AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06342

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06342.t1 MTR_3g097120 99.057 106 1 0 1 106 1 106 4.65e-77 222
MS.gene06342.t1 MTR_8g094980 69.159 107 26 2 7 106 1 107 2.01e-42 135
MS.gene06342.t1 MTR_3g092220 41.379 87 45 1 4 90 28 108 5.07e-17 70.9
MS.gene06342.t1 MTR_7g118010 40.244 82 43 1 9 90 23 98 8.66e-17 70.1
MS.gene06342.t1 MTR_8g026730 39.024 82 44 1 9 90 27 102 1.32e-16 69.7
MS.gene06342.t1 MTR_4g072220 41.463 82 39 2 2 82 19 92 5.43e-14 62.4
MS.gene06342.t1 MTR_2g043960 39.759 83 42 1 9 91 76 150 6.73e-14 63.9
MS.gene06342.t1 MTR_4g072890 42.857 77 35 2 5 80 22 90 1.10e-13 61.6
MS.gene06342.t1 MTR_4g072300 43.590 78 35 2 4 80 21 90 1.10e-13 61.6
MS.gene06342.t1 MTR_3g084250 42.308 78 36 2 4 80 20 89 1.26e-13 61.6
MS.gene06342.t1 MTR_7g405740 40.230 87 43 2 2 87 59 137 2.32e-13 62.4
MS.gene06342.t1 MTR_4g072940 41.772 79 37 2 5 82 53 123 2.58e-13 61.6
MS.gene06342.t1 MTR_4g072330 43.038 79 36 2 3 80 17 87 3.05e-13 60.5
MS.gene06342.t1 MTR_4g072250 43.590 78 34 2 4 80 21 89 4.43e-13 60.1
MS.gene06342.t1 MTR_4g072260 42.857 77 35 2 5 80 22 90 4.64e-13 60.1
MS.gene06342.t1 MTR_4g072240 42.308 78 36 2 4 80 21 90 5.73e-13 59.7
MS.gene06342.t1 MTR_4g072230 42.857 77 33 2 4 79 21 87 7.60e-13 59.3
MS.gene06342.t1 MTR_4g072570 40.506 79 38 2 3 80 19 89 9.88e-13 59.3
MS.gene06342.t1 MTR_4g072500 45.205 73 31 2 5 76 21 85 1.04e-12 59.3
MS.gene06342.t1 MTR_4g072820 45.333 75 32 2 8 81 19 85 1.44e-12 58.5
MS.gene06342.t1 MTR_8g461420 45.833 72 30 2 5 75 21 84 1.46e-12 58.9
MS.gene06342.t1 MTR_4g072640 44.595 74 32 2 4 76 20 85 1.70e-12 58.5
MS.gene06342.t1 MTR_3g098970 40.000 70 34 1 7 76 51 112 1.76e-12 60.1
MS.gene06342.t1 MTR_4g072870 44.595 74 32 2 4 76 21 86 2.22e-12 58.2
MS.gene06342.t1 MTR_3g084240 43.421 76 34 2 2 76 18 85 2.32e-12 58.2
MS.gene06342.t1 MTR_4g072660 41.333 75 35 2 3 76 14 80 2.35e-12 58.2
MS.gene06342.t1 MTR_4g124750 40.476 84 39 2 9 92 69 141 2.38e-12 59.7
MS.gene06342.t1 MTR_4g072880 41.026 78 37 2 4 80 21 90 2.46e-12 58.2
MS.gene06342.t1 MTR_3g084170 43.421 76 34 2 2 76 18 85 2.82e-12 58.2
MS.gene06342.t1 MTR_4g072480 43.243 74 33 2 4 76 20 85 3.99e-12 57.8
MS.gene06342.t1 MTR_3g084210 45.205 73 31 2 4 75 20 84 4.59e-12 57.4
MS.gene06342.t1 MTR_4g072370 43.590 78 35 2 4 80 18 87 4.67e-12 57.4
MS.gene06342.t1 MTR_3g110045 45.833 72 30 2 5 75 80 143 5.70e-12 58.5
