTAGTGTG+TGG 0.572339 tig0018459:+170533 None:intergenic
GTGCTAGTGTGTGGATGCAA+AGG 0.620695 tig0018459:+170542 None:intergenic
AGGAAGCTTGCAGTGTCACA+AGG 0.623585 tig0018459:-170573 Msa1366620:CDS
AAATGGGAGATCTCAACACA+TGG 0.662660 tig0018459:-170279 Msa1366620:CDS
GCTTATCGTTACCGACACCC+CGG 0.696996 tig0018459:+170474 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAATACTAATAGTAAAATA+AGG + tig0018459:170122-170141 None:intergenic 15.0%
!! AATTAAATTGCTGCAAAATA+AGG - tig0018459:170587-170606 Msa1366620:CDS 20.0%
!! TTCCTTTTGCATATACAATT+TGG + tig0018459:170167-170186 None:intergenic 25.0%
! AAACAAGAACAACAATGTTA+AGG - tig0018459:170185-170204 Msa1366620:CDS 25.0%
! AAACACATTTAGTACACAAA+TGG - tig0018459:170482-170501 Msa1366620:CDS 25.0%
! AACACATTTAGTACACAAAT+GGG - tig0018459:170483-170502 Msa1366620:CDS 25.0%
AGCCAAATTGTATATGCAAA+AGG - tig0018459:170162-170181 Msa1366620:CDS 30.0%
! TCAGATTGCATAGAAACTTT+TGG - tig0018459:170405-170424 Msa1366620:CDS 30.0%
AAGATGAACGAGAAGATGAA+AGG - tig0018459:170363-170382 Msa1366620:CDS 35.0%
! ATGCACTTGATGATCTTCAT+AGG - tig0018459:170430-170449 Msa1366620:CDS 35.0%
! TTTTTCCTTCAAACCCATCA+AGG + tig0018459:170557-170576 None:intergenic 35.0%
!! TGATGGGTTTGAAGGAAAAA+CGG - tig0018459:170557-170576 Msa1366620:CDS 35.0%
GATGATCTTCATAGGTCACT+TGG - tig0018459:170438-170457 Msa1366620:CDS 40.0%
AAATGGGAGATCTCAACACA+TGG - tig0018459:170499-170518 Msa1366620:CDS 40.0%
AATGAAGACACTTGCCTTGA+TGG - tig0018459:170540-170559 Msa1366620:CDS 40.0%
ATGAAGACACTTGCCTTGAT+GGG - tig0018459:170541-170560 Msa1366620:CDS 40.0%
! CGTCGATAAACTTGCTTCTA+CGG - tig0018459:170650-170669 Msa1366620:CDS 40.0%
! GTCGATAAACTTGCTTCTAC+GGG - tig0018459:170651-170670 Msa1366620:CDS 40.0%
! TAAACTTGCTTCTACGGGTT+TGG - tig0018459:170656-170675 Msa1366620:CDS 40.0%
! GTGTGTGGATGCAAAGGTTT+TGG + tig0018459:170233-170252 None:intergenic 45.0%
TGGAGAATTGTGCTAGTGTG+TGG + tig0018459:170248-170267 None:intergenic 45.0%
AGGAAGAACCCCAAGCAAAT+GGG - tig0018459:170275-170294 Msa1366620:CDS 45.0%
!! ATAGGTCACTTGGTGTGCTT+AGG - tig0018459:170448-170467 Msa1366620:CDS 45.0%
!! ACTTGCCTTGATGGGTTTGA+AGG - tig0018459:170549-170568 Msa1366620:CDS 45.0%
AGGAAGCTTGCAGTGTCACA+AGG - tig0018459:170205-170224 Msa1366620:CDS 50.0%
GTGCTAGTGTGTGGATGCAA+AGG + tig0018459:170239-170258 None:intergenic 50.0%
GCACAATTCTCCAACACAGC+AGG - tig0018459:170255-170274 Msa1366620:CDS 50.0%
CAGGAAGAACCCCAAGCAAA+TGG - tig0018459:170274-170293 Msa1366620:CDS 50.0%
TGGGGTTCTTCCTGCTGTGT+TGG + tig0018459:170268-170287 None:intergenic 55.0%
GCTTATCGTTACCGACACCC+CGG + tig0018459:170307-170326 None:intergenic 55.0%
GGCACGTGCCCATTTGCTTG+GGG + tig0018459:170286-170305 None:intergenic 60.0%
CGGCACGTGCCCATTTGCTT+GGG + tig0018459:170287-170306 None:intergenic 60.0%
CCAAGCAAATGGGCACGTGC+CGG - tig0018459:170285-170304 Msa1366620:CDS 60.0%
CAAGCAAATGGGCACGTGCC+GGG - tig0018459:170286-170305 Msa1366620:CDS 60.0%
AAGCAAATGGGCACGTGCCG+GGG - tig0018459:170287-170306 Msa1366620:CDS 60.0%
CCGGCACGTGCCCATTTGCT+TGG + tig0018459:170288-170307 None:intergenic 65.0%
ATGGGCACGTGCCGGGGTGT+CGG - tig0018459:170293-170312 Msa1366620:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0018459 gene 170102 170698 170102 ID=Msa1366620;Name=Msa1366620
tig0018459 mRNA 170102 170698 170102 ID=Msa1366620-mRNA-1;Parent=Msa1366620;Name=Msa1366620-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|198
tig0018459 exon 170102 170698 170102 ID=Msa1366620-mRNA-1:exon:15174;Parent=Msa1366620-mRNA-1
tig0018459 CDS 170102 170698 170102 ID=Msa1366620-mRNA-1:cds;Parent=Msa1366620-mRNA-1
Gene Sequence

>Msa1366620

ATGATTATAACATCACGCCTTATTTTACTATTAGTATTTCTTTCGTTCTCAACAAATACTAGCCAAATTGTATATGCAAAAGGAAACAAGAACAACAATGTTAAGGAAGCTTGCAGTGTCACAAGGTACCAAAACCTTTGCATCCACACACTAGCACAATTCTCCAACACAGCAGGAAGAACCCCAAGCAAATGGGCACGTGCCGGGGTGTCGGTAACGATAAGCGAAGTTAAGAATGTTCAAGCATATCTCACAAAATTAAAGATGAACGAGAAGATGAAAGGAAGAAACAGAGTTGCACTTTCAGATTGCATAGAAACTTTTGGCTATGCACTTGATGATCTTCATAGGTCACTTGGTGTGCTTAGGAAACTAAGCAAAAACACATTTAGTACACAAATGGGAGATCTCAACACATGGATTAGTGCAGCTCTTACTAATGAAGACACTTGCCTTGATGGGTTTGAAGGAAAAACGGAGAAGCAAATTAAATTGCTGCAAAATAAGGTTAAGAACGTGTCTTACATAACAAGTAACGCACTTGCTCTCGTCGATAAACTTGCTTCTACGGGTTTGGAAAGCATCACTGATCCATAG

Protein sequence

>Msa1366620

MIITSRLILLLVFLSFSTNTSQIVYAKGNKNNNVKEACSVTRYQNLCIHTLAQFSNTAGRTPSKWARAGVSVTISEVKNVQAYLTKLKMNEKMKGRNRVALSDCIETFGYALDDLHRSLGVLRKLSKNTFSTQMGDLNTWISAALTNEDTCLDGFEGKTEKQIKLLQNKVKNVSYITSNALALVDKLASTGLESITDP*