AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG043440

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG043440 MtrunA17_Chr8g0364021 89.189 148 14 2 1 146 31 178 9.32e-92 267
MsaG043440 MtrunA17_Chr5g0415031 54.023 87 40 0 4 90 33 119 5.85e-27 106
MsaG043440 MtrunA17_Chr8g0364231 54.118 85 39 0 6 90 34 118 2.80e-25 101
MsaG043440 MtrunA17_Chr6g0452001 49.515 103 48 2 2 103 54 153 3.53e-23 95.9
MsaG043440 MtrunA17_Chr6g0452021 50.588 85 41 1 8 92 37 120 3.71e-21 89.4
MsaG043440 MtrunA17_Chr1g0206781 46.341 82 44 0 8 89 5 86 2.35e-19 79.0
MsaG043440 MtrunA17_Chr1g0206771 42.105 95 52 1 7 101 9 100 2.74e-18 78.2
MsaG043440 MtrunA17_Chr1g0206771 48.571 70 36 0 13 82 94 163 2.29e-12 62.4
MsaG043440 MtrunA17_Chr3g0077881 41.284 109 57 3 8 109 2 110 3.49e-17 75.1
MsaG043440 MtrunA17_Chr3g0077881 44.578 83 44 2 5 85 90 172 1.31e-12 62.8
MsaG043440 MtrunA17_Chr3g0077891 49.383 81 40 1 5 84 90 170 5.15e-17 74.3
MsaG043440 MtrunA17_Chr3g0077891 41.284 109 57 2 8 109 2 110 1.36e-16 73.6
MsaG043440 MtrunA17_Chr3g0077941 50.649 77 37 1 8 83 2 78 4.64e-16 72.0
MsaG043440 MtrunA17_Chr3g0077941 45.556 90 41 2 7 95 91 173 4.86e-15 69.3
MsaG043440 MtrunA17_Chr3g0077911 50.000 74 36 1 7 79 83 156 6.61e-16 71.2
MsaG043440 MtrunA17_Chr3g0077911 39.773 88 48 2 8 93 2 86 2.21e-11 59.3
MsaG043440 MtrunA17_Chr1g0205821 37.500 88 55 0 5 92 90 177 2.45e-15 70.1
MsaG043440 MtrunA17_Chr1g0205821 42.254 71 41 0 13 83 12 82 2.07e-11 59.7
MsaG043440 MtrunA17_Chr3g0077861 49.315 73 36 1 8 79 84 156 3.23e-15 69.7
MsaG043440 MtrunA17_Chr1g0205811 40.449 89 53 0 1 89 1 89 7.19e-15 67.4
MsaG043440 MtrunA17_Chr4g0075861 40.449 89 51 1 8 94 83 171 7.42e-14 68.6
MsaG043440 MtrunA17_Chr4g0075861 44.156 77 41 1 7 83 167 241 2.82e-11 60.8
MsaG043440 MtrunA17_Chr4g0075861 44.156 77 40 1 13 89 11 84 5.07e-11 60.1
MsaG043440 MtrunA17_Chr1g0205861 35.965 114 62 2 6 113 8 116 1.11e-13 64.3
MsaG043440 MtrunA17_Chr7g0218911 40.000 75 39 1 18 92 2 70 1.66e-13 63.9
MsaG043440 MtrunA17_Chr4g0075971 38.202 89 53 1 8 94 83 171 5.07e-12 63.5
MsaG043440 MtrunA17_Chr4g0075971 44.156 77 40 1 13 89 11 84 7.12e-11 60.1
MsaG043440 MtrunA17_Chr7g0218891 41.026 78 44 1 14 89 185 262 4.25e-11 60.1
MsaG043440 MtrunA17_Chr2g0328701 37.895 95 52 2 13 107 28 115 4.26e-11 57.8
