AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57839

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57839.t1 MTR_7g106510 93.252 163 9 1 1 161 1 163 1.09e-105 311
MS.gene57839.t1 MTR_4g019670 89.571 163 15 1 1 161 1 163 1.24e-103 306
MS.gene57839.t1 MTR_3g093900 61.446 166 62 1 1 164 1 166 2.92e-65 209
MS.gene57839.t1 MTR_8g467500 61.486 148 51 2 13 158 13 156 8.00e-51 164
MS.gene57839.t1 MTR_3g466980 31.515 165 107 3 1 162 1 162 1.07e-22 90.5
MS.gene57839.t1 MTR_8g036130 36.434 129 78 1 6 130 3 131 3.33e-22 89.7
MS.gene57839.t1 MTR_5g075380 33.758 157 100 3 7 160 4 159 1.93e-21 85.5
MS.gene57839.t1 MTR_4g032620 34.426 122 78 1 6 125 3 124 1.03e-20 85.5
MS.gene57839.t1 MTR_4g031910 40.909 132 73 2 1 130 1 129 6.06e-20 83.2
MS.gene57839.t1 MTR_3g466830 31.333 150 100 2 6 152 2 151 1.40e-17 75.5
MS.gene57839.t1 MTR_2g035610 37.500 120 73 1 6 123 3 122 1.40e-17 74.3
MS.gene57839.t1 MTR_1g090710 31.579 114 77 1 6 118 3 116 2.66e-17 74.7
MS.gene57839.t1 MTR_4g032260 42.105 95 53 2 38 130 35 129 3.40e-17 74.3
MS.gene57839.t1 MTR_3g065100 37.607 117 71 1 6 120 3 119 3.57e-17 76.3
MS.gene57839.t1 MTR_2g016210 28.966 145 100 2 7 148 4 148 5.20e-17 75.9
MS.gene57839.t1 MTR_1g077390 31.579 114 77 1 6 118 3 116 3.77e-16 71.6
MS.gene57839.t1 MTR_4g028800 41.429 70 39 1 7 76 4 71 1.27e-15 68.2
MS.gene57839.t1 MTR_3g466890 28.105 153 107 2 6 155 2 154 2.07e-15 69.7
MS.gene57839.t1 MTR_5g047580 32.773 119 76 2 1 118 1 116 3.71e-15 68.9
MS.gene57839.t1 MTR_3g031240 27.826 115 81 1 6 118 3 117 1.21e-14 68.2
MS.gene57839.t1 MTR_3g031100 27.966 118 83 1 6 121 3 120 2.87e-14 68.6
MS.gene57839.t1 MTR_4g032290 37.895 95 57 1 38 130 35 129 4.74e-14 67.8
MS.gene57839.t1 MTR_4g063790 27.500 160 103 5 1 153 1 154 1.09e-13 65.5
MS.gene57839.t1 MTR_3g466930 30.645 124 83 2 35 155 2 125 1.42e-13 64.3
MS.gene57839.t1 MTR_1g084950 35.294 119 73 2 1 118 1 116 2.01e-13 64.7
MS.gene57839.t1 MTR_1g090697 30.252 119 79 2 1 118 1 116 2.67e-13 64.3
MS.gene57839.t1 MTR_3g466900 29.032 124 85 2 35 155 2 125 7.71e-13 62.4
MS.gene57839.t1 MTR_4g028720 34.127 126 82 1 6 130 3 128 9.26e-13 62.8
MS.gene57839.t1 MTR_1g077320 32.773 119 76 2 1 118 1 116 9.96e-13 62.8
MS.gene57839.t1 MTR_7g011950 32.061 131 85 2 1 130 1 128 3.46e-12 61.2
