AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001250 MtrunA17_Chr6g0481091 33.918 171 87 8 4 160 6 164 3.68e-19 83.2
MsaG001250 MtrunA17_Chr5g0405211 33.758 157 86 7 2 147 6 155 1.40e-16 77.4
MsaG001250 MtrunA17_Chr8g0345731 34.641 153 89 4 3 146 23 173 2.14e-16 74.3
MsaG001250 MtrunA17_Chr4g0054791 36.709 158 82 8 2 146 4 156 5.02e-16 75.5
MsaG001250 MtrunA17_Chr2g0309891 34.615 156 84 7 4 147 6 155 7.67e-16 75.5
MsaG001250 MtrunA17_Chr8g0361731 30.247 162 87 6 6 147 16 171 8.48e-16 75.5
MsaG001250 MtrunA17_Chr5g0400461 33.962 159 86 7 2 146 4 157 2.03e-15 73.9
MsaG001250 MtrunA17_Chr1g0197351 35.260 173 82 8 4 154 42 206 2.33e-15 74.7
MsaG001250 MtrunA17_Chr8g0372121 33.529 170 88 9 2 158 4 161 3.75e-15 73.2
MsaG001250 MtrunA17_Chr3g0128151 32.278 158 84 6 4 147 22 170 4.77e-15 73.9
MsaG001250 MtrunA17_Chr4g0050701 30.189 159 86 7 4 148 11 158 5.91e-15 70.9
MsaG001250 MtrunA17_Chr5g0417001 29.814 161 88 6 6 147 16 170 6.53e-15 73.2
MsaG001250 MtrunA17_Chr1g0201021 34.848 132 76 4 6 133 21 146 8.14e-15 73.2
MsaG001250 MtrunA17_Chr5g0428991 34.177 158 81 7 4 147 25 173 1.05e-14 72.8
MsaG001250 MtrunA17_Chr4g0047841 37.778 135 72 5 4 133 15 142 1.10e-14 72.0
MsaG001250 MtrunA17_Chr4g0018391 32.484 157 88 8 2 147 5 154 6.79e-14 69.7
MsaG001250 MtrunA17_Chr6g0453131 31.481 162 84 8 6 147 17 171 9.86e-14 69.7
MsaG001250 MtrunA17_Chr4g0056541 31.847 157 89 7 2 147 5 154 1.00e-13 69.3
MsaG001250 MtrunA17_Chr3g0109821 30.625 160 85 8 4 147 6 155 1.06e-13 69.7
MsaG001250 MtrunA17_Chr5g0433781 31.847 157 84 8 4 146 6 153 1.98e-13 68.9
MsaG001250 MtrunA17_Chr7g0263931 32.374 139 80 4 3 135 10 140 1.29e-12 65.9
MsaG001250 MtrunA17_Chr4g0038751 32.450 151 85 7 6 147 17 159 3.12e-12 64.7
MsaG001250 MtrunA17_Chr8g0359921 30.939 181 95 9 4 168 14 180 4.50e-12 64.3
MsaG001250 MtrunA17_Chr3g0139331 28.571 182 102 7 4 164 11 185 9.23e-12 63.5
MsaG001250 MtrunA17_Chr8g0345691 30.323 155 92 5 1 146 9 156 2.65e-11 62.4
MsaG001250 MtrunA17_Chr7g0252971 26.786 168 91 6 4 147 8 167 3.51e-11 62.0
MsaG001250 MtrunA17_Chr1g0183741 28.662 157 91 7 2 147 8 154 4.00e-11 61.2
MsaG001250 MtrunA17_Chr6g0453451 26.708 161 91 7 4 148 20 169 5.88e-11 61.2
MsaG001250 MtrunA17_Chr6g0484441 29.299 157 86 8 4 147 5 149 9.44e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001250 AT4G36160.2 34.706 170 93 7 4 162 14 176 1.26e-20 89.7
MsaG001250 AT4G36160.1 34.706 170 93 7 4 162 10 172 1.31e-20 89.4
MsaG001250 AT4G36160.3 34.706 170 93 7 4 162 10 172 1.31e-20 89.4
