AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG030240


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030240 MtrunA17_Chr6g0449851 90.402 323 22 2 1 322 1 315 0.0 596
MsaG030240 MtrunA17_Chr6g0457851 64.740 346 98 3 1 322 11 356 1.83e-157 444
MsaG030240 MtrunA17_Chr6g0449861 64.943 348 95 4 1 322 9 355 1.04e-153 434
MsaG030240 MtrunA17_Chr1g0212151 60.674 356 97 6 1 322 1 347 6.38e-140 399
MsaG030240 MtrunA17_Chr4g0059631 40.385 156 90 1 1 156 1 153 3.55e-35 128
MsaG030240 MtrunA17_Chr4g0022641 38.043 184 109 3 1 184 1 179 2.72e-34 129
MsaG030240 MtrunA17_Chr1g0212471 38.217 157 96 1 1 157 1 156 5.70e-33 120
MsaG030240 MtrunA17_Chr2g0303981 38.312 154 90 2 3 155 5 154 6.60e-30 112
MsaG030240 MtrunA17_Chr3g0107381 25.000 228 143 9 1 207 1 221 9.81e-14 69.3
MsaG030240 MtrunA17_Chr3g0134451 26.036 169 109 5 1 169 1 153 5.86e-13 68.6
MsaG030240 MtrunA17_Chr3g0125241 45.161 62 34 0 1 62 26 87 2.42e-12 65.1
MsaG030240 MtrunA17_Chr5g0425191 47.059 51 27 0 1 51 1 51 3.98e-12 62.0
MsaG030240 MtrunA17_Chr1g0159661 30.719 153 88 5 1 150 1 138 8.27e-12 63.2
MsaG030240 MtrunA17_Chr5g0404951 31.159 138 83 4 1 136 1 128 1.23e-11 63.5
MsaG030240 MtrunA17_Chr3g0107331 31.818 110 68 3 3 111 2 105 1.33e-11 62.0
MsaG030240 MtrunA17_Chr3g0107351 30.496 141 86 4 3 142 2 131 1.37e-11 62.0
MsaG030240 MtrunA17_Chr8g0379021 28.758 153 79 6 2 137 12 151 1.52e-11 62.4
MsaG030240 MtrunA17_Chr2g0279821 53.061 49 23 0 1 49 1 49 1.92e-11 63.2
MsaG030240 MtrunA17_Chr8g0380021 27.389 157 101 4 1 157 17 160 2.37e-11 62.8
MsaG030240 MtrunA17_Chr7g0246381 44.898 49 27 0 1 49 1 49 2.79e-11 58.5
MsaG030240 MtrunA17_Chr1g0173161 48.980 49 25 0 1 49 1 49 2.93e-11 58.9
MsaG030240 MtrunA17_Chr3g0107341 31.944 144 80 6 3 142 2 131 3.98e-11 60.8
MsaG030240 MtrunA17_Chr5g0427921 46.939 49 26 0 1 49 1 49 4.64e-11 57.8
MsaG030240 MtrunA17_Chr4g0014321 36.752 117 59 5 1 116 1 103 6.68e-11 61.6
MsaG030240 MtrunA17_Chr4g0044071 48.000 50 26 0 1 50 1 50 6.89e-11 58.9
MsaG030240 MtrunA17_Chr8g0377561 46.939 49 26 0 1 49 1 49 6.94e-11 58.5
MsaG030240 MtrunA17_Chr2g0308251 46.939 49 26 0 1 49 1 49 7.47e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG030240 AT5G55690.1 40.000 145 79 2 1 144 1 138 1.91e-25 103
MsaG030240 AT5G55690.2 40.000 145 79 2 1 144 1 138 1.91e-25 103
MsaG030240 AT5G58890.1 35.664 143 85 3 6 145 6 144 3.93e-19 86.3
MsaG030240 AT3G18650.1 35.075 134 75 4 16 144 31 157 8.77e-17 80.9
MsaG030240 AT1G22590.2 30.128 156 98 3 1 151 1 150 5.38e-14 69.3
MsaG030240 AT2G22630.1 55.102 49 22 0 1 49 1 49 1.67e-12 66.2
MsaG030240 AT2G22630.2 55.102 49 22 0 1 49 1 49 1.67e-12 66.2
MsaG030240 AT3G57390.3 31.852 135 70 4 1 119 1 129 1.95e-12 66.2
MsaG030240 AT3G57390.1 32.593 135 69 4 1 119 1 129 2.53e-12 66.2
MsaG030240 AT3G05860.2 30.097 103 65 3 1 102 1 97 1.44e-11 63.5
MsaG030240 AT3G05860.3 30.097 103 65 3 1 102 1 97 1.78e-11 63.9
MsaG030240 AT3G05860.1 30.097 103 65 3 1 102 1 97 1.94e-11 63.9
MsaG030240 AT5G20240.2 45.000 60 33 0 1 60 1 60 2.04e-11 61.6
MsaG030240 AT5G26650.1 31.193 109 68 3 5 112 3 105 2.27e-11 64.7
MsaG030240 AT3G57230.1 48.000 50 26 0 1 50 1 50 4.98e-11 62.4
MsaG030240 AT3G57230.4 48.000 50 26 0 1 50 1 50 4.98e-11 62.4
MsaG030240 AT4G37940.3 53.061 49 23 0 1 49 1 49 5.15e-11 61.2
MsaG030240 AT3G30260.1 48.000 50 26 0 1 50 1 50 5.20e-11 62.4
MsaG030240 AT4G37940.4 53.061 49 23 0 1 49 1 49 5.61e-11 61.6
MsaG030240 AT4G37940.1 53.061 49 23 0 1 49 1 49 5.96e-11 62.0
MsaG030240 AT5G20240.1 49.020 51 26 0 1 51 1 51 6.07e-11 61.6
MsaG030240 AT1G65300.1 30.275 109 69 3 5 112 4 106 8.25e-11 62.0

