AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene016737

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016737.t1 MTR_5g085390 93.074 231 13 3 1 229 1 230 5.65e-133 374
MS.gene016737.t1 MTR_6g011200 56.846 241 83 6 1 230 1 231 3.34e-80 241
MS.gene016737.t1 MTR_6g011250 63.121 141 50 1 1 139 1 141 3.81e-59 185
MS.gene016737.t1 MTR_6g011230 47.679 237 80 11 1 228 1 202 1.96e-55 176
MS.gene016737.t1 MTR_4g099230 63.910 133 43 1 10 142 3 130 1.34e-54 172
MS.gene016737.t1 MTR_6g004550 55.556 126 50 2 37 159 1 123 1.72e-37 128
MS.gene016737.t1 MTR_4g107450 54.717 106 47 1 8 113 9 113 2.04e-31 117
MS.gene016737.t1 MTR_8g017090 53.333 105 48 1 7 111 10 113 2.06e-29 112
MS.gene016737.t1 MTR_3g073690 45.098 102 55 1 10 111 10 110 4.10e-28 105
MS.gene016737.t1 MTR_7g033800 34.545 165 80 4 7 159 9 157 3.09e-27 102
MS.gene016737.t1 MTR_4g083680 32.164 171 97 5 10 178 16 169 4.53e-27 102
MS.gene016737.t1 MTR_3g452660 44.762 105 57 1 7 111 5 108 6.51e-27 105
MS.gene016737.t1 MTR_5g017950 43.810 105 58 1 7 111 6 109 1.12e-26 105
MS.gene016737.t1 MTR_8g040900 47.126 87 45 1 3 89 1 86 2.77e-26 102
MS.gene016737.t1 MTR_4g105170 42.056 107 60 2 7 112 9 114 1.32e-25 99.0
MS.gene016737.t1 MTR_6g005080 43.878 98 54 1 7 104 8 104 2.51e-25 97.1
MS.gene016737.t1 MTR_6g005070 43.878 98 54 1 7 104 7 103 3.71e-25 96.7
MS.gene016737.t1 MTR_3g077240 42.857 98 55 1 7 104 8 104 6.36e-25 97.4
MS.gene016737.t1 MTR_2g100020 45.283 106 57 1 8 113 18 122 6.98e-25 99.4
MS.gene016737.t1 MTR_5g083960 36.449 107 64 2 1 107 34 136 9.41e-25 97.1
MS.gene016737.t1 MTR_5g075020 38.938 113 64 3 1 112 38 146 1.26e-24 97.8
MS.gene016737.t1 MTR_5g075020 38.938 113 64 3 1 112 42 150 1.62e-24 97.4
MS.gene016737.t1 MTR_3g031660 36.441 118 74 1 10 127 8 124 3.96e-24 95.1
MS.gene016737.t1 MTR_5g093010 32.639 144 88 4 10 149 6 144 4.79e-24 94.0
MS.gene016737.t1 MTR_2g068760 42.105 95 50 2 10 104 14 103 8.35e-24 93.6
MS.gene016737.t1 MTR_2g093310 48.750 80 40 1 10 89 34 112 2.06e-23 93.6
MS.gene016737.t1 MTR_7g028905 37.864 103 63 1 10 112 6 107 7.18e-23 90.1
MS.gene016737.t1 MTR_3g094690 38.182 110 60 3 1 110 42 143 8.47e-23 93.2
MS.gene016737.t1 MTR_5g083230 42.169 83 47 1 7 89 4 85 2.35e-22 90.1
MS.gene016737.t1 MTR_5g083010 38.053 113 61 3 5 113 7 114 2.99e-22 90.1
MS.gene016737.t1 MTR_4g060950 43.158 95 52 2 10 103 25 118 5.67e-22 89.7
MS.gene016737.t1 MTR_3g071590 34.459 148 87 5 10 157 9 146 1.13e-21 88.2
