AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1298070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1298070 MtrunA17_Chr4g0055441 84.615 156 16 1 1 148 1 156 2.76e-94 269
Msa1298070 MtrunA17_Chr5g0439111 65.625 128 39 1 2 124 9 136 1.24e-50 161
Msa1298070 MtrunA17_Chr6g0452661 58.871 124 51 0 2 125 9 132 1.17e-47 154
Msa1298070 MtrunA17_Chr6g0452671 51.656 151 55 3 2 135 11 160 4.57e-47 151
Msa1298070 MtrunA17_Chr6g0452691 48.344 151 69 1 2 143 9 159 1.94e-45 146
Msa1298070 MtrunA17_Chr6g0449311 67.059 85 25 1 30 111 1 85 1.77e-34 117
Msa1298070 MtrunA17_Chr8g0342351 53.398 103 47 1 2 104 12 113 1.26e-30 110
Msa1298070 MtrunA17_Chr4g0059901 49.057 106 53 1 2 107 10 114 3.19e-30 110
Msa1298070 MtrunA17_Chr4g0058651 37.143 140 86 2 3 141 12 150 1.04e-28 103
Msa1298070 MtrunA17_Chr2g0330201 48.113 106 54 1 2 107 19 123 3.83e-28 105
Msa1298070 MtrunA17_Chr8g0353981 52.500 80 37 1 3 82 8 86 4.87e-27 100
Msa1298070 MtrunA17_Chr2g0311601 38.739 111 67 1 3 113 14 123 1.74e-26 97.4
Msa1298070 MtrunA17_Chr3g0117121 44.211 95 52 1 3 97 11 104 1.51e-25 96.3
Msa1298070 MtrunA17_Chr5g0402611 41.379 116 66 2 3 117 9 123 1.58e-25 99.0
Msa1298070 MtrunA17_Chr7g0227511 43.158 95 53 1 3 97 12 105 2.21e-25 95.1
Msa1298070 MtrunA17_Chr7g0225111 37.963 108 66 1 3 110 6 112 2.54e-25 93.2
Msa1298070 MtrunA17_Chr4g0043421 33.333 135 88 2 3 136 16 149 2.89e-25 94.7
Msa1298070 MtrunA17_Chr3g0115431 43.137 102 57 1 3 104 10 110 1.55e-24 94.4
Msa1298070 MtrunA17_Chr6g0449641 43.158 95 53 1 3 97 10 103 6.86e-24 90.5
Msa1298070 MtrunA17_Chr3g0106101 47.500 80 41 1 3 82 8 86 4.27e-23 89.4
Msa1298070 MtrunA17_Chr8g0374591 42.157 102 58 1 3 104 9 109 5.81e-23 87.8
Msa1298070 MtrunA17_Chr3g0097221 42.157 102 58 1 3 104 8 108 6.42e-23 91.3
Msa1298070 MtrunA17_Chr8g0374601 44.118 102 56 1 3 104 27 127 8.32e-23 90.9
Msa1298070 MtrunA17_Chr5g0437401 35.938 128 73 3 2 125 11 133 1.09e-22 88.2
Msa1298070 MtrunA17_Chr6g0449651 41.053 95 55 1 3 97 68 161 1.51e-22 88.6
Msa1298070 MtrunA17_Chr5g0437571 45.000 80 43 1 3 82 7 85 2.98e-22 87.0
Msa1298070 MtrunA17_Chr4g0030001 45.263 95 46 3 3 96 25 114 3.34e-22 87.4
Msa1298070 MtrunA17_Chr4g0040831 40.000 100 59 1 2 101 15 113 4.43e-22 87.4
Msa1298070 MtrunA17_Chr5g0438091 37.755 98 60 1 3 100 40 136 9.95e-22 86.3
Msa1298070 MtrunA17_Chr5g0444351 32.031 128 84 2 3 128 6 132 1.12e-21 84.7
Msa1298070 MtrunA17_Chr1g0200201 38.938 113 66 2 3 113 73 184 1.92e-21 86.3
Msa1298070 MtrunA17_Chr5g0432451 34.959 123 79 1 3 125 44 165 2.17e-20 83.6
Msa1298070 MtrunA17_Chr3g0113891 38.144 97 55 2 2 98 14 105 7.22e-20 81.3
Msa1298070 MtrunA17_Chr3g0114061 43.750 80 44 1 3 82 9 87 8.08e-20 80.5
Msa1298070 MtrunA17_Chr3g0129071 38.462 104 62 2 3 105 48 150 9.75e-20 82.0
Msa1298070 MtrunA17_Chr8g0351721 37.391 115 70 2 3 116 19 132 2.81e-19 80.5