MsaG043440 MtrunA17_Chr1g0205801 38.462 78 46 1 14 89 12 89 9.03e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG043440 AT1G24190.3 50.549 91 45 0 1 91 1 91 2.80e-24 99.4
MsaG043440 AT1G24190.2 50.549 91 45 0 1 91 1 91 3.00e-24 99.4
MsaG043440 AT1G24190.1 50.549 91 45 0 1 91 1 91 3.00e-24 99.4
MsaG043440 AT3G01320.2 48.936 94 48 0 8 101 51 144 1.79e-23 97.1
MsaG043440 AT3G01320.1 48.936 94 48 0 8 101 51 144 1.99e-23 96.7
MsaG043440 AT1G70060.2 47.778 90 47 0 1 90 1 90 2.25e-22 94.0
MsaG043440 AT1G70060.1 47.778 90 47 0 1 90 1 90 2.25e-22 94.0
MsaG043440 AT1G59890.2 50.000 82 41 0 14 95 45 126 4.44e-22 92.8
MsaG043440 AT1G59890.3 50.000 82 41 0 14 95 45 126 4.61e-22 92.8
MsaG043440 AT1G59890.1 50.000 82 41 0 14 95 45 126 5.13e-22 92.8
MsaG043440 AT1G59890.4 50.000 82 41 0 14 95 45 126 5.22e-22 92.8
MsaG043440 AT5G15020.1 47.872 94 48 1 8 101 46 138 4.77e-21 90.1
MsaG043440 AT5G15020.2 47.872 94 48 1 8 101 46 138 5.10e-21 89.7
MsaG043440 AT5G15025.1 50.633 79 39 0 10 88 43 121 3.86e-20 81.6
MsaG043440 AT1G10450.3 47.561 82 43 0 14 95 84 165 8.57e-19 83.6
MsaG043440 AT1G70030.3 44.706 85 47 0 3 87 11 95 9.82e-19 78.2
MsaG043440 AT1G10450.2 47.561 82 43 0 14 95 33 114 9.85e-19 83.2
MsaG043440 AT1G10450.1 47.561 82 43 0 14 95 33 114 9.85e-19 83.2
MsaG043440 AT1G70030.2 44.706 85 47 0 3 87 11 95 1.62e-18 77.8
MsaG043440 AT1G70030.1 45.122 82 45 0 6 87 3 84 5.64e-18 77.0
MsaG043440 AT5G15040.1 45.946 74 40 0 17 90 6 79 5.93e-17 72.4
MsaG043440 AT5G15040.3 45.946 74 40 0 17 90 6 79 5.93e-17 72.4
MsaG043440 AT5G15040.2 45.946 74 40 0 17 90 6 79 5.93e-17 72.4
MsaG043440 AT1G27220.1 44.444 81 44 1 3 82 2 82 9.09e-17 74.3
MsaG043440 AT4G12020.11 43.820 89 49 1 10 98 304 391 1.47e-16 77.0
MsaG043440 AT1G24200.1 44.565 92 48 1 1 92 1 89 2.06e-16 73.6
MsaG043440 AT4G12020.6 43.820 89 49 1 10 98 304 391 5.93e-16 75.5
MsaG043440 AT4G12020.8 43.820 89 49 1 10 98 304 391 5.93e-16 75.5
MsaG043440 AT4G12020.3 43.820 89 49 1 10 98 304 391 5.95e-16 75.5
MsaG043440 AT4G12020.1 43.820 89 49 1 10 98 304 391 5.99e-16 75.5
MsaG043440 AT4G12020.9 43.820 89 49 1 10 98 304 391 5.99e-16 75.5
MsaG043440 AT4G12020.4 43.820 89 49 1 10 98 304 391 6.07e-16 75.5
MsaG043440 AT4G12020.2 43.820 89 49 1 10 98 304 391 6.13e-16 75.5
MsaG043440 AT4G12020.7 43.820 89 49 1 10 98 304 391 6.28e-16 75.1
MsaG043440 AT4G12020.5 43.820 89 49 1 10 98 237 324 6.73e-16 75.1
