AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG028964

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028964 MtrunA17_Chr5g0439111 93.074 231 13 3 1 229 1 230 4.46e-133 374
MsaG028964 MtrunA17_Chr6g0452661 56.846 241 83 6 1 230 1 231 2.64e-80 241
MsaG028964 MtrunA17_Chr6g0452691 63.121 141 50 1 1 139 1 141 3.00e-59 185
MsaG028964 MtrunA17_Chr6g0452671 47.679 237 80 11 1 228 1 202 1.54e-55 176
MsaG028964 MtrunA17_Chr4g0055441 63.910 133 43 1 10 142 3 130 1.06e-54 172
MsaG028964 MtrunA17_Chr6g0449311 55.556 126 50 2 37 159 1 123 1.34e-37 128
MsaG028964 MtrunA17_Chr4g0059901 54.717 106 47 1 8 113 9 113 7.49e-32 117
MsaG028964 MtrunA17_Chr8g0342351 53.333 105 48 1 7 111 10 113 5.54e-30 112
MsaG028964 MtrunA17_Chr3g0115431 45.098 102 55 1 10 111 10 110 7.56e-28 105
MsaG028964 MtrunA17_Chr7g0227511 34.545 165 80 4 7 159 9 157 2.41e-27 102
MsaG028964 MtrunA17_Chr4g0043421 32.164 171 97 5 10 178 16 169 3.53e-27 102
MsaG028964 MtrunA17_Chr3g0097221 44.762 105 57 1 7 111 5 108 5.08e-27 105
MsaG028964 MtrunA17_Chr5g0402611 43.810 105 58 1 7 111 6 109 8.73e-27 105
MsaG028964 MtrunA17_Chr8g0353981 47.126 87 45 1 3 89 1 86 2.16e-26 102
MsaG028964 MtrunA17_Chr4g0058651 42.056 107 60 2 7 112 9 114 1.03e-25 99.0
MsaG028964 MtrunA17_Chr6g0449641 43.878 98 54 1 7 104 7 103 2.89e-25 96.7
MsaG028964 MtrunA17_Chr2g0311601 43.158 95 49 2 10 104 14 103 4.32e-25 96.7
MsaG028964 MtrunA17_Chr3g0117121 42.857 98 55 1 7 104 8 104 4.95e-25 97.4
MsaG028964 MtrunA17_Chr6g0449651 43.878 98 54 1 7 104 65 161 6.04e-25 97.4
MsaG028964 MtrunA17_Chr2g0330201 45.283 106 57 1 8 113 18 122 7.01e-25 99.8
MsaG028964 MtrunA17_Chr5g0438091 36.449 107 64 2 1 107 34 136 7.33e-25 97.1
MsaG028964 MtrunA17_Chr5g0432451 38.938 113 64 3 1 112 38 146 9.80e-25 97.8
MsaG028964 MtrunA17_Chr3g0106101 36.441 118 74 1 10 127 8 124 3.08e-24 95.1
MsaG028964 MtrunA17_Chr5g0444351 32.639 144 88 4 10 149 6 144 3.73e-24 94.0
MsaG028964 MtrunA17_Chr7g0225111 37.864 103 63 1 10 112 6 107 5.58e-23 90.1
MsaG028964 MtrunA17_Chr3g0129071 38.182 110 60 3 1 110 42 143 6.59e-23 93.2
MsaG028964 MtrunA17_Chr5g0437571 42.169 83 47 1 7 89 4 85 1.83e-22 90.1
MsaG028964 MtrunA17_Chr5g0437401 38.053 113 61 3 5 113 7 114 2.33e-22 90.1
MsaG028964 MtrunA17_Chr4g0030001 43.158 95 52 2 10 103 25 118 4.41e-22 89.7
MsaG028964 MtrunA17_Chr8g0374591 40.367 109 61 2 3 111 5 109 5.09e-22 87.8
MsaG028964 MtrunA17_Chr3g0114061 34.459 148 87 5 10 157 9 146 8.76e-22 88.2
MsaG028964 MtrunA17_Chr3g0113891 38.614 101 57 2 5 105 10 105 2.40e-21 87.8
MsaG028964 MtrunA17_Chr1g0200201 40.594 101 59 1 10 110 73 172 4.53e-21 87.8
MsaG028964 MtrunA17_Chr4g0040831 37.398 123 69 3 2 120 4 122 7.67e-21 86.7