MS.gene06342.t1 MTR_3g084190 43.056 72 32 2 5 75 21 84 8.06e-12 57.0
MS.gene06342.t1 MTR_8g096440 43.750 80 37 1 2 81 38 109 8.35e-12 58.2
MS.gene06342.t1 MTR_4g072600 45.946 74 31 2 4 76 15 80 9.18e-12 56.6
MS.gene06342.t1 MTR_1g061570 45.455 66 26 2 9 74 19 74 9.22e-12 57.4
MS.gene06342.t1 MTR_3g084230 45.833 72 30 2 5 75 21 84 9.28e-12 56.6
MS.gene06342.t1 MTR_3g117630 39.506 81 40 2 3 82 19 91 1.03e-11 56.6
MS.gene06342.t1 MTR_4g072910 49.275 69 26 2 9 76 35 95 1.07e-11 56.6
MS.gene06342.t1 MTR_5g008370 46.377 69 28 2 9 76 25 85 1.37e-11 57.4
MS.gene06342.t1 MTR_4g072730 38.667 75 37 2 3 76 19 85 1.66e-11 56.2
MS.gene06342.t1 MTR_4g072310 41.026 78 37 2 4 80 21 90 1.67e-11 56.2
MS.gene06342.t1 MTR_3g084180 39.241 79 39 2 3 80 19 89 2.13e-11 55.8
MS.gene06342.t1 MTR_3g084150 39.744 78 38 2 3 79 19 88 2.33e-11 55.8
MS.gene06342.t1 MTR_3g110038 39.024 82 41 2 2 82 18 91 2.51e-11 55.5
MS.gene06342.t1 MTR_4g072850 40.506 79 38 2 5 82 23 93 2.54e-11 55.5
MS.gene06342.t1 MTR_4g072530 42.466 73 33 2 5 76 21 85 2.55e-11 55.5
MS.gene06342.t1 MTR_4g072620 40.541 74 35 2 4 76 20 85 3.54e-11 55.1
MS.gene06342.t1 MTR_4g072830 41.026 78 37 2 4 80 18 87 6.19e-11 54.7
MS.gene06342.t1 MTR_4g072560 39.189 74 37 2 9 81 32 98 7.13e-11 54.7
MS.gene06342.t1 MTR_8g096500 43.590 78 34 2 12 89 52 119 7.30e-11 55.8
MS.gene06342.t1 MTR_4g072860 44.595 74 32 2 4 76 21 86 7.80e-11 54.3
MS.gene06342.t1 MTR_7g104940 41.667 72 34 1 10 81 51 114 8.67e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06342.t1 AT5G53590 41.975 81 44 1 9 89 46 123 2.63e-17 72.4
MS.gene06342.t1 AT2G46690 38.947 95 52 2 2 96 17 105 5.14e-17 70.9
MS.gene06342.t1 AT4G00880 41.558 77 39 1 8 84 27 97 7.69e-15 65.5
MS.gene06342.t1 AT3G61900 41.333 75 39 1 9 83 30 99 3.06e-14 64.3
MS.gene06342.t1 AT4G34780 42.857 77 38 2 7 82 26 97 3.54e-13 60.8
MS.gene06342.t1 AT4G22620 41.026 78 41 1 3 80 73 145 1.01e-12 60.8
MS.gene06342.t1 AT4G34790 43.478 69 32 2 9 76 39 101 2.71e-11 55.8
MS.gene06342.t1 AT3G43120 42.466 73 34 1 9 81 79 143 3.05e-11 57.0
MS.gene06342.t1 AT5G20810 44.118 68 30 1 9 76 79 138 3.61e-11 57.0
MS.gene06342.t1 AT4G34800 40.000 75 39 2 3 76 15 84 5.04e-11 55.1
MS.gene06342.t1 AT5G20810 44.118 68 30 1 9 76 79 138 7.34e-11 56.6
MS.gene06342.t1 AT4G12410 37.500 72 40 1 9 80 76 142 9.19e-11 55.8

