AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0936580

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936580 MtrunA17_Chr6g0452691 86.885 183 24 0 1 183 1 183 2.42e-119 335
Msa0936580 MtrunA17_Chr6g0452661 60.584 137 54 0 1 137 1 137 1.64e-54 173
Msa0936580 MtrunA17_Chr5g0439111 60.993 141 53 1 1 141 1 139 9.62e-51 163
Msa0936580 MtrunA17_Chr4g0055441 52.866 157 61 3 9 159 2 151 6.76e-49 155
Msa0936580 MtrunA17_Chr6g0452671 47.170 159 78 3 1 157 1 155 4.89e-41 137
Msa0936580 MtrunA17_Chr4g0059901 47.706 109 56 1 6 114 7 114 6.73e-28 105
Msa0936580 MtrunA17_Chr3g0097221 41.176 119 69 1 3 121 1 118 6.89e-26 100
Msa0936580 MtrunA17_Chr2g0311601 38.182 110 67 1 10 119 14 122 2.66e-25 95.9
Msa0936580 MtrunA17_Chr8g0353981 39.231 130 70 2 3 132 1 121 2.87e-25 97.4
Msa0936580 MtrunA17_Chr5g0437571 36.842 114 71 1 4 117 1 113 2.82e-24 93.2
Msa0936580 MtrunA17_Chr7g0227511 36.301 146 81 3 6 140 8 152 3.70e-24 93.2
Msa0936580 MtrunA17_Chr2g0330201 42.202 109 62 1 6 114 16 123 7.18e-24 95.5
Msa0936580 MtrunA17_Chr8g0374591 42.157 102 58 1 10 111 9 109 8.83e-24 90.9
Msa0936580 MtrunA17_Chr6g0449311 43.548 124 57 2 40 153 4 124 1.58e-23 90.9
Msa0936580 MtrunA17_Chr4g0043421 31.126 151 102 2 10 159 16 165 1.95e-23 91.3
Msa0936580 MtrunA17_Chr4g0030001 34.731 167 91 6 10 163 25 186 2.07e-23 91.7
Msa0936580 MtrunA17_Chr6g0449651 40.777 103 60 1 6 108 64 165 4.15e-23 91.3
Msa0936580 MtrunA17_Chr1g0200201 39.130 115 65 2 10 124 73 182 5.71e-23 91.7
Msa0936580 MtrunA17_Chr3g0114061 36.765 136 80 3 10 140 9 143 5.84e-23 89.7
Msa0936580 MtrunA17_Chr3g0106101 34.711 121 76 2 10 130 8 125 5.85e-23 90.1
Msa0936580 MtrunA17_Chr5g0402611 41.121 107 62 1 6 112 5 110 7.22e-23 93.2
Msa0936580 MtrunA17_Chr6g0449641 43.299 97 50 2 6 98 6 101 1.90e-22 88.2
Msa0936580 MtrunA17_Chr4g0058651 40.206 97 57 1 7 103 9 104 2.24e-22 89.0
Msa0936580 MtrunA17_Chr8g0342351 44.037 109 60 1 6 114 9 116 4.09e-22 90.1
Msa0936580 MtrunA17_Chr5g0438091 29.710 138 96 1 2 139 32 168 5.70e-22 88.2
Msa0936580 MtrunA17_Chr3g0117121 39.175 97 58 1 7 103 8 103 1.36e-21 87.0
Msa0936580 MtrunA17_Chr5g0432451 32.520 123 82 1 10 132 44 165 2.01e-21 87.4
Msa0936580 MtrunA17_Chr5g0444351 33.945 109 71 1 10 118 6 113 2.58e-21 85.1
Msa0936580 MtrunA17_Chr3g0129071 36.170 94 59 1 10 103 48 140 8.05e-21 86.3
Msa0936580 MtrunA17_Chr7g0225111 35.185 108 69 1 10 117 6 112 1.08e-20 82.8
Msa0936580 MtrunA17_Chr3g0115431 39.216 102 61 1 10 111 10 110 1.12e-20 85.5
Msa0936580 MtrunA17_Chr4g0040831 36.667 120 61 4 2 107 4 122 1.28e-18 79.7
Msa0936580 MtrunA17_Chr5g0437401 27.737 137 98 1 5 141 7 142 3.92e-18 77.8
