AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0836320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0836320 MtrunA17_Chr5g0402331 95.876 97 4 0 1 97 93 189 1.30e-61 185
Msa0836320 MtrunA17_Chr5g0402361 95.876 97 4 0 1 97 265 361 1.34e-59 186
Msa0836320 MtrunA17_Chr5g0402361 94.792 96 5 0 1 96 92 187 1.73e-57 180
Msa0836320 MtrunA17_Chr4g0044961 52.874 87 40 1 4 90 104 189 2.13e-26 96.3
Msa0836320 MtrunA17_Chr1g0161211 49.451 91 43 2 3 91 92 181 4.05e-22 85.5
Msa0836320 MtrunA17_Chr1g0161211 41.935 62 36 0 28 89 45 106 3.34e-11 57.0
Msa0836320 MtrunA17_Chr3g0111371 45.882 85 43 1 6 90 54 135 5.10e-22 83.6
Msa0836320 MtrunA17_Chr8g0391691 51.064 94 43 2 4 95 83 175 1.55e-21 83.6
Msa0836320 MtrunA17_Chr8g0391691 46.154 65 35 0 29 93 36 100 1.53e-12 60.1
Msa0836320 MtrunA17_Chr5g0434951 44.828 87 48 0 6 92 53 139 3.53e-21 81.3
Msa0836320 MtrunA17_Chr1g0169581 40.909 88 49 1 6 90 53 140 4.01e-19 76.3
Msa0836320 MtrunA17_Chr7g0245911 40.196 102 53 2 1 94 93 194 5.91e-18 74.7
Msa0836320 MtrunA17_Chr3g0121191 44.444 90 45 2 9 95 135 222 8.97e-18 74.7
Msa0836320 MtrunA17_Chr8g0392951 37.234 94 59 0 1 94 68 161 1.50e-17 72.8
Msa0836320 MtrunA17_Chr7g0256701 50.000 66 32 1 26 90 147 212 1.89e-17 73.6
Msa0836320 MtrunA17_Chr8g0351681 43.299 97 48 2 6 95 100 196 3.18e-17 72.8
Msa0836320 MtrunA17_Chr6g0482731 36.667 90 57 0 1 90 71 160 3.40e-17 72.0
Msa0836320 MtrunA17_Chr1g0169621 49.231 65 33 0 26 90 101 165 1.17e-16 70.5
Msa0836320 MtrunA17_Chr1g0188171 40.426 94 49 2 3 92 58 148 2.00e-15 67.0
Msa0836320 MtrunA17_Chr4g0033601 41.758 91 50 2 6 93 54 144 2.33e-15 66.6
Msa0836320 MtrunA17_Chr3g0116141 36.667 90 57 0 1 90 49 138 4.69e-15 65.9
Msa0836320 MtrunA17_Chr3g0116151 36.667 90 57 0 1 90 50 139 4.89e-15 65.9
Msa0836320 MtrunA17_Chr1g0185001 36.364 88 56 0 4 91 59 146 5.50e-15 65.9
Msa0836320 MtrunA17_Chr7g0256171 45.263 95 49 2 6 97 54 148 9.37e-15 65.5
Msa0836320 MtrunA17_Chr7g0254731 39.785 93 49 2 3 91 58 147 1.61e-14 64.7
Msa0836320 MtrunA17_Chr7g0254731 40.323 62 37 0 29 90 12 73 6.85e-11 55.1
Msa0836320 MtrunA17_Chr5g0396261 37.500 88 50 2 6 89 26 112 2.44e-14 63.2
Msa0836320 MtrunA17_Chr5g0440931 39.785 93 49 2 3 91 58 147 3.51e-14 63.5
Msa0836320 MtrunA17_Chr6g0460211 39.785 93 49 2 3 91 58 147 3.67e-14 63.5
Msa0836320 MtrunA17_Chr7g0225921 35.165 91 59 0 1 91 51 141 5.15e-14 63.2
Msa0836320 MtrunA17_Chr3g0093271 39.785 93 49 2 3 91 109 198 6.45e-14 63.9
Msa0836320 MtrunA17_Chr4g0057641 34.444 90 59 0 1 90 50 139 2.52e-13 61.2
Msa0836320 MtrunA17_Chr1g0166281 38.298 94 51 2 3 92 58 148 2.95e-13 61.2
Msa0836320 MtrunA17_Chr4g0057661 34.444 90 59 0 1 90 50 139 4.18e-13 60.8
Msa0836320 MtrunA17_Chr2g0329371 42.105 95 50 2 4 93 111 205 7.51e-13 61.2