MsaG001250 AT3G17730.1 31.771 192 104 9 4 181 6 184 7.78e-19 82.8
MsaG001250 AT3G49530.2 34.375 160 85 7 1 147 10 162 9.46e-19 84.3
MsaG001250 AT5G24590.2 37.500 160 80 7 1 147 10 162 9.90e-19 84.7
MsaG001250 AT3G49530.1 34.375 160 85 7 1 147 10 162 1.04e-18 84.7
MsaG001250 AT3G10490.1 36.538 156 81 6 4 147 27 176 3.56e-18 80.9
MsaG001250 AT3G10490.2 36.538 156 81 6 4 147 27 176 4.02e-17 80.1
MsaG001250 AT5G04410.1 34.483 174 93 8 4 163 9 175 1.11e-16 79.0
MsaG001250 AT4G17980.1 34.591 159 85 7 2 146 4 157 1.18e-16 77.0
MsaG001250 AT2G18060.3 34.194 155 84 7 4 147 9 156 1.43e-16 78.2
MsaG001250 AT2G18060.1 34.194 155 84 7 4 147 9 156 1.43e-16 78.2
MsaG001250 AT1G33060.1 34.545 165 83 7 1 150 21 175 1.48e-16 78.6
MsaG001250 AT1G33060.2 34.545 165 83 7 1 150 21 175 1.54e-16 78.6
MsaG001250 AT5G64530.2 36.364 132 70 4 4 135 3 120 2.04e-16 74.3
MsaG001250 AT3G10480.1 36.076 158 79 7 4 147 27 176 2.38e-16 77.8
MsaG001250 AT2G27300.1 32.667 150 90 6 1 146 11 153 3.94e-16 76.6
MsaG001250 AT4G17980.2 34.591 159 85 7 2 146 4 157 4.31e-16 75.9
MsaG001250 AT1G69490.1 32.099 162 85 7 2 147 7 159 5.84e-16 75.1
MsaG001250 AT5G64530.1 33.133 166 76 7 4 148 3 154 7.42e-16 73.6
MsaG001250 AT1G26870.1 34.969 163 78 8 6 147 18 173 7.45e-16 76.3
MsaG001250 AT3G10480.2 35.669 157 80 7 4 147 27 175 9.86e-16 75.9
MsaG001250 AT2G24430.2 32.484 157 84 7 4 147 16 163 2.99e-15 73.9
MsaG001250 AT2G24430.1 32.484 157 84 7 4 147 16 163 2.99e-15 73.9
MsaG001250 AT5G17260.1 28.889 180 99 9 4 163 6 176 5.02e-15 73.9
MsaG001250 AT5G22290.1 33.562 146 85 7 6 146 23 161 7.45e-15 72.8
MsaG001250 AT5G46590.1 32.911 158 87 6 2 146 4 155 9.37e-15 72.0
MsaG001250 AT3G44290.2 31.034 145 89 6 6 146 16 153 1.29e-14 70.9
MsaG001250 AT1G71930.2 31.609 174 99 8 1 162 6 171 1.45e-14 72.0
MsaG001250 AT1G71930.1 31.609 174 99 8 1 162 6 171 1.45e-14 72.0
MsaG001250 AT1G32510.1 32.099 162 89 6 2 146 4 161 1.55e-14 71.6
MsaG001250 AT1G54330.1 34.868 152 85 6 4 147 6 151 1.63e-14 71.6
MsaG001250 AT3G10500.1 33.333 168 92 7 1 154 6 167 1.66e-14 72.4
MsaG001250 AT3G44290.1 31.034 145 89 6 6 146 16 153 1.80e-14 71.6
MsaG001250 AT5G62380.2 31.875 160 87 8 1 147 4 154 2.27e-14 71.6
MsaG001250 AT5G62380.1 31.875 160 87 8 1 147 4 154 2.27e-14 71.6
MsaG001250 AT4G35580.1 33.333 162 89 8 1 150 6 160 2.71e-14 72.0
MsaG001250 AT4G35580.2 33.333 162 89 8 1 150 6 160 2.89e-14 71.6
MsaG001250 AT4G35580.3 33.333 162 89 8 1 150 6 160 3.21e-14 71.6