MS.gene57839.t1 MTR_1g090783 25.000 116 86 1 6 120 2 117 1.97e-11 59.3
MS.gene57839.t1 MTR_1g077300 33.333 114 75 1 6 118 3 116 5.05e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57839.t1 AT1G65300 36.697 109 67 1 6 112 2 110 1.29e-18 80.9
MS.gene57839.t1 AT2G40210 31.169 154 100 3 1 152 1 150 1.61e-15 73.2
MS.gene57839.t1 AT3G05860 29.927 137 90 3 1 134 1 134 2.91e-15 70.5
MS.gene57839.t1 AT3G05860 40.000 75 42 1 1 75 1 72 5.97e-15 70.5
MS.gene57839.t1 AT3G05860 40.000 75 42 1 1 75 1 72 7.92e-15 70.1
MS.gene57839.t1 AT5G06500 30.137 146 99 2 4 147 1 145 2.62e-14 68.6
MS.gene57839.t1 AT2G15660 30.065 153 90 5 5 152 3 143 6.20e-14 67.8
MS.gene57839.t1 AT2G28700 31.159 138 91 3 4 139 1 136 1.33e-13 67.4
MS.gene57839.t1 AT5G48670 35.593 118 72 2 6 120 3 119 2.19e-13 66.6
MS.gene57839.t1 AT5G26630 37.931 116 67 2 1 114 1 113 2.23e-13 65.5
MS.gene57839.t1 AT1G31630 32.174 115 75 2 6 118 2 115 2.50e-13 66.6
MS.gene57839.t1 AT1G65330 32.110 109 72 1 6 112 2 110 3.34e-13 65.9
MS.gene57839.t1 AT5G26650 30.702 114 77 1 7 118 2 115 6.46e-13 65.9
MS.gene57839.t1 AT1G31640 32.407 108 70 2 13 118 9 115 8.47e-13 65.5
MS.gene57839.t1 AT5G27960 30.702 114 77 1 7 118 2 115 1.45e-12 64.3
MS.gene57839.t1 AT1G22590 26.549 113 81 1 6 116 3 115 7.20e-12 60.5

Find 27 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTATTATTCTCAATCAATT+TGG 0.203967 6.1:-68869668 None:intergenic
TTGACTCAAACTTGGTTATT+AGG 0.223954 6.1:-68869843 None:intergenic
GATTGTCACATGCTCCATTT+TGG 0.244676 6.1:-68869734 None:intergenic
GAAAGGGTTGTTCACCAAAA+TGG 0.296295 6.1:+68869720 MS.gene57839:CDS
GAGGCTTGTGTGGTTGTGTT+TGG 0.314095 6.1:+68869769 MS.gene57839:CDS
AGAAAACGAAGAGACTTTAA+TGG 0.340960 6.1:+68869957 MS.gene57839:CDS
AGGCTTGTGTGGTTGTGTTT+GGG 0.371274 6.1:+68869770 MS.gene57839:CDS
GTGATACAAAACCATCAATA+TGG 0.392745 6.1:+68869797 MS.gene57839:CDS
ATAGGTGATGGCCATATTGA+TGG 0.399065 6.1:-68869808 None:intergenic
AATAACCAAGTTTGAGTCAA+TGG 0.421569 6.1:+68869846 MS.gene57839:CDS
CACATCCATTGACTCAAACT+TGG 0.433217 6.1:-68869851 None:intergenic
ATCAATATGGCCATCACCTA+TGG 0.448122 6.1:+68869810 MS.gene57839:CDS
GAAAACGAAGAGACTTTAAT+GGG 0.451096 6.1:+68869958 MS.gene57839:CDS
TGTGTGGTTGTGTTTGGGCC+AGG 0.454451 6.1:+68869775 MS.gene57839:CDS
GATGTCTAGGCATTTAGAAA+AGG 0.501336 6.1:+68870092 MS.gene57839:CDS