Find 28 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACCAAGCTTATGATGTTTA+TGG 0.111493 3.1:-77467137 MS.gene06342:CDS
TGCAGTTCAAGTGGGTTTAG+AGG 0.387862 3.1:-77467243 MS.gene06342:CDS
CAAGAAGATGAAAGTGAAGA+AGG 0.391141 3.1:-77467273 MS.gene06342:CDS
TGGTTATGGTTATGTTGGTT+AGG 0.415635 3.1:+77467032 None:intergenic
GACGATGCTGATGGTGGTTA+TGG 0.422891 3.1:+77467018 None:intergenic
GATGGTGGTTATGGTTATGT+TGG 0.451887 3.1:+77467027 None:intergenic
AAATTTCGAGTCAACAAGAA+TGG 0.461541 3.1:+77466976 None:intergenic
GGATGGTAAAGATAAGAGAT+AGG 0.469559 3.1:+77467179 None:intergenic
AAGAAGATGAAAGTGAAGAA+GGG 0.500937 3.1:-77467272 MS.gene06342:CDS
ATGATTTCCTTCATCTTCGA+TGG 0.519321 3.1:-77467073 MS.gene06342:CDS
CAATTCGCCATCGAAGATGA+AGG 0.535691 3.1:+77467066 None:intergenic
AGATGAAAGTGAAGAAGGGA+TGG 0.536875 3.1:-77467268 MS.gene06342:CDS
AGGAAATCATCCACAGAACA+TGG 0.538192 3.1:+77467086 None:intergenic
AGCCATAAACATCATAAGCT+TGG 0.538249 3.1:+77467135 None:intergenic
TGGAAGCTTGAGAGGACCAT+TGG 0.551787 3.1:+77467106 None:intergenic
TCAAGAAGACGCTTGAAAAG+TGG 0.553447 3.1:+77467158 None:intergenic
TCTCAAGCTTCCATGTTCTG+TGG 0.559981 3.1:-77467096 MS.gene06342:CDS
ACAGAACATGGAAGCTTGAG+AGG 0.564027 3.1:+77467098 None:intergenic
GGTTTAGAGGAAGAAGAAGA+AGG 0.564757 3.1:-77467230 MS.gene06342:CDS
GGGATGGCTTGCAGTTCAAG+TGG 0.572241 3.1:-77467252 MS.gene06342:CDS
GAATGGAAAATCAGAGCATG+AGG 0.588224 3.1:+77466993 None:intergenic
GCTTGAGAGGACCATTGGTA+TGG 0.590408 3.1:+77467111 None:intergenic
TTAGAGGAAGAAGAAGAAGG+TGG 0.598907 3.1:-77467227 MS.gene06342:CDS
GGATGGCTTGCAGTTCAAGT+GGG 0.612179 3.1:-77467251 MS.gene06342:CDS
GTTTATGGCTACCATACCAA+TGG 0.626042 3.1:-77467122 MS.gene06342:CDS
GAAGACGCTTGAAAAGTGGA+TGG 0.652650 3.1:+77467162 None:intergenic
CATGAGGAAGACGATGCTGA+TGG 0.669865 3.1:+77467009 None:intergenic
GAGGAAGACGATGCTGATGG+TGG 0.699924 3.1:+77467012 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAGATGAAAGTGAAGAA+GGG - chr3.1:77466998-77467017 MS.gene06342:CDS 30.0%
AGCCATAAACATCATAAGCT+TGG + chr3.1:77467138-77467157 None:intergenic 35.0%
ATGATTTCCTTCATCTTCGA+TGG - chr3.1:77467197-77467216 MS.gene06342:CDS 35.0%
CAAGAAGATGAAAGTGAAGA+AGG - chr3.1:77466997-77467016 MS.gene06342:CDS 35.0%
GACCAAGCTTATGATGTTTA+TGG - chr3.1:77467133-77467152 MS.gene06342:CDS 35.0%
GGATGGTAAAGATAAGAGAT+AGG + chr3.1:77467094-77467113 None:intergenic 35.0%
! TGGTTATGGTTATGTTGGTT+AGG + chr3.1:77467241-77467260 None:intergenic 35.0%
