AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93861

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93861.t1 MTR_1g105010 72.807 114 25 2 8 121 12 119 8.72e-51 157
MS.gene93861.t1 MTR_1g105960 45.783 83 40 1 13 95 2 79 5.09e-21 81.6
MS.gene93861.t1 MTR_1g105955 54.930 71 32 0 9 79 13 83 5.88e-20 80.9
MS.gene93861.t1 MTR_1g105955 54.286 70 32 0 11 80 94 163 4.25e-18 76.3
MS.gene93861.t1 MTR_1g104940 47.368 76 40 0 5 80 7 82 1.14e-19 78.6
MS.gene93861.t1 MTR_8g062700 50.000 76 38 0 5 80 35 110 1.59e-19 83.6
MS.gene93861.t1 MTR_8g062700 50.000 76 38 0 5 80 35 110 1.63e-19 83.6
MS.gene93861.t1 MTR_1g104960 46.250 80 43 0 1 80 88 167 9.17e-19 77.8
MS.gene93861.t1 MTR_1g104960 48.649 74 38 0 7 80 8 81 4.16e-14 65.9
MS.gene93861.t1 MTR_5g036670 49.315 73 37 0 8 80 39 111 9.63e-19 81.3
MS.gene93861.t1 MTR_1g104937 53.623 69 32 0 12 80 12 80 2.82e-18 74.7
MS.gene93861.t1 MTR_6g008970 44.444 90 43 2 8 97 59 141 3.08e-18 79.7
MS.gene93861.t1 MTR_7g089490 49.275 69 35 0 12 80 16 84 3.85e-18 74.7
MS.gene93861.t1 MTR_3g006125 45.455 88 43 2 2 84 170 257 8.31e-17 74.3
MS.gene93861.t1 MTR_3g006125 42.029 69 39 1 12 79 89 157 9.04e-11 57.8
MS.gene93861.t1 MTR_3g006065 51.515 66 31 1 11 75 89 154 3.28e-15 68.9
MS.gene93861.t1 MTR_3g006185 44.186 86 43 2 4 84 90 175 4.12e-15 68.2
MS.gene93861.t1 MTR_3g006185 42.029 69 39 1 12 79 8 76 5.68e-11 57.4
MS.gene93861.t1 MTR_6g008995 41.026 78 46 0 8 85 33 110 5.10e-15 70.5
MS.gene93861.t1 MTR_8g062350 43.210 81 44 1 1 79 1 81 8.13e-15 68.2
MS.gene93861.t1 MTR_7g013410 44.615 65 36 0 16 80 2 66 1.40e-14 66.2
MS.gene93861.t1 MTR_3g006150 51.515 66 31 1 11 75 89 154 1.76e-14 66.2
MS.gene93861.t1 MTR_3g006150 40.845 71 39 1 9 79 5 72 5.56e-11 57.0
MS.gene93861.t1 MTR_1g091047 49.231 65 32 1 11 74 8 72 5.89e-14 62.8
MS.gene93861.t1 MTR_4g133470 46.970 66 35 0 15 80 175 240 6.37e-14 66.2
MS.gene93861.t1 MTR_4g133470 46.575 73 39 0 8 80 85 157 7.04e-13 63.5
MS.gene93861.t1 MTR_4g133470 53.846 52 24 0 28 79 25 76 3.23e-11 58.9
MS.gene93861.t1 MTR_4g133300 47.945 73 38 0 8 80 85 157 8.75e-14 65.9
MS.gene93861.t1 MTR_4g133300 46.970 66 35 0 15 80 175 240 1.01e-13 65.9
MS.gene93861.t1 MTR_4g133300 53.846 52 24 0 28 79 25 76 3.99e-11 58.9
MS.gene93861.t1 MTR_1g104980 48.485 66 34 0 14 79 1 66 1.21e-13 64.3
MS.gene93861.t1 MTR_1g104980 48.485 66 34 0 15 80 73 138 2.40e-13 63.5
MS.gene93861.t1 MTR_3g006000 47.436 78 38 3 11 86 6 82 6.44e-13 60.5
MS.gene93861.t1 MTR_1g093310 41.667 72 36 1 9 80 6 71 8.09e-13 60.1
MS.gene93861.t1 MTR_3g006105 42.500 80 45 1 2 80 89 168 1.89e-12 61.6