Msa0936580 MtrunA17_Chr8g0374601 36.538 104 65 1 8 111 25 127 7.18e-18 79.0
Msa0936580 MtrunA17_Chr3g0113891 33.663 101 62 2 5 105 10 105 4.01e-16 72.4
Msa0936580 MtrunA17_Chr8g0337271 28.571 147 98 2 9 155 10 149 2.38e-15 70.9
Msa0936580 MtrunA17_Chr7g0260971 34.951 103 65 2 10 111 15 116 3.49e-15 70.9
Msa0936580 MtrunA17_Chr8g0351721 36.111 108 67 2 5 111 14 120 7.97e-15 69.7
Msa0936580 MtrunA17_Chr4g0046201 35.227 88 56 1 4 91 1 87 3.35e-14 68.9
Msa0936580 MtrunA17_Chr1g0184281 39.506 81 47 2 10 89 16 95 4.71e-14 67.4
Msa0936580 MtrunA17_Chr5g0435641 33.010 103 67 2 10 111 8 109 7.00e-14 66.6
Msa0936580 MtrunA17_Chr8g0374581 32.990 97 63 2 8 103 7 102 1.19e-13 66.6
Msa0936580 MtrunA17_Chr8g0351701 35.922 103 64 2 10 111 24 125 1.46e-13 66.6
Msa0936580 MtrunA17_Chr6g0460951 33.333 102 66 2 10 110 41 141 1.50e-13 66.2
Msa0936580 MtrunA17_Chr2g0326041 50.000 48 24 0 10 57 34 81 1.95e-13 63.2
Msa0936580 MtrunA17_Chr7g0245871 37.000 100 61 2 10 108 28 126 2.80e-13 65.9
Msa0936580 MtrunA17_Chr1g0184271 37.037 81 49 2 10 89 13 92 7.97e-13 64.7
Msa0936580 MtrunA17_Chr7g0261031 35.227 88 55 2 3 89 2 88 3.39e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936580 AT3G47870.1 50.459 109 53 1 6 114 33 140 7.14e-32 117
Msa0936580 AT3G26660.1 40.517 116 67 2 8 123 4 117 1.80e-27 100
Msa0936580 AT3G26620.1 40.952 105 61 1 8 112 4 107 1.08e-26 98.6
Msa0936580 AT1G65620.1 46.067 89 47 1 1 89 1 88 1.34e-24 95.5
Msa0936580 AT1G65620.4 46.067 89 47 1 1 89 1 88 1.34e-24 95.5
Msa0936580 AT1G65620.3 46.067 89 47 1 1 89 1 88 1.34e-24 95.5
Msa0936580 AT1G65620.5 46.067 89 47 1 1 89 1 88 1.34e-24 95.5
Msa0936580 AT1G65620.2 46.067 89 47 1 1 89 1 88 1.34e-24 95.5
Msa0936580 AT3G27650.1 45.000 100 50 2 6 101 36 134 2.28e-24 93.6
Msa0936580 AT2G30130.1 36.975 119 74 1 10 128 9 126 1.74e-23 92.4
Msa0936580 AT3G13850.1 44.144 111 61 1 8 118 35 144 2.77e-23 93.6
Msa0936580 AT5G66870.1 42.529 87 49 1 3 89 1 86 2.99e-22 91.7
Msa0936580 AT1G31320.1 43.750 80 44 1 10 89 14 92 7.57e-22 87.4
Msa0936580 AT5G63090.4 40.206 97 57 1 7 103 9 104 8.93e-22 87.8
Msa0936580 AT5G63090.3 40.206 97 57 1 7 103 9 104 8.93e-22 87.8
Msa0936580 AT5G63090.2 40.206 97 57 1 7 103 9 104 8.93e-22 87.8
Msa0936580 AT5G63090.1 40.206 97 57 1 7 103 9 104 8.93e-22 87.8
Msa0936580 AT2G28500.1 35.455 110 70 1 10 119 56 164 1.34e-21 88.6
Msa0936580 AT1G07900.1 36.735 98 61 1 10 107 34 130 2.77e-21 86.7
Msa0936580 AT2G40470.2 31.496 127 77 2 10 127 21 146 7.84e-21 85.5
Msa0936580 AT3G50510.1 38.318 107 65 1 5 111 8 113 7.93e-21 85.5
Msa0936580 AT3G50510.2 38.318 107 65 1 5 111 8 113 7.93e-21 85.5