Find 67 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTTCTTCATATCGATTT+TGG 0.101762 6:+5339816 None:intergenic
TCCCATGAATATCTACTTTA+TGG 0.106807 6:-5339676 MsaT030240.1:CDS
TTGTCTTTAGGCCATGTTTC+AGG 0.191776 6:+5340384 None:intergenic
GATGAATCTTACAATTCTTT+TGG 0.252372 6:-5340198 MsaT030240.1:CDS
AACAATTGAGGTCATTTATT+AGG 0.253713 6:-5340170 MsaT030240.1:CDS
TCTTGAACATCATAGGTCTT+AGG 0.310978 6:+5340306 None:intergenic
CCTTACTTGACCTCAAATTC+AGG 0.312584 6:-5340060 MsaT030240.1:CDS
AGGCTACTTCGTTCCATTCA+TGG 0.325169 6:+5339612 None:intergenic
AATATGCTTGCAAGGGTAAT+AGG 0.325548 6:+5339885 None:intergenic
ACTTTATGGATCCTATGATA+TGG 0.335816 6:-5339662 MsaT030240.1:CDS
CAACATATCCTTGGCCTTCA+AGG 0.352632 6:+5340409 None:intergenic
AAGCTCTCAACCTTCCCTTA+TGG 0.354140 6:-5339926 MsaT030240.1:CDS
TCAAGTAAGGAGAACTAATA+AGG 0.363002 6:+5340073 None:intergenic
GGGTCGTGGAAGAATATCTA+TGG 0.367126 6:-5340559 MsaT030240.1:CDS
GAGCTTTGTTCCAATTGAAT+TGG 0.369750 6:+5339943 None:intergenic
GCAAGCATATTGATGCTAAC+TGG 0.394885 6:-5339873 MsaT030240.1:CDS
GTAATAGGAGCTTTGTGAAC+TGG 0.402630 6:+5339900 None:intergenic
AAAATATTCTTGAACATCAT+AGG 0.416188 6:+5340299 None:intergenic
TATCCTTGGCCTTCAAGGTT+GGG 0.419769 6:+5340414 None:intergenic
CTGTATGCTCCCAACCTTGA+AGG 0.420817 6:-5340423 MsaT030240.1:CDS
TTGAATACTATCCATATCAT+AGG 0.430128 6:+5339651 None:intergenic
AACATCAACATCACAAAGAA+TGG 0.436469 6:+5340455 None:intergenic
ATCCATAAAGTAGATATTCA+TGG 0.445056 6:+5339674 None:intergenic
ACTATGACACAACAATTGAT+AGG 0.455411 6:-5340332 MsaT030240.1:CDS
GGAGGAGTAGGCATAGCAAT+AGG 0.462020 6:+5339721 None:intergenic
AAAGGATGGTTTAATAAAGA+AGG 0.462912 6:-5340490 MsaT030240.1:CDS
ATCTATGGAACTCATTCAAA+AGG 0.463531 6:-5340544 MsaT030240.1:CDS
CAACTGTTCAACTCCATGAA+TGG 0.470369 6:-5339625 MsaT030240.1:CDS
TTATCACAAATATTCATCAA+TGG 0.474002 6:+5339985 None:intergenic
TTTCCATTGTAATAGTATGA+TGG 0.479664 6:+5339766 None:intergenic
CCTGAATTTGAGGTCAAGTA+AGG 0.484340 6:+5340060 None:intergenic
AAAGTAGATATTCATGGGAT+AGG 0.486977 6:+5339680 None:intergenic
TTTCAGGTTCAACATATCCT+TGG 0.488478 6:+5340400 None:intergenic
TTTGTGAACTGGAAACCATA+AGG 0.489071 6:+5339911 None:intergenic
ATATCCTTGGCCTTCAAGGT+TGG 0.502086 6:+5340413 None:intergenic
GAAGTTGGTACCTGAATTTG+AGG 0.503776 6:+5340050 None:intergenic