MsaG043440 AT4G12020.10 43.820 89 49 1 10 98 304 391 6.74e-16 75.1
MsaG043440 AT1G27250.1 41.250 80 46 1 3 81 9 88 2.10e-15 69.7
MsaG043440 AT1G24210.1 38.462 78 43 1 10 87 10 82 5.63e-13 63.5
MsaG043440 AT1G27260.1 40.000 70 42 0 15 84 4 73 5.42e-12 62.4
MsaG043440 AT5G35610.1 38.144 97 59 1 6 102 2 97 1.45e-11 60.1
MsaG043440 AT1G23810.1 42.188 64 37 0 11 74 106 169 5.13e-11 59.7

Find 44 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTCCTCTTCTTGTGAAAT+TGG 0.130949 8:-45774273 None:intergenic
TCACATTCATCAAGAATCTT+AGG 0.163621 8:-45774300 None:intergenic
TTCATCAGATAAAGCGTAAA+AGG 0.168964 8:+45775910 MsaT043440.1:intron
TTCTGAAGGTTCAGATCAAC+TGG 0.314972 8:+45775985 MsaT043440.1:CDS
GTTCCTCTTCTTGTGAAATT+GGG 0.326386 8:-45774272 None:intergenic
CACATTCATCAAGAATCTTA+GGG 0.349697 8:-45774299 None:intergenic
AACATGCTAATGAGTTTGTT+AGG 0.381561 8:+45774436 MsaT043440.1:CDS
TGATGCCTTTGCATATCTTA+AGG 0.401654 8:+45773792 MsaT043440.1:CDS
ACAAACTCATTAGCATGTTC+AGG 0.401738 8:-45774432 None:intergenic
GAGGTGAAGGAGTTGTTTAA+AGG 0.403782 8:+45774195 MsaT043440.1:CDS
TGAAGGATTACAAAGATAAC+AGG 0.410405 8:+45773872 MsaT043440.1:CDS
AGGACATAATGATCTGATTA+CGG 0.410966 8:+45774215 MsaT043440.1:CDS
CCAAATGGTTCATTCCTTGA+TGG 0.420352 8:-45774405 None:intergenic
CTTCAGAAAGAACTGGATCT+TGG 0.440258 8:-45775970 None:intergenic
TGAGTTTGTTAGGAAAGTTA+AGG 0.441060 8:+45774446 MsaT043440.1:CDS
GGATGTCTTCAAAGAACAAA+TGG 0.447624 8:+45773822 MsaT043440.1:CDS
GGACATAATGATCTGATTAC+GGG 0.453739 8:+45774216 MsaT043440.1:CDS
TCTGAACCTTCAGAAAGAAC+TGG 0.455285 8:-45775977 None:intergenic
CCATCAAGGAATGAACCATT+TGG 0.482429 8:+45774405 MsaT043440.1:CDS
GGTCAGCACATGTTGATTCA+AGG 0.495257 8:-45775949 None:intergenic
GCATGTTCAGGTCCACCAAA+TGG 0.497913 8:-45774420 None:intergenic
CAAGATCCAGTTCTTTCTGA+AGG 0.500976 8:+45775971 MsaT043440.1:CDS
ATATGCAAAGGCATCATCTT+CGG 0.504699 8:-45773785 None:intergenic
AATCCCAATTTCACAAGAAG+AGG 0.518757 8:+45774269 MsaT043440.1:CDS
TCATCAGATAAAGCGTAAAA+GGG 0.524312 8:+45775911 MsaT043440.1:intron
CAATCTCCTCAGATGATGCT+TGG 0.539146 8:+45774363 MsaT043440.1:CDS
TGCATATCTTAAGGCAGTCA+AGG 0.543106 8:+45773801 MsaT043440.1:CDS
ATGTTGATTCAAGGTAAAGA+TGG 0.550744 8:-45775940 None:intergenic
TAATTACCATGATGTTGTAA+CGG 0.566432 8:+45774173 MsaT043440.1:CDS