Msa0936580 AT2G40470.1 31.496 127 77 2 10 127 46 171 1.15e-20 85.9
Msa0936580 AT1G16530.1 33.333 132 81 3 10 140 15 140 1.42e-20 84.0
Msa0936580 AT1G72980.1 40.164 122 69 2 6 124 10 130 2.33e-20 84.7
Msa0936580 AT2G23660.2 39.048 105 56 3 6 103 2 105 3.18e-20 86.3
Msa0936580 AT2G23660.3 39.048 105 56 3 6 103 2 105 3.18e-20 86.3
Msa0936580 AT2G23660.1 39.048 105 56 3 6 103 2 105 3.18e-20 86.3
Msa0936580 AT2G30340.2 36.170 94 59 1 10 103 54 146 3.71e-19 82.8
Msa0936580 AT2G30340.1 36.170 94 59 1 10 103 53 145 3.85e-19 82.4
Msa0936580 AT1G06280.1 35.514 107 63 3 8 112 23 125 4.22e-17 75.9
Msa0936580 AT3G11090.1 29.747 158 95 4 5 159 7 151 1.58e-16 73.6
Msa0936580 AT5G35900.1 28.571 154 96 4 10 154 6 154 3.47e-16 73.6
Msa0936580 AT2G19820.1 37.805 82 51 0 10 91 13 94 1.69e-15 69.7
Msa0936580 AT2G42430.1 40.741 81 46 2 10 89 16 95 1.28e-14 70.1
Msa0936580 AT4G00210.1 35.922 103 64 2 10 111 12 113 1.28e-14 69.7
Msa0936580 AT5G15060.1 39.189 74 44 1 10 82 18 91 2.61e-14 67.0
Msa0936580 AT3G03760.1 37.255 102 62 2 10 110 52 152 6.89e-14 68.2
Msa0936580 AT5G06080.1 29.139 151 94 4 10 156 8 149 4.06e-13 64.7
Msa0936580 AT4G00220.1 35.238 105 66 2 12 115 20 123 5.91e-13 65.1
Msa0936580 AT2G42440.1 35.227 88 55 2 3 89 1 87 8.49e-13 65.1
Msa0936580 AT2G45410.1 28.947 152 92 4 12 162 19 155 2.85e-12 62.8
Msa0936580 AT3G58190.1 38.272 81 48 2 10 89 12 91 4.62e-12 62.8
Msa0936580 AT2G45420.1 33.333 105 68 2 12 115 40 143 5.23e-11 60.1

Find 34 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGTTATTCACCAATATTT+AGG 0.310397 6_3:+7388697 Msa0936580:CDS
TTCCAATCGATAAACCAAAA+AGG 0.310892 6_3:+7388527 Msa0936580:CDS
AAGGATGGAATATTTGTTAC+TGG 0.328353 6_3:-7388838 None:intergenic
GACAATGTTCATAATTTGTT+TGG 0.383328 6_3:+7388553 Msa0936580:CDS
CATTCAATTCTTCGTTATCA+AGG 0.430545 6_3:-7388873 None:intergenic
TTCTGGATCAATATCCCAAC+CGG 0.435874 6_3:-7388917 None:intergenic
CACGTATCAAACCTAAATAT+TGG 0.439926 6_3:-7388708 None:intergenic
CTTTAGTAACTTCACTATGC+TGG 0.446441 6_3:-7388581 None:intergenic
GGTTTATCGATTGGAAAGTA+AGG 0.450274 6_3:-7388520 None:intergenic
CTGGAGGAGCGGTGGAAGGT+AGG 0.484199 6_3:-7388819 None:intergenic
TGGAGGAGCGGTGGAAGGTA+GGG 0.484588 6_3:-7388818 None:intergenic
CTTGATGGTGGTGTTGATGC+CGG 0.496790 6_3:+7388898 Msa0936580:CDS
CGATATAAAAGCCGATGCAA+TGG 0.498233 6_3:+7388618 Msa0936580:CDS
TGGTGGTGTTGATGCCGGTT+GGG 0.501743 6_3:+7388903 Msa0936580:CDS
CTTGCAAAATTCCCCGCTCA+TGG 0.503199 6_3:+7388667 Msa0936580:CDS
ATGGTGGTGTTGATGCCGGT+TGG 0.504635 6_3:+7388902 Msa0936580:CDS
ACATAGAAGAATATGAAGAA+AGG 0.510851 6_3:+7388953 Msa0936580:CDS