Msa1298070 MtrunA17_Chr8g0351701 37.864 103 62 2 3 104 24 125 4.42e-19 80.1
Msa1298070 MtrunA17_Chr7g0260971 37.500 104 63 2 3 105 15 117 9.11e-19 79.0
Msa1298070 MtrunA17_Chr6g0460951 37.255 102 62 2 3 103 41 141 1.79e-17 75.9
Msa1298070 MtrunA17_Chr8g0374581 39.216 102 60 2 3 103 9 109 6.57e-17 74.3
Msa1298070 MtrunA17_Chr6g0460941 38.202 89 53 2 3 90 8 95 4.58e-16 68.9
Msa1298070 MtrunA17_Chr7g0245871 36.000 100 62 2 3 101 28 126 5.38e-16 72.0
Msa1298070 MtrunA17_Chr4g0046201 36.667 90 56 1 2 91 6 94 8.77e-16 72.0
Msa1298070 MtrunA17_Chr1g0184281 35.354 99 62 2 3 100 16 113 2.27e-15 69.7
Msa1298070 MtrunA17_Chr2g0326041 54.167 48 22 0 3 50 34 81 9.10e-15 65.5
Msa1298070 MtrunA17_Chr5g0435641 30.769 104 70 2 2 104 7 109 1.16e-14 67.8
Msa1298070 MtrunA17_Chr8g0337271 29.921 127 84 3 1 123 9 134 2.21e-14 67.0
Msa1298070 MtrunA17_Chr7g0261031 33.333 99 64 2 3 100 9 106 2.02e-12 62.4
Msa1298070 MtrunA17_Chr1g0184271 31.313 99 66 2 3 100 13 110 3.26e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1298070 AT3G47870.1 51.961 102 48 1 2 103 36 136 6.13e-30 110
Msa1298070 AT3G13850.1 49.515 103 51 1 2 104 36 137 6.91e-28 104
Msa1298070 AT5G63090.4 42.718 103 58 1 3 105 12 113 2.52e-25 95.9
Msa1298070 AT5G63090.3 42.718 103 58 1 3 105 12 113 2.52e-25 95.9
Msa1298070 AT5G63090.2 42.718 103 58 1 3 105 12 113 2.52e-25 95.9
Msa1298070 AT5G63090.1 42.718 103 58 1 3 105 12 113 2.52e-25 95.9
Msa1298070 AT1G65620.1 47.500 80 41 1 3 82 10 88 6.65e-24 92.4
Msa1298070 AT1G65620.4 47.500 80 41 1 3 82 10 88 6.65e-24 92.4
Msa1298070 AT1G65620.3 47.500 80 41 1 3 82 10 88 6.65e-24 92.4
Msa1298070 AT1G65620.5 47.500 80 41 1 3 82 10 88 6.65e-24 92.4
Msa1298070 AT1G65620.2 47.500 80 41 1 3 82 10 88 6.65e-24 92.4
Msa1298070 AT1G31320.1 44.828 87 47 1 3 89 14 99 6.86e-24 91.7
Msa1298070 AT5G66870.1 41.176 102 59 1 3 104 8 108 7.17e-24 94.7
Msa1298070 AT3G27650.1 42.857 98 52 2 3 97 40 136 1.85e-23 90.1
Msa1298070 AT3G26660.1 39.216 102 61 1 3 104 6 106 6.24e-23 87.8
Msa1298070 AT3G26620.1 39.216 102 61 1 3 104 6 106 9.02e-23 87.4
Msa1298070 AT1G07900.1 44.681 94 47 2 3 96 34 122 1.92e-22 88.2
Msa1298070 AT1G72980.1 42.453 106 60 1 2 107 13 117 2.46e-22 88.6
Msa1298070 AT2G30130.1 38.136 118 69 3 3 120 9 122 6.09e-22 87.0
Msa1298070 AT3G11090.1 40.206 97 53 2 2 98 11 102 1.98e-21 85.1
Msa1298070 AT2G23660.2 34.014 147 92 3 3 148 6 148 3.62e-21 87.4
Msa1298070 AT2G23660.3 34.014 147 92 3 3 148 6 148 3.62e-21 87.4
Msa1298070 AT2G23660.1 34.014 147 92 3 3 148 6 148 3.62e-21 87.4
Msa1298070 AT2G28500.1 43.617 94 48 2 3 96 56 144 4.01e-21 85.9
Msa1298070 AT1G16530.1 32.680 153 84 5 3 143 15 160 5.49e-21 84.0
Msa1298070 AT2G40470.2 38.679 106 64 1 3 108 21 125 2.33e-20 83.2
Msa1298070 AT2G30340.2 35.294 119 76 1 3 121 54 171 2.68e-20 84.3
