AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene050277


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050277.t1 MTR_7g105220 99.174 121 1 0 1 121 1 121 3.99e-88 253
MS.gene050277.t1 MTR_8g036015 57.273 110 47 0 12 121 3 112 2.42e-42 137
MS.gene050277.t1 MTR_5g015500 60.396 101 40 0 12 112 307 407 1.87e-39 138
MS.gene050277.t1 MTR_5g015500 60.396 101 40 0 12 112 347 447 3.05e-39 138
MS.gene050277.t1 MTR_2g085075 53.097 113 52 1 10 121 461 573 3.88e-35 127
MS.gene050277.t1 MTR_2g023120 55.357 112 49 1 11 121 14 125 1.68e-31 116
MS.gene050277.t1 MTR_1g085560 56.881 109 42 4 17 121 97 204 9.48e-31 110
MS.gene050277.t1 MTR_7g110980 55.963 109 43 4 17 121 108 215 6.59e-30 108
MS.gene050277.t1 MTR_7g116340 52.632 114 42 4 19 121 18 130 7.40e-28 100
MS.gene050277.t1 MTR_8g040180 50.000 112 46 3 19 121 32 142 1.28e-27 100
MS.gene050277.t1 MTR_1g117010 51.852 108 47 4 18 121 93 199 1.35e-27 102
MS.gene050277.t1 MTR_1g117010 51.852 108 47 4 18 121 93 199 1.35e-27 102
MS.gene050277.t1 MTR_6g084140 45.455 110 53 1 12 114 3 112 3.16e-27 105
MS.gene050277.t1 MTR_6g084140 45.455 110 53 1 12 114 20 129 3.23e-27 105
MS.gene050277.t1 MTR_3g463900 51.754 114 43 4 19 121 48 160 8.20e-27 99.0
MS.gene050277.t1 MTR_8g079690 45.736 129 52 5 10 121 4 131 3.67e-26 100
MS.gene050277.t1 MTR_8g442420 44.545 110 54 1 12 114 3 112 6.75e-26 101
MS.gene050277.t1 MTR_4g075290 49.231 130 45 6 10 121 4 130 6.83e-26 95.5
MS.gene050277.t1 MTR_3g117750 51.282 117 41 5 18 121 25 138 1.92e-25 95.1
MS.gene050277.t1 MTR_3g070500 50.862 116 45 4 17 121 76 190 2.35e-25 95.9
MS.gene050277.t1 MTR_3g070500 52.778 108 39 4 17 113 76 182 1.18e-24 92.8
MS.gene050277.t1 MTR_4g086760 48.696 115 46 4 19 121 18 131 7.81e-24 93.6
MS.gene050277.t1 MTR_4g086760 48.696 115 46 4 19 121 18 131 1.06e-23 93.6
MS.gene050277.t1 MTR_4g086760 48.696 115 46 4 19 121 18 131 1.10e-23 93.2
MS.gene050277.t1 MTR_7g095750 49.558 113 44 4 21 121 23 134 1.19e-23 94.7
MS.gene050277.t1 MTR_4g073650 40.000 115 57 3 18 121 59 172 8.59e-21 83.6
MS.gene050277.t1 MTR_1g094065 34.862 109 65 2 13 121 83 185 3.24e-15 69.3
MS.gene050277.t1 MTR_3g107660 44.545 110 48 4 24 121 29 137 7.00e-15 69.7
MS.gene050277.t1 MTR_3g085705 50.000 68 30 2 54 121 32 95 1.87e-11 57.4
MS.gene050277.t1 MTR_1g035360 30.909 110 69 3 13 121 82 185 3.03e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene050277.t1 AT2G36130 87.603 121 15 0 1 121 1 121 2.28e-77 226
