AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0937660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0937660 MtrunA17_Chr6g0449651 93.662 142 9 0 1 142 58 199 1.20e-99 284
Msa0937660 MtrunA17_Chr6g0449641 88.571 140 16 0 2 141 1 140 4.52e-91 260
Msa0937660 MtrunA17_Chr7g0227511 86.607 112 15 0 3 114 4 115 1.29e-69 207
Msa0937660 MtrunA17_Chr3g0117121 79.130 115 24 0 1 115 1 115 8.40e-65 196
Msa0937660 MtrunA17_Chr4g0058651 80.374 107 21 0 8 114 9 115 8.33e-63 190
Msa0937660 MtrunA17_Chr5g0437571 52.055 146 59 1 8 142 4 149 7.10e-49 154
Msa0937660 MtrunA17_Chr4g0043421 63.810 105 38 0 9 113 14 118 2.15e-48 153
Msa0937660 MtrunA17_Chr2g0311601 57.025 121 44 1 9 129 12 124 4.14e-48 152
Msa0937660 MtrunA17_Chr3g0115431 64.602 113 40 0 2 114 1 113 6.15e-48 154
Msa0937660 MtrunA17_Chr5g0402611 65.455 110 38 0 4 113 2 111 1.40e-47 155
Msa0937660 MtrunA17_Chr8g0353981 68.750 112 33 1 2 113 1 110 1.46e-47 153
Msa0937660 MtrunA17_Chr3g0097221 65.138 109 38 0 5 113 2 110 2.29e-45 149
Msa0937660 MtrunA17_Chr3g0106101 53.600 125 56 1 8 130 5 129 4.51e-45 145
Msa0937660 MtrunA17_Chr3g0114061 51.429 140 59 2 7 137 5 144 8.27e-45 144
Msa0937660 MtrunA17_Chr5g0438091 58.879 107 44 0 7 113 36 142 1.27e-42 139
Msa0937660 MtrunA17_Chr3g0129071 60.000 105 42 0 9 113 46 150 1.56e-42 140
Msa0937660 MtrunA17_Chr3g0113891 67.010 97 32 0 7 103 11 107 3.49e-42 138
Msa0937660 MtrunA17_Chr5g0437401 63.208 106 39 0 7 112 8 113 3.80e-42 137
Msa0937660 MtrunA17_Chr4g0030001 45.070 142 65 2 9 137 23 164 1.94e-39 131
Msa0937660 MtrunA17_Chr5g0432451 57.143 112 48 0 9 120 42 153 1.37e-37 127
Msa0937660 MtrunA17_Chr7g0260971 58.333 108 44 1 4 110 8 115 2.86e-37 126
Msa0937660 MtrunA17_Chr1g0200201 55.446 101 45 0 11 111 73 173 7.78e-37 125
Msa0937660 MtrunA17_Chr1g0184281 58.491 106 43 1 7 111 12 117 5.88e-36 122
Msa0937660 MtrunA17_Chr7g0245871 60.000 95 37 1 10 103 27 121 9.73e-34 118
Msa0937660 MtrunA17_Chr8g0351721 56.731 104 44 1 8 110 16 119 1.75e-33 117
Msa0937660 MtrunA17_Chr8g0351701 54.286 105 47 1 10 113 23 127 1.98e-33 117
Msa0937660 MtrunA17_Chr6g0460951 50.962 104 50 1 9 111 39 142 4.95e-32 113
Msa0937660 MtrunA17_Chr5g0435641 53.608 97 44 1 9 104 6 102 9.12e-32 111
Msa0937660 MtrunA17_Chr5g0444351 49.000 100 51 0 11 110 6 105 1.34e-31 110
