AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0326250

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0326250 MtrunA17_Chr1g0197721 92.188 64 5 0 1 64 149 212 1.15e-34 122
Msa0326250 MtrunA17_Chr4g0059751 49.091 55 28 0 1 55 194 248 9.60e-16 69.3
Msa0326250 MtrunA17_Chr8g0369091 66.667 45 15 0 1 45 699 743 4.85e-15 67.4
Msa0326250 MtrunA17_Chr6g0478601 63.830 47 17 0 3 49 211 257 2.23e-14 65.5
Msa0326250 MtrunA17_Chr4g0018201 61.224 49 19 0 1 49 857 905 2.93e-14 65.5
Msa0326250 MtrunA17_Chr2g0309421 60.000 45 18 0 1 45 277 321 3.61e-14 65.1
Msa0326250 MtrunA17_Chr8g0335351 62.791 43 16 0 3 45 474 516 4.65e-14 64.7
Msa0326250 MtrunA17_Chr5g0428981 59.184 49 20 0 1 49 861 909 4.97e-14 64.7
Msa0326250 MtrunA17_Chr7g0245031 48.148 54 28 0 1 54 246 299 8.78e-14 63.9
Msa0326250 MtrunA17_Chr4g0030361 60.000 45 18 0 1 45 409 453 9.52e-14 63.9
Msa0326250 MtrunA17_Chr2g0312641 58.140 43 18 0 3 45 198 240 1.11e-13 63.5
Msa0326250 MtrunA17_Chr2g0285711 62.791 43 16 0 3 45 191 233 1.45e-13 63.2
Msa0326250 MtrunA17_Chr7g0250631 60.465 43 17 0 3 45 468 510 1.89e-13 63.2
Msa0326250 MtrunA17_Chr8g0381091 60.465 43 17 0 3 45 187 229 2.83e-13 62.4
Msa0326250 MtrunA17_Chr7g0227331 60.465 43 17 0 3 45 336 378 3.01e-13 62.4
Msa0326250 MtrunA17_Chr1g0179101 60.465 43 17 0 3 45 574 616 3.55e-13 62.4
Msa0326250 MtrunA17_Chr7g0266031 60.465 43 17 0 3 45 596 638 5.90e-13 61.6
Msa0326250 MtrunA17_Chr1g0153321 47.368 57 30 0 3 59 208 264 1.05e-12 60.8
Msa0326250 MtrunA17_Chr3g0080101 58.140 43 18 0 3 45 519 561 1.13e-12 60.8
Msa0326250 MtrunA17_Chr7g0234641 54.167 48 22 0 4 51 123 170 1.40e-12 60.5
Msa0326250 MtrunA17_Chr7g0261491 46.269 67 31 1 1 62 218 284 1.46e-12 60.5
Msa0326250 MtrunA17_Chr2g0327561 55.556 45 20 0 1 45 728 772 1.72e-12 60.1
Msa0326250 MtrunA17_Chr2g0321101 57.143 42 18 0 4 45 197 238 2.58e-12 59.7
Msa0326250 MtrunA17_Chr1g0183651 50.000 56 28 0 1 56 218 273 3.84e-12 59.3
Msa0326250 MtrunA17_Chr8g0338741 53.333 45 21 0 1 45 130 174 4.60e-12 58.9
Msa0326250 MtrunA17_Chr4g0013131 54.348 46 21 0 1 46 109 154 4.72e-12 58.9
Msa0326250 MtrunA17_Chr1g0167311 48.214 56 29 0 1 56 213 268 5.39e-12 58.9
Msa0326250 MtrunA17_Chr8g0346071 47.368 57 29 1 1 56 115 171 6.06e-12 58.5
Msa0326250 MtrunA17_Chr4g0063311 51.163 43 21 0 3 45 200 242 6.29e-12 58.5
Msa0326250 MtrunA17_Chr8g0356291 48.889 45 23 0 1 45 229 273 7.59e-12 58.5
Msa0326250 MtrunA17_Chr8g0346081 47.368 57 29 1 1 56 115 171 8.45e-12 58.2
Msa0326250 MtrunA17_Chr2g0290691 52.381 42 20 0 4 45 309 350 8.92e-12 58.2
Msa0326250 MtrunA17_Chr6g0449401 58.537 41 17 0 5 45 406 446 9.88e-12 58.2
Msa0326250 MtrunA17_Chr1g0167351 44.286 70 34 1 1 65 208 277 1.12e-11 57.8
Msa0326250 MtrunA17_Chr5g0428031 55.556 45 20 0 2 46 108 152 1.49e-11 57.4
