AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0969840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0969840 MtrunA17_Chr6g0449311 83.942 137 19 1 37 170 1 137 1.10e-65 197
Msa0969840 MtrunA17_Chr5g0439111 62.577 163 49 4 1 158 1 156 1.25e-60 187
Msa0969840 MtrunA17_Chr6g0452661 56.548 168 61 3 1 165 1 159 7.45e-59 184
Msa0969840 MtrunA17_Chr4g0055441 62.590 139 38 3 10 145 3 130 2.75e-53 166
Msa0969840 MtrunA17_Chr6g0452691 56.081 148 52 3 1 142 1 141 5.46e-53 166
Msa0969840 MtrunA17_Chr6g0452671 55.634 142 56 3 1 140 1 137 1.20e-46 151
Msa0969840 MtrunA17_Chr4g0059901 50.467 107 52 1 8 114 9 114 8.16e-32 115
Msa0969840 MtrunA17_Chr8g0342351 39.535 172 73 3 8 161 11 169 5.74e-31 112
Msa0969840 MtrunA17_Chr3g0097221 44.643 112 61 1 7 118 5 115 2.07e-26 101
Msa0969840 MtrunA17_Chr4g0058651 38.806 134 70 2 7 140 9 130 2.77e-26 98.6
Msa0969840 MtrunA17_Chr7g0227511 44.898 98 53 1 7 104 9 105 1.11e-25 96.7
Msa0969840 MtrunA17_Chr2g0330201 44.954 109 59 1 8 116 18 125 1.68e-25 99.4
Msa0969840 MtrunA17_Chr5g0402611 42.857 105 59 1 7 111 6 109 1.46e-24 97.1
Msa0969840 MtrunA17_Chr8g0353981 48.193 83 42 1 7 89 5 86 1.96e-24 94.7
Msa0969840 MtrunA17_Chr3g0115431 43.137 102 57 1 10 111 10 110 2.67e-24 94.4
Msa0969840 MtrunA17_Chr3g0117121 43.878 98 54 1 7 104 8 104 7.01e-24 92.4
Msa0969840 MtrunA17_Chr4g0043421 38.168 131 79 2 10 140 16 144 4.38e-23 90.1
Msa0969840 MtrunA17_Chr5g0444351 31.250 144 95 2 10 153 6 145 6.56e-23 88.6
Msa0969840 MtrunA17_Chr6g0449641 41.837 98 56 1 7 104 7 103 8.31e-23 88.6
Msa0969840 MtrunA17_Chr2g0311601 37.500 120 68 2 10 129 14 126 3.07e-22 87.4
Msa0969840 MtrunA17_Chr5g0437571 37.931 116 70 2 7 122 4 117 5.91e-22 87.0
Msa0969840 MtrunA17_Chr6g0449651 40.816 98 57 1 7 104 65 161 9.49e-22 87.0
Msa0969840 MtrunA17_Chr7g0225111 37.273 110 68 1 10 119 6 114 1.10e-21 84.7
Msa0969840 MtrunA17_Chr4g0030001 40.351 114 65 3 10 122 25 136 2.94e-21 85.9
Msa0969840 MtrunA17_Chr5g0437401 35.780 109 69 1 5 113 7 114 4.64e-21 84.7
Msa0969840 MtrunA17_Chr5g0438091 32.331 133 88 2 10 142 40 170 5.13e-21 85.1
Msa0969840 MtrunA17_Chr8g0374591 38.462 104 63 1 8 111 7 109 1.28e-20 82.4
Msa0969840 MtrunA17_Chr3g0106101 36.937 111 68 2 10 120 8 116 1.76e-20 83.2
Msa0969840 MtrunA17_Chr8g0374601 39.423 104 62 1 8 111 25 127 8.23e-20 83.6
Msa0969840 MtrunA17_Chr4g0040831 32.558 129 78 3 8 132 14 137 8.83e-20 82.0
Msa0969840 MtrunA17_Chr3g0114061 39.423 104 61 2 10 113 9 110 2.42e-19 80.1
Msa0969840 MtrunA17_Chr5g0432451 32.576 132 84 2 10 141 44 170 3.43e-19 81.3
Msa0969840 MtrunA17_Chr3g0113891 39.604 101 56 2 5 105 10 105 4.05e-19 80.1
Msa0969840 MtrunA17_Chr1g0200201 36.434 129 70 4 10 129 73 198 4.16e-19 80.9