MS.gene93861.t1 MTR_3g006105 38.554 83 50 1 12 93 8 90 9.35e-12 59.7
MS.gene93861.t1 MTR_1g109550 47.541 61 31 1 19 79 23 82 3.48e-12 60.1
MS.gene93861.t1 MTR_7g013380 44.286 70 37 1 12 79 185 254 5.80e-12 61.6
MS.gene93861.t1 MTR_7g013380 46.875 64 32 1 13 74 14 77 1.32e-11 60.5
MS.gene93861.t1 MTR_7g013380 44.615 65 34 1 12 74 99 163 1.34e-11 60.5
MS.gene93861.t1 MTR_2g097830 47.761 67 31 1 28 90 83 149 1.07e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93861.t1 AT1G24190 51.250 80 35 1 5 80 3 82 3.57e-21 88.2
MS.gene93861.t1 AT1G24190 51.250 80 35 1 5 80 3 82 3.63e-21 88.2
MS.gene93861.t1 AT1G24190 51.250 80 35 1 5 80 3 82 3.78e-21 88.2
MS.gene93861.t1 AT1G70060 52.055 73 35 0 8 80 10 82 1.09e-19 84.0
MS.gene93861.t1 AT1G70060 52.055 73 35 0 8 80 10 82 1.09e-19 84.0
MS.gene93861.t1 AT3G01320 47.945 73 38 0 8 80 53 125 3.78e-19 82.4
MS.gene93861.t1 AT3G01320 47.945 73 38 0 8 80 53 125 4.09e-19 82.4
MS.gene93861.t1 AT5G15020 45.333 75 41 0 8 82 48 122 4.57e-18 79.3
MS.gene93861.t1 AT5G15020 45.333 75 41 0 8 82 48 122 4.89e-18 79.3
MS.gene93861.t1 AT1G24200 38.739 111 59 3 1 109 1 104 5.12e-18 76.3
MS.gene93861.t1 AT1G59890 44.928 69 38 0 12 80 45 113 2.15e-15 71.6
MS.gene93861.t1 AT1G59890 44.928 69 38 0 12 80 45 113 2.17e-15 71.6
MS.gene93861.t1 AT1G59890 44.928 69 38 0 12 80 45 113 2.39e-15 71.6
MS.gene93861.t1 AT1G59890 44.928 69 38 0 12 80 45 113 2.39e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.47e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.62e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.65e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 235 308 2.67e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.70e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.72e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.72e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.75e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.77e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.77e-15 71.6
MS.gene93861.t1 AT4G12020 46.667 75 39 1 6 80 302 375 2.91e-15 71.2
MS.gene93861.t1 AT1G27250 39.506 81 49 0 9 89 18 98 5.90e-15 67.0
MS.gene93861.t1 AT5G15025 38.158 76 47 0 7 82 42 117 7.31e-15 66.2
MS.gene93861.t1 AT1G70030 41.558 77 43 1 8 82 18 94 3.10e-14 64.7
MS.gene93861.t1 AT1G70030 34.951 103 62 2 8 105 7 109 3.95e-14 65.5
MS.gene93861.t1 AT1G70030 41.558 77 43 1 8 82 18 94 6.76e-14 64.3
MS.gene93861.t1 AT1G27280 38.571 70 43 0 9 78 78 147 1.36e-12 62.4
MS.gene93861.t1 AT1G24230 43.478 69 38 1 7 74 9 77 1.38e-12 62.8
MS.gene93861.t1 AT1G10450 40.580 69 41 0 12 80 33 101 2.05e-12 63.2