MsaG028964 MtrunA17_Chr8g0374601 40.367 109 61 2 3 111 23 127 2.26e-20 87.0
MsaG028964 MtrunA17_Chr5g0435641 33.333 105 68 2 8 111 6 109 4.09e-17 76.6
MsaG028964 MtrunA17_Chr8g0374581 37.615 109 63 3 3 110 5 109 1.73e-16 75.5
MsaG028964 MtrunA17_Chr1g0184281 36.000 100 62 2 10 108 16 114 5.84e-16 73.9
MsaG028964 MtrunA17_Chr8g0351721 35.922 103 64 2 10 111 19 120 7.48e-16 73.6
MsaG028964 MtrunA17_Chr7g0260971 33.654 104 67 2 10 112 15 117 8.92e-16 73.6
MsaG028964 MtrunA17_Chr6g0460951 33.898 118 68 4 3 114 37 150 1.23e-15 73.2
MsaG028964 MtrunA17_Chr8g0337271 30.469 128 87 2 9 136 10 135 8.56e-15 70.5
MsaG028964 MtrunA17_Chr2g0326041 54.167 48 22 0 10 57 34 81 3.74e-14 65.9
MsaG028964 MtrunA17_Chr7g0245871 33.000 100 65 2 10 108 28 126 4.06e-14 69.3
MsaG028964 MtrunA17_Chr1g0184271 34.783 115 65 5 10 123 13 118 4.62e-14 68.9
MsaG028964 MtrunA17_Chr8g0351701 32.039 103 68 2 10 111 24 125 5.60e-14 68.9
MsaG028964 MtrunA17_Chr6g0460941 33.708 89 57 2 10 97 8 95 5.48e-13 63.2
MsaG028964 MtrunA17_Chr4g0046201 25.000 160 109 2 9 158 6 164 8.51e-13 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG028964 AT3G47870.1 56.863 102 43 1 9 110 36 136 4.08e-36 130
MsaG028964 AT3G13850.1 48.246 114 58 1 8 121 35 147 1.06e-29 112
MsaG028964 AT1G65620.1 30.348 201 130 2 7 207 7 197 1.55e-27 104
MsaG028964 AT1G65620.4 30.348 201 130 2 7 207 7 197 1.55e-27 104
MsaG028964 AT1G65620.3 30.348 201 130 2 7 207 7 197 1.55e-27 104
MsaG028964 AT1G65620.5 30.348 201 130 2 7 207 7 197 1.55e-27 104
MsaG028964 AT1G65620.2 30.348 201 130 2 7 207 7 197 1.55e-27 104
MsaG028964 AT5G66870.1 44.118 102 56 1 10 111 8 108 1.70e-26 104
MsaG028964 AT3G27650.1 42.342 111 62 2 7 116 37 146 2.32e-26 100
MsaG028964 AT2G40470.2 34.247 146 84 5 1 145 15 149 2.06e-25 99.0
MsaG028964 AT2G40470.1 34.247 146 84 5 1 145 40 174 4.42e-25 99.0
MsaG028964 AT1G72980.1 42.975 121 67 2 9 128 13 132 6.80e-25 98.2
MsaG028964 AT5G63090.4 40.566 106 62 1 7 112 9 113 8.39e-25 97.1
MsaG028964 AT5G63090.3 40.566 106 62 1 7 112 9 113 8.39e-25 97.1
MsaG028964 AT5G63090.2 40.566 106 62 1 7 112 9 113 8.39e-25 97.1
MsaG028964 AT5G63090.1 40.566 106 62 1 7 112 9 113 8.39e-25 97.1
MsaG028964 AT2G30340.2 37.037 108 64 2 1 108 48 151 5.15e-24 97.1
MsaG028964 AT2G30340.1 37.037 108 64 2 1 108 47 150 5.38e-24 97.1
MsaG028964 AT1G31320.1 47.500 80 41 1 10 89 14 92 5.56e-24 94.7
MsaG028964 AT1G07900.1 48.750 80 40 1 10 89 34 112 1.26e-22 91.7
MsaG028964 AT2G23660.2 41.176 102 59 1 10 111 6 106 2.67e-22 93.2
MsaG028964 AT2G23660.3 41.176 102 59 1 10 111 6 106 2.67e-22 93.2
MsaG028964 AT2G23660.1 41.176 102 59 1 10 111 6 106 2.67e-22 93.2