MS.gene016737.t1 MTR_3g094690 37.273 110 60 3 1 110 42 142 2.24e-21 89.4
MS.gene016737.t1 MTR_3g071420 38.614 101 57 2 5 105 10 105 3.09e-21 87.8
MS.gene016737.t1 MTR_8g079620 40.367 109 61 2 3 111 5 109 3.67e-21 88.6
MS.gene016737.t1 MTR_1g095850 40.594 101 59 1 10 110 73 172 5.83e-21 87.8
MS.gene016737.t1 MTR_8g079660 40.367 109 61 2 3 111 5 109 1.73e-20 87.4
MS.gene016737.t1 MTR_5g080470 33.333 105 68 2 8 111 6 109 5.28e-17 76.6
MS.gene016737.t1 MTR_8g079580 37.615 109 63 3 3 110 5 109 2.23e-16 75.5
MS.gene016737.t1 MTR_1g070220 36.000 100 62 2 10 108 16 114 7.55e-16 73.9
MS.gene016737.t1 MTR_8g036105 35.922 103 64 2 10 111 19 120 9.66e-16 73.6
MS.gene016737.t1 MTR_7g096530 33.654 104 67 2 10 112 15 117 1.15e-15 73.6
MS.gene016737.t1 MTR_6g027710 33.898 118 68 4 3 114 37 150 1.58e-15 73.2
MS.gene016737.t1 MTR_8g009730 30.469 128 87 2 9 136 10 135 1.11e-14 70.5
MS.gene016737.t1 MTR_6g027700 30.645 124 78 3 10 126 8 130 1.98e-14 70.1
MS.gene016737.t1 MTR_7g074990 33.000 100 65 2 10 108 21 119 3.14e-14 70.1
MS.gene016737.t1 MTR_1g070205 34.783 115 65 5 10 123 13 118 5.97e-14 68.9
MS.gene016737.t1 MTR_8g036085 32.039 103 68 2 10 111 24 125 7.24e-14 68.9
MS.gene016737.t1 MTR_4g088035 25.000 160 109 2 9 158 6 164 1.10e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene016737.t1 AT3G47870 56.863 102 43 1 9 110 36 136 3.95e-36 130
MS.gene016737.t1 AT3G13850 48.246 114 58 1 8 121 35 147 1.03e-29 112
MS.gene016737.t1 AT1G65620 30.348 201 130 2 7 207 7 197 1.51e-27 104
MS.gene016737.t1 AT1G65620 30.348 201 130 2 7 207 7 197 1.51e-27 104
MS.gene016737.t1 AT1G65620 30.348 201 130 2 7 207 7 197 1.51e-27 104
MS.gene016737.t1 AT1G65620 30.348 201 130 2 7 207 7 197 1.51e-27 104
MS.gene016737.t1 AT1G65620 30.348 201 130 2 7 207 7 197 1.51e-27 104
MS.gene016737.t1 AT5G66870 44.118 102 56 1 10 111 8 108 1.65e-26 104
MS.gene016737.t1 AT3G27650 42.342 111 62 2 7 116 37 146 2.25e-26 100
MS.gene016737.t1 AT2G40470 34.247 146 84 5 1 145 15 149 2.01e-25 99.0
MS.gene016737.t1 AT2G40470 34.247 146 84 5 1 145 40 174 4.30e-25 99.0
MS.gene016737.t1 AT1G72980 42.975 121 67 2 9 128 13 132 6.62e-25 98.2
MS.gene016737.t1 AT5G63090 40.566 106 62 1 7 112 9 113 8.17e-25 97.1
MS.gene016737.t1 AT5G63090 40.566 106 62 1 7 112 9 113 8.17e-25 97.1
MS.gene016737.t1 AT5G63090 40.566 106 62 1 7 112 9 113 8.17e-25 97.1
MS.gene016737.t1 AT5G63090 40.566 106 62 1 7 112 9 113 8.17e-25 97.1
MS.gene016737.t1 AT2G30340 37.037 108 64 2 1 108 48 151 5.02e-24 97.1