MS.gene93861.t1 AT1G10450 40.580 69 41 0 12 80 33 101 2.05e-12 63.2
MS.gene93861.t1 AT1G10450 40.580 69 41 0 12 80 84 152 2.25e-12 63.2
MS.gene93861.t1 AT1G27220 36.486 74 47 0 8 81 10 83 3.31e-12 60.8
MS.gene93861.t1 AT1G23810 42.188 64 37 0 9 72 106 169 5.31e-12 61.2
MS.gene93861.t1 AT1G24210 40.000 75 44 1 7 81 9 82 4.61e-11 57.4
MS.gene93861.t1 AT1G24250 42.188 64 37 0 9 72 117 180 7.11e-11 58.2

Find 27 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATAAAATATTAGAGATTT+TGG 0.199052 1.2:-77916920 MS.gene93861:CDS
TGAAAGTCCTAAGCGATTAC+AGG 0.315902 1.2:-77917170 MS.gene93861:CDS
AGGATGGAGGAGCTGTTTAA+AGG 0.330709 1.2:-77917114 MS.gene93861:CDS
AAGAACCCACCTGATCGAAT+AGG 0.409769 1.2:-77916994 MS.gene93861:CDS
CTCTGGGCAATGCAGGATAA+AGG 0.410594 1.2:-77917282 None:intergenic
AAACGCTATTGCTTCTTCCT+TGG 0.423218 1.2:+77917248 None:intergenic
CAGTGATGACACTGGAGAAA+AGG 0.440953 1.2:-77917037 MS.gene93861:CDS
TCACTGATTTGAGATGGCTT+TGG 0.444928 1.2:+77917054 None:intergenic
GGATGGAGGAGCTGTTTAAA+GGG 0.456905 1.2:-77917113 MS.gene93861:CDS
AGAACCCACCTGATCGAATA+GGG 0.457483 1.2:-77916993 MS.gene93861:CDS
ATTTGCGACCCTATTCGATC+AGG 0.474283 1.2:+77916985 None:intergenic
TTGAGATGGCTTTGGCGTAA+AGG 0.479351 1.2:+77917062 None:intergenic
AGTTAAACTTCTGTCTCAAA+AGG 0.482056 1.2:-77916944 MS.gene93861:CDS
TGCGACCCTATTCGATCAGG+TGG 0.509774 1.2:+77916988 None:intergenic
GCTAAAAGAATTGATATAGC+AGG 0.520011 1.2:-77917147 MS.gene93861:CDS
GTGTCATCACTGATTTGAGA+TGG 0.558119 1.2:+77917048 None:intergenic
GAAAGTCCTAAGCGATTACA+GGG 0.564984 1.2:-77917169 MS.gene93861:CDS
AGTTAAGTTTCAAGACAAGA+GGG 0.571152 1.2:-77917211 MS.gene93861:CDS
AAGTTAAGTTTCAAGACAAG+AGG 0.577150 1.2:-77917212 MS.gene93861:CDS
AGCAGGTGTGACAACAAGGA+TGG 0.585519 1.2:-77917130 MS.gene93861:CDS
GCGACCCTATTCGATCAGGT+GGG 0.613931 1.2:+77916989 None:intergenic
ATATAGCAGGTGTGACAACA+AGG 0.623415 1.2:-77917134 MS.gene93861:CDS
TCTCAAATCAGTGATGACAC+TGG 0.643527 1.2:-77917045 MS.gene93861:CDS
GCAATGCAGGATAAAGGTGG+TGG 0.647014 1.2:-77917276 MS.gene93861:CDS
AGGTGTGACAACAAGGATGG+AGG 0.648111 1.2:-77917127 MS.gene93861:CDS
TAAAGGTGGTGGTGTAACCA+AGG 0.651615 1.2:-77917265 MS.gene93861:CDS
TGGGCAATGCAGGATAAAGG+TGG 0.685630 1.2:-77917279 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGATAAAATATTAGAGATTT+TGG - chr1.2:77917253-77917272 MS.gene93861:CDS 15.0%
!!! TAAAATATTAGAGATTTTGG+AGG - chr1.2:77917256-77917275 MS.gene93861:CDS 20.0%
AAGTTAAGTTTCAAGACAAG+AGG - chr1.2:77916961-77916980 MS.gene93861:CDS 30.0%
AGTTAAACTTCTGTCTCAAA+AGG - chr1.2:77917229-77917248 MS.gene93861:CDS 30.0%