MS.gene050277.t1 AT1G01940 56.364 110 48 0 12 121 3 112 2.00e-41 134
MS.gene050277.t1 AT5G67530 57.426 101 43 0 12 112 346 446 1.23e-37 134
MS.gene050277.t1 AT4G33060 53.571 112 51 1 11 121 14 125 5.43e-36 128
MS.gene050277.t1 AT3G44600 52.101 119 56 1 4 121 469 587 2.95e-35 127
MS.gene050277.t1 AT3G62030 57.009 107 41 3 19 121 109 214 3.86e-29 106
MS.gene050277.t1 AT3G62030 57.009 107 41 3 19 121 108 213 4.30e-29 106
MS.gene050277.t1 AT3G62030 57.009 107 41 3 19 121 162 267 1.50e-28 105
MS.gene050277.t1 AT2G21130 51.587 126 42 5 7 121 14 131 2.59e-28 102
MS.gene050277.t1 AT4G38740 53.509 114 41 4 19 121 18 130 3.22e-28 101
MS.gene050277.t1 AT3G56070 52.632 114 42 3 19 121 18 130 7.38e-28 100
MS.gene050277.t1 AT3G56070 52.632 114 42 3 19 121 18 130 7.38e-28 100
MS.gene050277.t1 AT2G29960 50.862 116 45 4 17 121 44 158 4.43e-27 99.4
MS.gene050277.t1 AT2G29960 50.862 116 45 4 17 121 44 158 4.43e-27 99.4
MS.gene050277.t1 AT2G38730 49.206 126 49 5 10 121 32 156 5.65e-27 99.4
MS.gene050277.t1 AT1G53720 45.455 110 53 2 12 114 3 112 1.04e-26 101
MS.gene050277.t1 AT2G16600 52.542 118 40 5 17 121 17 131 3.29e-26 96.7
MS.gene050277.t1 AT3G55920 50.000 114 45 4 19 121 73 185 9.71e-26 96.7
MS.gene050277.t1 AT1G53720 45.455 110 53 2 12 114 3 112 1.15e-25 100
MS.gene050277.t1 AT4G34870 49.580 119 44 4 16 121 15 130 1.72e-25 94.7
MS.gene050277.t1 AT5G58710 49.138 116 47 3 17 121 47 161 2.39e-25 95.1
MS.gene050277.t1 AT3G63400 45.736 129 52 4 10 121 7 134 2.69e-25 98.6
MS.gene050277.t1 AT2G15790 49.565 115 45 4 19 121 18 131 2.75e-25 98.2
MS.gene050277.t1 AT5G13120 49.533 107 49 4 19 121 103 208 3.00e-25 96.3
MS.gene050277.t1 AT5G13120 49.533 107 49 4 19 121 107 212 3.88e-25 95.9
MS.gene050277.t1 AT3G63400 45.736 129 52 4 10 121 7 134 1.18e-24 97.8
MS.gene050277.t1 AT3G63400 45.736 129 52 4 10 121 7 134 1.18e-24 97.8
MS.gene050277.t1 AT3G63400 45.736 129 52 4 10 121 7 134 1.18e-24 97.8
MS.gene050277.t1 AT2G29960 45.690 116 41 5 17 121 44 148 1.26e-19 80.1
MS.gene050277.t1 AT4G34960 40.000 115 57 4 18 121 60 173 1.31e-19 80.9
MS.gene050277.t1 AT4G34960 42.056 107 50 4 18 113 60 165 1.44e-19 79.3
MS.gene050277.t1 AT2G16600 48.624 109 36 4 17 121 17 109 1.74e-18 76.3

Find 40 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTGACTTCCGTTAGTATT+AGG 0.209355 7.3:-9264954 None:intergenic
