AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0871690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0871690 MtrunA17_Chr6g0452691 87.978 183 22 0 1 183 1 183 6.41e-121 339
Msa0871690 MtrunA17_Chr6g0452661 61.314 137 53 0 1 137 1 137 1.04e-55 176
Msa0871690 MtrunA17_Chr5g0439111 60.993 141 53 1 1 141 1 139 1.10e-50 163
Msa0871690 MtrunA17_Chr4g0055441 52.866 157 61 4 9 159 2 151 1.46e-47 152
Msa0871690 MtrunA17_Chr6g0452671 45.294 170 85 3 1 163 1 169 4.58e-41 137
Msa0871690 MtrunA17_Chr4g0059901 48.624 109 55 1 6 114 7 114 4.61e-29 108
Msa0871690 MtrunA17_Chr3g0097221 42.017 119 68 1 3 121 1 118 5.44e-27 103
Msa0871690 MtrunA17_Chr2g0311601 39.091 110 66 1 10 119 14 122 1.39e-26 99.0
Msa0871690 MtrunA17_Chr8g0353981 40.000 130 69 2 3 132 1 121 2.24e-26 100
Msa0871690 MtrunA17_Chr5g0437571 37.719 114 70 1 4 117 1 113 1.54e-25 96.7
Msa0871690 MtrunA17_Chr7g0227511 36.986 146 80 3 6 140 8 152 3.05e-25 95.9
Msa0871690 MtrunA17_Chr6g0449311 44.355 124 56 2 40 153 4 124 3.75e-25 95.1
Msa0871690 MtrunA17_Chr2g0330201 43.119 109 61 1 6 114 16 123 4.55e-25 98.6
Msa0871690 MtrunA17_Chr4g0030001 35.329 167 90 6 10 163 25 186 8.54e-25 95.5
Msa0871690 MtrunA17_Chr1g0200201 40.000 115 64 2 10 124 73 182 1.52e-24 95.5
Msa0871690 MtrunA17_Chr4g0043421 34.091 132 76 2 10 131 16 146 1.62e-24 94.4
Msa0871690 MtrunA17_Chr6g0449651 41.748 103 59 1 6 108 64 165 2.15e-24 94.7
Msa0871690 MtrunA17_Chr3g0114061 37.500 136 79 3 10 140 9 143 3.46e-24 92.8
Msa0871690 MtrunA17_Chr3g0106101 35.537 121 75 2 10 130 8 125 4.41e-24 93.2
Msa0871690 MtrunA17_Chr8g0374591 42.157 102 58 1 10 111 9 109 7.93e-24 91.3
Msa0871690 MtrunA17_Chr5g0402611 42.056 107 61 1 6 112 5 110 1.02e-23 95.1
Msa0871690 MtrunA17_Chr6g0449641 44.330 97 49 2 6 98 6 101 1.66e-23 90.9
Msa0871690 MtrunA17_Chr4g0058651 41.237 97 56 1 7 103 9 104 1.90e-23 91.7
Msa0871690 MtrunA17_Chr5g0438091 31.034 145 85 4 2 139 32 168 2.21e-23 91.7
Msa0871690 MtrunA17_Chr8g0342351 44.954 109 59 1 6 114 9 116 3.08e-23 92.8
Msa0871690 MtrunA17_Chr5g0444351 34.862 109 70 1 10 118 6 113 8.13e-23 89.0
Msa0871690 MtrunA17_Chr3g0117121 40.206 97 57 1 7 103 8 103 1.40e-22 89.7
Msa0871690 MtrunA17_Chr5g0432451 33.333 123 81 1 10 132 44 165 1.84e-22 90.1
Msa0871690 MtrunA17_Chr7g0225111 36.111 108 68 1 10 117 6 112 3.22e-22 86.7
Msa0871690 MtrunA17_Chr3g0115431 40.196 102 60 1 10 111 10 110 6.73e-22 88.6
Msa0871690 MtrunA17_Chr3g0129071 37.234 94 58 1 10 103 48 140 7.60e-22 89.0
Msa0871690 MtrunA17_Chr4g0040831 37.500 120 60 4 2 107 4 122 9.30e-20 82.4
Msa0871690 MtrunA17_Chr5g0437401 28.467 137 97 1 5 141 7 142 3.68e-19 80.5
