AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1099080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1099080 MtrunA17_Chr7g0218891 80.460 174 34 0 1 174 49 222 6.75e-92 268
Msa1099080 MtrunA17_Chr7g0218891 77.344 128 29 0 1 128 135 262 1.63e-65 201
Msa1099080 MtrunA17_Chr7g0218891 74.815 135 34 0 40 174 2 136 7.98e-56 177
Msa1099080 MtrunA17_Chr3g0077911 43.925 107 58 2 13 118 51 156 1.55e-19 80.5
Msa1099080 MtrunA17_Chr3g0077911 35.200 125 77 3 53 174 3 126 4.25e-13 63.5
Msa1099080 MtrunA17_Chr4g0075861 33.333 174 107 4 1 174 43 207 6.83e-19 82.4
Msa1099080 MtrunA17_Chr4g0075861 40.000 115 62 4 13 125 135 244 2.47e-15 72.4
Msa1099080 MtrunA17_Chr4g0075861 34.513 113 68 3 64 176 20 126 2.97e-11 60.8
Msa1099080 MtrunA17_Chr8g0364231 44.860 107 55 3 67 171 56 160 7.42e-19 83.2
Msa1099080 MtrunA17_Chr8g0364231 36.441 118 71 3 1 116 76 191 2.64e-13 67.0
Msa1099080 MtrunA17_Chr3g0077891 42.105 114 59 2 13 120 55 167 1.40e-18 78.6
Msa1099080 MtrunA17_Chr3g0077891 40.000 130 70 3 51 174 8 135 2.98e-18 77.8
Msa1099080 MtrunA17_Chr3g0077861 43.636 110 54 3 13 118 51 156 1.13e-17 75.9
Msa1099080 MtrunA17_Chr3g0077861 36.364 121 73 3 57 174 7 126 1.42e-13 65.1
Msa1099080 MtrunA17_Chr4g0075971 32.759 174 108 4 1 174 43 207 2.79e-17 78.6
Msa1099080 MtrunA17_Chr4g0075971 39.370 127 70 4 1 125 123 244 2.04e-15 73.2
Msa1099080 MtrunA17_Chr3g0077881 37.692 130 73 3 51 174 8 135 4.04e-17 74.7
Msa1099080 MtrunA17_Chr3g0077881 37.719 114 64 2 13 120 55 167 1.12e-13 65.5
Msa1099080 MtrunA17_Chr5g0415031 39.091 110 57 3 67 171 57 161 7.72e-16 74.3
Msa1099080 MtrunA17_Chr1g0206771 41.905 105 54 2 70 174 33 130 9.50e-16 71.2
Msa1099080 MtrunA17_Chr1g0206771 38.017 121 66 3 1 120 50 162 3.48e-15 69.7
Msa1099080 MtrunA17_Chr3g0077941 37.984 129 73 3 51 174 8 134 1.45e-15 70.5
Msa1099080 MtrunA17_Chr3g0077941 39.831 118 65 4 13 125 55 171 1.08e-14 68.2
Msa1099080 MtrunA17_Chr1g0205831 37.607 117 58 2 13 129 48 149 8.08e-15 68.6
Msa1099080 MtrunA17_Chr1g0205831 33.333 123 61 4 54 174 5 108 2.56e-12 62.0
Msa1099080 MtrunA17_Chr6g0452001 35.385 130 72 4 47 171 59 181 2.58e-14 70.1
Msa1099080 MtrunA17_Chr6g0452021 34.711 121 75 2 51 171 43 159 5.52e-14 68.9
Msa1099080 MtrunA17_Chr1g0205821 34.821 112 69 2 13 122 59 168 5.60e-14 66.6
Msa1099080 MtrunA17_Chr1g0205821 32.540 126 79 3 51 174 13 134 1.05e-13 65.9
Msa1099080 MtrunA17_Chr1g0205811 41.237 97 51 2 52 144 15 109 5.88e-14 65.1
Msa1099080 MtrunA17_Chr1g0206781 30.827 133 64 2 43 175 3 107 9.92e-14 64.3
Msa1099080 MtrunA17_Chr1g0205801 44.156 77 41 1 52 128 13 87 1.33e-13 63.9