Msa0836320 MtrunA17_Chr4g0064231 47.826 69 34 1 27 93 151 219 1.11e-12 61.2
Msa0836320 MtrunA17_Chr4g0057651 34.444 90 59 0 1 90 50 139 1.63e-12 59.3
Msa0836320 MtrunA17_Chr8g0366401 31.579 95 61 1 3 93 63 157 1.81e-12 59.7
Msa0836320 MtrunA17_Chr6g0459231 32.967 91 61 0 1 91 52 142 2.24e-12 58.9
Msa0836320 MtrunA17_Chr7g0274101 39.560 91 54 1 3 92 58 148 3.30e-12 58.5
Msa0836320 MtrunA17_Chr8g0373691 40.625 64 38 0 27 90 51 114 1.62e-11 57.4
Msa0836320 MtrunA17_Chr8g0373691 32.955 88 58 1 4 90 100 187 1.78e-11 57.4
Msa0836320 MtrunA17_Chr7g0217621 43.373 83 43 2 12 92 119 199 1.64e-11 57.8
Msa0836320 MtrunA17_Chr7g0245231 41.176 68 40 0 23 90 24 91 2.70e-11 56.6
Msa0836320 MtrunA17_Chr6g0450921 43.077 65 37 0 26 90 26 90 3.11e-11 56.6
Msa0836320 MtrunA17_Chr4g0042491 47.619 63 33 0 28 90 113 175 8.61e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0836320 AT2G15680.1 50.575 87 42 1 4 90 97 182 2.25e-27 99.0
Msa0836320 AT1G24620.1 47.826 92 45 2 6 95 86 176 7.13e-23 87.4
Msa0836320 AT5G37770.1 42.105 95 50 1 4 93 64 158 5.68e-21 82.0
Msa0836320 AT5G37770.2 42.105 95 50 1 4 93 64 158 5.68e-21 82.0
Msa0836320 AT1G66400.1 41.935 93 47 2 4 91 62 152 4.21e-20 79.7
Msa0836320 AT1G18210.2 40.909 88 49 1 3 90 69 153 9.18e-19 76.3
Msa0836320 AT1G18210.2 39.437 71 43 0 27 97 21 91 9.57e-11 55.5
Msa0836320 AT1G18210.1 40.909 88 49 1 3 90 69 153 9.18e-19 76.3
Msa0836320 AT1G18210.1 39.437 71 43 0 27 97 21 91 9.57e-11 55.5
Msa0836320 AT5G17470.1 45.833 96 48 3 4 95 49 144 1.01e-18 75.9
Msa0836320 AT2G36180.1 46.875 96 46 3 4 95 47 141 1.99e-18 74.7
Msa0836320 AT5G42380.1 41.573 89 50 1 4 90 96 184 6.31e-18 74.7
Msa0836320 AT2G41410.1 43.421 76 41 2 19 93 136 210 1.39e-16 71.6
Msa0836320 AT4G14640.2 39.583 96 51 2 1 92 39 131 1.68e-16 69.7
Msa0836320 AT1G73630.1 39.080 87 50 1 4 90 67 150 3.23e-16 69.7
Msa0836320 AT4G14640.1 39.583 96 51 2 1 92 57 149 4.30e-16 68.9
Msa0836320 AT3G22930.1 39.130 92 55 1 1 91 79 170 5.40e-15 66.6
Msa0836320 AT3G03400.1 52.727 55 26 0 27 81 78 132 6.90e-15 65.5
Msa0836320 AT1G66410.4 39.785 93 49 2 3 91 22 111 7.06e-15 65.1
Msa0836320 AT1G66410.3 39.785 93 49 2 3 91 22 111 7.06e-15 65.1
Msa0836320 AT3G43810.4 39.785 93 49 2 3 91 22 111 1.25e-14 64.3
Msa0836320 AT3G43810.3 39.785 93 49 2 3 91 22 111 1.25e-14 64.3
Msa0836320 AT3G50360.1 38.889 90 52 2 4 90 72 161 1.50e-14 65.5
Msa0836320 AT3G50360.1 44.615 65 36 0 26 90 24 88 1.13e-11 58.2
Msa0836320 AT3G10190.1 39.773 88 52 1 4 90 118 205 1.52e-14 66.2
Msa0836320 AT5G37780.4 39.785 93 49 2 3 91 45 134 2.11e-14 64.3
Msa0836320 AT2G27030.3 39.175 97 52 2 3 95 58 151 2.33e-14 65.1
Msa0836320 AT5G21274.1 40.860 93 48 2 3 91 58 147 2.47e-14 64.3
Msa0836320 AT1G66410.1 39.785 93 49 2 3 91 58 147 2.63e-14 64.3