TCTCGCACCGTGCCCCTCTT+TGG 0.259093 7.3:+9264986 MS.gene050277:CDS
ATGAAGTTCCTACAAGTTCT+AGG 0.269440 7.3:-9264287 None:intergenic
ACTGACTTCCGTTAGTATTA+GGG 0.308819 7.3:-9264953 None:intergenic
AGAGGAGGAGAATCCATCTA+TGG 0.352009 7.3:+9264495 MS.gene050277:CDS
AGTTAAAGCATACCCATAGA+TGG 0.430770 7.3:-9264508 None:intergenic
GGTGGGGATCCCACTGGGAC+AGG 0.457978 7.3:+9264471 MS.gene050277:CDS
GATCCCACTGGGACAGGAAG+AGG 0.463282 7.3:+9264477 MS.gene050277:CDS
AAGCGCAGAAGGTGGTGCTC+CGG 0.493778 7.3:+9264115 MS.gene050277:CDS
GAGCTGAAGCACACTGGAGC+TGG 0.513405 7.3:+9264906 MS.gene050277:CDS
CCTCCTCTTCCTGTCCCAGT+GGG 0.517919 7.3:-9264480 None:intergenic
GATAAATTACCATCCAAAGA+GGG 0.534312 7.3:-9264999 None:intergenic
GCACCGTGCCCCTCTTTGGA+TGG 0.536332 7.3:+9264990 MS.gene050277:CDS
CGCAGAAGGTGGTGCTCCGG+AGG 0.537673 7.3:+9264118 MS.gene050277:CDS
AAAATGTGGGCAAGCGCAGA+AGG 0.539071 7.3:+9264104 None:intergenic
GAGTAGGATTTCATAGTACA+AGG 0.541774 7.3:+9264450 MS.gene050277:intron
AGGATTTCATAGTACAAGGT+GGG 0.556519 7.3:+9264454 MS.gene050277:intron
TCCTCCTCTTCCTGTCCCAG+TGG 0.564512 7.3:-9264481 None:intergenic
AATAATAATAATTACCTCGA+CGG 0.570411 7.3:-9264171 None:intergenic
TACAAGGTGGGGATCCCACT+GGG 0.581439 7.3:+9264466 MS.gene050277:CDS
GGTTACTCTAGAAACTTCCA+TGG 0.582783 7.3:+9264139 MS.gene050277:CDS
GTACAAGGTGGGGATCCCAC+TGG 0.586480 7.3:+9264465 MS.gene050277:CDS
AGCATGCACCTAGAACTTGT+AGG 0.588442 7.3:+9264279 MS.gene050277:CDS
AAACAAGAGCTGAAGCACAC+TGG 0.591406 7.3:+9264900 MS.gene050277:CDS
GAGGAGGAGAATCCATCTAT+GGG 0.597355 7.3:+9264496 MS.gene050277:CDS
TAAGTTCCACAGAATCATCA+AGG 0.601613 7.3:+9264343 MS.gene050277:CDS
AGATAAATTACCATCCAAAG+AGG 0.606617 7.3:-9265000 None:intergenic
GAAGTTTCTAGAGTAACCTC+CGG 0.610654 7.3:-9264134 None:intergenic
CCCACTGGGACAGGAAGAGG+AGG 0.622286 7.3:+9264480 MS.gene050277:CDS
CTCGACGGTGAATGAACCCA+TGG 0.626061 7.3:-9264156 None:intergenic
GGATTTCATAGTACAAGGTG+GGG 0.626995 7.3:+9264455 MS.gene050277:intron
TTCATTGAACTATCTCGTAG+AGG 0.631851 7.3:+9264305 MS.gene050277:CDS
TGAATACCTTGATGATTCTG+TGG 0.644502 7.3:-9264349 None:intergenic
AATGCTGGCCCTAATACTAA+CGG 0.646655 7.3:+9264945 MS.gene050277:CDS
TAGGATTTCATAGTACAAGG+TGG 0.656984 7.3:+9264453 MS.gene050277:intron
ATGTGGGCAAGCGCAGAAGG+TGG 0.657684 7.3:+9264107 MS.gene050277:CDS
CATGGGTTCATTCACCGTCG+AGG 0.657749 7.3:+9264157 MS.gene050277:CDS
GTTACTCTAGAAACTTCCAT+GGG 0.658204 7.3:+9264140 MS.gene050277:CDS