Msa0969840 MtrunA17_Chr3g0129071 36.735 98 61 1 10 107 48 144 1.01e-18 80.1
Msa0969840 MtrunA17_Chr7g0260971 38.835 103 61 2 10 111 15 116 5.65e-17 75.1
Msa0969840 MtrunA17_Chr8g0351721 34.862 109 69 2 4 111 13 120 1.69e-15 71.2
Msa0969840 MtrunA17_Chr7g0245871 35.354 99 62 2 10 107 28 125 7.58e-15 69.7
Msa0969840 MtrunA17_Chr8g0351701 33.981 103 66 2 10 111 24 125 1.05e-14 69.3
Msa0969840 MtrunA17_Chr1g0184281 36.364 99 61 2 10 107 16 113 1.39e-14 68.6
Msa0969840 MtrunA17_Chr4g0046201 37.500 88 54 1 9 96 6 92 2.95e-14 68.6
Msa0969840 MtrunA17_Chr6g0460951 33.333 102 66 2 10 110 41 141 4.13e-14 67.4
Msa0969840 MtrunA17_Chr8g0374581 34.615 104 66 2 8 110 7 109 3.31e-13 65.1
Msa0969840 MtrunA17_Chr6g0460941 35.227 88 55 2 10 96 8 94 3.91e-13 62.0
Msa0969840 MtrunA17_Chr1g0184271 27.703 148 94 4 10 156 13 148 4.54e-13 64.7
Msa0969840 MtrunA17_Chr5g0435641 27.928 111 78 2 7 116 5 114 2.66e-12 62.0
Msa0969840 MtrunA17_Chr2g0326041 50.000 48 24 0 10 57 34 81 1.23e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0969840 AT3G47870.1 55.769 104 45 1 9 112 36 138 4.79e-35 125
Msa0969840 AT3G13850.1 43.046 151 81 3 8 155 35 183 4.28e-31 113
Msa0969840 AT3G27650.1 42.000 100 57 1 7 106 37 135 4.07e-24 92.8
Msa0969840 AT5G63090.4 41.818 110 63 1 7 116 9 117 1.15e-23 92.0
Msa0969840 AT5G63090.3 41.818 110 63 1 7 116 9 117 1.15e-23 92.0
Msa0969840 AT5G63090.2 41.818 110 63 1 7 116 9 117 1.15e-23 92.0
Msa0969840 AT5G63090.1 41.818 110 63 1 7 116 9 117 1.15e-23 92.0
Msa0969840 AT3G26660.1 39.130 115 67 2 8 120 4 117 3.44e-23 89.0
Msa0969840 AT1G65620.1 46.988 83 43 1 7 89 7 88 3.71e-23 91.3
Msa0969840 AT1G65620.4 46.988 83 43 1 7 89 7 88 3.71e-23 91.3
Msa0969840 AT1G65620.3 46.988 83 43 1 7 89 7 88 3.71e-23 91.3
Msa0969840 AT1G65620.5 46.988 83 43 1 7 89 7 88 3.71e-23 91.3
Msa0969840 AT1G65620.2 46.988 83 43 1 7 89 7 88 3.71e-23 91.3
Msa0969840 AT5G66870.1 41.176 102 59 1 10 111 8 108 2.16e-22 91.7
Msa0969840 AT1G31320.1 45.263 95 48 2 5 96 6 99 5.00e-22 87.4
Msa0969840 AT3G26620.1 38.393 112 66 2 8 117 4 114 1.02e-21 85.5
Msa0969840 AT1G72980.1 41.071 112 64 2 9 119 13 123 2.10e-21 87.0
Msa0969840 AT1G07900.1 41.489 94 54 1 10 103 34 126 3.74e-20 83.2
Msa0969840 AT2G30130.1 40.385 104 60 2 10 113 9 110 2.15e-19 81.3
Msa0969840 AT2G28500.1 37.391 115 70 2 10 124 56 168 4.86e-19 81.3
Msa0969840 AT2G30340.2 38.776 98 59 1 10 107 54 150 6.76e-19 81.6
Msa0969840 AT2G30340.1 38.776 98 59 1 10 107 53 149 7.86e-19 81.3
Msa0969840 AT2G23660.2 40.594 101 59 1 10 110 6 105 1.18e-18 81.3
Msa0969840 AT2G23660.3 40.594 101 59 1 10 110 6 105 1.18e-18 81.3
Msa0969840 AT2G23660.1 40.594 101 59 1 10 110 6 105 1.18e-18 81.3
Msa0969840 AT2G40470.2 33.813 139 82 4 10 148 21 149 1.21e-18 79.3