ATTGGAAAGTAAGGAGCTAA+AGG 0.517863 6_3:-7388511 None:intergenic
AAATATTCCATCCTTTGCGT+TGG 0.521693 6_3:+7388846 Msa0936580:CDS
GAAGAATTGAATGACCTTGA+TGG 0.523446 6_3:+7388883 Msa0936580:CDS
AATAATTGAATCCATTGCAT+CGG 0.539959 6_3:-7388629 None:intergenic
ACACCAACACATCCATGAGC+GGG 0.540128 6_3:-7388679 None:intergenic
AGGTCATCCAACGCAAAGGA+TGG 0.555066 6_3:-7388853 None:intergenic
ATTTGTTACTGGAGGAGCGG+TGG 0.570982 6_3:-7388827 None:intergenic
GTTACTGGAGGAGCGGTGGA+AGG 0.573003 6_3:-7388823 None:intergenic
CGGCATCAACACCACCATCA+AGG 0.578433 6_3:-7388897 None:intergenic
TTCCCCGCTCATGGATGTGT+TGG 0.594749 6_3:+7388676 Msa0936580:CDS
AGGAGCGGTGGAAGGTAGGG+AGG 0.600825 6_3:-7388815 None:intergenic
ATCAAGGTCATCCAACGCAA+AGG 0.625046 6_3:-7388857 None:intergenic
GATGGAATATTTGTTACTGG+AGG 0.649452 6_3:-7388835 None:intergenic
AACACCAACACATCCATGAG+CGG 0.650255 6_3:-7388680 None:intergenic
AATATTTGTTACTGGAGGAG+CGG 0.656478 6_3:-7388830 None:intergenic
CACCAACACATCCATGAGCG+GGG 0.682848 6_3:-7388678 None:intergenic
GAATTGAATGACCTTGATGG+TGG 0.712886 6_3:+7388886 Msa0936580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GACAATGTTCATAATTTGTT+TGG + chr6_3:7388553-7388572 Msa0936580:CDS 25.0%
! AATAATTGAATCCATTGCAT+CGG - chr6_3:7388632-7388651 None:intergenic 25.0%
!!! GGATTCAATTATTTTTGAGT+CGG + chr6_3:7388639-7388658 Msa0936580:CDS 25.0%
!!! ATGTCTCTAAAAAAGTTTTC+TGG - chr6_3:7388937-7388956 None:intergenic 25.0%
! ACATAGAAGAATATGAAGAA+AGG + chr6_3:7388953-7388972 Msa0936580:CDS 25.0%
TTCCAATCGATAAACCAAAA+AGG + chr6_3:7388527-7388546 Msa0936580:CDS 30.0%
!!! AACCTTTTTGGTTTATCGAT+TGG - chr6_3:7388532-7388551 None:intergenic 30.0%
! TGAACATTGTCAAACCTTTT+TGG - chr6_3:7388544-7388563 None:intergenic 30.0%
!! GGTGTTATTCACCAATATTT+AGG + chr6_3:7388697-7388716 Msa0936580:CDS 30.0%
CACGTATCAAACCTAAATAT+TGG - chr6_3:7388711-7388730 None:intergenic 30.0%
!!! GTAGATTTTGTTGTTGTGAA+TGG - chr6_3:7388792-7388811 None:intergenic 30.0%
! AAGGATGGAATATTTGTTAC+TGG - chr6_3:7388841-7388860 None:intergenic 30.0%
CATTCAATTCTTCGTTATCA+AGG - chr6_3:7388876-7388895 None:intergenic 30.0%
ATTGGAAAGTAAGGAGCTAA+AGG - chr6_3:7388514-7388533 None:intergenic 35.0%
! GGTTTATCGATTGGAAAGTA+AGG - chr6_3:7388523-7388542 None:intergenic 35.0%
CTTTAGTAACTTCACTATGC+TGG - chr6_3:7388584-7388603 None:intergenic 35.0%
! AATATTTGTTACTGGAGGAG+CGG - chr6_3:7388833-7388852 None:intergenic 35.0%
! GATGGAATATTTGTTACTGG+AGG - chr6_3:7388838-7388857 None:intergenic 35.0%
AAATATTCCATCCTTTGCGT+TGG + chr6_3:7388846-7388865 Msa0936580:CDS 35.0%
GAAGAATTGAATGACCTTGA+TGG + chr6_3:7388883-7388902 Msa0936580:CDS 35.0%