Msa0326250 MtrunA17_Chr1g0187581 45.455 55 30 0 2 56 216 270 2.27e-11 57.0
Msa0326250 MtrunA17_Chr6g0453681 45.455 55 30 0 1 55 117 171 2.81e-11 56.6
Msa0326250 MtrunA17_Chr6g0468751 45.455 55 30 0 1 55 117 171 2.81e-11 56.6
Msa0326250 MtrunA17_Chr4g0047201 53.659 41 19 0 6 46 308 348 3.25e-11 56.6
Msa0326250 MtrunA17_Chr2g0304111 54.348 46 21 0 1 46 121 166 3.54e-11 56.6
Msa0326250 MtrunA17_Chr4g0032761 47.619 42 22 0 4 45 125 166 3.55e-11 56.6
Msa0326250 MtrunA17_Chr2g0299781 47.273 55 29 0 3 57 213 267 3.66e-11 56.6
Msa0326250 MtrunA17_Chr4g0074111 50.000 46 23 0 1 46 115 160 6.10e-11 55.8
Msa0326250 MtrunA17_Chr3g0135951 53.061 49 23 0 3 51 194 242 7.25e-11 55.5
Msa0326250 MtrunA17_Chr4g0075541 56.098 41 18 0 7 47 194 234 8.16e-11 55.5
Msa0326250 MtrunA17_Chr4g0047191 51.220 41 20 0 6 46 152 192 9.60e-11 55.1
Msa0326250 MtrunA17_Chr4g0047211 51.220 41 20 0 6 46 147 187 9.95e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0326250 AT5G04510.3 87.500 64 8 0 1 64 142 205 6.47e-35 120
Msa0326250 AT5G04510.2 87.500 64 8 0 1 64 142 205 1.45e-33 118
Msa0326250 AT5G04510.1 87.500 64 8 0 1 64 142 205 4.04e-33 118
Msa0326250 AT3G10540.1 85.938 64 9 0 1 64 143 206 3.04e-32 115
Msa0326250 AT5G58140.3 53.623 69 30 2 1 68 677 744 3.72e-16 71.2
Msa0326250 AT5G58140.6 53.623 69 30 2 1 68 677 744 4.11e-16 70.9
Msa0326250 AT5G58140.7 53.623 69 30 2 1 68 677 744 4.11e-16 70.9
Msa0326250 AT5G58140.5 53.623 69 30 2 1 68 677 744 4.11e-16 70.9
Msa0326250 AT5G58140.2 53.623 69 30 2 1 68 677 744 4.11e-16 70.9
Msa0326250 AT5G58140.1 53.623 69 30 2 1 68 677 744 4.11e-16 70.9
Msa0326250 AT5G62310.1 61.224 49 19 0 1 49 852 900 7.55e-15 67.4
Msa0326250 AT3G12690.1 60.000 45 18 0 1 45 285 329 3.34e-14 65.5
Msa0326250 AT3G12690.3 60.000 45 18 0 1 45 285 329 3.34e-14 65.5
Msa0326250 AT3G12690.2 60.000 45 18 0 1 45 285 329 3.34e-14 65.5
Msa0326250 AT3G17850.1 61.224 49 19 0 1 49 980 1028 3.61e-14 65.5
Msa0326250 AT1G48490.3 61.702 47 18 0 3 49 928 974 4.26e-14 65.1
Msa0326250 AT1G48490.2 61.702 47 18 0 3 49 928 974 4.26e-14 65.1
Msa0326250 AT1G48490.1 61.702 47 18 0 3 49 928 974 4.26e-14 65.1
Msa0326250 AT1G48490.4 61.702 47 18 0 3 49 929 975 4.51e-14 65.1
Msa0326250 AT2G44830.2 62.791 43 16 0 3 45 465 507 6.60e-14 64.7
Msa0326250 AT2G44830.3 62.791 43 16 0 3 45 465 507 6.60e-14 64.7
Msa0326250 AT2G44830.1 62.791 43 16 0 3 45 465 507 6.60e-14 64.7
Msa0326250 AT4G14350.3 47.059 68 31 1 1 63 217 284 1.36e-13 63.9
Msa0326250 AT4G14350.2 47.059 68 31 1 1 63 217 284 1.43e-13 63.5
Msa0326250 AT4G14350.1 47.059 68 31 1 1 63 217 284 1.43e-13 63.5
Msa0326250 AT4G14350.4 47.059 68 31 1 1 63 217 284 1.43e-13 63.5
Msa0326250 AT2G34650.1 62.791 43 16 0 3 45 182 224 1.46e-13 63.5