Msa0871690 MtrunA17_Chr8g0374601 37.500 104 64 1 8 111 25 127 5.49e-19 82.0
Msa0871690 MtrunA17_Chr3g0113891 37.647 85 52 1 5 89 10 93 4.40e-17 75.1
Msa0871690 MtrunA17_Chr7g0260971 35.922 103 64 2 10 111 15 116 2.43e-16 73.9
Msa0871690 MtrunA17_Chr8g0351721 37.037 108 66 2 5 111 14 120 1.94e-15 71.2
Msa0871690 MtrunA17_Chr1g0184281 40.741 81 46 2 10 89 16 95 3.87e-15 70.5
Msa0871690 MtrunA17_Chr5g0435641 33.981 103 66 2 10 111 8 109 3.88e-15 70.1
Msa0871690 MtrunA17_Chr8g0374581 33.333 102 66 2 10 110 9 109 5.04e-15 70.5
Msa0871690 MtrunA17_Chr6g0460951 34.314 102 65 2 10 110 41 141 9.58e-15 69.7
Msa0871690 MtrunA17_Chr8g0351701 36.893 103 63 2 10 111 24 125 2.80e-14 68.6
Msa0871690 MtrunA17_Chr4g0046201 34.314 102 59 2 4 105 1 94 3.25e-14 68.9
Msa0871690 MtrunA17_Chr8g0337271 27.891 147 99 2 9 155 10 149 6.76e-14 67.0
Msa0871690 MtrunA17_Chr1g0184271 38.272 81 48 2 10 89 13 92 7.12e-14 67.4
Msa0871690 MtrunA17_Chr7g0245871 38.000 100 60 2 10 108 28 126 7.43e-14 67.4
Msa0871690 MtrunA17_Chr2g0326041 50.000 48 24 0 10 57 34 81 2.31e-13 62.8
Msa0871690 MtrunA17_Chr7g0261031 36.364 88 54 2 3 89 2 88 2.68e-13 65.9
Msa0871690 MtrunA17_Chr6g0460941 38.272 81 48 2 10 89 8 87 8.35e-12 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0871690 AT3G47870.1 51.376 109 52 1 6 114 33 140 6.73e-33 120
Msa0871690 AT3G26660.1 41.379 116 66 2 8 123 4 117 8.24e-29 103
Msa0871690 AT3G26620.1 41.905 105 60 1 8 112 4 107 4.86e-28 102
Msa0871690 AT1G65620.1 47.191 89 46 1 1 89 1 88 1.12e-25 98.2
Msa0871690 AT1G65620.4 47.191 89 46 1 1 89 1 88 1.12e-25 98.2
Msa0871690 AT1G65620.3 47.191 89 46 1 1 89 1 88 1.12e-25 98.2
Msa0871690 AT1G65620.5 47.191 89 46 1 1 89 1 88 1.12e-25 98.2
Msa0871690 AT1G65620.2 47.191 89 46 1 1 89 1 88 1.12e-25 98.2
Msa0871690 AT3G27650.1 46.000 100 49 2 6 101 36 134 2.24e-25 96.3
Msa0871690 AT2G30130.1 37.815 119 73 1 10 128 9 126 7.50e-25 95.9
Msa0871690 AT3G13850.1 45.045 111 60 1 8 118 35 144 2.06e-24 96.7
Msa0871690 AT5G66870.1 43.678 87 48 1 3 89 1 86 2.87e-23 94.4
Msa0871690 AT2G28500.1 36.364 110 69 1 10 119 56 164 5.26e-23 92.0
Msa0871690 AT5G63090.4 41.237 97 56 1 7 103 9 104 7.48e-23 90.5
Msa0871690 AT5G63090.3 41.237 97 56 1 7 103 9 104 7.48e-23 90.5
Msa0871690 AT5G63090.2 41.237 97 56 1 7 103 9 104 7.48e-23 90.5
Msa0871690 AT5G63090.1 41.237 97 56 1 7 103 9 104 7.48e-23 90.5
Msa0871690 AT1G31320.1 45.000 80 43 1 10 89 14 92 8.32e-23 90.1
Msa0871690 AT1G07900.1 37.755 98 60 1 10 107 34 130 1.38e-22 90.1
Msa0871690 AT2G40470.2 32.283 127 76 2 10 127 21 146 2.76e-22 89.4
Msa0871690 AT2G40470.1 32.283 127 76 2 10 127 46 171 4.57e-22 89.4