AGCATATCACAACTCCATCA+AGG 0.566686 8:+45774391 MsaT043440.1:CDS
ATGTGAAATGACAATTCCAT+TGG 0.573688 8:+45774317 MsaT043440.1:CDS
TCAAGGAATGAACCATTTGG+TGG 0.574249 8:+45774408 MsaT043440.1:CDS
TGATGTTGTAACGGAGGTGA+AGG 0.575535 8:+45774182 MsaT043440.1:CDS
TGAGGAGATTGTGCATTGAG+AGG 0.583914 8:-45774351 None:intergenic
TCACCTCCGTTACAACATCA+TGG 0.592553 8:-45774179 None:intergenic
TTCAACATCTTTGCACCAAG+TGG 0.595995 8:+45774240 MsaT043440.1:CDS
CATTCATCAAGAATCTTAGG+GGG 0.605556 8:-45774297 None:intergenic
ACAAAGATGAGTACGAGTCA+AGG 0.614659 8:+45773748 None:intergenic
GACTGCCTTAAGATATGCAA+AGG 0.619589 8:-45773797 None:intergenic
ATTGGGATTTGATAACCACT+TGG 0.631213 8:-45774255 None:intergenic
ACATTCATCAAGAATCTTAG+GGG 0.631425 8:-45774298 None:intergenic
TTACCATGATGTTGTAACGG+AGG 0.669596 8:+45774176 MsaT043440.1:CDS
TCTTCACCAAGCATCATCTG+AGG 0.679479 8:-45774369 None:intergenic
AAGATGAGTACGAGTCAAGG+TGG 0.711763 8:+45773751 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 45773754 45776016 45773754 ID=MsaG043440
Chr8 mRNA 45773754 45776016 45773754 ID=MsaT043440.1;Parent=MsaG043440
Chr8 exon 45773754 45773893 45773754 ID=MsaT043440.1.exon1;Parent=MsaT043440.1
Chr8 CDS 45773754 45773893 45773754 ID=cds.MsaT043440.1;Parent=MsaT043440.1
Chr8 exon 45774170 45774467 45774170 ID=MsaT043440.1.exon2;Parent=MsaT043440.1
Chr8 CDS 45774170 45774467 45774170 ID=cds.MsaT043440.1;Parent=MsaT043440.1
Chr8 exon 45775918 45776016 45775918 ID=MsaT043440.1.exon3;Parent=MsaT043440.1
Chr8 CDS 45775918 45776016 45775918 ID=cds.MsaT043440.1;Parent=MsaT043440.1
Gene Sequence

>MsaT043440.1

ATGAGTACGAGTCAAGGTGGTAAGAAACTAACCGAAGATGATGCCTTTGCATATCTTAAGGCAGTCAAGGATGTCTTCAAAGAACAAATGGAAAACTATTCTTACTTTTTGAAAATAATGAAGGATTACAAAGATAACAGAATTAATTACCATGATGTTGTAACGGAGGTGAAGGAGTTGTTTAAAGGACATAATGATCTGATTACGGGATTCAACATCTTTGCACCAAGTGGTTATCAAATCCCAATTTCACAAGAAGAGGAACAACCCCCTAAGATTCTTGATGAATGTGAAATGACAATTCCATTGGAAGAATTAAAACCTCTCAATGCACAATCTCCTCAGATGATGCTTGGTGAAGAGCATATCACAACTCCATCAAGGAATGAACCATTTGGTGGACCTGAACATGCTAATGAGTTTGTTAGGAAAGTTAAGATAAAGCGTAAAAGGGACGTCACCATCTTTACCTTGAATCAACATGTGCTGACCAAGATCCAGTTCTTTCTGAAGGTTCAGATCAACTGGATCTTCTAG
Protein sequence

>MsaT043440.1

MSTSQGGKKLTEDDAFAYLKAVKDVFKEQMENYSYFLKIMKDYKDNRINYHDVVTEVKELFKGHNDLITGFNIFAPSGYQIPISQEEEQPPKILDECEMTIPLEELKPLNAQSPQMMLGEEHITTPSRNEPFGGPEHANEFVRKVKIKRKRDVTIFTLNQHVLTKIQFFLKVQINWIF*