CAAAATCGATATGAAGAAGA+AGG 0.504284 6:-5339815 MsaT030240.1:CDS
TGATGCTAACTGGACCCATC+AGG 0.505363 6:-5339863 MsaT030240.1:CDS
GATAACATTGCAAAAGAGAA+AGG 0.505631 6:-5340508 MsaT030240.1:CDS
TTGCCATCATACTATTACAA+TGG 0.513046 6:-5339769 MsaT030240.1:CDS
TTGTGAACTGGAAACCATAA+GGG 0.517232 6:+5339912 None:intergenic
TTGAATTGGCCAAAACCCTA+AGG 0.530156 6:+5339957 None:intergenic
TAAAGATGATGTATCCAACT+TGG 0.530838 6:-5340221 MsaT030240.1:CDS
CTTCAAGGTTGGGAGCATAC+AGG 0.533279 6:+5340424 None:intergenic
TAACATTAGCATTAACCTGA+TGG 0.537085 6:+5339848 None:intergenic
AGGTTTGCAAGATTCTGAAA+AGG 0.545328 6:+5339700 None:intergenic
TCCATAAAGTAGATATTCAT+GGG 0.546951 6:+5339675 None:intergenic
AGATTCTGAAAAGGAGGAGT+AGG 0.549609 6:+5339709 None:intergenic
TTAGCATCAATATGCTTGCA+AGG 0.558529 6:+5339877 None:intergenic
ATGCATACCAACATGTCTCA+AGG 0.563493 6:-5340021 MsaT030240.1:CDS
GGTATGCATGAGATTGAAGT+TGG 0.570442 6:+5340035 None:intergenic
TGTTCATAGAAAATGGGTCG+TGG 0.571043 6:-5340573 None:intergenic
TGAATTGGCCAAAACCCTAA+GGG 0.580427 6:+5339958 None:intergenic
ACATTGCAAAAGAGAAAGGA+TGG 0.582137 6:-5340504 MsaT030240.1:CDS
TTGTAAGATTCATCCCAAGT+TGG 0.584895 6:+5340207 None:intergenic
AACATTAGCATTAACCTGAT+GGG 0.586384 6:+5339849 None:intergenic
AAAGATGATGTATCCAACTT+GGG 0.588589 6:-5340220 MsaT030240.1:CDS
GCTCCCAACCTTGAAGGCCA+AGG 0.597883 6:-5340417 MsaT030240.1:CDS
TTTACAAAGTGCGTAAAGAG+AGG 0.599078 6:-5340245 MsaT030240.1:CDS
TTTGCAAGATTCTGAAAAGG+AGG 0.605154 6:+5339703 None:intergenic
TGCATACCAACATGTCTCAA+GGG 0.610432 6:-5340020 MsaT030240.1:CDS
TAGCATCAATATGCTTGCAA+GGG 0.621207 6:+5339878 None:intergenic
TGGTTTAATAAAGAAGGCAA+AGG 0.627278 6:-5340484 MsaT030240.1:CDS
GAACTGGAAACCATAAGGGA+AGG 0.661731 6:+5339916 None:intergenic
GATATGTTGAACCTGAAACA+TGG 0.676143 6:-5340395 MsaT030240.1:CDS
GCGAAAAGATGAATCACACA+AGG 0.690015 6:-5340103 MsaT030240.1:CDS
ATGGCCTAAAGACAAAAGAG+AGG 0.713382 6:-5340376 MsaT030240.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 5339615 5340583 5339615 ID=MsaG030240
Chr6 mRNA 5339615 5340583 5339615 ID=MsaT030240.1;Parent=MsaG030240
Chr6 exon 5339615 5340583 5339615 ID=MsaT030240.1.exon1;Parent=MsaT030240.1
Chr6 CDS 5339615 5340583 5339615 ID=cds.MsaT030240.1;Parent=MsaT030240.1
Gene Sequence