CGATATAAAAGCCGATGCAA+TGG + chr6_3:7388618-7388637 Msa0936580:CDS 40.0%
GAATTGAATGACCTTGATGG+TGG + chr6_3:7388886-7388905 Msa0936580:CDS 40.0%
TTCTGGATCAATATCCCAAC+CGG - chr6_3:7388920-7388939 None:intergenic 40.0%
AACACCAACACATCCATGAG+CGG - chr6_3:7388683-7388702 None:intergenic 45.0%
ATCAAGGTCATCCAACGCAA+AGG - chr6_3:7388860-7388879 None:intergenic 45.0%
CTTGCAAAATTCCCCGCTCA+TGG + chr6_3:7388667-7388686 Msa0936580:CDS 50.0%
ACACCAACACATCCATGAGC+GGG - chr6_3:7388682-7388701 None:intergenic 50.0%
! ATTTGTTACTGGAGGAGCGG+TGG - chr6_3:7388830-7388849 None:intergenic 50.0%
AGGTCATCCAACGCAAAGGA+TGG - chr6_3:7388856-7388875 None:intergenic 50.0%
!! CTTGATGGTGGTGTTGATGC+CGG + chr6_3:7388898-7388917 Msa0936580:CDS 50.0%
TTCCCCGCTCATGGATGTGT+TGG + chr6_3:7388676-7388695 Msa0936580:CDS 55.0%
CACCAACACATCCATGAGCG+GGG - chr6_3:7388681-7388700 None:intergenic 55.0%
CGGCATCAACACCACCATCA+AGG - chr6_3:7388900-7388919 None:intergenic 55.0%
!! ATGGTGGTGTTGATGCCGGT+TGG + chr6_3:7388902-7388921 Msa0936580:CDS 55.0%
!! TGGTGGTGTTGATGCCGGTT+GGG + chr6_3:7388903-7388922 Msa0936580:CDS 55.0%
TGGAGGAGCGGTGGAAGGTA+GGG - chr6_3:7388821-7388840 None:intergenic 60.0%
GTTACTGGAGGAGCGGTGGA+AGG - chr6_3:7388826-7388845 None:intergenic 60.0%
AGGAGCGGTGGAAGGTAGGG+AGG - chr6_3:7388818-7388837 None:intergenic 65.0%
CTGGAGGAGCGGTGGAAGGT+AGG - chr6_3:7388822-7388841 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 7388439 7388993 7388439 ID=Msa0936580;Name=Msa0936580
chr6_3 mRNA 7388439 7388993 7388439 ID=Msa0936580-mRNA-1;Parent=Msa0936580;Name=Msa0936580-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|184
chr6_3 exon 7388439 7388993 7388439 ID=Msa0936580-mRNA-1:exon:2373;Parent=Msa0936580-mRNA-1
chr6_3 CDS 7388439 7388993 7388439 ID=Msa0936580-mRNA-1:cds;Parent=Msa0936580-mRNA-1
Gene Sequence

>Msa0936580

ATGAATATCATGAAATCAAACAAAGTTTGTGCAGCATGCAAGTATCTAAGAAAAAAGTGTCACAAAGATTGTCCTTTAGCTCCTTACTTTCCAATCGATAAACCAAAAAGGTTTGACAATGTTCATAATTTGTTTGGTGTCTCCAGCATAGTGAAGTTACTAAAGAATATTAAAGACGACGATATAAAAGCCGATGCAATGGATTCAATTATTTTTGAGTCGGATATTCTTGCAAAATTCCCCGCTCATGGATGTGTTGGTGTTATTCACCAATATTTAGGTTTGATACGTGAGTCTGAAGAAGAGTTATATCACACACAAAGTTTACTAGCTATGTGTAAGATGAACAACCATTCACAACAACAAAATCTACATTCCTCCCTACCTTCCACCGCTCCTCCAGTAACAAATATTCCATCCTTTGCGTTGGATGACCTTGATAACGAAGAATTGAATGACCTTGATGGTGGTGTTGATGCCGGTTGGGATATTGATCCAGAAAACTTTTTTAGAGACATAGAAGAATATGAAGAAAGGATGCGTATGAATATTTAG
Protein sequence

>Msa0936580

MNIMKSNKVCAACKYLRKKCHKDCPLAPYFPIDKPKRFDNVHNLFGVSSIVKLLKNIKDDDIKADAMDSIIFESDILAKFPAHGCVGVIHQYLGLIRESEEELYHTQSLLAMCKMNNHSQQQNLHSSLPSTAPPVTNIPSFALDDLDNEELNDLDGGVDAGWDIDPENFFRDIEEYEERMRMNI*