MS.gene016737.t1 AT2G30340 37.037 108 64 2 1 108 47 150 5.24e-24 97.1
MS.gene016737.t1 AT1G31320 47.500 80 41 1 10 89 14 92 5.42e-24 94.7
MS.gene016737.t1 AT1G07900 48.750 80 40 1 10 89 34 112 1.22e-22 91.7
MS.gene016737.t1 AT2G23660 41.176 102 59 1 10 111 6 106 2.61e-22 93.2
MS.gene016737.t1 AT2G23660 41.176 102 59 1 10 111 6 106 2.61e-22 93.2
MS.gene016737.t1 AT2G23660 41.176 102 59 1 10 111 6 106 2.61e-22 93.2
MS.gene016737.t1 AT2G28500 48.750 80 40 1 10 89 56 134 3.89e-22 91.3
MS.gene016737.t1 AT3G26660 34.615 104 67 1 8 111 4 106 6.96e-22 87.4
MS.gene016737.t1 AT3G26620 32.174 115 77 1 8 122 4 117 7.34e-22 87.4
MS.gene016737.t1 AT1G16530 34.921 126 76 4 10 133 15 136 2.55e-21 87.4
MS.gene016737.t1 AT2G30130 36.522 115 71 2 10 124 9 121 2.60e-21 88.2
MS.gene016737.t1 AT3G50510 39.091 110 65 2 5 113 8 116 1.30e-20 86.3
MS.gene016737.t1 AT3G50510 39.091 110 65 2 5 113 8 116 1.30e-20 86.3
MS.gene016737.t1 AT1G06280 40.385 104 54 3 7 110 22 117 1.34e-20 86.7
MS.gene016737.t1 AT3G11090 35.644 101 60 2 5 105 7 102 3.33e-20 84.3
MS.gene016737.t1 AT5G15060 45.205 73 39 1 10 81 18 90 3.59e-17 75.9
MS.gene016737.t1 AT2G19820 40.000 80 48 0 10 89 13 92 3.96e-17 75.1
MS.gene016737.t1 AT4G00210 31.343 134 89 3 10 142 12 143 5.98e-16 74.3
MS.gene016737.t1 AT3G03760 35.294 102 64 2 10 110 52 152 1.26e-15 74.3
MS.gene016737.t1 AT5G35900 31.068 103 70 1 9 111 5 106 2.47e-15 72.4
MS.gene016737.t1 AT4G00220 32.673 101 66 2 12 111 20 119 8.11e-15 71.2
MS.gene016737.t1 AT2G42430 37.805 82 49 2 10 90 16 96 3.27e-14 70.1
MS.gene016737.t1 AT5G06080 30.597 134 81 4 9 141 7 129 1.04e-13 67.4
MS.gene016737.t1 AT2G31310 31.298 131 72 4 10 127 8 133 2.39e-13 66.6
MS.gene016737.t1 AT3G58190 32.039 103 68 2 10 111 12 113 7.16e-13 65.9
MS.gene016737.t1 AT2G45420 31.683 101 67 2 12 111 40 139 9.96e-13 66.2
MS.gene016737.t1 AT2G42440 30.303 99 67 2 10 107 8 105 1.31e-12 65.5
MS.gene016737.t1 AT2G45410 32.673 101 66 2 12 111 19 118 6.26e-12 62.8

Find 41 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTAAATATTGGGATATT+TGG 0.141273 5.2:-72735312 None:intergenic
TCACCAACATTGTTAAATAT+TGG 0.190888 5.2:-72735321 None:intergenic
CTTGGTGTTATTATGAATTA+TGG 0.198268 5.2:+72735168 MS.gene016737:CDS
AGCTAGAACAACATTTGATT+TGG 0.257325 5.2:+72735560 MS.gene016737:CDS
TCATTGCTTGATAATCCTTT+TGG 0.267871 5.2:-72735492 None:intergenic
CATGCTGCACAAGCCTTGTT+TGG 0.269582 5.2:-72734928 None:intergenic