>MsaT030240.1

ATGGGTCGTGGAAGAATATCTATGGAACTCATTCAAAAGGAGAGATCTAGAAAGATAACATTGCAAAAGAGAAAGGATGGTTTAATAAAGAAGGCAAAGGAATTTTCCATTCTTTGTGATGTTGATGTTTGTTTGATCCTGTATGCTCCCAACCTTGAAGGCCAAGGATATGTTGAACCTGAAACATGGCCTAAAGACAAAAGAGAGGTACAAAGAATTCTTCAAAATTACTATGACACAACAATTGATAGGCGTCCTAAGACCTATGATGTTCAAGAATATTTTAAGGAGAGGATGAAAAAAGTTGAATTAGAGATTTACAAAGTGCGTAAAGAGAGGTTAAAGATGATGTATCCAACTTGGGATGAATCTTACAATTCTTTTGGATATGAACAATTGAGGTCATTTATTAGGTTTTTGGATTCTAAGCTTGACGCATGTGATCAAAAGATGAATATGCGAAAAGATGAATCACACAAGGTCAATAACCTTATTAGTTCTCCTTACTTGACCTCAAATTCAGGTACCAACTTCAATCTCATGCATACCAACATGTCTCAAGGGAAAATTTACTCTCCATTGATGAATATTTGTGATAAAAATCCCTTAGGGTTTTGGCCAATTCAATTGGAACAAAGCTCTCAACCTTCCCTTATGGTTTCCAGTTCACAAAGCTCCTATTACCCTTGCAAGCATATTGATGCTAACTGGACCCATCAGGTTAATGCTAATGTTATGTATGATCCCAAAATCGATATGAAGAAGAAGGATGAAGCTGAAAATGATAAAAACTTGCCATCATACTATTACAATGGAAATGCAATGATAATGCAATCATATCCTATTGCTATGCCTACTCCTCCTTTTCAGAATCTTGCAAACCTATCCCATGAATATCTACTTTATGGATCCTATGATATGGATAGTATTCAAGCTCAACTGTTCAACTCCATGAATGGAACGAAGTAG

Protein sequence

>MsaT030240.1

MGRGRISMELIQKERSRKITLQKRKDGLIKKAKEFSILCDVDVCLILYAPNLEGQGYVEPETWPKDKREVQRILQNYYDTTIDRRPKTYDVQEYFKERMKKVELEIYKVRKERLKMMYPTWDESYNSFGYEQLRSFIRFLDSKLDACDQKMNMRKDESHKVNNLISSPYLTSNSGTNFNLMHTNMSQGKIYSPLMNICDKNPLGFWPIQLEQSSQPSLMVSSSQSSYYPCKHIDANWTHQVNANVMYDPKIDMKKKDEAENDKNLPSYYYNGNAMIMQSYPIAMPTPPFQNLANLSHEYLLYGSYDMDSIQAQLFNSMNGTK*