Msa0969840 AT2G40470.1 33.813 139 82 4 10 148 46 174 1.75e-18 79.7
Msa0969840 AT3G11090.1 35.354 99 63 1 5 103 7 104 1.91e-18 78.2
Msa0969840 AT1G16530.1 36.283 113 63 3 5 109 10 121 2.92e-18 77.8
Msa0969840 AT5G15060.1 45.946 74 39 1 10 82 18 91 1.24e-17 75.5
Msa0969840 AT1G06280.1 38.298 94 53 3 8 101 23 111 3.37e-16 73.2
Msa0969840 AT3G50510.1 37.143 105 64 2 10 113 13 116 5.20e-16 72.4
Msa0969840 AT3G50510.2 37.143 105 64 2 10 113 13 116 5.20e-16 72.4
Msa0969840 AT2G19820.1 34.343 99 62 1 1 96 1 99 6.26e-16 70.5
Msa0969840 AT2G42430.1 28.966 145 101 2 10 153 16 159 9.61e-16 72.8
Msa0969840 AT4G00210.1 33.333 138 84 4 10 145 12 143 1.76e-15 71.6
Msa0969840 AT3G58190.1 28.659 164 96 6 10 166 12 161 1.44e-14 68.9
Msa0969840 AT4G00220.1 34.286 105 67 2 12 115 20 123 2.15e-14 68.6
Msa0969840 AT2G42440.1 33.000 100 65 2 10 108 8 106 1.19e-13 67.0
Msa0969840 AT2G45420.1 33.333 105 68 2 12 115 40 143 1.69e-13 66.6
Msa0969840 AT3G03760.1 34.314 102 65 2 10 110 52 152 4.97e-13 65.5
Msa0969840 AT5G35900.1 28.431 102 72 1 10 111 6 106 1.75e-12 63.2
Msa0969840 AT2G31310.1 28.689 122 77 3 10 122 8 128 4.60e-12 61.6
Msa0969840 AT2G45410.1 35.644 101 63 2 12 111 19 118 7.82e-12 61.2

Find 18 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCACCAACATTGTTAAATAT+TGG 0.234385 6_4:+1241695 Msa0969830:intron
CTTTCTTCTTTGATATTTGC+AGG 0.243555 6_4:+1242078 Msa0969830:intron
TGGATGTCTTGGTCTTATTA+TGG 0.281895 6_4:-1241864 Msa0969840:CDS
GGTTTATCGGCTGGAAAATA+AGG 0.296290 6_4:+1242031 Msa0969830:intron
GCCAATGCTCATCGTTTGTT+TGG 0.347008 6_4:-1241998 Msa0969840:CDS
TAAGGAGCTAAAGGGAAATC+TGG 0.373984 6_4:+1242049 Msa0969830:intron
TTATTATAGTGATAATAATA+AGG 0.399138 6_4:+1241668 Msa0969830:intron
ATTCCAATATTTAACAATGT+TGG 0.448330 6_4:-1241698 Msa0969840:CDS
TCTTCTACATTTCTCTTCAT+CGG 0.464845 6_4:-1241753 Msa0969840:CDS
GGAATTGAAGAACTAGTAGA+AGG 0.471090 6_4:+1241716 Msa0969830:intron
TTCCCAAGTCATGGATGTCT+TGG 0.482571 6_4:-1241875 Msa0969840:CDS
GCTGGAAAATAAGGAGCTAA+AGG 0.488184 6_4:+1242040 Msa0969830:intron
CTGGAAAATAAGGAGCTAAA+GGG 0.491954 6_4:+1242041 Msa0969830:intron
AGACCAAGACATCCATGACT+TGG 0.541471 6_4:+1241872 Msa0969830:intron
ACCAAACAAACGATGAGCAT+TGG 0.553402 6_4:+1241997 Msa0969830:intron
CGTGCAAGATTCCCAAGTCA+TGG 0.565788 6_4:-1241884 Msa0969840:CDS
GACCAAGACATCCATGACTT+GGG 0.599785 6_4:+1241873 Msa0969830:intron
TTTGTTTGGTATTTCCAACA+TGG 0.612102 6_4:-1241984 Msa0969840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTATAGTGATAATAATA+AGG + chr6_4:1242069-1242088 Msa0969830:intron 10.0%
!! ATTCCAATATTTAACAATGT+TGG - chr6_4:1242036-1242055 Msa0969840:CDS 20.0%
!!! GAAGTCAATTATTTTTGAGT+CGG - chr6_4:1241822-1241841 Msa0969840:CDS 25.0%