TCCTTTAGCTCCTTATTTCC+CGG 0.285923 5.2:+72734984 MS.gene016737:CDS
GGAATTTGAGAACTAGTATA+AGG 0.287802 5.2:-72735291 None:intergenic
AATATCCGACTCAATAATTA+TGG 0.288561 5.2:-72735118 None:intergenic
CACCAACATTGTTAAATATT+GGG 0.294726 5.2:-72735320 None:intergenic
GGTTTATCGGCCGGGAAATA+AGG 0.295833 5.2:-72734994 None:intergenic
GCTAGAACAACATTTGATTT+GGG 0.363338 5.2:+72735561 MS.gene016737:CDS
AGCAACGCTCATCGTTTGTT+TGG 0.383470 5.2:+72735027 MS.gene016737:CDS
GGATGACAATTCTAATTTGA+TGG 0.388591 5.2:+72735467 MS.gene016737:CDS
CCTCATGATGTTAACTATAG+TGG 0.400420 5.2:+72735429 MS.gene016737:CDS
AGATATGTTAAAGCAGTCTA+TGG 0.416875 5.2:+72735191 MS.gene016737:CDS
CTTTAGTATCCTTTGTATGT+TGG 0.435097 5.2:-72735055 None:intergenic
CGTGCAAAATCTCCCGTTCA+TGG 0.444453 5.2:+72735141 MS.gene016737:CDS
ATCCCAATATTTAACAATGT+TGG 0.449694 5.2:+72735318 MS.gene016737:CDS
GACGACCTTGACGACCTTGA+TGG 0.456186 5.2:+72735522 MS.gene016737:CDS
ATTATCAAGCAATGAAGAAT+CGG 0.467820 5.2:+72735500 MS.gene016737:CDS
TCTAATTTGATGGTACCAAA+AGG 0.475215 5.2:+72735477 MS.gene016737:CDS
ACACCAAGACATCCATGAAC+GGG 0.497015 5.2:-72735153 None:intergenic
TTTGGTTTGATGATATTCAT+TGG 0.504277 5.2:-72734910 None:intergenic
TTGAGAACTAGTATAAGGTA+AGG 0.504496 5.2:-72735286 None:intergenic
TCTCCCGTTCATGGATGTCT+TGG 0.510462 5.2:+72735150 MS.gene016737:CDS
AAAGCAGTCTATGGAAGAGT+TGG 0.512156 5.2:+72735200 MS.gene016737:CDS
AAGGATACTAAAGGAAATCA+AGG 0.515917 5.2:+72735065 MS.gene016737:CDS
GCCGGGAAATAAGGAGCTAA+AGG 0.524058 5.2:-72734985 None:intergenic
CAACATACAAAGGATACTAA+AGG 0.551295 5.2:+72735056 MS.gene016737:CDS
GAGATCCATAATTATTGAGT+CGG 0.580015 5.2:+72735113 MS.gene016737:CDS
CCACTATAGTTAACATCATG+AGG 0.583308 5.2:-72735429 None:intergenic
GTTCATCAACACCACCATCA+AGG 0.592727 5.2:-72735536 None:intergenic
GAATATCATCAAACCAAACA+AGG 0.597163 5.2:+72734915 MS.gene016737:CDS
TTGGTGTTTCCAACATACAA+AGG 0.602738 5.2:+72735046 MS.gene016737:CDS
AACACCAAGACATCCATGAA+CGG 0.603796 5.2:-72735154 None:intergenic
CACCACCATCAAGGTCGTCA+AGG 0.611148 5.2:-72735527 None:intergenic
CATGATGTTAACTATAGTGG+TGG 0.632189 5.2:+72735432 MS.gene016737:CDS
TAGTGGTGGCGACTATGTCA+TGG 0.648101 5.2:+72735446 MS.gene016737:CDS
CACTATAGTTAACATCATGA+GGG 0.659397 5.2:-72735428 None:intergenic
GACCTTGACGACCTTGATGG+TGG 0.667335 5.2:+72735525 MS.gene016737:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GGATAATAATAATAATAATT+AGG - chr5.2:72735351-72735370 None:intergenic 10.0%
!!! ATATTATTATTTTCACTATT+GGG - chr5.2:72735372-72735391 None:intergenic 10.0%