Msa1099080 MtrunA17_Chr1g0205861 38.202 89 51 2 47 135 12 96 9.19e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1099080 AT1G24190.1 39.231 130 73 5 43 170 6 131 1.18e-16 77.4
Msa1099080 AT1G24190.1 34.646 127 78 5 1 124 48 172 6.14e-11 60.8
Msa1099080 AT1G24190.3 39.231 130 73 5 43 170 6 131 1.20e-16 77.4
Msa1099080 AT1G24190.3 34.646 127 78 5 1 124 48 172 6.70e-11 60.5
Msa1099080 AT1G24190.2 39.231 130 73 5 43 170 6 131 1.25e-16 77.0
Msa1099080 AT1G24190.2 34.646 127 78 5 1 124 48 172 6.20e-11 60.8
Msa1099080 AT1G70060.2 36.842 133 77 4 42 171 5 133 5.73e-16 75.1
Msa1099080 AT1G70060.1 36.842 133 77 4 42 171 5 133 5.73e-16 75.1
Msa1099080 AT5G15020.1 38.462 130 76 3 45 174 46 171 1.30e-15 74.3
Msa1099080 AT5G15020.2 38.462 130 76 3 45 174 46 171 1.35e-15 74.3
Msa1099080 AT1G70030.1 40.187 107 60 2 10 115 54 157 2.68e-15 70.1
Msa1099080 AT1G70030.1 34.646 127 73 4 48 171 8 127 5.46e-14 66.6
Msa1099080 AT3G01320.2 30.769 169 112 3 4 171 10 174 1.67e-14 70.9
Msa1099080 AT3G01320.2 27.273 176 120 4 1 174 91 260 4.01e-11 61.2
Msa1099080 AT3G01320.1 30.769 169 112 3 4 171 10 174 1.80e-14 70.9
Msa1099080 AT3G01320.1 27.273 176 120 4 1 174 91 260 4.09e-11 61.2
Msa1099080 AT1G59890.3 35.238 105 66 1 67 171 59 161 6.04e-14 69.3
Msa1099080 AT1G59890.1 35.238 105 66 1 67 171 59 161 6.28e-14 69.3
Msa1099080 AT1G59890.2 35.238 105 66 1 67 171 59 161 6.46e-14 69.3
Msa1099080 AT1G59890.4 35.238 105 66 1 67 171 59 161 6.90e-14 69.3
Msa1099080 AT1G10450.3 35.577 104 65 1 69 172 100 201 1.26e-12 65.5
Msa1099080 AT1G10450.3 31.884 138 91 2 1 138 118 252 1.90e-12 65.1
Msa1099080 AT1G10450.2 35.577 104 65 1 69 172 49 150 1.59e-12 65.5
Msa1099080 AT1G10450.2 31.884 138 91 2 1 138 67 201 2.16e-12 65.1
Msa1099080 AT1G10450.1 35.577 104 65 1 69 172 49 150 1.59e-12 65.5
Msa1099080 AT1G10450.1 31.884 138 91 2 1 138 67 201 2.16e-12 65.1
Msa1099080 AT1G24200.1 33.607 122 76 4 51 172 14 130 3.22e-11 59.7
Msa1099080 AT1G70030.2 33.036 112 68 3 48 156 19 126 3.74e-11 58.5
Msa1099080 AT1G70030.3 34.615 104 61 3 47 147 18 117 9.60e-11 57.0

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAACTTTCTGAATGTCTTTA+AGG 0.070134 7_3:+27351126 Msa1099080:CDS
AACATCATTGACAAATTCTT+TGG 0.315051 7_3:-27351418 None:intergenic
ATCTGAGGAGGAACAATCTC+TGG 0.416325 7_3:+27351018 Msa1099080:CDS
AGTAGTTCAATCTTGATATA+AGG 0.418112 7_3:-27351320 None:intergenic
TAACTTTCTGAATGTGTTGA+AGG 0.435901 7_3:+27351482 Msa1099080:CDS
AAGGGATTATTTGAAGGTCA+TGG 0.456386 7_3:+27350938 Msa1099080:CDS
GAATCTTGGTGAATTATTGA+AGG 0.480427 7_3:+27351275 Msa1099080:CDS
AGGATTGACGCTGCGAATCT+TGG 0.486810 7_3:+27351261 Msa1099080:intron
AGCTTGATTTCAAATCCATC+AGG 0.489510 7_3:-27350992 None:intergenic
AAATCTCAGTAAATTCTTGA+AGG 0.490603 7_3:+27350919 Msa1099080:CDS