MsaG001250 AT5G09330.5 31.977 172 89 8 2 155 4 165 7.70e-14 70.5
MsaG001250 AT5G09330.2 31.977 172 89 8 2 155 4 165 7.70e-14 70.5
MsaG001250 AT5G09330.4 31.977 172 89 8 2 155 4 165 7.70e-14 70.5
MsaG001250 AT5G09330.3 31.977 172 89 8 2 155 4 165 7.70e-14 70.5
MsaG001250 AT5G09330.1 31.977 172 89 8 2 155 4 165 7.70e-14 70.5
MsaG001250 AT1G62700.1 33.750 160 82 10 2 147 5 154 1.86e-13 69.3
MsaG001250 AT1G62700.2 33.750 160 82 10 2 147 5 154 1.86e-13 69.3
MsaG001250 AT5G39610.1 30.000 160 85 7 4 147 20 168 2.39e-13 68.2
MsaG001250 AT5G46590.2 33.813 139 81 5 2 135 4 136 2.52e-13 68.2
MsaG001250 AT4G27410.2 31.013 158 84 8 4 147 14 160 2.18e-12 65.5
MsaG001250 AT3G29035.1 31.429 140 78 6 4 136 24 152 3.86e-12 65.1
MsaG001250 AT1G61110.1 35.036 137 76 6 4 135 16 144 6.46e-12 64.3
MsaG001250 AT5G04395.1 29.932 147 83 7 4 134 28 170 7.91e-12 62.4
MsaG001250 AT1G76420.1 28.571 161 87 7 4 148 22 170 8.55e-12 63.9
MsaG001250 AT5G61430.1 29.375 160 86 7 4 147 16 164 1.19e-11 63.5
MsaG001250 AT5G07680.2 30.000 160 85 7 4 147 3 151 1.91e-11 63.2
MsaG001250 AT5G07680.1 30.000 160 85 7 4 147 17 165 2.11e-11 62.8
MsaG001250 AT3G15510.1 33.333 135 77 6 10 138 23 150 2.93e-11 62.8
MsaG001250 AT1G79580.3 31.818 154 89 7 4 147 17 164 4.19e-11 62.4
MsaG001250 AT1G79580.5 31.818 154 89 7 4 147 17 164 4.19e-11 62.4
MsaG001250 AT1G79580.4 31.818 154 89 7 4 147 17 164 4.19e-11 62.4
MsaG001250 AT1G79580.2 31.818 154 89 7 4 147 17 164 4.19e-11 62.4
MsaG001250 AT1G79580.1 31.818 154 89 7 4 147 17 164 4.19e-11 62.4
MsaG001250 AT3G15500.1 29.936 157 87 7 4 147 14 160 9.75e-11 60.8

Find 65 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATTTAAGCTTGCAATTA+TGG 0.141545 1:-17415691 MsaT001250.1:CDS
GGCACTGCAGGACTGGATTT+TGG 0.202792 1:-17421087 MsaT001250.1:CDS
CTCTGCACGGATCCATTCTT+TGG 0.268823 1:+17420756 None:intergenic
TCCCTCTTTATGTTCTATCT+TGG 0.300819 1:-17421001 MsaT001250.1:CDS
CTGGTAGTAGTGATGGTGGT+GGG 0.303392 1:-17420645 MsaT001250.1:CDS
TGGAGATGACAATGTGGTTT+TGG 0.323180 1:-17421032 MsaT001250.1:CDS
TCCATGGTTCTGACCTCATT+AGG 0.324328 1:-17421225 MsaT001250.1:CDS
GAATGGATCCGTGCAGAGTT+TGG 0.331686 1:-17420751 MsaT001250.1:CDS
GCTATGCTTCCACCTGGTGC+TGG 0.351315 1:-17421319 MsaT001250.1:CDS
CCATGGTTCTGACCTCATTA+GGG 0.355765 1:-17421224 MsaT001250.1:CDS
GGCATTACTCGAGACATTAA+TGG 0.390991 1:-17421055 MsaT001250.1:CDS
TGATGTCACTCGAAAACTTA+AGG 0.396017 1:-17420683 MsaT001250.1:CDS
TTTGATTGCCCTCCAAAGAA+TGG 0.411692 1:-17420768 MsaT001250.1:CDS