Msa1298070 AT2G30340.1 35.294 119 76 1 3 121 53 170 2.81e-20 84.3
Msa1298070 AT2G40470.1 38.679 106 64 1 3 108 46 150 3.42e-20 83.2
Msa1298070 AT3G50510.1 34.746 118 75 2 3 119 13 129 7.28e-20 82.0
Msa1298070 AT3G50510.2 34.746 118 75 2 3 119 13 129 7.28e-20 82.0
Msa1298070 AT5G35900.1 36.275 102 64 1 3 104 6 106 1.63e-19 81.3
Msa1298070 AT1G06280.1 39.326 89 53 1 2 90 24 111 7.90e-18 76.6
Msa1298070 AT5G15060.1 44.595 74 40 1 3 75 18 91 1.15e-17 74.7
Msa1298070 AT4G00210.1 33.333 135 81 3 3 129 12 145 6.90e-17 74.3
Msa1298070 AT4G00220.1 36.634 101 62 2 5 104 20 119 1.53e-16 73.6
Msa1298070 AT2G45420.1 35.644 101 63 2 5 104 40 139 4.39e-16 73.2
Msa1298070 AT2G19820.1 37.363 91 55 1 3 91 13 103 6.26e-16 69.7
Msa1298070 AT3G03760.1 36.275 102 63 2 3 103 52 152 1.75e-15 71.6
Msa1298070 AT2G42430.1 40.244 82 47 2 3 83 16 96 3.06e-15 70.5
Msa1298070 AT5G06080.1 34.021 97 62 2 2 97 7 102 1.60e-14 67.4
Msa1298070 AT2G45410.1 34.545 110 70 2 5 113 19 127 2.16e-14 67.4
Msa1298070 AT3G58190.1 33.333 132 78 4 3 131 12 136 3.00e-14 67.4
Msa1298070 AT2G31310.1 34.091 88 56 2 3 89 8 94 3.28e-13 64.3
Msa1298070 AT2G42440.1 34.694 98 59 3 3 96 8 104 1.37e-12 63.5

Find 23 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGCCTTGGCGAAGATTTC+TGG 0.170855 8_3:-58712675 None:intergenic
GAATCCATAGAACTTGTATT+TGG 0.194623 8_3:-58712957 None:intergenic
GGCGAAGATTTCTGGTTTAT+CGG 0.252911 8_3:-58712667 None:intergenic
GGTTTATCGGCTGGAAAATA+AGG 0.292366 8_3:-58712654 None:intergenic
TAAGGAGCTAAAGCGCAATT+TGG 0.321462 8_3:-58712636 None:intergenic
GCCAAGGCTCATCGTTTGTT+TGG 0.369225 8_3:+58712687 Msa1298070:CDS
AGGGAATCTTGCACGCATTT+CGG 0.384077 8_3:-58712793 None:intergenic
CGTGCAAGATTCCCTGCTAC+TGG 0.446694 8_3:+58712801 Msa1298070:CDS
GGAAAATGAGAACTAGTAGA+AGG 0.455012 8_3:-58712936 None:intergenic
TTCCCTGCTACTGGATGTCT+TGG 0.455177 8_3:+58712810 Msa1298070:CDS
AAGATTTCTGGTTTATCGGC+TGG 0.457749 8_3:-58712663 None:intergenic
GCACCAAGACATCCAGTAGC+AGG 0.478218 8_3:-58712813 None:intergenic
CTTTAGCATCTTCACCATGT+TGG 0.486560 8_3:-58712715 None:intergenic
CAATGATGGTGTTGATCCAC+AGG 0.524509 8_3:+58713007 Msa1298070:CDS
ACCAAACAAACGATGAGCCT+TGG 0.526005 8_3:-58712688 None:intergenic
ACAAAGGAAGCACAGTTGAA+TGG 0.540751 8_3:+58712981 Msa1298070:CDS
CTTGGTGCTATTCTTACATA+CGG 0.548699 8_3:+58712828 Msa1298070:CDS
TTTGTTTGGTGTTTCCAACA+TGG 0.590911 8_3:+58712701 Msa1298070:CDS
CACCAAGACATCCAGTAGCA+GGG 0.617241 8_3:-58712812 None:intergenic
TAAACCAGAAATCTTCGCCA+AGG 0.633091 8_3:+58712671 Msa1298070:CDS
AAGTTCTATGGATTCAACAA+AGG 0.663312 8_3:+58712965 Msa1298070:CDS
CAGTTGAATGGTGACAATGA+TGG 0.663930 8_3:+58712993 Msa1298070:CDS
AATGATGGTGTTGATCCACA+GGG 0.774862 8_3:+58713008 Msa1298070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTCCAAATACAAGTTCTA+TGG + chr8_3:58712953-58712972 Msa1298070:CDS 25.0%