TTACCATCCAAAGAGGGGCA+CGG 0.666255 7.3:-9264993 None:intergenic
ATAAATTACCATCCAAAGAG+GGG 0.671498 7.3:-9264998 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTAACATTTTTTTTTTT+TGG + chr7.3:9264238-9264257 MS.gene050277:intron 10.0%
!!! ATTTTGTCTTAAAATTTAGA+TGG + chr7.3:9264396-9264415 MS.gene050277:intron 15.0%
!! AAATGAAGTTGTTTATTCAA+AGG + chr7.3:9264787-9264806 MS.gene050277:intron 20.0%
!! AATAATAATAATTACCTCGA+CGG - chr7.3:9264174-9264193 None:intergenic 20.0%
!! AATGAAGTTGTTTATTCAAA+GGG + chr7.3:9264788-9264807 MS.gene050277:intron 20.0%
!! TAATCGTGTTATCATAATAT+GGG + chr7.3:9264557-9264576 MS.gene050277:intron 20.0%
!!! GTGTTGTTTTTTAATTACAT+TGG + chr7.3:9264418-9264437 MS.gene050277:intron 20.0%
! AATAACGAACAATGAAAATG+TGG - chr7.3:9264379-9264398 None:intergenic 25.0%
! ATGAAGTTGTTTATTCAAAG+GGG + chr7.3:9264789-9264808 MS.gene050277:intron 25.0%
! GTAATCGTGTTATCATAATA+TGG + chr7.3:9264556-9264575 MS.gene050277:intron 25.0%
!! ACATGTTCATAAACTGTTTT+CGG + chr7.3:9264641-9264660 MS.gene050277:intron 25.0%
!! TATCATAATATGGGTTTGTT+TGG + chr7.3:9264566-9264585 MS.gene050277:intron 25.0%
AAAACCCTAATTCTGTATCA+GGG - chr7.3:9264223-9264242 None:intergenic 30.0%
ATCAACTGACATAAACTGTT+TGG + chr7.3:9264607-9264626 MS.gene050277:intron 30.0%
TAAAACCCTAATTCTGTATC+AGG - chr7.3:9264224-9264243 None:intergenic 30.0%
TAAACCCTGATACAGAATTA+GGG + chr7.3:9264216-9264235 MS.gene050277:intron 30.0%
TCAACTGACATAAACTGTTT+GGG + chr7.3:9264608-9264627 MS.gene050277:intron 30.0%
TGAAGTTGTTTATTCAAAGG+GGG + chr7.3:9264790-9264809 MS.gene050277:intron 30.0%
TTAAACCCTGATACAGAATT+AGG + chr7.3:9264215-9264234 MS.gene050277:intron 30.0%
! ATTTTATCAATGGCTAATGC+TGG + chr7.3:9264930-9264949 MS.gene050277:CDS 30.0%
! CATTTTTGTATAAGCTGTCT+TGG - chr7.3:9264685-9264704 None:intergenic 30.0%
! TAATATGGGTTTGTTTGGAT+CGG + chr7.3:9264571-9264590 MS.gene050277:intron 30.0%
!! TTTAGCCACTTTGTTGTTTA+TGG + chr7.3:9264852-9264871 MS.gene050277:intron 30.0%
!!! ACATTGGTTTTTTGTTGAGT+AGG + chr7.3:9264434-9264453 MS.gene050277:intron 30.0%
AACTGACATAAACTGTTTGG+GGG + chr7.3:9264610-9264629 MS.gene050277:intron 35.0%
AGGATTTCATAGTACAAGGT+GGG + chr7.3:9264454-9264473 MS.gene050277:intron 35.0%
AGTTAAAGCATACCCATAGA+TGG - chr7.3:9264511-9264530 None:intergenic 35.0%
ATGAAGTTCCTACAAGTTCT+AGG - chr7.3:9264290-9264309 None:intergenic 35.0%
CAACTGACATAAACTGTTTG+GGG + chr7.3:9264609-9264628 MS.gene050277:intron 35.0%