Msa0871690 AT1G16530.1 34.091 132 80 3 10 140 15 140 8.54e-22 87.4
Msa0871690 AT3G50510.1 38.318 107 65 1 5 111 8 113 1.60e-21 87.4
Msa0871690 AT3G50510.2 38.318 107 65 1 5 111 8 113 1.60e-21 87.4
Msa0871690 AT1G72980.1 40.984 122 68 2 6 124 10 130 1.82e-21 87.8
Msa0871690 AT2G23660.2 41.584 101 51 3 10 103 6 105 3.23e-21 89.0
Msa0871690 AT2G23660.3 41.584 101 51 3 10 103 6 105 3.23e-21 89.0
Msa0871690 AT2G23660.1 41.584 101 51 3 10 103 6 105 3.23e-21 89.0
Msa0871690 AT2G30340.1 37.234 94 58 1 10 103 53 145 3.11e-20 85.5
Msa0871690 AT2G30340.2 37.234 94 58 1 10 103 54 146 3.13e-20 85.5
Msa0871690 AT1G06280.1 41.250 80 46 1 8 87 23 101 7.68e-18 77.8
Msa0871690 AT3G11090.1 33.333 114 74 2 5 117 7 119 1.79e-17 75.9
Msa0871690 AT2G42430.1 41.975 81 45 2 10 89 16 95 1.11e-15 72.8
Msa0871690 AT4G00210.1 35.156 128 74 4 10 129 12 138 1.44e-15 72.0
Msa0871690 AT5G15060.1 40.541 74 43 1 10 82 18 91 3.08e-15 69.3
Msa0871690 AT5G35900.1 27.333 150 103 3 6 154 2 146 3.26e-15 70.9
Msa0871690 AT2G19820.1 37.805 82 51 0 10 91 13 94 3.83e-15 68.9
Msa0871690 AT3G03760.1 38.235 102 61 2 10 110 52 152 4.27e-15 71.6
Msa0871690 AT4G00220.1 34.043 141 88 4 12 148 20 159 5.23e-14 68.2
Msa0871690 AT5G06080.1 29.801 151 93 5 10 156 8 149 6.96e-14 66.6
Msa0871690 AT2G42440.1 36.364 88 54 2 3 89 1 87 8.20e-14 67.8
Msa0871690 AT3G58190.1 35.185 108 62 4 10 112 12 116 3.52e-13 65.5
Msa0871690 AT2G31310.1 38.272 81 48 2 10 89 8 87 4.43e-13 64.7
Msa0871690 AT2G45420.1 34.286 105 67 2 12 115 40 143 1.22e-11 62.0
Msa0871690 AT2G45410.1 33.663 101 65 2 12 111 19 118 1.39e-11 60.8

Find 33 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGTTATTCACCAATATTT+AGG 0.310397 6_1:+6686890 Msa0871690:CDS
TTCCAATCGATAAACCAAAA+AGG 0.310892 6_1:+6686720 Msa0871690:CDS
AAGGATGGAATATTTGTTAC+TGG 0.328353 6_1:-6687031 None:intergenic
GACAATGTTCATAATTTGTT+TGG 0.383328 6_1:+6686746 Msa0871690:CDS
CATTCAATTCTTCGTTATCA+AGG 0.430545 6_1:-6687066 None:intergenic
CACGTATCAAACCTAAATAT+TGG 0.439926 6_1:-6686901 None:intergenic
CTTTAGTAACTTCACTATGC+TGG 0.446441 6_1:-6686774 None:intergenic
GGTTTATCGATTGGAAAGTA+AGG 0.450274 6_1:-6686713 None:intergenic
TTCTGGATCAATATCCCAAC+CGG 0.461965 6_1:-6687110 None:intergenic
CTGGAGGAGCGGTGGAAGGT+AGG 0.484199 6_1:-6687012 None:intergenic
TGGAGGAGCGGTGGAAGGTA+GGG 0.484588 6_1:-6687011 None:intergenic
CTTGATGGTGGTGTTGATGC+CGG 0.496790 6_1:+6687091 Msa0871690:CDS
CGATATAAAAGCCGATGCAA+TGG 0.498233 6_1:+6686811 Msa0871690:CDS
TGGTGGTGTTGATGCCGGTT+GGG 0.501743 6_1:+6687096 Msa0871690:CDS
ATGGTGGTGTTGATGCCGGT+TGG 0.504635 6_1:+6687095 Msa0871690:CDS