AGTTAAGTTTCAAGACAAGA+GGG - chr1.2:77916962-77916981 MS.gene93861:CDS 30.0%
GCTAAAAGAATTGATATAGC+AGG - chr1.2:77917026-77917045 MS.gene93861:CDS 30.0%
AAACGCTATTGCTTCTTCCT+TGG + chr1.2:77916928-77916947 None:intergenic 40.0%
ATATAGCAGGTGTGACAACA+AGG - chr1.2:77917039-77917058 MS.gene93861:CDS 40.0%
GAAAGTCCTAAGCGATTACA+GGG - chr1.2:77917004-77917023 MS.gene93861:CDS 40.0%
TCTCAAATCAGTGATGACAC+TGG - chr1.2:77917128-77917147 MS.gene93861:CDS 40.0%
TGAAAGTCCTAAGCGATTAC+AGG - chr1.2:77917003-77917022 MS.gene93861:CDS 40.0%
! TTTTAGCCCTGTAATCGCTT+AGG + chr1.2:77917013-77917032 None:intergenic 40.0%
!! GTGTCATCACTGATTTGAGA+TGG + chr1.2:77917128-77917147 None:intergenic 40.0%
!! TCACTGATTTGAGATGGCTT+TGG + chr1.2:77917122-77917141 None:intergenic 40.0%
AAGAACCCACCTGATCGAAT+AGG - chr1.2:77917179-77917198 MS.gene93861:CDS 45.0%
AGAACCCACCTGATCGAATA+GGG - chr1.2:77917180-77917199 MS.gene93861:CDS 45.0%
AGGATGGAGGAGCTGTTTAA+AGG - chr1.2:77917059-77917078 MS.gene93861:CDS 45.0%
ATTTGCGACCCTATTCGATC+AGG + chr1.2:77917191-77917210 None:intergenic 45.0%
CAGTGATGACACTGGAGAAA+AGG - chr1.2:77917136-77917155 MS.gene93861:CDS 45.0%
GGATGGAGGAGCTGTTTAAA+GGG - chr1.2:77917060-77917079 MS.gene93861:CDS 45.0%
! TAAAGGTGGTGGTGTAACCA+AGG - chr1.2:77916908-77916927 MS.gene93861:CDS 45.0%
!! TTGAGATGGCTTTGGCGTAA+AGG + chr1.2:77917114-77917133 None:intergenic 45.0%
AGCAGGTGTGACAACAAGGA+TGG - chr1.2:77917043-77917062 MS.gene93861:CDS 50.0%
AGGTGTGACAACAAGGATGG+AGG - chr1.2:77917046-77917065 MS.gene93861:CDS 50.0%
GCGACCCTATTCGATCAGGT+GGG + chr1.2:77917187-77917206 None:intergenic 55.0%
TGCGACCCTATTCGATCAGG+TGG + chr1.2:77917188-77917207 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 77916900 77917295 77916900 ID=MS.gene93861
chr1.2 mRNA 77916900 77917295 77916900 ID=MS.gene93861.t1;Parent=MS.gene93861
chr1.2 exon 77916900 77917295 77916900 ID=MS.gene93861.t1.exon1;Parent=MS.gene93861.t1
chr1.2 CDS 77916900 77917295 77916900 ID=cds.MS.gene93861.t1;Parent=MS.gene93861.t1
Gene Sequence

>MS.gene93861

ATGCAGGATAAAGGTGGTGGTGTAACCAAGGAAGAAGCAATAGCGTTTGTATGTGATGTAAAAGTTAAGTTTCAAGACAAGAGGGAAAAGTATGATGAATTTTTGAAAGTCCTAAGCGATTACAGGGCTAAAAGAATTGATATAGCAGGTGTGACAACAAGGATGGAGGAGCTGTTTAAAGGGCATTCAGATTTGATTTTGAAATTCAAATCCTTTACGCCAAAGCCATCTCAAATCAGTGATGACACTGGAGAAAAGGAAGAAGACACTGATGAACAGAAGAACCCACCTGATCGAATAGGGTCGCAAATTCAACTTATATCTCAAGAAGTTAAACTTCTGTCTCAAAAGGCTGATAAAATATTAGAGATTTTGGAGGAGAAGAAGCAAGCATAA
Protein sequence

>MS.gene93861.t1

MQDKGGGVTKEEAIAFVCDVKVKFQDKREKYDEFLKVLSDYRAKRIDIAGVTTRMEELFKGHSDLILKFKSFTPKPSQISDDTGEKEEDTDEQKNPPDRIGSQIQLISQEVKLLSQKADKILEILEEKKQA