AGATGAAAGTGAAGAAGGGA+TGG - chr3.1:77467002-77467021 MS.gene06342:CDS 40.0%
AGGAAATCATCCACAGAACA+TGG + chr3.1:77467187-77467206 None:intergenic 40.0%
GAATGGAAAATCAGAGCATG+AGG + chr3.1:77467280-77467299 None:intergenic 40.0%
GGTTTAGAGGAAGAAGAAGA+AGG - chr3.1:77467040-77467059 MS.gene06342:CDS 40.0%
GTTTATGGCTACCATACCAA+TGG - chr3.1:77467148-77467167 MS.gene06342:CDS 40.0%
TCAAGAAGACGCTTGAAAAG+TGG + chr3.1:77467115-77467134 None:intergenic 40.0%
TTAGAGGAAGAAGAAGAAGG+TGG - chr3.1:77467043-77467062 MS.gene06342:CDS 40.0%
! GATGGTGGTTATGGTTATGT+TGG + chr3.1:77467246-77467265 None:intergenic 40.0%
ACAGAACATGGAAGCTTGAG+AGG + chr3.1:77467175-77467194 None:intergenic 45.0%
CAATTCGCCATCGAAGATGA+AGG + chr3.1:77467207-77467226 None:intergenic 45.0%
GAAGACGCTTGAAAAGTGGA+TGG + chr3.1:77467111-77467130 None:intergenic 45.0%
TCTCAAGCTTCCATGTTCTG+TGG - chr3.1:77467174-77467193 MS.gene06342:CDS 45.0%
! TGCAGTTCAAGTGGGTTTAG+AGG - chr3.1:77467027-77467046 MS.gene06342:CDS 45.0%
CATGAGGAAGACGATGCTGA+TGG + chr3.1:77467264-77467283 None:intergenic 50.0%
GCTTGAGAGGACCATTGGTA+TGG + chr3.1:77467162-77467181 None:intergenic 50.0%
TGGAAGCTTGAGAGGACCAT+TGG + chr3.1:77467167-77467186 None:intergenic 50.0%
! GGATGGCTTGCAGTTCAAGT+GGG - chr3.1:77467019-77467038 MS.gene06342:CDS 50.0%
!! GACGATGCTGATGGTGGTTA+TGG + chr3.1:77467255-77467274 None:intergenic 50.0%
GAGGAAGACGATGCTGATGG+TGG + chr3.1:77467261-77467280 None:intergenic 55.0%
! GGGATGGCTTGCAGTTCAAG+TGG - chr3.1:77467018-77467037 MS.gene06342:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 77466986 77467306 77466986 ID=MS.gene06342
chr3.1 mRNA 77466986 77467306 77466986 ID=MS.gene06342.t1;Parent=MS.gene06342
chr3.1 exon 77466986 77467306 77466986 ID=MS.gene06342.t1.exon1;Parent=MS.gene06342.t1
chr3.1 CDS 77466986 77467306 77466986 ID=cds.MS.gene06342.t1;Parent=MS.gene06342.t1
Gene Sequence

>MS.gene06342

ATGCAGGAAGACAAGAAGATGAAAGTGAAGAAGGGATGGCTTGCAGTTCAAGTGGGTTTAGAGGAAGAAGAAGAAGGTGGTTCTTGCTCTCAGAAATTTGTCATACCTATCTCTTATCTTTACCATCCACTTTTCAAGCGTCTTCTTGACCAAGCTTATGATGTTTATGGCTACCATACCAATGGTCCTCTCAAGCTTCCATGTTCTGTGGATGATTTCCTTCATCTTCGATGGCGAATTGAGAAAGAATCTCCTAACCAACATAACCATAACCACCATCAGCATCGTCTTCCTCATGCTCTGATTTTCCATTCTTGTTGA
Protein sequence

>MS.gene06342.t1

MQEDKKMKVKKGWLAVQVGLEEEEEGGSCSQKFVIPISYLYHPLFKRLLDQAYDVYGYHTNGPLKLPCSVDDFLHLRWRIEKESPNQHNHNHHQHRLPHALIFHSC