!!! CATATTATTATTTTCACTAT+TGG - chr5.2:72735373-72735392 None:intergenic 15.0%
!! TTGTTAAATATTGGGATATT+TGG - chr5.2:72735315-72735334 None:intergenic 20.0%
! AATATCCGACTCAATAATTA+TGG - chr5.2:72735121-72735140 None:intergenic 25.0%
! ATCCCAATATTTAACAATGT+TGG + chr5.2:72735318-72735337 MS.gene016737:CDS 25.0%
! ATTATCAAGCAATGAAGAAT+CGG + chr5.2:72735500-72735519 MS.gene016737:CDS 25.0%
! CACCAACATTGTTAAATATT+GGG - chr5.2:72735323-72735342 None:intergenic 25.0%
! TCACCAACATTGTTAAATAT+TGG - chr5.2:72735324-72735343 None:intergenic 25.0%
!!! CATTTGATTTGGGAAAAAAA+AGG + chr5.2:72735571-72735590 MS.gene016737:CDS 25.0%
!!! CTTGGTGTTATTATGAATTA+TGG + chr5.2:72735168-72735187 MS.gene016737:CDS 25.0%
!!! GCTAAACATTTTTGGTTTAT+CGG - chr5.2:72735010-72735029 None:intergenic 25.0%
AAGGATACTAAAGGAAATCA+AGG + chr5.2:72735065-72735084 MS.gene016737:CDS 30.0%
AGATATGTTAAAGCAGTCTA+TGG + chr5.2:72735191-72735210 MS.gene016737:CDS 30.0%
AGCTAGAACAACATTTGATT+TGG + chr5.2:72735560-72735579 MS.gene016737:CDS 30.0%
CAACATACAAAGGATACTAA+AGG + chr5.2:72735056-72735075 MS.gene016737:CDS 30.0%
CACTATAGTTAACATCATGA+GGG - chr5.2:72735431-72735450 None:intergenic 30.0%
CTTTAGTATCCTTTGTATGT+TGG - chr5.2:72735058-72735077 None:intergenic 30.0%
GAATATCATCAAACCAAACA+AGG + chr5.2:72734915-72734934 MS.gene016737:CDS 30.0%
GAGATCCATAATTATTGAGT+CGG + chr5.2:72735113-72735132 MS.gene016737:CDS 30.0%
GGAATTTGAGAACTAGTATA+AGG - chr5.2:72735294-72735313 None:intergenic 30.0%
GGATGACAATTCTAATTTGA+TGG + chr5.2:72735467-72735486 MS.gene016737:CDS 30.0%
TTGAGAACTAGTATAAGGTA+AGG - chr5.2:72735289-72735308 None:intergenic 30.0%
! GCTAGAACAACATTTGATTT+GGG + chr5.2:72735561-72735580 MS.gene016737:CDS 30.0%
! TCTAATTTGATGGTACCAAA+AGG + chr5.2:72735477-72735496 MS.gene016737:CDS 30.0%
!! TCATTGCTTGATAATCCTTT+TGG - chr5.2:72735495-72735514 None:intergenic 30.0%
CATGATGTTAACTATAGTGG+TGG + chr5.2:72735432-72735451 MS.gene016737:CDS 35.0%
CCACTATAGTTAACATCATG+AGG - chr5.2:72735432-72735451 None:intergenic 35.0%
CCTCATGATGTTAACTATAG+TGG + chr5.2:72735429-72735448 MS.gene016737:CDS 35.0%
! TTGGTGTTTCCAACATACAA+AGG + chr5.2:72735046-72735065 MS.gene016737:CDS 35.0%
!! TGAGCGTTGCTAAACATTTT+TGG - chr5.2:72735018-72735037 None:intergenic 35.0%
!!! AACATTTTTGGTTTATCGGC+CGG - chr5.2:72735006-72735025 None:intergenic 35.0%
AAAGCAGTCTATGGAAGAGT+TGG + chr5.2:72735200-72735219 MS.gene016737:CDS 40.0%
AACACCAAGACATCCATGAA+CGG - chr5.2:72735157-72735176 None:intergenic 40.0%