Msa0937660 MtrunA17_Chr7g0225111 46.078 102 55 0 9 110 4 105 1.93e-31 108
Msa0937660 MtrunA17_Chr8g0374601 44.348 115 64 0 10 124 26 140 8.02e-31 111
Msa0937660 MtrunA17_Chr7g0261031 55.102 98 43 1 7 103 5 102 1.25e-30 109
Msa0937660 MtrunA17_Chr8g0374591 44.231 104 58 0 10 113 8 111 6.94e-30 105
Msa0937660 MtrunA17_Chr1g0184271 52.632 95 44 1 10 103 12 106 1.52e-29 107
Msa0937660 MtrunA17_Chr6g0452661 45.918 98 52 1 8 104 7 104 6.96e-29 105
Msa0937660 MtrunA17_Chr4g0059901 47.000 100 53 0 11 110 11 110 1.86e-28 105
Msa0937660 MtrunA17_Chr7g0245861 54.839 93 39 2 7 96 9 101 1.09e-27 99.8
Msa0937660 MtrunA17_Chr6g0452671 42.000 100 58 0 7 106 8 107 1.07e-26 99.0
Msa0937660 MtrunA17_Chr6g0452691 43.689 103 57 1 7 108 6 108 1.92e-26 97.8
Msa0937660 MtrunA17_Chr8g0374581 46.667 105 55 1 10 113 8 112 5.01e-26 98.2
Msa0937660 MtrunA17_Chr6g0460941 50.000 88 43 1 10 96 7 94 1.04e-25 93.6
Msa0937660 MtrunA17_Chr8g0342351 40.777 103 61 0 11 113 13 115 7.36e-24 93.2
Msa0937660 MtrunA17_Chr2g0330201 41.000 100 59 0 7 106 16 115 2.07e-23 92.8
Msa0937660 MtrunA17_Chr5g0439111 42.857 98 55 1 8 104 7 104 4.67e-22 87.8
Msa0937660 MtrunA17_Chr4g0040831 43.011 93 53 0 11 103 16 108 7.21e-22 86.7
Msa0937660 MtrunA17_Chr4g0055441 40.000 95 56 1 11 104 3 97 1.25e-21 84.7
Msa0937660 MtrunA17_Chr2g0326041 60.345 58 23 0 2 59 25 82 2.38e-21 82.0
Msa0937660 MtrunA17_Chr4g0046201 32.222 90 61 0 9 98 5 94 2.56e-15 70.5
Msa0937660 MtrunA17_Chr2g0326051 47.826 69 36 0 55 123 5 73 1.51e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0937660 AT3G27650.1 80.000 110 22 0 4 113 33 142 1.51e-65 196
Msa0937660 AT5G63090.4 79.825 114 22 1 1 113 1 114 3.90e-63 191
Msa0937660 AT5G63090.3 79.825 114 22 1 1 113 1 114 3.90e-63 191
Msa0937660 AT5G63090.2 79.825 114 22 1 1 113 1 114 3.90e-63 191
Msa0937660 AT5G63090.1 79.825 114 22 1 1 113 1 114 3.90e-63 191
Msa0937660 AT1G65620.1 66.379 116 39 0 2 117 1 116 1.26e-48 155
Msa0937660 AT1G65620.4 66.379 116 39 0 2 117 1 116 1.26e-48 155
Msa0937660 AT1G65620.3 66.379 116 39 0 2 117 1 116 1.26e-48 155
Msa0937660 AT1G65620.5 66.379 116 39 0 2 117 1 116 1.26e-48 155
Msa0937660 AT1G65620.2 66.379 116 39 0 2 117 1 116 1.26e-48 155
Msa0937660 AT2G30130.1 65.385 104 36 0 8 111 6 109 4.22e-48 154
Msa0937660 AT5G66870.1 63.717 113 39 1 2 114 1 111 1.97e-46 153