GAGTAGGATTTCATAGTACA+AGG + chr7.3:9264450-9264469 MS.gene050277:intron 35.0%
TAAGTCACCCAAAAAAACCT+AGG - chr7.3:9264816-9264835 None:intergenic 35.0%
TAAGTTCCACAGAATCATCA+AGG + chr7.3:9264343-9264362 MS.gene050277:CDS 35.0%
TAGGATTTCATAGTACAAGG+TGG + chr7.3:9264453-9264472 MS.gene050277:intron 35.0%
TTCATTGAACTATCTCGTAG+AGG + chr7.3:9264305-9264324 MS.gene050277:CDS 35.0%
! AACTGACTTCCGTTAGTATT+AGG - chr7.3:9264957-9264976 None:intergenic 35.0%
! ACTGACTTCCGTTAGTATTA+GGG - chr7.3:9264956-9264975 None:intergenic 35.0%
! GTTACTCTAGAAACTTCCAT+GGG + chr7.3:9264140-9264159 MS.gene050277:CDS 35.0%
! TGAATACCTTGATGATTCTG+TGG - chr7.3:9264352-9264371 None:intergenic 35.0%
! TGGAGCTGGTATTTTATCAA+TGG + chr7.3:9264920-9264939 MS.gene050277:CDS 35.0%
AATGCTGGCCCTAATACTAA+CGG + chr7.3:9264945-9264964 MS.gene050277:CDS 40.0%
CACTGCCATAAACAACAAAG+TGG - chr7.3:9264860-9264879 None:intergenic 40.0%
GGATTTCATAGTACAAGGTG+GGG + chr7.3:9264455-9264474 MS.gene050277:intron 40.0%
! GGTTACTCTAGAAACTTCCA+TGG + chr7.3:9264139-9264158 MS.gene050277:CDS 40.0%
!! GAAGTTTCTAGAGTAACCTC+CGG - chr7.3:9264137-9264156 None:intergenic 40.0%
AAACAAGAGCTGAAGCACAC+TGG + chr7.3:9264900-9264919 MS.gene050277:CDS 45.0%
AGAGGAGGAGAATCCATCTA+TGG + chr7.3:9264495-9264514 MS.gene050277:CDS 45.0%
AGCATGCACCTAGAACTTGT+AGG + chr7.3:9264279-9264298 MS.gene050277:CDS 45.0%
GAGGAGGAGAATCCATCTAT+GGG + chr7.3:9264496-9264515 MS.gene050277:CDS 45.0%
TGTTTATTCAAAGGGGGCCT+AGG + chr7.3:9264796-9264815 MS.gene050277:intron 45.0%
!!! AAAGGGGGCCTAGGTTTTTT+TGG + chr7.3:9264805-9264824 MS.gene050277:intron 45.0%
!!! AAGGGGGCCTAGGTTTTTTT+GGG + chr7.3:9264806-9264825 MS.gene050277:intron 45.0%
!!! TTTTAACATTTTTTTTTTTT+GGG + chr7.3:9264239-9264258 MS.gene050277:intron 5.0%
CATGGGTTCATTCACCGTCG+AGG + chr7.3:9264157-9264176 MS.gene050277:CDS 55.0%
CTCGACGGTGAATGAACCCA+TGG - chr7.3:9264159-9264178 None:intergenic 55.0%
TACAAGGTGGGGATCCCACT+GGG + chr7.3:9264466-9264485 MS.gene050277:CDS 55.0%
AAGCGCAGAAGGTGGTGCTC+CGG + chr7.3:9264115-9264134 MS.gene050277:CDS 60.0%
ATGTGGGCAAGCGCAGAAGG+TGG + chr7.3:9264107-9264126 MS.gene050277:CDS 60.0%
CCTCCTCTTCCTGTCCCAGT+GGG - chr7.3:9264483-9264502 None:intergenic 60.0%
GAGCTGAAGCACACTGGAGC+TGG + chr7.3:9264906-9264925 MS.gene050277:CDS 60.0%
GATCCCACTGGGACAGGAAG+AGG + chr7.3:9264477-9264496 MS.gene050277:CDS 60.0%