GACAATCTTATGCGGTATTG+AGG 0.507885 6.1:+68869750 MS.gene57839:CDS
TGAGAATAATACTCGAAGAA+AGG 0.533789 6.1:+68869678 MS.gene57839:CDS
ATTAGGTCTTCAGCCACCAT+AGG 0.558551 6.1:-68869826 None:intergenic
TGCTATAAGAGAAGATTGAA+AGG 0.560605 6.1:+68869703 MS.gene57839:CDS
AGATCACTAGGAAGATGTCT+AGG 0.577538 6.1:+68870079 MS.gene57839:CDS
TCAAGCGATTCTGCACATCA+TGG 0.589121 6.1:-68870032 None:intergenic
GCTATAAGAGAAGATTGAAA+GGG 0.594807 6.1:+68869704 MS.gene57839:CDS
TCTTCAGCCACCATAGGTGA+TGG 0.598675 6.1:-68869820 None:intergenic
ATGCGGTATTGAGGCTTGTG+TGG 0.625075 6.1:+68869759 MS.gene57839:CDS
ATGCATCAAATTGAAAACGA+AGG 0.641960 6.1:+68869988 MS.gene57839:CDS
AATATGGCCATCACCTATGG+TGG 0.644233 6.1:+68869813 MS.gene57839:CDS
GAGCATGTGACAATCTTATG+CGG 0.708478 6.1:+68869742 MS.gene57839:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTATTATTCTCAATCAATT+TGG - chr6.1:68869671-68869690 None:intergenic 20.0%
!! TTGAAAAAATTAAGATCACT+AGG + chr6.1:68870067-68870086 MS.gene57839:CDS 20.0%
!!! TTTCTTTTTTGATCTTTTCA+AGG - chr6.1:68869942-68869961 None:intergenic 20.0%
AATAACCAAGTTTGAGTCAA+TGG + chr6.1:68869846-68869865 MS.gene57839:CDS 30.0%
AGAAAACGAAGAGACTTTAA+TGG + chr6.1:68869957-68869976 MS.gene57839:CDS 30.0%
ATGCATCAAATTGAAAACGA+AGG + chr6.1:68869988-68870007 MS.gene57839:CDS 30.0%
GAAAACGAAGAGACTTTAAT+GGG + chr6.1:68869958-68869977 MS.gene57839:CDS 30.0%
GCTATAAGAGAAGATTGAAA+GGG + chr6.1:68869704-68869723 MS.gene57839:CDS 30.0%
GTGATACAAAACCATCAATA+TGG + chr6.1:68869797-68869816 MS.gene57839:CDS 30.0%
TATCCTCCAAAAAAGTCAAT+TGG - chr6.1:68869897-68869916 None:intergenic 30.0%
TGAGAATAATACTCGAAGAA+AGG + chr6.1:68869678-68869697 MS.gene57839:CDS 30.0%
TGCTATAAGAGAAGATTGAA+AGG + chr6.1:68869703-68869722 MS.gene57839:CDS 30.0%
TTGACTCAAACTTGGTTATT+AGG - chr6.1:68869846-68869865 None:intergenic 30.0%
!!! ATTGACTTTTTTGGAGGATA+AGG + chr6.1:68869897-68869916 MS.gene57839:CDS 30.0%
!!! TTGACTTTTTTGGAGGATAA+GGG + chr6.1:68869898-68869917 MS.gene57839:CDS 30.0%
GATGTCTAGGCATTTAGAAA+AGG + chr6.1:68870092-68870111 MS.gene57839:CDS 35.0%
!!! ATTGATGGTTTTGTATCACC+TGG - chr6.1:68869796-68869815 None:intergenic 35.0%
!!! GACTGACCAATTGACTTTTT+TGG + chr6.1:68869888-68869907 MS.gene57839:CDS 35.0%
!!! TGACCAATTGACTTTTTTGG+AGG + chr6.1:68869891-68869910 MS.gene57839:CDS 35.0%