! TCACCAACATTGTTAAATAT+TGG + chr6_4:1242042-1242061 Msa0969830:intron 25.0%
GGATATTCACAGAAAAAACA+AGG - chr6_4:1241624-1241643 Msa0969840:CDS 30.0%
CTTTCTTCTTTGATATTTGC+AGG + chr6_4:1241659-1241678 Msa0969830:intron 30.0%
TTTGTTTGGTATTTCCAACA+TGG - chr6_4:1241750-1241769 Msa0969840:CDS 30.0%
TCTTCTACATTTCTCTTCAT+CGG - chr6_4:1241981-1242000 Msa0969840:CDS 30.0%
CTGGAAAATAAGGAGCTAAA+GGG + chr6_4:1241696-1241715 Msa0969830:intron 35.0%
! TTTTAGCATCTTCACCATGT+TGG + chr6_4:1241767-1241786 Msa0969830:intron 35.0%
!! TGGATGTCTTGGTCTTATTA+TGG - chr6_4:1241870-1241889 Msa0969840:CDS 35.0%
GGAATTGAAGAACTAGTAGA+AGG + chr6_4:1242021-1242040 Msa0969830:intron 35.0%
TAAGGAGCTAAAGGGAAATC+TGG + chr6_4:1241688-1241707 Msa0969830:intron 40.0%
GCTGGAAAATAAGGAGCTAA+AGG + chr6_4:1241697-1241716 Msa0969830:intron 40.0%
! GGTTTATCGGCTGGAAAATA+AGG + chr6_4:1241706-1241725 Msa0969830:intron 40.0%
!!! AGCATTTTTGGTTTATCGGC+TGG + chr6_4:1241715-1241734 Msa0969830:intron 40.0%
!!! GGCGAGCATTTTTGGTTTAT+CGG + chr6_4:1241719-1241738 Msa0969830:intron 40.0%
ACCAAACAAACGATGAGCAT+TGG + chr6_4:1241740-1241759 Msa0969830:intron 40.0%
!!! TGAGCATTGGCGAGCATTTT+TGG + chr6_4:1241727-1241746 Msa0969830:intron 45.0%
GCCAATGCTCATCGTTTGTT+TGG - chr6_4:1241736-1241755 Msa0969840:CDS 45.0%
TTCCCAAGTCATGGATGTCT+TGG - chr6_4:1241859-1241878 Msa0969840:CDS 45.0%
GACCAAGACATCCATGACTT+GGG + chr6_4:1241864-1241883 Msa0969830:intron 45.0%
AGACCAAGACATCCATGACT+TGG + chr6_4:1241865-1241884 Msa0969830:intron 45.0%
CGTGCAAGATTCCCAAGTCA+TGG - chr6_4:1241850-1241869 Msa0969840:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 1241622 1242134 1241622 ID=Msa0969840;Name=Msa0969840
chr6_4 mRNA 1241622 1242134 1241622 ID=Msa0969840-mRNA-1;Parent=Msa0969840;Name=Msa0969840-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|170
chr6_4 exon 1241622 1242134 1241622 ID=Msa0969840-mRNA-1:exon:677;Parent=Msa0969840-mRNA-1
chr6_4 CDS 1241622 1242134 1241622 ID=Msa0969840-mRNA-1:cds;Parent=Msa0969840-mRNA-1
Gene Sequence

>Msa0969840

ATGGATATTCACAGAAAAAACAAGGCATGTGCAGCCTGCAAATATCAAAGAAGAAAGTGTACTCCAGATTTCCCTTTAGCTCCTTATTTTCCAGCCGATAAACCAAAAATGCTCGCCAATGCTCATCGTTTGTTTGGTATTTCCAACATGGTGAAGATGCTAAAATCTATTGACGATGATGATCATAAAGATGAAGCAATGAAGTCAATTATTTTTGAGTCGGAAATGCGTGCAAGATTCCCAAGTCATGGATGTCTTGGTCTTATTATGGAGTATCAAGATATGATAATTGAGTCTATGAAAGAGTTAGATCATGTAAAACAGTTACTAAGTTTGTGTAAGCTATCACAACAACAAAATCTTCTACATTTCTCTTCATCGGATCATTCTTCAGTACCTTCTACTAGTTCTTCAATTCCAATATTTAACAATGTTGGTGATGTTCCTTATTATTATCACTATAATAATGATACTATGATACTTCTAATGACATCATCTCTGATGTATGAATAA
Protein sequence

>Msa0969840

MDIHRKNKACAACKYQRRKCTPDFPLAPYFPADKPKMLANAHRLFGISNMVKMLKSIDDDDHKDEAMKSIIFESEMRARFPSHGCLGLIMEYQDMIIESMKELDHVKQLLSLCKLSQQQNLLHFSSSDHSSVPSTSSSIPIFNNVGDVPYYYHYNNDTMILLMTSSLMYE*