Msa0836320 AT5G37780.1 39.785 93 49 2 3 91 58 147 2.63e-14 64.3
Msa0836320 AT3G56800.1 40.860 93 48 2 3 91 58 147 2.72e-14 64.3
Msa0836320 AT2G41110.1 40.860 93 48 2 3 91 58 147 2.72e-14 64.3
Msa0836320 AT2G27030.1 40.860 93 48 2 3 91 58 147 2.72e-14 64.3
Msa0836320 AT2G41110.2 40.860 93 48 2 3 91 70 159 2.97e-14 64.7
Msa0836320 AT1G66410.2 39.785 93 49 2 3 91 68 157 3.46e-14 64.3
Msa0836320 AT5G37780.2 39.785 93 49 2 3 91 73 162 4.33e-14 64.3
Msa0836320 AT2G43290.1 39.583 96 50 2 6 93 114 209 4.76e-14 65.1
Msa0836320 AT3G43810.1 39.785 93 49 2 3 91 58 147 5.06e-14 63.5
Msa0836320 AT3G59440.1 39.796 98 51 3 1 93 95 189 5.14e-14 64.7
Msa0836320 AT5G37780.3 39.785 93 49 2 3 91 84 173 5.28e-14 64.3
Msa0836320 AT3G43810.2 38.614 101 53 3 3 97 58 155 9.08e-14 64.3
Msa0836320 AT1G05990.1 43.478 92 48 2 6 93 54 145 2.26e-13 62.0
Msa0836320 AT4G03290.1 40.000 95 51 2 6 94 54 148 2.22e-12 59.7
Msa0836320 AT1G32250.1 30.435 92 57 1 6 90 65 156 2.32e-12 59.7
Msa0836320 AT1G21550.1 35.714 98 49 3 9 92 57 154 3.36e-12 58.9
Msa0836320 AT1G76650.2 32.955 88 59 0 3 90 79 166 6.25e-12 58.5
Msa0836320 AT1G76650.1 32.955 88 59 0 3 90 89 176 7.65e-12 58.5
Msa0836320 AT1G76650.3 32.955 88 59 0 3 90 89 176 7.65e-12 58.5
Msa0836320 AT3G07490.1 38.947 95 55 2 6 97 54 148 8.71e-12 58.2
Msa0836320 AT4G12860.1 46.269 67 34 1 33 97 82 148 1.32e-11 57.4
Msa0836320 AT3G03000.1 31.111 90 60 1 6 93 69 158 2.83e-11 57.0
Msa0836320 AT2G41100.2 33.945 109 53 3 4 94 23 130 5.46e-11 56.6
Msa0836320 AT1G76640.1 43.077 65 37 0 26 90 19 83 9.75e-11 55.5

Find 23 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCAAGTATTTGATATAAA+TGG 0.216373 5_4:+9801482 Msa0836320:CDS
CATAGACTTTAAAGAGTTCA+TGG 0.277650 5_4:+9801406 Msa0836320:CDS
CCTTAGTGCTTGTAAGAAAA+TGG 0.341545 5_4:+9801568 Msa0836320:CDS
AACTGTCTCAAATATTTAAG+AGG 0.427192 5_4:+9801528 Msa0836320:CDS
TCTCAAATATTTAAGAGGTT+AGG 0.448139 5_4:+9801533 Msa0836320:CDS
GTGAAAGGGGTTGACGGTGA+TGG 0.473054 5_4:+9801590 Msa0836320:CDS
CTTGTAAGAAAATGGTGAAA+GGG 0.492061 5_4:+9801576 Msa0836320:CDS
TAGATTTGAATGAGTTTACA+AGG 0.501078 5_4:+9801624 Msa0836320:CDS
AAAATGGTGAAAGGGGTTGA+CGG 0.504340 5_4:+9801584 Msa0836320:CDS
GCCATCTTTGTCAGAGCCCA+TGG 0.507089 5_4:-9801381 None:intergenic
GTATTTGATATAAATGGTGA+TGG 0.547891 5_4:+9801488 Msa0836320:CDS
GAGTTCATGGAAATGTTCAA+TGG 0.548455 5_4:+9801419 Msa0836320:CDS
AATGGCAAGAAATGTGCCTA+AGG 0.556472 5_4:+9801656 Msa0836320:CDS
GGGTAGTAAGATAAAAGAAG+AGG 0.559838 5_4:+9801445 Msa0836320:CDS
GCTTGTAAGAAAATGGTGAA+AGG 0.569070 5_4:+9801575 Msa0836320:CDS
GGGGTTGACGGTGATGGAGA+TGG 0.573082 5_4:+9801596 Msa0836320:CDS
ATGGAAATGTTCAATGGAGA+GGG 0.592453 5_4:+9801425 Msa0836320:CDS
CATGGAAATGTTCAATGGAG+AGG 0.594726 5_4:+9801424 Msa0836320:CDS
TTTACAAGGATGATGATGAA+TGG 0.601621 5_4:+9801638 Msa0836320:CDS