Msa0326250 AT1G79250.1 55.556 45 20 0 1 45 246 290 1.59e-13 63.5
Msa0326250 AT1G79250.3 55.556 45 20 0 1 45 246 290 1.59e-13 63.5
Msa0326250 AT1G79250.2 55.556 45 20 0 1 45 246 290 1.59e-13 63.5
Msa0326250 AT1G79250.4 55.556 45 20 0 1 45 246 290 1.59e-13 63.5
Msa0326250 AT1G30640.3 50.000 52 26 0 1 52 125 176 2.03e-13 63.2
Msa0326250 AT1G16440.1 55.556 45 20 0 1 45 215 259 2.32e-13 63.2
Msa0326250 AT1G45160.1 59.574 47 19 0 3 49 770 816 2.77e-13 62.8
Msa0326250 AT1G30640.2 50.000 52 26 0 1 52 218 269 2.80e-13 62.8
Msa0326250 AT1G30640.1 50.000 52 26 0 1 52 218 269 2.80e-13 62.8
Msa0326250 AT5G03640.2 62.791 43 16 0 3 45 643 685 3.01e-13 62.8
Msa0326250 AT5G03640.1 62.791 43 16 0 3 45 643 685 3.01e-13 62.8
Msa0326250 AT1G45160.2 59.574 47 19 0 3 49 770 816 3.17e-13 62.8
Msa0326250 AT3G27580.2 58.140 43 18 0 3 45 284 326 7.16e-13 61.6
Msa0326250 AT3G27580.1 58.140 43 18 0 3 45 284 326 7.16e-13 61.6
Msa0326250 AT3G23310.1 53.704 54 25 0 1 54 218 271 9.14e-13 61.2
Msa0326250 AT5G40030.1 55.814 43 19 0 3 45 216 258 9.18e-13 61.2
Msa0326250 AT1G53700.1 57.143 42 18 0 4 45 197 238 9.71e-13 61.2
Msa0326250 AT3G52890.2 58.140 43 18 0 3 45 640 682 1.44e-12 60.8
Msa0326250 AT3G52890.4 58.140 43 18 0 3 45 640 682 1.44e-12 60.8
Msa0326250 AT3G52890.1 58.140 43 18 0 3 45 640 682 1.44e-12 60.8
Msa0326250 AT3G52890.3 58.140 43 18 0 3 45 640 682 1.44e-12 60.8
Msa0326250 AT4G24400.1 46.552 58 30 1 2 59 108 164 1.59e-12 60.8
Msa0326250 AT1G03920.2 51.786 56 27 0 1 56 122 177 1.64e-12 60.8
Msa0326250 AT4G24400.2 43.548 62 34 1 2 63 108 168 1.71e-12 60.5
Msa0326250 AT1G03920.1 51.786 56 27 0 1 56 235 290 2.14e-12 60.5
Msa0326250 AT1G03920.3 51.786 56 27 0 1 56 235 290 2.14e-12 60.5
Msa0326250 AT5G55910.2 53.488 43 20 0 3 45 211 253 2.19e-12 60.5
Msa0326250 AT5G55910.1 53.488 43 20 0 3 45 211 253 2.19e-12 60.5
Msa0326250 AT4G26610.1 53.488 43 20 0 3 45 225 267 2.19e-12 60.5
Msa0326250 AT2G36350.1 59.524 42 17 0 4 45 662 703 2.39e-12 60.1
Msa0326250 AT3G14370.1 54.762 42 19 0 4 45 191 232 2.79e-12 60.1
Msa0326250 AT2G26980.2 56.522 46 20 0 1 46 112 157 4.60e-12 58.9
Msa0326250 AT3G08730.1 42.593 54 31 0 1 54 232 285 5.16e-12 59.3
Msa0326250 AT3G08730.2 42.593 54 31 0 1 54 232 285 5.16e-12 59.3
Msa0326250 AT2G26980.3 56.522 46 20 0 1 46 112 157 6.07e-12 58.9
Msa0326250 AT2G26700.1 52.381 42 20 0 4 45 192 233 6.43e-12 58.9
Msa0326250 AT2G26980.1 56.522 46 20 0 1 46 112 157 6.43e-12 58.9
Msa0326250 AT3G44610.1 43.478 69 31 3 4 64 182 250 9.53e-12 58.5
Msa0326250 AT2G20470.2 50.000 56 28 0 1 56 222 277 1.05e-11 58.5
Msa0326250 AT2G20470.1 50.000 56 28 0 1 56 222 277 1.05e-11 58.5
Msa0326250 AT3G45780.2 55.556 45 20 0 1 45 763 807 1.19e-11 58.2
Msa0326250 AT3G45780.1 55.556 45 20 0 1 45 763 807 1.19e-11 58.2