Msa0937660 AT2G23660.2 62.617 107 40 0 7 113 2 108 3.47e-46 152
Msa0937660 AT2G23660.3 62.617 107 40 0 7 113 2 108 3.47e-46 152
Msa0937660 AT2G23660.1 62.617 107 40 0 7 113 2 108 3.47e-46 152
Msa0937660 AT1G31320.1 69.318 88 27 0 9 96 12 99 1.27e-43 141
Msa0937660 AT2G30340.1 55.752 113 50 0 9 121 51 163 1.95e-42 141
Msa0937660 AT2G30340.2 55.752 113 50 0 9 121 52 164 2.56e-42 141
Msa0937660 AT1G16530.1 61.538 104 39 1 9 111 13 116 1.66e-41 136
Msa0937660 AT3G11090.1 57.658 111 45 1 7 117 8 116 6.26e-41 134
Msa0937660 AT1G07900.1 46.667 135 66 1 9 137 32 166 7.02e-41 135
Msa0937660 AT2G40470.2 62.857 105 39 0 9 113 19 123 2.07e-40 134
Msa0937660 AT2G40470.1 62.857 105 39 0 9 113 44 148 4.02e-40 134
Msa0937660 AT2G28500.1 45.223 157 63 3 9 142 54 210 8.10e-40 134
Msa0937660 AT3G26620.1 46.721 122 59 1 11 132 6 121 2.47e-38 126
Msa0937660 AT3G26660.1 45.902 122 60 1 11 132 6 121 1.17e-37 125
Msa0937660 AT3G03760.1 55.769 104 45 1 9 111 50 153 4.75e-35 122
Msa0937660 AT2G42430.1 56.190 105 45 1 7 110 12 116 3.32e-34 119
Msa0937660 AT5G06080.1 50.926 108 52 1 9 115 6 113 3.85e-33 115
Msa0937660 AT4G00210.1 60.000 95 37 1 10 103 11 105 1.09e-32 115
Msa0937660 AT4G00220.1 57.576 99 41 1 13 110 20 118 1.38e-32 115
Msa0937660 AT2G45420.1 57.576 99 41 1 13 110 40 138 7.62e-32 114
Msa0937660 AT2G45410.1 46.667 135 65 3 13 140 19 153 1.27e-30 109
Msa0937660 AT3G58190.1 53.125 96 44 1 10 104 11 106 1.63e-30 109
Msa0937660 AT2G31310.1 52.083 96 45 1 9 103 6 101 1.97e-30 108
Msa0937660 AT3G50510.1 45.283 106 58 0 8 113 10 115 7.25e-30 107
Msa0937660 AT3G50510.2 45.283 106 58 0 8 113 10 115 7.25e-30 107
Msa0937660 AT2G42440.1 49.495 99 49 1 7 104 4 102 1.68e-29 107
Msa0937660 AT3G47870.1 38.182 110 68 0 1 110 27 136 1.64e-25 99.0
Msa0937660 AT3G13850.1 40.777 103 61 0 11 113 37 139 2.63e-25 97.4
Msa0937660 AT5G35900.1 43.000 100 57 0 11 110 6 105 1.86e-24 93.6
Msa0937660 AT1G72980.1 40.187 107 64 0 4 110 7 113 1.21e-22 89.4
Msa0937660 AT1G06280.1 48.052 77 40 0 11 87 25 101 3.29e-20 82.8
Msa0937660 AT4G22700.1 34.921 126 80 2 11 135 6 130 4.34e-18 77.0
Msa0937660 AT2G19820.1 36.264 91 57 1 7 96 9 99 4.63e-16 70.1
Msa0937660 AT5G15060.1 36.986 73 44 1 11 81 18 90 2.33e-12 60.8
Msa0937660 AT3G27940.3 29.245 106 75 0 10 115 5 110 1.09e-11 59.3