GAGAGACGGCACTGCAGGAC+TGG 0.427179 1:-17421094 MsaT001250.1:CDS
CCCACTGACGAGATACTTGT+TGG 0.432459 1:-17421289 MsaT001250.1:CDS
AAAACACGGCACACAACAAA+AGG 0.436311 1:+17420789 None:intergenic
GCTGGTAGTAGTGATGGTGG+TGG 0.451886 1:-17420646 MsaT001250.1:CDS
GATGTCACTCGAAAACTTAA+GGG 0.453296 1:-17420682 MsaT001250.1:CDS
CTATGCTTCCACCTGGTGCT+GGG 0.456622 1:-17421318 MsaT001250.1:CDS
GCTGGGGCTGGTAGTAGTGA+TGG 0.467052 1:-17420652 MsaT001250.1:CDS
TACTTGTTGGCTACTACCTT+AGG 0.477557 1:-17421276 MsaT001250.1:CDS
GGTGGTGGGGCTGCTGAGCA+AGG 0.481889 1:-17420631 MsaT001250.1:intron
TGCACGGATCCATTCTTTGG+AGG 0.483554 1:+17420759 None:intergenic
CGATCGGGTCATACTCATAC+AGG 0.485419 1:+17421194 None:intergenic
TACTGCTTCACTGCCAAAGT+TGG 0.486292 1:-17421121 MsaT001250.1:CDS
CCGTCTCTCACTGCCAACTT+TGG 0.487719 1:+17421108 None:intergenic
TTCCAAGATAGAACATAAAG+AGG 0.498797 1:+17420999 None:intergenic
AGGACGCTGTCAGAACAAAC+TGG 0.499874 1:-17420967 MsaT001250.1:CDS
TGGTAGTAGTGATGGTGGTG+GGG 0.505536 1:-17420644 MsaT001250.1:CDS
GCAGTGAGAGACGGCACTGC+AGG 0.521491 1:-17421099 MsaT001250.1:CDS
TGCATTGGCTGACAAGCCTC+AGG 0.522270 1:-17420930 MsaT001250.1:intron
GCCAACAAGTATCTCGTCAG+TGG 0.527034 1:+17421288 None:intergenic
ATTGCAAGCTTAAATTGCTC+CGG 0.527174 1:+17415696 None:intergenic
ACCTTCTTCAACATCAGATA+AGG 0.528743 1:+17420726 None:intergenic
ATTGTCGATGGTATAGTAGA+AGG 0.534238 1:+17421156 None:intergenic
GTGGGGAGAAACCCAGCACC+AGG 0.542796 1:+17421307 None:intergenic
GAACAGGTTCAGAATTTCCA+TGG 0.547755 1:-17421241 MsaT001250.1:CDS
GAGGTATATGACAATTCGAT+CGG 0.559279 1:+17421178 None:intergenic
CCACGTGGAAGCTATAACGC+CGG 0.563222 1:-17415715 MsaT001250.1:CDS
ACAGGTTCAGCTCCCTAATG+AGG 0.565571 1:+17421212 None:intergenic
GCACGGATCCATTCTTTGGA+GGG 0.571238 1:+17420760 None:intergenic
GCAATGGCTATGCTTCCACC+TGG 0.574224 1:-17421325 MsaT001250.1:CDS
AGGTATATGACAATTCGATC+GGG 0.577727 1:+17421179 None:intergenic
CCAACAAGTATCTCGTCAGT+GGG 0.578284 1:+17421289 None:intergenic
CTATCTTGGAAATTCTGTGA+AGG 0.589080 1:-17420987 MsaT001250.1:CDS
ACTATACCATCGACAATCGT+AGG 0.602081 1:-17421150 MsaT001250.1:CDS
GGGGCTGGTAGTAGTGATGG+TGG 0.602818 1:-17420649 MsaT001250.1:CDS
CCCTAATGAGGTCAGAACCA+TGG 0.604440 1:+17421224 None:intergenic
ATAAGGCTCCAAACTCTGCA+CGG 0.610087 1:+17420743 None:intergenic
ATGTCACTCGAAAACTTAAG+GGG 0.610861 1:-17420681 MsaT001250.1:CDS
ATTTAAGCTTGCAATTATGG+AGG 0.617003 1:-17415688 MsaT001250.1:CDS
GTCGATGGTATAGTAGAAGG+AGG 0.618515 1:+17421159 None:intergenic