Msa0326250 AT3G08720.1 42.593 54 31 0 1 54 238 291 1.20e-11 58.2
Msa0326250 AT3G08720.3 42.593 54 31 0 1 54 238 291 1.20e-11 58.2
Msa0326250 AT3G08720.4 42.593 54 31 0 1 54 238 291 1.20e-11 58.2
Msa0326250 AT3G08720.2 42.593 54 31 0 1 54 238 291 1.20e-11 58.2
Msa0326250 AT2G20470.3 50.000 56 28 0 1 56 222 277 1.20e-11 58.2
Msa0326250 AT2G26980.5 56.522 46 20 0 1 46 112 157 1.26e-11 58.2
Msa0326250 AT4G33080.2 52.941 51 24 0 1 51 192 242 1.26e-11 58.2
Msa0326250 AT4G33080.1 52.941 51 24 0 1 51 192 242 1.34e-11 58.2
Msa0326250 AT5G09890.1 44.068 59 33 0 1 59 200 258 1.46e-11 58.2
Msa0326250 AT5G09890.2 44.068 59 33 0 1 59 200 258 1.49e-11 58.2
Msa0326250 AT1G30270.3 54.348 46 21 0 1 46 32 77 1.59e-11 57.8
Msa0326250 AT2G26980.4 56.522 46 20 0 1 46 122 167 1.73e-11 57.8
Msa0326250 AT1G30270.2 54.348 46 21 0 1 46 129 174 1.80e-11 57.8
Msa0326250 AT1G30270.1 54.348 46 21 0 1 46 129 174 1.97e-11 57.8
Msa0326250 AT3G20830.1 42.857 49 28 0 4 52 130 178 2.46e-11 57.4
Msa0326250 AT1G01140.3 52.174 46 22 0 1 46 117 162 3.02e-11 57.0
Msa0326250 AT1G01140.1 52.174 46 22 0 1 46 117 162 3.30e-11 57.0
Msa0326250 AT1G01140.2 52.174 46 22 0 1 46 117 162 3.33e-11 57.0
Msa0326250 AT4G30960.1 52.174 46 22 0 1 46 121 166 3.67e-11 57.0
Msa0326250 AT3G29160.1 47.273 55 29 0 1 55 118 172 3.95e-11 56.6
Msa0326250 AT3G29160.2 47.273 55 29 0 1 55 118 172 3.95e-11 56.6
Msa0326250 AT3G01090.3 45.455 55 30 0 1 55 117 171 4.11e-11 56.6
Msa0326250 AT3G01090.1 45.455 55 30 0 1 55 117 171 4.11e-11 56.6
Msa0326250 AT5G10930.1 54.348 46 21 0 1 46 110 155 4.59e-11 56.6
Msa0326250 AT3G01090.2 45.455 55 30 0 1 55 140 194 4.82e-11 56.6
Msa0326250 AT3G29160.3 47.273 55 29 0 1 55 118 172 5.33e-11 56.2
Msa0326250 AT5G21222.1 44.444 54 30 0 1 54 111 164 6.36e-11 56.2
Msa0326250 AT5G21222.2 44.444 54 30 0 1 54 111 164 6.36e-11 56.2
Msa0326250 AT5G21222.4 44.444 54 30 0 1 54 111 164 6.36e-11 56.2
Msa0326250 AT5G21222.3 44.444 54 30 0 1 54 111 164 6.36e-11 56.2
Msa0326250 AT5G47750.1 52.381 42 20 0 4 45 294 335 7.01e-11 56.2
Msa0326250 AT2G19400.1 45.614 57 31 0 3 59 205 261 8.57e-11 55.8

Find 8 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATATTAAAATAGCTGATTT+TGG 0.157219 2_4:+35829134 Msa0326250:CDS
CATTTGGAAGGACAGTAATT+TGG 0.270247 2_4:-35829181 None:intergenic
TCTTGAATACATACATAGTT+TGG 0.294404 2_4:+35828982 Msa0326250:CDS
AACTTACCTGATGCTGCATT+TGG 0.332330 2_4:-35829197 None:intergenic
CTTGAATACATACATAGTTT+GGG 0.409234 2_4:+35828983 Msa0326250:CDS
GTCCTTCCAAATGCAGCATC+AGG 0.463630 2_4:+35829191 Msa0326250:CDS
AACTTGTTACTTACAAATGA+AGG 0.482816 2_4:+35829110 Msa0326250:CDS
TACCTGATGCTGCATTTGGA+AGG 0.567959 2_4:-35829193 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATTAAAATAGCTGATTTT+GGG + chr2_4:35829135-35829154 Msa0326250:CDS 15.0%