TATTTGATATAAATGGTGAT+GGG 0.605312 5_4:+9801489 Msa0836320:CDS
GCCATGGGCTCTGACAAAGA+TGG 0.632822 5_4:+9801380 None:intergenic
TTGTAAGAAAATGGTGAAAG+GGG 0.653751 5_4:+9801577 Msa0836320:CDS
TGATGGGAAAATCAATGCTG+AGG 0.707496 5_4:+9801505 Msa0836320:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCAAGTATTTGATATAAA+TGG + chr5_4:9801482-9801501 Msa0836320:CDS 15.0%
!! TATTTGATATAAATGGTGAT+GGG + chr5_4:9801489-9801508 Msa0836320:CDS 20.0%
! GTATTTGATATAAATGGTGA+TGG + chr5_4:9801488-9801507 Msa0836320:CDS 25.0%
! AACTGTCTCAAATATTTAAG+AGG + chr5_4:9801528-9801547 Msa0836320:CDS 25.0%
! TCTCAAATATTTAAGAGGTT+AGG + chr5_4:9801533-9801552 Msa0836320:CDS 25.0%
! TAGATTTGAATGAGTTTACA+AGG + chr5_4:9801624-9801643 Msa0836320:CDS 25.0%
! CATAGACTTTAAAGAGTTCA+TGG + chr5_4:9801406-9801425 Msa0836320:CDS 30.0%
CTTGTAAGAAAATGGTGAAA+GGG + chr5_4:9801576-9801595 Msa0836320:CDS 30.0%
TTGTAAGAAAATGGTGAAAG+GGG + chr5_4:9801577-9801596 Msa0836320:CDS 30.0%
! TTTACAAGGATGATGATGAA+TGG + chr5_4:9801638-9801657 Msa0836320:CDS 30.0%
GAGTTCATGGAAATGTTCAA+TGG + chr5_4:9801419-9801438 Msa0836320:CDS 35.0%
ATGGAAATGTTCAATGGAGA+GGG + chr5_4:9801425-9801444 Msa0836320:CDS 35.0%
GGGTAGTAAGATAAAAGAAG+AGG + chr5_4:9801445-9801464 Msa0836320:CDS 35.0%
! CCATTTTCTTACAAGCACTA+AGG - chr5_4:9801571-9801590 None:intergenic 35.0%
CCTTAGTGCTTGTAAGAAAA+TGG + chr5_4:9801568-9801587 Msa0836320:CDS 35.0%
GCTTGTAAGAAAATGGTGAA+AGG + chr5_4:9801575-9801594 Msa0836320:CDS 35.0%
CATGGAAATGTTCAATGGAG+AGG + chr5_4:9801424-9801443 Msa0836320:CDS 40.0%
TGATGGGAAAATCAATGCTG+AGG + chr5_4:9801505-9801524 Msa0836320:CDS 40.0%
AAAATGGTGAAAGGGGTTGA+CGG + chr5_4:9801584-9801603 Msa0836320:CDS 40.0%
GTGAAAGGGGTTGACGGTGA+TGG + chr5_4:9801590-9801609 Msa0836320:CDS 55.0%
!! GGGGTTGACGGTGATGGAGA+TGG + chr5_4:9801596-9801615 Msa0836320:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 9801383 9801676 9801383 ID=Msa0836320;Name=Msa0836320
chr5_4 mRNA 9801383 9801676 9801383 ID=Msa0836320-mRNA-1;Parent=Msa0836320;Name=Msa0836320-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|-1|0|1|-1|1|1|0|97
chr5_4 exon 9801383 9801676 9801383 ID=Msa0836320-mRNA-1:exon:4373;Parent=Msa0836320-mRNA-1
chr5_4 CDS 9801383 9801676 9801383 ID=Msa0836320-mRNA-1:cds;Parent=Msa0836320-mRNA-1
Gene Sequence

>Msa0836320

ATGGGCTCTGACAAAGATGGCTTCATAGACTTTAAAGAGTTCATGGAAATGTTCAATGGAGAGGGTAGTAAGATAAAAGAAGAGGAGATTAAGAGTGCTTTTCAAGTATTTGATATAAATGGTGATGGGAAAATCAATGCTGAGGAACTGTCTCAAATATTTAAGAGGTTAGGAGAGAGTTGTAGCCTTAGTGCTTGTAAGAAAATGGTGAAAGGGGTTGACGGTGATGGAGATGGTCTTATAGATTTGAATGAGTTTACAAGGATGATGATGAATGGCAAGAAATGTGCCTAA
Protein sequence

>Msa0836320

MGSDKDGFIDFKEFMEMFNGEGSKIKEEEIKSAFQVFDINGDGKINAEELSQIFKRLGESCSLSACKKMVKGVDGDGDGLIDLNEFTRMMMNGKKCA*