GCCTTATCTGATGTTGAAGA+AGG 0.619001 1:-17420727 MsaT001250.1:CDS
CCAAAGTTGGCAGTGAGAGA+CGG 0.623168 1:-17421108 MsaT001250.1:CDS
TCCAAGATAGAACATAAAGA+GGG 0.626576 1:+17421000 None:intergenic
GAATTGCCTACGATTGTCGA+TGG 0.629431 1:+17421144 None:intergenic
GTTGAAGAAGGTGATGCTGC+TGG 0.630740 1:-17420715 MsaT001250.1:CDS
GGGAGAAACCCAGCACCAGG+TGG 0.671634 1:+17421310 None:intergenic
GATTATGTACGAGTATGCAT+TGG 0.682043 1:-17420945 MsaT001250.1:CDS
ATTACTCGAGACATTAATGG+TGG 0.700868 1:-17421052 MsaT001250.1:CDS
TGTCACTCGAAAACTTAAGG+GGG 0.705876 1:-17420680 MsaT001250.1:CDS
CCGGCGTTATAGCTTCCACG+TGG 0.714144 1:+17415715 None:intergenic
TGACAATGTTGTCTTCCACG+TGG 0.721449 1:-17415730 MsaT001250.1:CDS
CAACAAGTATCTCGTCAGTG+GGG 0.741470 1:+17421290 None:intergenic
TAATGGTGGAGATGACAATG+TGG 0.781339 1:-17421038 MsaT001250.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 17415674 17421344 17415674 ID=MsaG001250
Chr1 mRNA 17415674 17421344 17415674 ID=MsaT001250.1;Parent=MsaG001250
Chr1 exon 17415674 17415772 17415674 ID=MsaT001250.1.exon3;Parent=MsaT001250.1
Chr1 CDS 17415674 17415772 17415674 ID=cds.MsaT001250.1;Parent=MsaT001250.1
Chr1 exon 17420632 17420814 17420632 ID=MsaT001250.1.exon2;Parent=MsaT001250.1
Chr1 CDS 17420632 17420814 17420632 ID=cds.MsaT001250.1;Parent=MsaT001250.1
Chr1 exon 17420931 17421344 17420931 ID=MsaT001250.1.exon1;Parent=MsaT001250.1
Chr1 CDS 17420931 17421344 17420931 ID=cds.MsaT001250.1;Parent=MsaT001250.1
Gene Sequence

>MsaT001250.1

ATGGCTATGCTTCCACCTGGTGCTGGGTTTCTCCCCACTGACGAGATACTTGTTGGCTACTACCTTAGGAACAAAAATAGCGAACAGGTTCAGAATTTCCATGGTTCTGACCTCATTAGGGAGCTGAACCTGTATGAGTATGACCCGATCGAATTGTCATATACCTCCTTCTACTATACCATCGACAATCGTAGGCAATTCTACTGCTTCACTGCCAAAGTTGGCAGTGAGAGACGGCACTGCAGGACTGGATTTTGGATGAAGAAGGGCATTACTCGAGACATTAATGGTGGAGATGACAATGTGGTTTTGGGTCAAAAGTCCCTCTTTATGTTCTATCTTGGAAATTCTGTGAAGGACGCTGTCAGAACAAACTGGATTATGTACGAGTATGCATTGGCTGACAAGCCTCAGGCTCCTTTTGTTGTGTGCCGTGTTTTTGATTGCCCTCCAAAGAATGGATCCGTGCAGAGTTTGGAGCCTTATCTGATGTTGAAGAAGGTGATGCTGCTGGTGATGACTCTGATGTCACTCGAAAACTTAAGGGGGCTGGGGCTGGGGCTGGTAGTAGTGATGGTGGTGGGGCTGCTGAGCAAGGCGAGTTATGTTGCATTTCTTGACAATGTTGTCTTCCACGTGGAAGCTATAACGCCGGAGCAATTTAAGCTTGCAATTATGGAGGAAGATCTTATCTGA
Protein sequence

>MsaT001250.1

MAMLPPGAGFLPTDEILVGYYLRNKNSEQVQNFHGSDLIRELNLYEYDPIELSYTSFYYTIDNRRQFYCFTAKVGSERRHCRTGFWMKKGITRDINGGDDNVVLGQKSLFMFYLGNSVKDAVRTNWIMYEYALADKPQAPFVVCRVFDCPPKNGSVQSLEPYLMLKKVMLLVMTLMSLENLRGLGLGLVVVMVVGLLSKASYVAFLDNVVFHVEAITPEQFKLAIMEEDLI*