Msa0937660 AT3G27940.1 29.245 106 75 0 10 115 5 110 1.09e-11 59.3
Msa0937660 AT3G27940.2 29.245 106 75 0 10 115 5 110 1.09e-11 59.3

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATGTTCACAAAGTATT+TGG 0.212072 6_3:+9118766 Msa0937660:CDS
GCAAACTTATGAGGCTCTTC+TGG 0.277156 6_3:-9118745 None:intergenic
AATCCTTGCTTCAGCTTCAT+AGG 0.299183 6_3:-9118860 None:intergenic
GGCTCTTCTGGTGGGAAATA+AGG 0.304156 6_3:-9118733 None:intergenic
TTGTAGCATCAAGTTCCTTT+TGG 0.323860 6_3:-9118945 None:intergenic
CGCTTCAAGGACAACTCTTT+AGG 0.341714 6_3:+9118920 Msa0937660:CDS
TGAACATTTGCAAACTTATG+AGG 0.383834 6_3:-9118754 None:intergenic
ATGTCATTGCTGAAATTTGA+AGG 0.464467 6_3:-9119051 None:intergenic
GGAGCTATTTCAGCGCTTCA+AGG 0.465943 6_3:+9118907 Msa0937660:CDS
ATGAAGTCTTACCTCATCAA+AGG 0.530030 6_3:+9118815 Msa0937660:CDS
ACAACTCTTTAGGCTCCAAA+AGG 0.536437 6_3:+9118930 Msa0937660:CDS
AACTTATGAGGCTCTTCTGG+TGG 0.540828 6_3:-9118742 None:intergenic
TGAAGTCTTACCTCATCAAA+GGG 0.542775 6_3:+9118816 Msa0937660:CDS
AATCCAGTGTATGGTTGTGT+TGG 0.555823 6_3:+9118886 Msa0937660:CDS
TGTCATTGCTGAAATTTGAA+GGG 0.589927 6_3:-9119050 None:intergenic
AGAAACTTGCAAGCAGCACA+TGG 0.591215 6_3:-9118676 None:intergenic
ACTTATGAGGCTCTTCTGGT+GGG 0.610191 6_3:-9118741 None:intergenic
ACTGTATCCTCCCTTTGATG+AGG 0.610482 6_3:-9118826 None:intergenic
GCTCCAACACAACCATACAC+TGG 0.615806 6_3:-9118889 None:intergenic
TTGCCTATGAAGCTGAAGCA+AGG 0.624248 6_3:+9118857 Msa0937660:CDS
TGGAGAATTTGAGTAGCTTG+AGG 0.626001 6_3:-9118656 None:intergenic
AGTCTTACCTCATCAAAGGG+AGG 0.699522 6_3:+9118819 Msa0937660:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGAACATTTGCAAACTTATG+AGG - chr6_3:9118757-9118776 None:intergenic 30.0%
! GCAAATGTTCACAAAGTATT+TGG + chr6_3:9118766-9118785 Msa0937660:CDS 30.0%
AGGATTAAAAATCCAGTGTA+TGG + chr6_3:9118877-9118896 Msa0937660:CDS 30.0%
!! TTGATTCGTTTTACTCATGA+AGG + chr6_3:9118976-9118995 Msa0937660:CDS 30.0%
TGTCATTGCTGAAATTTGAA+GGG - chr6_3:9119053-9119072 None:intergenic 30.0%
ATGTCATTGCTGAAATTTGA+AGG - chr6_3:9119054-9119073 None:intergenic 30.0%
AAGGTGCAAAAATGCAATCT+TGG - chr6_3:9118717-9118736 None:intergenic 35.0%
ATGAAGTCTTACCTCATCAA+AGG + chr6_3:9118815-9118834 Msa0937660:CDS 35.0%
TGAAGTCTTACCTCATCAAA+GGG + chr6_3:9118816-9118835 Msa0937660:CDS 35.0%
! TTGTAGCATCAAGTTCCTTT+TGG - chr6_3:9118948-9118967 None:intergenic 35.0%