TTCTTGAAGGGATTATTTGA+AGG 0.491097 7_3:+27350932 Msa1099080:CDS
CAGCTTGATTTCAAATCCAT+CGG 0.495338 7_3:-27351349 None:intergenic
AGCTTGATTTCAAATCCATC+GGG 0.513708 7_3:-27351348 None:intergenic
TTATTGAAGGGATTATTTCA+AGG 0.513778 7_3:+27351288 Msa1099080:CDS
AATCTTGGTGAATTATTGAA+GGG 0.514858 7_3:+27351276 Msa1099080:CDS
TTGAACTACTTCATGCCTGA+TGG 0.515459 7_3:+27350977 Msa1099080:CDS
AATCTCAGTAAATTCTTGAA+GGG 0.520509 7_3:+27350920 Msa1099080:CDS
AATCAAGCTGCCATCGGAGG+AGG 0.529195 7_3:+27351362 Msa1099080:CDS
AGAGATTCTTCCTCCTCCGA+TGG 0.570247 7_3:-27351372 None:intergenic
TTGAACTACTTCATGCCCGA+TGG 0.579628 7_3:+27351333 Msa1099080:CDS
ATTTATTCAAGTTAATCAGA+GGG 0.582516 7_3:+27351449 Msa1099080:CDS
GATTTATTCAAGTTAATCAG+AGG 0.587296 7_3:+27351092 Msa1099080:CDS
GATTTATTCAAGTTAATCAG+AGG 0.587296 7_3:+27351448 Msa1099080:CDS
TGAAATCAAGCTGCCATCGG+AGG 0.588675 7_3:+27351359 Msa1099080:CDS
TGAAATCAAGCTTCTATCTG+AGG 0.589635 7_3:+27351003 Msa1099080:CDS
ATTTATTCAAGTTAATCAGA+GGG 0.591574 7_3:+27351093 Msa1099080:CDS
TGAAGGATTACAAGAGACAA+AGG 0.594478 7_3:+27351499 Msa1099080:CDS
ATTTGAAATCAAGCTGCCAT+CGG 0.624832 7_3:+27351356 Msa1099080:CDS
AATCAAGCTTCTATCTGAGG+AGG 0.631110 7_3:+27351006 Msa1099080:CDS
TTAAGGATTACAAAACACAA+AGG 0.659829 7_3:+27351143 Msa1099080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAATATAATAAAAAAATAG+TGG - chr7_3:27351184-27351203 None:intergenic 10.0%
!!! TTTTTTATTATATTGTGAAA+TGG + chr7_3:27351188-27351207 Msa1099080:intron 10.0%
!!! ATTTATTCAAGTTAATCAGA+GGG + chr7_3:27351093-27351112 Msa1099080:CDS 20.0%
!!! ATTTATTCAAGTTAATCAGA+GGG + chr7_3:27351093-27351112 Msa1099080:CDS 20.0%
! AAATCTCAGTAAATTCTTGA+AGG + chr7_3:27350919-27350938 Msa1099080:CDS 25.0%
! AATCTCAGTAAATTCTTGAA+GGG + chr7_3:27350920-27350939 Msa1099080:CDS 25.0%
!! GATTTATTCAAGTTAATCAG+AGG + chr7_3:27351092-27351111 Msa1099080:CDS 25.0%
! TAACTTTCTGAATGTCTTTA+AGG + chr7_3:27351126-27351145 Msa1099080:CDS 25.0%
! TTAAGGATTACAAAACACAA+AGG + chr7_3:27351143-27351162 Msa1099080:CDS 25.0%
! AATCTTGGTGAATTATTGAA+GGG + chr7_3:27351276-27351295 Msa1099080:CDS 25.0%
! TTATTGAAGGGATTATTTCA+AGG + chr7_3:27351288-27351307 Msa1099080:CDS 25.0%
! AGTAGTTCAATCTTGATATA+AGG - chr7_3:27350967-27350986 None:intergenic 25.0%
! AACATCATTGACAAATTCTT+TGG - chr7_3:27351065-27351084 None:intergenic 25.0%
!! GATTTATTCAAGTTAATCAG+AGG + chr7_3:27351092-27351111 Msa1099080:CDS 25.0%
TTCTTGAAGGGATTATTTGA+AGG + chr7_3:27350932-27350951 Msa1099080:CDS 30.0%
! GACAAATTCTTTCGCATTTT+TGG - chr7_3:27351056-27351075 None:intergenic 30.0%
GAATCTTGGTGAATTATTGA+AGG + chr7_3:27351275-27351294 Msa1099080:CDS 30.0%