MsaG028964 AT2G28500.1 48.750 80 40 1 10 89 56 134 3.99e-22 91.3
MsaG028964 AT3G26660.1 34.615 104 67 1 8 111 4 106 7.13e-22 87.4
MsaG028964 AT3G26620.1 32.174 115 77 1 8 122 4 117 7.52e-22 87.4
MsaG028964 AT1G16530.1 34.921 126 76 4 10 133 15 136 2.61e-21 87.4
MsaG028964 AT2G30130.1 36.522 115 71 2 10 124 9 121 2.66e-21 88.2
MsaG028964 AT3G50510.1 39.091 110 65 2 5 113 8 116 1.33e-20 86.3
MsaG028964 AT3G50510.2 39.091 110 65 2 5 113 8 116 1.33e-20 86.3
MsaG028964 AT1G06280.1 40.385 104 54 3 7 110 22 117 1.38e-20 86.7
MsaG028964 AT3G11090.1 35.644 101 60 2 5 105 7 102 3.41e-20 84.3
MsaG028964 AT5G15060.1 45.205 73 39 1 10 81 18 90 3.67e-17 75.9
MsaG028964 AT2G19820.1 40.000 80 48 0 10 89 13 92 4.04e-17 75.1
MsaG028964 AT4G00210.1 31.343 134 89 3 10 142 12 143 6.11e-16 74.3
MsaG028964 AT3G03760.1 35.294 102 64 2 10 110 52 152 1.29e-15 74.3
MsaG028964 AT5G35900.1 31.068 103 70 1 9 111 5 106 2.52e-15 72.4
MsaG028964 AT4G00220.1 32.673 101 66 2 12 111 20 119 8.27e-15 71.2
MsaG028964 AT2G42430.1 37.805 82 49 2 10 90 16 96 3.34e-14 70.1
MsaG028964 AT5G06080.1 30.597 134 81 4 9 141 7 129 1.06e-13 67.4
MsaG028964 AT2G31310.1 31.298 131 72 4 10 127 8 133 2.43e-13 66.6
MsaG028964 AT3G58190.1 32.039 103 68 2 10 111 12 113 7.29e-13 65.9
MsaG028964 AT2G45420.1 31.683 101 67 2 12 111 40 139 1.01e-12 66.2
MsaG028964 AT2G42440.1 30.303 99 67 2 10 107 8 105 1.33e-12 65.5
MsaG028964 AT2G45410.1 32.673 101 66 2 12 111 19 118 6.36e-12 62.8

Find 40 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTAAATATTGGGATATT+TGG 0.141273 5:-71237716 None:intergenic
TCACCAACATTGTTAAATAT+TGG 0.190888 5:-71237725 None:intergenic
CTTGGTGTTATTATGAATTA+TGG 0.198268 5:+71237572 MsaT028964.1:CDS
AGCTAGAACAACATTTGATT+TGG 0.257325 5:+71237964 MsaT028964.1:CDS
TCATTGCTTGATAATCCTTT+TGG 0.267871 5:-71237896 None:intergenic
CATGCTGCACAAGCCTTGTT+TGG 0.269582 5:-71237332 None:intergenic
TCCTTTAGCTCCTTATTTCC+CGG 0.285923 5:+71237388 MsaT028964.1:CDS
GGAATTTGAGAACTAGTATA+AGG 0.287802 5:-71237695 None:intergenic
AATATCCGACTCAATAATTA+TGG 0.288561 5:-71237522 None:intergenic
CACCAACATTGTTAAATATT+GGG 0.294726 5:-71237724 None:intergenic
GGTTTATCGGCCGGGAAATA+AGG 0.295833 5:-71237398 None:intergenic
GCTAGAACAACATTTGATTT+GGG 0.363338 5:+71237965 MsaT028964.1:CDS
AGCAACGCTCATCGTTTGTT+TGG 0.383470 5:+71237431 MsaT028964.1:CDS
GGATGACAATTCTAATTTGA+TGG 0.388591 5:+71237871 MsaT028964.1:CDS
CCTCATGATGTTAACTATAG+TGG 0.400420 5:+71237833 MsaT028964.1:CDS
AGATATGTTAAAGCAGTCTA+TGG 0.416875 5:+71237595 MsaT028964.1:CDS
CTTTAGTATCCTTTGTATGT+TGG 0.435097 5:-71237459 None:intergenic
CGTGCAAAATCTCCCGTTCA+TGG 0.444453 5:+71237545 MsaT028964.1:CDS
ATCCCAATATTTAACAATGT+TGG 0.449694 5:+71237722 MsaT028964.1:CDS