GTACAAGGTGGGGATCCCAC+TGG + chr7.3:9264465-9264484 MS.gene050277:CDS 60.0%
TCCTCCTCTTCCTGTCCCAG+TGG - chr7.3:9264484-9264503 None:intergenic 60.0%
CCCACTGGGACAGGAAGAGG+AGG + chr7.3:9264480-9264499 MS.gene050277:CDS 65.0%
TCTCGCACCGTGCCCCTCTT+TGG + chr7.3:9264986-9265005 MS.gene050277:CDS 65.0%
CGCAGAAGGTGGTGCTCCGG+AGG + chr7.3:9264118-9264137 MS.gene050277:CDS 70.0%
GGTGGGGATCCCACTGGGAC+AGG + chr7.3:9264471-9264490 MS.gene050277:CDS 70.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 9264107 9265011 9264107 ID=MS.gene050277
chr7.3 mRNA 9264107 9265011 9264107 ID=MS.gene050277.t1;Parent=MS.gene050277
chr7.3 exon 9264107 9264178 9264107 ID=MS.gene050277.t1.exon1;Parent=MS.gene050277.t1
chr7.3 CDS 9264107 9264178 9264107 ID=cds.MS.gene050277.t1;Parent=MS.gene050277.t1
chr7.3 exon 9264269 9264364 9264269 ID=MS.gene050277.t1.exon2;Parent=MS.gene050277.t1
chr7.3 CDS 9264269 9264364 9264269 ID=cds.MS.gene050277.t1;Parent=MS.gene050277.t1
chr7.3 exon 9264456 9264517 9264456 ID=MS.gene050277.t1.exon3;Parent=MS.gene050277.t1
chr7.3 CDS 9264456 9264517 9264456 ID=cds.MS.gene050277.t1;Parent=MS.gene050277.t1
chr7.3 exon 9264878 9265011 9264878 ID=MS.gene050277.t1.exon4;Parent=MS.gene050277.t1
chr7.3 CDS 9264878 9265011 9264878 ID=cds.MS.gene050277.t1;Parent=MS.gene050277.t1
Gene Sequence

>MS.gene050277

ATGTGGGCAAGCGCAGAAGGTGGTGCTCCGGAGGTTACTCTAGAAACTTCCATGGGTTCATTCACCGTCGAGGTAATTATTATTATTTTAATTTTTTTAATTCGTTCGTTAAACCCTGATACAGAATTAGGGTTTTAACATTTTTTTTTTTTGGGTTTTTAGTTGTACTACAAGCATGCACCTAGAACTTGTAGGAACTTCATTGAACTATCTCGTAGAGGTTATTACGACAACGTTAAGTTCCACAGAATCATCAAGGTATTCATCTTCCACATTTTCATTGTTCGTTATTTTGTCTTAAAATTTAGATGGTGTTGTTTTTTAATTACATTGGTTTTTTGTTGAGTAGGATTTCATAGTACAAGGTGGGGATCCCACTGGGACAGGAAGAGGAGGAGAATCCATCTATGGGTATGCTTTAACTCATCATCGTTATGTTAATTGTGTTTGTAATCGTGTTATCATAATATGGGTTTGTTTGGATCGGCTTATTTTCGCTTATCAACTGACATAAACTGTTTGGGGGAACTTATGACATGTTCATAAACTGTTTTCGGCTTATTTTCATAAGCTCTCCAAGACAGCTTATACAAAAATGATTTGACTTTATTTTATCTTTTGATATAGAAATAGCTTATATATAAGTGCTTATTTTGATAAGCGCTTATGCTATAAGCTGCAAATGAAGTTGTTTATTCAAAGGGGGCCTAGGTTTTTTTGGGTGACTTATGAGTTATCAATTCAATTTAGCCACTTTGTTGTTTATGGCAGTGCTAAATTTGAAGATGAGATTAAACAAGAGCTGAAGCACACTGGAGCTGGTATTTTATCAATGGCTAATGCTGGCCCTAATACTAACGGAAGTCAGTTCTTTATTACTCTCGCACCGTGCCCCTCTTTGGATG

Protein sequence

>MS.gene050277.t1

MWASAEGGAPEVTLETSMGSFTVELYYKHAPRTCRNFIELSRRGYYDNVKFHRIIKDFIVQGGDPTGTGRGGESIYGAKFEDEIKQELKHTGAGILSMANAGPNTNGSQFFITLAPCPSLD