AGATCACTAGGAAGATGTCT+AGG + chr6.1:68870079-68870098 MS.gene57839:CDS 40.0%
ATCAATATGGCCATCACCTA+TGG + chr6.1:68869810-68869829 MS.gene57839:CDS 40.0%
GAAAGGGTTGTTCACCAAAA+TGG + chr6.1:68869720-68869739 MS.gene57839:CDS 40.0%
GACAATCTTATGCGGTATTG+AGG + chr6.1:68869750-68869769 MS.gene57839:CDS 40.0%
GAGCATGTGACAATCTTATG+CGG + chr6.1:68869742-68869761 MS.gene57839:CDS 40.0%
! ATAGGTGATGGCCATATTGA+TGG - chr6.1:68869811-68869830 None:intergenic 40.0%
! GATTGTCACATGCTCCATTT+TGG - chr6.1:68869737-68869756 None:intergenic 40.0%
!! CACATCCATTGACTCAAACT+TGG - chr6.1:68869854-68869873 None:intergenic 40.0%
AATATGGCCATCACCTATGG+TGG + chr6.1:68869813-68869832 MS.gene57839:CDS 45.0%
AGGCTTGTGTGGTTGTGTTT+GGG + chr6.1:68869770-68869789 MS.gene57839:CDS 45.0%
ATTAGGTCTTCAGCCACCAT+AGG - chr6.1:68869829-68869848 None:intergenic 45.0%
TCAAGCGATTCTGCACATCA+TGG - chr6.1:68870035-68870054 None:intergenic 45.0%
GAGGCTTGTGTGGTTGTGTT+TGG + chr6.1:68869769-68869788 MS.gene57839:CDS 50.0%
TCTTCAGCCACCATAGGTGA+TGG - chr6.1:68869823-68869842 None:intergenic 50.0%
! ATGCGGTATTGAGGCTTGTG+TGG + chr6.1:68869759-68869778 MS.gene57839:CDS 50.0%
TGTGTGGTTGTGTTTGGGCC+AGG + chr6.1:68869775-68869794 MS.gene57839:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 68869637 68870137 68869637 ID=MS.gene57839
chr6.1 mRNA 68869637 68870137 68869637 ID=MS.gene57839.t1;Parent=MS.gene57839
chr6.1 exon 68869637 68870137 68869637 ID=MS.gene57839.t1.exon1;Parent=MS.gene57839.t1
chr6.1 CDS 68869637 68870137 68869637 ID=cds.MS.gene57839.t1;Parent=MS.gene57839.t1
Gene Sequence

>MS.gene57839

ATGACAAGAATCAGAAAAAAGAAGATCACATCCAAATTGATTGAGAATAATACTCGAAGAAAGGCGTGCTATAAGAGAAGATTGAAAGGGTTGTTCACCAAAATGGAGCATGTGACAATCTTATGCGGTATTGAGGCTTGTGTGGTTGTGTTTGGGCCAGGTGATACAAAACCATCAATATGGCCATCACCTATGGTGGCTGAAGACCTAATAACCAAGTTTGAGTCAATGGATGTGCAGTCGAAAAATAAGACTGACCAATTGACTTTTTTGGAGGATAAGGGCAAAAAACTTGAAGCAAGCCTTGAAAAGATCAAAAAAGAAAACGAAGAGACTTTAATGGGAGTTTATATGCATCAAATTGAAAACGAAGGTAAATCTTTAGATGATTTTGACCATGATGTGCAGAATCGCTTGATTGCTTTTACTCTTGAAAAAATTAAGATCACTAGGAAGATGTCTAGGCATTTAGAAAAGGAGATTTTGCCTCTTGAAAATTAA
Protein sequence

>MS.gene57839.t1

MTRIRKKKITSKLIENNTRRKACYKRRLKGLFTKMEHVTILCGIEACVVVFGPGDTKPSIWPSPMVAEDLITKFESMDVQSKNKTDQLTFLEDKGKKLEASLEKIKKENEETLMGVYMHQIENEGKSLDDFDHDVQNRLIAFTLEKIKITRKMSRHLEKEILPLEN