TAACTTTCTGAATGTGTTGA+AGG + chr7_3:27351482-27351501 Msa1099080:CDS 30.0%
AAGGGATTATTTGAAGGTCA+TGG + chr7_3:27350938-27350957 Msa1099080:CDS 35.0%
AGCTTGATTTCAAATCCATC+AGG - chr7_3:27350995-27351014 None:intergenic 35.0%
TGAAATCAAGCTTCTATCTG+AGG + chr7_3:27351003-27351022 Msa1099080:CDS 35.0%
AGCTTGATTTCAAATCCATC+GGG - chr7_3:27350995-27351014 None:intergenic 35.0%
CAGCTTGATTTCAAATCCAT+CGG - chr7_3:27351352-27351371 None:intergenic 35.0%
! ATTTGAAATCAAGCTGCCAT+CGG + chr7_3:27351356-27351375 Msa1099080:CDS 35.0%
TGAAGGATTACAAGAGACAA+AGG + chr7_3:27351499-27351518 Msa1099080:CDS 35.0%
TTGAACTACTTCATGCCTGA+TGG + chr7_3:27350977-27350996 Msa1099080:CDS 40.0%
AATCAAGCTTCTATCTGAGG+AGG + chr7_3:27351006-27351025 Msa1099080:CDS 40.0%
ATCTGAGGAGGAACAATCTC+TGG + chr7_3:27351018-27351037 Msa1099080:CDS 45.0%
TTGAACTACTTCATGCCCGA+TGG + chr7_3:27351333-27351352 Msa1099080:CDS 45.0%
!!! ATTTTTTTATTATATTTTGT+AGG + chr7_3:27351241-27351260 Msa1099080:intron 5.0%
AGGATTGACGCTGCGAATCT+TGG + chr7_3:27351261-27351280 Msa1099080:intron 50.0%
TGAAATCAAGCTGCCATCGG+AGG + chr7_3:27351359-27351378 Msa1099080:CDS 50.0%
AGAGATTCTTCCTCCTCCGA+TGG - chr7_3:27351375-27351394 None:intergenic 50.0%
AATCAAGCTGCCATCGGAGG+AGG + chr7_3:27351362-27351381 Msa1099080:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 27350908 27351536 27350908 ID=Msa1099080;Name=Msa1099080
chr7_3 mRNA 27350908 27351536 27350908 ID=Msa1099080-mRNA-1;Parent=Msa1099080;Name=Msa1099080-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|0|0|1|1|0.5|2|0|176
chr7_3 exon 27350908 27351164 27350908 ID=Msa1099080-mRNA-1:exon:5780;Parent=Msa1099080-mRNA-1
chr7_3 exon 27351263 27351536 27351263 ID=Msa1099080-mRNA-1:exon:5781;Parent=Msa1099080-mRNA-1
chr7_3 CDS 27350908 27351164 27350908 ID=Msa1099080-mRNA-1:cds;Parent=Msa1099080-mRNA-1
chr7_3 CDS 27351263 27351536 27351263 ID=Msa1099080-mRNA-1:cds;Parent=Msa1099080-mRNA-1
Gene Sequence

>Msa1099080

ATCGATGATGCAAATCTCAGTAAATTCTTGAAGGGATTATTTGAAGGTCATGGAGATCTTATATCAAGATTGAACTACTTCATGCCTGATGGATTTGAAATCAAGCTTCTATCTGAGGAGGAACAATCTCTGGAGCATTTTGTAGCCAAAAATGCGAAAGAATTTGTCAATGATGTTAAGTGTAGATTTATTCAAGTTAATCAGAGGGATAAGTATGATAACTTTCTGAATGTCTTTAAGGATTACAAAACACAAAGGATTGACGCTGCGAATCTTGGTGAATTATTGAAGGGATTATTTCAAGGTCATAGAGACCTTATATCAAGATTGAACTACTTCATGCCCGATGGATTTGAAATCAAGCTGCCATCGGAGGAGGAAGAATCTCTTGAACATTCTGAAGAAAAAACTACCAAAGAATTTGTCAATGATGTTAAGTGTAGATTTATTCAAGTTAATCAGAGGGAAAAGTATGTTAACTTTCTGAATGTGTTGAAGGATTACAAGAGACAAAGGTTTGATCATTTGTGA
Protein sequence

>Msa1099080

IDDANLSKFLKGLFEGHGDLISRLNYFMPDGFEIKLLSEEEQSLEHFVAKNAKEFVNDVKCRFIQVNQRDKYDNFLNVFKDYKTQRIDAANLGELLKGLFQGHRDLISRLNYFMPDGFEIKLPSEEEESLEHSEEKTTKEFVNDVKCRFIQVNQREKYVNFLNVLKDYKRQRFDHL*