ACATAGAAGAATATGAAGAA+AGG 0.510851 6_1:+6687146 Msa0871690:CDS
ATTGGAAAGTAAGGAGCTAA+AGG 0.517863 6_1:-6686704 None:intergenic
GAAGAATTGAATGACCTTGA+TGG 0.523446 6_1:+6687076 Msa0871690:CDS
CGTGCAAAATTCCCCGCTCA+TGG 0.527145 6_1:+6686860 Msa0871690:CDS
AATAATTGAATCCATTGCAT+CGG 0.539959 6_1:-6686822 None:intergenic
ACACCAACACATCCATGAGC+GGG 0.540128 6_1:-6686872 None:intergenic
AGGTCATACAACGCAAAGGA+TGG 0.566621 6_1:-6687046 None:intergenic
ATTTGTTACTGGAGGAGCGG+TGG 0.570982 6_1:-6687020 None:intergenic
GTTACTGGAGGAGCGGTGGA+AGG 0.573003 6_1:-6687016 None:intergenic
CGGCATCAACACCACCATCA+AGG 0.578433 6_1:-6687090 None:intergenic
TTCCCCGCTCATGGATGTGT+TGG 0.594749 6_1:+6686869 Msa0871690:CDS
AGGAGCGGTGGAAGGTAGGG+AGG 0.600825 6_1:-6687008 None:intergenic
ATCAAGGTCATACAACGCAA+AGG 0.642184 6_1:-6687050 None:intergenic
GATGGAATATTTGTTACTGG+AGG 0.649452 6_1:-6687028 None:intergenic
AACACCAACACATCCATGAG+CGG 0.650255 6_1:-6686873 None:intergenic
AATATTTGTTACTGGAGGAG+CGG 0.656478 6_1:-6687023 None:intergenic
CACCAACACATCCATGAGCG+GGG 0.682848 6_1:-6686871 None:intergenic
GAATTGAATGACCTTGATGG+TGG 0.712886 6_1:+6687079 Msa0871690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GACAATGTTCATAATTTGTT+TGG + chr6_1:6686746-6686765 Msa0871690:CDS 25.0%
! AATAATTGAATCCATTGCAT+CGG - chr6_1:6686825-6686844 None:intergenic 25.0%
!!! GGATTCAATTATTTTTGAGT+CGG + chr6_1:6686832-6686851 Msa0871690:CDS 25.0%
! ACATAGAAGAATATGAAGAA+AGG + chr6_1:6687146-6687165 Msa0871690:CDS 25.0%
TTCCAATCGATAAACCAAAA+AGG + chr6_1:6686720-6686739 Msa0871690:CDS 30.0%
!!! AACCTTTTTGGTTTATCGAT+TGG - chr6_1:6686725-6686744 None:intergenic 30.0%
! TGAACATTGTCAAACCTTTT+TGG - chr6_1:6686737-6686756 None:intergenic 30.0%
!! GGTGTTATTCACCAATATTT+AGG + chr6_1:6686890-6686909 Msa0871690:CDS 30.0%
CACGTATCAAACCTAAATAT+TGG - chr6_1:6686904-6686923 None:intergenic 30.0%
!!! GTAGATTTTGTTGTTGTGAA+TGG - chr6_1:6686985-6687004 None:intergenic 30.0%
! AAGGATGGAATATTTGTTAC+TGG - chr6_1:6687034-6687053 None:intergenic 30.0%
CATTCAATTCTTCGTTATCA+AGG - chr6_1:6687069-6687088 None:intergenic 30.0%
! ATGTCTCTAAAAAAGTCTTC+TGG - chr6_1:6687130-6687149 None:intergenic 30.0%
ATTGGAAAGTAAGGAGCTAA+AGG - chr6_1:6686707-6686726 None:intergenic 35.0%
! GGTTTATCGATTGGAAAGTA+AGG - chr6_1:6686716-6686735 None:intergenic 35.0%
CTTTAGTAACTTCACTATGC+TGG - chr6_1:6686777-6686796 None:intergenic 35.0%
! AATATTTGTTACTGGAGGAG+CGG - chr6_1:6687026-6687045 None:intergenic 35.0%
! GATGGAATATTTGTTACTGG+AGG - chr6_1:6687031-6687050 None:intergenic 35.0%
GAAGAATTGAATGACCTTGA+TGG + chr6_1:6687076-6687095 Msa0871690:CDS 35.0%