!!! CATATTAAAATAGCTGATTT+TGG + chr2_4:35829134-35829153 Msa0326250:CDS 20.0%
! TCTTGAATACATACATAGTT+TGG + chr2_4:35828982-35829001 Msa0326250:CDS 25.0%
! CTTGAATACATACATAGTTT+GGG + chr2_4:35828983-35829002 Msa0326250:CDS 25.0%
!!! AACTTGTTACTTACAAATGA+AGG + chr2_4:35829110-35829129 Msa0326250:CDS 25.0%
! AGTGATACATCGTGATTTTA+AGG + chr2_4:35829006-35829025 Msa0326250:CDS 30.0%
!!! TGATTTTAAGGTAGCTCTAT+GGG + chr2_4:35829018-35829037 Msa0326250:intron 30.0%
TACTGCATTATTGCCATATA+TGG + chr2_4:35829048-35829067 Msa0326250:intron 30.0%
! TTTTCACACATAGCCATATA+TGG - chr2_4:35829064-35829083 None:intergenic 30.0%
!!! TTTTTTTTACCCTGTTAGAG+TGG + chr2_4:35829299-35829318 Msa0326250:intron 30.0%
!!! TTTTTTTACCCTGTTAGAGT+GGG + chr2_4:35829300-35829319 Msa0326250:intron 30.0%
! ATTTTCTTGTAGTGAGAGAT+CGG + chr2_4:35829346-35829365 Msa0326250:intron 30.0%
!!! GTGATTTTAAGGTAGCTCTA+TGG + chr2_4:35829017-35829036 Msa0326250:intron 35.0%
CATTTGGAAGGACAGTAATT+TGG - chr2_4:35829184-35829203 None:intergenic 35.0%
AACTTACCTGATGCTGCATT+TGG - chr2_4:35829200-35829219 None:intergenic 40.0%
AATGCAGCATCAGGTAAGTT+AGG + chr2_4:35829200-35829219 Msa0326250:intron 40.0%
TCAGGTAAGTTAGGAGCAAA+TGG + chr2_4:35829209-35829228 Msa0326250:intron 40.0%
TACCTGATGCTGCATTTGGA+AGG - chr2_4:35829196-35829215 None:intergenic 45.0%
GCTGAAAACCCACTCTAACA+GGG - chr2_4:35829311-35829330 None:intergenic 45.0%
AGCTGAAAACCCACTCTAAC+AGG - chr2_4:35829312-35829331 None:intergenic 45.0%
GTCCTTCCAAATGCAGCATC+AGG + chr2_4:35829191-35829210 Msa0326250:CDS 50.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 35828944 35829371 35828944 ID=Msa0326250;Name=Msa0326250
chr2_4 mRNA 35828944 35829371 35828944 ID=Msa0326250-mRNA-1;Parent=Msa0326250;Name=Msa0326250-mRNA-1;_AED=0.84;_eAED=0.84;_QI=0|0|0|0.33|0.5|0.66|3|0|68
chr2_4 exon 35828944 35829027 35828944 ID=Msa0326250-mRNA-1:exon:11054;Parent=Msa0326250-mRNA-1
chr2_4 exon 35829104 35829212 35829104 ID=Msa0326250-mRNA-1:exon:11055;Parent=Msa0326250-mRNA-1
chr2_4 exon 35829358 35829371 35829358 ID=Msa0326250-mRNA-1:exon:11056;Parent=Msa0326250-mRNA-1
chr2_4 CDS 35828944 35829027 35828944 ID=Msa0326250-mRNA-1:cds;Parent=Msa0326250-mRNA-1
chr2_4 CDS 35829104 35829212 35829104 ID=Msa0326250-mRNA-1:cds;Parent=Msa0326250-mRNA-1
chr2_4 CDS 35829358 35829371 35829358 ID=Msa0326250-mRNA-1:cds;Parent=Msa0326250-mRNA-1
Gene Sequence

>Msa0326250

GACGAGGCACGATTTTATGCAGCTGAAGTTGTCGATGCTCTTGAATACATACATAGTTTGGGAGTGATACATCGTGATTTTAAGTCAGAGAACTTGTTACTTACAAATGAAGGACATATTAAAATAGCTGATTTTGGGAGTGTGAAGACTATGCAAGATAGCCAAATTACTGTCCTTCCAAATGCAGCATCAGTGAGAGATCGGTAA
Protein sequence

>Msa0326250

DEARFYAAEVVDALEYIHSLGVIHRDFKSENLLLTNEGHIKIADFGSVKTMQDSQITVLPNAASVRDR*