GAATCCATAGAACTTGTATT+TGG - chr8_3:58712960-58712979 None:intergenic 30.0%
AAGTTCTATGGATTCAACAA+AGG + chr8_3:58712965-58712984 Msa1298070:CDS 30.0%
!! TTTGTTTGGTGTTTCCAACA+TGG + chr8_3:58712701-58712720 Msa1298070:CDS 35.0%
!! CTTGGTGCTATTCTTACATA+CGG + chr8_3:58712828-58712847 Msa1298070:CDS 35.0%
GGAAAATGAGAACTAGTAGA+AGG - chr8_3:58712939-58712958 None:intergenic 35.0%
TAAGGAGCTAAAGCGCAATT+TGG - chr8_3:58712639-58712658 None:intergenic 40.0%
! GGTTTATCGGCTGGAAAATA+AGG - chr8_3:58712657-58712676 None:intergenic 40.0%
!! AAGATTTCTGGTTTATCGGC+TGG - chr8_3:58712666-58712685 None:intergenic 40.0%
!! GGCGAAGATTTCTGGTTTAT+CGG - chr8_3:58712670-58712689 None:intergenic 40.0%
TAAACCAGAAATCTTCGCCA+AGG + chr8_3:58712671-58712690 Msa1298070:CDS 40.0%
CTTTAGCATCTTCACCATGT+TGG - chr8_3:58712718-58712737 None:intergenic 40.0%
! ACAAAGGAAGCACAGTTGAA+TGG + chr8_3:58712981-58713000 Msa1298070:CDS 40.0%
CAGTTGAATGGTGACAATGA+TGG + chr8_3:58712993-58713012 Msa1298070:CDS 40.0%
!! AATGATGGTGTTGATCCACA+GGG + chr8_3:58713008-58713027 Msa1298070:CDS 40.0%
ACCAAACAAACGATGAGCCT+TGG - chr8_3:58712691-58712710 None:intergenic 45.0%
AGGGAATCTTGCACGCATTT+CGG - chr8_3:58712796-58712815 None:intergenic 45.0%
!! CAATGATGGTGTTGATCCAC+AGG + chr8_3:58713007-58713026 Msa1298070:CDS 45.0%
TGAGCCTTGGCGAAGATTTC+TGG - chr8_3:58712678-58712697 None:intergenic 50.0%
GCCAAGGCTCATCGTTTGTT+TGG + chr8_3:58712687-58712706 Msa1298070:CDS 50.0%
TTCCCTGCTACTGGATGTCT+TGG + chr8_3:58712810-58712829 Msa1298070:CDS 50.0%
CACCAAGACATCCAGTAGCA+GGG - chr8_3:58712815-58712834 None:intergenic 50.0%
CGTGCAAGATTCCCTGCTAC+TGG + chr8_3:58712801-58712820 Msa1298070:CDS 55.0%
GCACCAAGACATCCAGTAGC+AGG - chr8_3:58712816-58712835 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 58712594 58713040 58712594 ID=Msa1298070;Name=Msa1298070
chr8_3 mRNA 58712594 58713040 58712594 ID=Msa1298070-mRNA-1;Parent=Msa1298070;Name=Msa1298070-mRNA-1;_AED=0.54;_eAED=0.54;_QI=0|-1|0|1|-1|1|1|0|148
chr8_3 exon 58712594 58713040 58712594 ID=Msa1298070-mRNA-1:exon:16888;Parent=Msa1298070-mRNA-1
chr8_3 CDS 58712594 58713040 58712594 ID=Msa1298070-mRNA-1:cds;Parent=Msa1298070-mRNA-1
Gene Sequence

>Msa1298070

ATGGCTTGTGCAGCATGCAAATATCAAAGAAGAAAGTGTTCTCCAAATTGCGCTTTAGCTCCTTATTTTCCAGCCGATAAACCAGAAATCTTCGCCAAGGCTCATCGTTTGTTTGGTGTTTCCAACATGGTGAAGATGCTAAAGAATATTGATGATGATCATCTAAAAGATGAAGCAATGAAATCAATTATCTTTGAGTCCGAAATGCGTGCAAGATTCCCTGCTACTGGATGTCTTGGTGCTATTCTTACATACGGAGATGAGTTAAAGAAGTCTCTTGAAGAGTTAGATCATGTAAGAAATCTACTAGCTTATTGTAAACAACATAATCTTTCTTCTGCACCTTCTACTAGTTCTCATTTTCCAAATACAAGTTCTATGGATTCAACAAAGGAAGCACAGTTGAATGGTGACAATGATGGTGTTGATCCACAGGGAAAACCTTAA
Protein sequence

>Msa1298070

MACAACKYQRRKCSPNCALAPYFPADKPEIFAKAHRLFGVSNMVKMLKNIDDDHLKDEAMKSIIFESEMRARFPATGCLGAILTYGDELKKSLEELDHVRNLLAYCKQHNLSSAPSTSSHFPNTSSMDSTKEAQLNGDNDGVDPQGKP*