CGATATAAAAGCCGATGCAA+TGG + chr6_1:6686811-6686830 Msa0871690:CDS 40.0%
ATCAAGGTCATACAACGCAA+AGG - chr6_1:6687053-6687072 None:intergenic 40.0%
GAATTGAATGACCTTGATGG+TGG + chr6_1:6687079-6687098 Msa0871690:CDS 40.0%
TTCTGGATCAATATCCCAAC+CGG - chr6_1:6687113-6687132 None:intergenic 40.0%
AACACCAACACATCCATGAG+CGG - chr6_1:6686876-6686895 None:intergenic 45.0%
AGGTCATACAACGCAAAGGA+TGG - chr6_1:6687049-6687068 None:intergenic 45.0%
ACACCAACACATCCATGAGC+GGG - chr6_1:6686875-6686894 None:intergenic 50.0%
! ATTTGTTACTGGAGGAGCGG+TGG - chr6_1:6687023-6687042 None:intergenic 50.0%
!! CTTGATGGTGGTGTTGATGC+CGG + chr6_1:6687091-6687110 Msa0871690:CDS 50.0%
CGTGCAAAATTCCCCGCTCA+TGG + chr6_1:6686860-6686879 Msa0871690:CDS 55.0%
TTCCCCGCTCATGGATGTGT+TGG + chr6_1:6686869-6686888 Msa0871690:CDS 55.0%
CACCAACACATCCATGAGCG+GGG - chr6_1:6686874-6686893 None:intergenic 55.0%
CGGCATCAACACCACCATCA+AGG - chr6_1:6687093-6687112 None:intergenic 55.0%
!! ATGGTGGTGTTGATGCCGGT+TGG + chr6_1:6687095-6687114 Msa0871690:CDS 55.0%
!! TGGTGGTGTTGATGCCGGTT+GGG + chr6_1:6687096-6687115 Msa0871690:CDS 55.0%
TGGAGGAGCGGTGGAAGGTA+GGG - chr6_1:6687014-6687033 None:intergenic 60.0%
GTTACTGGAGGAGCGGTGGA+AGG - chr6_1:6687019-6687038 None:intergenic 60.0%
AGGAGCGGTGGAAGGTAGGG+AGG - chr6_1:6687011-6687030 None:intergenic 65.0%
CTGGAGGAGCGGTGGAAGGT+AGG - chr6_1:6687015-6687034 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 6686632 6687186 6686632 ID=Msa0871690;Name=Msa0871690
chr6_1 mRNA 6686632 6687186 6686632 ID=Msa0871690-mRNA-1;Parent=Msa0871690;Name=Msa0871690-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|184
chr6_1 exon 6686632 6687186 6686632 ID=Msa0871690-mRNA-1:exon:2101;Parent=Msa0871690-mRNA-1
chr6_1 CDS 6686632 6687186 6686632 ID=Msa0871690-mRNA-1:cds;Parent=Msa0871690-mRNA-1
Gene Sequence

>Msa0871690

ATGAATATCATGAAATCAAACAAAGTTTGTGCAGCATGCAAGTATCTAAGAAAAAAGTGTCACAAAGATTGTCCTTTAGCTCCTTACTTTCCAATCGATAAACCAAAAAGGTTTGACAATGTTCATAATTTGTTTGGTGTCTCCAGCATAGTGAAGTTACTAAAGAATATTAAAGACGACGATATAAAAGCCGATGCAATGGATTCAATTATTTTTGAGTCGGATATTCGTGCAAAATTCCCCGCTCATGGATGTGTTGGTGTTATTCACCAATATTTAGGTTTGATACGTGAGTCTGAAGAAGAGTTATATCGCACACAAAGTTTACTAGCTATGTGTAAGATGAACAACCATTCACAACAACAAAATCTACATTCCTCCCTACCTTCCACCGCTCCTCCAGTAACAAATATTCCATCCTTTGCGTTGTATGACCTTGATAACGAAGAATTGAATGACCTTGATGGTGGTGTTGATGCCGGTTGGGATATTGATCCAGAAGACTTTTTTAGAGACATAGAAGAATATGAAGAAAGGATGCGTATGAATATTTAG
Protein sequence

>Msa0871690

MNIMKSNKVCAACKYLRKKCHKDCPLAPYFPIDKPKRFDNVHNLFGVSSIVKLLKNIKDDDIKADAMDSIIFESDIRAKFPAHGCVGVIHQYLGLIRESEEELYRTQSLLAMCKMNNHSQQQNLHSSLPSTAPPVTNIPSFALYDLDNEELNDLDGGVDAGWDIDPEDFFRDIEEYEERMRMNI*