! TCCTTTAGCTCCTTATTTCC+CGG + chr5.2:72734984-72735003 MS.gene016737:CDS 40.0%
!!! ACATTTTTGGTTTATCGGCC+GGG - chr5.2:72735005-72735024 None:intergenic 40.0%
ACACCAAGACATCCATGAAC+GGG - chr5.2:72735156-72735175 None:intergenic 45.0%
AGCAACGCTCATCGTTTGTT+TGG + chr5.2:72735027-72735046 MS.gene016737:CDS 45.0%
GTTCATCAACACCACCATCA+AGG - chr5.2:72735539-72735558 None:intergenic 45.0%
CGTGCAAAATCTCCCGTTCA+TGG + chr5.2:72735141-72735160 MS.gene016737:CDS 50.0%
GCCGGGAAATAAGGAGCTAA+AGG - chr5.2:72734988-72735007 None:intergenic 50.0%
GGTTTATCGGCCGGGAAATA+AGG - chr5.2:72734997-72735016 None:intergenic 50.0%
TCTCCCGTTCATGGATGTCT+TGG + chr5.2:72735150-72735169 MS.gene016737:CDS 50.0%
! TAGTGGTGGCGACTATGTCA+TGG + chr5.2:72735446-72735465 MS.gene016737:CDS 50.0%
!! CATGCTGCACAAGCCTTGTT+TGG - chr5.2:72734931-72734950 None:intergenic 50.0%
CACCACCATCAAGGTCGTCA+AGG - chr5.2:72735530-72735549 None:intergenic 55.0%
GACCTTGACGACCTTGATGG+TGG + chr5.2:72735525-72735544 MS.gene016737:CDS 55.0%
GACGACCTTGACGACCTTGA+TGG + chr5.2:72735522-72735541 MS.gene016737:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 72734913 72735608 72734913 ID=MS.gene016737
chr5.2 mRNA 72734913 72735608 72734913 ID=MS.gene016737.t1;Parent=MS.gene016737
chr5.2 exon 72734913 72735608 72734913 ID=MS.gene016737.t1.exon1;Parent=MS.gene016737.t1
chr5.2 CDS 72734913 72735608 72734913 ID=cds.MS.gene016737.t1;Parent=MS.gene016737.t1
Gene Sequence

>MS.gene016737

ATGAATATCATCAAACCAAACAAGGCTTGTGCAGCATGCAAGTATCAAAGAAGAAAGTGTTCAAGTGAGTGTCCTTTAGCTCCTTATTTCCCGGCCGATAAACCAAAAATGTTTAGCAACGCTCATCGTTTGTTTGGTGTTTCCAACATACAAAGGATACTAAAGGAAATCAAGGACGACGATCAAAAAGATGATGCGATGAGATCCATAATTATTGAGTCGGATATTCGTGCAAAATCTCCCGTTCATGGATGTCTTGGTGTTATTATGAATTATGGAGATATGTTAAAGCAGTCTATGGAAGAGTTGGATCATGTAAAAACGTTACTAGCTTATTGTAACGATTTACAACAAAAACAACATCTTCATTCTTCCTTACCTTATACTAGTTCTCAAATTCCAAATATCCCAATATTTAACAATGTTGGTGATGTTCCTAATTATTATTATTATTATCCCAATAGTGAAAATAATAATATGATGAGAGCATCTTCTTCTTATATTAGTGACATCATCCCTCATGATGTTAACTATAGTGGTGGCGACTATGTCATGGATGACAATTCTAATTTGATGGTACCAAAAGGATTATCAAGCAATGAAGAATCGGACGACCTTGACGACCTTGATGGTGGTGTTGATGAACAAGCTAGAACAACATTTGATTTGGGAAAAAAAAGGAAGATTTTCAGATAG
Protein sequence

>MS.gene016737.t1

MNIIKPNKACAACKYQRRKCSSECPLAPYFPADKPKMFSNAHRLFGVSNIQRILKEIKDDDQKDDAMRSIIIESDIRAKSPVHGCLGVIMNYGDMLKQSMEELDHVKTLLAYCNDLQQKQHLHSSLPYTSSQIPNIPIFNNVGDVPNYYYYYPNSENNNMMRASSSYISDIIPHDVNYSGGDYVMDDNSNLMVPKGLSSNEESDDLDDLDGGVDEQARTTFDLGKKRKIFR