! CATGAAGGTTCTTTTTCTCT+TGG + chr6_3:9118991-9119010 Msa0937660:CDS 35.0%
TGGAGAATTTGAGTAGCTTG+AGG - chr6_3:9118659-9118678 None:intergenic 40.0%
AATCCTTGCTTCAGCTTCAT+AGG - chr6_3:9118863-9118882 None:intergenic 40.0%
AATCCAGTGTATGGTTGTGT+TGG + chr6_3:9118886-9118905 Msa0937660:CDS 40.0%
ACAACTCTTTAGGCTCCAAA+AGG + chr6_3:9118930-9118949 Msa0937660:CDS 40.0%
! GGTTCTTTTTCTCTTGGTCT+TGG + chr6_3:9118997-9119016 Msa0937660:CDS 40.0%
AGAAACTTGCAAGCAGCACA+TGG - chr6_3:9118679-9118698 None:intergenic 45.0%
ACTTATGAGGCTCTTCTGGT+GGG - chr6_3:9118744-9118763 None:intergenic 45.0%
AACTTATGAGGCTCTTCTGG+TGG - chr6_3:9118745-9118764 None:intergenic 45.0%
GCAAACTTATGAGGCTCTTC+TGG - chr6_3:9118748-9118767 None:intergenic 45.0%
AGTCTTACCTCATCAAAGGG+AGG + chr6_3:9118819-9118838 Msa0937660:CDS 45.0%
ACTGTATCCTCCCTTTGATG+AGG - chr6_3:9118829-9118848 None:intergenic 45.0%
TTGCCTATGAAGCTGAAGCA+AGG + chr6_3:9118857-9118876 Msa0937660:CDS 45.0%
CGCTTCAAGGACAACTCTTT+AGG + chr6_3:9118920-9118939 Msa0937660:CDS 45.0%
GGCTCTTCTGGTGGGAAATA+AGG - chr6_3:9118736-9118755 None:intergenic 50.0%
GCTCCAACACAACCATACAC+TGG - chr6_3:9118892-9118911 None:intergenic 50.0%
! GGAGCTATTTCAGCGCTTCA+AGG + chr6_3:9118907-9118926 Msa0937660:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 9118649 9119077 9118649 ID=Msa0937660;Name=Msa0937660
chr6_3 mRNA 9118649 9119077 9118649 ID=Msa0937660-mRNA-1;Parent=Msa0937660;Name=Msa0937660-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|142
chr6_3 exon 9118649 9119077 9118649 ID=Msa0937660-mRNA-1:exon:2915;Parent=Msa0937660-mRNA-1
chr6_3 CDS 9118649 9119077 9118649 ID=Msa0937660-mRNA-1:cds;Parent=Msa0937660-mRNA-1
Gene Sequence

>Msa0937660

ATGATGGCCTCAAGCTACTCAAATTCTCCATGTGCTGCTTGCAAGTTTCTAAGAAGAAAATGCAACCAAGATTGCATTTTTGCACCTTATTTCCCACCAGAAGAGCCTCATAAGTTTGCAAATGTTCACAAAGTATTTGGTGCAAGCAATGTTAGCAAAATTCTTAATGAAGTCTTACCTCATCAAAGGGAGGATACAGTGAATTCTCTTGCCTATGAAGCTGAAGCAAGGATTAAAAATCCAGTGTATGGTTGTGTTGGAGCTATTTCAGCGCTTCAAGGACAACTCTTTAGGCTCCAAAAGGAACTTGATGCTACAAATGCTGATTTGATTCGTTTTACTCATGAAGGTTCTTTTTCTCTTGGTCTTGGACAATTTCACTCTGATGACTTTTTAAATTACCCTTCAAATTTCAGCAATGACATGTGA
Protein sequence

>Msa0937660

MMASSYSNSPCAACKFLRRKCNQDCIFAPYFPPEEPHKFANVHKVFGASNVSKILNEVLPHQREDTVNSLAYEAEARIKNPVYGCVGAISALQGQLFRLQKELDATNADLIRFTHEGSFSLGLGQFHSDDFLNYPSNFSNDM*