GACGACCTTGACGACCTTGA+TGG 0.456186 5:+71237926 MsaT028964.1:CDS
ATTATCAAGCAATGAAGAAT+CGG 0.467820 5:+71237904 MsaT028964.1:CDS
TCTAATTTGATGGTACCAAA+AGG 0.475215 5:+71237881 MsaT028964.1:CDS
ACACCAAGACATCCATGAAC+GGG 0.497015 5:-71237557 None:intergenic
TTTGGTTTGATGATATTCAT+TGG 0.504277 5:-71237314 None:intergenic
TCTCCCGTTCATGGATGTCT+TGG 0.510462 5:+71237554 MsaT028964.1:CDS
AAAGCAGTCTATGGAAGAGT+TGG 0.512156 5:+71237604 MsaT028964.1:CDS
AAGGATACTAAAGGAAATCA+AGG 0.515917 5:+71237469 MsaT028964.1:CDS
GCCGGGAAATAAGGAGCTAA+AGG 0.524058 5:-71237389 None:intergenic
CAACATACAAAGGATACTAA+AGG 0.551295 5:+71237460 MsaT028964.1:CDS
GAGATCCATAATTATTGAGT+CGG 0.580015 5:+71237517 MsaT028964.1:CDS
CCACTATAGTTAACATCATG+AGG 0.583308 5:-71237833 None:intergenic
GTTCATCAACACCACCATCA+AGG 0.592727 5:-71237940 None:intergenic
GAATATCATCAAACCAAACA+AGG 0.597163 5:+71237319 MsaT028964.1:CDS
TTGGTGTTTCCAACATACAA+AGG 0.602738 5:+71237450 MsaT028964.1:CDS
AACACCAAGACATCCATGAA+CGG 0.603796 5:-71237558 None:intergenic
CACCACCATCAAGGTCGTCA+AGG 0.611148 5:-71237931 None:intergenic
CATGATGTTAACTATAGTGG+TGG 0.632189 5:+71237836 MsaT028964.1:CDS
TAGTGGTGGCGACTATGTCA+TGG 0.648101 5:+71237850 MsaT028964.1:CDS
CACTATAGTTAACATCATGA+GGG 0.659397 5:-71237832 None:intergenic
GACCTTGACGACCTTGATGG+TGG 0.667335 5:+71237929 MsaT028964.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 71237317 71238012 71237317 ID=MsaG028964
Chr5 mRNA 71237317 71238012 71237317 ID=MsaT028964.1;Parent=MsaG028964
Chr5 exon 71237317 71238012 71237317 ID=MsaT028964.1.exon1;Parent=MsaT028964.1
Chr5 CDS 71237317 71238012 71237317 ID=cds.MsaT028964.1;Parent=MsaT028964.1
Gene Sequence

>MsaT028964.1

ATGAATATCATCAAACCAAACAAGGCTTGTGCAGCATGCAAGTATCAAAGAAGAAAGTGTTCAAGTGAGTGTCCTTTAGCTCCTTATTTCCCGGCCGATAAACCAAAAATGTTTAGCAACGCTCATCGTTTGTTTGGTGTTTCCAACATACAAAGGATACTAAAGGAAATCAAGGACGACGATCAAAAAGATGATGCGATGAGATCCATAATTATTGAGTCGGATATTCGTGCAAAATCTCCCGTTCATGGATGTCTTGGTGTTATTATGAATTATGGAGATATGTTAAAGCAGTCTATGGAAGAGTTGGATCATGTAAAAACGTTACTAGCTTATTGTAACGATTTACAACAAAAACAACATCTTCATTCTTCTTTACCTTATACTAGTTCTCAAATTCCAAATATCCCAATATTTAACAATGTTGGTGATGTTCCTAATTATTATTATTATTATCCCAATAGTGAAAATAATAATATGATGAGAGCATCTTCTTCTTATATTAGTGACATCATCCCTCATGATGTTAACTATAGTGGTGGCGACTATGTCATGGATGACAATTCTAATTTGATGGTACCAAAAGGATTATCAAGCAATGAAGAATCGGACGACCTTGACGACCTTGATGGTGGTGTTGATGAACAAGCTAGAACAACATTTGATTTGGGAAAAAAAAGGAAGATTTTCAGATAG
Protein sequence

>MsaT028964.1

MNIIKPNKACAACKYQRRKCSSECPLAPYFPADKPKMFSNAHRLFGVSNIQRILKEIKDDDQKDDAMRSIIIESDIRAKSPVHGCLGVIMNYGDMLKQSMEELDHVKTLLAYCNDLQQKQHLHSSLPYTSSQIPNIPIFNNVGDVPNYYYYYPNSENNNMMRASSSYISDIIPHDVNYSGGDYVMDDNSNLMVPKGLSSNEESDDLDDLDGGVDEQARTTFDLGKKRKIFR*